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This Week in PNAS: May 25, 2010

Researchers in China report in PNAS this week their method for "constructing ultrahigh-density linkage maps composed of high-quality SNPs based on low-coverage sequences of recombinant inbred lines." The team's first step was to elucidate high-quality SNPs and perform a Bayesian inference in order to genotype the lines in the mapping populations using the SNPs, assisted by a hidden Markov model. The team constructed a ultrahigh-density linkage map "using 238 recombinant inbred lines derived from a cross between two rice varieties," and suggest that their method is "generally applicable in genetic map construction with low-coverage sequence data."

In the PNAS Early Edition, researchers in Seattle report that the hoxa3a orthologues between the mouse and zebrafish models have non-equivalent protein functions in vivo. "We demonstrate that zebrafish hoxa3a expressed from the mouse Hoxa3 locus can substitute for mouse Hoxa3 in some tissues, but has distinct or null phenotypes in others," the authors write, adding that the mouse and zebrafish Hox protein functions have "diverged considerably since their last common ancestor" and evolved independently.

An interdisciplinary team of pharmacogenomicists, molecular biologists, and geneticists say their discovery that "alternative splicing regulates mouse embryonic stem cell pluripotency and differentiation." To determine the roles of alternative splicing and alternative promoter selection, the team investigated reciprocal exon-exon junctions on a genome-wide scale in differentiating mouse ESCs via microarrays. Their consequent analysis of the transcription factor Tcf3 in knock-down cells revealed distinct differentiation outcomes in ESCs. They suggest that their study "illustrate[s] a critical role for AS in the specification of ES cells," among other things.

Finally, researchers in Japan report that the Mohawk — Mkx — atypical homeobox gene is a regulator of tendon differentiation in vivo. Using a mouse model, the team shows that "Mkx plays a critical role in tendon differentiation by regulating type I collagen production in tendon cells."

The Scan

Not as High as Hoped

The Associated Press says initial results from a trial of CureVac's SARS-CoV-2 vaccine suggests low effectiveness in preventing COVID-19.

Finding Freshwater DNA

A new research project plans to use eDNA sampling to analyze freshwater rivers across the world, the Guardian reports.

Rise in Payments

Kaiser Health News investigates the rise of payments made by medical device companies to surgeons that could be in violation of anti-kickback laws.

Nature Papers Present Ginkgo Biloba Genome Assembly, Collection of Polygenic Indexes, More

In Nature this week: a nearly complete Ginkgo biloba genome assembly, polygenic indexes for dozens of phenotypes, and more.