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This Week in Nucleic Acids Research: Oct 13, 2010

In an advance online article published in Nucleic Acids Research this week, a trio of researchers at Harvard Medical School describes improved and complete enrichment, co-amplification at lower denaturation temperature PCR — or ice-COLD-PCR — which they say "enables rapid amplification and robust enrichment for low-abundance unknown DNA mutations." The team tested the efficacy of ice-COLD-PCR by enriching regions of TP53 in serially diluted mutant and wild-type DNA mixtures. When compared with conventional- and COLD-PCR, ice-Cold PCR "enriched all mutation types and allowed identification of mutation abundances down to 1 percent, and 0.1 percent by Sanger sequencing or pyrosequencing," the authors write.

Researchers at Auburn University in Alabama and at Iowa State University present cBARBEL, a catfish genome database, in Nucleic Acids Research this week. The catfish breeder and researcher bioinformatics entry location database "serves as a comprehensive, integrative platform for all aspects of catfish genetics, genomics and related data resources," the authors write. Currently, cBARBEL contains a contig viewer with SNP information overlay, BLAST-based search functions, and a visualization of genetic linkages in the ictalurid catfish.

Investigators at the University of Toronto this week describe "evidences for increased expression variation of duplicate genes in budding yeast." Specifically, Dong Dong and colleagues show that "trans-regulation effect[s] can explain [a] larger fraction of the expression variation than cis-regulation," which is "true for both duplicate genes and singleton genes," they write. Dong et al. also report that duplicate genes affected by cis-acting regulation have more genetic diversity in their promoters and coding regions than singleton genes, while duplicate and singleton genes under trans-acting regulation "are differentially regulated by chromatin regulators and transcription factors."

Also in Nucleic Acids Research this week, investigators at the New Jersey Medical School describe the "evolution and expression of the snaR family of small non-coding RNAs." Upon investigating snaR genes and their expression in humans and primates, Andrew Parrott and his colleagues now infer that "snaR evolved from the left monomer of the primate-specific Alu SINE family" and that "snaRs participate in tissue- and species-specific regulation of cell growth and translation," they write.

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.