Week in Review: December 8–12

A new stem cell state; bird genome bonanza; antibiotic resistance in the wild; the DNA “loop-ome”

Dec 12, 2014
Tracy Vence

DNA loops mapped

ADRIAN SANBORN, EREZ LIEBERMAN AIDENAn international team has completed the highest-resolution map yet of how nuclear DNA forms loops to fit inside the cell. The work was published in Cell this week (December 11).

This latest map is “a landmark in the field of genome architecture,” said the University of California, San Diego’s Bing Ren, who was not involved in the work.

“This huge dataset will be used as a highly valuable resource for many researchers to mine and address all sorts of questions related to the functioning of our genome,” added Wouter de Laat of the Hubrecht Institute in the Netherlands, who also did not participate in the study.

Fuzzy stem cells

PETER D. TONGEResearchers in Canada and their international colleagues have reprogrammed a new type of stem cell, called “F-class,” which can differentiate into all three embryonic precursor tissues but differs from other induced pluripotent stem cells. The team described these cells in Nature this week (December 10).

“In some ways, F-class cells are a prototype of stem cells for disease research and therapeutic approaches: they grow faster and under simpler conditions than iPS cells,” study coauthor Thomas Preiss of Australian National University in Canberra told The Scientist.

Stem cell biologist Paul Knoepfler of the University of California, Davis, who was not involved in the work, added: “This opens up the idea that there may be different kinds of pluripotent stem cells.”

Avian family tree

AAAS/CARLA SCHAFFERScientists published 45 bird genomes across various journals this week (December 11), plus phylogenomic analyses revealing, among other things, how the animals lost their teeth and why avian genomes tend to be smaller than those of other vertebrates.

“The relationships of modern birds have proved very hard to disentangle, and they are still much debated. The new work provides the first authoritative, consensual resolution of the problem,” vertebrate paleontologist Mike Benton of the University of Bristol, who was not involved in the project, told The Scientist. “The key to the new endeavor is that these studies are based on whole genome analyses, whereas previous phylogenomic efforts have used selected genes only.”

Antibiotic resistance gone wild

JURGI CRISTÓBAL-AZKARATEGenes associated with antibiotic resistance have long been found in livestock, and have even been found in some wild animals. But a team led by investigators in Mexico City was surprised to find just how widespread antibiotic resistance genes were among diverse species of wildlife sampled in the jungles near Veracruz. Their work was published in PLOS ONE in September.

Researchers are unsure exactly how these animals accrued such drug resistance. “We are completely in the dark [about] which kind of processes led to this type of resistance,” said study coauthor Carlos Amábile-Cuevas of Mexico’s Fundación Lusara.

Other news in life science:

PubPeer Pushes Back
The founders of the post-publication peer review website file a motion to quash an academic’s subpoena for user information.

New Ruling on Old Misconduct Case
The Office of Research Integrity has finally pointed the finger in a case of suspected data manipulation in a 2006 Science paper.

Europe Softens on GM Crops
A new agreement in the European Union allows genetically engineered crops to be approved without member-state votes, likely allowing several GMO foods to enter the market.

Evolution in Oil Droplets
For the first time, researchers have mimicked biological evolution using chemicals instead of living organisms.

New NIH IRB Guidelines Proposed
A draft policy from the US National Institutes of Health suggests that clinical studies performed at multiple sites should be reviewed by a single institutional review board.