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This Week in PLOS: Nov 14, 2016

In PLOS Genetics, researchers from Spain, France, Japan, and the Netherlands track methylation in human gametes, pre-implantation embryos, and placental tissue, providing evidence for transient maintenance of some differentially methylated regions originating in human oocytes in placental tissue. Using available bisulfite and RNA sequencing data for human gametes, pre-implantation embryos, placental tissue, and somatic tissue, the team uncovered tens of thousands of differentially methylated regions. While almost all of the differentially methylated regions from sperm cells were reprogrammed by the blastocyst stage, some 80 percent of the methylated sites persisted from oocytes. Methylation and expression in placental tissue appeared to be polymorphic, in part reflecting epigenetic and imprinting patterns from maternal gametes.

A PLOS One paper by Colombian and American investigators describes microRNAs associated with kidney damage in individuals with systemic lupus erythematosus. The team used barcoded miRNA sequencing to test blood plasma samples from 140 individuals with lupus and 40 without, identifying 89 miRNAs that appeared to be present at different levels in patients with a form of lupus-related kidney damage called lupus nephritis compared with the healthy controls. When they took a closer look at this set, the researchers further homed in on a set of five validated miRNAs that can distinguish between systemic lupus erythematosus cases with or without kidney damage with 70 percent specificity and 97 percent sensitivity.

Finally, a team from the US and China demonstrates the feasibility of using environmental DNA in residual saliva samples to non-invasively follow brown bears in the wild. As they report in PLOS One, the researchers collected swab samples from 156 partially consumed Pacific salmon carcasses from sites in Southeast Alaska, comparing DNA patterns in the samples with those found in almost 300 scat samples from the same sites. They were able to successfully extract, amplify, and genotype bear DNA 92 scat swab samples and 97 fish samples, particularly salmon brain case or bite hole sites that may have contained more brown bear saliva. Based on their results, the authors argue that "swabbing of food remains or consumed baits from other animals may be an additional cost-effective, and valuable tool in the study of the ecology and population biology of many elusive and/or wide-ranging species."