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This Week in PNAS: Jul 24, 2012

This post has been updated to clarify that scientists from France and Japan discuss the genome of Aeropyrum coil-shaped virus, of Aeropyrum pernix, not the hyperthermophilic archaeon itself.

In a paper published online in advance in PNAS this week, a team led by investigators at the Broad Institute shows that using whole-genome sequencing is a powerful approach for association studies in Senegalese parasites — an approach that it took to identify genetic changes associated with the parasites' in vitro response to 12 antimalarials. "Based on the success of the analysis presented in this study, and on the demonstrated shortcomings of array-based approaches, we argue for a complete transition to sequence-based GWAS for small, low linkage-disequilibrium genomes like that of [Plasmodium] falciparum," the researchers write.

Elsewhere in this week's Early Edition, scientists from France and Japan report on the 24,893 nucleotide-circular genome of Aeropyrum coil-shaped virus, of the hyperthermophilic archaeon Aeropyrum pernix, which is "double that of the largest known ss[single-stranded]DNA genome," they write.

Hyung-June Woo and Jaques Reifman from the US Army Medical Research and Materiel Command this week present "a quantitative quasispecies theory-based model of virus escape mutation under immune selection," they write. Woo and Reidman add that "by explicitly representing epitope mutations and thus providing a genotype-phenotype map, the quasispecies theory can form the basis of a detailed sequence-specific model of real-world viral pathogens evolving under immune selection."

Also in PNAS this week, researchers in France and Portugal use population genetics modeling and remote-sensing analyses to "address the question of the origin of open habitats in the Daraina region in northern Madagascar," and present evidence to suggest that, contrary to popular thought, land cover changes there were not necessarily anthropogenic. Rather, the team found that "the golden-crowned sifaka (Propithecus tattersalli), a forest-dwelling lemur, underwent a strong population contraction before the arrival of the first humans, hence excluding an anthropogenic cause." Still, the researchers add that their study "does not preclude the later role played by humans in other regions in which recent lemur bottlenecks have been observed."

The Scan

Team Tracks Down Potential Blood Plasma Markers Linked to Heart Failure in Atrial Fibrillation Patients

Researchers in BMC Genomics found 10 differentially expressed proteins or metabolites that marked atrial fibrillation with heart failure cases.

Study Points to Synonymous Mutation Effects on E. Coli Enzyme Activity

Researchers in Nature Chemistry saw signs of enzyme activity shifts in the presence of synonymous mutations in a multiscale modeling analysis of three Escherichia coli genes.

Team Outlines Paternal Sample-Free Single-Gene Approach for Non-Invasive Prenatal Screening

With data for nearly 9,200 pregnant individuals, researchers in Genetics in Medicine demonstrate the feasibility of their carrier screening and reflex single-gene non-invasive prenatal screening approach.

Germline-Targeting HIV Vaccine Shows Promise in Phase I Trial

A National Institutes of Health-led team reports in Science that a broadly neutralizing antibody HIV vaccine induced bnAb precursors in 97 percent of those given the vaccine.