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This Week in PLoS : Jul 9, 2012

Writing in PLoS One, researchers in France report on their detection of the Staphylococcus aureus delta-toxin using whole-cell MALDI-TOF mass spectrometry in a series of 168 clinical isolates and 23 unrelated glycopeptide-intermediate strains.

In the same journal, Arizona State University's Roy Curtiss and his colleagues compare the genome of the UK-1 strain of Salmonella enterica serovar Typhimurium with those of other S. Typhimurium strains, finding "many interesting genetic and genomic variations specific to UK-1," they write. Among those variations is a UK-1-specific gene deletion that the researchers found "exhibited a significant decrease in oral virulence in BALB/c mice."

Over in PLoS Computational Biology this week, Cornell University's Diana Chang and Alon Keinan show that, in human genome-wide association studies, "synthetic associations tend to be further away from the underlying risk alleles compared to 'natural associations' (i.e. associations due to underlying common causal variants), but to a much lesser extent than previously predicted, with both the age and the effect size of the risk allele playing a part in this phenomenon." Chang and Keinan also show that associated allele frequency may be an indicator of synthetic associations.

And in PLoS Genetics, the HudsonAlpha Institute for Biotechnology's Gregory Barsh and his colleagues present guidelines for GWAS. These guidelines are intended to "emphasize work in which genetic approaches and genetic logic help us learn more about biology," such that "regardless of the species or the population being studied, genetic arguments should stand on their own," Barsh et al. write.

The Scan

Octopus Brain Complexity Linked to MicroRNA Expansions

Investigators saw microRNA gene expansions coinciding with complex brains when they analyzed certain cephalopod transcriptomes, as they report in Science Advances.

Study Tracks Outcomes in Children Born to Zika Virus-Infected Mothers

By following pregnancy outcomes for women with RT-PCR-confirmed Zika virus infections, researchers saw in Lancet Regional Health congenital abnormalities in roughly one-third of live-born children.

Team Presents Benchmark Study of RNA Classification Tools

With more than 135 transcriptomic datasets, researchers tested two dozen coding and non-coding RNA classification tools, establishing a set of potentially misclassified transcripts, as they report in Nucleic Acids Research.

Breast Cancer Risk Related to Pathogenic BRCA1 Mutation May Be Modified by Repeats

Several variable number tandem repeats appear to impact breast cancer risk and age at diagnosis in almost 350 individuals carrying a risky Ashkenazi Jewish BRCA1 founder mutation.