Duke Research Blog

Following the people and events that make up the research community at Duke.

Category: News Release

Lemur Research Gets a Gut Check

Baby Coquerel’s sifaka

Clinging to her mom, this baby Coquerel’s sifaka represents the only lemur species at the Duke Lemur Center known to fall prey to cryptosporidium, a microscopic parasite that causes diarrhea that can last for a week or more. The illness wipes out much of the animals’ gut microbiome, researchers report, but fecal transplants can help them recover. Photo by David Haring, Duke Lemur Center.

DURHAM, N.C. — “Stool sample collector” is not a glamorous way to introduce oneself at a party. But in the course of their research, gut microbiologists Erin McKenney and Lydia Greene have spent a lot of time waiting for animals to relieve themselves.

They estimate they have hundreds of vials of the stuff, from a dozen primate species including lemurs, baboons and gorillas, sitting in freezers on the Duke University campus.

The researchers aren’t interested in the poop per se, but in the trillions of bacteria inhabiting the gastrointestinal tract, where the bugs help break down food, produce vitamins and prevent infection.

A few years ago, McKenney and Greene started collecting stool samples at the Duke Lemur Center to see how the microbial makeup of lemurs’ guts varies from birth to weaning, and as their diets change over the seasons. And what happens when they get sick?

Illustration of Cryptosporidium, a widespread intestinal parasite that causes diarrhea in people, pets, livestock and wildlife worldwide. Courtesy of the U.S. Centers for Disease Control.

Illustration of Cryptosporidium, a widespread intestinal parasite that causes diarrhea in people, pets, livestock and wildlife worldwide. Courtesy of the U.S. Centers for Disease Control.

Between 2013 and 2016, ten of the lemurs they were studying contracted cryptosporidium, or “crypto” for short, a waterborne parasite that causes diarrhea in people, pets, livestock and wildlife worldwide.

All of the infected animals were Coquerel’s sifakas — the only lemur species out of roughly 20 at the Duke Lemur Center known to fall prey to the parasite — and most of them were under five years old when they fell ill.

Animals that tested positive were moved into separate holding areas away from other animals and visitors. Keepers wore protective suits, gloves, face masks and booties while working in the animals’ enclosures to prevent infection.

All of the animals eventually recovered. Along the way, six of the affected animals were treated with antibiotics, and three were also fed a slurry of saline and feces from a healthy relative.

McKenney and Greene collected stool samples before, during and after infection for up to two months. They used a technique called 16S ribosomal RNA sequencing to identify the types of bacteria in the samples based on their genes, and compared the results with those of 35 unaffected individuals.

In a healthy gut microbiome, “good” bacteria in the gut compete with “bad” microbes for space and nutrients, and secrete substances that inhibit their growth.

The guts of sick and recovering sifakas are host to a very different assortment of microbes than those of unaffected animals, the researchers found.

Not surprisingly, both crypto infection, and antibiotic treatment, wiped out much of the animals’ gut flora — particularly the bacterial groups Bifidobacterium, Akkermansia, Succinivibrio and Lachnospiraceae.

Even after the infections cleared, most animals took another several weeks to stabilize and return to normal levels of gut biodiversity, with younger animals taking longer to recover.

The only animals that made a full comeback within the study period were those that received a fecal transplant, suggesting that the treatment can help restore gut bacterial diversity and speed recovery.

The patterns of gut recolonization following crypto infection mirrored those seen from birth to weaning, said McKenney, now a postdoctoral researcher at North Carolina State University.

The researchers hope their findings will help control and prevent crypto outbreaks in captive primates. Because lemurs are more closely related to humans than lab mice are, the research could also help scientists understand how the gut microbiome protects humans from similar infections and facilitates recovery.

“Thanks to bioinformatics and advances in sequencing, the microbiome gives us a window into the health of these animals that we’ve never had before,” said Greene, a graduate student in ecology at Duke.

They published their findings June 15, 2017, in the journal Microbial Ecology in Health and Disease.

Duke evolutionary anthropology professors Christine Drea and Anne Yoder were senior authors on this study. This research was supported by the National Science Foundation (1455848) and the Duke Lemur Center Directors Fund.

CITATION:  “Down for the Count: Cryptosporidium Infection Depletes Gut Microbiota in Coquerel’s Sifakas,” Erin McKenney, Lydia Greene, Christine Drea and Anne Yoder. Microbial Ecology in Health and Disease, June 15, 2017. http://dx.doi.org/10.1080/16512235.2017.1335165

Post by Robin Smith, science writer, Office of News & Communications

Seed Grants Pair Scientists at Duke and RTI International

The original intent of Funds Launching Alliances for Research Exploration (FLARE) had been to provide seed funding to one research project that joins Duke University scientists with those at RTI International, a global non-profit research institution in the Research Triangle Park.

In the end, the proposals were so good that Duke Vice Provost for Research Larry Carin and RTI President and CEO Wayne Holden decided they had to fund two.

The goal of the seed funding, which was announced last week, is to create new collaborations that would be attractive to federal funding. Each team will receive $100,000 in seed funding.

Kirsten Corazzini of the Duke School of Nursing and Michael Lepore of RTI will co-lead a project on improving nursing home care.

Kirsten Corazzini of the Duke School of Nursing and Michael Lepore of RTI will co-lead a project on improving nursing home care.

One of the winning ideas is a team combining Duke’s department of sociology and School of Nursing with RTI’s public health and health policy researchers. They’ll be examining methods to improve nursing home care through patient-directed  planning. After a year of theoretical framing and data collection, the group hopes to pursue an R21 application with the National Institute of Nursing Research (NINR).

This group will be led by Duke’s Kirsten Corazzini, PhD, an Associate Professor of Nursing, and Michael Lepore, PhD, Senior Health Policy & Health Services Researcher at RTI.

(Clockwise from upper left) RTI's Brooks Depro and William Studabaker will join Duke's Jim Zhang and Christopher Timmins in a study about air quality around fracking operations.

(Clockwise from upper left) RTI’s Brooks Depro and William Studabaker will join Duke’s Jim Zhang and Christopher Timmins in a study about air quality around fracking operations.

The second winning proposal will do air quality assessments before shale gas fracking operations have begun in a local area. This combines Duke economist Christopher Timmins, Ph.D. and Jim Zhang, Ph.D. of the Nicholas School of Environment with RTI economist Brooks Depro, Ph.D. and research chemist William Studabaker, Ph.D.

They plan to apply data visualization and an exploration of correlations with identifiable sources of local air pollution (especially toxics, VOC’s and particulates) and characteristics of local populations. Documenting ambient pollution before fracking starts will be critical to accurately measuring the air quality effects of the practice. This group intends to approach NIH for funding after the pilot program.

Pain-Sensing Gene Named for Rocky

Guest Post By Sheena Faherty, graduate student in Biology

How do our neurons discriminate between a punch to the face or a kiss on the cheek? Between something potentially harmful, and something pleasant?

A new study published this week in Current Biology offers an answer by describing a previously uncharacterized gene required for pain sensing.

This work comes out of Dan Tracey’s lab at the Duke Institute for Brain Sciences. They named the gene balboa in honor of fictional prizefighter Rocky Balboa and his iconic immunity to pain.

Stallone as Rocky

Float like a drosophila, sting like a …oh, never mind.

The researchers found that the balboa gene is only active in pain-sensing neurons and is required for detection of painful touch responses. Without it, neurons can’t distinguish between something harmful and something pleasant.

Does the ultimate prize of naming of the gene inspire any boxing matches between lab mates?

“In the fly community, we are allowed to have these creative gene names, so discussions about the decision on naming are more fun than argumentative,” Tracey says.

Tracey’s lab is concerned with sensory neurobiology, the study of how neurons transform cues from the surrounding environment to signals that can be interpreted by the brain. Ultimately, the lab group hopes to identify the underlying molecular mechanisms that are involved in our sense of touch.

Pugilistic fly artwork designed by Jason Wu, a neurobiology graduate student in Jorg Grandl's lab

Pugilistic fly artwork designed by Jason Wu, a neurobiology graduate student in Jorg Grandl’s lab

“It’s unclear what happens during that moment of touch sensation when sensory neurons detect and convert a touch stimulus into a nerve impulse,” said graduate student Stephanie Mauthner, who is the lead author on the Rocky paper. “It’s also ambiguous how nerves are capable of discriminating the threshold of touch intensity.”

Although the fruit fly has a relatively simple central nervous system, Tracey’s group uses it as model because it has many of the same neural circuits that the human brain has.

“[Our goal was to figure out] what molecular components are required for pain neurons to detect harsh touch responses and what is the mechanism for performing this task,” Mauthner said.

Using fluorescent cells, their study also shows that balboa interacts with another protein of the same family named pickpocket. They’re hopeful that this gene duo can be a potential target for pain medications that could discriminate between different sites of pain throughout the body.

Pain relievers such as aspirin or ibuprofen work broadly throughout the whole body—with no discrimination to where the pain is actually occurring. But, by working towards the exact molecular mechanism of pain signaling, genes like balboa and pickpocket are potential candidates for more targeted therapeutics.

Grad student Stephanie Mauthner, hangs out with one of her many vials of flies (courtesy of Stephanie Mauthner)

Grad student Stephanie Mauthner hangs out with one of her many vials of flies (courtesy of Stephanie Mauthner)

CITATION: “Balboa Binds to Pickpocket In Vivo and Is Required for Mechanical Nociception in Drosophila Larvae,” Stephanie E. Mauthner, Richard Y. Hwang, Amanda H. Lewis, Qi Xiao, Asako Tsubouchi, Yu Wang, Ken Honjo, J.H. Pate Skene, Jörg Grandl, W. Daniel Tracey Jr. Current Biology, Dec. 15, 2014. DOI: http://dx.doi.org/10.1016/j.cub.2014.10.038

Copper Nanowires Now Match Performance of Leading Competitor

Images of the first and last stages (intermediate photo excluded) of the copper nanowire growth as seen through a transmission electron microscope. Interestingly, though not visible here, the nanowires are pink. (Photo: Shengrong Ye)

Images of the first and last stages of the copper nanowire growth as seen through a transmission electron microscope. Interestingly, though not visible here, the nanowires are pink. (Photo: Shengrong Ye)

 

By Erin Weeks

Copper nanowires are one step closer to becoming a low-cost substitute for the transparent conductor in solar cells, organic LEDs and flexible, electronic touch screens. A team at Duke has succeeded in making transparent conductors from copper nanowires that are only 1% less transparent than the conventional material, indium-tin oxide (ITO).

Copper is 1000 times more abundant and 100 times cheaper than indium, the main ingredient in ITO, but for years copper nanowires have lagged behind in terms of transmittance.

Assistant chemistry professor Benjamin Wiley’s lab has fixed that — simply by changing the aspect ratio, or the proportion of length to diameter, of the nanowires. The findings were reported recently in the journal Chemical Communications.

“We finally have something competitive with ITO in terms of performance, and we got there by increasing the nanowire aspect ratio,” Wiley said.

Using a special growth solution, Wiley’s lab can “sprout” the nanowires in under half an hour and at normal atmospheric pressure. Further tweaking the synthesis, the team was able to prompt the nanowires to grow long and uniform in diameter, instead of tapered and baseball bat-shaped, which have lower aspect ratios.

The paper also includes the images of copper nanowire growth as observed in real time, the first time such observations have been published.

Still, at least one kink remains before the nanowire technology will be attractive for commercial production. The copper nanowires are susceptible to corrosive oxidation, which Wiley’s team has tried to remedy by coating the nanowires with materials like nickel. Unfortunately, a nickel coating reduces the transparency of the nanowire films.

“So now we’re trying to figure out ways to protect the nanowires without decreasing the performance,” Wiley said. “We’re focused on getting the same performance, but having more stability.”

Citation: “A rapid synthesis of high aspect ratio copper nanowires for high-performance transparent conducting films.” Shengrong Ye, Aaron Rathmell, et al. Chemical Communications, March 11, 2014. DOI:10.1039/c3cc48561g.

New Course Offers Lessons from Lasering Priceless Art

Duke graduate student Tana Villafana and chief conservator at the NC Museum of Art William Brown stand over The Crucifixion (inset). (Photo: Martin Fischer)

Duke graduate student Tana Villafana and chief conservator at the NC Museum of Art William Brown stand over The Crucifixion (inset). (Photo: Martin Fischer)

By Erin Weeks

A group of chemists at Duke University has gained recognition in recent years for shooting lasers at medieval artwork — technology that allows a harmless peek at the many layers and materials in a painting and offers insight into long gone eras and artists. Now, Duke students will have the chance to learn from this pioneering work at the intersection of chemistry and art history in a new course on the science of color.

The course coincides with the publication of the first scientific measurements from the laser work, reported Jan. 20 in the Proceedings of the National Academy of Sciences.

“The images we have now are enormously better than a year ago,” said Warren S. Warren, head of the lab performing the imaging and the James B. Duke professor of chemistry. He and fellow Duke authors, grad student Tana Villafana and associate research professor Martin Fischer, have not only demonstrated the technology works — they’ve shown it works at an incredible level of detail, telling the difference, for example, between nearly identical pigments.

But lasering The Crucifixion by Puccio Cappano was just the start, as the team envisions countless more cultural applications of the technology. Given enough funding and manpower, they could visualize ancient scrolls of text too fragile to unroll, reveal the bright colors that once adorned Greek statues, learn the secrets of China’s terracotta warriors, and even detect the beginnings of pigment degradation in aging artwork.

There are talented people in art conservation, Warren said, whose work could benefit from more advanced technology, and there are talented people at the cutting-edge of laser science looking for meaningful ways to apply their inventions. For the past several years, Warren’s lab has brought these people together.

Now, he hopes to accomplish something similar with students at Duke. Warren, Fischer, and another chemistry instructor, Adele DeCruz, are teaming up to teach “The Molecular, Physical, and Artistic Bases of Color” in the second half of spring semester.

The class will visit the Nasher Museum of Art, the North Carolina Museum of Art in Raleigh, and possibly even the National Gallery of Art in Washington, D.C, to learn first-hand from art conservators and working artists. Students can expect to learn about how humans have used and made pigments over the millennia; how color works at a molecular level; and the basics of how human vision, microscopes, cameras, and lasers all see or image color.

Students can register for the half course, CHM 590, until the add/drop deadline for classes on January 22. “Students should not be scared off by the course number,” Warren said. “The prerequisite is one college-level science course, and the intent is to make both the science and artistic components accessible to a broad audience.”

Funding for the research was provided by National Science Foundation grant CHE-1309017.

CITATION: “Femtosecond pump-probe microscopy generates virtual cross-sections in historic artwork.” Tana E. Villafana, William P. Brown, et al. Proceedings of the National Academy of Sciences, Jan. 20, 2014. Doi: 10.1071/pnas.1317230111

Early Primate Leaping Set Stage for Human Airtime

By Ashley Yeager

From primate ancestors that leaped like a dwarf lemur is where we got our ability to jump, a new study suggests. Photo courtesy of Mireya Mayor.

Primate ancestors that leaped like a dwarf lemur may be where we got our ability to jump, a new study suggests. (Photo courtesy of Mireya Mayor and Shaquille O’Neal).

Over a puddle, up to the basket, off the high dive — we all take leaps from time to time.

Now, new research suggests that this acrobatic lifestyle began far back in our evolution, when the earliest primates were first emerging on Earth.

“What this study suggests to us is that a very unusual and impressively acrobatic lifestyle jumping through the trees set us on the road to evolving many of features we recognize today in primates, including humans,” says Duke evolutionary anthropologist Doug Boyer.

Boyer and colleagues measured the ankle bones of 73 living and 38 extinct species of primates and found that throughout primate evolution, even our earliest ancestors were developing the bone structure to support long jumps. The results appear July 3 in PLoS ONE.

From the data, the scientists concluded that the ankle mechanics for better leaping in primates began to evolve around 55-60 million years ago. Boyer says natural selection seemed to favor a lifestyle of increasingly acrobatic locomotion in trees, including leaping long distances rapidly between branches.

Scientists had previously noticed that exceptional leapers had unusually elongated ankles. Boyer’s study, however, is the first to simultaneously test for effects of both body mass and behavior on ankle-bone elongation.

The team found a trade-off between body mass and ankle elongation. At larger body masses, ankles were proportionally shorter regardless of behavior. Yet, among animals of similar body size, the leapers had proportionally longer ankles, Boyer says. This was true among even fairly large primates, a contradiction to scientists’ earlier view that there was no behavioral benefit of ankle elongation for bigger animals.

The study is also the first to look at incremental evolutionary changes leading from our earliest primate ancestors to all the modern living forms. Whether leaping was an important behavior for the earliest primates has been controversial.

From their fossil data, Boyer and colleagues could see that early primates were not specialized leapers. “For the most part many of them were generalists, clamoring around on trees, jumping around now and then, but possibly preferring to scamper rather than make huge leaps,” he says.

The ankle bone serves a fulcrum to launch leapers' into the air. The longer the lever, the better the jump, in most cases. Credit: Doug Boyer, Duke.

The ankle bone serves a fulcrum to launch leapers’ into the air. The longer the lever, the better the jump, in most cases. Credit: Doug Boyer, Duke.

This particular conclusion was not new. But the researchers’ approach — looking at incremental evolution — allowed them to see more of a change. “The earliest primates were already better leapers than their ancestors, and the data show their descendents became even better yet,” he explains.

The measurements also suggest that initial elongation of the bones for specialized leaping evolved two independent times in primates – once in lemur ancestors and once in the ancestor of tarsiers, monkeys, apes and other anthropoids like us.

The study didn’t directly address human leaping, and it doesn’t mean humans with longer ankles are better leapers. But, Boyer notes, it’s not out of the range of possibility.

Citation: “Evolution and allometry of calcaneal elongation in living and extinct primates.” Boyer, D. et al. July 3, 2013. PLoS ONE. doi: 10.1371/journal.pone.0067792

Steve Koonin to speak March 8

Official portrait of Steven E. Koonin, former Under-Secretary for Science of the United States Department of Energy. Credit: DOE.

Want to know what we should do to address America’s energy challenges?

Come hear the ideas of  Steve Koonin, a former chief scientist at British Petroleum and more recently the Under Secretary for Science at the Department of Energy. He’ll speak at Duke at 5:15 p.m. on March 8, 2012. The lecture will be held in room 2231 of the French Family Science Center.

Koonin, an MIT-minted theoretical physicist and currently a researcher at the Institute for Defense Analyses in Washington D.C., will talk about strategies to incorporate alternative and renewable energy sources into our energy profile. The lecture is free and open to the public.

The talk is part of the university-hosted Symposium on Electroweak Nuclear Physics, a two-day science conference to explore the latest experiments and ideas on matter and how it behaves at ordinary temperatures — quite the opposite of what’s being studied at the Large Hadron Collider and other high-energy particle accelerators.

The symposium is being held in honor of Jefferson Lab deputy director for science R. D. McKeown’s sixtieth birthday.

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