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This Week in PLOS: Sep 19, 2016

In PLOS Genetics, an international team led by investigators in the UK, Finland, and Norway explores the respective roles of gene regulatory elements and genes in the accessory and core genomes of Escherichia coli populations from ST131, a pathogenic lineage involved in infections outside of the intestine. Using 228 E. coli ST131 genome sequences representing isolates from birds, domestic animals, and clinical samples, the researchers teased apart pan-genome structures for the lineage. Along with clues to drug resistance in ST131 subtypes, their analyses suggest E. coli gains access to larger accessory gene collections as it becomes adept at colonizing multiple host species.

For a paper in PLOS Neglected Tropical Diseases, researchers from the University of Maryland and elsewhere describe transcriptome patterns in skin biopsy samples from individuals with Leishmania braziliensis infections. The team used RNA sequencing to assess skin biopsies from eight individuals with early cutaneous leishmaniasis infections and 17 late cutaneous leishmaniasis cases. The meta-transcriptomic profiles differed between individuals with or without L. braziliensis transcripts, the study's authors note, particularly when it came to transcripts related to B cell activation and other immune response. "Biopsies without detectable parasite transcripts showed decreased evidence for B cell activation, but increased expression of antimicrobial genes and genes encoding skin barrier functions," they write.

Finally, a team from the Netherlands, Greece, and elsewhere considers population patterns for biomarkers used to guide drug use and predicting drug toxicity. As they report in PLOS One, the researchers used array-based genotyping to scrutinize more than 1,900 potential pharmacogenomic biomarkers falling in 231 genes, in more than 1,100 individuals from 18 European populations. The frequency of several clinically important pharmacogenomic marker alleles often varied from one population to the next, they found, including seven markers that were previously implicated in response to dozens of approved drugs.

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