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This Week in PNAS: Jul 2, 2013

In a study slated to appear online this week in the Proceedings of the National Academy of Sciences, researchers from the Rockefeller University used a metagenomic sequencing-based method to find new natural product-producing genes in soil microbial communities. After isolating microbial DNA from a soil sample, the team created a clone library that was then assessed by amplicon sequencing and subsequently compared with known natural product-related genes. In the sample from New Mexico's Chihuahuan Desert, for example, the study's authors found clusters of genes similar to those used to produce natural products with established anti-tumor and immunosuppressant activity, prompting them to propose that "previously undetected biosynthetic gene clusters with potential biomedical relevance are very common in the environment."

The presence of genes involved in vitamin B5 biosynthesis may help some Campylobacter bacteria become more adept at colonizing cattle, according to another PNAS study. An international team took a genome-wide association study approach to finding potential genetic contributors to specificity for cattle or chicken hosts in bacteria from two Campylobacter species that appear in the animal gut microbiome and can cause food-borne illness in humans in some instances. Using sequence type data and genome sequences for 192 C. jejuni or C. coli isolates from cattle, chicken, clinical samples, and other sources, researchers narrowed in seven genes that seem to mediate host preferences in the bugs. Of those, three genes — found in cattle-associated Campylobacter — belonged to a vitamin B5 biosynthesis pathway.

Researchers from Yale and Stanford Universities used an RNA interference screen to catalog genes contributing to stem cell differentiation into neural lineage cells for an upcoming PNAS online study. The team subjected differentiating human embryonic stem cells to pools of short hairpin RNAs targeting more than 1,800 genes. With the help of deep sequencing, the investigators were able to tally up genes needed for normal neural progenitor cell formation and maintenance — a list that included known neurodevelopmental genes and genes participating in RNA granule formation as well as players in neurodegenerative conditions that appear late in life.