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PLOS Papers Take on Population Substructure, Immune Deficiency-Related Rubella, More

In PLOS Genetics, researchers from McGill University describe a computational approach for finding fine-scale population structure details. The "uniform manifold approximation and project," or UMAP, is a non-linear, dimension-reducing method that "creates a neighborhood around each individual's genetic coordinates and identifies a pre-selected number of neighbors to build high dimensional manifolds" with genotyping data, the team says. The investigators used UMAP to find population substructures with genotyping data in three available datasets, for example, including a Hispanic population cluster found in data from the Health and Retirement Study that coincided with mountainous regions of the western US. Based on these and other data, the authors suggest UMAP "helps reveal patterns of covariation between geography, phenotypes, and genotypes."

A team from the US Centers for Disease Control and Prevention and elsewhere take a look at rubella virus-associated inflammatory nodules, known as chronic granulomas, which were found in children with primary immune deficiencies. As they report for a paper appearing in PLOS Pathogens, the researchers initially identified the so-called "immunodeficiency-related, vaccine-derived rubella viruses" (iVDRV) structures in skin biopsy samples from a handful of individuals with immune deficiency. Using genome sequences for iVDRV samples from four individuals with iVDRV and a reference rubella vaccine sequence, the authors saw signs of continued iVDRV evolution within each individual. They noted that the evolutionary rates appeared to outpace that of wild type rubella viruses, perhaps due to "continuous viral replication and selection during chronic infection in a single individual."

For a paper appearing in PLOS One, investigators in France present findings from a proteomics-based analysis of prostate cell lines spanning several prostate cancer subtypes. Using mass spectrometry coupled with "stable isotope labeling with amino acids in culture" or SILAC, labeling, the team assessed protein and phosphoproteome patterns in four cell lines, uncovering some proteins and phosphosites that were consistent across cell lines and others that varied from one cell line to another. "Further data integration in a molecular network highlighted the differentially expressed pathways," the authors note, "in particular migration and invasion, RNA splicing, DNA damage repair response, and transcription regulation."