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This Week in PLoS: May 3, 2010

In PLoS Computational Biology, Australian researchers report that they developed a new method to study recombination in closely related HIV genomes. Their approach takes advantage of the small changes that can occur in the HIV genome that do not affect viral proteins or how infective the virus is. With this marker system, they then developed mathematical tools that measure the recombination rate while taking into consideration background recombination and template switching.

Duke researchers identified four gene regions connected with lipoprotein-associated phospholipase A2 levels in the blood, which is linked to atherosclerosis. Drawing on data collected as part of the Framingham study, they conducted a genome-wide association study of Lp-PLA2 activity and mass. The four loci that reached genome-wide significance were: the APOE/APOC1 region on chromosome 19, CELSR2/PSRC1 on chromosome 1, SCARB1 on chromosome 12, and ZNF259/BUD13 in the APOA5/APOA1 gene region on chromosome 11.

Viennese researchers looked into the role reversible histone acetylation has in transcriptional regulation of transposable elements. The researchers treated mouse cells with a histone deacetylase inhibitor and then monitored the expression levels of 10 different transposons. They found that VL30 transposons would reactivate when histone acetylation increased. The researchers also add that histone H3 phosphorylation, which occurs in response to stress, is needed for the acetylation-dependent activation of VL30 element. "Our finding that HDAC inhibition can reactivate VL30 elements in mice might indicate that other TEs or non-coding elements could also respond to an epigenetic therapy in humans," they write. "Therefore, careful evaluation of potential effects beyond the deregulation of single copy genes will be an important issue for future studies."

Finally, an editorial in PLoS Medicine from a group of medical journal editors discuss the principles of comparative effectiveness research as well as standards for CER. They write that "the principal goal of CER is to allow decision makers (patients, clinicians, purchasers, and policy makers) to make informed decisions on specific health practices" and that CER should be applied to a "broad range of interventions, tests, and strategies" as well as include "new data, old data newly analyzed, and systematic reviews of existing research." On the conducting and reporting end of CER, the editors encourage following established reporting as well as making CER studies freely available in a repository such as PubMed Central.

The Scan

Alzheimer's Risk Gene Among Women

CNN reports that researchers have found that variants in MGMT contribute to Alzheimer's disease risk among women but not men.

Still Hanging Around

The Guardian writes that persistent pockets of SARS-CoV-2 in the body could contribute to long COVID.

Through a Little Spit

Enteric viruses like norovirus may also be transmitted through saliva, not just the fecal-oral route, according to New Scientist.

Nature Papers Present Method to Detect Full Transcriptome, Viruses Infecting Asgard Archaea, More

In Nature this week: VASA-seq approach to detect full transcriptome, analysis of viruses infecting Asgard archaea, and more.