Week in Review: October 7–11

Nobels awarded for vesicle trafficking and computational chemistry; building 3-D microbial communities; mislabeled microbes cause retractions

By | October 11, 2013

Nobel week celebrates greatness

WIKIMEDIA, JONATHUNDERIt’s Nobel season again. On Monday (October 7), the Nobel Assembly at Karolinska Institutet in Sweden crowned James Rothman, Randy Schekman, and Thomas Südhof the winners of the 2013 Nobel Prize in Medicine or Physiology for helping to unravel the details of the cellular transport system. When Schekman, a professor at the University of California, Berkeley, got the call before dawn, he “snapped to attention,” he told The Scientist. “My heart started to race.”

“They’re three very different people. Each is very intelligent, very purposeful and driven,” said Dartmouth University’s Bill Wickner, who received a call from Schekman that morning to share the good news. “I love each one of them. They're fun, they love to talk shop. They’re good listeners as well as speakers.”

Then on Wednesday (October 9), the Nobel Assembly awarded its annual prize in chemistry to Martin Karplus, Michael Levitt, and Arieh Warshel for the development of computer-based methods to model complex systems. The three winners began using computer modeling to predict the outcomes of diverse chemical reactions in the 1970s and continued to refine the computational methodologies throughout their careers.

“With powerful computers it’s quicker to try to calculate how your small molecule will bind to your target,” said Johan Åqvist of Uppsala University in Sweden, who did a postdoc with Arieh Warshel at the University of Southern California. “In a sense it’s really powerful because you can see the fine details like how individual atoms move and calculate how much they contribute to interactions.”

Researcher is open about retractions

WIKPEDIA, IRRI IMAGESTwo papers have been retracted, including a 2009 Science paper cited 131 times, and lead author Pamela Ronald wants everyone to know. She began announcing the suspected problems with her work to colleagues at conferences as soon as she figured out that the research was tainted. “There was never any question . . . that we do anything different than retract the paper if it was wrong,” Ronald told The Scientist. “We didn’t want to mislead anyone else.”

Ronald, a plant geneticist at the University of California, Davis, led a team of researchers who claimed to have identified a bacterial molecule recognized by the immune system of rice plants. But after failing to replicate the results, the lab realized that two of the bacterial strains were mislabeled, and some of the work was based on an unreliable test. Both studies, the 2009 Science paper and a 2011 study published in PLOS ONE, have now been retracted.

The field applauds Ronald’s openness in this situation. “I feel absolutely confident that there was no intentional cheating,” said Markus Albert, a plant biologist from the University of Tubingen. And Ivan Oransky, a journalist who monitors scientific retractions through his blog Retraction Watch, noted the strides such honesty could make towards gaining the public’s trust. “Some scientists worry that retractions lead to a mistrust of science,” he told The Scientist, “but when handled appropriately the way Ronald’s have been, they only boost public confidence in research.”

Culturing bacteria in 3-D

J. CONNELL ET AL., UNIVERSITY OF TEXAS AT AUSTINResearchers at the University of Texas at Austin have developed a way to keep microbes localized within a 3-dimensional environment in order to test how population structure influences bacteria. “In microbial populations, there’s cooperation and there’s cheating and there’s competition, and so understanding how these very complicated things actually function is not something you can just do in a petri dish or a bulk broth,” said Bryan Kaehr, a bioengineer at Sandia National Laboratories and a former postdoc in lead author Jason Shear’s lab. “In order for us to ever really understand cell communication in a meaningful way, you really have to organize populations like this—at this scale, the scale of cells.”

The team’s strategy involves the cross-linking of a gelatin mold upon exposure to the laser of a 3-D printer. Once the bacteria are seeded into the gelatin and allowed to settle at random, the researchers can print a “house” that can entrap certain groups of cells. As those cells proliferate, they form colonies of varying densities, at different orientations to other bacterial groups.

“This is the beauty of the technique—that it allows you to create any 3-D structure,” said engineer Aleksandr Ovsianikov of the Vienna University of Technology in Austria, who was not involved in the study. “So you have total freedom [of design].”

Where are the Ashkenazi Jews from?

FLICKR, ADAM BAKERThe Ashkenazi Jews, which account for the majority of today’s Jewish population, are traditionally believed to have descended from the ancient tribes of Israel. This  supposition has been supported by studies of Y chromosomal DNA, which have suggested a likely origin of male Ashkenazis in the Near East. Previous analyses of the mitochondrial genome also suggested a Near East origin for Ashkenazi females. But a study of mitochondrial DNA published this week challenges this idea, finding evidence that female Ashkenazi Jews descended from prehistoric Europeans. European women, they suggest, could have converted as the Ashkenazi population migrated through the content some 2,000 years ago or earlier. “We found that most of the maternal lineages . . . emanate from Europe,” said coauthor Martin Richards, an archaeogeneticist at the University of Huddersfield in the U.K.

But some researchers have their doubts, calling into question the mitochondrial DNA data used in the new study, as well as the analysis itself. “These analyses really do not have any formal statistical inference about evolutionary history in them,” Goldstein wrote in an e-mail to The Scientist. “They are based on direct interpretations of where one finds different [mitochondrial DNA] types today.  And so the analyses are largely impressionistic.”

Advice for giving scientific talks

SXC.HU, VIXSScientific presentations, given at countless conferences around the world every year, are too often rushed, unreadable, and generally incomprehensible, argued David Rubenson, associate director for administration and strategic planning at the Stanford Cancer Institute. But there are ways to improve, he said. Rubenson suggested eight steps to biomedical researchers; in a nutshell: be realistic. Consider what you can cover in the limited amount of time that you have, he said, and think about what your audience will be able to digest in that time. And, of course, don’t forget to practice: “The worst words in science may be, ‘I’ll write the presentation on the airplane.’ There is no substitute for dry runs that include tough critics.”

More news in life science:

Science, Stalled

As the government shutdown rolls on, field seasons are in jeopardy, meetings are missed, and academia steps in to fill some voids.

Fake Paper Exposes Failed Peer Review

The widespread acceptance of an atrocious manuscript, fabricated by an investigative journalist, reveals the near absence of quality at some journals.

Progress for First Malaria Vaccine

Following successful clinical trials, GlaxoSmithKline says it will submit its malaria vaccine for European regulatory approval

Open Data Helps Citations

A study has shown that papers with publicly available data are more likely to be cited than papers with unavailable data.

Fecal Pills

A study shows that fecal transplants in an oral capsule form are an effective treatment for Clostridium difficile infection.

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