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

Category: Biology Page 1 of 27

Modeling Biology: Ruby Kim’s Research on the Math of Physiological Cycles

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What lies at the intersection of mathematics and biology? Freshly-minted math PhD Ruby Kim and her work on mathematically modeling human dopamine cycles.

Ruby Kim, recent Duke PhD graduate

Kim’s work has centered around her creation of a math model to predict how a person’s dopamine levels ebb and flow over the course of a day “to understand the general mechanics of how disruptions in the (biological) clock lead to disruptions in dopamine.”

She said there is a pretty long history of mathematicians using differential equations to see how different clock genes and proteins change over the course of a day’s circadian cycle. Yet, no previous models have connected the circadian clock – controlled by the brain’s suprachiasmatic nucleus – to dopamine levels. And Kim tells me that work suggesting dopamine changes throughout the day are likely controlled by the internal circadian clock itself is “relatively new.”

The first step in Kim’s work was validating scientists’– or “experimentalists,” as Kim dubs them –  hypotheses about dopamine and dopaminergic enzyme cycling.

Many physiological processes are controlled via circadian rhythms and the internal clock in humans, as well as other organisms.

“But I’d like this work to help experimentalists go one step further and be able to test out hypotheses more easily.” For example, Kim says that her model has the potential to reveal other fascinating phenomena, such as how drug treatments or different genetic mutations may impact circadian rhythm or dopamine. This is thanks to the multifaceted layers of Kim’s model.

“From a mathematical perspective, the math model is very interesting. It has a lot of interesting dynamics,” she says. “Not only does it show nice, 24-hour rhythms, it shows both steady state behavior… but then also behavior that’s really wild – something called quasi-periodic behavior, where the internal clock is significantly different than the external 24-hour light-dark cycle.”

“This leads to oscillatory behavior that’s not periodic,” she says. These sorts of quasi-periodic behaviors have been observed in experiments and misunderstood, but they can be computed.

Kim emphasized the experimental and clinical implications of her work. Dopamine is involved in learning and motivation and is also linked a plethora of psychiatric conditions like Parkinson’s, ADHD, and schizophrenia. “Patients with these conditions often also experience circadian disruptions,” Kim says. “That’s a pretty big symptom.”

Kim began her academic career in her home state of California at Pomona College as a pre-med math major. “I had always been intrigued by human physiology. And math was one of the subjects I was also pretty drawn to. I just didn’t appreciate it much because throughout high school and the beginning of undergrad, I didn’t see any direct applications,” Kim told me.

The marriage of her love for math with her intrigue in biology actually began at Duke when Kim attended a mathematical biology workshop during the summer after her sophomore year. “I had never heard of math biology before that.”

After working on a brief project to model sleep apnea in infants at the workshop, Kim returned to California and took up math modeling courses in her following semesters of undergrad. One of her professors, Ami E. Radunskaya, PhD, was extremely supportive and introduced Kim to a lot of “cool biological problems.” Kim went on to do research with Radunskaya, modeling tumor-immune interactions. This experience, Kim says, “kind of just threw me into academia.” The project gave way to an undergraduate thesis with Radunskaya that analyzed the long-term behavior of this tumor growth and treatment model.

Radunskaya then suggested that Kim pursue grad school. “I kind of applied on a whim,” Kim said, “It wasn’t something I had specifically imagined for myself.” Kim mentioned how no one from her home community had really ever gone to grad school and so it was not something she had ever “explicitly” thought about before.

Using mathematics to fight cancer | Department of Mathematics | University  of Washington
An abstract of Radunskaya’s work on mathematical modeling and understanding tumor-immune interactions to address cancer.

In her search for a graduate program, Kim applied to math programs, as well as those that were interdisciplinary. “I ended up choosing Duke because I really liked my advisor,” Kim told me. While Kim’s advisor Michael Reed, PhD “does a lot of interesting math,” Kim wanted to work with him because math isn’t his focus – understanding “really complex biological systems using mathematical language is.”

“A lot of times you see people who do things at the intersection of math and biology that are more motivated from a mathematical standpoint … that’s just not what I’m interested in personally. I’m very interested in finding an interesting biological problem and then applying whatever mathematical tools I have.”

While at Duke, Kim was foundational to founding the university’s chapter of the Association for Women in Math (AWM). During her undergrad, Kim “had a really great experience with AWM,” finding both a community of women mathematicians and a network of women professors who were involved in the chapter.

At Duke, there wasn’t a chapter “but quite a few people who were interested in starting and being part of one.” This organization, which is open to people of any gender identity, heads mentorship programming that brings undergrads, grad students, postdocs, and professors together, organizes conferences, and contributes to their central focus of community building in math.

Outside of her research, Kim spends most of her free time taking care of foster pups, which she describes as “extremely rewarding but also very tiring.” Her most recent foster, a four-month-old puppy, eavesdropped on our interview as he took a nap.

This fall, Kim will begin a post-doc with the University of Michigan’s math department as she “wanted to keep studying circadian rhythms with faculty who are really great in that area.”

Post by Cydney Livingston, Class of 2022

Vernal, Ephemeral, Spring Beauty by Any Other Name

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Nicki Cagle, Ph.D., with perfoliate bellwort, an ephemeral forest plant also known as wild oats (Uvularia perfoliata).

“Ephemeral” is one of my favorite words. It conjures up images of vernal pools and fireflies and flowers in spring. It comes from ephēmeros, a Greek word meaning “lasting a day.” English initially used it in a scientific sense, to refer to fevers and then in reference to short-lived organisms like flowers or insects. Today “ephemeral” is most often used to describe anything fleeting or short-lived.

The term “spring ephemeral,” for instance, refers to flowers that are visible for only a short time each spring before they disappear.

Nicki Cagle, Ph.D, a senior lecturer in the Nicholas School of the Environment, led a spring ephemeral workshop in the Korstian Division of Duke Forest on a Friday afternoon in late March. The workshop was hosted by DSER, the Duke student chapter of the Society for Ecological Restoration. We focused on identifying herbaceous plant species and families, particularly spring ephemerals.

“Spring ephemerals are perennials that emerge early in the spring and then grow, reproduce, and disappear from the surface of the forest floor in just a few short weeks,” Cagle explains. We also found several species that aren’t technically ephemerals but still bloom in early spring — before the tree canopy emerges and plunges the floor into shade.

Oxalis violacea, a species of wood sorrel.

The first plant Cagle points out is Oxalis violacea, a type of wood sorrel. “This particular species will have purple flowers,” she says. The genus name, Oxalis, refers to the plant’s oxalic acid content. “You can nibble on it,” but “you don’t want to nibble on it too much.” Oxalic acid, which is also found in common foods like spinach, gives the leaves a pleasant, lemony taste, but it can cause problems if eaten in excess.

Common bluet (Houstonia caerulea).

When we come across a patch of lovely, pale violet flowers with yellow centers, Cagle challenges the workshop participants to determine which family it belongs to. She offers two options: Rubiaceae, a large family that often has either opposite or whorled leaves and four to five petals and which includes familiar plants like coffee, or Violaceae, a very small plant family whose members “tend to have everything in fives” (like petals, stamens, and sepals) and often have basal leaves. Answer: Rubiaceae. This particular species is Houstonia caerulea, the common bluet. Its yellow centers help distinguish it from related species like the summer bluet, tiny bluet, and purple bluet. If anything, Cagle says, the plant’s presence is “an indicator of disturbance,” but it’s still good to have around.

Here’s the little brown jug (Hexastylis arifolia).

Next we come across two species in the Hexastylis genus. They are sometimes called wild ginger, but the name is misleading. Hexastylis species are not related to the ginger you buy in the store, which is in a completely different family. Hexastylis is, however, in the same family as the Asarum genus, which Cagle thinks of as “proper” wild ginger. Asarum and Hexastylis have traditionally been used as food and medicine, but they also contain toxins. According to Cagle, they belong to “one of the few plant families that have fossilized remains in the United States,” even dating back to the late Cretaceous Period.

The two species we see are Hexastylis arifolia, the little brown jug, and Hexastylis minor which looks similar but “tends to have a much more rounded form.” Like many spring ephemerals, Hexastylis is often dispersed by ants. The seeds have elaiosomes, fatty deposits that ants find attractive.

“We have a lot of different violets of varying origins” in this area. According to Cagle, this one is likely to be a common blue violet, Viola sororia.

There’s a patch of violets near the Hexastylis plants. “We have a lot of different violets… of varying origins” around here, Cagle says. Many of the native species have both a purple form and a variety that’s white with purple striping. Other species in the violet family come in different colors altogether, and Cagle says many of those are of European origin.

The Johnny-jump-up pansy, for instance, can have “funkier colors,” like yellow or pinkish purple and is native to Europe and Asia. Violets can be hard to identify. Some species are distinguished mainly by characteristics like the lobes (projections in leaves with gaps between them) or the hairiness of the leaves. The bird’s foot violet and wood violet, for example, “tend to have really deep lobes.”

Cagle says the violet we’re looking at is likely the common blue violet, characterized by smooth leaves and petals, purple or purple-and-white flowers, and rounded or slightly arrow-shaped leaves.

The Cranefly orchid (Tipularia discolor) reproduces later in the year. The purple on the bottom of the leaves, and sometimes on the top as well (see right), helps protect the plant from sunlight and herbivores.

The orchid family, Orchidaceae, is one of the largest families of flowering plants in the world. Many of its members are tropical, including the Vanilla genus, but “we do have a number of native orchids” here as well, including yellow and pink lady’s slipper orchids, putty-root, and the cranefly orchid.

The cranefly orchid, Tipularia discolor, isn’t yet in bloom, but we come across the leaves several times on our walk. According to Cagle, Tipularia discolor “isn’t actually a spring ephemeral” because it reproduces later in the year. However, “it’s ephemeral in its own way,” the leaves disappear by the time it flowers. Cagle says the plant’s scientific name can remind you what to look for: “‘Tip-’ because you’re going to tip this leaf over” to look at the underside and “discolor” because the leaves are a striking purple underneath. Some of the ones we see are purple on top as well. Cagle explains that the purple coloration serves as sunscreen and protection from critters that eat plants.

The plant gets its common name (and its scientific genus name, interestingly) from its delicate flowers, which are supposed to resemble craneflies. When the plant blooms, “the flowers are so delicate and so subtle that most of the time you miss them.” Pollinators like Noctuid moths, on the other hand, find the flowers easily and often. Cranefly orchids even have “specialized seed structures” that “get fused onto insects [such as the moths]… and carried off.”

Rue anemone (Thalictrum thalictroides or Anemonella thalictroides).
Cagle with giant chickweed (Stellaria pubera).

The rue anemone, unlike the cranefly orchid, is a true spring ephemeral. It belongs to a more “primitive” family and has lots of petals in a spiral arrangement. The species is also known as windflower “because they flutter and dance as the breeze comes through.” Cagle mentions that the plant is “usually pollinated by flies and little bees” and serves as an important food source for insects in early spring. But “how do these even exist” in a forest with so many plant-eating deer? Many spring ephemerals, Cagle explains, have “some really potent toxins” that protect them from large herbivores.

We stop briefly to examine perfoliate bellwort, also known as wild oats (Uvularia perfoliata), and giant (or star) chickweed. Chickweed is in the pink family, named not for the color but because “the petals… [look] as if they’re cut by ‘pinking shears,’” which have saw-toothed blades that leave notches in fabric.

Trout lily (Erythronium umbilicatum). According to Cagle, “No spring ephemeral walk is actually complete without finding some trout lilies.”

Near the end of our walk, we find several trout lilies. That’s fortunate. “No spring ephemeral walk is actually complete without finding some trout lilies,” Cagle says.

Unsurprisingly, trout lilies belong to the lily family. “Their flower structure,” Cagle says, “is very symmetrical” with three petals and three sepals. In trout lilies, the sepals resemble petals, too. This particular species is Erythronium umbilicatum. The species name, umbilicatum, refers to its “really long peduncle,” or flower stalk, which “allows the seed to actually touch the ground.” The seed is dimpled, Cagle says, “like a little belly button.” The name “trout lily,” meanwhile, refers to the mottled pattern on the leaves.

Spring beauty (Claytonia virginica), “a quintessential spring ephemeral.”

At the base of a tree near a small river, Cagle points out a flower called spring beauty (Claytonia virginica), “a quintessential spring ephemeral.” Some flowers, like the common bluet we saw earlier, thrive in disturbed areas, but plants like the spring beauty need rich, undisturbed habitat. That makes them good indicator species, species that can help scientists gauge environmental conditions and habitat quality. When a natural area is being restored, for example, scientists can measure restoration progress by comparing the “restoration site” to an undisturbed “reference site.”

According to Cagle, the spring beauty is pollinated by “bee flies… flies that kind of look like bees.” After pollination, the flowers turn pink. Cagle says this is common among ephemerals. One theory is that the color change signifies which flowers have already been pollinated, but others think it’s just a result of senescence, or aging.

Spring beauties are also “photonastic,” meaning they open and close in response to changing light conditions. “There is some evidence that the Iroquois would eat this plant in order to prevent conception,” Cagle says, but today the plant—like many spring ephemerals—is under protection in some areas. Human activities, sadly, have contributed to the decline of too many spring ephemerals.

Alum root (Heuchera americana) near the end of the walk. According to Cagle, its roots can be used “to form mordant for dyes.” Members of the Saxifrage family, which includes alum root, often have five petals, five sepals, and five stamens.

Not all of the plants we saw are spring ephemerals. Some, although they bloom in early spring, “wouldn’t technically be considered ephemeral because their leaves stick around even if their blooms don’t last long.” True ephemerals, on the other hand, “are plants that just seem to disappear off the face of the planet (or the forest floor) after a few weeks,” Cagle says. Only three of the species we found during the workshop are true ephemerals: the windflower, trout lily, and spring beauty. However, these aren’t the only spring ephemerals found in the area. Cagle’s personal favorite is bloodroot, with its “bright white petals” and pollen “that looks like it’s glowing.”

Next time you’re in the woods, keep your eyes out for ephemerals and other early spring flowers, but look quickly. They won’t be here for long.

By Sophie Cox

Post and Photos by Sophie Cox, Class of 2025

Kinsie Huggins: the Future Doctor Who Could Shot-Put

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From shot-putting, to helping conduct two research studies, to being selected for a cardiology conference, meet: Kinsie Huggins. She is from Houston, Texas, currently majoring in Biology and minoring in Psychology with a Pre-Med track here at Duke. With such a simple description, one can already see how bright her future is!

“I want to be a pediatrician and work with kids,” Huggins says. “When I was younger, I lived in Kansas, and in my area, there were no black pediatricians. My mother decided to go far to find one and I really bonded with my pediatrician. One day, I made a pact with her in that I would become a pediatrician too so that I can also inspire other little girls like me of my color and other minority groups.”

Having such a passion to let African-American and minority voices be heard, Huggins is also part of the United Black Athletes, using her shot-put platform to make sure these voices are heard in the athletics department.

And while she may be a top-notch sportswoman, she is also just as impressive when it comes to her studies and research. One of her projects focuses on the field of nephrology – the study of kidneys and kidney disease. She and a pediatric nephrologist are currently working on studying rare kidney diseases and the differences in DNA correlating to these diseases.

Kinsie is also a researcher at GRID (Genomics Race Identity Difference), which studies the sickle cell trait in the NCAA. With the sudden deaths of college athletes from periods of over-exhaustion during conditioning, there has been a rise in attention of sickle cell trait and its impact on athletes. At first, the NCAA implemented a policy that made it mandatory for college athletes to get tested for sickle cell in 2010, but some were wary about the lack of scientific validity in such claims. Now, the NCAA has funded GRID to conduct such research.

The difference of Normal red blood cell and sickle cell (CDC).

 “We are analyzing the policy (athletes need to be tested for sickle cell), interviewing athletes in check-ups, and looking at data to see if the policy is working out for athletes and their performance/health,” Huggins explains.

With such an impressive profile, it doesn’t go without saying that Huggins didn’t go unnoticed. The American College of Cardiology (ACC) select high school and college students interested in the field of medicine and have them attend a conference in Washington D.C. to hear about research presentations, groundbreaking results of late-breaking clinical trials, and lectures in the field. Having worked hard, Huggins was selected to be part of the Youth Scholars program from the ACC and was invited to the conference on April 2-4. 

Let’s wish Kinsie the best of luck at the conference and on her future research!

Post by Camila Cordero, Class of 2025

Quorum Sensing: The Social Network of Bacteria

Dr. Bonnie L. Bassler, the Chair of Molecular Biology at Princeton University, is an advocate for diversity in science.

Bonnie Bassler of Princeton University

Throughout her presentation of the Ingrid Daubechies Lecture on Jan. 31 during Research Week, she emphasized that the diversity of her scientific team allowed every lab member to contribute to different steps of the process of studying quorum sensing, a form of microbial communication. (Watch her talk.)

Bacteria are everywhere. They’re sitting at the tables you sit at, burrowing in the clothes you wear and unfortunately, also crawling around on your skin. For a long time, they’ve had a pretty bad reputation, and for good reason! They have caused plagues that have wiped out masses across the globe, driven up breath mint sales by thriving in your mouth and mutated into every biologist’s Boogeyman when you try to kill them with antibiotics – super bugs!

However, the bacterial redemption arc is also quite compelling. “Good guy” bacteria in the gut help us break down food, produce essential vitamins and also sometimes fight off their evil siblings.

So, good or bad, the impact of bacteria in our daily lives is undeniable. But how does a microscopic little being have the capacity to influence the macroscopic world so greatly?

It doesn’t. At least, not by itself.

Lactococcus lactis is one of the starter bacteria in a cheese culture!

A bacterium never works alone because its strength lies in its numbers! Groupwork and communication (as any Pratt star going through recruiting season will swear to their interviewers) are what make bacteria so powerful. A bacterium by its lonesome will act differently than a bacterium surrounded by its daughters, sisters and cousins (bacterial family tree dynamics can get a little unusual).

Knowing that bacteria optimize their behaviors to work efficiently in a group answers the question of how they are so powerful, but it raises another.

How do bacteria know when they have company?

In a world where social media helps us stay connected, it is easy to take rapid status updates for granted. But for tech-deprived microbial colony, how does one member gauge the population of their surroundings? This question is one that Bassler’s lab answered: with a special chemical compound called autoinducers.

Autoinducers are little chemical signaling molecules that each bacterium sends out into its immediate environment. These molecules allow for quorum sensing, or cell-to-cell communication, to take place among bacteria.

Basic quorum sensing: How bacteria know who’s around them. (Nidhi Srivaths)

Every bacterium senses changes in the concentration of these autoinducers in their surroundings. Sensing a sudden increase in autoinducer concentration will change a bacterium’s gene expression, protein synthesis, and consequently, behavior. It will adapt to group behavior, while a bacterium that senses a drop in autoinducers will adapt to individual behavior.

Bacteria not only sense how many others are around them but also who their neighbors are. Autoinducers are universal to both Gram positive and negative bacteria and are unique to the type of bacteria that produce them.

This provides the bacterium with qualitative information on the population of its surroundings. Are they friends or foes?

Quorum sensing also includes nametags so bacteria can tell friend from foe. (Nidhi Srivaths)

In marine vibrio (a genus of Gram-negative bacteria), Bassler’s lab found that quorum sensing could perform intra-species, intra-genus and inter-species identification. This additional information helps the microbes adjust their behavior – from being friendly and supportive towards their relatives to being aggressive and competitive with their enemies.

Bassler provided a real-world perspective on quorum sensing. One species of the vibrio genus, Vibrio cholerae, is responsible for causing Cholera a deadly food and water-borne disease that has plagued low- and middle-income countries for centuries.

When the cholera bacteria enter the host, they are highly virulent and create a sticky biofilm around themselves that helps them clump into aggregates. Their cell density increases with bacterial division until the bacteria sense a certain concentration of autoinducers. Then their gene expression is modified to reduce virulence and biofilm production and the bacterial gene expression patterns shift to escape mechanisms. The bacteria soon break out in large numbers in search of a new host. (Their human host has voluminous, watery diarrhea in response and that becomes the vector for infecting new hosts.)

While the sequence of events that occurred in a cholera infection was known, the discovery of quorum sensing in V. cholerae opens doors for possible treatments, Bassler said. As bacterial communication sets the cycle of infection and division in motion, interfering with the autoinducers produced or disrupting bacteria’s ability to sense them sets the stage for innovative therapies for several infectious diseases.

Quorum sensing is another step towards understanding the world of the tiny microorganisms that influence our world and Bassler and her team are another example of the incredible research that can come from diverse teams in science.

Post by Nidhi Srivaths, Class of 2024

Medicine Under a Microscope

Duke Research Week 2022 featured a range of speakers from across all disciplines. The Lefkowitz Distinguished Lecture on January 31st highlighted some of our favorite things here at Duke Research Blog: ingenuity and perspective. 

Dr. Huda Yahya Zoghbi’s career spans decades; her Wikipedia page sports an “Awards and Honors” section that takes up my entire computer screen. She is a geneticist, neuroscientist, pediatric neurologist, pharmaceutical executive, and literature lover. Her presentation kicked off 2022 Research Week with a discussion of her work on Rett Syndrome. (View the session)

Rett Syndrome is a rare genetic disorder. The gene that researchers identified as the driver of the syndrome is MeCP2, which is especially active in brain cells. Certain mutations of this one gene can be responsible for a loss of speech, development issues, and persistent fidgeting. 

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The MeCP2 protein. Image: Wikipedia Commons

Children with Rett Syndrome faced chronic misdiagnosis, and even with proper care were limited by a lack of research.

Duke’s Dr. Robert Lefkowitz introduced Zoghbi at the beginning of the seminar and explained how she came to become the leading expert on this relatively unknown disorder. After completing medical school in Beirut in the midst of the ravaging Lebanese Civil War, she came to Texas Children’s Hospital, where she was able to observe and diagnose her first case of the syndrome, a process spurred by a simple interest in a newly-published journal article.

Holistic knowledge of Rett Syndrome is completely dependent on genetic research. A mutation on the MeCP2 gene causes errors in transcription, the reading out of DNA in your cells which leads to the production of proteins.

The mutated gene’s MeCP2 protein is then lacking the ability to do its job, which is helping other genes be expressed, or actively transcribed.

It’s a vicious cycle; like when you go to sleep late one night, so you sleep in the next day, then go to sleep late the next night, then sleep in the next day, and so forth.

In order to simulate and measure the effect of different kind of mutations on the MeCP2 gene, Zoghbi and her team studied genetically modified mice. While Rett Syndrome is caused by a lack of MeCP2 function, an overactive MeCP2 gene causes MeCP2 duplication syndrome. Varying degrees of gene efficiency then produce varying degrees of severity in the syndrome’s traits, with fatality at either end of the curve.  

Varying degrees of phenotype severity.

Zoghbi’s talk focused mainly on the mechanics of the disorder on a genetic level, familiar territory to both Nobel Laureate Lefkowitz and Duke Medicine Dean Mary Klotman, who shared some discussion with Zoghbi.

This medicine on a microscale is applicable to treating genetic disorders, not just identifying them. Zoghbi has been able to experimentally correct MeCP2 duplication disorder in mice by modifying receptors in a way that reverses the effects of the disorder.

The symptoms of Rett Syndrome are physical; they present themselves as distinct phenotypes of a subtle difference in genotype that’s too small to see. The field of genetics in medicine is responsible for making that connection.

Post by Olivia Ares, Class 2025

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Materials For a Changing World… What is That?

Everything in our world is made from materials, meaning life is enabled by material development and efficiency. In today’s society, from constant technological revolution to the global pandemic, life as we know it is always evolving. But as the world around us evolves, the materials around us also need to evolve to keep up with current demands. But how? As a part of Duke University’s annual Research Week on Feb. 3, researchers from a multitude of practices offered their wisdom and research.

Moderated by Dr. Catherine L. Brinson, Ph.D., the panel hosted three Duke Scholars and their research on ‘Materials for a Changing World’. “The development of new materials can really be key in solving some of the more critical challenges of our time,” Brinson maintained.

Dr. David Beratan explaining his research on bio-machines and their material efficiency.

The first scholar to present was R.J Reynolds distinguished professor of chemistry, Dr. David N Beratan, Ph.D. His research concerns the transition from soft, wet, and tiny research machines to more durable, long-term research machines in the science field. “The machines of biology tend to be stochastic and floppy rather than deterministic and hard,” Beratan began. “They’re messy and there are lots of moving parts. They’re intrinsically noisy and error-prone, etc…They’re very different from the kinds of things you see under the hood of your car, and we’d really like to understand how they work and what lessons we might derive from them for our world.” His complex research and research group have aided in bridging the gap in knowledge regarding the transition of biological functional machines to synthetic ones.

Dr.Rubinstein presenting his research on materials at Duke’s Pratt School of Engineering in 2019.

The panel continued with Aleksandar S. Vesic Distinguished Professor in mechanical engineering, Dr. Michael Rubinstein, Ph.D. His research involves the development of self-healing materials across multiple spectrums. “What you want to think about is materials that can heal themselves,” he stated. “If there’s a crack or a failure in a material, we would like the material to heal itself without external perturbation involvement. So it could be done by the other diffusion of molecules across some physical approaches, or by a chemical approach where you have bonds that were broken to the form.” His research on this possibility has made strides in the scientific field, especially in a time of such ecological stress and demand for materials.

Dr. Segura talking with Dr. Brinson on her research involving self-healing materials.

The panel concluded with biomedical engineering professor Dr. Tatiana Segura, Ph.D. Segura talked about work they are doing at their lab regarding materials that can be used to heal the human body after damage or injury. She began by mentioning that “we are a materials lab and that’s what we’re interested in designing. So what are we inspired by? Well, we are really inspired by the ability of our body to heal.” At her lab, a primary motivation is healing disabilities after a stroke. “Sometimes you have something that you deal with for a long time no matter how your body healed. And that inspires us to consider how do we actually engage this process with materials to make it go better and actually make our body heal in a way that we can promote repair and regeneration.” Understanding this process is a complex one, she explained, but one that she believes is crucial in understanding the design of the material.

‘Materials for a Changing World’ was yet another extremely powerful speaker series offered this year during Duke Research Week. Our world is changing, and our materials need to keep up. With the help of these experts, material innovation has a bright future.

Written by Skylar Hughes
Class of 2025

Finding the Tipping Point for Coastal Wetlands

Cypress swamp, eastern North Carolina. Photo by Steve Anderson, Duke

DURHAM, N.C. — The Albemarle-Pamlico Peninsula covers more than 2,000 square miles on the North Carolina coastal plain, a vast expanse of forested swamps and tea-colored creeks. Many people would probably avoid this place, whose dense thickets of cane and shrubs and waterlogged soils can slow a hike to a crawl.

“It’s hard fieldwork,” says Duke researcher Steve Anderson. “It gets really dense and scratchy. That, plus the heat and humidity mixed with the smell of sulfur and the ticks and the poison ivy; it just kind of adds up.”

But to Anderson and colleagues from Duke and North Carolina State University, these bottomlands are more than impenetrable marsh and muck and mosquitoes. They’re also a barometer of change.

Researchers surveying plants in Alligator River National Wildlife Refuge in 2016. Photo by Mathew Stillwagon, North Carolina State University

Most of the area they study lies a mere two to three feet above sea level, which exposes it to surges of ocean water — 400 times saltier than freshwater — driven inland by storms and rising seas. The salt deposits left behind when these waters recede build up year after year, until eventually they become too much for some plants to cope with.

Trudging in hip waders through stunted shrubs and rotting tree stumps, Anderson snaps a picture with his phone of a carpet of partridge berry trailing along the forest floor. In some parts of the peninsula, he says, the soils are becoming so salty that plants like these can no longer reproduce or are dying off entirely.

Along the North Carolina coast, understory plants such as this partridge berry (left) are quickly ceding ground to species such as this bigleaf marsh-elder (right) as the soils become too salty for them to thrive. Credit: Steve Anderson

In a recent study the team, led by professors Justin Wright and Emily Bernhardt of Duke, and Marcelo Ardón of NC State, surveyed some 112 understory plants in the region, making note of where they were found and how abundant they were in relation to salt levels in the soil.

The researchers identified a ‘tipping point,’ around 265 parts per million sodium, where even tiny changes in salinity can set off disproportionately large changes in the plants that live there.

Above this critical threshold, the makeup of the marsh floor suddenly shifts, as plants such as wax myrtle, swamp bay and pennywort are taken over by rushes, reeds and other plants that can better tolerate salty soils.

Certain dwindling plants could be an early warning sign that salt is poisoning inland waters, researchers say. Credit: Steve Anderson

The hope is that monitoring indicator species like these could help researchers spot the early warning signs of salt stress, Anderson says.

This research was supported by grants from the National Science Foundation (DEB1713435, DEB 1713502, and Coastal SEES Collaborative Research Award Grant No. 1426802).

CITATION: “Salinity Thresholds for Understory Plants in Coastal Wetlands,” Anderson, S. M., E. A. Ury, P. J. Taillie, E. A. Ungberg, C. E. Moorman, B. Poulter, M. Ardón, E. S. Bernhardt, and J. P. Wright. Plant Ecology, Nov. 24, 2021. DOI: 10.1007/s11258-021-01209-2.

Salt is poisoning the soils past a point of no return for some marsh plants; one team is trying to pinpoint the early warning signs. By Steve Anderson.

Blake Fauskee and the ‘Little Typos’ of Fern DNA

Blake Fauskee, third-year Biology PhD student, initially pitched his graduate project to advisor Kathleen Pryer (Ph.D.) as an undergrad.

Fauskee, who researches RNA editing sites in ferns, told me about the project that he’s been working on for the last several years. His research could push back against the idea that DNA is the end-all, be-all molecule for encoding life as we know it.

Blake Fauskee, third-year Biology PhD student

Fauskee broke down RNA editing for me. “RNA editing is this extra step in the whole central dogma, the whole gene expression process, that happens in plant organellar DNA,” he said. This process takes place in plant mitochondrial and chloroplast genomes.

Fauskee uses a lot of metaphors to describe his work, which I find both helpful and admirable. Science can often be dense and lack feasible connections to processes that most of us are familiar with. “Basically, in [plant] DNA, there are little typos almost. The wrong nucleotide is encoded at certain spots. When those genes are going to be expressed, they get turned into RNA and then other proteins from the nucleus come in and find the little typos so that in the end you get the correct protein.”

This image shows a simplified diagram of how RNA editing works.

Fauskee calls RNA editing an “interesting and strange process” that neither animals nor humans have. His work attempts to study the evolution of this process, the patterns of RNA editing, and why it came to be. He uses DNA and RNA sequence data and the help of computational tools to do his work. He explains that when sequencing DNA, you can think of the fragmented base pairs “as little puzzle pieces.”

“So, I take all those little puzzle pieces and try to put back together the chloroplast genome, which is about 150,000 base pairs. It’s like a thousand-piece puzzle.”

Next, he figures out where the fern’s gene sequences are on the DNA strands, making use of genomic databases that contain known genomes. He then aligns RNA sequences to the genes he has mapped. Fauskee looks for the “typos” or “little differences” between the DNA and RNA: “That’s how we find the RNA editing sites.” Finally, he evaluates how the proteins would be changed by the typos in the DNA if the RNA was not edited after being transcribed.

“So, a lot of these fern genes will have a STOP codon right in the middle, which is really, really bad if you don’t fix because you are only going to get half a protein,” Fauskee said. STOP codons signal to the protein-building ribosomes that the protein is finished once it reads this portion of the RNA. Fauskee explained that these types of errors are the ones would expect organisms to lose, but it turns out they are the ones that are conserved in ferns. “Is there an extra function there? Is it helpful? Is it adaptive?” Fauskee asked.

An image of different ferns.

Comparative analyses between fern species are important. By looking at whether there are common editing sites and common amino acid changes, Fauskee says, “we’re trying to understand if certain editing sites may be advantageous and what kinds of fluctuation we see between certain types of changes.”

Fauskee underscored the importance of his work. “RNA editing is a really interesting process that kind of undermines what I learned in molecular biology…They always tell you DNA is the bedrock, it’s the be-all, end-all. But what happens when the DNA is wrong? What’s the other added layer on this?”

Simply put, Fauskee, says that because of RNA editing, “We have to rethink central dogma a little bit.” In some plants, 10% of all their gene products contribute to RNA editing, Fauskee tells me. “That’s a big chunk and that’s got to be important,” Fauskee said, “Why would evolution keep such a burden going?”

Biology’s central dogma is the idea that DNA is transcribed into RNA and then translated into proteins. RNA editing adds an extra step before translation and protein production.

There may also be implications for how RNA editing sites affect the way that genetic relationships are mapped through phylogenetics. If differences between the DNA of different species at RNA editing sites, this could be misleading. Though the DNA indicates a change in base pair, RNA editing could lead to the same output in protein despite the seeming change. “If you took [RNA editing] into account,” Fauskee says, “does it give you a different answer?”

Fauskee studies ferns because of the amount of editing sites found in these plants. While flowering plants have lost editing sites over time, ferns have not. “For RNA editing, you can look at all angiosperms (flowering plants) and for the whole chloroplast genome, they might have 30-50 RNA editing sites. When you get into ferns, that number jumps up to 300-500 and I am trying to understand why.”

Botanical science first captured Fauskee’s interest while he completed his undergraduate degree in his home state at the University of Minnesota Duluth (UMD). As a sophomore at UMD, Fauskee was taken under the wing of Amanda Grusz (Ph.D.). Grusz received her PhD in biology from Duke and worked under Pryer during her own time at the university. “I’m like my advisor’s academic grandson, which is kind of funny.” Clara Howell, who is part of Fauskee’s PhD cohort and who I spoke with last Fall, is also an academic grandchild in her own lab.

Being an “academic grandson” has worked out well for Fauskee. His key advice to me for any person considering a PhD, “Make sure your advisor is not someone you just admire as a scientist, but as a person.” On a day-to-day basis, Fauskee says that advisor Katheen Pryer “is pretty hands off” but is also “one of the most supportive people ever. I’m pretty much the driver of my own ship. If I am falling off the road, she’ll push me back on the road, but she’ll give me freedom to swerve around on that road.”

Fauskee also emphasized a piece of wisdom that Pryer passed down to him. “If whatever you’ve got going on is working and everyone else is doing something different, who cares?” he said.

Though Fauskee says that “lab work can be frustrating,” getting his long analyses to run after wrangling lots of data is very rewarding. Fauskee, who does not have a background in coding or computer languages, likes to “tell people that [his] floor of biology combined is one competent coder.” When he’s not stealing bits of his biology neighbor’s code, Fauskee loves to attend Duke Basketball games and is a fan of the television show Survivor.

Post by Cydney Livingston, Class of 2022

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

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

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

Emily Levy, an almost-PhD in Duke Biology

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Post by Cydney Livingston, Class of 2022

LowCostomy: the Low-Cost Colostomy Bag for Africa

It’s common for a Pratt engineering student like me to be surrounded by incredible individuals who work hard on their revolutionary projects. I am always in awe when I speak to my peers about their designs and processes.

So, I couldn’t help but talk to sophomore Joanna Peng about her project: LowCostomy.

Rising from the EGR101 class during her freshman year, the project is about building  a low-cost colostomy bag — a device that collects excrement outside the patient after they’ve had their colon removed in surgery. Her device is intended for use in under-resourced Sub-Saharan Africa.

“The rates in colorectal cancer are rising in Africa, making this a global health issue,” Peng says. “This is a project to promote health care equality.”

The solution? Multiple plastic bags with recycled cloth and water bottles attached, and a beeswax buffer.

“We had to meet two criteria: it had to be low cost; our max being five cents. And the second criteria was that it had to be environmentally friendly. We decided to make this bag out of recycled materials,” Peng says. 

Prototype of the LowCostomy bag

For now, the team’s device has succeeded in all of their testing phases. From using their professor’s dog feces for odor testing, to running around Duke with the device wrapped around them for stability testing, the team now look forward to improving their device and testing procedures.

“We are now looking into clinical testing with the beeswax buffer to see whether or not it truly is comfortable and doesn’t cause other health problems,” Peng explains.

Poster with details of the team’s testing and procedures

Peng’s group have worked long hours on their design, which didn’t go unnoticed by the National Institutes of Health (NIH). Out of the five prizes they give to university students to continue their research, the NIH awarded Peng and her peers a $15,000 prize for cancer device building. She is planning to use the money on clinical testing to take a step closer to their goal of bringing their device to Africa.

Peng shows an example of the beeswax port buffer (above). The design team of Amy Guan, Alanna Manfredini, Joanna Peng, and Darienne Rogers (L-R).

“All of us are still fiercely passionate about this project, so I’m excited,” Peng says. “There have been very few teams that have gotten this far, so we are in this no-man’s land where we are on our own.”

She and her team continue with their research in their EGR102 class, working diligently so that their ideas can become a reality and help those in need.

Post by Camila Cordero, Class of 2025

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