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This Week in PLoS: Nov 16, 2009

David Shulenburger of the Association of Public and Land-Grant Universities in Washington, D.C. has written an article for PLoS Biology on the need for university public access mandates. Following on the steps of Harvard, MIT, and the University of Kansas, three schools that require all their science to be publicly accessible, the Association of Public and Land-Grant Universities, the Association of American Universities, the Association of Research Libraries, and the Coalition for Networked Information are several organizations actively rooting for public access, advising "that serious campus discussion on the topic occur." The perspective goes on to defend public access versus open access, as scientists and publishers continue to grapple with finding the best business model.

Research from Mu Gao and Jeffrey Skolnick at the Georgia Institute of Technology has produced DNA-Binding-Domain-Threader (DBD-Threader), a threading-based method "for the prediction of DNA-binding domains and associated DNA-binding protein residues." Applying their computational method genome-wide, they tested more than 18,500 protein sequences and predicted more than 1,600 to have DNA-binding function. When they compared their results to existing GO annotations, they found that about 30 percent of their predictions are new. Their work appears this week in PLoS Computational Biology.

University of California San Diego's Kun Zhang and Harvard University's George Church are senior authors on work in PLoS Genetics this week that's developed a method for finding tissue-specific gene expression regulatory variants in human iPS cells. Using padlock probes and deep sequencing, they showed that "allele-specific expression is both cell type and genotype-dependent, but the majority of detectable allele-specific expression loci remains consistent despite large changes in the cell type or the experimental condition following iPS reprogramming, except on the X-chromosome." Their method, they say, will enable detection of genome-wide variants using only a skin biopsy.

Juha Kere and Outi Hovatta of the Karolinska Institute and Karolinska University Hospital, respectively, have performed transcriptome profiling of human pre-implantation development states. Using microarrays on 397 human oocytes and embryos at six developmental stages, they found that pre-implantation development consists of two main transitions, "from metaphase-II oocyte to 4-cell embryo where mainly the maternal genes were expressed, and from 8-cell embryo to blastocyst with down-regulation of the maternal genes and up-regulation of embryonic genes," they write in the abstract at PLoS One.

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.