Biology | Duke Research Blog

Fossil Primate Director Becomes a Fossil Primate Himself

May 20th, 2013

Gregg Gunnell directs the fossil primate division of the Duke Lemur Center.

By Karl Leif Bates

A newly discovered 25 million-year-old monkey fossil has been named for Gregg Gunnell, director of the Duke Lemur Center’s Division of Fossil Primates.

The thing is, Nsungwepithecus gunnelli, might turn out to be a pig. “It might be a ‘porky-pithecus,’ ” Gunnell said with a laugh. ”Early monkeys and early pigs looked remarkably alike.”

The fossil, from southwestern Tanzania, consists of a single molar. But it displays nine characteristics that would distinguish it from other Old World monkeys, according to Nancy Stevens, a paleontologist at Ohio University in Athens, Ohio who was the lead author on a paper about the discovery in Nature.

Gunnell’s monkey was found at a site in the Rukwa Rift Basin along with another new monkey fossil, Rukwapithecus fleaglei, for which scientists have a jaw and three teeth. It too has nine distinguishing features.

An artist's conception of the two newly named 25.2 million year old fossil monkeys described in Nature. (credit: Mauricio Anton)

An artist’s conception of the two newly named 25.2 million year old fossil monkeys described in Nature. Gregg Gunnell is the guy on the right. (credit: Mauricio Anton)

Gunnell said Stevens named the monkey after him to honor his role in helping her become a paleontologist. When Stevens was an undergraduate at Michigan State University, and Gunnell worked in the museum at the University of Michigan, he took Stevens and her now-husband and co-author Patrick O’Connor along on archaeological digs in Wyoming. Apparently the lessons stuck.

N. gunnelli is actually Gunnell’s third species. He was earlier honored by the naming of a bat and an extinct tillodont, which was, he reluctantly explains, a rather pig-like little animal.

“I’m hoping that this pig really is a monkey — that’ll improve my self-image,” he said.

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Hope for Understanding Ourselves Goes to the Dogs

April 29th, 2013

By Ashley Yeager

Brian Hare and Evan MacLean, co-directors of Duke’s Canine Cognition Center, play with Lilu, a labradoodle. Credit: Ashley Yeager, Duke.

Lilu, a beautiful brown poodle-labradoodle mix, couldn’t sit still. Scents of pizza and peanut butter dog treats and the sights of new people easily distracted her.

The ADD behavior could be one trait that made her fail out of service-dog training.

“Six out of every ten dogs wash out of service training. But it’s hard right now for scientists to understand why,” said Duke evolutionary anthropologist Evan MacLean, co-director of the university’s Canine Cognition Center.

He, along with biological anthropologist Brian Hare and geneticist Misha Angrist spoke about ‘Genes, Brains and Games’ in man’s best friend as part of the Science and Society Journal Club on April 26.

MacLean and Hare explained that dogs have taken on many jobs in human society, acting as everything from pets, to our eyes and ears to being like coal-mine canaries searching for hidden bombs and missing people.

“Dog vocations require different sets of cognitive skills,” MacLean said. He studies military dogs, looking for traits that make them more suited for service tasks than pets like Lilu.

MacLean would ultimately like to identify the genetic components that underlie the characteristics suited for each type of job that a dog might do.

Scientists are interested in correlating dogs’ cognitive traits to their associated genes because the animals are “the most exquisite example of artificial selection,” Angrist said.

In Portuguese water dogs, for example, just six substitutions in individual DNA bases of the dogs explain variations in body size. In humans, nearly every gene could factor into height. It’s the same challenge that makes understanding human cognition and intelligence difficult at the genetic level.

Of course, defining cognition and intelligence at the conceptual level isn’t so clear cut either. “It’s so hard for people, journalists and the general public, to understand multiple intelligences,” Hare said.

He explained that at a basic level, cognition is the ability to make inferences, and that when we think of intelligence we think of IQ and standardized tests. These tests, however, measure only one type of intelligence. They don’t measure the ability to empathize, to verbalize a new idea or to put two completely separate ideas together to form a new one, which are other, important facets of intelligence, or really multiple intelligences.

At the Canine Cognition Center, and through the citizen science website Dognition, Hare and MacLean use standardized tests to study the variation in dogs’ intelligence. The tests, unlike the SAT or ACT, “cast a wide net across skills sets dogs could use for different vocations,” Hare said.

Dogs like Lilu, he added, are “really the hope of the world” for understanding cognition.

Visible Thinking 2013!

April 24th, 2013

By Pranali Dalvi

Students explain their research to peers and faculty at Visible Thinking 2013 in the French Family Science Center. Photo credit: Pranali Dalvi

On April 19, Duke undergrads gathered in the French Family Science Center for Visible Thinking 2013.

The event showcases the exciting research undergraduates are doing in every discipline from the biological sciences to the humanities. For many students, it was also a celebration of several semesters and summers of hard work. Like seasoned scientists, students explained their research to their mentors, peers and prospective Dukies during the annual poster session.

Renata Dinamarco, a Trinity senior, studied the entrepreneurial preparedness of small businesses in Pembroke Pines, Florida.

Renata Dinamarco, Trinity’13. Photo credit: Pranali Dalvi

People are moving to the newer, western front of the city, so the eastern portion of Pembroke Pines is being redeveloped. Many people believed business owners in the east were underprepared as compared to the west when it came to opening small businesses.

When Renata interviewed 55 small business owners, she found that there was no statistical difference between entrepreneurs in the east versus the west. But, she did find that business owners in the east were more likely to view the city government negatively. Renata’s study of the demographics of small business populations is important for making informed policy decisions.

Christine Tsai, Trinity’14. Photo credit: Pranali Dalvi

Junior Christine Tsai studied the expression of gut-specific genes three days after fertilization in zebrafish. In a healthy developing embryo, epithelial cells line the internal organs.

To explore what genes are turned on and off during the development of the cells, Tsai compared gene expression from the gut cells to gene expression of cells from the entire body. Zebrafish have clear embryos that develop quickly, making them easy to study and use as a system to study genetics.

“I plan to continue conducting undergraduate research and know that the techniques and skills I have acquired and continue to develop through my research will further my understanding of processes in cell and molecular biology,” she said.

Ben Finkel, Trinity’13. Photo credit: Pranali Dalvi

For his honors thesis in evolutionary anthropology, Ben Finkel worked in Dr. Brian Hare’s lab combining his interest in education outreach with his passion for conservation. Finkel’s project examines how portrayals of chimpanzees as either aggressive or affiliative can affect our conservation perception. Through his research, Finkel wanted to understand how media steers conservation beliefs. He found that people were less likely to promote conservation of chimanzees if they showed aggressive behaviors rather than affiliative behaviors.

For more from Visible Thinking, check out my video about senior Emily Ngan who studies the brain’s immune system cells and their role in addiction.

Students Create Multimedia Ocean Conservation Text

April 16th, 2013

By Ashley Yeager

This screenshot shows one of the opening page of of Johnston's new iBook. Image courtesy of Dave Johnston, Duke.

This screenshot shows one of the opening pages of a chapter in Johnston’s new iBook. Image courtesy of Dave Johnston, Duke.

Duke marine biologist Dave Johnston and his students are back in business on iTunes.

They’ve just released The View From Below, a free iBook for middle school students and teachers that uses multimedia and classroom exercises to discuss overfishing, marine debris, climate change, invasive species and other issues related to marine conservation.

This is Johnston’s second digital textbook. His first was Cachalot, an iPad textbook covering the latest science of marine mammals like whales, dolphins and seals. Experts contributed the text, images and open-access papers.

The View From Below, however, is a bit different.

Undergraduate students in Johnston’s Marine Conservation Service Learning class wrote the book using Apple’s iBooks authoring tool. Johnston and Tom Schultz, Director of the Marine Conservation Molecular Facility at Duke’s Marine Lab, edited it.

“There are a lot of people exploring the use of the iBooks platform for student-generated content, among other development platforms,” Johnston says. “I don’t think we’ve seen many that focus on marine science yet though, and I’m pretty sure it’s the first marine conservation textbook written by students on the iTunes store.”

Johnston says the class chose to use the iBooks software because the technology is free, easy to use and provides “great templates to get things going quickly.” The software also works well because Duke’s Marine Lab has an iPad loaner program, making the tablet the platform of choice for developing and testing the textbook.

The middle school that the service learning class works with also has access to iPads for students and instructors, so the audience was there for the iPad format, Johnston adds.

His students chose to write the book as the class project to spur learning and discussion about some of the most serious problems facing Earth’s oceans.

“As the text indicates, all life on earth is ultimately supported by the ocean, so we need to take care of it,” he says.

More on Human Evolution This Week

April 8th, 2013

Churchill displays the right hand of the adult female callled MH2. Her arm is complete from fingers to shoulder blade and collar bone.

One of the researchers displays the right hand of the adult female called MH2. Her arm is complete from fingers to shoulder blade and collar bone. Credit: University of Witwatersrand.

By Karl Leif Bates

Followers of the saga of human evolution are in for a treat later this week.

Duke’s Steven Churchill and an international team of colleagues will soon publish the second wave of papers from their analysis of two South African specimens called Australopithecus sediba.

We can’t tell you the details of what’s in the papers just yet because of the journal’s embargo policy, but trust us — it’s pretty cool!

UPDATE 4/12/2013 — The embargo has lifted, so details of the findings and a recorded interview with two of the scientists can be found on the Duke Research site. END UPDATE

At 2 p.m. on Thursday 4/11, you can tune into a Google+ Hangout to hear Churchill and Boston University’s Jeremy DeSilva describe the latest findings and ask your own questions.

Join the Hangout from 2 to 2:30 p.m. http://bit.ly/DukeGooglePlus

This latest round of analysis goes deeper into several areas of the anatomy of the two spectacularly complete A. sediba specimens and turns up some surprises.

~~This blog will also have a more complete report, going live right around that time, so come on back.~~

Two of Churchill’s former undergrad students, 2012 graduates Tawnee Sparling and Kelly Ostrofsky, are among the authors on the new papers. You can hear them talk about their work in this video.

The story of how scientists discovered the two specimens is pretty cool too — CBS Sixty Minutes did a segment on that a couple of years ago. View it here.

And here’s Churchill in a Sept., 2011 segment describing what the specimens are and what they might represent.

Australopithecus sediba – Steve Churchill Sept. 2011

Making sense of smells

March 18th, 2013

By Prachiti Dalvi

Nobel Laureate Dr. Richard Axel, who visited Duke on March 14, 2013.

“A good scientist has to have a nose for which field to work in,” cancer researcher Bernard Weinstein once told his mentee Dr. Richard Axel.

It was a saying Axel took quite literally.

He and Linda Buck won the 2004 Nobel Prize in Physiology or Medicine for discovering the cell receptors that run our sensory system for olfaction, or the sense of smell.

Axel first stepped into the research world when he took a job as a glass washer to support himself during his undergraduate years at Columbia University. After a few broken test tubes and dirty beakers, he was fired as a glass washer and, instead, rehired to do research. He went on to publish three papers as an undergraduate, including one where he was senior author.

In 1979, he earned his medical degree from Johns Hopkins University. He then returned to Columbia, and in 1977 he, along with Michael Wigler and Saul Silverstein, discovered a way to insert foreign DNA into a host cell to produce particular proteins.

The finding grew into to the field of molecular cloning and earned Axel a spot in the National Academy of Sciences at 37.

Axel moved on to study how the brain represents the external world. This is a central issue in philosophy, psychology and neuroscience. But unlike, vision and touch, which have at least two dimensions in the external world, information about odors has no dimensionality at all.

So, how is smell represented in the various smell centers of the brain? Axel explained what scientists know about the representations during a March 14 lecture sponsored by the Ruth K. Broad Foundation and the Chancellor’s Lecture Series.

Pathway of odor perception (courtesy of nobelprize.org)

The process starts in the nose, where different kinds of smell-sensing cells line the nasal cavity. Each type of smell-sensing cell expresses only one of about 1400 odor-receptor genes. The cells expressing a given gene are randomly distributed through the nasal tissue and send projections back through the skull into the olfactory bulb.

This bulb is essentially first relay station for sensing smell in the brain. The incoming information gets consolidated in a part of the bulb called the glomerulus. There a given odor receptor activates nerve fibers called glomeruli. They send signals to higher brain regions, which then create a topographic map of incoming odors.

This topographic map is similar, or conserved, in all individuals of a species, Axel said.

His lab at Columbia is now focused on understanding how the sense of smell is established during development, how it may change over time and how certain smells can elicit specific thoughts and behaviors.

Summer camp inspires allergy research

March 5th, 2013

By Ashley Mooney

Courtesy of Nicole Leung.

For some undergraduates, research ideas stem from summer camp.

Junior Nicole Leung, a biology major concentrating on pharmacology, is doing an independent study on allergies and pediatric immunology. She works in Dr. Wesley Burks’ lab at the University of North Carolina in Chapel Hill and explained that her interest in allergies first started when she was a volunteer at a summer camp.

“I was taking care of a little boy who was allergic to so many foods and he had to carry an epi-pen around with him all the time,” she said. “It was my first exposure to such a serious problem with allergies.”

“It was really hard for me to see a boy who was so close to being normal be completely abnormal during camp,” she said, adding that because of the boy’s severe allergies, he was very shy and had a hard time making friends.

Leung saw the challenge of severe allergies again in college when a gluten allergy started to affect her freshman-year roommate.

Now, Leung is trying to understand whether people can develop a long-term tolerance to food allergies, even though there is currently no cure for allergic diseases. The lab is also developing immune-system therapies to sensitize patients to allergens and see how long they can withstand the allergic effects.

“Very little is known about allergies, but they tell a lot about our immune system,” she said, adding that “as the human population grows, I think that allergies are going to be a major concern in the future, so this field has great potential.”

In Leung’s previous research, she compared several allergy tests to find which best predicts the severity of allergic reactions. Most common allergy tests, like the skin-prick test and the blood-based ImmunoCAP test, do not determine how severely people may be allergic to certain substances.

Courtesy of Nicole Leung.

“They only will tell you that you’re allergic but you might not have a reaction to it,” she said.

Using a statistical analysis, Leung found that the basophil activation test has a much higher correlation to severity than the skin-prick or ImmunoCAP tests.

“With the basophil activation test, we mix allergens in blood and try to see whether a certain allergen will cause basophils to degranulate and release histamines, which is what triggers the allergy symptoms,” she said. “Because these activated basophils expose CD63 molecules on their surface, we can determine the percentage activated and use cutoff points to identify whether the person is allergic.”

She added that the test only requires a small amount of blood and is a relatively quick procedure. But there are still questions of how it can be applied to clinical practice.

For Leung, the hardest aspect of research is digging through background information to find out how to move her project forward.

“None of the articles point you to a clear answer, and that is the most challenging part of research. But it is also the most exciting part because you get to test your own hypotheses,” she said.

Besides her allergy research, Leung also works in a neuroeconomics lab that looks at risky decision-making in gambling. The lab uses eye trackers to measure how much a test subject’s eyes dilate and how often they shift their eyes between two choices—one risky option, and one safer one.

Although Leung said she has a more direct role in the design and implementation of her allergy research, she said she enjoys meeting and interacting with the families who participate the neuroeconomics study.

Tracking the cell transitions that cause cancer

March 4th, 2013

By Ashley Mooney

Courtesy of Tristan Bepler.

Researchers think that for cancer to develop, damaged cells have to undergo certain transitions that cause them to spread, or metastasize.

Junior Tristan Bepler, a biology and computer science major, is testing this hypothesis, studying two types of cell transitions scientists have linked to the spread of cancer. He works in the lab of Mariano Garcia-Blanco, professor of molecular genetics and microbiology, and looks at the mesenchymal-to-epithelial transition, or MET, and the epithelial-to-mesenchymal transition, or EMT. Mesenchymal cells are more motile, while epithelial cells tend to be fixed in rows.

The hypothesis is that when epithelial cells form tumors, like in colon, prostate or breast cancer, the cells at the edge of the tumor have to turn to mesenchymal cells for the cancer metastasize. Then, “the mesenchymal cells can leave the tumor, get into the blood stream and spread around your body,” Bepler said.

In order for cells to latch onto cells in new locations, they have to transition back to epithelial cells through MET. Bepler’s research focuses on whether MET or EMT are necessary for metastasis.

Most of Bepler’s daily activities involve culturing cells and handling the rats the lab uses in for the research.

The scientists grow tumors in the rats, they inject them under the skin on their flank. “When we’re growing tumors, we have to measure the size of the tumors and weigh the rats to make sure they’re not gaining too much weight,” Bepler said. “Once the tumors get too large, we have to sacrifice the rats and dissect them. We collect their tumors and their lungs, then we can section them and look at fluorescence, which is how we track MET and EMT.”

Although the project is in the basic sciences, it has the potential for clinical use. If EMT is necessary for diseased cells to spread, drugs that block the transition may be effective in treating certain types of cancer. Clinical application is still a long way down the road, though, Bepler said.

Choosing to study metastasis, rather than viruses, which the lab also investigates, “really wasn’t driven by a desire to study cancer at the time,” Bepler said. “I really didn’t know anything, so I decided I would do the cancer side.”

A Durham, N.C. native, Bepler began his lab work the summer before his freshman year. “When you first start working in the lab, you basically work as a lab tech. Your mentor says, ‘do this experiment,’ and you do the experiment,” he said. “It’s sometimes hard to feel like what you’re doing is important or like you’re really involved in the project because you’re just working as a lab tech, you’re not intellectually involved.”

“The key is to get into the biology of what’s going on or think about the experiments and then it becomes a lot more interesting, because after a while you come up with good ideas for experiments, and you become a little more independent and can do your own experiments,” he said.

Bepler added that he prefers working with rats, as opposed to mice, because they are more friendly and do not bite as often.