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This Week in PNAS: Jul 13, 2010

In the PNAS Early Edition this week, researchers at the University of Victoria and the National Institute of Allergy and Infectious Diseases report that they've inserted nine "essential genes" from Arctic bacteria into mammalian pathogenic bacteria "to construct stable, temperature-sensitive bacterial vaccines." One ligA gene, the team writes, "was shown to render Francisella tularensis, Salmonella enterica, and Mycobacterium smegmatis temperature-sensitive." Three temperature-sensitive strains of F. tularenis "were shown to induce protective immunity after vaccination at a cool body site," the authors write.

A European research team this week reports their reconstruction of the Candidatus Nitrospira defluvii genome, and suggest that its metagenome "illuminates the physiology and evolution of globally important nitrite-oxidizing bacteria." The researchers suggest their study shows that Nitrospira evolved from microaerophillic — or even anaerobic — ancestors, based on the "reverse tricarboxylic acid cycle as the pathway for CO2 fixation and the lack of most classical defense mechanisms against oxidative stress."

Walter Reisner at McGill University and his international colleagues describe the "power of denaturation mapping as a single-molecule technique" in PNAS this week. "By partially denaturing YOYO-1-labeled DNA in nanofluidic channels with a combination of formamide and local heating, we obtain a sequence-dependent 'barcode' corresponding to a series of local dips and peaks in the intensity trace along the extended molecule," the authors write, adding that this is an effect of the physics of local denaturation. Reisner et al. suggest that their technique is cognizant of sequence variation "without requiring enzymatic labeling or a restriction step."

Also in this week's PNAS, researchers at the Duke University Medical Center show that DNA mismatch repair protein PMS2 "endonuclease activity has distinct biological functions and is essential for genome maintenance and tumor suppression," a finding they've determined using endonuclease-deficient Pms2E702K knock-in mice. These murine models showed increased mutation rates and a strong predisposition for cancer, the authors write, adding that class-switch recombination was hindered in Pms2EK/EK B cells, "indicating a specific role in Ig diversity."

The Scan

NFTs for Genome Sharing

Nature News writes that non-fungible tokens could be a way for people to profit from sharing genomic data.

Wastewater Warning System

Time magazine writes that cities and college campuses are monitoring sewage for SARS-CoV-2, an approach officials hope lasts beyond COVID-19.

Networks to Boost Surveillance

Scientific American writes that new organizations and networks aim to improve the ability of developing countries to conduct SARS-CoV-2 genomic surveillance.

Genome Biology Papers on Gastric Cancer Epimutations, BUTTERFLY, GUNC Tool

In Genome Biology this week: recurrent epigenetic mutations in gastric cancer, correction tool for unique molecular identifier-based assays, and more.