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This Week in PNAS: Sep 16, 2009

Maite Novoa and Frédéric Bigeya at INRA in Montpellier, France, led work that appears this week in the Proceedings of the National Academy of Sciences showing that gene transfer occurs between Saccharomyces and non-Saccharomyces species. Upon sequencing the genome of the commercial wine yeast S. cerevisiae EC1118, they identified three large regions involved in key wine fermentation functions. Phylogenetic analysis showed that one of these regions came from a species related to Saccharomyces, while the two other regions were of non-Saccharomyces origin. "Our results suggest that these [gene transfer] processes are favored by ecologic proximity and are involved in the molecular adaptation of wine yeasts to conditions of high sugar, low nitrogen, and high ethanol concentrations," they say.

Researchers led by those at Columbia University Medical Center blended linkage analysis with studies of fine-level chromosomal variation in Afrikaner families to show that individually rare inherited CNVs are more frequent in cases with familial schizophrenia. Performing high-density linkage analysis, they found a region on chromosome 13q34 that can be linked to schizophrenia in some families, and in other families, they found genome-wide significant linkage to chromosome 1p36.

Sichuan University scientists studied how PSF protein and VL30-1 RNA, a mouse retroelement noncoding RNA, affect proto-oncogene transcription, cell proliferation, and tumorigenesis in mice. Using gene transfection to overexpress and shRNA transfection to decrease expression of these genes, their results show that "PSF is a major tumor-suppressor protein and VL30-1 RNA is a major tumor-promoter RNA in mice," says the abstract.

Finally, big news published yesterday is that opportunistic pathogens, like non-tuberculous mycobacteria, including Mycobacterium avium, are found at levels 100 times higher than normal in some showerheads. Using grant money donated for work to detect how microbes might be used in a terrorist attack, the University of Colorado's Norman Pace analyzed rRNA gene sequences from 45 showerhead sites around the US. The work showed that there are more than 15 kinds of bacteria, mostly harmless, in showerheads, but that showers in New York are particularly infected with M. avium. Pace says the people with compromised immune or pulmonary systems should be concerned, but that switching from a plastic to metal showerhead can improve the situation. The New York Times adds insight, and our sister publication, GenomeWeb Daily News, reports further.

The Scan

Study Tracks Responses in Patients Pursuing Polygenic Risk Score Profiling

Using interviews, researchers in the European Journal of Human Genetics qualitatively assess individuals' motivations for, and experiences with, direct-to-consumer polygenic risk score testing.

EHR Quality Improvement Study Detects Demographic-Related Deficiencies in Cancer Family History Data

In a retrospective analysis in JAMA Network Open, researchers find that sex, ethnicity, language, and other features coincide with the quality of cancer family history information in a patient's record.

Inflammatory Bowel Disease Linked to Gut Microbiome Community Structure Gradient in Meta-Analysis

Bringing together data from prior studies, researchers in Genome Biology track down microbial taxa and a population structure gradient with ties to ulcerative colitis or Crohn's disease.

Ancient Greek Army Ancestry Highlights Mercenary Role in Historical Migrations

By profiling genomic patterns in 5th century samples from in and around Himera, researchers saw diverse ancestry in Greek army representatives in the region, as they report in PNAS.