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This Week in PNAS: Dec 29, 2010

In this week's PNAS Early Edition, the Broad Institute's David Jaffe and his colleagues describe ALLPATHS-LG, a genome assembly algorithm that uses data from massively parallel sequencers. Using ALLPATHS-LG on Illumina data, Jaffe et al. found that their assembly accuracy was higher than that achieved with capillary-based sequencing.

In another PNAS paper published online in advance this week, researchers at Switzerland's University of Basel show that the ultraconserved RNA 338 is aberrantly expressed in a both murine and human hepatocellular carcinoma cell lines, and suggest that its associated 590-base pair RNA gene, TUC338, may play a role in the pathobiology of hepatocellular carcinoma. Transcribed ultraconserved non-coding RNAs, the authors write, represent "a unique class of genes involved in [hepatocellular carcinoma]."

A team led by investigators at the National Institute of Allergy and Infectious Diseases reports that "genetic susceptibility to systemic lupus erythematosus protects against cerebral malaria in mice" in PNAS this week. As immune mechanisms appear to protect lupus-prone mice during parasitic infections – due to "a deficiency in FcγRIIB or overexpression of Toll-like receptor 7" – these animals show improved survival in malarial infections, the authors write.

Researchers at the University of New Mexico School of Medicine and their collaborators show that "methylation of histone H3 lysine 36 enhances DNA repair by non-homologous end-joining." More specifically, when screening for histone methylation post-DNA double-strand break induction using ionizing radiation, the team identified H3K36me2 as "the major event." In human cell system experiments, the researchers saw that "the DNA repair protein Metnase ... localized to an induced DSB and directly mediated the formation of H3K36me2 near the induced DSB." H3K36 dimethylation "improved the association of early DNA repair components, including NBS1 and Ku70, with the induced DSB and enhanced DSB repair," the authors write.

The Scan

Not Yet a Permanent One

NPR says the lack of a permanent Food and Drug Administration commissioner has "flummoxed" public health officials.

Unfair Targeting

Technology Review writes that a new report says the US has been unfairly targeting Chinese and Chinese-American individuals in economic espionage cases.

Limited Rapid Testing

The New York Times wonders why rapid tests for COVID-19 are not widely available in the US.

Genome Research Papers on IPAFinder, Structural Variant Expression Effects, Single-Cell RNA-Seq Markers

In Genome Research this week: IPAFinder method to detect intronic polyadenylation, influence of structural variants on gene expression, and more.