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This Week in PNAS: Dec 1, 2015

Editor's Note: Some of the articles described below are not yet available at the PNAS site, but they are scheduled to be posted some time this week. 

In the early, online edition of the Proceedings of the National Academy of Sciences, University of California, San Diego, researchers consider genetic variants that seem to show protective effects against late-onset Alzheimer's disease and related dementia. By bringing together sequences for dozens of primate genomes, data from the 1000 Genomes Project, and expression profiles from human and chimp blood samples, the team found evidence that an Alzheimer's protective variant detected in past genome-wide association studies has been derived in humans, as have other gene variants suspected of diminishing neurodegenerative risk in individuals who are past their reproductive prime. From these findings, the study's authors speculate that "[s]election by inclusive fitness may be strong enough to favor alleles that protect against cognitive decline in post-reproductive humans."

A team from Japan and France delve into the gene repertoire of ancestral animal stem cells for another PNAS paper. After identifying more than 17,400 transcripts in Ephydatia fluviatilis using transcriptome sequencing on samples taken at different stages during the demosponge's development, the researchers focused on expression patterns in totipotent E. fluviatilis archeocyte cells compared to those in the sponge's other cell types. When they compared the genes expressed in the totipotent cells with those present in the Hydra cnidarian and in the flatworm Schmidtea mediterranea, authors of the study argue that most stem cell-related genes were present prior to the advent of early animals, though ancestral version of such genes seem to have been subject to pronounced post-transcriptional regulation rather than DNA regulators.

Researchers from the Chinese Academy of Sciences and elsewhere explore the DNA methylation consequences of whole-genome duplication in rice. The team did whole-genome bisulfite sequencing, transcript sequencing, and small RNA sequencing on an autotetraploid rice plant that had been produced from the diploid Oryza sativa subspecies indica cultivar Aijiaonante and self-pollinated for four dozen generations. When they compared patterns in the autotetraploid plant with those present in the diploid parent plant, the investigators uncovered methylation shifts affecting transposable elements in rice plants that had undergone whole-genome duplication, along with changes in nearby gene expression and alterations in small interfering RNA abundance. "Collectively," they write, "our findings suggest that chromosome doubling induces methylation variation in [transposable elements] that affect gene expression and may become a 'genome shock' response factor to help neoautopolyploids adapt to genome-dosage effects."