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This Week in PNAS: Aug 11, 2015

Editor's Note: Some of the articles described below are not yet available at the PNAS site, but they are scheduled to be posted some time this week.

In the early, online version of the Proceedings of the National Academy of Sciences, researchers from Switzerland and Germany describe sets of genes associated with different aspects of memory, based on a genome-wide association study and gene set enrichment analysis for thousands of young adults whose memory and related cognitive skills had been assessed using recognition, recall, and other memory tests. From gene set enrichment patterns in 1,239 individuals from the discovery set, the team identified seven sets of genes that appeared to contribute to one of the traits considered. Four of the gene set associations — including an association between amine compound solute carrier transport genes and learning rate — were confirmed through testing on hundreds more individuals. Other gene sets coincided with individuals' memory improvement after repetition, memory maintenance, and more.

Investigators from French Guiana and the US pinpoint a new mutation in the chloroquine resistance transporter gene pfct that can restore drug sensitivity to Plasmodium falciparum parasites in regions where chloroquine is no longer used as a first-line malaria treatment. Focusing on isolates collected in French Guiana during the 17 years after chloroquine was no longer used there, the team did a genome-wide association study of 580 chloroquine-sensitive or -resistant P. falciparum parasites carrying a classic resistance allele in the pfct gene. The search led to a second mutation in pfct that appears to have emerged in around 2002, eventually restoring chloroquine sensitivity to most P. falciparum parasites in the region, but diminished their response to another drug called piperaquine.

Finally, a team from Australia and the US takes a look at how well missense mutation effect predictions match up with measurable phenotypes in mutagen-exposed mice that had been exome sequenced. In mice carrying potentially disruptive point mutations in nearly two-dozen essential immune genes or in the TP53 gene, the researchers saw the mutant phenotypes predicted from the PolyPhen2 database for only a fraction of the mouse alterations. The study's authors say the results "highlight an important gap in our ability to relate genotype to phenotype in clinical genome sequencing: the inability to differentiate immediately clinically relevant mutations from nearly neutral mutations."