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This Week in Nature: Aug 5, 2010

In an advance online publication of Nature this week, an international research team presents its draft genome sequence for the sponge Amphimedon queenslandica. The A. queenslandica genome, the authors write, is "remarkably similar to other animal genomes in content, structure, and organization." The team also suggests that sequencing the sponge genome deduced "genomic events linked to the origin and early evolution of animals." The investigators note that "many of the genes associated with the emergence of animals are also implicated in cancer."

Investigators at the University of Michigan and their international colleagues this week report the identification of 95 loci significantly associated with plasma lipids — include 59 novel associations — which they've elucidated in a genome-wide association study of more than 100,000 individuals of European ancestry. "The 95 loci contribute not only to normal variation in lipid traits but also to extreme lipid phenotypes and have an impact on lipid traits in three non-European populations (East Asians, South Asians and African Americans)," the authors add. The team validated three of the novel genes — GALNT2, PPP1R3B, and TTC39B — using mouse models.

Another team led by researchers at the University of Michigan shows that "reporter genes introduced into the genome of various human embryonic carcinoma-derived cell lines by L1 [LINE-1] retrotransposition are rapidly and efficiently silenced either during or immediately after their integration." Specifically, using an EC cell line treated with histone deacetylase inhibitors, the authors found that "reactivation of the reporter gene was correlated with changes in chromatin status at the L1 integration site." The team suggests that ECs are unique from many differentiated cells in that they've been shown to "silence reporter genes delivered by L1 retrotransposition."

Also in Nature this week, investigators at the University of Washington in Seattle and their colleagues outline Foldit — a multiplayer online computer game that functions to predict protein structures — marking its debut in the literature. "Foldit players interact with protein structures using direct manipulation tools and user-friendly versions of algorithms from the Rosetta structure prediction methodology, while they compete and collaborate to optimize the computed energy," the authors write, adding that non-scientist players "develop a rich assortment of new strategies and algorithms." Washington's Seth Cooper et al. suggest that Foldit represents a "powerful new approach to solving computationally limited scientific problems."

The Scan

Study Finds Sorghum Genetic Loci Influencing Composition, Function of Human Gut Microbes

Focusing on microbes found in the human gut microbiome, researchers in Nature Communications identified 10 sorghum loci that appear to influence the microbial taxa or microbial metabolite features.

Treatment Costs May Not Coincide With R&D Investment, Study Suggests

Researchers in JAMA Network Open did not find an association between ultimate treatment costs and investments in a drug when they analyzed available data on 60 approved drugs.

Sleep-Related Variants Show Low Penetrance in Large Population Analysis

A limited number of variants had documented sleep effects in an investigation in PLOS Genetics of 10 genes with reported sleep ties in nearly 192,000 participants in four population studies.

Researchers Develop Polygenic Risk Scores for Dozens of Disease-Related Exposures

With genetic data from two large population cohorts and summary statistics from prior genome-wide association studies, researchers came up with 27 exposure polygenic risk scores in the American Journal of Human Genetics.