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This Week in PNAS: Jun 24, 2014

Researchers from Stanford and Yale Universities report on an approach that combines short and long read sequence data to produce a personal transcriptome with allele-specific resolution. Using Pacific Biosciences and Illumina sequencing technologies, the team sequenced transcripts from lymphoblastoid cell lines that had been generated with samples from three individuals in a parent-child trio. As reported yesterday by GenomeWeb Daily News, the method made it possible to pick out gene expression, splicing, and SNP patterns in the samples, providing haplotype profiles for the child in the trio. The data also linked genetic variants influencing gene expression, revealing examples of differential allelic expression and differential allelic isoforms.

The bloody diarrhea-causing pathogen Shigella flexneri consumes large quantities of pyruvate or other compounds produced by the host cell's glycolytic pathway, another PNAS study suggests. Swiss researchers turned to metabolic, proteomic, and genetic profiling to look at the metabolic effects of S. flexneri infection in human cells. Their results suggest that infected human cells keep pumping out products via normal metabolic pathways. But the output of these pathways seems to be slurped up by S. flexneri, they note, providing energy to the pathogen and keeping host pathways relatively intact.

A team from the US, France, and Spain performed comparative genomics on almost three dozen basidiomycetes fungi to explore differences between so-called white rot fungi, which can degrade plant lignin, and brown rot fungi, which degrades cellulose and hemicellulose in plants, but not lignin. This difference had previously been attributed to differences in peroxidase enzymes present in the fungi — a pattern the researchers explored further using genome sequences for 33 fungi that did or did not decay wood. In contrast to past results, the comparison failed to find sequences for peroxidase enzymes associated with lignin degradation in some white rot fungi, prompting the study's authors to argue that "the prevailing paradigm of white rot vs. brown rot does not capture the diversity of fungal wood decay mechanisms."