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This Week in PNAS: Mar 5, 2013

In the early, online edition of the Proceedings of the National Academy of Sciences, Uppsala University's Ulf Gyllensten and colleagues describe genetic variants that appear to affect peptide levels in the human blood proteome. The team assessed SNP patterns in more than 1,000 Swedish individuals, while using mass spectrometry to characterize and quantify peptides in their blood. The genome-wide association study led to apparent "protein quantitative trait loci," or pQTLs, for 60 peptides representing just over twodozen proteins. Those involve argue that the potential for using high-throughput proteomic and genomic schemes to assess genetic influences on the proteome "opens up the possibility for systemic studies of the functional importance of specific genetic variants on the protein."

Our sister publication GenomeWeb Daily News has more on the study, here.

A trio of researchers from the University of Georgia takes a peek at gene function in the methanogenic archaeal species Methanococcus maripaludis using transposon-mediated mutagenesis and deep sequencing. The team mapped transposon insertion sites in the M. maripaludis genome in mutant lines, using this information to gain clues about whether various genes are essential or beneficial for the bug's growth under given conditions. "Although definitive assignments of essentiality still require detailed analyses of each gene, the methodology generates hypotheses about the nature of specific genes and a great deal of insight into specific questions regarding methanogens," study authors say, "as well as more general questions about the genetics, biochemistry, and physiology of archaea."

Members of the Alzheimer's Disease Neuroimaging Initiative and collaborators report on findings from a modified GWAS designed to pin down variants contributing to brain connectivity. The group started by doing brain scans on dozens of identical or non-identical twin pairs as a means of teasing apart heritable aspects of brain networks. Using this information, together with genotyping data, researchers unearthed variants with apparent ties to brain connectivity. Among them: a SNP near the SPON1 gene that appeared to influence brain structure and dementia risk in follow-up analyses. From these and other findings, study authors concluded that the connectome/genome-wide screening approach "offers substantial promise to discover genes affecting brain connectivity and risk for brain diseases."