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This Week in PNAS: Sep 8, 2009

In PNAS this week, scientists at Zurich's Institute of Microbiology used community proteogenomics to study the physiology of phyllosphere bacteria. Analyzing the bacterial communities on the leaves of soybean, clover, and Arabidopsis, they found a "high consistency" on the three different plants, "both with respect to the predominant community members (including the alphaproteobacterial genera Sphingomonas and Methylobacterium) and with respect to their proteomes," the abstract says.

In work led by Joseph Nevins at the Duke Institute for Genome Sciences and Policy, his team found that a "combination of histological and genomic analyses can uncover substantial heterogeneity in mammary tumor formation and therefore highlight aspects of tumor phenotype not evident in the population as a whole." Analysis of Myc-induced mammary tumors in mouse models showed that the high level of tumor heterogeneity was caused by activating Ras mutations and that two major histological subtypes showed differences in two cell signaling pathways, β-catenin and Stat3.

Japanese scientists, partly led by those at the RIKEN Advanced Science Institute, developed a genetically encoded FRET-based indicator to watch histone acetylation in live cells. The indicator showed changes in the acetylation state of both K5 and K8 in histone H4, and they used it to watch the changes in histone H4 acetylation levels during mitosis, among other things.

Finally, researchers led by first authors Kenji Nakata and Barbara Lipska at NIH show that splice variants of the Disrupted-In-Schizophrenia-1 gene are associated with schizophrenia. Looking at DISC1 transcripts in adult and fetal human brain from normal and patients with schizophrenia, they found that there were many alternatively spliced transcripts, including groups lacking exon 3, exons 7 and 8, an exon 3 insertion variant, and intergenic splicing between TSNAX and DISC1. They also found that certain risk-associated SNPs were linked to expression of several of the alternatively spliced transcripts.

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.