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This Week in PNAS : Jun 26, 2012

In a paper appearing in this week's PNAS Early Edition, a team led by investigators at the Salk Institute for Biological Studies in La Jolla, Calif., shows that, in response to salicylic acid exposure, transposon-associated differentially methylated regions in Arabidopsis thaliana that are accompanied by the upregulation of 21-nt siRNAs are often coupled to transcriptional changes of the transposon and/or the proximal gene. "We report an unexpected role for DNA methylation in regulation of the Arabidopsis thaliana immune system," the authors write.

Scientists at three research institutions in California show in a genome-wide analysis of glucocorticoid receptor-binding sites in mouse that "p85α plays a critical role in glucocorticoid-induced insulin resistance and muscle atrophy in C2C12 myotubes," as they report online in advance in PNAS this week.

University of Washington's David Russell and his colleagues elsewhere report their use of in vivo gene targeting to "insert an enhancer-promoter element at an imprinted chromosome 12 locus in mice, thereby converting [approximately] 1 in 20,000 normal hepatocytes into a focus of HCC [hepatocellular carcinoma] with a single genetic modification." Russell et al. say that while the distinct phenotypic and prognostic subclasses of human HCC have been difficult to reproduce in animal experiments, their current study suggests future applications of in vivo gene targeting for "studying various tumors in diverse animal species."

The "heavy use of equations impedes communication among biologists," write Tim Fawcett and Andrew Higginson from the University of Bristol in PNAS this week. In an analysis of how the use of mathematical equations affects the scientific impact of studies in ecology and evolution, Fawcett and Higginson show that the "density of equations in an article has a significant negative impact on citation rates, with papers receiving 28 percent fewer citations overall for each additional equation per page in the main text," they write.

The Scan

Germline-Targeting HIV Vaccine Shows Promise in Phase I Trial

A National Institutes of Health-led team reports in Science that a broadly neutralizing antibody HIV vaccine induced bnAb precursors in 97 percent of those given the vaccine.

Study Uncovers Genetic Mutation in Childhood Glaucoma

A study in the Journal of Clinical Investigation ties a heterozygous missense variant in thrombospondin 1 to childhood glaucoma.

Gene Co-Expression Database for Humans, Model Organisms Gets Update

GeneFriends has been updated to include gene and transcript co-expression networks based on RNA-seq data from 46,475 human and 34,322 mouse samples, a new paper in Nucleic Acids Research says.

New Study Investigates Genomics of Fanconi Anemia Repair Pathway in Cancer

A Rockefeller University team reports in Nature that FA repair deficiency leads to structural variants that can contribute to genomic instability.