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This Week in PNAS: May 24, 2011

By resequencing 630 gene fragments of rice chromosomes from wild and cultivated accessions, researchers led by New York University's Michael Purugganan were able to infer the evolutionary history of rice, as they report in this week's PNAS. The team took both a diffusion-based approach to model the SNP data and a Bayesian evolutionary approach for its phylogenetic analyses. These studies, the team says, suggest a single origin of rice that dates to about 8,200 to 13,500 years ago.

Researchers from the University of Texas Southwestern Medical Center in Dallas report that clustered DNA damage leads to chromosome breakage. Using immunofluorescence, they stained the repair proteins XRCC1, 53BP1, and hOGG1 as a means to study double-stranded breaks, single-stranded breaks, and base damage as well as repair in human cells. As they report in PNAS, the researchers found that "a large fraction of 53BP1, XRCC1, and hOGG1 foci colocalized in cells irradiated with Fe and Si ions, but not in H2O2-treated cells, suggesting that the colocalized IRIF represents the sites of clustered DNA lesions." The researchers add that "difficulties associated with clustered DNA damage repair and checkpoint release before the completion of clustered DNA damage repair appear to promote genome instability that may lead to carcinogenesis."

Gregory Sims and Sung-Hou Kim constructed two whole-genome phylogenies of the Escherichia coli/Shigella group through an alignment-free genome comparison that uses feature frequency profile approach, as they report in PNAS. One phylogeny is "based on the compositions of all possible features of length l = 24" and the other is "based on the compositions of core features with low frequency and low variability." In one phylogeny, Sims and Kim report, Shigella appears as a single clade, though in the other, it appears to be comprised of two subclades. "In both FFP trees, the basal group of the E. coli/Shigella phylogeny is the B2 phylogroup, which contains primarily uropathogenic strains, suggesting that the E. coli/Shigella ancestor was likely a facultative or opportunistic pathogen," they add.

Finally, there's a Q&A with Eric Lander in this week's online early edition of PNAS that focuses on the role of sequencing in medicine, and the need to sequence a million genomes. "As the cost of genome sequencing drops to $1,000, the cost for each disease would be about $10 million. When you think about how much money is spent on schizophrenia or other diseases, doesn’t it make sense to invest to find all of the human genetic information that is potentially relevant to the disease?" Lander says. He cautions, though, that there won't be immediate changes to how medicine is done. "It took more than 50 years to go from the germ theory of disease to the widespread availability of antibiotics or from the idea that cholesterol might play a causal role in heart disease to the widespread use of lipid lowering drugs," he adds. "I think we can do better, but we should be clear with the public that truly transforming medicine is not an overnight affair."

The Scan

Transcriptomic, Epigenetic Study Appears to Explain Anti-Viral Effects of TB Vaccine

Researchers report in Science Advances on an interferon signature and long-term shifts in monocyte cell DNA methylation in Bacille Calmette-Guérin-vaccinated infant samples.

DNA Storage Method Taps Into Gene Editing Technology

With a dual-plasmid system informed by gene editing, researchers re-wrote DNA sequences in E. coli to store Charles Dickens prose over hundreds of generations, as they recount in Science Advances.

Researchers Model Microbiome Dynamics in Effort to Understand Chronic Human Conditions

Investigators demonstrate in PLOS Computational Biology a computational method for following microbiome dynamics in the absence of longitudinally collected samples.

New Study Highlights Role of Genetics in ADHD

Researchers report in Nature Genetics on differences in genetic architecture between ADHD affecting children versus ADHD that persists into adulthood or is diagnosed in adults.