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This Week in PLoS: May 16, 2011

In PLoS Genetics this week, researchers across Brazil report sequencing the genome of an Herbaspirillum seropedicae strain, a diazotrophic endophyte "capable of colonizing intercellular spaces of grasses such as rice and sugar cane." Through the Paraná State Genome Programme, the team sequenced the 5,513,887 basepair genome of H. seropedicae strain SmR1, which it found is "a highly versatile microorganism with capacity to metabolize a wide range of carbon and nitrogen sources and with possession of four distinct terminal oxidases." Furthermore, the team identified genes for hemagglutinins, hemolysins, and adhesins, as well as a gene "coding for ACC deaminase, which may be involved in modulating the associated plant ethylene-signaling pathway," it writes.

A team led by investigators at the Universidad Peruana Cayetano Heredia in Lima, Peru, reports in PLoS Neglected Tropical Diseases this week on its comparative gene expression analysis of five phenotypically diverse clinical isolates of Leishmania braziliensis throughout its life cycle. Using real-time PCR, the team "tested 12 genes encoding proteins with roles in transport, thiol-based redox metabolism, cellular reduction, RNA poly(A)-tail metabolism, cytoskeleton function and ribosomal function" in each isolate. The researchers found that, in general, the regulation of gene expression in L. braziliensis "essentially occurs around the stationary phase of promastigotes," though the genes involved vary by isolate. Given its analysis, the team says that for L. braziliensis, "results obtained on an individual strain are not necessarily representative of a given species."

Over in PLoS One, investigators at Canada's BC Cancer Agency show that massively parallel sequencing is a "highly sensitive method for detecting putative infectious agents associated with human tissues," and that the technique — which "provides the opportunity to sample the transcriptome of a given tissue comprehensively" — affords sensitive detection of "human RNA-seq libraries spiked with decreasing amounts of an RNA-virus."

In another PLoS One paper, researchers in Spain report their proof-of-concept study on deep- versus population-sequencing of "HIV-1-infected individuals with previous triple-class virological failure who also developed virologic failure to deep salvage therapy." The team sequenced seven patients using both techniques, and they found that, while deep sequencing detected all mutations found by population sequencing, it "did not consistently modify the susceptibility predictions achieved with population sequencing for darunavir, tipranavir, or raltegravir," the authors write. Overall, the team says that "in this subset of heavily pre-treated individuals, deep sequencing improved the assessment of genotypic resistance to etravirine, but did not consistently provide additional information on darunavir, tipranavir or raltegravir susceptibility."

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.