Duke Research Blog

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

Category: Animals (Page 1 of 18)

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

From Sunfish-Seeker to Planet-Saver: Dr. Tierney Thys

Marine biologist Tierney Thys believes that science make us superheroes. In her words, the tools of science are the superpowers that “allow us to explore worlds that are invisible to the naked eye.”

As a National Geographic Explorer, Research Associate at the California Academy of Sciences, and, in my humble opinion, one of the most effective, passionate science communicators out there, she may as well be a superhero already.

Dr. Tierney Thys snorkels with some aquatic research subjects. Photo credit: Tierney Thys.

Thys, an alumna of Duke’s Biology Department, presented at the Marine Science and Conservation Leaders’ (MSCL) inaugural Marine Science Symposium on Saturday, March 25. She was one of four featured speakers — all women in STEM— whose research interests range from marine biology to physical oceanography.

Though she discussed her own research and life story in depth, the main point Thys drove home was the importance of (and science behind) powerful science communication.

Like most marine biologists, Thys’ love for the ocean began when she was a child. She received her Ph.D. from Duke in 1998, an endeavor which, she said, “looked interminable while [she] was in the midst of grad school but, in retrospect, was just a blink of an eye.”

Among the many fun tidbits she has gleaned studying ocean science are the following:

  • As adults, humans retain a lot of characteristics from our fish-like time in the womb; e.g. “we can thank fish for washboard abs.”
  • Humans, for all our obsession with large brains, have nothing on the African elephantfish, which has a “higher brain weight to body weight ratio than any other vertebrate.”
  • Fish had the gender continuum “totally nailed” before it became trendy among humans, with fish of many species having the ability to change sex at will.

Thys, right, and her dissertation advisor, Dr. Stephen Wainwright, left. Photo credit: Tierney Thys.

Her most impactful lesson out of Duke, however, came from her dissertation advisor Stephen Wainwright, James B. Duke Professor emeritus of zoology. Wainwright is the founder of Duke’s Bio-Design Studio, an art studio within a scientific research laboratory employing a full-time sculptor “to create three-dimensional working models of biological systems for research,” as reported by Duke Magazine. Exposure to this unique melding of disciplines in the final stages of Thys’ education set her on what she said was “an eclectic career path” that would also seek to fuse the artistic and the scientific.

Thys’ research specialty out of graduate school is the Mola mola, more commonly known as the Ocean sunfish—the heaviest bony fish on the planet. According to Thys, sunfish can grow to “60 million times their starting weight,” the equivalent of a human child growing to the weight of six Titanic ships. The heaviest Mola ever caught weighed over 5000 lbs., though, surprisingly, jellies (what most folks would call jellyfish) comprise most of the adult sunfish’s diet.

Thys hailed pop-off satellite tags as the “superpower” of science that allows her to track sunfish through the world ocean, generating data that can improve environmental protection of the species.

A fun graphic Thys used in her presentation to explain the technology of pop-off tags for tracking Mola mola, pictured right. Photo credit: Mike Johnson.

“Studying the sunfish has eclipsed studying any other fish for me. [They’re ] a massive part of the bycatch in driftnet fisheries all over the world—[but] we need to keep our jelly-eaters intact. With data, we can figure out the [sunfish] hotspots, and work to protect those areas,” Thys said.

Thys has tackled this problem herself by adapting the discipline-blending approach of her advisor, Wainwright. She has primarily used filmmaking to bridge the gap between the arts and sciences, playing key roles in high-profile documentary projects meant to improve public understanding of marine science, technology, and conservation. These include the Strange Days on Planet Earth series with National Geographic, The Shape of Life series with PBS, and several short documentary films. She has also collaborated with dance companies to create conservation-oriented dance productions, K-6 schools for educational art projects, and prisons to improve inmates’ scientific literacy with nature imagery—all to widen the scope of her science-education efforts. Thys supports her creative ideas with science itself:

“One very large filter exists between our conscious mind and subconscious mind, she said. “Our conscious mind can only process a tiny amount of the information gathered by our subconscious mind.”

“A good story can cut through these filters and light up our brains in new ways,” Thys said “By using different forms of art to tell stories infused with scientific information, we can message in profound ways. We can reach people who might not otherwise be interested or receptive to science. The arts are not a luxury, but rather a powerful vehicle for helping message, teach and share our vital scientific findings,” Thys said.

A mural Thys made with students out of bottle caps at a California elementary school, one of Thys’ many efforts to spread public awareness of scientific issues. Photo credit: Tierney Thys.

As though she hadn’t already empowered everyone in the audience to save the world, Thys concluded with a compelling piece of advice: “Be a part of something much bigger than yourself.”

Post by Maya Iskandarani

Young Scientists, Making the Rounds

“Can you make a photosynthetic human?!” an 8th grader enthusiastically asks me while staring at a tiny fern in a jar.

He’s not the only one who asked me that either — another student asked if Superman was a plant, since he gets his power from the sun.

These aren’t the normal questions I get about my research as a Biology PhD candidate studying how plants get nutrients, but they were perfect for the day’s activity –A science round robin with Durham eighth-graders.

Biology grad student Leslie Slota showing Durham 8th graders some fun science.

After seeing a post under #scicomm on Twitter describing a public engagement activity for scientists, I put together a group of Duke graduate scientists to visit local middle schools and share our science with kids. We had students from biomedical engineering, physics, developmental biology, statistics, and many others — a pretty diverse range of sciences.

With help from David Stein at the Duke-Durham Neighborhood Partnership, we made connections with science teachers at the Durham School of the Arts and Lakewood Montessori school, and the event was in motion!

The outreach activity we developed works like speed dating, where people pair up, talk for 3-5 mins, and then rotate. We started out calling it “Science Speed Dating,” but for a middle school audience, we thought “Science Round-Robin” was more appropriate. Typically, a round-robin is a tournament where every team plays each of the other teams. So, every middle schooler got to meet each of us graduate students and talk to us about what we do.

The topics ranged from growing back limbs and mapping the brain, to using math to choose medicines and manipulating the different states of matter.

The kids were really excited for our visit, and kept asking their teachers for the inside scoop on what we did.

After much anticipation, and a little training and practice with Jory Weintraub from the Science & Society Initiative, two groups of 7-12 graduate students armed themselves with photos, animals, plants, and activities related to our work and went to visit these science classes full of eager students.

First-year MGM grad student Tulika Singh (top right) brought cardboard props to show students how antibodies match up with cell receptors.

“The kids really enjoyed it!” said Alex LeMay, middle- and high-school science teacher at the Durham School of the Arts. “They also mentioned that the grad students were really good at explaining ideas in a simple way, while still not talking down to them.”

That’s the ultimate trick with science communication: simplifying what we do, but not talking to people like they’re stupid.

I’m sure you’ve heard the old saying, “dumb it down.” But it really doesn’t work that way. These kids were bright, and often we found them asking questions we’re actively researching in our work. We don’t need to talk down to them, we just need to talk to them without all of the exclusive trappings of science. That was one thing the grad students picked up on too.

“It’s really useful to take a step back from the minutia of our projects and look at the big picture,” said Shannon McNulty, a PhD candidate in Molecular Genetics and Microbiology.

The kids also loved the enthusiasm we showed for our work! That made a big difference in whether they were interested in learning more and asking questions. Take note, fellow scientists: share your enthusiasm for what you do, it’s contagious!

Another thing that worked really well was connecting with the students in a personal way. According to Ms. LeMay, “if the person seemed to like them, they wanted to learn more.” Several of the grad students would ask each student their names and what they were passionate about, or even talk about their own passions outside of their research, and these simple questions allowed the students to connect as people.

There was one girl who shared with me that she didn’t know what she wanted to do when she grew up, and I told her that’s exactly where I was when I was in 8th grade too. We then bonded over our mutual love of baking, and through that interaction she saw herself reflected in me a little bit; making a career in science seem like a possibility, which is especially important for a young girl with a growing interest in science.

Making the rounds in these science classrooms, we learned just as much from the students we spoke to as they did from us. Our lesson being: science outreach is a really rewarding way to spend our time, and who knows, maybe we’ll even spark someone who loves Superman to figure out how to make the first photosynthesizing super-person!

Guest post by Ariana Eily , PhD Candidate in Biology, shown sharing her floating ferns at left.

 

Seeing Nano

Take pictures at more than 300,000 times magnification with electron microscopes at Duke

Sewer gnat head

An image of a sewer gnat’s head taken through a scanning electron microscope. Courtesy of Fred Nijhout.

The sewer gnat is a common nuisance around kitchen and bathroom drains that’s no bigger than a pea. But magnified thousands of times, its compound eyes and bushy antennae resemble a first place winner in a Movember mustache contest.

Sewer gnats’ larger cousins, horseflies are known for their painful bite. Zoom in and it’s easy to see how they hold onto their furry livestock prey:  the tiny hooked hairs on their feet look like Velcro.

Students in professor Fred Nijhout’s entomology class photograph these and other specimens at more than 300,000 times magnification at Duke’s Shared Material & Instrumentation Facility (SMIF).

There the insects are dried, coated in gold and palladium, and then bombarded with a beam of electrons from a scanning electron microscope, which can resolve structures tens of thousands of times smaller than the width of a human hair.

From a ladybug’s leg to a weevil’s suit of armor, the bristly, bumpy, pitted surfaces of insects are surprisingly beautiful when viewed up close.

“The students have come to treat travels across the surface of an insect as the exploration of a different planet,” Nijhout said.

Horsefly foot

The foot of a horsefly is equipped with menacing claws and Velcro-like hairs that help them hang onto fur. Photo by Valerie Tornini.

Weevil

The hard outer skeleton of a weevil looks smooth and shiny from afar, but up close it’s covered with scales and bristles. Courtesy of Fred Nijhout.

fruit fly wing

Magnified 500 times, the rippled edges of this fruit fly wing are the result of changes in the insect’s genetic code. Courtesy of Eric Spana.

You, too, can gaze at alien worlds too small to see with the naked eye. Students and instructors across campus can use the SMIF’s high-powered microscopes and other state of the art research equipment at no charge with support from the Class-Based Explorations Program.

Biologist Eric Spana’s experimental genetics class uses the microscopes to study fruit flies that carry genetic mutations that alter the shape of their wings.

Students in professor Hadley Cocks’ mechanical engineering 415L class take lessons from objects that break. A scanning electron micrograph of a cracked cymbal once used by the Duke pep band reveals grooves and ridges consistent with the wear and tear from repeated banging.

cracked cymbal

Magnified 3000 times, the surface of this broken cymbal once used by the Duke Pep Band reveals signs of fatigue cracking. Courtesy of Hadley Cocks.

These students are among more than 200 undergraduates in eight classes who benefitted from the program last year, thanks to a grant from the Donald Alstadt Foundation.

You don’t have to be a scientist, either. Historians and art conservators have used scanning electron microscopes to study the surfaces of Bronze Age pottery, the composition of ancient paints and even dust from Egyptian mummies and the Shroud of Turin.

Instructors and undergraduates are invited to find out how they could use the microscopes and other nanotech equipement in the SMIF in their teaching and research. Queries should be directed to Dr. Mark Walters, Director of SMIF, via email at mark.walters@duke.edu.

Located on Duke’s West Campus in the Fitzpatrick Building, the SMIF is a shared use facility available to Duke researchers and educators as well as external users from other universities, government laboratories or industry through a partnership called the Research Triangle Nanotechnology Network. For more info visit http://smif.pratt.duke.edu/.

Scanning electron microscope

This scanning electron microscope could easily be mistaken for equipment from a dentist’s office.

s200_robin.smith

Post by Robin Smith

Evolutionary Genetics Shaping Health and Behavior

Dr. Jenny Tung is interested in the connections between genes and behavior: How does behavior influence genetic variation and regulation and how do genetic differences influence behavior?

A young Amboseli baboon hitches a ride with its mother. (Photo by Noah Snyder-Mackler)

A young Amboseli baboon hitches a ride with its mother. (Photo by Noah Snyder-Mackler)

An assistant professor in the Departments of Evolutionary Anthropology and Biology at Duke, Tung is interested in evolution because it gives us a window into why the living world is the way it is. It explains how organisms relate to one another and their environment. Genetics explains the actual molecular foundation for evolutionary change, and it gives part of the answer for trait variation. Tung was drawn as an undergrad towards the combination of evolution and genetics to explain every living thing we see around us; she loves the explanatory power and elegance to it.

Tung’s longest collaborative project is the Amboseli Baboon Research Project (ABRP), located in the Amboseli ecosystem of East Africa. She co-leads it with Susan Alberts, chair of evolutionary anthropology at Duke, Jeanne Altmann at Princeton, and Beth Archie at Notre Dame.

Tung has spent months at a time on the savannah next to Mount Kilimanjaro for this project. The ABRP monitors hundreds of baboons in several social groups and studies social processes at several levels. Recently the project has begun to include genetics and other aspects of baboon biology, including the social behaviors within the social groups and populations, and how these behaviors have changed along with the changing Amboseli ecosystem. Tung enjoys different aspects of all of her projects, but is incredibly grateful to be a part of the long-term Amboseli study.

Jenny Tung

Jenny Tung is an assistant professor in evolutionary anthropology and biology.

The process of discovery excites Tung. It is hard for her to pin down a single thing that makes research worth it, but “new analyses, discussions with students who teach me something new, seeing a great talk that makes you think in a different way or gives you new research directions to pursue” are all very exciting, she said.

Depending on the project, the fun part varies for her; watching a student develop as a scientist through their own project is rewarding, and she loves collaborating with extraordinary scientists. Specific sets of collaborators make the research worth it. “When collaborations work, you really push each other to be better scientists and researchers,” Tung said.

Raechel ZellerGuest post by Raechel Zeller, North Carolina School of Science and Math, Class of 2017

Aging Gracefully, and Cheaply, in a Small Space

The old joke is, “We’ve cured cancer several times — in mice!”

But the trouble with our favorite lab animal is that they aren’t nearly as close to humans as we had hoped.

Researchers who are working on human longevity obviously need a model organism — they can’t keep their funding going for 100 years to see how a person dies. And other primates aren’t ideal, either; they’re also pretty long-lived and expensive to house, besides.

microcebus mouse lemurs

Mouse lemurs at a lab outside Paris eagerly lap up their calories. Sometimes it’s great being in the control group. (CNRS photo)

So what if you had a primate that was relatively short-lived, say 13 years tops, and quite small, say 100 grams, a bit bigger than a mouse? Behold the Mouse Lemur, Microcebus, the smallest member of the primate family.

In a pair of presentations Friday during the Duke Lemur Center’s 50th Anniversary scientific symposium, gerontologists Fabien Pifferi of the French national lab CNRS, and Steven Austad, chair of biology at the University of Alabama-Birmingham (UAB), made their arguments for how well “le microcèbe” might work in studying aging in humans.

Pifferi works at one of two mouse lemur breeding colonies in France, which is housed in an elegant old chateau in Brunoy, a suburb southeast of Paris. There, a 450-member breeding colony of grey mouse lemurs produces about 100 pups a year, and the scientists have devised many clever, non-invasive ways to test their physical and mental abilities as they age.

“It seems like their normal aging is very similar to humans,” Pifferi said. But about 20 percent of the tiny lemurs follow a different trajectory, marked by the formation of brain plaques, atrophy of the brain and cognitive declines. It’s not exactly Alzheimer’s disease, he said, but it may be a useful scientific model of human aging.

Aging, UAB’s Austad began, is already the number one health challenge on the planet and will remain so for the foreseeable future. We need a good research model to understand not just how to achieve longevity, but how to live healthy longer, he said.

Filbert, a grey mouse lemur, was born at the Duke Lemur Center in June 2013, weighing less than two cubes of sugar. He should still be around in 2023 at least.

Filbert, a grey mouse lemur, was born at the Duke Lemur Center in June 2013, weighing less than two cubes of sugar.

Citing some early studies on using calorie restriction and rapamycin to increase longevity, Austad said mouse lemurs may be “a mid-way model between mice and humans.”

The CNRS colony at Brunoy tried to replicate a study on calorie restriction and longevity that had yielded mixed results in other animals. The mouse lemurs in the experimental condition thrived.

“I saw this colony last year,” Lemur Center Director Anne Yoder said. “The one remaining control animal was old and feeble and sort of pathetic. The four calorie-restricted animals were bouncing around, they were glossy.” Though suffering age-related blindness at that point, they were very much alive and frisky, Pifferi added.

“I think the mouse lemur is a great intermediate to do these sorts of studies,”  Austad said.

But, as you may imagine, some members of the lemur community who have dedicated their lives to preserving rare and critically endangered lemurs might struggle with the idea of  breeding up mouse lemurs to use as lab animals, even if the tests are non-invasive. Nobody asked hostile questions, but the discussion is sure to continue.

Karl Leif BatesPost by Karl Leif Bates

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