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This Week in PLOS: Nov 16, 2015

In PLOS Genetics, researchers from Harvard University, the Broad Institute, and elsewhere describe a recombination density-based scheme for calibrating mutation rates in human genomes. The team applied the approach — which relies on clues from fine-scale recombination mapping to track mutation accumulations — to diploid genome sequences from eight individuals from non-African populations. The mutation rate estimates resulting from this method were consistent with split times between human populations and between humans and other great apes that were intermediate, falling between those previously calculated from family pedigrees or phylogenetic analyses.

A Trinity College, Dublin- and University of Liverpool-led team used RNA sequencing to take a look at gene expression and transcript utilization patterns in Salmonella enterica pathogens from the Typhimurium serovar during mouse macrophage infections. As they report in PLOS Pathogens, the researchers scrutinized transcriptional and gene expression patterns in S. Typhimurium strain 4/74, identifying genes, small RNAs, and transcriptional start sites at play in the bug during the first eight hours of mouse macrophage infection. The resulting data, placed in an online resource called SalComMac, are expected to offer clues to the factors involved in S. Typhimurium virulence.

Finally, in PLOS One, American and Israeli researchers present a pathogen typing method based on single molecule analyses done with solid-state nanopores, which they applied to bugs such as Mycobacterium tuberculosis and methicillin-resistant Staphylococcus aureus. "[T]he solid-state nanopore diagnostic platform may be used to detect large insertions or deletions, small insertions or deletions, and even single-nucleotide variations in DNA," the team writes, noting that "Bayesian classification of test samples can provide highly confident pathogen typing results based on only a few tens of independent single-molecule events."