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This Week in PNAS: Oct 18, 2016

In the early online edition of the Proceedings of the National Academy of Sciences, Harvard University and Genia Technologies' George Church leads a team presenting a single-molecule sequencing strategy built around a polymerase enzyme and alpha-hemolysin-based nanopore inserted into a lipid bilayer. The researchers sequenced stretches of tagged DNA moving through the pore with the help of a complementary metal oxide semiconductor electrode array that had the lipid bilayer on its surface. In their proof-of-principle experiments, they measured each tagged base hundreds of times to distinguish the signals they produced from background noise in the system. "Coupling protein catalysis and nanopore-based detection to an electrode array could provide the foundation of a highly scalable, single-molecule, electronic DNA-sequencing platform," the team writes.

A University of California, San Diego team takes a look at newly generated and steady-state transcripts in developing Arabidopsis thaliana seedlings. The researchers used global nuclear run-on sequencing, 5' global nuclear run-on sequencing, and RNA sequencing, respectively, to sequence nascent RNA and unravel RNA polymerase patterns, map transcription start sites, and assess steady state transcript levels in six-day-old A. thaliana seedlings. "Our modified method to map engaged RNA polymerases and nascent transcripts in primary tissues paves the way for comparative and response studies," the authors write.

Finally, Canadian researchers report on phosphoproteomic patterns found in mouse models of a heart disease called dilated cardiomyopathy, which is characterized by heart enlargement, weakening, and life threatening declines in heart function. From mass spectrometry- and affinity capture-based analyses of nearly 1,900 heart-related phosphoproteins, close to 3,900 phosphopeptides and almost 3,600 proteins overall in mouse heart tissue, the team notes that transgenic mice showing early signs of dilated cardiomyopathy had altered signaling by Notch-1 and other pathways compared to wild-type mice from the same litter. The group also confirmed these findings in its follow-up immuno-blotting and immunofluorescence experiments.