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

Tag: biology

Jason Dinh Once Collected Cicadas, Now He Researches Snapping Shrimp

Jason Dinh’s research career began unintentionally with a semester at Duke’s Marine Lab. A current fourth-year PhD candidate in Duke’s Biology Department, Dinh ventured to the Marine Lab for a mental reset in the spring of his sophomore year as a Duke undergraduate. “While I was there, I realized that people can just get paid to ask questions about how the world works,” Dinh told me, “And I really didn’t know that was a thing that you could do.” Maybe this is what I want to do, he thought.

Jason Dinh, fourth-year PhD candidate in Duke Biology Department

Dinh spent his remaining undergraduate summers investigating the impacts of soundscapes on oyster and fish larvae development. Now, he studies snapping shrimp – a small oceanic species that is “one of the biggest sound producers in the ocean,” bested only by toothed whales.

Dinh first became aware of snapping shrimp during his undergraduate research. He told me that you can find snapping shrimp “basically anywhere, from the equator up to Virginia or maybe North Carolina.” While conducting research on ocean sounds and oyster and fish larvae, Dinh noticed the frequent snapping sounds of the snapping shrimp when he placed underwater microphones. “We didn’t really know what they were doing,” Dinh said.

An image of a species of snapping shrimp like Dinh works with.

The male snapping shrimp is asymmetrical with one very large claw and one that is regular-sized. The large claw has a tiny hook on the end and when the shrimp clamps down or “snaps” the claw, the top half latches into the bottom, shooting out an air bubble at sixty miles per hour that “essentially boils the water behind it,” producing the loud snapping noise in its wake. When many shrimp are snapping at once, it sounds almost like the frying grease when cooking bacon, Dinh tells me. (Click here to watch a video of the snapping shrimp in action.)

At first, researchers suspected the bubble from the snap was a means of stunning prey, but “It turns out that snapping shrimp also fight each other,” Dinh said. And when fighting, male snapping shrimp shoot the air bubbles at one another. The bigger the shrimp’s body size, the larger the snapping claw and the louder the snapping sound.

An image of two snapping shrimp facing off.

Going into his PhD, Dinh wanted to continue his undergraduate work in acoustics and figure out novel ways animals were producing sounds. His investigation of the snapping shrimp took him in new directions, however. Through his projects, Dinh has conducted work on the costs and benefits that keep the claw size as an honest indicator of shrimp size in competitions and approached a plethora of questions from the physiological and physical mechanisms of sending and assessing snaps, up to the evolutionary implications of the sexual selection for claw size.

“I don’t think I really knew I wanted to do research until right before I applied for grad school,” Dinh said at the beginning of our conversation. He remembers being a child curious about nature and bringing in “hundreds of cicadas” and “random critters into the house.” A few decades later and his research is centered on living creatures, which is both a rewarding and tricky process.

“Live animals are going to do what live animals want to do,” Dinh stated simply. “One thing my advisor always tells us is that you don’t get to tell the animal what to do, it tells you what you are going to do.” This has certainly held true for Dinh. While he has had many detailed and well-planned experimental ideas, he says he’s ultimately ended up doing what the “animals told him they were willing and happy to do in the lab.” However, along the way Dinh basks in the “joys in tiny discoveries in the process of research.”

I asked Dinh how he ended up at Duke in the first place and why he chose to stick around for his PhD. “So I ended up at Duke for undergrad because I really liked basketball, which is a really bad reason to choose a school.” But ultimately, this choice “paid off really well because my first year was the last year we won the National Championship,” Dinh said. He traveled to Indianapolis for the event which he says was the “best basketball game of [his] life.”

Dinh decided to do his PhD at Duke because of how deeply he admires his advisor, Sheila Patek (PhD), as a scientist. “I think she’s just a wonderful, passionate, passionate defender of basic science and just doing science because more knowledge is good for society,” Dinh elaborated, “Sheila’s also a staunch and fearless advocate for her students.” Though Dinh considers himself an “outlier” in the lab – primarily a behavioral ecologist in a lab of researchers investigating biomechanics – the way that Patek approaches science is the way that he wants to approach science as well.

Like Alice falling down the rabbit hole in Alice in Wonderland, Dinh compares the diving explorations of science as being a “professional rabbit holer.” Science consists of picking questions further and further apart and leaning into research findings to tunnel into topics.

“I feel like science is being a professional rabbit holer,” Dinh stated. While Dinh is on the pursuit of the weapon size and fighting strategies of snapping shrimp, he doesn’t know exactly where he wants to head next, following the completion of his PhD. Like the snapping shrimp that collect information about their opponents to make an informed decision about engaging in fights, Dinh says he is conducting a sort of Bayesian method of his own. He’s assessing his experiences as he goes and sorting out the right next step for him.

A fan of the meditative art of writing, long morning walks with his dog, and reality TV, Dinh appreciates being “on the frontier of what we know” and is sure to let his deep-rooted curiosity about the natural world continue to guide him.

By Cydney Livingston

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

How did it get up there?

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

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

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

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

A toothed whale clears its blowhole. Photo by Friedrich Frühling

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

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

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

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

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

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

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

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

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

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

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

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

Read more about weird whale skulls.

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

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

Post by Marie Claire Chelini PhD, Duke Biology

Tracking Tiny Moving Targets

This squiggly line shows the path taken by a snippet of DNA as it might move around within the soupy interior of a cell. Duke’s Kevin Welsher and colleagues have developed a technique that turns a microscope into a ‘flight tracker’ for molecules, making it possible to follow the paths of viruses and other particles thousands of times smaller than the period at the end of this sentence. Until now, such techniques have required particles to be tethered to make sure they stay within the field of view. But the Welsher lab has developed a way to lock on to freely moving targets and track them for minutes at a time.

Researchers created a tiny circuit through a single water molecule, and here’s what they found

Graphic by Limin Xiang, Arizona State University

Many university labs may have gone quiet amid coronavirus shutdowns, but faculty continue to analyze data, publish papers and write grants. In this guest post from Duke chemistry professor David Beratan and colleagues, the researchers describe a new study showing how water’s ability to shepherd electrons can change with subtle shifts in a water molecule’s 3-D structure:

Water, the humble combination of hydrogen and oxygen, is essential for life. Despite its central place in nature, relatively little is known about the role that single water molecules play in biology.

Researchers at Duke University, in collaboration with Arizona State University, Pennsylvania State University and University of California-Davis have studied how electrons flow though water molecules, a process crucial for the energy-generating machinery of living systems. The team discovered that the way that water molecules cluster on solid surfaces enables the molecules to be either strong or weak mediators of electron transfer, depending on their orientation. The team’s experiments show that water is able to adopt a higher- or a lower-conducting form, much like the electrical switch on your wall. They were able to shift between the two structures using large electric fields.

In a previous paper published fifteen years ago in the journal Science, Duke chemistry professor David Beratan predicted that water’s mediation properties in living systems would depend on how the water molecules are oriented.

Water assemblies and chains occur throughout biological systems. “If you know the conducting properties of the two forms for a single water molecule, then you can predict the conducting properties of a water chain,” said Limin Xiang, a postdoctoral scholar at University of California, Berkeley, and the first author of the paper.

“Just like the piling up of Lego bricks, you could also pile up a water chain with the two forms of water as the building blocks,” Xiang said.

In addition to discovering the two forms of water, the authors also found that water can change its structure at high voltages. Indeed, when the voltage is large, water switches from a high- to a low-conductive form. In fact, it is may be possible that this switching could gate the flow of electron charge in living systems.

This study marks an important first step in establishing water synthetic structures that could assist in making electrical contact between biomolecules and electrodes. In addition, the research may help reveal nature’s strategies for maintaining appropriate electron transport through water molecules and could shed light on diseases linked to oxidative damage processes.

The researchers dedicate this study to the memory of Prof. Nongjian (NJ) Tao.

CITATION: “Conductance and Configuration of Molecular Gold-Water-Gold Junctions Under Electric Fields,” Limin Xiang, Peng Zhang, Chaoren Liu, Xin He, Haipeng B. Li, Yueqi Li, Zixiao Wang, Joshua Hihath, Seong H. Kim, David N. Beratan and Nongjian Tao. Matter, April 20, 2020. DOI: 10.1016/j.matt.2020.03.023

Guest post by David Beratan and Limin Xiang

Combining Up-Close Views of Science, Nature With the Magic of Light

Zinnia stamen by Thomas Barlow, Duke University

Thomas Barlow ’21 finds inspiration in small everyday things most people overlook: a craggy lichen growing on a tree, a dead insect, the light reflected by a pane of glass. Where we might see a flower, Barlow looks past the showy pink petals to the intricate parts tucked within.

The 20-year-old is a Duke student majoring in biology. By day, he takes classes and does research in a lab. But in his spare time, he likes to take up-close photographs using objects he finds outside or around the lab: peach pits, fireflies. But also pipettes, pencils.

A handheld laser pointer and flitting fireflies become streaks of light in this long-exposure image in Duke Forest. By Thomas Barlow.

Barlow got interested in photography in middle school, while playing around with his dad’s camera. His dad, a landscape architect, encouraged the hobby by enlisting him to take photos of public parks, gardens and playgrounds, which have been featured on various architects’ websites and in national publications such as Architecture Magazine. But “I always wanted to get closer, to see more,” Barlow said.

In high school he started taking pictures of still lifes. But he didn’t just throw flowers and fruit onto a backdrop and call it art. His compositions were a mishmash of insects and plants arranged with research gadgets: glass tubes, plastic rulers, syringes, or silicon wafers like those used for computer chips.

“I like pairing objects you would never find together normally,” Barlow said. “Removing them from their context and generating images with interesting textures and light.”

Sometimes his mother sends him treasures from her garden in Connecticut to photograph, like the pale green wings of a luna moth. But mostly he finds his subjects just steps from his dorm room door. It might be as easy as taking a walk through Duke Gardens or going for one of his regular runs in Duke Forest.

Having found, say, a flower bud or bumblebee, he then uses bits of glass, metal, mirrors and other shiny surfaces — “all objects that interact with light in some interesting way” – to highlight the interaction of light and color.

“I used to be really obsessed with dichroic mirrors,” pieces of glass that appear to change colors when viewed from different angles, Barlow said. “I thought they were beautiful objects. You can get so many colors and reflections out of it, just by looking at it in different ways.”

In one pair of images, the white, five-petaled flowers of a meadow anemone are juxtaposed against panels of frosted glass, a pipette, a mechanical pencil.

Another image pair shows moth wings. One is zoomed in to capture the fine details of the wing scales. The other zooms out to show them scattered willy-nilly around a shimmering pink circle of glass, like the remnants of a bat’s dinner plate.

Luna moth wings and wing scales with dichroic mirror, Thomas Barlow

For extreme close-ups, Barlow uses his Canon DSLR with a microscope objective mounted onto the front of a tube lens. Shooting this close to something so small isn’t just a matter of putting a bug or flower in front of the camera and taking a shot. To get every detail in focus, he takes multiple images of the same subject, moving the focal point each time. When he’s done he’s taken hundreds of pictures, each with a different part of the object in focus. Then he merges them all together.

At high magnification, Barlow’s flower close-ups reveal the curly yellow stamens of a zinnia flower, and the deep red pollen-producing parts of a tiger lily.

“I love that you can see the spikey pollen globules,” Barlow said.

Stomata and pollen on the underside of a tiger lily stamen, by Thomas Barlow

When he first got to Duke he was taking photos using a DIY setup in his dorm room. Then he asked some of the researchers and faculty he knew if there was anything photography-related he could do for their labs.

“I knew I was interested in nature photography and I wanted to practice it,” Barlow said.

One thing led to another, and before long he moved his setup to the Biological Sciences building on Science Drive, where he’s been photographing lichens for Daniele Armaleo and Jolanta Miadlikowska, both lichenologists.

“A lichen photo might not seem like anything special to an average person,” Barlow said. “But I think they’re really stunning.”

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