Biopython: freely available Python tools for computational molecular biology and bioinformatics

Summary: The Biopython project is a mature open source international collaboration of volunteer developers, providing Python libraries for a wide range of bioinformatics problems. Biopython includes modules for reading and writing different sequence file formats and multiple sequence alignments, dealing with 3D macro molecular structures, interacting with common tools such as BLAST, ClustalW and EMBOSS, accessing key online databases, as well as providing numerical methods for statistical learning. Availability: Biopython is freely available, with documentation and source code at www.biopython.org under the Biopython license. Contact: All queries should be directed to the Biopython mailing lists, see www.biopython.org/wiki/[email protected]

Evidence for directional selection at a novel major histocompatibility class I marker in wild common frogs (Rana temporaria) exposed to a viral pathogen (Ranavirus).

(c) 2009 Teacher et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.Whilst the Major Histocompatibility Complex (MHC) is well characterized in the anuran Xenopus, this region has not previously been studied in another popular model species, the common frog (Rana temporaria). Nor, to date, have there been any studies of MHC in wild amphibian host-pathogen systems. We characterise an MHC class I locus in the common frog, and present primers to amplify both the whole region, and specifically the antigen binding region. As no more than two expressed haplotypes were found in over 400 clones from 66 individuals, it is likely that there is a single class I locus in this species. This finding is consistent with the single class I locus in Xenopus, but contrasts with the multiple loci identified in axolotls, providing evidence that the diversification of MHC class I into multiple loci likely occurred after the Caudata/Anura divergence (approximately 350 million years ago) but before the Ranidae/Pipidae divergence (approximately 230 mya). We use this locus to compare wild populations of common frogs that have been infected with a viral pathogen (Ranavirus) with those that have no history of infection. We demonstrate that certain MHC supertypes are associated with infection status (even after accounting for shared ancestry), and that the diseased populations have more similar supertype frequencies (lower F(ST)) than the uninfected. These patterns were not seen in a suite of putatively neutral microsatellite loci. We interpret this pattern at the MHC locus to indicate that the disease has imposed selection for particular haplotypes, and hence that common frogs may be adapting to the presence of Ranavirus, which currently kills tens of thousands of amphibians in the UK each year

Temporal and spatial instability in neutral and adaptive (MHC) genetic variation in marginal salmon populations

The role of marginal populations for the long-term maintenance of species’ genetic diversity and evolutionary potential is particularly timely in view of the range shifts caused by climate change. The Centre-Periphery hypothesis predicts that marginal populations should bear reduced genetic diversity and have low evolutionary potential. We analysed temporal stability at neutral microsatellite and adaptive MHC genetic variation over five decades in four marginal Atlantic salmon populations located at the southern limit of the species’ distribution with a complicated demographic history, which includes stocking with foreign and native salmon for at least 2 decades. We found a temporal increase in neutral genetic variation, as well as temporal instability in population structuring, highlighting the importance of temporal analyses in studies that examine the genetic diversity of peripheral populations at the margins of the species’ range, particularly in face of climate change

Single-Walled Carbon Nanotube (SWCNT)-induced interstitial fibrosis in the lungs of rats is associated with increased levels of PDGF mRNA and the formation of unique intercellular carbon structures that bridge alveolar macrophages In Situ

BACKGROUND: Nanotechnology is a rapidly advancing industry with many new products already available to the public. Therefore, it is essential to gain an understanding of the possible health risks associated with exposure to nanomaterials and to identify biomarkers of exposure. In this study, we investigated the fibrogenic potential of SWCNT synthesized by chemical vapor deposition using cobalt (Co) and molybdenum (Mo) as catalysts. Following a single oropharyngeal aspiration of SWCNT in rats, we evaluated lung histopathology, cell proliferation, and growth factor mRNAs at 1 and 21 days post-exposure. Comparisons were made to vehicle alone (saline containing a biocompatible nonionic surfactant), inert carbon black (CB) nanoparticles, or vanadium pentoxide (V(2)O(5)) as a known inducer of fibrosis. RESULTS: SWCNT or CB caused no overt inflammatory response at 1 or 21 days post-exposure as determined by histopathology and evaluation of cells (>95% macrophages) in bronchoalveolar lavage (BAL) fluid. However, SWCNT induced the formation of small, focal interstitial fibrotic lesions within the alveolar region of the lung at 21 days. A small fraction of alveolar macrophages harvested by BAL from the lungs of SWCNT-exposed rats at 21 days were bridged by unique intercellular carbon structures that extended into the cytoplasm of each macrophage. These "carbon bridge" structures between macrophages were also observed in situ in the lungs of SWCNT-exposed rats. No carbon bridges were observed in CB-exposed rats. SWCNT caused cell proliferation only at sites of fibrotic lesion formation as measured by bromodeoxyuridine uptake into alveolar cells. SWCNT increased platelet-derived growth factor (PDGF)-A, PDGF-B, and PDGF-C mRNA levels significantly at 1 day as measured by Taqman quantitative real-time RT-PCR. At 21 days, SWCNT did not increase any mRNAs evaluated, while V(2)O(5 )significantly increased mRNAs encoding PDGF-A, -B, and -C chains, PDGF-Rα, osteopontin (OPN), connective tissue growth factor (CTGF), and transforming growth factor (TGF)-β1. CONCLUSION: Our findings indicate that SWCNT do not cause lung inflammation and yet induce the formation of small, focal interstital fibrotic lesioins in the alveolar region of the lungs of rats. Of greatest interest was the discovery of unique intercellular carbon structures composed of SWCNT that bridged lung macrophages. These "carbon bridges" offer a novel and easily identifiable biomarker of exposure

Respiratory syncytial virus infection reduces lung inflammation and fibrosis in mice exposed to vanadium pentoxide

<p>Abstract</p> <p>Background</p> <p>Vanadium pentoxide (V₂O₅) exposure is a cause of occupational bronchitis and airway fibrosis. Respiratory syncytial virus (RSV) is a ubiquitous pathogen that causes airway inflammation. It is unknown whether individuals with pre-existing respiratory viral infection are susceptible to V₂O₅-induced bronchitis. We hypothesized that respiratory viral infection will exacerbate vanadium-induced lung fibrosis.</p> <p>Methods</p> <p>In this study we investigated the effect of RSV pre- or post-exposure to V₂O₅in male AKR mice. Mice were pre-exposed by intranasal aspiration to RSV or media vehicle prior to intranasal aspiration of V₂O₅or saline vehicle at day 1 or day 7. A parallel group of mice were treated first with V₂O₅or saline vehicle at day 1 and day 7 then post-exposed to RSV or media vehicle at day 8.</p> <p>Results</p> <p>V₂O₅-induced airway inflammation and fibrosis were decreased by RSV pre- or post-exposure. Real time quantitative RT-PCR showed that V₂O₅significantly increased lung mRNAs encoding pro-fibrogenic growth factors (TGF-β1, CTGF, PDGF-C) and collagen (Col1A2), but also increased mRNAs encoding anti-fibrogenic type I interferons (IFN-α, -β) and IFN-inducible chemokines (CXCL9 and CXCL10). RSV pre- or post-exposure caused a significantly reduced mRNAs of pro-fibrogenic growth factors and collagen, yet reduced RNA levels of anti-fibrogenic interferons and CXC chemokines.</p> <p>Conclusions</p> <p>Collectively these data suggest that RSV infection reduces the severity of V₂O₅-induced fibrosis by suppressing growth factors and collagen genes. However, RSV suppression of V₂O₅-induced IFNs and IFN-inducible chemokines suggests that viral infection also suppresses the innate immune response that normally serves to resolve V₂O₅-induced fibrosis.</p

The surged faradic stimulation to the pelvic floor muscles as an adjunct to the medical management in children with rectal prolapse

<p>Abstract</p> <p>Background</p> <p>To assess the role of the surged faradic stimulation to the pelvic floor muscles as an adjunct to the conservative management in the children of idiopathic rectal prolapse</p> <p>Methods</p> <p><it>Study design</it>: Prospective</p> <p><it>Setting</it>: Pediatric Surgery Department, Pt BD Sharma, Post Graduate Institute of Medical Sciences, Rohtak</p> <p><it>Subjects</it>: 47 consecutive children with idiopathic rectal prolapse attending the Pediatric Surgery out patient department from July 2005 to June 2006</p> <p><it>Methodology</it>: The information pertaining to duration and the extent of rectal prolapse, predisposing or associated medical conditions, results of local clinical examination were noted. Surged faradic stimulation using modified intraluminal rectal probe, was given on the alternate days. The conventional conservative medical management was also continued. The extent of relief and the number of the sittings of faradic stimulation required were noted at various stages of follow-ups</p> <p><it>Statistical Methods</it>: Mean values between those completely cured and others; poor responders and others were compared with t-test and proportions were compared with Chi square test. The p-value < 0.05 was considered statistically significant.</p> <p>Results</p> <p>The mean number of sittings in the completely cured group (n = <b>28</b>(64%)) was (12.4 ± 7.8) and was comparable with very poor responder (n = 6(13%). There was higher percentage of relief (76%) at the first follow up (at 15 days) in completely cured Vs other (37%) and also the poor responders showed (20%) Vs other (68%) and was statistically significant.</p> <p>Conclusion</p> <p>With use of faradic stimulation, even the long-standing rectal prolapse can be fully cured. The follow up visit at 2 weeks is very important to gauge the likely success of this modality in treatment of the patients with rectal prolapse. Those showing poor response at this stage may require alternative treatment or take a long time to get cured</p

Pneumoconiosis and respiratory problems in dental laboratory technicians: Analysis of 893 dental technicians

Objectives: To explore the rate of pneumoconiosis in dental technicians (DTP) and to evaluate the risk factors. Material and Methods: Data of 893 dental technicians, who were admitted to our hospital in the period January 2007–May 2012, from 170 dental laboratories were retrospectively examined. Demographic data, respiratory symptoms, smoking status, work duration, working fields, exposure to sandblasting, physical examination findings, chest radiographs, pulmonary function tests and high-resolution computed tomography results were evaluated. Results: Dental technicians’ pneumoconiosis rate was 10.1% among 893 cases. The disease was more common among males and in those exposed to sandblasting who had 77-fold higher risk of DTP. The highest profusion subcategory was 3/+ (according to the International Labour Organization (ILO) 2011 standards) and the large opacity rate was 13.3%. Conclusions: To the best of our knowledge, it was the largest DTP case series (N = 893/90) in the literature in English. Health screenings should be performed regularly for the early diagnosis of pneumoconiosis, which is an important occupational disease for dental technicians