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This Week in PNAS: Jan 25, 2011

This week in the PNAS Early Edition, an international research team led by investigators at the University of British Columbia reports "insights, from genome and transcriptome analyses, into how [Grosmannia clavigera] tolerates conifer-defense chemicals, including oleoresin terpenoids, as they colonize a host tree." G. clavigera, the authors note, is a "critical component of" the current mountain pine beetle outbreak, as it is in symbiosis with mountain pine beetle, but pathogenic in lodgepole pine trees. Using RNA-seq, the team found that "terpenoids induce a substantial antimicrobial stress in Gc ... the fungus may detoxify these chemicals by using them as a carbon source," which, among other insights gained from the G. clavigera genome and transcriptome, represents a "major step toward understanding the biological interactions between the tripartite MPB/fungus/forest system."

The University of Texas Health Science Center's Daneen Schaeffer and Ambro van Hoof present their analysis of the "different nuclease requirements for exosome-mediated degradation of normal and non-stop mRNAs" in yeast. More specifically, the team demonstrates that "the endo- and exonuclease activities of the exosome are both capable of rapidly degrading non-stop mRNAs and ribozyme-cleaved mRNAs." In in vitro experiments, "the endonuclease domain of the exosome is active only under non-physiological conditions," but in vivo, Schaeffer and van Hoof observed "activity ... sufficient for the rapid degradation of nonstop mRNAs," they report in PNAS this week.

In another paper published online in advance this week, researchers at the King Abdullah University of Science and Technology in Saudi Arabia demonstrate the ability to engineer transcription activator-like family of type III effector-based hybrid nucleases that can generate site-specific double-strand breaks and, consequently, they propose that these nucleases show potential for future site-specific genome modifications. In its PNAS article, the team reports its creation of a Hax3-based hybrid TALE nuclease, which it says "can bind to its target sequence in vitro and ... cleave double-stranded DNA in vitro if the DNA binding sites have the proper spacing and orientation."

Bert Vogelstein at the Johns Hopkins Kimmel Cancer Center and his international colleagues report on the potential of "mutant proteins as cancer-specific biomarkers" in PNAS this week. Vogelstein et al. show that peptides expressed from both normal and mutant alleles are detectable by "selected reaction monitoring of their product ions using a triple-quadrupole mass spectrometer." To demonstrate the efficacy of its approach, the team quantified "the number and fraction of mutant Ras protein present in cancer cell lines" as well as in clinical specimens. Based on its results, the team proposes that "this approach could prove useful for diagnostic applications."

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.