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This Week in PLOS: Nov 24, 2014

In PLOS Genetics, National Institutes of Health researchers report on loci linked to aggressive prostate cancer, which they identified through systems biology-based analyses on mouse models of the disease. Through quantitative trait locus testing on descendants of crosses involving transgenic mice designed to be prone to neuroendocrine prostate cancer, the team narrowed in on sites in the genome that seemed to be associated with aggressive prostate cancer. Microarray profiling on more than 100 mouse tumors, together with the candidate QTLs, made it possible to find nearly three dozen genes linked to aggressive disease, including a handful of genes with altered expression in aggressive human prostate tumors.

Bacterial contamination is common in RNA sequence data generated from human tissues in the clinical setting, according to an opinion paper in PLOS Pathogens. Researchers from Tulane University and elsewhere considered RNA sequence datasets for almost 200 human cancer samples and dozens more normal human tissue samples. From that data, the study's authors determined that "substantial bacterial contamination is routinely found in existing human-derived RNA-seq datasets that likely arises from environmental sources." A recent PeerJ study described contamination by bacterial sequences in publicly available genome assemblies, as reported in GenomeWeb last week.

A team from Spain performed metabolic profiling on heart tissue and blood samples from mice infected with the Chagas disease-causing pathogen Trypanosoma cruzi. As they report in PLOS Neglected Tropical Diseases, the researchers used mass spectrometry, liquid chromatography, and other methods to track metabolite profiles in plasma and heart samples collected from female mice infected with T. cruzi for two or three weeks. The search uncovered 200 compounds found at distinct levels in heart tissue sample from infected mice — including a jump in levels of compounds involved in processes such as glucose uptake and fatty acid synthesis — along with another 100 compound showing differential representation in infected mouse plasma.