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This Week in PNAS: Dec 11, 2012

In the early, online edition of the Proceedings of the National Academy of Sciences, a University of Colorado, Argonne National Laboratory, and Northern Arizona University-led team reports on the composition and functional attributes of soil microbial communities found in a range of biomes. Using 16S ribosomal RNA sequencing and metagenomic sequencing, the researchers looked at 16 microbe communities from soil samples taken in cold or hot deserts, forests, grasslands, or tundra environments, classifying these microbiomes based on their apparent functional protein profiles, phylogeny, and taxonomy. The findings point to distinct soil communities in desert biomes, for instance, where microbes tended to have a bolstered repertoire of genes involved in osmoregulation and dormancy, but fewer antibiotic resistance and nutrient cycling genes.

Researchers from the US and Israel explore the fail-safe mechanisms that help maintain transcriptional silencing of regions influenced by the tumor suppressor p53 in the mouse genome. The team defined parts of the genome that are subject to DNA methylation-based silencing in the presence of p53, showing that the slew of repeats and non-coding RNAs transcribed in the absence of p53 go on to trigger an interferon response that ultimately leads to apoptosis. "[T]his work reveals roles for p53 and [interferon] that are key for genetic stability," study authors say, "and therefore relevant to both tumorigenesis and the evolution of species."

Researchers from the Natural History Museum, London, and the University of Exeter explore gene fission and fusion events in the genomes of more than 100 fungi. Starting from 63 gene fusions found in at least two of the nine fungal genomes they tested initially, the investigators followed the fate of these genes in 115 fungal genomes. Through phylogenetic and comparative analyses of these genomes, for instance, the team was able to detect 110 instances in which the fusions underwent gene fission — a process that appears to result from gene separation, degeneration, or duplication. "[W]e identify multiple mechanisms that drive gene fission," the study's authors write, "and that do not require complex simultaneous evolutionary events, suggesting that gene fissions play a hitherto underestimated role in gene evolution."

The Scan

Genes Linked to White-Tailed Jackrabbits' Winter Coat Color Change

Climate change, the researchers noted in Science, may lead to camouflage mismatch and increase predation of white-tailed jackrabbits.

Adenine Base Editor Targets SCID Mutation in New Study

Researchers from the University of California, Los Angeles, report in Cell that adenine base editing was able to produce functional T lymphocytes in a model of severe combined immune deficiency.

Researchers Find Gene Affecting Alkaline Sensitivity in Plants

Researchers from the Chinese Academy of Science have found a locus affecting alkaline-salinity sensitivity, which could aid in efforts to improve crop productivity, as they report in Science.

International Team Proposes Checklist for Returning Genomic Research Results

Researchers in the European Journal of Human Genetics present a checklist to guide the return of genomic research results to study participants.