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

Category: Animals Page 1 of 16

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

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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

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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

Carrying On a Legacy of “Whimsical” Gardening

A contorted hardy orange tree (Poncirus trifoliata) in the Charlotte Brody Discovery Garden. The brightly colored structures in the background are pollinator houses.

On Wednesday, September 15, the Sarah P. Duke Gardens hosted a drop-in event in the Charlotte Brody Discovery Garden, an area near the main entrance with a focus on organic and sustainable gardening. This part of Duke Gardens is almost ten years old, but Wednesday’s event, led by curator Jason Holmes and horticulturist Nick Schwab, showcased what makes it unique.

The entrance to the Charlotte Brody Discovery Garden is marked by a lovely arbor draped with vines. Inside, the winding paths are lined with flowers, fruiting trees, and beds of herbs and vegetables. Bees and butterflies flit here and there, bright against the rainy sky.

Holmes finds me admiring a display of carnivorous plants. He introduces himself and shows me around.

Flirting with danger: a fly perches on a Venus flytrap. The Venus flytrap is a carnivorous plant native only to parts of the Carolinas.

One of the first things I notice is the array of pollinator houses scattered amongst flowers and attached to wooden structures. Many plants rely on pollinators to reproduce, and the pollinator houses can help attract native species like mason bees and leaf-cutter wasps, but Holmes says they have another purpose as well: bringing awareness to the importance of pollinators.

Along with the pollinator houses, which are designed to attract native bees, the Charlotte Brody Discovery Garden has beehives for honey bees. Though honey bees are not originally native to the New World, they are important pollinators, and their populations are declining. Like many native bees, honey bees are threatened in part by habitat loss and pesticide use, but gardeners and landowners can help.

The Charlotte Brody Discovery Garden is only about an acre in size, but exploring it feels like walking through a museum, a new exhibit around every corner. Over here, raised beds of hot peppers, organized by level of spiciness. (“I don’t do spicy,” says Holmes, but even Schwab, who has sampled the garden’s hottest peppers, tells me he often finds the less spicy ones to be more enjoyable.) Over there, clusters of pumpkins. Despite the steamy day, the pumpkins are a reminder that fall is coming. I’ve been noticing subtle hints of fall for weeks—brisk mornings, breezes that send dry leaves skittering across pavement—but despite these tantalizing harbingers of autumn, some days still seem distinctly summery. As it turns out, this garden is experiencing a similar transition.

A recipe for “Peri-Peri Sauce” within a display of hot peppers. Peppers are common in many cuisines, but they are originally native to tropical America.

Holmes and Schwab, along with other dedicated gardeners, are in the process of phasing out summer vegetables like okra, melons, cucumbers, zucchini, and eggplant and planting crops like cabbage, broccoli, and cauliflower in anticipation of cooler weather.

Change is something of a constant in the garden. Holmes likes to tell everyone who works with him that “every day’s going to be different.” When I ask if he has a favorite season in the garden, Holmes mentions two: “I love the cool-down of fall, and I love the rebirth of spring.” As for winter, Holmes describes it as a period of much-needed rest—for both the garden and the gardeners.

Potted succulents and clusters of bright orange pumpkins add to the garden’s whimsical feel.

The Charlotte Brody Discovery Garden is a fully functioning garden, donating most of its produce to the Food Bank of Central and Eastern North Carolina, but it is also a space for discovery. Since its inception in 2012, the garden has sought to foster curiosity about gardening and the natural world.

The garden also houses a chicken coop, which Holmes says is constructed out of recycled materials from local factories. Holmes picks up a white silkie chicken, holding her gently before prompting her to join the others in the enclosure outside. He tells me she’s acting “broody,” exhibiting a tendency to behave as though she is incubating eggs.

Jason Holmes with one of the chickens. Holmes also cares for chickens at his home, but not because he wants to eat their eggs. He considers them “companions” instead.

When I ask Holmes about Charlotte Brody, he describes a woman who lived in Kinston, North Carolina, and invited kids to her home to learn about organic gardening and discover its joys for themselves. Holmes says Brody had a “whimsical, free approach” to gardening.

“Whimsical” describes this garden well. Tiny, orange spheres dangling from bushes. A tree frog peering out from a pollinator house. Hand-written signs nestled amongst peppers, offering recipes for “Peri-Peri Sauce” and “Hot Honey.” Everything from cacti to chickens to oranges coexisting peacefully in the same garden.

Before I leave, I linger under the arbor. The sun streams through the dome above me. The frog is still hiding in the same pollinator house as before. Looking around, I see more than a small garden. I see the legacy of a woman who devoted her time to gardening joyfully and sustainably and teaching others to do the same.

The arbor at the entrance to the Charlotte Brody Discovery Garden. Despite the rain earlier in the afternoon, the sun had come out again by the time I left.

Jason Holmes, Nick Schwab, and the many workers and volunteers who have put their time and effort into this garden are continuing that legacy. Holmes hopes that visitors will find inspiration here, whatever that means to them. I know I did, and next time I come back, I’ll wander the paths and notice the changing seasons, ready to be inspired again.

By Sophia Cox, Class of 2025

New Blogger Nhu Bui: Discovering Science Communication

My name is Nhu Bui, pronounced “New Buoy.” I’m a sophomore from Cypress, Texas hoping to major in Environmental Science & Policy and English (that’s only two, I promise), and I’m thrilled to join the Duke Research Blog team.

Thanh-Nhu Bui, Nhu for short

I’ve loved science ever since I could waddle into my backyard to catch ladybugs and earthworms. For the longest time, I was convinced I was going to be a zookeeper, or maybe a veterinarian – anything that would allow me to work with animals. (I also toyed with the idea of becoming a physician, treating the most ferocious of creatures.) But I also knew that reading and writing were my fortes and that I was always happier in a library than in a laboratory. 

In high school, I joined the speech and debate team. My primary (and favorite) event was informative speaking: 10 minutes of educational entertainment on a topic of choice. I always chose to speak on environmental issues – from bees to coral reefs – and I loved it. The event was my perfect storm of science and communications… so imagine my excitement upon entering college and discovering that science communication is a whole thing.

Some highlights of my informative visual aids

With the blog, I hope to be able to discover new interests and explore my intrigues across the wide world of research at Duke University. But most importantly, I hope to be able to hone my craft. Effective science communication is more crucial than ever; issues like climate change and vaccination impact every aspect of life, but the public’s view of science is mired in perceptions of bias and manipulation. While science and politics are inextricable, trust and awareness are critical for a functioning society.

Of course, constantly questioning the world is also critical – it’s the foundation of scientific discovery – but as with everything, it’s all about balance. Who knows where that balance is? I’m still looking for it myself, but I’m hoping that joining the Duke Research Blog will help me on the way. 

Keeping a respectful distance while admiring monkeys.

Outside of my love for science and writing, here are the most important things to know about me: my favorite movies are Paddington 1 and 2 (can’t choose), my top genre on Spotify is show tunes (I’ve never done theater), and I once walked through a Whataburger drive-thru (it’s a Texas thing). 

Thanks for getting to know me, and I hope to see you back on the blog soon!

Post by Nhu Bui, Class of 2024

New Blogger Sophie Cox: Keep Asking Questions

Typing with one hand, especially my left hand, is not easy, but my right hand is currently occupied by freeze-dried mealworms and, momentarily, by a chittering wild bird.

My eagle-eyed supervisor is a Carolina wren, South Carolina’s official state bird.

“You have babies, don’t you?” I mutter as a small, brown bird with a white eyestripe wraps her long toes around my fingers.

She doesn’t answer–she never does–but she flutters repeatedly to my socked feet and from there to my hand, where she selects a mealworm and then flies to a flower box on my neighbor’s mailbox.

This bird and her mate are the pair of Carolina wrens who have spent the past year training me to hand-feed them. Life hack: if you’re being cornered by wild birds every time you step outside, I suggest keeping a bag of dried mealworms in your pocket.

I want to investigate the flower box, but I don’t want to betray the trust I’ve worked so hard to build. Instead, I wait until my little friend finishes her ritual before approaching the mailbox.

Among the fake hydrangea blossoms, I see a scruffy head poking out. Judging by its size, the youngster looks about ready to leave the nest. With a smile, I turn and walk away.

Along with observing wildlife, I enjoy reading, writing, playing board games, and spending time outside.

My name is Sophie, and I’m a freshman at Duke. At home in upstate South Carolina, I can often be found smearing fruity, fermenting moth bait onto tree trunks at dusk or curled up in a hammock swing with a good book while the Carolina wrens do their best to distract me.

They each have their own personalities (which is partly how I tell them apart), but both birds strike me as curious and even intelligent.

Lately, I’ve been wondering if Carolina wrens belong on the growing list of animals believed to possess theory of mind, the ability to understand mental states and to recognize that others’ thoughts and beliefs can differ from one’s own.

I have always associated the natural world with a sense of wonder that borders on enchantment.

Perhaps unsurprisingly, I plan to major in biology. My lifelong aspiration to study science hasn’t faded, but science should be accessible to everyone, scientists or not. That is partly why I want to work for Duke’s research blog.

If the coronavirus pandemic has taught us anything, it’s the importance of having access to accurate information we can trust. Too often, data is manipulated and obscured, twisting facts and turning science into a political minefield. That should never be acceptable. My favorite news
sources are those that effectively bridge the gap between academia and the general public, providing information that is digestible and engaging without sacrificing scientific integrity.

Judging by the articles I have read, Duke’s research blog has a similar mission, and it’s a mission I firmly believe in.

Science is full of unanswered questions. At its simplest, my goal for the future is the same as it was ten years ago: to answer some of those questions.

This summer, I worked as a counselor and nature instructor at a residential summer camp. Campers often approached me throughout the day to enthusiastically describe their encounters with click beetles, squirrels, and frogs. I saw in their eyes the same exhilaration I feel when the Carolina wrens’ amber eyes meet mine or when a shimmery, pale golden moth flutters across my pajamas and then disappears soundlessly into the night, as beautiful and ephemeral as a
moonbeam.

One young boy, a seven-year-old who reminded me of myself at his age, was fascinated by my field guide to insects and spiders of North America. Again and again, he’d point to an insect or spider or worm, then hand the field guide to me and wait for me to find the right page. At one point, he even retrieved the book from my backpack. I don’t know if he could read, but he knew what the book was for, and he cared. He could neither hear nor speak, but maybe, in the end, it didn’t matter. You don’t need words to flip over stones and marvel at the life hidden beneath.

People want scientific knowledge. Studying science — and not just as scientists — brings us so tantalizingly close to the mysterious, the undiscovered, the unknown. Science is more than petri dishes, graphs, and Latin jargon. It is a world full of questions waiting to be asked. In my own scientific writing, mostly in the form of nature journals, I strive to be methodical but not impersonal. My goal as a blogger is similar: to be accurate and objective without sacrificing the mystery and excitement that makes science so engaging to begin with.

After college, I hope to pursue ecological field research. In the meantime, I’ll keep exploring. I’ll keep flipping over stones. I’ll keep talking to the wrens, even if they never talk back, and wondering what they’re thinking when their gaze meets mine. In short, I’ll keep asking questions. I think you should, too.

Post by Sophie Cox, Class of 2025

Two Ways to Weird: How Whale Noses Moved to the Top of Their Head

A blue whale skeleton suspended in London’s Natural History Museum

Odd skulls are nothing new to V. Louise Roth, a professor in the Department of Biology. Much of her research centers on how animals’ shapes and sizes evolve and develop, so weirdly shaped bones are at the core of her work. But when Ph.D. student Rachel Roston drew her attention to the peculiarities of whale skulls, even Roth was astounded.

“There are some pretty weird mammal skulls out there,” Roth said. “I have studied morphological development in elephants, which are also kind of a crazy choice, but in terms of which bone goes where I think cetaceans are the weirdest ones.”

Cetaceans are the group that includes baleen whales – such as humpback whales – and toothed whales – such as dolphins and killer whales. Unlike almost all other vertebrate animals, cetaceans don’t breathe out of their mouths or from a nose placed in front of their face, but from a blowhole located on top of their head.

How did it get up there?

Rachel Roston, a graduate student in the Duke Biology department, recently published a paper with Professor Louise Roth, about some of the ways dolphin, whale and porpoise skulls break the rules of anatomy.

A new study published in the Journal of Anatomy by Roth and Roston, now a postdoctoral researcher at the University of Washington, reveals how whale and dolphin skulls undergo a complete transformation through their embryonic and fetal development, resulting in a re-orientation of their nasal passages.

What’s more, there’s not just one way to do it: baleen whales and toothed whales move their nostrils to the tops of their heads in two very different ways.

“It’s not just that they are developing the same thing in different ways,” said Roston, who led this work as part of her Ph.D. in Biology at Duke. “Looking from the outside of the body all you see is that both of them have their nose on the top of their head, but when you look inside their skulls, they are actually totally different blowholes.”

A toothed whale clears its blowhole. Photo by Friedrich Frühling

To figure out which bone went where and in which way, Roston looked at CT scans of baleen and toothed whales’ embryos in different stages of development and drew a dotted timeline of anatomical changes through the animals’ development.

Early-stage embryos look very much alike in most vertebrate animals: small, with a disproportionally large head, big eyes and oral and nasal cavities in the front of their face. As the embryos develop, they take different paths and become more and more similar to their own species.

Most of them keep their noses and their mouths in front of their face, but dolphins and whales transform their whole heads to change the direction of their nasal passage while keeping the snout facing forward.

“We think of the nostrils as something you find at the tip of the snout,” Roth said. “But whales go through some key changes in bone orientation that decouple one from the other.”

“It’s like looking at a cubist Picasso painting,” Roston said. “The eyes, nose and mouth are all there, but their relationships to each other are completely distorted.”

Whale embryos at different developmental stages. The white arrow shows how the nasal cavity shifts position through embryonic development.

This internal shuffling requires that the parts forming the roof of the embryo’s mouth move away from those that form its nasal passage. Initially parallel in small young embryos, they end up at an angle of about 45 degrees in baleen whales. In toothed whales this final angle is even wider, closer to 90 degrees.

In baleen whales, a key rotation happens at the back of the skull, where it meets the spine. Rather than being perpendicular to the ground, as in the head of a dog, the back of the skull is tilted forward towards the snout.

In toothed whales, the point of inflexion for this rotation is in the middle of the head. A bone in the center of the skull changes shape, curving upwards as the nasal passage ends facing up.

Roston and Roth both say that museum collections and non-destructive scanning techniques, such as CT scans, were key for this project because whale embryo specimens are difficult to come by. When a gravid female dies, small embryos often go unnoticed in their mother’s massive carcass. But older fetuses are larger than your typical sedan, making them difficult to preserve intact and store in museums. The few specimens found in museums must therefore be studied with the proverbial velvet gloves, or, in this case, CT scans.

“In science you always question ‘how come no one’s done this before?’” Roston said. “Here, it was because specimens are precious, so you don’t want to cut them up and destroy them.”

“Sometimes we’re looking at museum specimens that are 100 years old. This was an opportunity to describe them in a way that I hope will still be useful 100 years from now.”

Read more about weird whale skulls.

The research was funded by Duke University. Roston has also been supported by the National Institutes of Health.

CITATION: “Different Transformations Underlie Blowhole and Nasal Passage Development in a Toothed Whale (Odontoceti: Stenella attenuata) and a Baleen Whale (Mysticeti: Balaenoptera physalus),” Rachel A. RostonV. Louise Roth, Journal of Anatomy. DOI: 10.1111/joa.13492

Post by Marie Claire Chelini PhD, Duke Biology

In Drawers of Old Bones, New Clues to the Genomes of Lost Giants

DNA extracted from a 1,475-year-old jawbone reveals genetic blueprint for one of the largest lemurs ever.

By teasing trace amounts of DNA from this partially fossilized jawbone, nearly 1,500 years after the creature’s death, scientists have managed to reconstruct the first giant lemur genome. Credit: University of Antananarivo and George Perry, Penn State

If you’ve been to the Duke Lemur Center, perhaps you’ve seen these cute mouse- to cat-sized primates leaping through the trees. Now imagine a lemur as big as a gorilla, lumbering its way through the forest as it munches on leaves.

It may sound like a scene from a science fiction thriller, but from skeletal remains we know that at least 17 supersized lemurs once roamed the African island of Madagascar. All of them were two to 20 times heftier than the average lemur living today, some weighing up to 350 pounds.

Then, sometime after humans arrived on the island, these creatures started disappearing.

The reasons for their extinction remain a mystery, but by 500 years ago all of them had vanished.

Coaxing molecular clues to their lives from the bones and teeth they left behind has proved a struggle, because after all this time their DNA is so degraded.

But now, thanks to advances in our ability to read ancient DNA, a giant lemur that may have fallen into a cave or sinkhole near the island’s southern coast nearly 1,500 years ago has had much of its DNA pieced together again. Researchers believe it was a slow-moving 200-pound vegetarian with a pig-like snout, long arms, and powerful grasping feet for hanging upside down from branches.

A single jawbone, stored at Madagascar’s University of Antananarivo, was all the researchers had. But that contained enough traces of DNA for a team led by George Perry and Stephanie Marciniak at Penn State to reconstruct the nuclear genome for one of the largest giant lemurs, Megaladapis edwardsi, a koala lemur from Madagascar.

Ancient DNA can tell stories about species that have long since vanished, such as how they lived and what they were related to. But sequencing DNA from partially fossilized remains is no small feat, because DNA breaks down over time. And because the DNA is no longer intact, researchers have to take these fragments and figure out their correct order, like the pieces of a mystery jigsaw puzzle with no image on the box.

Bones like these are all that’s left of Madagascar’s giant lemurs, the largest of which weighed in at 350 pounds — 20 times heftier than lemurs living today. Credit: Matt Borths, Curator of the Division of Fossil Primates at the Duke Lemur Center

Hard-won history lessons

The first genetic study of M. edwardsi, published in 2005 by Duke’s Anne Yoder, was based on DNA stored not in the nucleus — which houses most of our genes — but in another cellular compartment called the mitochondria that has its own genetic material. Mitochondria are plentiful in animal cells, which makes it easier to find their DNA.

At the time, ancient DNA researchers considered themselves lucky to get just a few hundred letters of an extinct animal’s genetic code. In the latest study they managed to tease out and reconstruct some one million of them.

“I never even dreamed that the day would come that we could produce whole genomes,” said Yoder, who has been studying ancient DNA in extinct lemurs for over 20 years and is a co-author of the current paper.

For the latest study, the researchers tried to extract DNA from hundreds of giant lemur specimens, but only one yielded enough useful material to reconstitute the whole genome.

Once the creature’s genome was sequenced, the team was able to compare it to the genomes of 47 other living vertebrate species, including five modern lemurs, to identify its closest living relatives. Its genetic similarities with other herbivores suggest it was well adapted for grazing on leaves.

Despite their nickname, koala lemurs weren’t even remotely related to koalas. Their DNA confirms that they belonged to the same evolutionary lineage as lemurs living today.

To Yoder it’s another piece of evidence that the ancestors of today’s lemurs colonized Madagascar in a single wave.

Since the first ancient DNA studies were published, in the 1980s, scientists have unveiled complete nuclear genomes for other long-lost species, including the woolly mammoth, the passenger pigeon, and even extinct human relatives such as Neanderthals.

Most of these species lived in cooler, drier climates where ancient DNA is better preserved. But this study extends the possibilities of ancient DNA research for our distant primate relatives that lived in the tropics, where exposure to heat, sunlight and humidity can cause DNA to break down faster.

“Tropical conditions are death to DNA,” Yoder said. “It’s so exciting to get a deeper glimpse into what these animals were doing and have that validated and verified.”

See them for yourself

Assembled in drawers and cabinets cases in the Duke Lemur Center’s Division of Fossil Primates on Broad St. are the remains of at least eight species of giant lemurs that you can no longer find in the wild. If you live in Durham, you may drive by them every day and have no idea. It’s the world’s largest collection.

In one case are partially fossilized bits of jaws, skulls and leg bones from Madagascar’s extinct koala lemurs. Nearby are the remains of the monkey-like Archaeolemur edwardsi, which was once widespread across the island. There’s even a complete skeleton of a sloth lemur that would have weighed in at nearly 80 pounds, Palaeopropithecus kelyus, hanging upside down from a branch.

Most of these specimens were collected over 25 years between 1983 and 2008, when Duke Lemur Center teams went to Madagascar to collect fossils from caves and ancient swamps across the island.

“What is really exciting about getting better and better genetic data from the subfossils, is we may discover more genetically distinct species than only the fossil record can reveal,” said Duke paleontologist Matt Borths, who curates the collection. “That in turn may help us better understand how many species were lost in the recent past.”

They plan to return in 2022. “Hopefully there is more Megaladapis to discover,” Borths said.

A fossil site in Madagascar. Courtesy of Matt Borths, Duke Lemur Center Division of Fossil Primates

CITATION: “Evolutionary and Phylogenetic Insights From a Nuclear Genome Sequence of the Extinct, Giant, ‘Subfossil’ Koala Lemur Megaladapis Edwardsi,” Stephanie Marciniak, Mehreen R. Mughal, Laurie R. Godfrey, Richard J. Bankoff, Heritiana Randrianatoandro, Brooke E. Crowley, Christina M. Bergey, Kathleen M. Muldoon, Jeannot Randrianasy, Brigitte M. Raharivololona, Stephan C. Schuster, Ripan S. Malhi, Anne D. Yoder, Edward E. Louis Jr, Logan Kistler, and George H. Perry. PNAS, June 29, 2021. DOI: 10.1073/pnas.2022117118.

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