Kumbaya and All That… Until Thursday!

By Karl Leif Bates

You wouldn’t know it from the war drums banging over at ESPN this week in advance of Thursday night’s football showdown, or the hairy eyeball the frat boys give you for wearing the wrong shirt in Chapel Hill, but our two fine institutions, Duke and UNC-Chapel Hill, are actually very good friends and close collaborators. …At the faculty level, at least.

A February 2013 map showing which blue Facebook users follow during March Madness. (We're huge in NW Arizona, okay?)

A February 2013 map showing which blue Facebook users follow during March Madness. (We’re huge in NW Arizona, okay?)

It’s quite common for a major research paper coming out of either campus to include collaborators from the other Tier 1 research university just 10 miles away. It only makes sense. When the ARRA Stimulus funding was on the table a few years ago, the two pulled together on all sorts of projects to bring about $400 million in federal tax dollars back to the Triangle.

And now, a new program announced just a few weeks ago will actually pay researchers from both schools to be friends! Can you imagine?

A Chapel Hill taunt. (Not actually supported by the data, but whatever.)

A Chapel Hill taunt. (Not actually supported by the data, but whatever.)

Duke’s Translational Medicine Institute (DTMI) and the North Carolina Translational and Clinical Sciences Institute (NC TraCS) are awarding $50,000 grants to research projects that are trying to speed laboratory medical findings into the clinic or the population. (That’s what “translation” means.) The only catch is that the application has to include one co-investigator from each school.

“I think that although we come from different ends of Tobacco Road and our different shades of blue compete passionately in sports, when it comes to translating medical progress and health care to the community, we can be very collaborative,” Jennifer Li of the Duke Translational Medicine Institute told the DTMI newsletter.

Just look at those long faces! Poor kids. A Duke buzzer-beater will do that to you.

Just look at those long faces! Poor kids. A Duke buzzer-beater will do that to you.

Naturally, the newsletter then had to quote a Tarheel: “On a scientific basis, collaborative teams are formed based on shared interests and complimentary resources, skills and experiences,” said John Buse, deputy director of the NC Translational and Clinical Sciences Institute. “The hope (is) that the sum is greater than the parts.”

Perhaps, Dr. Buse, perhaps. But what’s the fun in that?

GO DUKE !

World Domination in a Loaf of Bread

By Robin Smith

If baker’s yeast could take over the world, the bread leavener’s world domination might look like this time-lapse movie produced by a team led by Duke biologist Nicolas Buchler:

Their report in the Nov. 5, 2014, issue of the journal Molecular Biology of the Cell shows time-lapse images of yeast cells under a microscope as one cell grows and divides into two, and two into four, and so on.

To watch the budding yeasts in action, the researchers inserted a gene for an enzyme that gives fireflies their characteristic yellow light into the yeasts’ DNA.

It normally takes one yeast cell about 90 minutes to grow and divide into two new cells. But in the time-lapse movie, the process is compressed into a few seconds.

The yellow dots show genes being turned on and off in the nucleus of each cell.

The approach allows scientists to track the activation and deactivation of genes over a tiny cell’s fast life cycle more accurately than standard labeling techniques using other glowing proteins, the researchers say.

CITATION: “Measuring fast gene dynamics in single cells with timelapse luminescence microscopy,” Mazo-Vargas, A., Park, H., Aydin, M. and N. Buchler. Molecular Biology of the Cell, November 5, 2014.

All Ears for Corn Genetics

By Nonie Arora

“Technology is progress” and “new is better” seem to be mantras in some fields of research. However, when it comes to fields of genetically modified corn, we might be wise to think otherwise.

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Dr. Mary Eubanks and Students at the Campus Farm. Credit: Nonie Arora

Duke biology professor Dr. Mary Eubanks spoke to a group of Duke students, community members, and a farmer from Togo about corn genetics in a workshop held Friday, Oct. 24 at the Duke Campus Farm. Dr. Eubanks founded her own seed genetics company (Sun Dance Genetics LLC) and is a leading advocate for changing the way we grow corn.

Dr. Eubanks became intrigued by the origins of corn while studying the origins of agriculture and the start of American civilization in an archaeology PhD program. She realized that she wouldn’t be able to answer her questions about what she considered to be this “great botanical mystery” without an understanding of genetics. To uncover this mystery, she pursued a postdoctoral program in corn genetics. Based on her experimentation, she developed the hypothesis that maize domestication involved something called intergeneric hybridization, or crossing between plants in different genera.

European Corn Borner attacks Maize. Credit: Wikimedia commons

European Corn Borner attacks Maize. Credit: Wikimedia commons

During her career, Dr. Eubanks also worked in regulatory affairs and learned about the devastating effects of chemical pesticides. She became an advocate for sustainable agriculture: finding ways to develop pest-resistant corn without genetic engineering. She has successfully transferred natural resistance to the worst insect pests of corn — corn rootworm and European corn borer.

In contrast to using natural breeding methods to create new lines of corn, genetically modifying organisms could have negative effects on human health, according to Dr. Eubanks. Dr. Eubanks believes that the inserter and promoter sequences that are used to get the genes to express the foreign proteins can lead to antibiotic resistance and intestinal issues for humans.

The group was surprised by her description of her own anaphylactic shock reaction to Bt-corn, a GMO. Her own personal history of the allergic reaction made her think of the potential reactions our bodies could be having to GMOs. Dr. Eubanks described how it was problematic that genes being introduced to the crop came from other organisms and that humans haven’t evolved a tolerance to the proteins the genes encode. This could lead to potential allergenicity in humans. According to Dr. Eubanks, it is possible that there has been horizontal gene transfer between plasmids — small molecules used to insert genes from one organism to the next — and the human gut.

When asked about the regulations regarding GMOs, Dr. Eubanks explained that the FDA is in charge of the labeling and GMOs are generally regarded as safe so long as they are substantially equivalent to the other food product. The industry is very opposed to the labeling of GMOs and 90% of the corn, cotton, and soy available has some GMO product in it, according to Dr. Eubanks. She believes that not enough is being done to regulate the industry.

We were intrigued by her discussion of food security and funding for interventions. She described that a lot of international work on food security highly promotes technology and the big industry agricultural model. Dr. Eubanks believes we need to change our paradigm from thinking that the most advanced technological options are always best to considering an ecological intensification approach. Such an approach seeks to design more productive, sustainable production systems that are well suited to their environments by better understanding how nature functions. Her current work is helping bring food security to South Sudan through corn that is pest-resistant and drought-tolerant.

 

Scents Are Key to Lemur Nightlife

LEMUR SUPERPOWER #457:  Some lemurs can safely digest cyanide in amounts sufficient to kill an elephant. Others can enter hibernation-like states to survive periods when food and water are in short supply. To add to their list of superpowers, lemurs also have especially keen powers of scent.

Buried in the nose of Fuggles the mouse lemur are specialized pheromone receptors that help her distinguish friend from foe in the dark of night, when mouse lemurs are active.

By Robin Ann Smith

If you could pick one superpower, consider taking inspiration from lemurs. Some lemurs can safely digest cyanide in amounts that would kill an elephant. Others can enter hibernation-like states to survive periods when food and water are in short supply. Still others have keen powers of scent, with the ability to find mates and avoid enemies in the darkness by smell alone.

Research by biologist and Duke Lemur Center director Anne Yoder suggests that the molecular machinery for sniffing out pheromones — much of which has gone defunct in humans and many other primates — is still alive and well in lemurs and lorises, our distant primate cousins.

Lemurs use scents to mark the boundaries of their territories, distinguish males from females and figure out whether another animal is friend or foe. When a lemur gets a whiff of another animal, specialized pheromone receptors in the lining of the nose transmit the information to the brain, triggering instinctive urges like mating, defense and avoiding predators.

The receptors are proteins encoded by a family of genes called V1Rs. First identified in rats in the mid-1990s, V1R genes are found in animals ranging from lampreys to humans. But the proportion of these pheromone-detection genes that actually functions varies greatly from one species to the next, Yoder said last week in a roundtable discussion hosted by Duke’s Science & Society program.

Randy the ring-tailed lemur scent-marks his territory. Photo by David Haring.

Randy the ring-tailed lemur scent-marks his territory. Photo by David Haring.

Studies suggest that as much as 90% to 100% of the pheromone-detection genes in humans consist of disabled pieces of DNA, called pseudogenes.

“Our pheromone-detection genes are so boring — we don’t have many of them, and almost all of them are broken,” Yoder said.

But in lemurs and lorises — whose ancestors split off from the rest of the primate family tree more than 60 million years ago — the proportion of pheromone-detection genes that is still intact is much higher.

In a study published this year, Yoder and colleagues analyzed the DNA of 19 species and subspecies of lemurs and lorises, looking for subtle differences in their V1R genes. They found that one group — the mouse lemurs — has the highest proportion of intact V1R sequences of any mammal yet studied.

To find out which genes are linked to which scents, Yoder and her colleagues plan to take DNA sequences from pheromone-detecting genes in lemurs, insert them into mice, and expose the mice to different scents to see how they respond.

An ability to sniff out the right mates — and avoid being seduced by the wrong suitors — may have served as a mating barrier that allowed lemur species to diverge after arriving in their island home of Madagascar, helping to explain how the more than 70 living species of lemurs came to be, Yoder says.

Duke Undergraduate Research Society. Hit them up.

By Lyndsey Garcia

I have a confession: I have never personally been interested in performing research. I love to read, listen, and talk about research and latest developments, but never saw myself micropipetting or crunching raw data in the lab. But after attending the Duke Undergraduate Research Society (DURS) Kickoff, they got me to sign up for their listserve!

DURS Executive Board: (from left to right) Joseph Kleinhenz, Syed Adil, Lillian Kang, Dr. Huntington Willard, Sammie Truong, John Bentley

DURS Executive Board: (from left to right) Joseph Kleinhenz, Syed Adil, Lillian Kang, Dr. Huntington Willard, Sammie Truong, John Bentley

The kickoff highlighted DURS’s leading man, Dr. Huntington Willard. He was a biology pre-med undergraduate at Harvard for 3 years until he was introduced to genome research, which quickly became his life’s passion.

In 2002, Willard launched the Institute for Genome Sciences and Policy at Duke, which grew to more than 100 faculty and 300 staff members. The institute unfortunately met its end this past June, but Willard continues his love and passion for genome research here at Duke, and with Duke undergraduate students.

Before creating IGSP, Willard had only interacted with medical and graduate students during his research. But at Duke he had his first opportunity to engage with  undergrads.

“The best thing at Duke is the undergrads and I wanted to take advantage of the best thing at Duke,” he says.

Willard explains his love for research by explaining the inherent differences between all Duke students and those Duke students who perform research. All Duke students love to learn and are interested in what they are learning, but Duke students who research are questioners. He says they want to know more than what is given in the textbook. They constantly go between B and C on the test because there could be valid reasons for both, but we just don’t know why yet. They aren’t afraid to delve into uncharted territories where there is no safety net of certainty.

Willard says many of these young researchers seem to follow his own motto: “This is so cool. I want to know how it works.”

Willard’s talk already had me inspired, but then I got to hear from the executive board of DURS. Each member explained the research they are involved with on campus and how they got there. They explained how they sent tons of emails to professors and received no responses and gave anecdotes about switching labs because it wasn’t what they wanted.

They also expanded on what DURS offers to undergraduates. The program connects professors and undergraduates for potential research positions, sets up workshops to help make networking contacts, pairs young undergrads with experienced undergrads to mentor and give advice, and helps one realize that no one came out of the womb with lab experience, so don’t be discouraged by not having any at first.

“This is exactly why I came to Duke. It’s a great university with amazing research opportunities and now I can’t wait to get started.” – Freshman Jaclyn Onufrey.

So my takeaway from Duke Undergraduate Research Society was:

1)      Are you interested in questioning the unknown?

2)      Do you want to be part of discovering something new?

3)      Don’t know where to start?

If any of those aspects apply to you, it’s definitely worth hitting up DURS!

Duke Undergrads Sink Their Teeth into Evolution Research

Undergraduates Ben Schwartz (left) and Amalia Cong (center) have spent the past year studying enamel evolution in the labs of Christine Wall (right) and Greg Wray (not pictured).

Undergraduates Ben Schwartz (left) and Amalia Cong (center) have spent the past year studying enamel evolution in the labs of Christine Wall (right) and Greg Wray (not pictured).

By Erin Weeks

The evolution of thick tooth enamel helped turn our species into hard food-chomping omnivores, and two undergraduates are taking a bite out of research to unravel how that happened. Amalia Cong and Ben Schwartz are building on the work of a recent paper that identified precisely where in the human genome natural selection worked to give our species thick tooth enamel. The original study looked only at the potential role of four genes with a known role in tooth development — so now the team is broadening their scope.

“They’re really excited to expand out and push the envelope on new genes,” said Christine Wall, associate research professor of evolutionary anthropology and one of the authors of the paper, along with professor of biology Greg Wray.

Cong and Schwartz arrived in the Wall and Wray labs last summer through a special research session at Duke, the Howard Hughes Vertical Integration Partners (VIP) Program. For ten weeks, they received a crash course in primate evolutionary genomics.

“They had very little time, and the progress they made was astounding,” Wall said. “The success that they had is really a testament to how hard they worked. This has developed into their own research.”

“We’ve begun to expand our tooth enamel gene analysis to include proteins in conjunction with the RNA in order to gain a more holistic understanding of the evolutionary differences that exist between chimpanzees and humans,” Schwartz said. He will continue to work in the lab through this summer, turning the work into a senior thesis.

“One of our goals was to look at the relative expression of these few genes,” Schwartz said, which they’ve done by comparing tooth development in primates of different ages. “Our results correlated very heavily with known functions of these genes in other animals, such as rats.”

The experience has given both students a taste for research, which they hope to continue doing after graduating from Duke. Cong, who hails from a small city outside of Toronto, will be attending dental school in the fall, while Baltimore native Schwartz is interested in pursuing a joint MD/PhD.