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This Week in PLoS: Dec 6, 2010

In a PLoS Genetics paper published this week, researchers at Australia's University of Queensland, along with their international collaborators, show that variants associated with ankylosing spondylitis — at 1q32 and STAT3 — suggest a genetic overlap between the inflammatory arthritic condition and Crohn's disease. The team interrogated 53 markers from 30 Crohn's-associated genomic regions in a population of 2,773 unrelated individuals affected by ankylosing spondylitis and 2,215 controls. Using a Cochran-Armitage statistical test for trend, the researchers identified significant overlap between ankylosing spondylitis and Crohn's, suggesting "common aetiopathogenic pathways" for both, and strengthening the notion that common risk variants are involved across various diseases.

Hakon Hakonarson and his colleagues at the Children's Hospital of Philadelphia report in PLoS One this week that duplication of 5q35.1, which harbors the SLIT3 gene, "predisposes to major depressive disorder." This duplication, Hakonarson et al. write, represents a highly penetrant variant; SLIT3 duplication, the team suggests, "is a novel association which explains a definitive proportion of the largely unknown etiology of MDD."

Based on their analysis of "sequences from metagenomic databases, Marseillevirus and three new viruses extending the Mimiviridae family to generate the phylogenetic trees of eight proteins involved in different steps of DNA processing," researchers at France's Université de la Méditerranée propose a fourth domain of life, which suggests "a single common origin for nucleocytoplasmic large DNA viruses." Using phyletic pattern analysis methods, the researchers obtained data to support the "existence of a clade containing NCLDVs clearly distinct from that of Eukarya, Bacteria, and Archaea." In addition, the authors suggest that the "core genome of the NCLDV is as ancient as the three currently accepted domains of life."

Lisa Meadows and her colleagues at the University of Cambridge challenge the notion that gene "expression neighborhoods are a feature of eukaryotic genome organization" in this week's PLoS Biology. More specifically, Meadows et al. disrupted three male-specific Drosophila gene expression neighborhoods by targeted chromosomal inversions. Then, using whole-transcriptome microarray analysis and RT-qPCR, the team compared the manipulated flies against "their non-inverted, but otherwise identical, progenitors." The team saw "no significant differences in the expression of genes that define each of the neighborhoods," a finding that undercuts "models explaining neighborhood organization in terms of local sequence interactions, enhancer crosstalk, or short-range chromatin effects," at least in this specific context.

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.