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This Week in PNAS: Dec 31, 2013

Researchers led by Cornell University's Alon Keinan report in the Proceedings of the National Academy of Sciences that the human population has increased by about 100-fold during the past 3,000 years to 4,000 years. By focusing on regions of the human gene that are under neutral selective pressures and examining them in people with homogenous ancestry, they devised models showing that people have been experiencing a 3.4 percent population growth rate per generation for about the last 140 generations. "These models can inform studies of natural selection, the architecture of complex diseases, and the methods that should best be used for genotype-phenotype mapping," they add.

GenomeWeb Daily News has more on this study here.

Researchers led by the University of Texas' Jeffrey Barrick describe in PNAS this week the recursive genome-wide recombination and sequencing method they developed to study what mutations in a strain of Escherichia coli helped the organism to use citrate as a carbon source. This strain of E. coli developed the ability to use citrate over some 31,500 generations, and by using their REGRES approach and backcrosses, Barrick and his colleagues found that strains with only citT and dctA mutations could fully use citrate. "Overall, our discovery of the mechanism of a key refinement step in the evolution of a metabolic innovation highlights the degree to which interactions between alleles shape the evolution of complex traits and emphasizes the need for novel whole-genome methods to explore such relationships," the researchers add.

The Foundation for Applied Molecular Evolution's Steven Benner and his colleagues report that they combined artificially expanded genetic information systems (AEGIS) with systematic evolution of ligands by exponential enrichment (SELEX) experiment to develop AEGIS oligonucleotides that bind to a line of breast cancer cells. From this, they developed an apatamer, called ZAP-2012, made from six different — the standard G, A, C, and T, as well as nonstandard P and Z nucleotides.

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.