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This Week in Science: Jan 28, 2011

In Science this week, a team led by investigators at the US Department of Energy Joint Genome Institute reports its discovery of 27,755 putative carbohydrate-active genes among cow rumen microbes through metagenomic sequencing. The team also found that these genes "expressed 90 candidate proteins, of which 57 percent were enzymatically active against cellulosic substrates," which may have implications for future studies on "industrial-scale conversion of cellulosic biomass into biofuels." Further, the DOE JGI-led team assembled and validated 15 genomes for microbes that participate in the deconstruction of cellulosic biomass.

Mark Enright at the UK-based firm Biocontrol Ltd. and Imperial College London's Brian Spratt discuss "the genomic view of bacterial diversification." High-throughput, large-scale genomic approaches have thus far allowed investigators to obtain "a mass of information about the population and evolutionary biology of any bacterial — or archaeal — species at a modest and rapidly falling cost," Enright and Spratt write, adding their expectation that "exciting times lie ahead for the integration of bacterial genome data, epidemiology, and evolution."

Anthony James at the University of California, Irvine, says in this week's Science that it's important that the public be informed that researchers working with emerging genetics technologies "are aggressively supporting the formulation of best practices for their safe, efficient, ethical, and regulated application, and are reaching out to experts from a range of relevant disciplines for advice and counsel." James says that though investigators have not yet "achieved harmonized international standards" for the use of these technologies, "we are much closer than people realize." It'd be a tragedy, he adds, were the process of developing these standards "to stifle creativity in the development of not only genetics-based solutions, but all truly novel approaches that seek to reduce" the health threats that other diseases pose.

And in Science Signaling, investigators at the University of Texas Southwestern Medical Center and Weill Cornell Medical College in New York report results from their genome-wide RNAi screen of cultured murine cells. Among other things, the team established previously unknown associations between the Hedgehog and Wnt signaling pathways as well as "genes linked to developmental malformations, diseases of premature tissue degeneration, and cancer." The team also found that Stk11, the kinase also known as Lkb1, is a "critical mediator in both the Hh and the Wnt pathways," it reports.

The Scan

Study Points to Tuberculosis Protection by Gaucher Disease Mutation

A mutation linked to Gaucher disease in the Ashkenazi Jewish population appears to boost Mycobacterium tuberculosis resistance in a zebrafish model of the lysosomal storage condition, a new PNAS study finds.

SpliceVault Portal Provides Look at RNA Splicing Changes Linked to Genetic Variants

The portal, described in Nature Genetics, houses variant-related messenger RNA splicing insights drawn from RNA sequencing data in nearly 335,700 samples — a set known as the 300K-RNA resource.

Automated Sequencing Pipeline Appears to Allow Rapid SARS-CoV-2 Lineage Detection in Nevada Study

Researchers in the Journal of Molecular Diagnostics describe and assess a Clear Labs Dx automated workflow, sequencing, and bioinformatic analysis method for quickly identifying SARS-CoV-2 lineages.

UK Team Presents Genetic, Epigenetic Sequencing Method

Using enzymatic DNA preparation steps, researchers in Nature Biotechnology develop a strategy for sequencing DNA, along with 5-methylcytosine and 5-hydroxymethylcytosine, on existing sequencers.