Bio Saga Blog - A Chronicle of Life Sciences & Informatics

"Molecular Tweeting" Could Hold the Key to Busting Superbugs A broader understanding of bacterial social networks might help scientists combat antibiotic resistance Indeed interesting, although bit old article, sounded very interesting. Just stumbled on it this morning!  

Listeria TDRM Database http://www.lmtdrm.com/ . Please keep your comments and suggestions flowing in  kamesh@pronetinformatix.com The genus  Listeria  consists of a group of gram-positive bacteria of low G+C content closely related to  Bacillus, Clostridium, Enterococcus, Streptococcus,  and  Staphylococcus .  Listeria spp.   are facultative anaerobic rods of 0.4 by 1 to 1.5 µm that do not form spores, have no capsule and are motile at 10 to 25°C.  Listeria spp .  is isolated from a diversity of environmental sources, including soil, water, effluents, a large variety of foods, and the feces of humans and animals. The genus  Listeria  currently includes eight species:  L. monocytogenes ,  L. ivanovii ,  L. seeligeri , L.rocourtiace ,  L. innocua ,  L. welshimeri ,  L. marthii   and  L. grayi . Two of these species  L. monocytogenes  and  L. ivanovii  are potential...

Microbial Genomes Curator @ Computercraft Corporation--Maryland (US).  Submitted by Computercraft Corporation; posted on Saturday, March 17, 2012 RESPONSIBILITIES: Computercraft seeks a microbiologist to work with a team of software developers and biologists on microbial genome analysis including pan-genome, protein clusters, phylogenetic tree and more. This is a technically challenging position requiring experience in genome sequencing and annotation. A background in comparative genome analysis such as alignments and tree building is a plus. Our scientists work with genomic experts at the NIH's National Center for Biotechnology Information (NCBI) to create and enhance a suite of databases and tools available to researchers worldwide. Teamwork interaction and excellent organizational skills are essential for this detail-oriented position, as is scientific problem-solving with a results-oriented focus. REQUIREMENTS: * PhD in molecular biology, microbiology, or related field * ...

BIBI automates DNA sequence analysis for bacterial identification in the clinical field. BIBI relies on the use of BLAST and CLUSTAL W programs applied to different subsets of sequences extracted from GenBank. These sequences are filtered and stored in a new database, which is adapted to bacterial identification. For further details refer : http://umr5558-sud-str1.univ-lyon1.fr/ lebibi/lebibi.cgi

The Department of Energy's Joint Genome Institute has chosen 41 research projects out of 152 applicants to use its sequencing services under its 2012 Community Sequencing Program, JGI said Thursday. Researchers for this year's CSP program, which provides the scientific community with access to JGI's high-throughput sequencing technologies, proposed projects to study plant-microbe interactions, how microbes are involved in carbon capture and greenhouse gas emission, and metagenomics. “These selections truly take advantage of the DOE JGI’s massive-scale sequencing and data analysis capabilities,” DOE JGI Director Eddy Rubin said in a statement.  “The projects span the globe and the unexplored branches of the tree of life, and promise to yield a better understanding of the interplay between climate, ecosystem, and organism.  Still other projects are targeting improvements in biofuel feedstock production, focusing on the potential of microorganisms to improve feedstock growth a...

Abstract Whole genome amplification by the multiple displacement amplification (MDA) method allows sequencing of DNA from single cells of bacteria that cannot be cultured. Assembling a genome is challenging, however, because MDA generates highly nonuniform coverage of the genome. Here we describe an algorithm tailored for short-read data from single cells that improves assembly through the use of a progressively increasing coverage cutoff. Assembly of reads from single  Escherichia coli  and  Staphylococcus aureus  cells captures >91% of genes within contigs, approaching the 95% captured from an assembly based on many  E. coli  cells. We apply this method to assemble a genome from a single cell of an uncultivated SAR324 clade of Deltaproteobacteria, a cosmopolitan bacterial lineage in the global ocean. Metabolic reconstruction suggests that SAR324 is aerobic, motile and chemotaxic. Our approach enables acquisition of genome assemblies for individual uncu...

BioTorrents, a website that allows open access sharing of scientific data and uses the popular BitTorrent peer-to-peer file sharing technology. BioTorrents allows files to be transferred rapidly due to the sharing of bandwidth across multiple institutions and provides more reliable file transfers due to the built-in error checking of the file sharing technology. BioTorrents contains multiple features, including keyword searching, category browsing, RSS feeds, torrent comments, and a discussion forum. AVAILABILITY: BioTorrents is available at http://www.biotorre nts.net/ REFERENCE: A complete description of BioTorrents is described in the manuscript at http://www.plosone. org/article/ info:doi/ 10.1371/journal. pone.0010071

The National Institutes of Health has awarded 970 stimulus grants worth more than $625 million — around 14 percent of total NIH stimulus grant funding to date — to projects that fall within the broad family of 'omics disciplines, according to a preliminary analysis of the NIH funding database conducted by GenomeWeb Daily News . As of Sept. 30, the close of the fiscal year, the National Institutes of Health had awarded a total of $5 billion in stimulus funding — nearly half of the $10 billion appropriation that NIH will disburse over two years under the American Recovery and Reinvestment Act of 2009 . The $5 billion figure includes both grants and contracts, however. For grants alone, NIH had awarded approximately $4.4 billion via 12,789 ARRA grants as of Oct. 7, according to the database. The 970 grants awarded to 'omics projects comprise 7.5 percent of the stimulus grants awarded so far, but the total funding awarded to these projects makes up 14 percent of NIH ARRA grant ...

In a paper called "Metagenome Annotation Using a Distributed Grid of Undergraduate Students" I just love this title! It's nerdy and cute, all at the same time. Says Sandra Porter . The paper describes a class where students from Marseilles University investigate the function of unidentified genes from a Global Ocean Sampling experiment. All the sequences are obtained from the environmental sequence division at the NCBI . French researchers describe their strategy for teaching undergraduate-level bioinformatics using cutting-edge genomic data and a Web-based learning tool. The students then annotated real metagenomic sequences from the Global Ocean Sampling experiment. "In return for their much-needed help sorting out oodles of DNA data, the undergrads gain a practical knowledge of the work involved in doing bioinformatics and metagenomics, and, most importantly of all, they get to experience what it's like to do real research," says Karen James at the Be...

In Heidelberg, Germany, today researchers from eight countries and the European Commission announced the formation of a new research enterprise, the International Human Microbiome Consortium (IHMC), which will sequence the genomes of tens of thousands of microorganisms that live in and on the human body and that influence human health. Initial funding of more than US$200 million is being provided by the U.S. National Human Genome Research Institute (NHGRI) and the European Commission (EC). Jane Peterson, associate director of extramural research at the NHGRI, said international collaboration is very important in advancing science, and that “the sum is more than the parts.” Participants in the IHMC have agreed in principle to the free and open release of data and resources, and the coordination of research plans, as well as to sharing innovative developments, she reported. Data from microbiome research already being conducted by the NIH Human Microbiome Project and the EC Metagenomics ...