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This Week in Nucleic Acids Research : Aug 10, 2011

In a paper published online in advance in Nucleic Acids Research this week, a team led by investigators at the New Jersey Medical School, present an "impartial evaluation of measurements of leukocyte telomere length by Southern blot of the terminal restriction fragments and quantitative PCR of telomere DNA content, expressed as the ratio of telomeric product [to] single copy gene product." In addition to presenting the results of its measurements of leukocyte telomere length assessments using this approach, the team also discusses "the ramifications of these findings with regard to measurements of telomere length/DNA content in epidemiological/clinical circumstances."

The University of Zurich's Nicole Wilson and Esther Stoeckli this week report their generation of "novel plasmid vectors that contain cell type-specific promoters/enhancers to drive the expression of a fluorescent marker," which, when followed directly by a miR30-RNAi transcript, "allow for direct tracing of cells experiencing gene silencing by the bright fluorescence." Further, the team suggests that the level of knockdown achieved using this vector-based approach "is sufficient to reproduce the expected pathfinding defects upon perturbation of genes with known axon guidance functions."

In another Nucleic Acids Research advance online publication, researchers at the University of Calgary and elsewhere show that ionizing radiation-induced phosphorylation of human polynucleotide kinase/phosphatase by the DNA-dependent protein kinase and ataxia-telangiectasia mutated, or ATM, regulates its function in double-strand break repair. In its in vivo study, the team found that the "inactivation of DNA-PK [DNA-dependent protein kinase] and/or ATM led to reduced PNKP [polynucleotide kinase/phosphatase] at DNA damage sites."

Researchers in Taiwan show that, by integrating three experimental data sets — "including cap analysis of gene expression tags, TSS [transcriptional start sites] Seq libraries, and H3K4me3 chromatin signature derived from high-throughput sequencing analysis of gene initiation" — they were able to identify 847 human miRNA transcriptional start sites. The team also presents a "machine learning-based Support Vector Machine model ... to systematically identify representative TSSs for each miRNA gene," in its recent Nucleic Acids Research paper.

The Scan

Missed Early Cases

A retrospective analysis of blood samples suggests early SARS-CoV-2 infections may have been missed in the US, the New York Times reports.

Limited Journal Editor Diversity

A survey finds low diversity among scientific and medical journal editors, according to The Scientist.

How Much of a Threat?

Science writes that need for a provision aimed at shoring up genomic data security within a new US bill is being questioned.

PNAS Papers on Historic Helicobacter Spread, Brain Development, C. difficile RNAs

In PNAS this week: Helicobacter genetic diversity gives insight into human migrations, gene expression patterns of brain development, and more.