Week in Review: August 25–29

Sequencing the Ebola outbreak; optogenetic memory manipulation; monitoring post-publication peer review; yeast-based opioid production; even more ENCODE

By | August 29, 2014

Ninety-nine Ebola genomes

STEPHEN GIREResearchers at Harvard University and their international colleagues have sequenced 99 Ebola virus genomes isolated from the blood of 78 patients in Sierra Leone—one of four countries at the center of the ongoing, largest-ever Ebola outbreak—and made them available online within days. Their analysis of all the sequences was published in Science this week (August 28).

“This analysis will provide the backbone for tracking the virus as it spreads, and to see if future outbreaks outside of these countries are connected both epidemiologically and genetically,” emerging infectious diseases researcher Matthew Frieman from the University of Maryland School of Medicine who was not involved in the work told The Scientist in an e-mail. “The ability to deep sequence virus samples rapidly, inexpensively, and safely has opened up a window in to genomic surveillance that did not exist before.”

Optogenetically controlled memory switch

WIKIMEDIA, MARK HARKINInvestigators at MIT have used optogenetics to make mice enjoy spending time in a place they were previously conditioned to fear, according to results published in Nature this week (August 27). The team was able to switch the animals’ memories by manipulating connections between neurons in the hippocampus and amygdala.

Elizabeth Phelps, a professor of psychology and neural science at New York University who was not involved in the work, called the results “an exciting advance in our understanding of the malleability of memory.”

Do journals monitor post-publication peer review?

FLICKR, MINISTERIO TIC COLOMBIAThe Scientist asked editors at a handful of journals whether they monitor comments related to papers they’ve published on post-publication peer review websites like PubPeer. Some do, some don’t.

“Some of the editors may monitor PubPeer,” Monica Bradford, executive editor at Science, told The Scientist. “However, we have not set up a routine, consistent process for monitoring the site.”

PLOS does “keep an eye on PubPeer,” said David Knutson, the organization’s public relations manager, “but we would prefer that readers alert the editors directly about any concerns they may have about PLOS publications.”

In a comment posted to the story, reader Eric J. Murphy wrote: “As an Editor-in-Chief of a society journal, I have never examined PubPeer nor will I do so.” Read Murphy’s reasoning and participate in the conversation in the comments.

Producing opioids in engineered yeast

WIKIMEDIA, RAINIS VENTAUsing bacterial and poppy plant genes, scientists at Stanford University have engineered yeast synthesize naturally occurring opiates and semisynthetic opioids from precursor molecules. Their work was published in Nature Chemical Biology this week (August 24).

“The authors have demonstrated that it is possible to develop a technology platform in yeast that allows the transformation of [the opiate alkaloid] thebaine to a variety of opiate drugs by mixing and matching microbial and plant enzymes,” biochemist Neil Bruce from the University of York, U.K., told The Scientist in an e-mail. “This is elegant piece of synthetic biology . . . and demonstrates that it may ultimately be possibly to generate a [complete] morphinian biosynthetic pathway in yeast.”

ENCODE/modENCODE data dump

NHGRIFour papers published concurrently in Nature this week (August 27) have nearly doubled the data output of the Encyclopedia of DNA Elements (ENCODE) and model organism ENCODE (modENCODE) projects.

Geneticist William Bush of Case Western Reserve University in Ohio who was not involved with the studies told The Scientist: “What’s really striking about these papers is that they find ways in which we can map similarities in genomic function between key model organisms that are often used in lab research.”

Other news in life science:

How Long Is Too Long?
Readers discuss the varied amounts of time they’ve waited for journals to respond to or act on their concerns regarding published papers.

Predatory Journal Trading on Former Name
Experimental & Clinical Cardiology, a once well-respected journal, now is publishing anything that comes with a payment of $1,200.

RIKEN to Regroup Following STAP Saga
The Japanese institution will downsize, rename, and relaunch the research center at the heart of the stimulus-triggered acquisition of pluripotency controversy.

Social Data for Ebola Surveillance
Algorithms that map social media posts and mobile phone data can help researchers track epidemics.

NIH Issues Genomic Data Sharing Rules
Updated guidelines expand upon existing policy to include more kinds of data.

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