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This Week in PLoS: Apr 26, 2010

In PLoS One this week, researchers at the Department of Energy's Joint Genome Institute and the University of Arizona report the completed sequence of Candidatus Sulcia meulleri, obtained from an uncultured single cell. "Single cell genomics is a novel culture-independent approach, which enables access to the genetic material of an individual cell," the authors write of their approach; they isolated an individual Sulcia cell for single-cell shotgun sequencing, and amplified the whole genome using multiple displacement amplification. By independently shotgun sequencing and assembling the Sulcia genome pooled from bateriomes using a standard metagenomic approach, the team was able to verify the validity of their single cell genome sequence. "This study demonstrates the power of single cell genomics to generate a complete, high quality, non-composite reference genome within an environmental sample, which can be used for population genetic analyzes," the authors conclude.

Also in PLoS One, Amit Khachane and Paul Harrison at McGill University describe their method for classifying and annotating potentially functional long, non-coding RNAs in mammals. By using the available existing cDNA data sets for humans and mice, Khachane and Harrison identified 78 lncRNAs that originate from the same protein-coding genes in both species. "We further identified orthologous protein-coding genes that are contributing to the pool of lncRNAs; of which, genes implicated in carcinogenesis are significantly over-represented," the team writes, adding that their study demonstrates that lncRNAs "could play an important role in cancer pathomechanisms."

In PLoS Genetics this week, investigators from the University of Virginia and Johns Hopkins University report their "microarray-based genetic screen for yeast chronological aging factors." Using the Saccharomyces cerevisiae model, the team performed a large-scale functional screen for genes that regulate lifespan. They identified viable haploid genes using DNA barcode sequences. "Viable mutants in the aging population were selected at several time points and then detected using a microarray DNA hybridization technique that quantifies abundance of the barcode tags," the authors write, adding that their work "will greatly aid in the elucidation of mechanisms that cells and organisms utilize in slowing down the aging process."

An interdisciplinary research team from the University of California, Los Angeles says that the hypomethylation of a LINE-1 promoter activates an alternate transcript of the MET oncogene in bladder cancer cases. Erika Wolff and her colleagues demonstrate — for the first time — "that hypomethylation of retrotransposons can cause altered gene expression in humans." Their study also shows that LINE-1 hypomethylation may also play a role in disease predisposition.

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.