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This Week in PLOS: Feb 22, 2016

In PLOS Genetics, researchers from Finland and Sweden describe recurrent mutations that they detected in uterine leiomyosarcoma tumors using exome sequencing. In comparing protein-coding sequences in 19 uterine leiomyosarcoma tumors with matched normal samples, the team uncovered 43 genes that were mutated more than once. The top culprits were the TP53, ATRX, and MED12 genes, which were mutated in 33 percent, 26 percent, and 21 percent of the tumors, respectively. And in follow-up experiments on 44 tumors, the study's authors saw a dip in ATRX protein levels a little more than half the time, leading to a so-called "alternative lengthening of telomeres" phenotype that they suspect may be susceptible to treatment with existing ATR inhibitor drugs.

A Scottish team takes a look at the interplay between host genetics and methane production by microbes in cattle rumen for another PLOS Genetics paper. In particular, the researchers tracked differences in methane emissions, archaea abundance, microbial community membership, and microbial gene content in rumen samples from cattle from different breed crosses and diet groups. Their research demonstrates that host genetics do play an apparent role in features such as feed conversion efficiency and methane emission. "[G]enetic selection of low-emitting animals is a viable option based on a newly developed selection criterion," the authors write. "The experimental data provided a comprehensive insight into the host additive genetic influence on the microbiome, the impact of nutrition on genetics and the microbiome, and the effect of metagenomic microbial genes on the analyzed traits."

Finally, Italian researchers reporting in PLOS One discuss findings from a whole-genome sequencing study on a European strain of an infectious laryngotracheitis virus (ILTV) that can cause contagious respiratory conditions in chickens. Using two commercial chicken embryo origin vaccines and three samples collected from ILTV-infected chickens during outbreaks in Italy in 1980, 2007, and 2011, the team put together five full ILTV genomes with reads generated on Roche 454 instruments. When they compared the sequences to one another and to ILTV isolates sequenced previously, the researchers saw between 99.996 percent and 99.99 percent similarity between the strains. However, their analysis also highlighted SNP and insertion changes suspected of influencing virulence and attenuation of the virus in vaccine strains.

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