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This Week in PNAS: Dec 15, 2009

In a paper in the Proceedings of the National Academy of Sciences this week, scientists at CNRS in Paris have used network analysis to study the structure and evolution of genetic diversity. Studying about 119,000 homologous DNA families taken from 111 cellular genomes and 165,529 phage, plasmid, and environmental virome sequences, they found that plasmids, not viruses, were "key vectors of genetic exchange between bacterial chromosomes, both recently and in the past," they say.

In other work, researchers look at the diversity of microbial communities from the abyssal sea floor. Led by first author Frank Scheckenbach at the University of Cologne, they sampled eukaryotic microbes from all three abyssal plains of the southeastern Atlantic Ocean, including the Angola, Cape, and Guinea Abyssal Plains, from depths of 5,000 meters, and found "great phylogenetic diversity." Many clones were affiliated with parasitic species.

Scientists led by NCI's Jing Huang used a genome-wide approach to discover a connection between the p53 and the Wnt signaling pathways in mouse embryonic stem cells. Using ChIP-chip and gene expression microarrays, they found that the Wnt signaling pathway "is significantly overrepresented in p53-regulated genes in mESCs" and that activation of this pathway inhibits the differentiation of mESCs.

At the University of California, Berkeley, and Lawrence Berkeley National Laboratory, researchers compared feature frequency profiles (FFPs) of whole proteomes to construct a "whole-proteome phylogeny of prokaryotes." They constructed the FFP trees with whole proteomes of 884 prokaryotes, 16 unicellular eukaryotes, and 2 random sequences, and present a simplified proteome FFP tree of monophyletic class or phylum with branch support.

Using single-molecule and stopped-flow FRET analysis, scientists led by Smita Patel at the University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical School were able to observe the initiation-to-elongation transition of T7 RNA polymerase. They show that the "slow steps of transcription initiation, including DNA scrunching/RNAP-promoter rotational changes during 5- to 8-nt synthesis, not the major conformational changes, dictate the overall rate of [elongation] formation in T7 RNAP."

Finally, a team of American and French researchers led by Didier Raoult at the Université de la Méditerranée in Marseille have sequenced the genome of a large virus, now named the Marseillevirus, living inside the amoeba Acanthamoeba polyphaga. A story at GenomeWeb Daily News has the full scoop.

The Scan

NFTs for Genome Sharing

Nature News writes that non-fungible tokens could be a way for people to profit from sharing genomic data.

Wastewater Warning System

Time magazine writes that cities and college campuses are monitoring sewage for SARS-CoV-2, an approach officials hope lasts beyond COVID-19.

Networks to Boost Surveillance

Scientific American writes that new organizations and networks aim to improve the ability of developing countries to conduct SARS-CoV-2 genomic surveillance.

Genome Biology Papers on Gastric Cancer Epimutations, BUTTERFLY, GUNC Tool

In Genome Biology this week: recurrent epigenetic mutations in gastric cancer, correction tool for unique molecular identifier-based assays, and more.