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This Week in PNAS: Oct 9, 2012

An international team led by investigators at the French National Institute for Agricultural Research, the US Department of Energy's Joint Genome Institute, and the Wellcome Trust Centre for Human Genetics presents results from a genome sequencing study of the button mushroom, Agaricus bisporus, in the early, online issue of the Proceedings of the National Academy of Sciences. The team generated draft genome sequences for two A. bisporus representatives — a cultivated European strain from the A. bisporus variety bisporus and a California strain from the burnetti variety that makes it home in the leaf litter around woody plants. By folding in transcriptome data for different mushroom developmental stages and for mushrooms grown on different substrates, the group uncovered clues about the fungal adaptations that the mushroom uses for growth in humic acid-rich environments, including genes coding for enzymes involved in the decomposition of leaves and other plant materials.

Adult stress levels and socio-economic status during childhood appear to influence some DNA methylation differences that exist between individuals within a community, according to a study by researchers at the University of British Columbia, Simon Fraser University, and Stanford University. The researchers performed array-based DNA methylation profiling on peripheral mononuclear white blood cells from 92 individuals between the ages of 24 and 45 from a community in and around Vancouver, Canada. When they looked at how methylation patterns at the promoters of nearly 14,500 human genes corresponded to individuals' gene expression profiles, blood composition, early-life socio-economic status and so on, the researchers found several factors that seemed to coincide with inter-individual methylation differences. These included the proportion of different white blood cell types present in the individuals' sample, their stress hormone output sex, age, and ethnicity as well as experiences such as childhood poverty and stress during adulthood. Even so, the DNA methylation differences detected often did not coincide with gene expression shifts at nearby genes, the researchers reported, "suggesting a more complex relationship than anticipated."

Another PNAS study looks at the bacterioplankton communities present in ocean samples collected in the Antarctic and the Arctic. By sequencing the V6 region of the 16S ribosomal RNA gene, Desert Research Institute investigators Alison Murray and colleagues from several centers around the world catalogued the bacteria found in surface or deep water bacterioplankton communities in the Southern and Arctic Oceans. The researchers then looked at how deep-water and shallow-water communities in the 20 Southern Ocean samples and the 24 Arctic Ocean samples tested compared with one another and with four-dozen samples collected at lower latitude ocean sites. "Our results suggest differences in environmental conditions at the poles and different selection mechanisms controlling surface and deep ocean community structure and diversity," the study's authors say. "Surface bacterioplankton may be subjected to more short-term variable conditions, whereas deep communities appear to be structured by longer water-mass residence times and connectivity through ocean circulation."

The Scan

Genome Sequences Reveal Range Mutations in Induced Pluripotent Stem Cells

Researchers in Nature Genetics detect somatic mutation variation across iPSCs generated from blood or skin fibroblast cell sources, along with selection for BCOR gene mutations.

Researchers Reprogram Plant Roots With Synthetic Genetic Circuit Strategy

Root gene expression was altered with the help of genetic circuits built around a series of synthetic transcriptional regulators in the Nicotiana benthamiana plant in a Science paper.

Infectious Disease Tracking Study Compares Genome Sequencing Approaches

Researchers in BMC Genomics see advantages for capture-based Illumina sequencing and amplicon-based sequencing on the Nanopore instrument, depending on the situation or samples available.

LINE-1 Linked to Premature Aging Conditions

Researchers report in Science Translational Medicine that the accumulation of LINE-1 RNA contributes to premature aging conditions and that symptoms can be improved by targeting them.