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This Week in PNAS: Jan 10, 2012

Harvard University's X. Sunney Xie and his colleagues present what they call a "truly digital" RNA-seq approach. "Following reverse transcription, a large set of barcode sequences is added in excess, and nearly every cDNA molecule is uniquely labeled by random attachment of barcode sequences to both ends," Xie et al. write in a paper published online in advance in PNAS this week. Post PCR, the researchers use paired-end deep sequencing to read the barcodes and cDNA sequences. "Rather than counting the number of reads, RNA abundance is measured based on the number of unique barcode sequences observed for a given cDNA sequence," the authors add. This allowed them to count with "single-copy resolution despite sequence-dependent bias and PCR-amplification noise." Overall, the Harvard group says its approach is "analogous to digital PCR but amendable to quantifying a whole transcriptome."

An international team led by investigators at ETH Zürich in Switzerland shows that "gut inflammation can boost horizontal gene transfer between pathogenic and commensal Enterobacteriaceae." In a mouse colitis model, the team found that "pathogen-driven inflammatory responses in the gut can generate transient enterobacterial blooms in which conjugative transfer occurs at unprecedented rates."

In another paper published online in advance this week, Inyup Paik, Seungchan Yang, and Giltsu Choi at the Korea Advanced Institute of Science and Technology show that the Pfr form of phytochrome interacts with the cytosolic protein PENTA1, inhibiting translation of protochlorophyllide reductase mRNA. Paik, Yang, and Choi say that their results "demonstrate that phytochromes transmit light signals to regulate not only transcription in the nucleus through PIFs [phytochrome-interacting basic helix-loop-helix transcription factors], but also translation in the cytosol through PNT1."

Elsewhere in this week's PNAS Early Edition, investigators at the University of Glasgow and the University of Exeter report their investigation of lifelong telomere length in zebra finches. "We found telomere length at 25 d [days] to be a very strong predictor of realized lifespan," the authors write.

The Scan

Vaccine Update Recommended

A US Food and Drug Administration panel recommends booster vaccines be updated to target Omicron, CNBC reports.

US to Make More Vaccines for Monkeypox Available

The US is to make nearly 300,000 vaccine doses available in the coming weeks to stem the spread of human monkeypox virus, according to NPR.

Sentence Appealed

The Associated Press reports that Swedish prosecutors are appealing the sentence given to a surgeon once lauded for transplanting synthetic tracheas but then convicted of causing bodily harm.

Genome Biology Papers on COVID-19 Effector Genes, Virtual ChIP-seq, scDART

In Genome Biology this week: proposed COVID-19 effector genes, method to predict transcription factor binding patterns, and more.