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This Week in PNAS: Sep 1, 2015

In the early, online edition of the Proceedings of the National Academy of Sciences, an international team led by investigators in Saudi Arabia and the US present results from a genome sequencing study of the sea anemone Aiptasia, which is expected to serve as a model organism for understanding the symbiotic relationships that make up coral reefs. After putting together an almost 260 million base genome for Aiptasia, the researchers compared it with other anthozoan animals, uncovering Aiptasia-specific genes, expanded gene families, and genomic rearrangements that may contribute to Aiptasia's close ties to symbiotic dinaflagellate algae living within them. Our sister publication GenomeWeb Daily News has more on the study here.


A team from Albert Einstein College of Medicine and the Universityof California at Berkeley describe a CRISPR/Cas9-based scheme for labeling specific sites in the genome so their three-dimensional organization and orientation can be visualized. The approach — known as Cas9-mediated fluorescence in situ hybridization, or CASFISH — relies on the CRISPR/Cas9 system to act as probes to label portions of the genome without altering their composition by fluorescently labeling Cas9 proteins that no longer have nuclease enzyme activity. The researchers demonstrated the feasibility of this approach by using CASFISH to label sequences in both repetitive and non-repetitive portions of the genome.


Finally, researchers from the US and Japan outline the genome mining method that they used to search for potentially useful natural products in the genomes of more than 10,000 actinomycetes bacteria. Using some 2,500 actinomycetes isolates from their own lab and roughly 7,500 isolates from the Agricultural Research Service Culture Collection, the team did PCR- and draft genome sequencing-based searches for pepM, a gene coding for a phosphoenolpyruvate mutase enzyme that has been linked to the production of a group of bioactive compounds known as phosphonic acids. The PCR-based screen picked up more than 400 suspected phosphonate producers, the study's authors explain, while genome sequencing verified the pepM gene's presence in 278 of the strains falling into 64 different groups.

The Scan

Machine Learning Helps ID Molecular Mechanisms of Pancreatic Islet Beta Cell Subtypes in Type 2 Diabetes

The approach helps overcome limitations of previous studies that had investigated the molecular mechanisms of pancreatic islet beta cells, the authors write in their Nature Genetics paper.

Culture-Based Methods, Shotgun Sequencing Reveal Transmission of Bifidobacterium Strains From Mothers to Infants

In a Nature Communications study, culture-based approaches along with shotgun sequencing give a better picture of the microbial strains transmitted from mothers to infants.

Microbial Communities Can Help Trees Adapt to Changing Climates

Tree seedlings that were inoculated with microbes from dry, warm, or cold sites could better survive drought, heat, and cold stress, according to a study in Science.

A Combination of Genetics and Environment Causes Cleft Lip

In a study published in Nature Communications, researchers investigate what combination of genetic and environmental factors come into play to cause cleft lip/palate.