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This Week in PLoS: Apr 5, 2010

Australian researchers led by Cathy Jensen looked into whether SNPs associated with risk of multiple sclerosis also affect the severity of the disease. To do so, they genotyped seven SNPs in more than a thousand people with MS and correlated that with clinical outcome measures such as age of onset, MS severity score, and the time interval between first demyelinating event and first relapse. The researchers found no association between those clinical outcomes and the SNPs under study. "In this population, our study provided no evidence that MS severity or progression was altered by recently confirmed risk alleles in MS sufferers," they report in PLoS One.

Mike Snyder and his colleagues report in PLoS Pathogens that they used RNA-seq to examine why Acinetobacter baumannii becomes more virulent in the presence of ethanol. They found that 70 genes have different gene expression levels in the presence of ethanol. Snyder and his colleagues propose that the increased virulence is because of increased metabolic capacity and higher expression of stress response factors. They also found that phospholipase C may act acts as a virulence factor in A. baumannii.

In PLoS Genetics, researchers from the University of Chicago found that SNPs associated with a complex trait are more likely to be eQTLs. By analyzing a database of results from GWAS, the researchers also note that there are susceptibility loci to still be found for some complex disorders and "that can be more easily discovered and characterized by annotating SNPs with information on eQTL scores," they write. The reseracheres add: "Use of information on expression appears to benefit our understanding of not only more tractable disorders, such as Crohn's disease and autoimmune disorders, for which relatively large numbers of loci have already been identified at the cost of genotyping 10,000 or fewer samples, but also for less tractable disorders such as hypertension and bipolar disease."

Petras Kundrotas and Ilya Vakse report their analysis of high-throughput protein interaction models in PLoS Computational Biology. They determined the accuracy of the protein binding sites predicted by models developed using BLASTPGP and NEST. The researchers found that about "50% of complexes with the interfaces modeled by high-throughput techniques had accuracy suitable for meaningful docking experiments."

The Scan

Genome Sequences Reveal Range Mutations in Induced Pluripotent Stem Cells

Researchers in Nature Genetics detect somatic mutation variation across iPSCs generated from blood or skin fibroblast cell sources, along with selection for BCOR gene mutations.

Researchers Reprogram Plant Roots With Synthetic Genetic Circuit Strategy

Root gene expression was altered with the help of genetic circuits built around a series of synthetic transcriptional regulators in the Nicotiana benthamiana plant in a Science paper.

Infectious Disease Tracking Study Compares Genome Sequencing Approaches

Researchers in BMC Genomics see advantages for capture-based Illumina sequencing and amplicon-based sequencing on the Nanopore instrument, depending on the situation or samples available.

LINE-1 Linked to Premature Aging Conditions

Researchers report in Science Translational Medicine that the accumulation of LINE-1 RNA contributes to premature aging conditions and that symptoms can be improved by targeting them.