1.
SNPdbe: Constructing an nsSNP functional impacts database.
Source
TUM, Bioinformatics - I12, Informatik, Boltzmannstr. 3, 85748 Garching, Germany, TUM Graduate School of Information Science in Health (GSISH), Boltzmannstr. 11, 85748 Garching, Germany, Department of Biochemistry and Microbiology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, NJ 08901, USA.
Abstract
SUMMARY:
Many existing databases annotate experimentally characterized single nucleotide polymorphisms (SNPs). Each non-synonymous SNP (nsSNP) changes one amino acid in the gene product (single amino acid substitution; SAAS). This change can either affect protein function or be neutral in that respect. Most polymorphisms lack experimental annotation of their functional impact. Here, we introduce SNPdbe - SNP database of effects, with predictions of computationally annotated functional impacts of SNPs. Database entries represent nsSNPs in dbSNP and 1000 Genomes collection, as well as variants from UniProt and PMD. SAASs come from more than 2600 organisms; "human" being the most prevalent. The impact of each SAAS on protein function is predicted using the SNAP and SIFT algorithms and augmented with experimentally derived func-tion/structure information and disease associations from PMD, OMIM and UniProt. SNPdbe is consistently updated and easily augmented with new sources of information. The DB is available as a MySQL dump and via a web front-end that allows searches with any combination of organism names, sequences and mutation IDs.
AVAILABILITY:
http://www.rostlab.org/services/snpdbe
CONTACT:
snpdbe@rostlab.org.
- PMID:
- 22210871
- [PubMed - as supplied by publisher]
Small-Molecule Inhibitor Starting Points Learned From Protein-Protein Interaction Inhibitor Structure.
Source
Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15260, USA.
Abstract
MOTIVATION:
Protein-protein interactions (PPIs) are a promising, but challenging target for pharmaceutical intervention. One approach for addressing these difficult targets is the rational design of small-molecule inhibitors that mimic the chemical and physical properties of small clusters of key residues at the protein-protein interface. The identification of appropriate clusters of interface residues provides starting points for inhibitor design and supports an overall assessment of the susceptibility of PPIs to small-molecule inhibition.
RESULTS:
We extract Small-Molecule Inhibitor Starting Points (SMISPs) from protein-ligand and protein-protein complexes in the Protein Data Bank (PDB). These SMISPs are used to train two distinct classifiers, a support vector machine and an easy to interpret exhaustive rule classifier. Both classifiers achieve better than 70% leave-one-complex-out cross-validation accuracy and correctly predict SMISPs of known PPI inhibitors not in the training set. A PDB-wide analysis suggests that nearly half of all PPIs may be susceptible to small-molecule inhibition.
AVAILABILITY:
http://pocketquery.csb.pitt.edu.
CONTACT:
dkoes@pitt.edu.
- PMID:
- 22210869
- [PubMed - as supplied by publisher]
VarSifter: Visualizing and analyzing exome-scale sequence variation data on a desktop computer.
Source
National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
Abstract
SUMMARY:
VarSifter is a graphical software tool for desktop computers that allows investigators of varying computational skills to easily and quickly sort, filter, and sift through sequence variation data. A variety of filters and a custom query framework allow filtering based on any combination of sample and annotation information. By simplifying visualization and analyses of exome-scale sequence variation data, this program will help bring the power and promise of massively-parallel DNA sequencing to a broader group of researchers.Availability and Implementation: VarSifter is written in Java, and is freely available in source and binary versions, along with a User Guide, athttp://research.nhgri.nih.gov/software/VarSifter/.
CONTACT:
mullikin@mail.nih.gov
SUPPLEMENTARY INFORMATION:
Additional figures and methods available online at the journal's website.
- PMID:
- 22210868
- [PubMed - as supplied by publisher]
CytoSEED: a Cytoscape plugin for viewing, manipulating and analyzing metabolic models created by the Model SEED.
Source
Computer Science Department, Hope College, Holland, Michigan, 49423, USA.
Abstract
SUMMARY:
CytoSEED is a Cytoscape plugin for viewing, manipulating and analyzing metabolic models created using the Model SEED. The CytoSEED plugin enables users of the Model SEED to create informative visualizations of the reaction networks generated for their organisms of interest. These visualizations are useful for un-derstanding organism-specific biochemistry and for highlighting the results of flux variability analysis experiments.Availability and Implementation: Freely available for download on the web at http://sourceforge.net/projects/cytoseed/. Implemented in Java SE 6 and supported on all platforms that support Cytoscape.
CONTACT:
dejongh@hope.edu
SUPPLEMENTARY INFORMATION:
Installation instructions, a tutorial, and full-size figures are available athttp://www.cs.hope.edu/cytoseed/.
- PMID:
- 22210867
- [PubMed - as supplied by publisher]
influx_s: increasing numerical stability and precision for metabolic flux analysis in isotope labeling experiments.
Source
Université de Toulouse; INSA,UPS,INP; LISBP, 135 Avenue de Rangueil, F-31077 Toulouse, France.
Abstract
MOTIVATION:
The problem of stationary metabolic flux analysis based on isotope labelling experiments first appeared in the early 1950s and was basically solved in early 2000s. Several algorithms and software packages are available for this problem. However, the generic stochastic algorithms (simulated annealing or evolution algorithms) currently used in these software require a lot-of time to achieve acceptable precision. For deterministic algorithms, a common drawback is the lack of convergence stability for ill-conditioned systems or when started from a random point.
RESULTS:
In this paper, we present a new deterministic algorithm whith significantly increased numerical stability and accuracy of flux estimation compared to commonly used algorithms. It requires relatively short CPU time (from several seconds to several minutes with a standard PC architecture) to estimate fluxes in the central carbon metabolism network of E.Coli.
AVAILABILITY:
The software package influx_s implementing this algorithm is distributed under an OpenSource licence at http://metasys.insa-toulouse.fr/software/influx/
CONTACT:
Jean-Charles.Portais@insa-toulouse.fr
SUPPLEMENTARY INFORMATION:
- PMID:
- 22210866
- [PubMed - as supplied by publisher]
Efficient large-scale protein sequence comparison and gene matching to identify orthologs and co-orthologs.
Source
Department of Biochemistry and Molecular Biology, ARC Centre of Excellence in Structural and Functional Microbial Genomics and Clayton School of Information Technology, Monash University, VIC 3800, Australia.
Abstract
Broadly, computational approaches for ortholog assignment is a three steps process: (i) identify all putative homologs between the genomes, (ii) identify gene anchors and (iii) link anchors to identify best gene matches given their order and context. In this article, we engineer two methods to improve two important aspects of this pipeline [specifically steps (ii) and (iii)]. First, computing sequence similarity data [step (i)] is a computationally intensive task for large sequence sets, creating a bottleneck in the ortholog assignment pipeline. We have designed a fast and highly scalable sort-join method (afree) based on k-mer counts to rapidly compare all pairs of sequences in a large protein sequence set to identify putative homologs. Second, availability of complex genomes containing large gene families with prevalence of complex evolutionary events, such as duplications, has made the task of assigning orthologs and co-orthologs difficult. Here, we have developed an iterative graph matching strategy where at each iteration the best gene assignments are identified resulting in a set of orthologs and co-orthologs. We find that the afree algorithm is faster than existing methods and maintains high accuracy in identifying similar genes. The iterative graph matching strategy also showed high accuracy in identifying complex gene relationships. Standalone afree available from http://vbc.med.monash.edu.au/∼kmahmood/afree. EGM2, complete ortholog assignment pipeline (including afree and the iterative graph matching method) available from http://vbc.med.monash.edu.au/∼kmahmood/EGM2.
- PMID:
- 22210858
- [PubMed - as supplied by publisher]
Discovery and mapping of a new expressed sequence tag-single nucleotide polymorphism and simple sequence repeat panel for large-scale genetic studies and breeding of Theobroma cacao L.
Source
1 CIRAD, UMR 1334 AGAP, TA 108/03-34398, Montpellier Cedex 5, France.
Abstract
Theobroma cacao is an economically important tree of several tropical countries. Its genetic improvement is essential to provide protection against major diseases and improve chocolate quality. We discovered and mapped new expressed sequence tag-single nucleotide polymorphism (EST-SNP) and simple sequence repeat (SSR) markers and constructed a high-density genetic map. By screening 149 650 ESTs, 5246 SNPs were detected in silico, of which 1536 corresponded to genes with a putative function, while 851 had a clear polymorphic pattern across a collection of genetic resources. In addition, 409 new SSR markers were detected on the Criollo genome. Lastly, 681 new EST-SNPs and 163 new SSRs were added to the pre-existing 418 co-dominant markers to construct a large consensus genetic map. This high-density map and the set of new genetic markers identified in this study are a milestone in cocoa genomics and for marker-assisted breeding. The data are available at http://tropgenedb.cirad.fr.
- PMID:
- 22210604
- [PubMed - as supplied by publisher]
MTCID: A database of genetic polymorphisms in clinical isolates of Mycobacterium tuberculosis.
Source
School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India.
Abstract
Tuberculosis (TB) is a major cause of morbidity and mortality throughout the world, particularly in developing countries. The response of the patients and treatment outcome depends, in addition to diagnosis, appropriate and timely treatment and host factors, on the virulence of Mycobacterium tuberculosis and genetic polymorphism prevalent in clinical isolates of the bacterium. A number of studies have been carried out to characterize clinical isolates of M. tuberculosis obtained from TB patients. However, the data is scattered in a large number of publications. Though attempts have been made to catalog the observed variations, there is no database that has been developed for cataloging, storing and dissemination of genetic polymorphism information. MTCID (M. tuberculosis clinical isolate genetic polymorphism database) is an attempt to provide a comprehensive repository to store, access and disseminate single nucleotide polymorphism (SNPs) and spoligotyping profiles of M. tuberculosis. It can be used to automatically upload the information available with a user that adds to the existing database at the backend. Besides it may also aid in maintaining clinical profiles of TB and treatment of patients. The database has 'search' features and is available at http://ccbb.jnu.ac.in/Tb.
Copyright © 2011 Elsevier Ltd. All rights reserved.
- PMID:
- 22209237
- [PubMed - as supplied by publisher]
A cost-effective and field-ready potentiostat that poises subsurface electrodes to monitor bacterial respiration.
Source
Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY 14853, USA.
Abstract
Here, we present the proof-of-concept for a subsurface bioelectrochemical system (BES)-based biosensor capable of monitoring microbial respiration that occurs through exocellular electron transfer. This system includes our open-source design of a three-channel microcontroller-unit (MCU)-based potentiostat that is capable of chronoamperometry, which laboratory tests showed to be accurate within 0.95±0.58% (95% Confidence Limit) of a commercial potentiostat. The potentiostat design is freely available online: http://angenent.bee.cornell.edu/potentiostat.html. This robust and field-ready potentiostat, which can withstand temperatures of -30°C, can be manufactured at relatively low cost ($600), thus, allowing for en-masse deployment at field sites. The MCU-based potentiostat was integrated with electrodes and a solar panel-based power system, and deployed as a biosensor to monitor microbial respiration in drained thaw lake basins outside Barrow, AK. At three different depths, the working electrode of a microbial three-electrode system (M3C) was maintained at potentials corresponding to the microbial reduction of iron(III) compounds and humic acids. Thereby, the working electrode mimics these compounds and is used by certain microbes as an electron acceptor. The sensors revealed daily cycles in microbial respiration. In the medium- and deep-depth electrodes the onset of these cycles followed a considerable increase in overall activity that corresponded to those soils reaching temperatures conducive to microbial activity as the summer thaw progressed. The BES biosensor is a valuable tool for studying microbial activity in situ in remote environments, and the cost-efficient design of the potentiostat allows for wide-scale use in remote areas.
Copyright © 2011 Elsevier B.V. All rights reserved.
- PMID:
- 22209069
- [PubMed - as supplied by publisher]
MotifMap: integrative genome-wide maps of regulatory motif sites for model species.
Abstract
ABSTRACT:
BACKGROUND:
A central challenge of biology is to map and understand gene regulation on a genome-wide scale. For any given genome, only a small fraction of the regulatory elements embedded in the DNA sequence have been characterized, and there is great interest in developing computational methods to systematically map all these elements and understand their relationships. Such computational efforts, however, are significantly hindered by the overwhelming size of non-coding regions and the statistical variability and complex spatial organizations of regulatory elements and interactions. Genome-wide catalogs of regulatory elements for all model species simply do not yet exist.
RESULTS:
The MotifMap system uses databases of transcription factor binding motifs, refined genome alignments, and a comparative genomic statistical approach to provide comprehensive maps of candidate regulatory elements encoded in the genomes of model species. The system is used to derive new genome-wide maps for yeast, fly, worm, mouse, and human. The human map contains 519,108 sites for 570 matrices with a False Discovery Rate of 0.1 or less. The new maps are assessed in several ways, for instance using high-throughput experimental ChIP-seq data and AUC statistics, providing strong evidence for their accuracy and coverage. The maps can be usefully integrated with many other kinds of omic data and are available at http://motifmap.igb.uci.edu/.
CONCLUSIONS:
MotifMap and its integration with other data provide a foundation for analyzing gene regulation on a genome-wide scale, and for automatically generating regulatory pathways and hypotheses. The power of this approach is demonstrated and discussed using the P53 apoptotic pathway and the Gli hedgehog pathway as examples.
- PMID:
- 22208852
- [PubMed - as supplied by publisher]
Effects on muscle performance of NSAID treatment with Piroxicam versus placebo in geriatric patients with acute infection-induced inflammation. A double blind randomized controlled trial.
Abstract
ABSTRACT:
BACKGROUND:
Inflammation is the main cause of disease-associated muscle wasting. In a previous single blind study we have demonstrated improved recovery of muscle endurance following celecoxib treatment in hospitalized geriatric patients with acute infection. Here we further evaluate NSAID treatment with piroxicam in a double blind RCT and investigate the role of cytokines and heat shock proteins (Hsp) with respect to muscle performance. We hypothesized that NSAID treatment would preserve muscle performance better than antibiotic treatment alone, by reducing infection-associated inflammation and by increasing expression of cytoprotective Hsp.
METHODS:
Consecutive admissions to the geriatric ward were screened. 30 Caucasian patients, median age 84.5 years, with acute infection-induced inflammation and serum levels of CRP > 10 mg/L were included and randomized to active treatment with 10 mg piroxicam daily or placebo. Assessment comprised general clinical and biochemical parameters, 25 cytokines in serum, intra- and extracellular Hsp27 and Hsp70, Elderly Mobility Scale (EMS) scores, grip strength (GS), fatigue resistance (FR) and lean body mass (LBM). Patients were evaluated until discharge with a maximum of 3 weeks after treatment allocation.
RESULTS:
EMS scores, FR and grip work (GW), a measure taking into account GS and FR, significantly improved with piroxicam, but not with placebo. Early decreases in IL-6 serum levels with piroxicam correlated with better muscle performance at week 2. Basal expression of Hsp27 in monocytes without heat challenge (WHC) was positively correlated with FR at baseline and significantly increased by treatment with piroxicam compared to placebo. Profound modifications in the relationships between cytokines or Hsp and changes in muscle parameters were observed in the piroxicam group.
CONCLUSIONS:
Piroxicam improves clinically relevant measures of muscle performance and mobility in geriatric patients hospitalized with acute infection-induced inflammation. Underlying mechanisms may include modifications in the cytokine network and increases in monocytic expression of cytoprotective Hsp27. Trial registration Current Controlled Trials (ISRCTN58517443) http://www.controlled-trials.com/ISRCTN58517443/
- PMID:
- 22208783
- [PubMed - as supplied by publisher]
A new strategy for better genome assembly from very short reads.
Abstract
ABSTRACT:
BACKGROUND:
With the rapid development of the next generation sequencing (NGS) technology, large quantities of genome sequencing data have been generated. Because of repetitive regions of genomes and some other factors, assembly of very short reads is still a challenging issue.
RESULTS:
A novel strategy for improving genome assembly from very short reads is proposed. It can increase accuracies of assemblies by integrating de novo contigs, and produce comparative contigs by allowing multiple references without limiting to genomes of closely related strains. Comparative contigs are used to scaffold de novo contigs. Using simulated and real datasets, it is shown that our strategy can effectively improve qualities of assemblies of isolated microbial genomes and metagenomes.
CONCLUSIONS:
With more and more reference genomes available, our strategy will be useful to improve qualities of genome assemblies from very short reads. Some scripts are provided to make our strategy applicable athttp://code.google.com/p/cd-hybrid/.
- PMID:
- 22208765
- [PubMed - as supplied by publisher]
SPINE-D: Accurate Prediction of Short and Long Disordered Regions by a Single Neural-Network Based Method.
Source
School of Informatics, Indiana University Purdue University, Indianapolis, IN 46202, USA. yqzhou@iupui.edu.
Abstract
Short and long disordered regions of proteins have different preference for different amino acid residues. Different methods often have to be trained to predict them separately. In this study, we developed a single neural-network-based technique called SPINE-D that makes a three-state prediction first (ordered residues and disordered residues in short and long disordered regions) and reduces it into a two-state prediction afterwards. SPINE-D was tested on various sets composed of different combinations of Disprot annotated proteins and proteins directly from the PDB annotated for disorder by missing coordinates in X-ray determined structures. While disorder annotations are different according to Disprot and X-ray approaches, SPINE-D's prediction accuracy and ability to predict disorder are relatively independent of how the method was trained and what type of annotation was employed but strongly depend on the balance in the relative populations of ordered and disordered residues in short and long disordered regions in the test set. With greater than 85% overall specificity for detecting residues in both short and long disordered regions, the residues in long disordered regions are easier to predict at 81% sensitivity in a balanced test dataset with 56.5% ordered residues but more challenging (at 65% sensitivity) in a test dataset with 90% ordered residues. Compared to eleven other methods, SPINE-D yields the highest area under the curve (AUC), the highest Mathews correlation coefficient for residue-based prediction, and the lowest mean square error in predicting disorder contents of proteins for an independent test set with 329 proteins. In particular, SPINE-D is comparable to a meta predictor in predicting disordered residues in long disordered regions and superior in short disordered regions. SPINE-D participated in CASP 9 blind prediction and is one of the top servers according to the official ranking. In addition, SPINE-D was examined for prediction of functional molecular recognition motifs in several case studies. The server and databases are available athttp://sparks.informatics.iupui.edu/.
- PMID:
- 22208280
- [PubMed - in process]
Cambrian archaeocyathan metazoans: revision of morphological characters and standardization of genus descriptions to establish an online identification tool.
Source
CNRS (UMR 7207, centre de recherche sur la paléobiodiversité et les paléoenvironnements), Laboratoire Informatique et Systématique, MNHN Département Histoire de la Terre, Bâtiment de Géologie, CP48, 57 rue Cuvier, 75005 Paris (France).
Abstract
Archaeocyatha represent the oldest calcified sponges and the first metazoans to build bioconstructions in association with calcimicrobes. They are a key group in biology, evolutionary studies, biostratigraphy, paleoecology and paleogeography of the early Cambrian times. The establishing of a new standardized terminology for archaeocyathans description has permitted the creation of the first knowledge base in English including descriptions of all archaeocyathan genera. This base, using the XPER² software package, is an integral part of the -Archaeocyatha- a knowledge base website, freely available at url http://www.infosyslab.fr/archaeocyatha. The website is composed of common information about Archaeocyatha, general remarks about the knowledge base, the description of the 307 genera recognized with images of type-specimens of type-species for each genus, as well as additional morphological data, an interactive free access key and its user guide.The automatic analysis and comparison of the digitized descriptions have identified some genera with highly similar morphology. These results are a great help for future taxonomic revisions and suggest a number of possible synonymies that require further study.
Engaging the broader community in biodiversity research: the concept of the COMBER pilot project for divers in ViBRANT.
Source
Institute of Marine Biology and Genetics, Hellenic Centre for Marine Research, 71003 Heraklion, Crete, Greece.
Abstract
This paper discusses the design and implementation of a citizen science pilot project, COMBER (Citizens' Network for the Observation of Marine BiodivERsity, http://www.comber.hcmr.gr), which has been initiated under the ViBRANT EU e-infrastructure. It is designed and implemented for divers and snorkelers who are interested in participating in marine biodiversity citizen science projects. It shows the necessity of engaging the broader community in the marine biodiversity monitoring and research projects, networks and initiatives. It analyses the stakeholders, the industry and the relevant markets involved in diving activities and their potential to sustain these activities. The principles, including data policy and rewards for the participating divers through their own data, upon which this project is based are thoroughly discussed. The results of the users analysis and lessons learned so far are presented. Future plans include promotion, links with citizen science web developments, data publishing tools, and development of new scientific hypotheses to be tested by the data collected so far.
Scratchpads 2.0: a Virtual Research Environment supporting scholarly collaboration, communication and data publication in biodiversity science.
Source
Natural History Museum, Cromwell Road, London, SW7 5BD, U.K.
Abstract
The Scratchpad Virtual Research Environment (http://scratchpads.eu/) is a flexible system for people to create their own research networks supporting natural history science. Here we describe Version 2 of the system characterised by the move to Drupal 7 as the Scratchpad core development framework and timed to coincide with the fifth year of the project's operation in late January 2012. The development of Scratchpad 2 reflects a combination of technical enhancements that make the project more sustainable, combined with new features intended to make the system more functional and easier to use. A roadmap outlining strategic plans for development of the Scratchpad project over the next two years concludes this article.
Pulsatile versus continuous administration of oxytocin for induction and augmentation of labor: two randomized controlled trials.
Source
Division of Women's Health, King's College London, Women's Health Academic Centre, King's Health Partners, St Thomas' Hospital Campus, London, England, UK.
Abstract
OBJECTIVE:
To determine whether pulsatile oxytocin infusion improves delivery outcome in women requiring induction or augmentation of labor.
STUDY DESIGN:
Two related randomized controlled trials undertaken in 2 inner-city United Kingdom university hospitals (ISRCTN72773405; http://www.isrctn.org/). Women were randomly assigned to a pulsatile or continuous infusion protocol. Primary outcome: cesarean section rate (induction trial); operative delivery rate (augmentation trial).
RESULTS:
For induction, cesarean section rates were similar in women receiving pulsatile (n = 264, 38.3%) vs continuous infusion of oxytocin (n = 257; 37.7%; risk ratio, 1.01; 95% confidence interval, 0.81-1.26; P = .903), but associated with increased "infusion to time of delivery" intervals (P < .001) in the pulsatile group. For augmentation, pulsatile infusion resulted in higher operative delivery rates (70.1%, n = 251) vs continuous infusion (62.7%, n = 249; risk ratio, 1.12; 95% confidence interval, 0.99-1.27; P = .077) and increased neonatal morbidity.
CONCLUSION:
For induction, pulsatile infusion of oxytocin is effective, but conferred little clinical benefit. Pulsatile infusion is not recommended for augmentation.
Copyright © 2012 Mosby, Inc. All rights reserved.
Difficult phylogenetic questions: more data, maybe; better methods, certainly.
Source
Département de Biochimie, Centre Robert-Cedergren, Université de Montréal, Succursale Centre-Ville, Montréal, Québec H3C 3J7, Canada. herve.philippe@umontreal.ca.
Abstract
ABSTRACT: Contradicting the prejudice that endosymbiosis is a rare phenomenon, Husník and co-workers show in BMC Biology that bacterial endosymbiosis has occured several times independently during insect evolution. Rigorous phylogenetic analyses, in particular using complex models of sequence evolution and an original site removal procedure, allow this conclusion to be established after eschewing inference artefacts that usually plague the positioning of highly divergent endosymbiont genomic sequences.See research article http://www.biomedcentral.com/1741-7007/9/87.
The bending of cell sheets - from folding to rolling.
Source
Department of Biology, 241 Gilmer Hall, University of Virginia, Charlottesville, VA 22904, USA. rek3k@virginia.edu.
Abstract
ABSTRACT: The bending of cell sheets plays a major role in multicellular embryonic morphogenesis. Recent advances are leading to a deeper understanding of how the biophysical properties and the force-producing behaviors of cells are regulated, and how these forces are integrated across cell sheets during bending. We review work that shows that the dynamic balance of apical versus basolateral cortical tension controls specific aspects of invagination of epithelial sheets, and recent evidence that tissue expansion by growth contributes to neural retinal invagination in a stem cell-derived, self-organizing system. Of special interest is the detailed analysis of the type B inversion in Volvox reported in BMC Biology by Höhn and Hallmann, as this is a system that promises to be particularly instructive in understanding morphogenesis of any monolayered spheroid system.See research article: http://www.biomedcentral.com/1741-7007/9/89.
Multilocus Sequence Typing (MLST) and Phylogenetic Analysis of Propionibacterium acnes.
Source
Department of Biomedicine, Faculty of Health Sciences, Aarhus University, Wilhelm Meyers allé 4,DK-8000 Aarhus C, Denmark.
Abstract
Propionibacterium acnes is a commensal of human skin but is also implicated in the pathogenesis of acne vulgaris and in biofilm-associated infections of medical devices and endophthalmitis, and in infections of bone and dental root canals. Recent studies associate P. acnes with prostate cancer. As the species includes evolutionary lineages with distinct association with health and disease, there is a need for a high-resolution typing scheme. Recently, two MLST schemes were reported, one based on nine and one based on seven housekeeping genes. In the present study, the two schemes were compared with reference to a phylogenetic tree based on 78 P. acnes genomes and their gene contents. Further support for a basically clonal population structure of P. acnes and a scenario of global spread of epidemic clones of P. acnes was obtained. Compared with the Belfast scheme, the Aarhus MLST scheme (http://pacnes.mlst.net/) based on nine genes offers significantly enhanced resolution and phylogenetic inferences more concordant with analyses based on a comprehensive sampling of the entire genomes, their gene contents, and their putative pathogenic potential
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