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

Category: Biology Page 1 of 29

Why Do Some Dogs Need High Chairs, and How Can Genetics Help?

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Jake, a German shepherd dog in a Bailey chair. Dogs with megaesophagus must eat in a vertical position to help food travel to their stomachs.
Photo credit: Beth Grant

Some dogs have to eat in a high chair—or, more specifically, a Bailey Chair. The chair keeps them in a vertical position while they eat so that gravity can do the work their bodies can’t: moving food from the mouth to the stomach.

These dogs have megaesophagus, an esophagus disorder that can prevent dogs from properly digesting food and absorbing nutrients. When you swallow a bite of food, it travels down a muscular tube, the esophagus, to the stomach. In humans, the esophagus is vertical, so our esophageal muscles don’t have to fight against gravity. But because dogs are quadrupeds, a dog’s esophagus is more horizontal, so “there is a greater burden on peristaltic contractions to transport the food into the stomach.” In dogs with megaesophagus, the esophagus is dilated, and those contractions are less effective. Instead of moving properly into the stomach, food can remain in the esophagus, exacerbating the problem and preventing proper digestion and nutrient absorption. 

Leigh Anne Clark, Ph.D., an associate professor at Clemson University, recently spoke at Duke about megaesophagus in dogs and its genetic underpinnings. She has authored dozens of publications on dog genetics, including five cover features. Her research primarily involves “[mapping] alleles and genes that underlie disease in dogs.” In complex diseases like megaesophagus, that’s easier said than done. “This disease has a spectrum,” Clark says, and “Spoiler: that makes it more complicated to map.”

Clinical signs of megaesophagus, or mega for short, include regurgitation, coughing, loss of appetite, and weight loss. (We might use the word “symptom” to talk about human conditions, but “a symptom is something someone describes—e.g., I feel nauseous. But dogs can’t talk, so we can only see ‘clinical signs.’”) Complications of mega can include aspiration pneumonia and, in severe cases, gastroesophageal intussusception, an emergency situation in which dogs “suck their stomach up into their esophagus.”

Leigh Anne Clarke of Clemson University

Sometimes megaesophagus resolves on its own with age, but when it doesn’t it requires lifelong management. Mega has no cure, but management can involve vertical feeding, smaller and more frequent meals, soft foods, and sometimes medication. Even liquid water can cause problems, so some dogs with mega receive “cubed water,” made by adding a “gelatinous material” to water, instead of a normal water bowl.

In dogs, mega can be either congenital, meaning present at birth, or acquired. In cases of acquired megaesophagus, the condition is “usually secondary to something else,” and the root cause is often never determined. (Humans can get mega, too, but as with acquired mega in dogs, mega in humans is usually caused by a preexisting condition. The best human comparison, according to Clark, might be achalasia, a rare disorder that causes difficulty swallowing.) Clark’s current research focuses on the congenital form of the disease in dogs.

Her laboratory recently published a paper investigating the genetic foundation of mega. Unlike some diseases, mega isn’t caused by just one genetic mutation, so determining what genes might be at play required some genetic detective work. “You see mega across breeds,” Clark says, which suggests an environmental component, but the disease is more prevalent in some breeds than others. For instance, 28 percent of all diagnoses are in German shepherds. That was a “red flag” indicating that genes were at least partly responsible.

Clark and her collaborators chose to limit their research study to German shepherds. Despite including a wide range of dogs in the study, they noticed that males were significantly overrepresented. Clark thinks that estrogen, a hormone more abundant in females, may have a protective effect against mega.

Clark and her team performed a genome-wide association study (GWAS) to look for alleles that are more common in dogs with mega. One allele that turned out to be a major risk factor was a variant of the MCHR2 gene, which plays a role in feeding behaviors. In breeds where mega is overrepresented, like German shepherds, “we have a situation where the predominant allele in the population is also the risk allele,” says Clark.

Using the results of the study, they developed a test that can identify which version of the gene a given dog has. The test, available at veterinary testing companies, is designed “to help breeders reduce the frequency of the risk allele and to plan matings that are less likely to produce affected puppies.”

Post by Sophie Cox, Class of 2025

Duke’s Most-Cited — The Scholars Other Scientists Look To

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It’s not enough to just publish a great scientific paper.

Somebody else has to think it’s great too and include the work in the references at the end of their paper, the citations. The more citations a paper gets, presumably the more important and influential it is. That’s how science works — you know, the whole standing-on-the-shoulders-of-giants thing.

So it always comes as a chest swelling affirmation for Dukies when we read all those Duke names on the annual list of Most Cited Scientists, compiled by the folks at Clarivate.

This year is another great haul for our thought-leaders. Duke has 30 scientists among the nearly 7,000 authors on the global list, meaning their work is among the top 1 percent of citations by scientific field and year, according to Clarivate’s Web of Science citation index.

As befits Duke’s culture of mixing and matching the sciences in bold new ways, most of the highly cited are from “cross-field” work.

Duke’s Most Cited Are:

Biology and Biochemistry

Charles A. Gersbach       

Robert J. Lefkowitz         

Clinical Medicine

Christopher Bull Granger             

Pamela S. Douglas           

Adrian F. Hernandez      

Manesh R. Patel               

Eric D. Peterson

Cross-Field

Chris Beyrer

Stefano Curtarolo

Renate Houts 

Tony Jun Huang  

Ru-Rong Ji

Jie Liu

Jason Locasale  

Edward A. Miao

David B. Mitzi    

Christopher B. Newgard

John F. Rawls   

Drew T. Shindell

Pratiksha I. Thakore       

Mark R. Wiesner              

Microbiology

Barton F. Haynes             

Neuroscience and Behavior

Quinn T. Ostrom              

Pharmacology and Toxicology

Evan D. Kharasch

Plant and Animal Science

Xinnian Dong    

Sheng Yang He                 

Psychiatry and Psychology

Avshalom Caspi

William E. Copeland

E. Jane  Costello               

Terrie E. Moffitt

Social Sciences

Michael J. Pencina          

John W. Williams              

Congratulations, one and all! You’ve done us proud again.

“Of Sound Mind”: a Discussion of the Hearing Brain

“To me [this image] captures the wonder, the awe, the beauty of sound and the brain that tries to make sense of it,” said professor Nina Kraus, Northwestern University researcher and author of “Of Sound Mind: How Our Brain Constructs a Meaningful Sonic World.”

Stop. What do you hear?

We might not always think about the sounds around us, but our brains are always listening, said Northwestern University professor Nina Kraus.

Kraus, auditory researcher and author of “Of Sound Mind: How Our Brain Constructs a Meaningful Sonic World,” spoke via Zoom to a Duke audience in October. She has published more than four hundred papers on the auditory system in humans and other animals and how it’s affected by conditions like autism, aging, and concussion. She discussed some of her findings and how “the sound mind” affects us in our day-to-day lives.

One of the slides from Kraus’s presentation. We can think of sound as having many “ingredients.”

“I think of the sound mind as encompassing how we think, how we move, how we sense, and how we feel,” Kraus said. We live in a “visually dominated world,” but for hearing people, sound plays an important role in language, music, rhythm, and how we perceive the world.

One of the slides from Kraus’s presentation. The human auditory system involves not just the ears but also several regions of the brain. The “hearing brain” engages movement, cognition, and emotions along with interpreting direct sensory input from all senses.

Kraus discussed the auditory system and how much of what we think of as hearing takes place in the brain. We can think of sound as signals outside the head and electricity as signals inside the head (neural processing). When those two merge, learning occurs, and we can make sound-to-meaning connections.

Another slide from Kraus’s presentation. In an experiment, teaching rabbits to associate a sound with meaning (in this case, more carrots) changed patterns of neuron firing in the auditory cortex, even in individual neurons. “Same sound, same neuron, and yet the neuron responded differently… because now there’s a sound-to-meaning connection,” Kraus said.

Despite how sensitive our neurons and brains are to sound, things can get lost in translation. Kraus studies how conditions like concussions and hearing loss can adversely affect auditory processing. Even among healthy brains, we all hear and interpret sounds differently. People have unique “sonic fingerprints” that are relatively stable over time within an individual brain but differ between people. These patterns of sound recognition are apparent when scientists record brain responses to music or other sounds.

“One of the biological measures that we have been using in human and in animal models,” Kraus said, is FFR (frequency following response) to speech. FFR-to-speech can be used to analyze an individual’s auditory processing system. It also allows scientists to convert brain responses back into sound waves. “The sound wave and the brainwave resemble each other, which is just remarkable.”

One of Kraus’s slides. Technology called frequency following response (FFR) can be used to convert brain waves back into original sound (like a song).

This technology helps reveal just how attuned our brains are to sound. When we hear a song, our brain waves respond to everything from the beat to the melody. Those brain waves are so specific to that particular song or sound that when scientists convert the brain waves back into sound, the resulting music is still recognizable.

When scientists try this on people who have experienced a concussion, for instance, the recreated music can sound different or garbled. Experiments that compare healthy and unhealthy brains can help reveal what concussions do to the brain and our ability to interpret sound. But not everything that affects auditory processing is bad.

Musical training is famously good for the brain, and experiments done by Kraus and other scientists support that conclusion. “The musician signature—something that develops over time—” has specific patterns, and it can enhance certain components of auditory processing over time. Making music might also improve language skills. “The music and language signatures really overlap,” Kraus said, “which is why making music is so good for strengthening our sound mind.” Kids who can synchronize to a beat, for example, tend to have better language skills according to some of the experiments Kraus has been involved with.

Musicians are also, on average, better at processing sound in noisy environments. Musicians respond well in quiet and noisy environments. Non-musicians, on the other hand, respond well in quiet environments, but that response “really breaks down” in noisy ones.

Interestingly, “Making music has a lifelong impact. Making music in early life can strengthen the sound mind when one is seventy or eighty years old.”

A slide from Kraus’s presentation. Musicians tend to be better at processing sounds in noisy environments.

Exercise, too, can improve auditory processing. “Elite division 1 athletes have especially quiet brains” with less neural noise. That’s a good thing; it lets incoming information “stand out more.”

In experiments, healthy athletes also have a more consistent response over time across multiple trials, especially women.

These benefits aren’t limited to elite athletes, though. According to Kraus, “Being fit and flexible is one of the best things you can do for your brain,” Kraus said.

Kraus and her team have a regularly updated website about their work. For those who want to learn more about their research, they have a short video about their research approach and an online lecture Kraus gave with the Kennedy Center.

Nina Kraus with a piano. “Science is a deeply human endeavor,” she said, “and I think we often forget that. It’s made by people.”
Photo courtesy of Kraus and colleague Jenna Cunningham, Ph.D.
Post by Sophie Cox, Class of 2025

The Need for Title IX in STEM

The Panel:

In recognition of the 50th anniversary of Title IX, which was intended to make sex discrimination in education illegal, a panel of Duke women met on Thursday, September 29 to talk about whether Title IX could change STEM, (Science Technology, Engineering and Math). Unfortunately, the answer was not simple.

But just through the sharing of the statistics relevant to this problem, the stories, and their solutions, one could start to understand the depth of this problem. One takeaway was that all women in STEM, whether they be student, professor, or director, have faced gender discrimination.

The student panelists after a successful forum

Down to the Statistics:

Dr. Sherryl Broverman, a Duke professor of the practice in biology and global health, gave the audience an overview. Of all of Duke’s regular ranked, tenured-track faculty, only 30% are women. In contrast, women make up 60% of the non-tenure track faculty. Dr. Broverman said men are promoted in Duke at a higher frequency. This is especially seen with the associate professor title because, on average, men are associate professors for 4 to 5 years; whereas women are associate professors for up to 9 years.

To give an example, senior Nasya Bernard-Lucien, a student panelist who studied Biomedical Engineering and then Neuroscience informed me that she has had a total of two women professors in her entire STEM career. This is a common pattern here at Duke because taking a STEM class that has a woman professor is as rare as finding a non-stressed Duke student.

Dr. Kisha Daniels (left) and Dr. Whitney McCoy (right)

The Beginning of a Girl’s Career in STEM

This disproportionate demographic of women professors in STEM is not a new occurrence with Duke or the rest of the world because the disproportion of women in STEM can be seen as early as middle school. Two of the student panelists noted that during their middle school career, they were not chosen to join an honors STEM program and had to push their school’s administration when they asked to take more advanced STEM classes.

Dr. Kisha Daniels, an associate professor of the practice in education said on a faculty panel that one of her daughters was asked by her male peers, “what are you doing here?” when she attended her middle school’s honors math class. Gender discrimination in STEM begins in early childhood, and it extends its reach as long as women continue to be in a STEM field, and that is particularly evident here at Duke.

Women in STEM at Duke

Dr. Sherryl Broverman

The last panel of the Title IX @ 50 event was the student panel which consisted of undergraduate and graduate students. Even though they were all from different backgrounds, all acknowledged the gender disparity within STEM classes.

Student Bentley Choi said she was introduced to this experience of gender discrimination when she first arrived at Duke from South Korea. She noted how she was uncomfortable and how it was hard to ask for help while being one of the few women in her physics class. One would have hoped that Duke would provide a more welcoming environment to her, but that is not the case, and it is also not an isolated incident. Across the panel, all of the women have experienced discomfort in their STEM classes due to being one of the few girls in there.

The Future of Title IX

How can Title IX change these issues? Right now, Title IX and STEM are not as connected as they need to be; in fact, Title IX, in the past, has been used to attack programs created to remedy the gender disparity in STEM. So, before Title IX can change STEM, it needs to change itself.

Title IX needs to address that this problem is a systemic issue and not a standalone occurrence. However, for this change to happen, Dr. Whitney McCoy, a research scientist in Child and Family Policy, said it perfectly, “we need people of all backgrounds to voice the same opinion to create policy change.”

So, talk to your peers about this issue because the more people who understand this situation, the chances of creating a change increases. The last thing that needs to occur is that 50 years in the future, there will be similar panels like this one that talk about this very issue, and there are no panels that talk about how we, in the present, fixed it.

Post by Jakaiyah Franklin, Class of 2025

Do Snakes Have Tails? and Other Slithery Questions

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 redbelly snake (Storeria occipitomaculata), 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. 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 Alex: Pipetting Writer from Coastal SC

When I write about myself, it always reads like a poorly crafted match.com zinger. Boring, awkward, and something along the lines of:

I’m Alex. Aquarius. Love dogs, classic rock, old NCIS episodes. $1 Goodwill paperback thrillers, marked with “Happiest 53rd Richard! All my love, Janet” and “8/17/2005, Saw this and thought of you!” And I like to ask myself why Steven King’s Carrie conjures up thoughts of said person? Who’s Richard? How’s Janet?

I also love coffee. And tea. Peppermint, of course. Irish breakfast, sure. Chamomile, why not. But I think I really just like collecting mugs — hearty ceramics, dainty porcelain, hand-painted, non-dishwashable, chipped, stained monstrosities. It might be a problem though (as I don’t have much shelf space).

Favorite genre of film? It’s got to be anything in the Meg Ryan romcom cinematic universe. Or the Brat Pack coming-of-age cannon. Breakfast Club, St. Elmo’s Fire, About Last Night, Pretty in Pink. Really just the Judd Nelson je ne sais quoi.

My dog and I celebrating her 11th birthday this summer!

I think my 2nd grade superlative was “Wormiest Bookworm,” whatever that means. That might’ve been the year I read every Nancy Drew book in the library and founded the neighborhood’s first and only detective business. I do wish I could say I’ve Jules Verne’d the world in 80 days — circumnavigating all five nebulous oceans, frozen Arctic plains, Swiss peaks, and continental slopes; Phileas Fogging my way through the Mediterranean, aperitivo in hand. But I’m a bit unworldly in the geographic sense. I’ve only been out of the country once to boat up next to Niagara Falls, wearing a thin, plastic poncho and an I <3 Canada tee (though I’ve possibly made it a second time to Canada after getting lost on the circumference of a lake in Vermont).

I’ve only ever lived in Charleston, SC, never straying too far from its labyrinth of intercostals and waterways, its Theseus-like shrimpers, gliding into port. At Duke, I spend half my time majoring in molecular/cellular biology and the other lamenting my landlockedness, missing Charleston’s temperate sea breeze.

Beach in the middle of winter

Growing up there was all briny inlet and Waffle House, midnight bacon, butter pats, cordgrass, molting blue crab, churches on every street corner and in every denomination, weak coffee and greasy hash brown breakfast, September hurricanes, salt, cicadas, farm stands packed with peaches, a once-in-a-hundred year 6-inch snowfall that closed school for two weeks.

On Saturdays, I sharktooth-hunted with my sisters in pluff mud plots now developed (strangers tend to find the smell of the marsh pungent, but I think it’s character building). Fished for red drum. Searched for pearls in half-mooned oyster mouths. Kayaked down creeks.

Charleston’s a literary city, or so I’ve always heard. I think Edgar Allen Poe’s ghost haunts a cobble-stoned alley downtown or something like that. And if not an alley then a quaint B&B, its porch bearing creaky rocking chairs and purple coneflower. I went to an arts-specialized middle and high school for creative writing, wrote some bad poetry in my formative years and a couple of questionable short films, then went to college and somehow fell into the field of cell bio and now I spend a decent chunk of my free time researching genetic heart disease in a campus lab. Feeding cardiomyocytes via gentle pipette like they’re sea monkeys.

I like to picture the act of writing and that of science as similar — fraternal twins or first cousins — and I don’t think it a coincidence that early philosophers were our first physicians, mathematicians, physicists, chemists, etc. Both fields challenge us to pose questions about our world, about its inhabitants, its oddities, its nuances. We just go about answering them differently.

For this reason, I’m incredibly excited to join Duke’s Research Blog, to write about science and innovation, to poeticize protein structures or to search for lyricism in neuronal action potentials the way a deep sea troller searches for the elusive giant squid. I just think there’s something so wonderful about learning new things, cradling little curiosities that often lead nowhere, and doing so through an accessible, enjoyable medium.

Post by Alex Clifford, Class of 2024

What Are Lichens, and Why Does Duke Have 160,000 of Them?

Saxicolous lichens (lichens that grow on stones) from the Namib Desert, and finger lichen, Dactylina arctica (bottom left insert), common in the Arctic, on display in Dr. Jolanta Miadlikowska’s office. The orange color on some of the lichen comes from metabolites, or secondary chemicals produced by different lichen species. The finger lichen is hollow.

Lichens are everywhere—grayish-green patches on tree bark on the Duke campus, rough orange crusts on desert rocks, even in the Antarctic tundra. They are “pioneer species,” often the first living things to return to barren, desolate places after an extreme disturbance like a lava flow. They can withstand extreme conditions and survive where nearly nothing else can. But what exactly are lichens, and why does Duke have 160,000 of them in little envelopes? I reached out to Dr. Jolanta Miadlikowska and Dr. Scott LaGreca, two lichen researchers at Duke, to learn more.

Dr. Jolanta Miadlikowska looking at lichen specimens under a dissecting microscope. The pale, stringy lichen on the brown bag is whiteworm lichen (Thamnolia vermicularis), used to make “snow tea” in parts of China.

According to Miadlikowska, a senior researcher, lab manager, and lichenologist in the Lutzoni Lab (and one of the Instructors B for the Bio201 Gateway course) at Duke, lichens are “obligate symbiotic associations,” meaning they are composed of two or more organisms that need each other. All lichens represent a symbiotic relationship between a fungus (the “mycobiont”) and either an alga or a cyanobacterium or both (the “photobiont”). They aren’t just cohabiting; they rely on each other for survival. The mycobiont builds the thallus, which gives lichen its structure. The photobiont, on the other hand, isn’t visible—but it is important: it provides “food” for the lichen and can sometimes affect the lichen’s color. The name of a lichen species refers to its fungal partner, whereas the photobiont has its own name.

Lichen viewed through a dissecting microscope. The black speckles visible on some of the orange lichen lobes are a “lichenicolous” fungus that can grow on top of lichen. There are also “endolichenic fungi… very complex fungal communities that live inside lichen,” Miadlikowska says. “We don’t see them, but they are there. And they are very interesting.”

Unlike plants, fungi can’t perform photosynthesis, so they have to find other ways to feed themselves. Many fungi, like mushrooms and bread mold, are saprotrophs, meaning they get nutrients from organic matter in their environment. (The word “saprotroph” comes from Greek and literally means “rotten nourishment.”) But the fungi in lichens, Miadlikowska says, “found another way of getting the sugar—because it’s all about the sugar—by associating with an organism that can do photosynthesis.” More often than not, that organism is a type of green algae, but it can also be a photosynthetic bacterium (cyanobacteria, also called blue-green algae). It is still unclear how the mycobiont finds the matching photobiont if both partners are not dispersed together. Maybe the fungal spores (very small fungal reproductive unit) “will just sit and wait” until the right photobiont partner comes along. (How romantic.) Some mycobionts are specialists that “can only associate with a few or a single partner—a ‘species’ of Nostoc [a cyanobacterium; we still don’t know how many species of symbiotic and free-living Nostoc are out there and how to recognize them], for example,” but many are generalists with more flexible preferences. 

Two species of foliose (leaf-like) lichens from the genus Peltigera. In the species on the left (P. canina), the only photobiont is a cyanobacterium from the genus Nostoc, making it an example of bi-membered symbiosis. In the species on the right (P. aphthosa), on the other hand, the primary photobiont is a green alga (which is why the thallus is so green when wet). In this case, Nostoc is a secondary photobiont contained only in the cephalodia—the dark, wart-like structures on the surface. With two photobionts plus the mycobiont, this is an example of tri-membered symbiosis.

Lichens are classified based on their overall thallus shape. They can be foliose (leaf-like), fruticose (shrubby), or crustose (forming a crust on rocks or other surfaces). Lichens that grow on trees are epiphytic, while those that live on rocks are saxicolous; lichens that live on top of mosses are muscicolous, and ground-dwelling lichens are terricolous. Much of Miadlikowska’s research is on a group of cyanolichens (lichens with cyanobacteria partners) from the genus Peltigera. She works on the systematics and evolution of this group using morphology-, anatomy-, and chemistry-based methods and molecular phylogenetic tools. She is also part of a team exploring biodiversity, ecological rules, and biogeographical patterns in cryptic fungal communities associated with lichens and plants (endolichenic and endophytic fungi). She has been involved in multiple ongoing NSF-funded projects and also helping graduate students Ian, Carlos, Shannon, and Diego in their dissertation research. She spent last summer collecting lichens with Carlos and Shannon and collaborators in Alberta, Canada and Alaska. If you walk in the sub basement of the Bio Sciences building where Bio201 and Bio202 labs are located, check out the amazing photos of lichens (taken by Thomas Barlow, former Duke undergraduate) displayed along the walls! Notice Peltigera species, including some new to science, described by the Duke lichen team.

Lichens have value beyond the realm of research, too. “In traditional medicine, lichens have a lot of use,” Miadlikowska says. Aside from medicinal uses, they have also been used to dye fabric and kill wolves. Some are edible. Miadlikowska herself has eaten them several times. She had salad in China that was made with leafy lichens (the taste, she says, came mostly from soy sauce and rice vinegar, but “the texture was coming from the lichen.”). In Quebec, she drank tea made with native plants and lichens, and in Scandinavia, she tried candied Cetraria islandica lichen (she mostly tasted the sugar and a bit of bitterness, but once again, the lichen’s texture was apparent).

In today’s changing world, lichens have another use as well, as “bioindicators to monitor the quality of the air.” Most lichens can’t tolerate air pollution, which is why “in big cities… when you look at the trees, there are almost no lichens. The bark is just naked.” Lichen-covered trees, then, can be a very good sign, though the type of lichen matters, too. “The most sensitive lichens are the shrubby ones… like Usnea,” Miadlikowska says. Some lichens, on the other hand, “are able to survive in anthropogenic places, and they just take over.” Even on “artificial substrates like concrete, you often see lichens.” Along with being very sensitive to poor air quality, lichens also accumulate pollutants, which makes them useful for monitoring deposition of metals and radioactive materials in the environment.

Dr. Scott LaGreca with some of the 160,000 lichen specimens in Duke’s herbarium.

LaGreca, like Miadlikoska, is a lichenologist. His research primarily concerns systematics, evolution and chemistry of the genus Ramalina. He’s particularly interested in “species-level relationships.” While he specializes in lichens now, LaGreca was a botany major in college. He’d always been interested in plants, in part because they’re so different from animals—a whole different “way of being,” as he puts it. He used to take himself on botany walks in high school, and he never lost his passion for learning the names of different species. “Everything has a name,” he says. “Everything out there has a name.” Those names aren’t always well-known. “Some people are plant-blind, as they call it…. They don’t know maples from oaks.” In college he also became interested in other organisms traditionally studied by botanists—like fungi. When he took a class on fungi, he became intrigued by lichens he saw on field trips. His professor was more interested in mushrooms, but LaGreca wanted to learn more, so he specialized in lichens during grad school at Duke, and now lichens are central to his job. He researches them, offers help with identification to other scientists, and is the collections manager for the lichens in the W.L. and C.F. Culberson Lichen Herbarium—all 160,000 of them.

The Duke Herbarium was founded in 1921 by Dr. Hugo Blomquist. It contains more than 825,000 specimens of vascular and nonvascular plants, algae, fungi, and, of course, lichens. Some of those specimens are “type” specimens, meaning they represent species new to science. A type specimen essentially becomes the prototype for its species and “the ultimate arbiter of whether something is species X or not.” But how are lichens identified, anyway?

Lichenologists can consider morphology, habitat, and other traits, but thanks to Dr. Chicita Culberson, who was a chemist and adjunct professor at Duke before her retirement, they have another crucial tool available as well. Culbertson created a game-changing technique to identify lichens using their chemicals, or metabolites, which are often species-specific and thus diagnostic for identification purposes. That technique, still used over fifty years later, is a form of thin-layer chromatography. The process, as LaGreca explains, involves putting extracts from lichen specimens—both the specimens you’re trying to identify and “controls,” or known samples of probable species matches—on silica-backed glass plates. The plates are then immersed in solvents, and the chemicals in the lichens travel up the paper. After the plates have dried, you can look at them under UV light to see if any spots are fluorescing. Then you spray the plates with acid and “bake it for a couple hours.” By the end of the process, the spots of lichen chemicals should be visible even without UV light. If a lichen sample has traveled the same distance up the paper as the control specimen, and if it has a similar color, it’s a match. If not, you can repeat the process with other possible matches until you establish your specimen’s chemistry and, from there, its identity. Culberson’s method helped standardize lichen identification. Her husband also worked with lichens and was a director of the Duke Gardens.

Thin-layer chromatography plates in Dr. LaGreca’s office. The technique, created by Dr. Chicita Culberson, helps scientists identify lichens by comparing their chemical composition to samples of known identity. Each plate was spotted with extracts from different lichen specimens, and then each was immersed in a different solvent, after which the chemicals in the extracts travel up the plate . Each lichen chemical travels a characteristic distance (called the “Rf value”) in each solvent. Here, the sample in column 1 on the rightmost panel matches the control sample in column 2 in terms of distance traveled up the page, indicating that they’re the same species. The sample in column 4, on the other hand, didn’t travel as far as the one in column 5 and has a different color. Therefore, those chemicals (and species) do not match.

LaGreca shows me a workroom devoted to organisms that are cryptogamic, a word meaning “hidden gametes, or hidden sex.” It’s a catch-all term for non-flowering organisms that “zoologists didn’t want to study,” like non-flowering plants, algae, and fungi. It’s here that new lichen samples are processed. The walls of the workroom are adorned with brightly colored lichen posters, plus an ominous sign warning that “Unattended children will be given an espresso and a free puppy.” Tucked away on a shelf, hiding between binders of official-looking documents, is a thin science fiction novel called “Trouble with Lichen” by John Wyndham.

The Culberson Lichen Herbarium itself is a large room lined with rows of cabinets filled with stacks upon stacks of folders and boxes of meticulously organized lichen samples. A few shelves are devoted to lichen-themed books with titles like Lichens De France and Natural History of the Danish Lichens.

Each lichen specimen is stored in an archival (acid-free) paper packet, with a label that says who collected it, where, and on what date. (“They’re very forgiving,” says LaGreca. “You can put them in a paper bag in the field, and then prepare the specimen and its label years later.”) Each voucher is “a record of a particular species growing in a particular place at a particular time.” Information about each specimen is also uploaded to an online database, which makes Duke’s collection widely accessible. Sometimes, scientists from other institutions find themselves in need of physical specimens. They’re in luck, because Duke’s lichen collection is “like a library.” The herbarium fields loan requests and trades samples with herbaria at museums and universities across the globe. (“It’s kind of like exchanging Christmas presents,” says LaGreca. “The herbarium community is a very generous community.”)

Duke’s lichen collection functions like a library in some ways, loaning specimens to other scientists and trading specimens with institutions around the world.

Meticulous records of species, whether in databases of lichens or birds or “pickled fish,” are invaluable. They’re useful for investigating trends over time, like tracking the spread of invasive species or changes in species’ geographic distributions due to climate change. For example, some lichen species that were historically recorded on high peaks in North Carolina and elsewhere are “no longer there” thanks to global warming—mountain summits aren’t as cold as they used to be. Similarly, Henry David Thoreau collected flowering plants at Walden Pond more than 150 years ago, and his samples are still providing valuable information. By comparing them to present-day plants in the same location, scientists can see that flowering times have shifted earlier due to global warming. So why does Duke have tens of thousands of dried lichen samples? “It comes down to the reproducibility of science,” LaGreca says. “A big part of the scientific method is being able to reproduce another researcher’s results by following their methodology. By depositing voucher specimens generated from research projects in herbaria like ours, future workers can verify the results” of such research projects. For example, scientists at other institutions will sometimes borrow Duke’s herbarium specimens to verify that “the species identification is what the label says it is.” Online databases and physical species collections like the herbarium at Duke aren’t just useful for scientists today. They’re preserving data that will still be valuable hundreds of years from now.

Meet New Blogger Jakaiyah, an infectious disease enthusiast

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

Expanding the SCOPE of Medical Education

It may be hard to put your finger on it, but Duke often allows students to connect their classes to something more personal.

The university’s emphasis on interdisciplinary education is a major initiative that colors students’ academic experiences. While there are many examples of these connections between people, classes, fields, and departments, few so tangibly represent those connections like The SCOPES Project, which connects arts and humanities to medical education at Duke.

Beneath the Surface by Mihir Patel, 2022. Image Courtesy of SCOPES.

Art and medicine can exist in entirely different worlds. They can appeal to different people and tell different stories. But why be simple when you can be, well… stunning? They can be integrated to form something powerful, and that’s precisely what SCOPES leadership members Isa DeLaura, Raluca Gosman, Mason Seely, David Stevens, and Lindsay Olson aimed to do. 

“It is encouraging as an upperclassman who previously participated in this program to see rising students continue the tradition of incorporating the humanities into medical practice,” Mason Seeley says. The generational aspect of the project seems to contribute to its personality; participants bring their own perspectives to their work only to walk away with dozens more. 

“Having a creative outlet has helped me process interactions with patients and the difficulties of the profession, and celebrate happy moments as well,” says Isa DeLaura.

“The goal is to give artists creative freedom to explore their relationships with their patients with whatever medium and in whatever style works best for them. As such, every year the feel is entirely based on the decisions of the artists.”

Isa DeLaura, MS3+

David Stevens insists that the artists “resist… forces of depersonalization in compelling and beautiful ways.”

The project is inspired and supported by yet another interdisciplinary Duke initiative called APPLE (Appreciating Patient Perspectives through Longitudinal Encounters), which connects medical students with patients living with chronic illnesses. The artists/medical students/empaths-in-training then attended multiple creative workshops and developed art pieces to reflect their patients’ personal experiences. But this year’s 6th annual SCOPES exhibition looks a bit different from past years’ (which are conveniently available online for your viewing pleasure).

Having attended many an art opening myself, I am unashamed to say that much of my enjoyment comes from the cheeseplates (and the excitement in the air, but that’s besides the point). Some exhibitions opt for a traditional charcuterie, some marked Kirkland Signature and others displayed on a handmade butcherblock. The point of fingerfoods is to encourage the attendees to stand up, walk around, and interact with the masses. But it also encourages attendees to “just stop by,” making the affair all the less intimate.

Following limitations on group gatherings Duke enforced during COVID, the SCOPES team decided to apply their newfangled interdisciplinary/revolutionary/innovative thinking to the art opening itself: They held a banquet. 

“I loved the way this turned out,” says DeLaura. “It was very personal and made for great discussion and comradery.” 

Fences, Rivers, Walls by Taylor Yoder, 2022. Image Courtesy of SCOPES.

“SCOPES has provided an opportunity to reflect on my experiences as a first-year medical student while also exploring new ways to combine various art forms to create my vision,” says Taylor Yoder, who created Fences, Rivers, Walls, pictured above. “I hope to continue shooting film throughout my medical education and career.”

I was particularly (although wrongfully) surprised about the variety in the exhibit. While the artists attended the same workshops and worked with patients through the same program, they took radically different approaches to their creations. Esme Trahair, a second-year medical student, was a humanities major in undergrad. Her piece combines historical perspectives with modern (although antiquated) mechanisms, emphasizing “the importance of remembering and learning from historical, outdated medical teachings.”

For the Record by Esme Trahair, 2022. Image Courtesy of SCOPES.

The work features a variety of perspectives, but also some clear motifs that could be key takeaways for future medical providers. Like Yoder, artist Kreager Taber explores the patient’s value of “home.” Exploring these motifs could allow for more personal, “upstream” healthcare. 

This year’s SCOPES exhibition is held in the Mars Gallery in the Duke University Hospital Concourse. It is an initiative of the Trent Center for Bioethics, Humanities & History of Medicine at the Duke University School of Medicine. It will be on display August 9-September 29, and available for viewing online at this link. 

P.S. If you are an MS1 student interested in participating in SCOPES, I have a link for you!

Post by Olivia Ares, Class of 2025

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

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.

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