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This Week in PNAS: Apr 28, 2009

Published in the most recent issue of PNAS, scientists at the University of Illinois at Urbana-Champaign have used molecular dynamics simulations to model the community interaction networks between tRNA and aminoacyl tRNA synthetase of a bacterial glutamyl-tRNA synthetase and an archaeal leucyl-tRNA synthetase complex. They found a large number of suboptimal communication networks between the molecule and enzyme and that "residues and nucleotides in the majority of pathways for intercommunity signal transmission are evolutionarily conserved and are predicted to be important for allosteric signaling."

In early online, scientists from UCSF's Department of Pharmaceutical Chemistry looked into the ability of molecular docking to predict target-ligand hits from a large-scale screen. Covering a library of more than 137,000 possible ligand fragments docked against the structure of β-lactamase, they found a 48 percent hit rate that "compares very favorably with 'lead-like' docking and high-throughput screening against the same enzyme."

Also in early online, scientists at Princeton University performed a quantitative genome-scale analysis of protein localization in Caulobacter crescentus. Using fluorescent protein fusions, they identified nearly 300 localized proteins, up to 10-fold more than were previously characterized, they say in the abstract. They then measured protein distribution by using their "projected system of internal coordinates from interpolated contours (PSICIC) image analysis toolkit," which they say can be readily applied to other systems.

Finally, a consortium of researchers fine-mapped a common variant in the MSMB gene on chromosome 10q11.2 to be associated with prostate cancer susceptibility. Following on two GWAS that identified the SNP rs10993994, in this study they used HapMap SNPs to fine-map across a region flanking rs10993994 with 13 tag SNPs in 6,118 prostate cancer cases and 6,105 controls of European origin from the CGEMS project. Further functional studies showed that indeed, rs10993994 " remained the most strongly associated marker with prostate cancer risk."

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.