Research Scholar

2022 Undergraduate Research Scholar


Arches National Park, Moab, UT.

“My hero is my brother,” says Tiffany Do of her brother Anthony. “He’s the first in my family to graduate from the University of Utah. I look up to him because he’s gone through the trials in being a first-generation student and has helped me overcome some of those obstacles.”

Those obstacles can be daunting. Students who are first-generation college students talk about not knowing what even the right questions are to ask. Others talk about experiencing “imposter syndrome”—chronically feeling as though they are, any moment, about to be found out as someone who doesn’t belong in college.

So it makes sense that Do, who is a senior majoring in biology, would see her brother as a welcome guide to what can seem like an intimidating if not an impossible mountain to climb. But there were others who helped prepare this Taylorsville, Utah native to succeed at the college level, including her AP biology teacher Paige Ehler and her chemistry and biotechnology teacher Kristin Lillywhite who encouraged her to study the life sciences. And too, once Do arrived on campus, the ACCESS Scholars program also aided her in finding a home in STEM. The program, based in the College of Science, provided a scholarship as well as a network and experience with presenting her research at a symposium. As a senior she now works as an ACCESS mentor for others.

The results have been gratifying. Earlier this year Do had the experience of publishing her first paper in Intersect, an international Science, Technology, and Society research journal run by undergraduate students at Stanford University and supported by the Program in STS at Stanford. The journal welcomes undergraduate, graduate, and PhD submissions at the intersection of history, culture, sociology, art, literature, business, law, health, and design with science and technology, and its submissions are not exclusive to Stanford affiliates and generally span several continents.

Her article, co-authored with eight others, is titled Barriers to Accessibility of Algal Biofuels, a “companion piece to algal biofuel research with the goal of synthesizing relevant, contemporary considerations about how to expand algal biofuel to a modern society.”

That she is now published is perhaps a testament to the rich experience she’s had at the U in more than one research lab, including Dr. Catherine Loc-Carrillo’s Micro-Phage Epi Lab, Dr. James Van Etten Chlorovirus Lab and, currently, in the mycology lab under the direction of SBS’s Dr. Bryn Dentinger at Utah Museum of Natural History.

“I wasn’t sure what I wanted to research at first,” she concedes when she was first accepted at the U. “I was given a list of labs I could be a part of for my honors thesis and I reached out to the Dentinger Lab.” She simply found it fascinating that it was a lab that studied fungi.

“I have been gaining skills in culturing fungi, extracting nucleic acids, and quantifying the abundance and integrity of extractions,” she explains while currently conducting “a culture growth experiment grown under varying conditions that mimic ecological stressors, to induce a stress response in ectomycorrhizal fungi,” a form of symbiotic relationship that occurs between a fungal symbiont, or mycobiont, and the roots of various plant species.

 

Tiffany Do

“My hero is my brother,” says Tiffany Do of her brother Anthony. “He’s the first in my family to graduate from the University of Utah. I look up to him because he’s gone through the trials in being a first-generation student and has helped me overcome some of those obstacles.”

 

When asked to explain something interesting that most people don’t know about fungi, she explains how ectomycorrhizal fungi “form mutualistic relationships with trees. They play a key role in the nutrient cycle and there is still a lot to learn in understanding these organisms”

That said, she continues, “I’m still exploring what I really want to do once I graduate at the U.”

Meanwhile, Do is “paying it forward,” as she is “passionate about helping students especially first-gen in finding their place on campus.”

In addition to her ACCESS Scholarship she has seen nine other awards come her way, including most recently, a Research Scholars Award funded by the Mountaineer Endowment at the School of Biological Sciences. The award will help her this summer and fall semester complete her honors thesis.

Outside of class and lab work, Do is active in the Asian American Student Association (AASA), a student-led organization at the U that celebrates and promotes awareness of Asian cultures. “My family [members were] … refugees from Vietnam. This organization is a great way for me to connect with others that have similar backgrounds while also expanding my knowledge of other cultures.” She also takes advantage of Utah’s outdoor recreation as she loves to rock climb. This activity has proven a release from the trials of the pandemic which has affected her—as it has all of us.

“It’s hard to connect and keep in contact [with other people] when everything was online.” Related to that, her advice to other undergraduates or those considering attending college is “to reach out for help. As someone who has a hard time reaching out and sharing my struggles, I learned the hard way that it was necessary in my own life. There are people willing to be there for you, you just have to be willing to put in that trust. There are advisors and friends that are willing to listen.”

And for Tiffany Do, there’s also been her “hero” brother who graduated this year in mathematics and quantitative analysis of markets & organizations before securing work. He continues to help show his sister the way.

by David Pace, first published @ biology.utah.edu.

PAYTON UTZMAN

Payton Utzman


Many people wouldn’t see a direct line between working on John Deere tractors in rural Washington State and working on a DNA repair enzyme that functions to prevent cancer in humans.

But that’s the unlikely trajectory of Payton Utzman BS’22 who after graduating from the School of Biological Sciences headed off to join Nabla Bio at a 15,000-square-foot state-of-the-art wet laboratory and co-working space for high-potential biotech and life science ventures at Harvard University.

“We are a small team of nine scientists,” says Utzman, “working to synthesize therapeutic antibodies that are designed by artificial intelligence. It has been an amazing experience so far learning so many new skills and applying my undergraduate research experience in such a useful way.”

 

Payton Utzman BS'22

"The elegant and candid relationship between the structure of a protein and its corresponding function resembled my understanding of how metal parts assembled into an engine can produce incredible amounts of power."

 

Granted, it wasn’t a just a bounce from the spring seat of a John Deere tractor in Pullman, WA to Boston. But Utzman’s mechanically-oriented mind found a formidably gratifying corollary in biochemistry and structural biology in the Horvath lab. “I spent my childhood weekends helping my father and grandfather maintain various tractors and machinery. By the time I graduated high school, I was a self-taught mechanic, having restored an old pickup and rebuilding the engine through the guidance of a manual,” he remembers. “When I was exposed to the microscopic world of proteins, I was amazed by the enzymatic function of these biological machines. The elegant and candid relationship between the structure of a protein and its corresponding function resembled my understanding of how metal parts assembled into an engine can produce incredible amounts of power. I was then intrigued to learn more about the world of proteins and motivated to join Dr. Horvath’s research team in learning a protein mechanistically functions to repair DNA.”

In addition to making discoveries in DNA repair, the Horvath Lab, headed up by principal investigator and SBS Associate Professor Martin Horvath, applies structural methods and biochemistry to make discoveries in Chronic Neuropathic Pain that may lead to the use of non-opioid drugs. For the DNA repair project the lab studies the atomic resolution structure of MutY, [a human gene that encodes a DNA glycosylase], to understand how this enzyme recognizes and removes Adenine in OG:A base pairs.”

Says Utzman, “to better understand the mechanism of MutY, we are interested in learning about the evolution of this enzyme over millions of years. This led us to studying MutY enzymes from microbes at The Lost City Hydrothermal Field, a site similar to conditions in which life may have been conceived on Earth.” Samples from the Lost City have been collected by another SBS professor William “Billy” Brazelton, a unique partnership with marine biology and the unique mineral structures at the bottom of the Mid-Atlantic.

From these samples containing MutY-encoding genes, Utzman and his colleagues were excited to locate microbes that survive off of energy created from a geochemical reaction involving rocks and water, one of the discoveries that would lead to a better understanding of the nature of cancer.

“One of the most valuable assets of the University of Utah is the large amount of cutting-edge research occurring on campus,” says Utzman of his four years in Utah and his seven semesters as a teaching assistant. “I am so thankful for the research opportunities given to me by the U which have paved the way for me to actually have an impact on treating disease and impacting lives.”


Video on Payton Utzman’s 2020 research - “A Structural Analysis of the LC MutY Metagenome”.

Since exchanging leather work gloves in rural America for the rubber-gloved hands of the science researcher, Utzman has learned how to think critically and solve difficult problems. “I am passionate about getting kids interested in science and showing the amazing problems we can solve by blending scientific disciplines with creativity.”

Pursuant to that interest, Utzman worked together with other dedicated STEM students at the U to found the student-led STEM Tutoring program at the U to provide free tutoring to high school students in the greater Salt Lake City area. Not surprisingly, Utzman believes that the future of medicine is molecular. And while his professional ambition is to continue studying the function of proteins to one day help develop therapeutics to treat disease, he is also driven to outreach–-both in elevating the uninitiated to the scientific method (and critical thinking) and in science communication for the public.

The U graduate is quick to reference Dr. Anthony Fauci, the physician-scientist and immunologist serving as the director of the National Institute of Allergy and Infectious Diseases and the Chief Medical Advisor to the President. During the past three years the young scientist saw Fauci as the country’s undisputed spirit guide through the coronavirus pandemic. “His perseverance to help people and communicate scientific truth is inspiring,” says Utzman who finds the short-statured but brilliant (and reportedly fit) octogenarian as his “hero.”

For Utzman, the greatest advice he can give up-and-coming scientists at the U and elsewhere, is to learn how to learn. “The pandemic was a difficult time for all of us, and it was devastating that the virus affected so many lives. I think one of the biggest take-aways from the pandemic was the importance of scientific research and clear communication with the public. My advice for other students would be to learn how to read and to understand research publications.”

Embedded now in the next chapter of his life, Utzman has secured an excellent foundation. The Beta Theta Pi was a two-time Undergraduate Research Opportunities Program (UROP) Scholar, an SBS Research Scholar in 2021 and recipient of the Continuing Student School Scholarship in 2020. Additionally, he was lead author of a paper published in the University of Utah Undergraduate Research Journal.

Though far from the farm fields outside Pullman, Washington, the grease monkey in Utzman apparently is forever. He says that despite long days at the bench studying that “elegant and candid relationship between the structure of a protein structure and its corresponding function” he can still become absorbed by those other metal parts, the ones in trucks and motorcycles that coalesce so intricately–those other machines that can kick out a lot of power, but on the level of a combustion engine.

And this just in from Beantown: Payton Utzman is working on yet another engine–training for the Boston Marathon.

At age 81, Dr. Fauci–known to “kill it” on the treadmill at the gym–would be proud.

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Biomimetic Cephalopods

Biomimetic Cephalopods


Bringing ancient animals back to life—as robots.

In a university swimming pool, scientists and their underwater cameras watch carefully as a coiled shell is released from a pair of metal tongs. The shell begins to move under its own power, giving the researchers a glimpse into what the oceans might have looked like millions of years ago when they were full of these ubiquitous animals.

This isn’t Jurassic Park, but it is an effort to learn about ancient life by recreating it. In this case, the recreations are 3-D-printed robots designed to replicate the shape and motion of ammonites, marine animals that both preceded and were contemporaneous with the dinosaurs.

 

David Peterman

"Evolution dealt them a very unique mode of locomotion after liberating them from the seafloor with a chambered, gas-filled conch. These animals are essentially rigid-bodied submarines propelled by jets of water."

 

The robotic ammonites allowed the researchers to explore questions about how shell shapes affected swimming ability. They found trade-offs between stability in the water and maneuverability, suggesting that the evolution of ammonite shells explored different designs for different advantages rather than converged toward a single best design.

“These results reiterate that there is no single optimum shell shape,” says David Peterman, a postdoctoral fellow in the University of Utah’s Department of Geology and Geophysics.

The study is published in Scientific Reports and supported by the National Science Foundation.

Bringing ammonites to “life”

For years, Peterman and Kathleen Ritterbush, assistant professor of geology and geophysics, have been exploring the hydrodynamics, or physics of moving through the water, of ancient shelled cephalopods, including ammonites. Cephalopods today include octopuses and squid, with only one group sporting an external shell—the nautiluses.

Before the current era, cephalopods with shells were everywhere. Although their rigid coiled shells would have impacted their free movement through the water, they were phenomenally successful evolution-wise, persisting for hundreds of millions of years and surviving every mass extinction.

“These properties make them excellent tools to study evolutionary biomechanics,” Peterman says, “the story of how benthic (bottom-dwelling) mollusks became among the most complex and mobile group of marine invertebrates. My broader research goal is to provide a better understanding of these enigmatic animals, their ecosystem roles, and the evolutionary processes that have shaped them.”

Peterman and Ritterbush previously built life-sized 3-D weighted models of cone-shaped cephalopod shells and found, through releasing them in pools, that the ancient animals likely lived a vertical life, bobbing up and down through the water column to find food. These models’ movements were governed solely by buoyancy and the hydrodynamics of the shell.

But Peterman has always wanted to build models more similar to living animals.

Diagram of a Biometic Cehalapod.

“I have wanted to build robots ever since I developed the first techniques to replicate hydrostatic properties in physical models, and Kathleen strongly encouraged me as well,” Peterman says. “On-board propulsion enables us to explore new questions regarding the physical constraints on the life habits of these animals.”

Buoyancy became Peterman’s chief challenge. He needed the models to be neutrally buoyant, neither floating nor sinking. He also needed the models to be water-tight, both to protect the electronics inside and to prevent leaking water from changing the delicate buoyancy balance.

But the extra work is worth it. “New questions can be investigated using these techniques,” Peterman says, “including complex jetting dynamics, coasting efficiency, and the 3-D maneuverability of particular shell shapes.”

Three kinds of shells

The researchers tested robotic ammonites with three shell shapes. They’re partially based on the shell of a modern Nautilus and modified to represent the range of ancient ammonites’ shell shapes. The model called a serpenticone had tight whorls and a narrow shell, while the sphaerocone model had few thick whorls and a wide, almost spherical shell. The third model, the oxycone, was somewhere in the middle: thick whorls and a narrow, streamlined shell. You can think of them occupying a triangular diagram, representing “end-members” of different shell characteristics.

“Every planispiral cephalopod to ever exist plots somewhere on this diagram,” Peterman says, allowing the properties for in-between shapes to be estimated.

Once the 3-D-printed models were built, rigged and weighted, it was time to go to the pool. Working first in the pool of Geology and Geophysics professor Brenda Bowen and later in the U’s Crimson Lagoon, Peterman and Ritterbush set up cameras and lights underwater and released the robotic ammonites, tracking their position in 3-D space throughout around a dozen “runs” for each shell type.

No perfect shell shape

By analyzing the data from the pool experiments, the researchers were looking for the pros and cons associated with each shell characteristic.

“We expected there to be various advantages and consequences for any particular shapes,” Peterman says. “Evolution dealt them a very unique mode of locomotion after liberating them from the seafloor with a chambered, gas-filled conch. These animals are essentially rigid-bodied submarines propelled by jets of water.” That shell isn’t great for speed or maneuverability, he says, but coiled-shell cephalopods still managed remarkable diversity through each mass extinction.

“Throughout their evolution, externally shelled cephalopods navigated their physical limitations by endlessly experimenting with variations on the shape of their coiled shells,” Peterman says.

So, which shell shape was the best?

David Peterman

“The idea that one shape is better than another is meaningless without asking the question—‘better at what?’” Peterman says. Narrower shells enjoyed less drag and more stability while traveling in one direction, improving their jetting efficiency. But wider, more spherical shells could more easily change directions, spinning on an axis. This maneuverability may have helped them catch prey or avoid slow predators (like other shelled cephalopods).

Peterman notes that some interpretations consider many ammonite shells as hydrodynamically “inferior” to others, limiting their motion too much.

“Our experiments, along with the work of colleagues in our lab, demonstrate that shell designs traditionally interpreted as hydrodynamically ‘inferior’ may have had some disadvantages but are not immobile drifters,” Peterman says. “For externally shelled cephalopods, speed is certainly not the only metric of performance.” Nearly every variation in shell design iteratively appears at some point in the fossil record, he says, showing that different shapes conferred different advantages.

“Natural selection is a dynamic process, changing through time and involving numerous functional tradeoffs and other constraints,” he says, “Externally-shelled cephalopods are perfect targets to study these complex dynamics because of their enormous temporal range, ecological significance, abundance, and high evolutionary rates.”

Find the full study @ Nature.com.

 

by Paul Gabrielsen, first published in @TheU.