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This Week in PNAS: Nov 30, 2010

In this week's PNAS Early Edition, a public-private research consortium of investigators at plant research institutes as well as beer and whiskey producers across Europe reports its mapping of 15 traits across about 500 barley crop cultivars genotyped with more than 1,500 SNPs. The team found "high levels of linkage disequilibrium within and between chromosomes" and "common alleles of high penetrance" across the cultivars. Then, to determine the applicability of genome-wide association mapping paired with comparative analysis to "resolve traits to candidate polymorphism level in unsequenced genomes," such as that of barley, the team fine-mapped anthocyanin pigmentation at an interval that contains three genes; the investigators found that the putative anthocyanin pathway gene HvbHLH1 is "diagnostic for lack of anthocyanin" in the plant.

Bart Bryant and his colleagues at the University of California, Riverside, show that "miR-275 is indispensable for blood digestion and egg development in the mosquito Aedes aegypti." Female A. aegypti with antagomir-mediated miR-275 depletion show "severe defects in blood digestion, fluid excretion, and egg development," Bryant et al. write, adding that their study has "uncovered the critical importance of microRNAs in controlling blood-meal-activated physiological events required for completion of egg development in mosquito disease vectors."

Researchers at McGill University in Montreal report their "identification of differential translation in genome-wide studies" online in PNAS this week. Nahum Sonenberg and his collaborators show that, "when combined with a variance shrinkage method for estimating error variance, analysis of partial variance has ... greater statistical power" as it identifies "fewer genes as translationally regulated resulting merely from unrealistically low variance estimates rather than from large changes in translational activity." To correct for cytosolic mRNA levels in genome-wide analyses of translational control, Sonenberg et al. suggest this combination of techniques is "applicable to datasets obtained from both the commonly used polysome microarray method and the sequencing-based ribosome profiling method."

Also, researchers in Germany describe a method to regulate selected loci using de novo-engineered transcription activator-like effector-type transcription factors. Using TALE transcription factors from the bacterial genus Xanthomonas as a model, the team shows that those differing in repeat-variable diresidues — of 34/35-amino acid repeat units — and non-repeat-variable diresidues showed differential DNA-binding specificity of the chimeras. Based on their investigations, the researchers suggest that "one needs only to modify the RVDs to generate designer TALEs to activate transcription of user-defined target genes."

The Scan

CDC Calls Delta "Variant of Concern"

CNN reports the US Centers for Disease Control and Prevention now considers the Delta variant of SARS-CoV-2 to be a "variant of concern."

From FDA to Venture Capital

Former FDA Commissioner Stephen Hahn is taking a position at a venture capital firm, leading some ethicists to raise eyebrows, according to the Washington Post.

Consent Questions

Nature News writes that there are questions whether informed consent was obtained for some submissions to a database of Y-chromosome profiles.

Cell Studies on Multimodal Single-Cell Analysis, Coronaviruses in Bats, Urban Microbiomes

In Cell this week: approach to analyze multimodal single-cell genomic data, analysis of bat coronaviruses, and more.