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This Week in PLOS: Dec 5, 2016

In PLOS Genetics, researchers from the US, Brazil, and China used a combination of RNA sequencing and chromatin immunoprecipitation sequencing on primary human liver cells to gauge response to metformin, a drug used to treat type 2 diabetes and other conditions. The team tracked expressed transcripts and sequences associated with active or repressive histone marks in hepatocytes exposed to metformin or control compounds to narrow in on candidate metformin response genes and regulatory sequences for more detailed analyses. "Our findings provide a genome-wide representation of metformin hepatic response, highlight important sequences that could be associated with inter-individual variability in glycemic response to metformin and identify novel [type 2 diabetes] treatment candidates," the authors write.

A team from Fudan University and the Chinese Center for Disease Control and Prevention describe an array-based strategy for detecting protozoa species in the blood in a PLOS Neglected Tropical Diseases paper. The researchers compared a microarray with more than 100 probes, corresponding to conserved regions in protozoans such as Plasmodium, Leishmania, or Trypanosoma, with PCR- or sequencing-based methods for identifying 18 protozoan species. Their results suggest the array method could pick up almost 92 percent of blood protozoa with sensitivity beyond 82 percent and at least 95 percent specificity.

Researchers at the University of Nebraska present a comparison of a draft rhesus macaque genome and an improved macaque genome for a PLOS One study. The team considered the protein-coding genes that were annotated in each version of the genome, for example, looking at the relationship between these genes and their apparent orthologs in the human genome. In particular, the study's authors note that the draft version of the rhesus macaque genome contained gene sequences that did not turn up in the improved genome, suggesting that "spurious sequences must be filtered out from evolutionary analyses to obtain correct results."