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Around the Literature: June 2010

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Pig Patterns

Larson G, Liu R, Zhao X, et al. (2010). Patterns of East Asian pig domestication, migration, and turnover revealed by modern and ancient DNA. PNAS. 107(17): 7686-7691.

This paper details the analysis of more than 1,500 modern and 18 ancient pig DNA sequences sampled across East Asia to provide evidence for the long-term genetic continuity between modern and ancient Chinese domestic pigs. The authors also demonstrate the presence of several genetically distinct and widespread wild boar populations that have not contributed maternal genetic material to modern domestic stocks. "The overall findings provide the most complete picture yet of pig evolution and domestication in East Asia, and generate testable hypotheses regarding the development and spread of early farmers in the Far East," the authors write. DNA

Motifs in MS

Beck J, Urnovitz HB, Saresella M, et al. (2010). Serum DNA motifs predict disease and clinical status in multiple sclerosis. Journal of Molecular Diagnostics. 12(3): 312-319.

Beck and her colleagues use newly available mass sequencing and assembly technologies to identify unique cell-free DNA motifs in the blood of patients with multiple sclerosis. Although coding genes distinguish relapsing-remitting MS — the most common MS clinical syndrome — and its clinical activity, several repeat sequences consistently differ in all MS patients and clinical status versus the database of healthy patients. The authors suggest that their findings show "that DNA motifs observed in serum are characteristic of relapsing-remitting MS and disease activity and are promising as a clinical tool in monitoring patient responses to treatment."

Conserved Methylation

Zemach A, McDaniel IE, et al. (2010). Genome-wide evolutionary analysis of eukaryotic DNA methylation. Science. E-pub.

The authors describe their quantification of DNA methylation in 17 eukaryotic genomes, and their consequent discovery that gene body methylation is conserved between plants and animals — whereas selective methylation of transposons is not. They show that methylation of plant transposons in the CHG context extends to green algae, and present evidence for the RNA-directed DNA methylation of fungal genes. Their data demonstrates that extant DNA methylation systems are assortments of conserved and derived features, and suggest that "gene body methylation is an ancient property of eukaryotic genomes," according to Zemach et al.

Biomarker Submission

Dieterle F, Sistare F, Goodsaid F, et al. (2010). Renal biomarker qualification submission: a dialogue between the FDA-EMEA and Predictive Safety Testing Consortium. Nature Biotechnology. (28): 455-462.

Researchers outline their 2007 submission of urinary renal safety biomarkers for Food and Drug Administration and European Medicines Agency review. They summarize the Predictive Safety Testing Consortium's renal biomarker submission, their analyses and conclusions, and examine new standards and practices identified through the qualification review process at FDA and EMEA. The paper provides guidelines for future regulatory submissions for biomarkers of other organs and tissues currently under investigation by the PSTC.

The Scan

US Supports Patent Waivers

NPR reports that the Biden Administration has announced its support for waiving intellectual property protections for SARS-CoV-2 vaccines.

Vaccines Versus Variants

Two studies find the Pfizer-BioNTech SARS-CoV-2 vaccine to be effective against viral variants, and Moderna reports on booster shots to combat variants.

CRISPR for What Ails You

The Wall Street Journal writes that CRISPR-based therapies could someday be used to treat common conditions like heart attacks.

Nature Papers Review Integration of Single-Cell Assay Data, Present Approach to Detect Rare Variants

In Nature this week: review of ways to integrate data from single-cell assays, and more.