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This Week in PLOS: Jan 7, 2013

In PLOS One, an international team led by investigators in Australia and the UK outlines a strategy for sequencing the malaria-causing parasite Plasmodium vivax from clinical samples. The approach involves filtering out patient's white blood cells before a short parasite-culturing stint from the cells that remain, researchers say, steps that curb human DNA contamination while upping the proportion of parasite DNA available for sequencing. In the new study, for instance, the team demonstrated that it could sequence the notoriously difficult-to-culture P. vivax parasite to high coverage — both in terms of genome depth and breadth — using samples from nearly two dozen patients.

A team from Spain and the US — including representatives from Pacific Biosciences — used single-molecule real-time sequencing with the PacBio RS instrument to profile methylation patterns at single-base resolution in two human pathogens from the genus Mycoplasma. As they report in PLOS Genetics, the investigators focused on the non-gonococcal urethritis-causing pathogen M. genitalium and M. pneumoniae, a culprit in some pneumonia cases. Analyses of pathogens in exponential and stationary phases of growth uncovered two sequence motifs that are particularly prone to methylation in one or both of the species. Those involved say the study "demonstrates the unique capability of SMRT sequencing to directly sequence and profile the methylome of a whole microbial genome, allowing for unprecedented progress towards understanding the role of epigenomics in the world of prokaryotes."

Finally, the University of Michigan's Mercedes Pascual and colleagues from the US and the UK look at factors affecting genetic diversity and antigen profiles in influenza A from the H3N2 subtype in PLOS Pathogens. Using information on influenza A mutation rates, levels of competition, and so on, the researchers came up with models consistent with known influenza H3N2 phylodynamics. Within this framework, they found, "a limited antigenic space can explain the observed phylogenetic patterns and … a limited mutation rate is a key property underlying the dynamic of (H3N2) influenza."

The Scan

Study Links Evolution of Longevity, Social Organization in Mammals

With the help of comparative phylogenetics and transcriptomics, researchers in Nature Communications see ties between lifespan and social organization in mammals.

Tumor Microenvironment Immune Score Provides Immunotherapy Response, Prognostic Insights

Using multiple in situ analyses and RNA sequence data, researchers in eBioMedicine have developed a score associated with immunotherapy response or survival.

CRISPR-Based Method for Finding Cancer-Associated Exosomal MicroRNAs in Blood

A team from China presents in ACS Sensors a liposome-mediated membrane fusion strategy for detecting miRNAs carried in exosomes in the blood with a CRISPR-mediated reporter system.

Drug Response Variants May Be Distinct in Somatic, Germline Samples

Based on variants from across 21 drug response genes, researchers in The Pharmacogenomics Journal suspect that tumor-only DNA sequences may miss drug response clues found in the germline.