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This Week in PLoS: Nov 22, 2010

In a PLoS Genetics paper published this week, the University of Oxford's Aris Katzourakis and Robert Gifford identify 10 non-retroviral endogenous viral elements — including "the first endogenous representatives of double-stranded RNA" — in animal genomes. Using an in silico approach, Katzourakis and Gifford analyzed these endogenous viral elements across multiple host species. Phylogenetic and genomic studies revealed that "genetic material derived from all known viral genome types and replication strategies can enter the animal germ line," the authors write, which indicates a "more significant evolutionary role for gene flow from virus to animal genomes than has previously been recognized."

In profiling DNA methylation in total peripheral blood leukocytes and T-lymphocytes from adults with Down syndrome and controls on a microarray platform, researchers at the Columbia University Medical Center and their colleagues "found gene-specific CpG methylation abnormalities in DS, with many of the differentially methylated genes having known or predicted roles in lymphocyte development and function." The team validated significant methylation differences between Down syndrome and control PBLs in eight genes via bisulfite sequencing and methylation-sensitive pyrosequencing; bisulfite sequencing also confirmed differential methylation of NOD2/CARD15 between Down syndrome and control T-cells. These methylation differences, the authors suggest, represent a "recurrent and functionally relevant downstream response to trisomy 21 in human cells."

Over in PLoS One, investigators at France's Université Victor Segalen Bordeaux report that the button mushroom Agaricus bisporus cox1 gene is "the longest mitochondrial gene and the largest reservoir of mitochondrial group 1 introns." At a length of 29,902 nucleotides, the A. bisporus cox1 gene "exhibits a peculiar dynamics of intron keeping and catching, leading to the largest collection of mitochondrial group I introns reported to date in a eukaryote," the authors write.

By mapping genotype-epigenotype interactions in the context of type 2 diabetes by methylated DNA immunoprecipitation on targeted arrays and validating them with pyrosequencing, researchers in the UK and New Zealand found that methylation differences between women with type 2 diabetes and female controls is "driven by the coordinated phase of CpG-creating SNPs across the risk haplotype." The team found haplotype-specific methylation in a 7.7 kb region that contains a highly conserved non-coding element, which had "previously been validated as a long-range enhancer, supported by the histone H3K4me1 enhancer signature." The team writes that their study demonstrates how SNP data generated by GWAS can be integrated with epigenomic methylation information demystify the genotype-epigenotype interactions that underlie common complex diseases.

The Scan

Not Kept "Clean and Sanitary"

A Food and Drug Administration inspection uncovered problems with cross contamination at an Emergent BioSolutions facility, the Wall Street Journal reports.

Resumption Recommendation Expected

The Washington Post reports that US officials are expected to give the go-ahead to resume using Johnson & Johnson's SARS-CoV-2 vaccine.

Canada's New Budget on Science

Science writes that Canada's new budget includes funding for the life sciences, but not as much as hoped for investigator-driven research.

Nature Papers Examine Single-Cell, Multi-Omic SARS-CoV-2 Response; Flatfish Sequences; More

In Nature this week: single-cell, multi-omics analysis provides insight into COVID-19 pathogenesis, evolution of flatfish, and more.