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This Week in PNAS: Mar 17, 2015

Editor's Note: Some of the articles described below are not yet available at the PNAS site, but they are scheduled to be posted some time this week.

In the early, online edition of the Proceedings of the National Academy of Sciences, researchers from the University of Texas at Austin present an essential genome for the opportunistic pathogen Pseudomonas aeruginosa, based on sequence data for transposon insertion mutagenesis strains of P. aeruginosa grown under normal lab conditions or in sputum samples from individuals with cystic fibrosis. By comparing essential genomes, the team found genes that are required for growth in the lab but not in sputum and vice versa. The study's authors also saw hints that gene function and gene architecture may shift slightly in the bug depending on its environment.

In another study slated to appear in PNAS, a team from the US and Sweden used a combination of exome sequencing and targeted sequencing to characterize mutation patterns in dozens of insulinomas —  pancreatic tumors that excrete excess insulin. The researchers identified recurrent mutations in the transcription factor gene YY1 through exome sequencing on matched tumor-normal samples from seven individuals with benign insulinomas. Targeted testing on additional benign or malignant insulinomas uncovered similar mutations in seven of 43 cases, while the group's chromatin immunoprecipitation sequencing experiments indicated that the glitch alters the DNA binding motif recognized by the YY1 gene product.

Finally, researchers from the US and France describe co-selected genes that appear to contribute to herbivore resistance adaptations in a range of Arabidopsis thaliana strains from different parts of western Europe. The team focused on nearly 600 A. thaliana accessions, using mass spectrometry to measure levels of glucosinolate compounds that Arabidopsis and related plants used to defend themselves against herbivores. When they folded in SNP data, the investigators found that genetic shifts at just a few key loci seemed to explain a significant proportion of the defense chemical adaptations.