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This Week in PNAS: Nov 22, 2011

In this week's PNAS Early Edition, the University of Alberta's Ling-ju Lin and Michael Schultz discuss promoter-targeted Rtt109 repression of ARG1 via "silencing a pathway of transcriptional activation that depends on ASF1." Lin and Schultz show that the intensity of ARG1 transcription "at its induced and repressed set points is controlled by different mechanisms of functional interplay between Rtt109 and Asf1."

Researchers in Northwestern University's materials science department this week present "an approach that combines scanning probe block copolymer lithography with site-selective immobilization strategies to create arrays of proteins down to the single-molecule level with arbitrary pattern control." The team used scanning probe block copolymer lithography to "synthesize individual sub-10-nm single crystal gold nanoparticles that can act as scaffolds for the adsorption of functionalized alkylthiol monolayers, which facilitate the immobilization of specific proteins," it says, adding that "the number of protein molecules that adsorb onto the nanoparticles is dependent upon particle size; when the particle size approaches the dimensions of a protein molecule, each particle can support a single protein." The team adds that, in principle, its approach is "applicable to many parallelized cantilever and cantilever-free scanning probe molecular printing methods."

An international team led by investigators at the University of California, San Diego, present a computationally efficient implementation of direct-coupling analysis, or DCA, which can be used to evaluate the "accuracy of contact prediction by DCA for a large number of protein domains, based purely on sequence information," the authors write. The team also presents evidence to suggest that "contacts predicted by DCA can be used as a reliable guide to facilitate computational predictions of alternative protein conformations, protein complex formation, and even the de novo prediction of protein domain structures, contingent on the existence of a large number of homologous sequences."

Members of the China Plant BOL Group show in a paper published online in advance in PNAS this week that "ITS/ITS2 should be incorporated into the core barcode for seed plants." The group also discusses the importance of "sampling multiple individuals and using markers with different modes of inheritance" when investigating plant genomes. "In cases where it is difficult to amplify and directly sequence ITS in its entirety, just using ITS2 is a useful backup because it is easier to amplify and sequence this subset of the marker," the authors write.