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This Week in PNAS: Jul 28, 2009

In PNAS this week, European scientists studied how cytoskeleton proteins affect viral DNA replication in bacteria. Using fusion proteins and fluorescence microscopy, they were able to show that the actin-like MreB cytoskeleton protein of E. coli and Bacillus subtilis is required for efficient viral DNA replication. It works by localizing the B. subtilis phage DNA and replication machinery to the cell membrane. "Importantly, we show that MreB interacts directly with the [phage] membrane-protein p16.7, responsible for attaching viral DNA at the cell membrane," they write.

Others have used genomic analysis to study pediatric acute myeloid leukemia. In one paper from scientists at St. Jude Children's Research Hospital, they used SNP arrays and candidate gene resequencing on 111 children with de novo AML and found that there are few genetic changes, with a mean 2.38 somatic copy number changes per leukemia. Surprising, they say, is that 34 percent of the leukemias had no copy number changes and 28 percent of the leukemias with recurrent translocations showed no sequence or numerical abnormalities. In another study, a collaboration involving over 20 researchers used array CGH on 86 AML genomes as a complement to karotype analysis to find a total of 201 somatic copy number alterations, making that a mean of 2.34 CNAs per genome.

In work led by UC Berkeley's Michael Marletta, researchers found that DNA aptamers that can bind to heme "efficiently inhibit in vitro hemozoin formation catalyzed by either a model lipid system or parasite-derived extracts just as or more potently than chloroquine," suggesting that these can be used as tools to study functional pathways in the malaria parasite, Plasmodium falciparum.

Scientists at the University of Adelaide have characterized the distribution of retrotransposons and simple sequence repeats in the bovine genome. Among other things, they found that the cow genome has typical repeats found in placental mammals, but also a significant number of "long interspersed nuclear element RTE (BovB) elements proposed to have been horizontally transferred from squamata," they write in the abstract. Looking further, they found that only a few of them are likely to retrotranspose.

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.