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This Week in Science: Mar 16, 2012

This week, Science publishes technical comments from three groups on a May 2011 paper from the University of Pennsylvania School of Medicine's Mingyao Li et al., "Widespread RNA and DNA sequence differences in the human transcriptome." Claudia Kleinman and Jacek Majewski at McGill University say that "common sources of systematic errors in high-throughput sequencing technology, which were not properly accounted for in this study, explain most of the claimed differences" between DNA and messenger RNA in human cells that Li et al. reported. Meanwhile, the University of Chicago's Joseph Pickrell and his colleagues show that "at least 88 percent of these sequence mismatches can likely be explained by technical artifacts such as errors in mapping sequencing reads to a reference genome, sequencing errors, and genetic variation," and Cold Spring Harbor Laboratory's Wei Lin et al. say that "a deeper analysis of the sequencing data is required to discern true differences between RNA and DNA from potential artifacts."

In response, Li and her colleagues report having repeated their analysis "using two different sequence alignment methods," and also having "carried out additional experiments including whole genome DNA sequencing." They say that their results were "consistent with our finding of widespread RNA-DNA sequence differences."

Elsewhere in this week's Science, a team of researchers in France and the UK and a separate group in the US provide structural evidence for how transfer-messenger RNA, or tmRNA, rescues ribosomes stalled on defective messenger RNAs in bacteria. Cajetan Neubauer et al. present the "crystal structure of a tmRNA fragment, SmpB, and elongation factor Tu bound to the ribosome at 3.2 angstroms resolution," while Matthieu Gagnon et al. report "a 3.2 angstrom-resolution crystal structure of the rescue factor YaeJ bound to the Thermus thermophilus 70S ribosome in complex with the initiator tRNAifMet and a short mRNA."

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.