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This Week in PLoS: Jun 22, 2009

Just out in PLoS One, scientists from the Stazione Zoologica Anton Dohrn in Italy published a paper on mapping SNPs and indels on Venter's chromosomes 17 through 22. The authors compared those to the human reference genome and found that insertions and deletions were more likely to occur in GC-rich regions. They conclude, "Our study strongly suggests that the distribution of insertions/deletions is due to the structure of chromatin which is mostly open in gene-rich, GC-rich isochores, and largely closed in gene-poor, GC-poor isochores."

Also in PLoS One, a large team of researchers looked at 340 SNPs representing candidate genes in ovarian cancer, finding the most significant association for the SNP rs2107425 on chromosome 11p15.5. That SNP has previously been linked to breast cancer susceptibility. Another paper reports the genome sequence of Mycobacterium abscessus, an emerging pathogen which has a 5 Mb circular chromosome with nearly 5,000 predicted coding sequences, according to the abstract.

In PLoS Computational Biology, scientists at Princeton used microarray data for C. elegans to generate predictions of tissue-specific gene expression, which they then validated experimentally. "These patterns of tissue-specific expression are more accurate than existing high-throughput experimental studies for nearly all tissues; they also complement existing experiments by addressing tissue-specific expression present at particular developmental stages and in small tissues," the authors write.

Two papers in PLoS Genetics report on large-scale studies of Drosophila. Senior author Steven Brenner and his colleagues developed a method to analyze the effects of alternative splicing combined with nonsense-mediated mRNA decay, specifically looking at genes whose expression can be down-regulated after they've been transcribed. They turned up 45 genes that met their criteria; that set includes "a number that are central to the cell's regulatory processes, including translation, RNA splicing, and cell cycle progression," the authors write. And in this paper from senior author Alexander Bishop, scientists used RNAi screening to identify genes involved in damage survival response in cells. The authors went on to examine the resulting pathway information in mouse, and found that "identification of pathways can facilitate comparative biology analysis when direct gene/orthologue comparisons fail," they write.

The Scan

CDC Calls Delta "Variant of Concern"

CNN reports the US Centers for Disease Control and Prevention now considers the Delta variant of SARS-CoV-2 to be a "variant of concern."

From FDA to Venture Capital

Former FDA Commissioner Stephen Hahn is taking a position at a venture capital firm, leading some ethicists to raise eyebrows, according to the Washington Post.

Consent Questions

Nature News writes that there are questions whether informed consent was obtained for some submissions to a database of Y-chromosome profiles.

Cell Studies on Multimodal Single-Cell Analysis, Coronaviruses in Bats, Urban Microbiomes

In Cell this week: approach to analyze multimodal single-cell genomic data, analysis of bat coronaviruses, and more.