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This Week in PLoS: Oct 9, 2009

Scientists have added more than 10 percent new genes to the yeast ribosome biogenesis pathway in work appearing this week in PLoS Biology. Zhihua Li at the University of Texas, Austin, is first author on a paper that used network-guided genetics, "an approach for associating candidate genes with biological processes that capitalizes on recent advances in functional genomic and proteomic studies," to identify additional ribosomal biogenesis genes, says the abstract. After a number of assays, the team confirmed at least 15 new genes, which are involved in ribosomal subunit maturation, ribosomal particle association, and ribosomal subunit nuclear export, and for processing 5S, 7S, 20S, 27S, and 35S rRNAs.

Scientists at the University of Bordeaux have determined the minimal number of genes for a pathogen, "providing further insight into the composition of hypothetical minimal gene sets needed for life." In their work, which was published this week in PLoS Genetics, they compared the genomes of three bacteria that infect the human urogenital tract, the newly sequenced Mycoplasma hominis, M. genitalium, and Ureaplasma parvum. The M. hominis genome, they found, contains an "unusual major energy-producing pathway through arginine hydrolysis," which suggests to them that M. hominis and U. parvum exchanged genes at some point. Their comparison determined the minimal set of genes needed in M. hominis to be 256.

In work out of Forest Rohwer's lab at San Diego State University, researchers performed the first metagenomic study of DNA viral communities in the airways of diseased and non-diseased people. Examining sequences from sputum DNA viral communities in five people with cystic fibrosis and five without, the scientists found that on the whole, there was little diversity of viruses, with "an average richness of 175 distinct viral genotypes," they write. "The majority of viral diversity was uncharacterized." In fact, CF eukaryotic viral communities were dominated by a few viruses, including human herpesviruses and retroviruses. Their work appears in PLoS One.

A study in PLoS Pathogens looked into the transcriptional control of carbohydrate metabolism in Candida albicans, a fungal pathogen in humans, and identified two factors, Tye7p and Gal4p, as key regulators of glycolysis. Using ChIP-chip and transcription profiling, the National Research Council of Canada's Malcolm Whiteway led the work that found that both Tye7p and Gal4p bind the promoter sequences of glycolytic genes. However, they regulate unique sets of genes: Tye7p activates genes involved in trehalose, glycogen, and glycerol metabolism while Gal4p regulates the pyruvate dehydrogenase complex. "This suggests that Tye7p represents the key transcriptional regulator of carbohydrate metabolism in C. albicans and Gal4p provides a carbon source-dependent fine-tuning of gene expression while regulating the metabolic flux between respiration and fermentation pathways," they say.

The Scan

Gone, But Now Reconstructed SARS-CoV-2 Genomes

In a preprint, a researcher describes his recovery of viral sequences that had been removed from a common database.

Rare Heart Inflammation Warning

The Food and Drug Administration is adding a warning about links between a rare inflammatory heart condition and two SARS-CoV-2 vaccines, Reuters reports.

Sandwich Sampling

The New York Times sent tuna sandwiches for PCR analysis.

Nature Papers Describe Gut Viruses, New Format for Storing Quantitative Genomic Data, More

In Nature this week: catalog of DNA viruses of the human gut microbiome, new dense depth data dump format to store quantitative genomic data, and more.