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This Week in PLOS: Jun 12, 2017

In PLOS Genetics, researchers from France, Japan, and Belgium present findings from a genome sequencing and comparative genomics study of root-knot nematodes in the Meloidogyne genus, focusing on ameioitic, asexual representatives that might offer clues about asexual root-knot nematodes that plague agricultural plants. By comparing the genome assemblies for three Meloidogyne species with one another and with available sequences from other nematodes, the team saw hints that Meloidogyne representatives with mitotic asexual reproductive strategies seem to have an uptick in transposable elements in their genomes relative to species that reproduce sexually, spurring speculation that plasticity in the parasites might stem from hybridization, polyploidy, and enhanced transposable element levels.

A University of Alberta-led team describes microRNAs showing enhanced expression in brain tissue from individuals with HIV-associated neurocognitive disorder (HAND), a group of neurological conditions known to manifest themselves in up to one-quarter of HIV/AIDS cases. As they report in PLOS Pathogens, the researchers did array-based miRNA analyses in postmortem brain tissue from 20 individuals with HAND and 10 individuals with HIV/AIDS who did not have such neurological complications. A comparison of brain miRNA patterns in these groups led to a dozen upregulated miRNAs in individuals with HAND — including miRNAs believed to target peroxisome biogenesis players — and five miRNAs with lower-than-usual expression in the HAND group.

Researchers from the US and the Netherlands report on somatic mutations detected through exome sequencing on matched tumor and normal samples from dozens of individuals with uveal melanoma for a paper appearing in PLOS One. Based on sequencing 52 primary tumor samples and three metastases from the liver, the team narrowed in on recurrent alterations affecting genes such as GNAQ, GNA11, BAP1, and SF3B1, and EIF1AX. The group went on to explore the latter mutations in more detail by tinkering with levels of normal or mutant EIF1AX in uveal melanoma cell lines and by sequencing RNA transcripts in cells containing portions of the mutated gene.