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This Week in PLoS: Jun 21, 2010

In PLoS One this week, an international research team reports the "variability in the incidence of miRNAs and genes in fragile sites and the role of repeats and CpG islands in the distribution of genetic material," which they've elucidated using statistical models. The researchers found that fragile sites are denser in miRNAs on average, and that there's a "positive correlation between fragility and repeats, and between miRNAs and CpG islands."

Also in PLoS One, Anke Treuner-Lange at the Institut für Mikrobiologie und Molekularbiologie in Germany compares the phosphatomes of the multicellular myxobacterian Myxococcus xanthus and Sorangium cellulosum with other prokaryotic genomes. Treuner-Lange constructed phylogenetic trees to position the M. xanthus and S. cellulosum sequences relative to protein phosphatases of other organisms, and found that "there has been a greater expansion of [eukaryotic-like protein kinases] than [protein phosphatases] in multicellular myxobacteria."

In PLoS Neglected Tropical Diseases, researchers at the J. Craig Venter Institute and their collaborators report their new assembly, re-annotation, and consequent analyses of the Entamoeba histolytica genome, which revealed "new genomic features and protein content information." Hernan Lorenzi et al. write that their genome annotation "represents a more refined and accurate blueprint of the pathogen genome, and provides an upgraded tool as reference for the study of many important aspects of E. histolytica biology, such as genome evolution and pathogenesis."

Researchers at the University of Minnesota and their colleagues used mass spec-based quantitative proteomics to decipher myosin and actin as "promising saliva biomarkers for distinguishing pre-malignant oral lesions" in a study published in PLoS One this week. Using bionformatic approaches and validation via western blotting of candidate proteins from patient saliva samples, the authors found that "exfoliated epithelial cells from the subjects' saliva … showed increased myosin and actin abundance in those with malignant lesions," suggesting that their method could be a non-invasive screening tool "to detect oral cancer early."

The Scan

Gone, But Now Reconstructed SARS-CoV-2 Genomes

In a preprint, a researcher describes his recovery of viral sequences that had been removed from a common database.

Rare Heart Inflammation Warning

The Food and Drug Administration is adding a warning about links between a rare inflammatory heart condition and two SARS-CoV-2 vaccines, Reuters reports.

Sandwich Sampling

The New York Times sent tuna sandwiches for PCR analysis.

Nature Papers Describe Gut Viruses, New Format for Storing Quantitative Genomic Data, More

In Nature this week: catalog of DNA viruses of the human gut microbiome, new dense depth data dump format to store quantitative genomic data, and more.