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This Week in PNAS: Oct 2, 2018

A Sanford Burnham Prebys Medical Discovery Institute-led team describes copy number variants occurring midway through neurogenesis in the cerebral cortex in a mouse model. Using a single-cell, whole-genome sequencing method with transposases-based amplification, the researchers assessed hundreds of individual cells in developing or fully formed cerebral cortex samples from dozens of mice, using a machine learning informatics method to toss out false-positive CNVs. Their search uncovered thousands of new CNVs — many spanning less than a million bases of sequence — that became more prominent during neurogenesis. "These data demonstrate the existence of myriad CNVs, which genomically diversify neural cells before incorporation into the mature organization of the brain," the authors write. GenomeWeb has more on this, here.

University of Ottawa researchers explore drivers of genetic and phenotypic variation in the opportunistic pathogen Pseudomonas aeruginosa, which often causes opportunistic infections in individuals with cystic fibrosis. The team followed a dozen parallel populations of P. aeruginosa, grown in the lab under a range of cystic fibrosis-relevant conditions for hundreds of generations. Based on their findings, the investigators suggest that "nutritional complexity and reduced dispersal can drive evolutionary diversification of P. aeruginosa independent of other features of the [cystic fibrosis] lung such as an active immune system or the presence of competing microbial species."

A team from China and Australia reports on DNA demethylase enzyme mutations in rice that appear to boost the nutritional value of the grains by prompting the production of a thicker-than-usual layer of protein-, vitamin-, and mineral-rich material on the outside of the seed, known as the aleurone. After screening for thickened aleurone in tens of thousands of grains from more than 6,000 mutant rice plants, the researchers characterized the nutritional content of such seeds and used map-based cloning to narrow in on an alteration affecting an intron of the DNA demethylase-coding gene OsROS1. Their subsequent bisulfite sequencing analyses suggest that this mutation bumps up methylation at some sites in the genome, including regions that dial down expression of transcription factors suspected of contributing to aleurone differentiation.