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

Category: Animals Page 1 of 16

Do Snakes Have Tails? and Other Slithery Questions

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Dhruv Rungta, a member of the Wild Ones club, with a ring-necked snake during a herpetology walk with Dr. Nicki Cagle in the Duke Forest.
Upper left: Dr. Nicki Cagle holding a ring-necked snake. Photo by Montana Lee, another Wild Ones member.

On a sunny Friday in September, Dr. Nicki Cagle led a herpetology walk in the Duke Forest with the Wild Ones. The Wild Ones is an undergraduate club focused on increasing appreciation for the natural world through professor-led outings. Herpetology is the study of reptiles and amphibians.

Dr. Cagle is a senior lecturer in the Nicholas School of the Environment at Duke and the Associate Dean of Diversity, Equity, and Inclusion. Along with teaching courses on environmental education and natural history, she is also the science advisor for a citizen science project focused on reptiles and amphibians, or herpetofauna, in the Duke Forest. Volunteers monitor predetermined sites in the Duke Forest and collect data on the reptiles and amphibians they find.

“We get a sense of abundance, seasonality… and how the landscape is affecting what we’re seeing,” Dr. Cagle says. There is evidence that herp populations in the Duke Forest and elsewhere are decreasing.

Dr. Nicki Cagle flipping over a cover board with members of the Wild Ones. The cover boards are used to monitor reptiles and amphibians for a citizen science project in the Duke Forest.

The project relies on transects, “a sampling design… where you have a sampling spot at various intervals” along a line of a predetermined length. In this case, the sampling spots are “traps” meant to attract reptiles and amphibians without harming them. Each site has a large board lying on the ground. “Different herps are more likely to be found under different objects,” Dr. Cagle explains, so the project uses both wooden and metal cover boards.

But why would snakes and other herps want to hide under cover boards, anyway? Reptiles and amphibians are “cold-blooded” animals, or ectotherms. They can’t regulate their own body temperature, so they have to rely on their environment for thermoregulation. Snakes might sun themselves on a rock on cold days, for instance, or hide under a conveniently placed wooden board to escape the heat.

Salamanders that use the cover boards might be attracted to the moist environment, while “snakes will tend to go under cover boards either to hide — like if they’re about to molt and they’re more vulnerable — to look for prey, or just to maintain the proper temperature,” Dr. Cagle says.

Citizen scientists typically check the boards once a week and not more than twice a week. Volunteers have to avoid checking the traps too often because of a phenomenon called “trap shyness,” where animals might start avoiding the traps because they’ve learned to associate them with pesky humans flipping the boards over and exposing their otherwise cozy resting places. By checking the traps less frequently, scientists can reduce the likelihood of that and minimize disturbance to the animals they’re studying.

The first snake we saw was a worm snake, dark above with a pink stomach.

Dr. Cagle gave the Wild Ones a behind-the-scenes tour of some of the cover boards. Using a special, hooked tool conveniently stashed in a PVC pipe next to the first cover board, we flipped each board over and looked carefully underneath it for slithery movements. We didn’t find any under the first several cover boards.

But then, under a large sheet of metal, we saw a tiny snake squirming around in the leaf litter. There was a collective intake of breath and exclamations of “snake!”

Dr. Cagle captured it and held it carefully in her hands. Snakes, especially snakes as young as this one, can be all too easily crushed. We gathered around to look more closely at the baby snake, a species with the adorable name “worm snake.” It was dark above with a strikingly pink underside. The pink belly is a key field mark of worm snakes. Earth snakes are also found around here and look similar, but they tend to have tan bellies.

After a minute or two, the worm snake made a successful bid for freedom and wriggled back under the board, disappearing from sight almost immediately.

Crossing over a dry “intermittent stream,” which Dr. Cagle describes as “the running-water equivalent of a vernal pool.” A vernal pool is a temporary wetland that is dry for much of the year.

Some of the cover boards revealed other animals as well. We found a caterpillar chrysalis attached to one and several holes — probably made by small mammals — under another.

Whatever made the holes, we can safely assume it wasn’t a snake. According to Dr. Cagle, the term “snakehole” is misleading. Most snakes don’t make their own holes, though some of them do use existing holes made by other animals. One exception is the bull snake, which is known for digging.

We found a young five-lined skink sunning itself on top of one of the metal cover boards. (Thermoregulation!) Juvenile five-lined skinks are colloquially known as blue-tailed skinks, but the name is somewhat misleading — the adults don’t have blue tails at all.

The snakes we were looking for, meanwhile, were often elusive. Some vanished under the leaf litter before we could catch them. Sometimes it was hard to tell whether we were even looking at a snake at all.

“What are you?” Dr. Cagle muttered at one point, crouching down to get a better look at what was either a stick-esque snake or a snake-esque stick. “Are you an animal? Or are you just a wet something?” (Just a wet something, it turned out.)

The Duke Forest is a valuable community resource with a complicated history. “We know that slavery was practiced on at least four properties” in the Duke Forest, Dr. Cagle says, and the forest is located on the traditional hunting grounds of several indigenous peoples. The interpretive signs along the Shepherd Nature Trail, which we walked part of during our herpetology outing, were designed in collaboration with the Occaneechi Band of Saponi. Today, the Duke Forest is used for research, recreation, timber management, and wildlife management and conservation.

Later on, we found at least three young ring-necked snakes (Diadophis punctatus) under different cover boards. One of them was particularly cooperative, so we passed it around the group. (“All snakes can bite,” Dr. Cagle reminded us, but “some have the tendency to bite less,” and this species “has the tendency not to bite.”) Its small, lithe body was surprisingly strong. The little snake wrapped tightly around one of my fingers and seemed content to chill there. A living, breathing, reptilian ring. That was definitely a highlight of my day.

The faint, dark line on this ring-necked snake’s underside (on the bottom of the loop) is the anal vent. Everything below that point (farther from the head) is considered the official tail of a snake.

If you’ve ever wondered if snakes have tails, the answer is yes. The official cut-off point, Dr. Cagle says, is the anal vent. Everything below that is tail. In between flipping over cover boards and admiring young snakes, we learned about other herps. Near the beginning of our walk, someone asked what the difference is between a newt and a salamander.

“A newt is a type of salamander,” Dr. Cagle says, “but newts have an unusual life cycle where they spend part of their life cycle on land… and that is called their eft phase.” As adults, they return to the water to breed.

We learned that copperheads “tend to be fatter-bodied for their length” and that spotted salamanders cross forest roads in large numbers on warm, rainy nights in early spring when they return to wetlands to breed.

Students holding a ring-necked snake. Above: Kelsey Goldwein (left), Gurnoor Majhail (one of the co-presidents of the Wild Ones), and Simran Sokhi (background on right). Below: Emily Courson (left) and Barron Brothers.

Perhaps the most interesting herp fact of the day came near the end of our walk when one of the students asked how you can tell the sex of a snake. Apparently there are two ways. You can measure a snake’s tail (males usually have longer tails), or you can insert a metal probe, blunted at the end, into a snake’s anal vent. Scientists can determine the sex of the snake by how deep the probe goes. It goes farther into the anal vent if the snake is a male. Why is that? Because male snakes have hemipenes — not two penises, exactly, but “an analogous structure that allows the probe to slide between the two and go farther” than it would in a female snake. The more you know…

Looking for snakes on a herpetology outing with Dr. Cagle and the Wild Ones. Photograph by Gurnoor Majhail.

Disclaimer: Handling wild snakes may result in snake bites. It can also be stressful to the snakes. Furthermore, some snakes in this area are venomous, and it’s probably best to familiarize yourself with those before getting close to snakes rather than afterward. Snakes are amazing, but please observe wildlife safely and responsibly.

Bonus snake! I saw this adorable fellow on the Duke Campus and thought it was an earthworm at first. Dr. Cagle thinks it might be a rough earth snake. I did not check to see if it had a tan belly.
Post by Sophie Cox, Class of 2025

Meet New Blogger Jakaiyah, an infectious disease enthusiast

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Hello, my name is Jakaiyah Franklin, and I am a sophomore here at Duke University. In terms of my major, I am undecided, but I do know my passion lies in biology, science communication, and environmental science.

Outside of classes, I am the treasurer for the Duke Chapter of the NAACP and LLC leader for the Stem Pathways for Inclusion, Readiness, and Excellence (SPIRE) program. Last year I was the stage manager for two Hoof n Horn productions.

This is the Rocky Horror Picture Show company after finishing our last show.

This year, I will start a research position along with this research blogging position.

In a more personal sense, I am the youngest of three and a proud aunt. Right now, I say I am from Texas, even though I have lived in Georgia, South Carolina, Germany, and presently North Carolina. If someone ever asked me, I would say that Germany holds my most memorable memories; however, I have grown into a better version of myself in each place I have lived. Other than school, I like to read and watch House of the Dragon and the earlier seasons of The Game of Thrones. I prefer to study outside or in a place where natural light is abundant. I also love learning new things pertaining to science, specifically infectious diseases.

My view of Muhuru Bay, Kenya, where I spent the summer after my first year at Duke. That’s Lake Victoria in the distance.

I find diseases fascinating, and I believe they are our natural predators. I want to be able to not only understand them, but also, I want to help prevent them. If one were to have a favorite type of disease to study, mine would be zoonotic diseases. They are interesting because the act of a virus being able to jump from a host like a rat to a human is captivating to me.

After graduating from Duke, I want to earn a master’s in public health or a Ph.D. in epidemiology, virology, or infectious disease to feed my curiosity about diseases. However, before I can even decide what Ph.D. or master’s I want to earn, my current goal is to decide on my major.

Jakaiyah Franklin

I do like to think ahead, so, for my very distant career, I know I want to be able to see infectious diseases in both the lab and in the places where they are infecting populations. I want my research to be digestible for the general population because, as seen with both COVID and Monkeypox, science can be easily misinterpreted if not delivered appropriately. I want to prevent this occurrence from happening to me by learning more about science communication and actively improving my communication skills.

I hope this blogging position will expose me to infectious disease research or general public health research. With this new understanding of the research, I hope this position will also educate me on how to inform others so that they can enjoy and understand the science.

Post by Jakaiyah Franklin, Class of 2025

Predicting What Extinctions Could Mean for Lemurs and the Forests They Call Home

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New research shows that lemurs and their food trees are tightly linked in ecological networks, and that the extinction of lemurs will have cascading effects on ecosystem functions.

The Critically Endangered black-and-white ruffed lemur, Varecia variegata, is one of the lemurs that eats the most fruit. When they consume the fruit, they pass the whole far from the mother tree, effectively aiding in seed dispersal. Photo credit: Laura De Ara

Lemurs are the primates found only on Madagascar. They are unique in many ways, and like many organisms, they fit in complex ecological networks. These networks include interactions between lemurs and their food trees. Many interactions are beneficial, or mutualistic; for example, lemurs eat the fruits of trees and disperse their seeds, providing a critical service to the trees. If lemurs go extinct — 98% of species are threatened with extinction due to human activities — the links in the ecological network will be severed, with potentially negative impacts on the trees.

Research published in the Journal of Animal Ecology by Ph.D. student Camille DeSisto, of the Duke University Nicholas School of the Environment, and James Herrera, from the Duke Lemur Center, shows how tightly linked lemurs and trees are in their interaction networks, and the negative impacts of extinction on network resilience. If lemurs do in fact disappear, many trees will be left without a way to disperse their seeds, and may not be able to reproduce effectively.

DeSisto and Herrera used advanced techniques in social network analysis, including exponential random graph models, to test which traits of lemurs and trees predict their probability of interaction. The lemurs with the highest probability of interactions with trees were large, fruit-eating species with a short gestation length, occurring in arid habitats, and with a threat status of Least Concern. Closely related plants were more likely to interact with the same lemur species than distantly related plants, but closely related lemurs were not more likely to interact with the same plant genus.

Simulated lemur extinction tended to increase network structure in some properties, including connectance (% of realized interactions out of all possible interactions) and modularity (how many unique cliques or subcommunities form in the network), but decrease nestedness (the tendency for specialists which feed on only a few trees to be a subset of generalists which feed on many trees) and robustness (tolerance to future extinctions), compared to pre‐extinction networks. Networks were more tolerant to plant than lemur extinctions.

The silky sifaka, Propithecus candidus, is one of the most endangered primates in the world. Unlike some lemurs, the sifaka have antagonistic relationships with trees, eating leaves and prey on seeds, rather than pass them intact. Photo credit: Laura De Ara.

By simulating the loss of lemur and plant species, the authors could predict how network structure will erode over time if threatened lemurs and trees go extinct. The results showed that if the most well-connected lemurs in the network were to disappear, the percentage of trees with interactions would quickly decline, compared to scenarios in which lemurs were removed randomly or if the least-well connected lemurs went extinct. Given the threat status and geographic range size of lemurs, the percentage of trees that would lose their interacting lemurs would be greater than that expected if lemur extinctions were random.

The bamboo lemur, Hapalemur occidentalis, is a highly specialized species, eating mostly bamboo leaves. They do, however, occasionally eat fruits, and often spread the seeds effectively. Photo credit: Laura De Ara

Results also showed that if lemurs go extinct, the resilience of the networks to further disturbance would decrease. This indicates that the current links between lemurs and trees are critical to the stability of these complex ecological networks.

To prevent the loss of key ecosystem functions like seed dispersal, it is critically important to protect lemurs and trees, which depend so crucially on one another for survival. DeSisto is currently conducting field research in Madagascar, studying how well seeds germinate when eaten by lemurs. She created a tree nursery in the forest to grow the seeds obtained from lemur feces, and already has several species germinating. Interestingly, she is also showing how lemurs disperse the seeds of vines, which are an important yet understudied food source when tree fruits are not available. She will continue her research across multiple seasons, to determine how changes in plant phenology affect seed dispersal patterns.

Author Camille DeSisto and assistant Feno Telessy examine the seeds germinating from lemur feces.
Amazingly, seeds from lemur feces are already germinating after only one month. Some tree seeds take months or even a year before germinating.

Many conservation programs are currently striving to safeguard Madagascar forests and the diverse species found only in these natural habitats. The Duke Lemur Center has an active conservation program in the northeast, called the DLC-SAVA Conservation Initiative. This program takes a community-based approach to conservation, partnering closely with local stakeholders and actors to develop projects that address the needs of both lemurs and people. By co-creating projects that include alternative and sustainable livelihood strategies, both nature and people benefit from conservation. Natural ecosystems provide important services for people, including locally, such as protecting watersheds and pollinators, as well as globally, such as carbon sequestration. Without the native forests, and the lemurs that call those forests home, people would lose the valuable and irreplaceable services forests provide.

CITATION: “Drivers and Consequences of Structure in Plant–Lemur Ecological Networks,” Camille DeSisto and James Paul Herrera. Journal of Animal Ecology, July 15, 2022. DOI: 10.1111/1365-2656.13776.

Lemur Gut Isn’t One Ecosystem, It’s Many

Lemurs like Ferdinand are leaf-eating machines, says Duke microbiome researcher Lydia Greene. Credit: Lydia Greene

DURHAM, N.C. — A jungle. A rainforest. A wetland. A wilderness. Researchers have used various metaphors to describe the complex, interconnected community of microbes (most of them bacteria) living inside your body, and all over it too.

If you were to count up all the trillions of cells inside and out, we are more bacteria than human. Fortunately, perhaps, the microbes that make a cozy home inside your nose, or clinging to your teeth, aren’t the same ones that are living behind your ear or busily multiplying in your belly button.

The same is true for our distant primate cousins the lemurs, particularly in their guts, say researchers Lydia Greene and Erin McKenney in a new study.

Lemurs rely on gut microbes to digest their leafy diets, explains Greene, a research scientist at the Duke Lemur Center. Microbes in lemurs’ GI tracts help ferment plant fiber, detoxify plant chemical defenses, and synthesize vitamins and nutrients that lemurs can’t make for themselves. Our own gut bugs do many of the same things for us.

Greene and McKenney study how lemur gut bacteria are shaped by what lemurs eat, how they evolved and the complexity of the route microbes travel through the body. They hope to better understand how these microorganisms keep lemurs healthy, or — when they’re out of balance — make them sick.

Researchers who do this kind of work spend a lot of time collecting poop. For good reasons, says McKenney, an assistant professor at North Carolina State University. Scientists can learn about lemurs by what they leave behind, and poop can be collected repeatedly without harming the animals. But for this study the team tried something different, made possible by a one-of-a-kind biobank:

When an animal dies at the Duke Lemur Center, veterinary staff determine the cause of death, and blood and tissue samples that might be important for research or education are collected and preserved.

Today, the collection holds thousands of samples, collected over decades from more than two dozen species of rare and endangered primates, which the center stores in super cold freezers in their headquarters in North Carolina. It’s a frozen ark maintained at up to minus 80 degrees Celsius, with redundant backup power.

In the event that any one of these species goes extinct, and the last living parts of them are gone, future generations will still be able to study the genetic and other information they left behind.

Using this bank, the team sampled several sites in the bowels of 52 deceased lemurs, including dwarf lemurs, aye-ayes, ruffed lemurs, bamboo lemurs, brown lemurs, ring-tailed lemurs and sifakas.

A trip through a lemur’s GI tract is a journey through a varied landscape. The long, twisting route from the stomach through the small intestine to the colon serves numerous functions, filtering, digesting, absorbing, detoxifying, fermenting.

Not all lemur guts work the same: Fruit-eaters, like ruffed lemurs, generally have short, simple guts. If you stretched them out, they’d be five times their body length — not much shorter than ours, relative to body size. Leaf-eaters like sifakas have more complex GI tracts with relatively longer colons and a leaf-fermentation pouch called a cecum. Their guts are the lemur champions — up to 16 times body length.

Having whole lemurs to study instead of just poo enabled the researchers to sample different regions of the gut to figure out what kinds of microbes were present in each spot. They used genetic sequencing technology to identify microbes and compare their relative abundance in different sites.

Sampling along the digestive tract, they found that different spots along this long, twisting pathway have their own communities of bacteria doing different kinds of jobs. The complex ecosystem lurking in a lemur’s small intestine, for example, isn’t the same as the microbial menagerie setting up camp in their colon.

Levels of biodiversity varied too. The stomach supports less microbial life because fewer species can tolerate its acidic digestive juices. But if the upper regions of the gut are a garden, the lower regions are more like a tropical rainforest. About two dozen types of bacteria were more abundant in the cecum and colon than elsewhere. Lemurs with relatively longer lower guts host the richest microbiomes, to better ferment high-fiber foods.

“We probably couldn’t have detected these relationships without such an extensive comparative dataset,” McKenney said.

“This kind of lemur research can really only be done at the Duke Lemur Center,” Greene said.

Rodelinda, a Coquerel’s sifaka lemur, munches on leaves at the Duke Lemur Center. Credit: Lydia Greene.

This research was supported by the National Science Foundation (DBI PRFB 1906416) and by a Duke Lemur Center Director’s fund.

CITATION: “Gut Site and Gut Morphology Predict Microbiome Structure and Function in Ecologically Diverse Lemurs,” Lydia K. Greene, Erin A. McKenney, William Gasper, Claudia Wrampelmeier, Shivdeep Hayer, Erin E. Ehmke, & Jonathan B. Clayton. Microbial Ecology, May 14, 2022. DOI: 10.1007/s00248-022-02034-4

Symposium Explores How People and Nature are Inextricably Entwined

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The massive Keeler Oak, a white oak (Quercus alba) in New Jersey.

An April symposium at Grainger Hall, People and Nature, brought a diverse set of speakers, both from Duke and other U.S. institutions, to examine the relationship between human culture and land and to discuss pressing issues such as environmental justice. The session was organized by PhD students Nicholas School of the Environment and the biology department.

Paul Manos of Duke Biology

Professor Paul Manos of Duke Biology told us  how oaks, ubiquitous tree species in temperate regions, can make people think about nature. A walk in the woods looking at the different oaks can result in a fascinating journey of natural history. For those who are curious enough, an inquiry into the lives of oaks will take them deep into topics such as evolutionary history, leaky species boundaries, plant-animal interactions, among others, Manos said. Keeping true to the theme of the symposium, Manos explored some hypotheses about the first time that humans had contact with oaks, and how this relationship unfolded ever since.

Orue Gaoue of Tennessee-Knoxville

Associate Professor Orou G. Gaoue of the University of Tennessee, Knoxville,  took us through a detailed case study of human and plant interactions with long-term data from the country of Benin, in Africa. He showed how the harvest of the African mahogany (Khaya senegalensis) affects human demography and even the marriage dynamics of the Fulani people, with many other insights into the intertwined relationship of the locals and their harvest.

Andrew Curley of Arizona

Central to the morning sessions were the rights of nature and the granting of personhood to non-humans, which is common in the cosmology of many indigenous cultures. For instance, Andrew Curley, assistant professor at the University of Arizona, mentioned in his talk that the O’odham people in the Sonoran Desert confer the Saguaro cactus personhood status. His talk exposed how colonial dynamics have created climate catastrophes and drought around the Colorado River, how indigenous peoples have to navigate these foreign systems, and how they understand their relationship with the land and water.

Michelle Carter, a first-year Masters of Environmental Management (MEM) student at Duke, examined the feasibility of the rights of nature in the US legal system. These rights allow certain natural features (e.g. rivers) to stand as a sole party in litigation and recover damages on their behalf. However, effective application and the enforcement of policy have been lacking.

The second part of the symposium focused on environmental justice. Duke Ph.D. student Maggie Swift presented a land acknowledgement which was divided into three parts: recognition of the violent history of the past; an understanding of the present with a celebration of the lives and achievements of current indigenous peoples; and a call to action so that participants were encouraged to financially support native-led organizations.  Links for donations and more information can be found on the symposium website. The land acknowledgement was followed by a brief presentation on the project Unearthing Duke Forest  that explores the human history surrounding Duke Forest.

Why is it important to jointly consider people and nature in your work? What insights do you gain in your work by taking this approach?

People & NAture
Christine Folch of Duke Cultural Anthropology

Assistant professor Christine Folch, from Duke’s Department of Cultural Anthropology provided an analysis of the discourse around climate change. At the center was the question “do you believe in climate change?” which has ingrained the element of doubt and the ability of the speaker to say “no, I don’t.”  

Associate professor Louie Rivers III, from NC State University,  gave a talk on perceived environmental risks and their influence on social justice. He pointed out that these questions  could be dismissed by certain groups such as black farmers, who are concerned and disproportionally affected by environmental issues but might not relate to how the question is addressed.

Sherri White-Williamson, Environmental Justice Policy director at NC Conservation Network, explained the concept of environmental justice and provided concrete examples of how certain policies (e.g. federal housing/lending policies or interstate highway systems) can create inequalities that leave communities of color to bear the exposure of environmental degradation. She also made us aware that this year is the 40th anniversary of the birth of the US environmental justice movement that started when an African-American community  in Warren County, North Carolina organized to fight a hazardous waste landfill.

No exploration of people and nature would be complete without including the seas. A team of three students at the Duke University Marine Lab, undergrad Maddie Paris, second-year MEM Claire Huang, and Ph.D. student Rebecca Horan, presented two case studies of social and ecological outcomes linked to education and outreach interventions conducted in tropical marine environments.

Their first case study was on turtle education in Grenada, West Indies. Here a 10-week summer program for local children ages 9-12 created an improved understanding of marine turtle biology and its connection to the health of the ocean and their communities. The second case study was a 4-week training course for fisher people and fisheries officers in Mtwara, Tanzania. These participants increased their skills in monitoring the local reefs and were better equipped to educate their communities on marine environmental issues.

The symposium ended with two open questions for the audience, which should be considerations for anyone doing environmental research:  Why is it important to jointly consider people and nature in your work? What insights do you gain in your work by taking this approach?

Guest post by Rubén Darío Palacio, Ph.D. 2022 in Conservation Biology from the Nicholas School of the Environment, and science director of conservation non-profit Fundacion Ecotonos in Colombia.

A Conversation with Emily Levy, Soon-to-Be Biology PhD

Emily Levy studies how the physical and social environments that baboons experience affect their physiology and life outcomes. The Massachusetts native, who works under advisor Susan Alberts (PhD), is in the final year of her Biology PhD and will defend her thesis later this Spring.

Though Duke’s in-person classes have been delayed until next week, I caught up with Levy over Zoom. The wall of her home office displays a fascinating Russian map of Chicago from the cold war era that shows bridges with their weight capacity. Levy tells me that she had no idea how her husband, who is from Evanston, found the map.

Emily Levy, an almost-PhD in Duke Biology

Levy’s research stems from the Amboseli Baboon Research Project – a nearly 50-year-old, ongoing study of wild baboons in Kenya. Duke’s Alberts has been studying these baboons for over 35 years and is a renowned primatologist involved with the project. Alberts’ lab collaborates with field researchers in Kenya to receive data and samples that are imperative to much of their work.

“Something that I really appreciate about Susan and the way she runs the lab is that she starts first-year grad students on a starter project,” Levy told me. Following a discussion about Levy’s interests, this project led to her first work on dominance rank, stress levels, and what this means physiologically for baboons. Levy also “poked around” at how scientists study dominance rank and found that the methods used for assessing rank “matter a lot.”

In her more recent project, Levy is trying to figure out what early life environments mean for adulthood in baboons. “So, we know that baboons that experience a really harsh early life, if they survive to adulthood, have really, really reduced lifespans as adults – like half as long – as baboons that had no adverse events,” Levy said.

“I’m focusing on two hypotheses to get at what might be happening under the skin that could have something to do with longer term effects on health and mortality.” One hypothesis is that a tough early life environment, especially nutritional stress, could stunt baboon growth and impinge adult activities like foraging or maintaining dominance rank. The other hypothesis proposes that early life adversity disrupts immune development, leading to an immune system that is either always inflamed or produces an overpowering inflammatory response when a baboon does get sick.

The second hypothesis is one that has been supported by human research, but Levy’s preliminary results “are the exact opposite.” This highlights one facet of the importance of her research: Its implications and parallels to human health and mortality. But Levy says her research is also “cool because it’s just cool” and appreciates what her work may add to basic science beyond human application.

In her journey to Duke, Levy said that she “tried a few ways of studying” animals before arriving at the work she conducts now.  Levy, who really liked animals, enjoyed time outside, and was “hooked on biology” in high school, began her undergraduate career at Williams College with this in mind. “In college, I took biology and neuroscience and then took animal behavior my sophomore year and was like Oooo, this is cool!,” Levy exclaimed with a big smile on her face, “And it felt sort of light-bulby.”

Along the journey to her PhD, Levy studied plants and insect pollinators and spent a few weeks in Madagascar in a tent filled with fleas. Though Levy said that these experiences of field work became “one of my favorite things about my job,” they also helped shape her trajectory as a scientist as she figured out which model systems and research questions “did and did not spark her joy.”

It was during her undergraduate thesis assessing social behavior in rats that she felt a strong “click” for studying social behavior in animals. Taking a couple years to work in a clinical research lab that conducted work on autism in humans, Levy enjoyed working on research to aid in special needs people. “But pretty quickly,” Levy said, “I was like, Alright, I don’t want to study humans for my whole life.”

“I’d basically been crossing things off my list up until this point,” Levy continued, “I now knew I wanted to study social animal behavior in non-human animals.” In her year away from research, Levy worked as an outdoor educator in Wyoming while she applied to grad school with this study plan in mind. Her time in Jackson Hole, Wyoming narrowed her interests even more, pushing her towards behavioral ecology because of her observation of an amazing, unbroken natural ecosystem.

Levy says she ultimately ended up at Duke because “the Baboon Project is amazing,” “Susan Alberts is amazing,” and “the Duke Biology Department is really wonderful.”

While Levy enjoys working with Alberts and mentoring undergraduates, as well as using grant writing as a “fun way to develop really exciting ideas and hypotheses,” she also shared some of her frustrations with me. “Science is very slow — often, not always — and a project from start to finish takes a long time. And the publication process is so long. I struggle with that pace sometimes” Additionally, as someone who was raised to never take herself too seriously, Levy also said that she has felt a lot of pressure in grad school to take herself more seriously than she should as part of academic culture.

Levy loves teaching and her hope is to become a faculty member at a small liberal arts college or undergraduate institution following a post-doc, for which she is currently in the application process. Through this future work, Levy aspires to “bring undergrads through the scientific process.”

In her time away from the lab and science, Emily is an avid baker. “One of my goals in grad school has been to acknowledge and own what I am good at, and I know I am good at baking,” Levy said with a grin. Chocolate chip cookies are her specialty.

If she could give any aspiring science PhDs a word of advice, Levy offered that you should have fun and “pay attention to the non-intellectual, as well as intellectual, things that you enjoy most.” As exemplified by her path to figuring out what exactly it was in science that inspired her, Levy says not to worry as much about figuring out where you are going, and when, but reaping the lessons and insights of the experiences along the way.

Post by Cydney Livingston, Class of 2022

Science Behind the Scenes: Get To Know a Zebrafish Lab Technician

It’s 7:30 a.m. on a Sunday morning, and Mark McDonough is making a very familiar journey through a very unfamiliar mode. With the light rain pelting down on his gelled hair, he’s walking the 2-mile trek from East Campus to West Campus. The C1 doesn’t run until 8:30 a.m. on weekends, and his job is simply too important to wait for Duke-provided transportation.

Since his third week as a freshman, Mark has held the position of Lab Technician at the Duke University School of Medicine Zebrafish Core Facilities. Through the job, which he earned via the university’s work-study program, Mark has had the opportunity to make his college experience more affordable while completing the behind-the-scenes work that keeps the university’s labs running.

Upon arriving at work every morning, Mark spends anywhere from thirty minutes to an hour cleaning the filters on the fish tanks, after which he removes feces and inserts food. These three tasks are just a microcosm of his duties as a lab technician, but without them, a majority of his assigned fish would die before their biological characteristics could be fully measured.

As a freshman, Mark McDonough (pictured) has had the opportunity to work in a lab that does cutting-edge research.

Mark’s day-to-day responsibilities are similar to those of many lab technicians. Hundreds of Duke’s affiliated research labs make use of living subjects and biological specimens which must be sheltered, fed, and closely monitored. Without the presence of lab technicians, studies involving these subjects could lead to inconsequential or misleading results.

Mark’s supervisor, Z-Core Facilities Manager Karina Olivieri, fully understands the importance of the three lab technicians in her five zebrafish facilities. Says Olivieri, technicians ensure the “health of the fish and quality of their water so that researchers can collect measurements and make valuable insights.” As the demand for zebrafish grows on Duke’s campus, she expects the number of lab technician roles to grow as well. This trend will likely not be unique to Duke.

The zebrafish’s see-through embryo, rapid life cycle, and well-documented genome make it a “model organism” for biological experiments.

Nationwide, demand for lab technicians has accelerated in many of the largest research corporations and academic institutions. According to the Foundation for Biomedical Research, almost every U.S. drug must pass through animal testing in order to reach FDA approval, meaning that larger amounts of living specimens must be preserved as the pharmaceutical industry grows. The rising presence of these experimental subjects may be why the Bureau of Labor Statistics reports that lab technician roles are increasing at a rate of 11%, which beats the national average for STEM occupations.

Though lab technicians don’t present work at prestigious conferences or see their names printed at the top of cutting-edge research articles, their work is pivotal for ensuring that innovative research can be conducted at Duke and beyond. So in the unlikely event that you recognize a passing stranger as a lab technician, make sure to thank them for their service to the Duke community. They keep the university’s vibrant research scene – and its fish – thriving.

Post by Shariar Vaez-Ghaemi, class of 2025

When the gut’s internal ecosystem goes awry, could an ancient if gross-sounding treatment make it right?

Lemur researchers make a case for fecal transplants to reduce the side effects of antibiotics. Photo by David Haring, Duke Lemur Center.

Dr. Cathy Williams knew something wasn’t right. The veterinarian had felt off for weeks after her 2014 trip to Madagascar.

At first she just felt bloated and uncomfortable and wasn’t interested in eating much. But eventually she developed a fever and chills that sent her to the emergency room.

When tested, doctors found that what she had wasn’t just a stomach bug. She was suffering from an infection of Clostridium difficile, a germ that causes severe diarrhea and abdominal pain and can quickly become life-threatening if not treated promptly.

“It was horrible,” Williams said.

The condition is often triggered when antibiotics disrupt the normal balance of bacteria that inhabit the gut, allowing “bad” bacteria such as C. difficile to multiply unchecked and wreak havoc on the intestines.

To get her infection under control, Williams asked her doctors if they could try an approach she and other veterinarians had used for decades to treat lemurs with digestive problems at the Duke Lemur Center. The procedure, known as a fecal microbiota transplant, involves taking stool from a healthy donor and administering it to the patient to add back “good” microbes and reset the gut.

At the time it was considered too experimental for clinical use in human cases like Williams’. She was prescribed the standard treatment and was sent home from the hospital, though she wouldn’t feel well enough to go back to work for another month. But now new research in lemurs is confirming what Williams and others long suspected: that this ancient if gross-sounding treatment can help an off-kilter gut microbiome get back to normal.

In a recent study in the journal Animal Microbiome, a research team led by Duke professor Christine Drea, former PhD student Sally Bornbusch and colleagues looked at the gut microbiomes of 11 healthy ring-tailed lemurs over a four-month period after receiving a seven-day course of the broad-spectrum antibiotic amoxicillin.

The lemurs were split into two experimental groups. One was a wait-and-see group, with continued follow-up but no further treatment after the antibiotics. The other group was given a slurry of their own feces, collected prior to antibiotic treatment and then mixed with saline and fed back to the same animal after their course of antibiotics was over.

“It sounds crazy,” Williams said. But she has used a similar procedure since the 1990s to treat illnesses in Coquerel’s sifaka lemurs, whose infants are known to eat their mother’s poop during weaning — presumably to get the microbes they’ll need to transition to solid food.

A baby Coquerel’s sifaka tries some of her first solid foods. Photo by David Haring.

Drea, Bornbusch and team used genetic sequencing techniques to track changes in the lemurs’ gut microbiome before, during and after treatment.

As expected, even a single course of antibiotics caused the numbers of microbes in their guts to plunge compared with controls, briefly wiping out species diversity in both experimental groups before returning to baseline.

“Antibiotics had dramatic effects, even in healthy animals,” Drea said.

But in terms of which types of bacteria bounced back and when, the patterns of recovery in the two groups were different. Lemurs that received the “poop soup” treatment started to stabilize and return to their pre-antibiotic microbiome within about two weeks. In contrast, the bacterial composition in the wait-and-see group continued to fluctuate, and still hadn’t quite returned to normal even after four months of observation.

This kind of therapy isn’t new. Reports of using fecal transplants to treat people suffering from food poisoning or diarrhea date back as far as fourth century China. The evidence for its effectiveness in captive settings has Bornbusch advocating for freezing stool at Smithsonian’s National Zoo, where she is now a postdoctoral fellow.

“If we can bank feces from animals when they’re healthy, that can be a huge benefit down the road,” Bornbusch said. “It can help the animals get better, faster.”

And now if any of her lemur patients were to get sick with C. difficile like she did, Williams said, “I would absolutely go with a fecal microbiota transplant.”

“People are put off by it,” Drea said, “But the disgust for this approach might actually have been holding up a fairly cheap and useful cure.”

Ring-tailed lemurs at the Duke Lemur Center in North Carolina. Photo by David Haring, Duke Lemur Center

This research was supported by the National Science Foundation (BCS 1749465), the Duke Lemur Center Director’s Fund, and the Duke Microbiome Center.

CITATION: “Antibiotics and Fecal Transfaunation Differentially Affect Microbiota Recovery, Associations, and Antibiotic Resistance in Lemur Guts,” Sally L. Bornbusch, Rachel L. Harris, Nicholas M. Grebe, Kimberly Roche, Kristin Dimac-Stohl, Christine M. Drea. Animal Microbiome, Oct. 1, 2021. DOI: 10.1186/s42523-021-00126-z.

By Robin Ann Smith

The Life of a Biology Ph.D. Student, Clara Howell

Clara Howell and I meet to chat on a lovely October afternoon under the trees of the Bryan Center Plaza. In my final Fall at Duke as an undergraduate, I am happy to connect with Clara, a third-year PhD student in the biology department. We meet on the auspices that I want to learn more about her trek through academia and her current work in the Nowicki lab for this very profile piece. “I’ve never been written about before,” Clara says to me. I suspect that, though most grad students’ work is totally cool, most of them never have.

Clara Howell, Ph.D. student, conducting field work.

Clara talks with her hands as she lays out her current work for me. Right now, she is studying sexual selection and infection in different bird species. Duke biology professor Steve Nowicki, one of Clara’s advisors, has done a lot of work on honesty in communication systems between animals. Most species, Clara tells me, rely on honest signals for mate choice, because it benefits females to be able to discern between low- and high-quality mates, and it benefits high quality males to be able to advertise their quality. In general, animal signals should be reliable. Clara’s other advisor, biology professor and chair of evolutionary anthropology Susan Alberts, specializes in life history trade-offs of signaling: Animals only have so many resources and they must make choices about how to use them. A male bird, that is, for example, fighting an infection, cannot devote as many resources to sexual signaling as an uninfected male.

“But,” Clara says, with an increasingly bright smile on her face, “There is an interesting period of time right after an animal is exposed to a potential pathogen where it’s not immediately clear if the bird’s sexual signals will be honest. This is because it could be most advantageous for animals – especially males – to continue devoting every resource possible for sexual signaling, even if it means ignoring a pathogen that will eventually kill them.”

The punchline is, the male swamp sparrows and zebra finches that Clara studies might benefit from “lying” about being sick. By ignoring an arising infection and devoting one’s energy to maintaining strong sexual signaling, these male birds may be tricking females into thinking they are perfectly healthy mates with no sickness in sight. So far, Clara has been recording the songs of male birds following an injection of bacterial cell walls to stimulate their immune response. “The real kicker will be when I test females and see how and if they discern between the songs of sick and healthy males.”

“When we started to social distance at the beginning of the pandemic in March 2020, before any of us knew how long this would last, I wondered whether other animals do the same thing,” Clara said. When COVID-19 put a pause to Clara’s original work, she found inspiration in the pandemic itself to think about cues of sickness in other animal species besides our own – an idea she saw other scientists starting to buzz about.

Before grad school, Clara studied neuroscience and English at Tulane University in New Orleans. She worked in an evolutionary biology lab with former Duke Ph.D. Elizabeth Derryberry beginning in sophomore year and did her honor’s thesis in Derryberry’s lab on connections between novel foraging tasks and mate preferences in zebra finches. And Clara loved her advisor so much that she decided to follow Derryberry to the University of Tennessee as a grad student in the same year she earned her bachelor’s degree.

“What about your English major?” I asked Clara. “I was a very nerdy, book-ish child,” she replied, “I wanted to read more in college.” Her background in English has turned out to be quite useful for her work in the sciences. “Having really great scientific ideas and not being able to tell people about them is pretty useless,” she said with a short laugh. These English skills have been useful for grant writing too. That’s right – I asked Clara to tell me about the less glamorous parts of being a grad student.

“The process of finding money is something I wish people talked about more,” Clara said as she wrapped her long ponytail through her hands. The through line: “If you want to do your own ideas, you have to find your own money,” she stated plainly. The process of finding money takes up a considerable amount of her time and most grants she has applied for she does not end up getting. But because she enjoys writing, she says it’s not so bad. Though Clara wishes departments were more open about research funding policies and that there were more internal grants, she’s never thought of grant writing as a waste of time. “A lot of the time when I write grants, I’m really clarifying ideas. It’s definitely helpful,” she tells me.

Grant writing takes up a considerable amount of time for most science Ph.D. students.

Clara’s advice to anyone interested in a science Ph.D. is to truly consider getting a master’s degree beforehand. “It might not be the right choice for everyone,” Clara said, “But I found the transition from undergrad to graduate school really difficult. I spent most of my master’s degree just learning how to be a grad student and figuring out how academia works, which meant that when I started my Ph.D. I could focus much more on what I wanted to research.” The time in her master’s program also helped her home in on her central interests in biology. And oh, she also recommends noise-canceling headphones, her “favorite possession.”

Although she says she is still working on figuring out her work-life balance, Clara likes being able to set her own schedule and how each week is so different from the next. Outside of lab, Clara claims she is the stereotype of ecology and evolutionary biology grad students: She enjoys rock-climbing, board games, and craft breweries. You might have to go to the Biological Sciences building to find Clara. “I haven’t broached the other areas of campus,” she said, “Undergrads are sort of scary. They use language I don’t understand, and they are all so stylish. They make me feel old.” Old at 26, the life of the biology Ph.D.

How To Hold a Bee and Not Get Stung

Pictured from left to right are Lindsey Weyant, Andrew McCallum, and Will Marcus.

On Saturday, September 25, the Wild Ones club hosted an insect-themed outing with Fred Nijhout, an entomology professor at Duke. We visited a pond behind the Biological Sciences Building bordered by vegetation. Apparently, the long grasses and flowers are prime habitat for insects, which are often attracted to sunny areas and edge habitat. Along with several other students, I practiced “sweeping” for insects by swishing long nets through vegetation, a delightfully satisfying activity, especially on such a gorgeous fall day.

A species of skipper feeding on a flower. According to Fred Nijhout, the best way to distinguish butterflies (including skippers) from moths is by looking for knobbed antennae, characteristic of butterflies but not moths.

Professor Nijhout says much of his research focuses on butterflies and moths, but the insect biology class he teaches has a much broader focus. So does this outing. In just a couple hours, our group finds a wide array of species.

A milkweed bug (left) and a soldier beetle, two of the species we saw on Sunday.

Many of the insects we see belong to the order Hemiptera, a group sometimes referred to as “true bugs” that includes more than 80,000 species. We find leafhoppers that jump out of our nets while we’re trying to look at them, a stilt-legged bug that moves much more gracefully on its long legs than I ever could on stilts, spittlebugs that encase themselves in foam as larvae and then metamorphose into jumping adults sometimes called froghoppers, and yet another Hemipteran with a wonderfully whimsical name (just kidding): the plant bug.

Professor Nijhout shows us a milkweed leaf teeming with aphids (also in the order Hemiptera) and ants. He explains that this is a common pairing. Aphids feed on the sap in leaf veins, which is nutrient-poor, so “they have special pumps in their guts that get rid of the water and the sugars” and concentrate the proteins. In the process, aphids secrete a sugary substance called honeydew, which attracts ants.

The honeydew excreted as a waste product by the aphids provides the ants with a valuable food source, but the relationship is mutualistic. The presence of the ants affords protection to the aphids. Symbiosis, however, isn’t the only means of avoiding predation. Some animals mimic toxic look-alikes to avoid being eaten. Our group finds brightly colored hoverflies, which resemble bees but are actually harmless flies, sipping nectar from flowers. Professor Nijhout also points out a brightly colored milkweed bug, which looks toxic because it is.

Sixteen species of hoverfly, all of which are harmless. Note that hoverflies, like all flies, have only one pair of wings, whereas bees have two.
Image from Wikipedia user Alvesgaspar (GNU Free Documentation License, Creative Commons license).

Humans, too, can be fooled by things that look dangerous but aren’t. As it turns out, even some of our most basic ideas about risk avoidance—like not playing with bees or eating strange berries—are sometimes red herrings. When we pass clusters of vibrant purple berries on a beautyberry bush, Professor Nijhout tells us they’re edible. “They’re sweet,” he says encouragingly. (I wish I could agree. They’re irresistibly beautiful, but every time I’ve tasted them, I’ve found them too tart.) And on several occasions, to the endless fascination of the Wild Ones, he catches bees with his bare hands and offers them to nearby students. Male carpenter bees (which can be identified by the patch of yellow on their faces) have no stinger, and according to Professor Nijhout, their mandibles are too weak to penetrate human skin. It’s hard not to flinch at the thought of holding an angry bee, but there’s a certain thrill to it as well. When I cup my hands around one of them, I find the sensation thoroughly pleasant, rather like a fuzzy massage. The hard part is keeping them from escaping; it doesn’t take long for the bee to slip between my hands and fly away.

Professor Nijhout in his element, about to capture a male carpenter bee (below) by hand.

The next day, I noticed several bees feeding on a flowering bush on campus. Eager to test my newfound knowledge, I leaned closer. Even when I saw the telltale yellow faces of the males, I was initially hesitant. But as I kept watching, I felt more wonder than fear. For perhaps the first time, I noticed the way their buzzy, vibrating bodies go momentarily still while they poke their heads into blossoms in search of the sweet nectar inside. Their delicate wings, blurred by motion when they fly, almost shimmer in the sunlight while they feed.

Gently, I reached out and cupped a male bee in my hands, noticing the way his tiny legs skittered across my fingers and the soft caress of his gossamer wings against my skin. When I released him, his small body lifted into the air like a fuzzy UFO.

I realize this new stick-my-face-close-to-buzzing-bees pastime could backfire, so I don’t necessarily recommend it, especially if you have a bee allergy, but if you’re going to get face-to-face with a carpenter bee, you might at least want to check the color of its face.

Damla Ozdemir, a member of the Wild Ones, with a giant cockroach in Professor Nijhout’s classroom.

If you could hold all the world’s insects in one hand and all the humans in the other, the insects would outweigh us. More than 900,000 species of insects have been discovered, and there may be millions more still unknown to science. Given their abundance and diversity, even the experts often encounter surprises.“Every year I see things I’ve never seen before,” Professor Nijhout told us. Next time you step outside, take a closer look at your six-legged company. You might be surprised by what you see.

By Sophie Cox, Class of 2025

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