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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.