studentspotlight

Eliza Diggins

March 16, 2022

Eliza Diggins

Eliza Diggins is a sophomore working on a double major in applied mathematics and physics. As a freshman, she participated in the Science Research Initiative (SRI) program, sponsored by the College of Science. The SRI puts students in a lab to do research as soon as they arrive on campus. After Eliza was admitted to the program, she began working with Fred Adler, professor of mathematics and of biology in the Department of Mathematics and in the School of Biological Sciences.

We caught up with Eliza for a chat.

How did you become interested in both math and physics?
Math and physics have both had a special place in my heart for most of my life. Even back in elementary school, math and science always held my attention more than other subjects. I began to actively study physics in middle school and never looked back.

Could you tell us about the kind of research you did in the SRI program with Dr. Adler?
I worked with Professor Adler modeling how COVID-19 virions move in the human airway. We constructed mathematical descriptions of the fluid motion to predict how differences in lung physiology would affect the distribution of virion absorption and, consequently, the severity of infection.

What do you enjoy about being at the U and in the Math and Physics Departments?
I enjoy being a part of both departments because the classroom environment is very positive, and the professors are always willing to engage with students. In addition to my time spent in the classroom, I teach English as a Second Language to adult students at the Guadalupe School.

What has it been like to work on your degree during the pandemic?
Working on a degree during a pandemic has been both a blessing and a curse. I've had more time to focus on my research and learning on my own time, which has left me very well prepared for future endeavors from an academic standpoint. Unfortunately, that additional time comes at the expense of many of the quintessential experiences of college.

Any career plans after you graduate?
My short-term plans are largely focused on getting into a good graduate program to study theoretical physics. In the long run, I'd like to have a career in academia so that I can focus full time on my research interests.

Any hobbies or interests outside of math and physics?
Outside of academic pursuits, I spend a lot of time outdoors. I'm passionate about hiking and running and spend a lot of time white-water rafting with my family. I also have a passion for herpetology, and I own two poison dart frogs!

by Michele Swaner, first published @ math.utah.edu

Sarmishta Kannan

February 23, 2022

Sarmishta Kannan

In the entrance of the Eccles Health Sciences Education building.

For Sarmishta Diraviam Kannan, HBS’17, the journey to her “dream school” – the University’s School of Medicine – spanned about 25 years and some 8,780 miles.

Sarmishta was born in Tamil Nadu, India, which is located on the southern tip of the Indian sub-continent. In addition to the long history of the Tamil people, Tamil Nadu is famous for its temples, festivals, and celebration of the arts.

When Sarmishta was just nine years old, her family immigrated to the United States. They settled in Boston where her father worked for GE Healthcare. In 2008, the family moved to Salt Lake City, near the corporate headquarters of GE Healthcare, while her father continued his career with the company.

Sarmishta, who was then 12 years old and in junior high school, was still mastering English as a second language and adjusting to social norms and public education systems in America.

It was a difficult time for Sarmishta, but her “dream” was beginning to form.

Sarmishta graduated from Hillcrest High School, in Midvale, in 2013 with the International Baccalaureate (IB) diploma.

“The IB diploma is a rigorous program, and I was the only one to take the higher-level courses in all three sciences of physics, chemistry and biology,” says Sarmishta. “It was through the IB program that I found my passion in the sciences, especially biological sciences, and completing the IB program prepared me well for college.”

Sarmishta decided to attend the U as an undergraduate because of the abundance of research opportunities and the Honors degree option in Biology which gave her the chance to perform long-term research that culminated with an Undergraduate Thesis. Plus, it put her in close proximity to the School of Medicine.

The “dream” was clear now and within reach.

“The Honors thesis requires involvement in research that finishes with writing a paper on a particular research project. That experience was valuable to me as I got the opportunity to be involved in a research project from start to finish,” says Sarmishta.

She worked with Dr. Kevin Jones at the Huntsman Cancer Institute to help discover the roles that lysosomes and autophagy play in alveolar soft parts sarcoma, clear cell sarcoma, and synovial sarcoma.

“In the Jones lab, it was fascinating for me to see how researchers used experimental data to understand cancer biology. So, I decided to pursue sarcoma research for my thesis,” says Sarmishta.

“I investigated the hypothesis that Alveolar Soft Parts Sarcoma (ASPS) and Clear Cell Sarcoma (CCS) morphology is attributed to lysosomes and that these cancers up-regulate autophagy genes using autophagy as a survival mechanism,” says Sarmishta.

“I learned to design investigations and troubleshoot various lab protocols to gather data and test the hypothesis. Critically analyzing the data supported the hypothesis that ASPS and CCS contain abundant autophagic lysosomes. However, it raised further questions indicating more research was necessary to better understand autophagy’s role in ASPS and CCS.”

“Writing my thesis taught me to build an evidence-based argument based on my data, critically analyze the work of others, synthesize new ideas for further research, and effectively communicate complex topics,” says Sarmishta.

Her thesis abstract was published in the 2016 University of Utah Undergraduate Research Journal. She also presented her thesis to Utah legislators at the Research on Capitol Hill event in 2017 and at Undergraduate Research Symposiums in 2016 and 2017.

After graduating with an Honors degree in Biology, she continued to work in the Jones lab as a full-time Lab Technician before starting medical school. She worked on various projects including writing a review manuscript on sarcomagenesis, titled Genetic Drivers and Cells of Origin in Sarcomagenesis, which was published in early 2021 in the Journal of Pathology.

She also worked on a project that focused on modeling synovial sarcoma metastasis in mouse models. Sarmishta was listed as a co-author on that paper and was published in the Journal of Experimental Medicine.

In the meantime, Sarmishta applied to the School of Medicine in 2019 and in 2020 and was accepted in 2020.

Finally, her “dream” was realized.

Today, Sarmishta is about halfway through her second year of the MD program at the University’s School of Medicine.

“It has been a very fulfilling experience so far! I am grateful to have the opportunity to follow my passion, learn about the human body, help and support people going through healthcare challenges. I am excited to start my clinical years where I get to rotate through various specialties in the hospital and apply all the knowledge I have been learning to patient care,” says Sarmishta.

In addition to school, she enjoys reading, painting, watching movies and singing.

In fact, Sarmishta is a classically-trained Carnatic singer. Carnatic music is a traditional system of music from India that provides a nearly limitless array of melodic patterns. It emphasizes vocal performance.

“I started singing when I was five and my parents enrolled me in Carnatic music classes in India. I continued my training after moving to the United States,” says Sarmishta.

“I perform publicly at the local Hindu Temple and at Indian festivals. One of my most cherished experiences was performing a Hindu song at the 6th Parliament of World Religions event, that was held in Salt Lake City.”

Sarmishta is scheduled to complete the MD program in 2024.

“A new dream is already forming,” she says.

 

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Sahar Kanishka

April 30, 2021

Undergraduate Research Award

Sahar Kanishka

Biology major receives 2021 Outstanding Undergraduate Researcher Award.

Sahar Kanishka remembers daily where her family came from, where they are now, and what opportunity there is for her at the School of Biological Sciences (SBS).

“I’ve always wanted to be a doctor ever since I was younger,” she recently explained in a video interview. “Because my family’s from Afghanistan and they actually fled from the Soviet invasion, they were telling me how the medical resources over there were very scarce when they were escaping. Like things we take for granted here [in the United States]. I want to be able to give back in some way. And that’s my way of giving back, becoming a doctor and contributing what I’ve learned here.”

What Kanishka, now in her junior year as an honors student, is learning happens largely in the Gagnon lab at the SBS where she and her colleagues are studying vertebrate lineage and cell fate choice along with cell signaling and genome engineering. Their subject model is the living zebrafish with which they are attempting to answer the question of how biology builds an animal with millions of cells. The question is complicated by the fact that those millions of cells are continually sharing information while shape-shifting at the same time.

Zebrafish

A living organism is the culmination of science turning chaos and cacophony into a kind of marvelous symphony. Using CRISPR-Cas9 gene-editing technology, the Gagnon lab is busy marking cells with a genetic barcode that could later be used to trace the lineage of cells that in the zebrafish are similar to other vertebrates, including humans.

The micro “scissors” of CRISPR is no longer just being used to decode the genome, but to make a version, readable to humans, of what cells are doing in real time and how. It’s research that’s contributing to a sea change in genomic studies, and Kanishka is there at the bench experiencing it firsthand. The way Jamie Gagnon, Principal Investigator who holds the Mario Cappechi Endowed Chair at SBS, puts it, the research Kanishka is doing “may lead to a holy grail method for developmental biology—the ability to record developmental history, in living animals, with molecular and spatial resolution.”

Little wonder then that the Undergraduate Research Program at the University of Utah chose Kanishka for this year’s award. In his nomination letter Gagnon, who referred to Kanishka as having “transitioned quickly into an independent scientist," also wrote that he has been “impressed with Sahar’s poise, focus and commitment to research over the last year, which has been particularly challenging for our undergraduate researchers… . Sahar is already the face of STEM research in the College.”

Kanishka’s journey at the U threaded through ACCESS, a signature program of the College of Science. It was a scholarship and mentorship experience that led to re-figuring what research could be. Instead of working primarily on a computer in isolation and doing anatomy lessons from a book, ACCESS and SBS provided her with a hands-on approach in its full cadaver lab. As a pre-med student hoping to earn a joint medical degree and doctorate, Kanishka’s turn as a teaching assistant to professor Mark Nielsen gave her added invaluable experience. ACCESS also gave her a practical skill set, like creating her first research poster and then presenting it publicly.

The ACCESS program

The same has been true in the Gagnon lab where she says you are free to mold your research experience to your own expectations. Research at the U “fosters an environment of curiosity of real research. It’s really beautiful,” she says, “to have someone [like Gagnon] believe in you like that.” This, she concedes, in spite of feeling at times like an imposter as the child of an immigrant family and as a woman. She’s had to “learn through lots of struggles.”

Some lessons from those struggles have been hard won. “You can’t just put science in a box and tell it what to do,” she explains. “I have to allow it the freedom to seek to understand the world rather than to just understand me.” Her joint undergraduate degree in business administration speaks to Kanishka’s sense of the intersectionality of all learning. She was especially impressed with a recent visit by Reshma Shetty, the inaugural SBS Distinguished Lab Alumni who worked with Baldomera “Toto” Olivera in his lab and is a co-founder of Boston-based Gingko Bioworks, a bio-engineering start-up.

But the ballast in Kanishka’s life--both that of her academic career’s and that of her personal story’s--continues to be family. That includes not only her younger sister and parents here in Utah, but also her extended family in Afghanistan and beyond. “I hate that we’re separated by distance,” she says, referring to her overseas cousins, aunts and uncles as “my other parents and siblings. I owe everything to them. They mean everything to me.”

Until she and her extended family are all at least on the same side of the globe, Kanishka has both advice and a caution for her undergraduate colleagues. “Figure out if you want to do something by actually doing it,” she advises, recommending internships for high schoolers not bound for college, including through a program she helps facilitate as a volunteer called Talent Ready Utah. “College can be a business,” she warns, “pumping out students” for a job market they may not resonate with or even prosper in.

But Sahar Kanishka is optimistic about things as well. When asked about the pandemic and the social and economic upheaval, she proffers a winning smile, while adding, “I’m excited to see how college will change and adapt.”

 
by David Pace
 

Beckman Abstract

  • Lineage tracing in zebrafish with CRISPR prime editing (S. Kanishka)
    All embryos develop from a single cell. We use lineage tracing to map the relationships between individual cells and back to the initial founding cell. These lineage trees can help us understand how cells acquire their fates during normal development, and how that can go wrong in human disease. An emerging method for lineage tracing in embryos uses cellular barcodes. Cellular barcodes individually tag cells with a unique set of mutations specific to that cell. As cell divisions occur, the barcode is passed on to the progeny cells and a lineage tree can constructed based on cells that share similar barcodes. The CRISPR-Cas9 system for gene editing is an ideal tool for creating a huge diversity of cellular barcodes in embryos. However there are limitations with CRISPR-Cas9, including unpredictable indel formation and difficulties in recovering barcodes from cells. In this project, a modified CRISPR system known as prime editing will be applied in zebrafish, and utilized for lineage tracing. Prime editing allows for precise genome editing by inserting user-specified genetic sequences at a target site in the genome. I hypothesize that we can use prime editing to insert a huge library of user-specified barcodes into the genome of developing zebrafish. Because these barcodes are defined by the experimenter, they can be recovered at the end of the experiment using RNA in situ hybridization. In principle, lineage tracing with prime editing will allow us to discover the spatial arrangement of related cells in intact embryos and tissues. We hope to use lineage tracing with prime editing to understand the mechanisms of heart regeneration in zebrafish.

2021 Churchill Scholar

April 8, 2021

Six in a Row!

Isaac Martin brings home the U's sixth straight Churchill Scholarship.

For the sixth consecutive year a College of Science student has received the prestigious Churchill Scholarship to study at the University of Cambridge in the United Kingdom. Isaac Martin, a senior honors student majoring in mathematics and physics, is one of only 17 students nationally to receive the award this year.

Martin’s designation ties Harvard’s six-year run of consecutive Churchill Scholars (1987-1992) and is second only to Princeton’s seven-year streak (1994-2000).

“Isaac’s recognition as a Churchill Scholar is the result of years of remarkable discipline and dedication to a field of study that he loves,” said Dan Reed, senior vice president for Academic Affairs.

Martin decided to apply for a Churchill Scholarship as a freshman, after meeting for lunch with Michael Zhao, a 2017 Churchill Scholar who unexpectedly passed away in 2018.

“I am positively delighted and quite flabbergasted to receive the scholarship,” Martin says, “but I wish I could phone Michael to thank him for making the opportunity known to me. His legacy lives on in the undergraduate program of the math department here at Utah, where many others like me have greatly benefited from the example he set.”

Martin, a recipient of an Eccles Scholarship and a 2020 Barry Goldwater Scholarship, remembers as a kindergartener trying to write down the biggest number in existence and, as an eighth grader, suddenly understanding trigonometry after hours of reading on Wikipedia.

“That sensation of understanding, the feeling that some tiny secret of the universe was suddenly laid bare before me – that’s something I’ve only felt while studying math and physics, and it’s a high I will continue to chase for the rest of my life,” he says.

Books by Carl Sagan and Jim Baggott also kindled his love of math and physics, and after several years of self-directed study in middle and high school and a year at Salt Lake Community College, Martin enrolled at the U as a mathematics and physics double major.

After early undergraduate experiences in the research labs of physics professors Vikram Deshpande and Yue Zhao, Martin found himself gravitating more toward mathematics. He completed a Research Experience for Undergraduates (REU) at UC Santa Barbara studying almost Abelian Lie groups, which have applications in cosmology and crystallography, under Zhirayr Avetisyan. This experience resulted in Martin’s first research paper. He later completed another REU at the University of Chicago.

“This research was incredibly rewarding because while it applied to physics, the work itself was firmly rooted in the realm of pure math.” Martin says.

Returning to Utah, Martin worked with professors Karl Schwede and Thomas Polstra to study F-singularities, and developed this work into a single-author paper and his currently-in-progress honors thesis with professor Anurag Singh.

“I would not be where I am today without the incredible faculty at Utah and their willingness to devote time to undergraduates,” Martin says.

At Cambridge, Martin hopes to study algebraic geometry, number theory and representation theory (“in that order,” he says) in pursuit of a master’s degree in pure mathematics.

“I’m particularly interested in learning as much as I can about mirror symmetry, which I intend to make my essay topic,” he adds. “I also plan to drink a lot of tea and to buy one of those Sherlock Holmes coats. I will also begrudgingly begin using the term ‘maths’ but I promise to stop the instant I board a plane back to the U.S. in 2022.”

After he returns from Cambridge, Martin plans to earn a doctoral degree in pure mathematics and enter academia, using his experiences in many different educational systems including U.S. and British public schools, homeschooling and online learning, to broaden opportunities for students from a diversity of backgrounds.

“My past has molded me into who I am today,” he says, “and I hope I can use my experiences to create programs in STEM for opportunity-starved students, whether they are held back due to non-traditional schooling or to socio-economic factors.”

 

by Paul Gabrielsen - First Published in @theU

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2021 Research Scholar

March 31, 2021

2021 Research Scholar

For Karrin Tennant, recipient of the 2021 College of Science Research Scholar Award, the never-ending story of environmental science has plenty of plot twists. A member of the Anderegg lab in the School of Biological Sciences (SBS) which studies the intersection of ecosystems and climate change, Tennant has been busy working in the area of nighttime water loss in plants. The work tests a major hypothesis in the field and has the potential to greatly advance our understanding of plant physiology. The award is given annually to the College’s most outstanding senior undergraduate researcher. Tennant will be honored at the College Convocation May 6th and receive a $1,000 award, a plaque commemorating this achievement, and a one-year membership in the American Association for the Advancement of Science (AAAS), which includes a one-year subscription to Science.

In his letter of support, Assistant Professor Bill Anderegg and Principal Investigator says, “Karrin has blown me away with her incredible independence, creativity, dedication, initiative, and intellectual maturity. Her Biology Honors research is incredibly exciting, eminently publishable, and on par with advanced and successful Ph.D. students I have mentored.”

Karrin Tennant

One of those plot twists includes nighttime transpiration through tiny pores known as stomata on the underside of tree leaves. Photosynthesis, the process by which green plants and some other organisms use sunlight to synthesize foods from carbon dioxide and water, clearly happens during the day. But why and how do trees like the Black Cottonwood in the Pacific Northwest, continue to draw H20 from the ground at night? "What's the ecological value of this happening?" Tennant asks. At night "can trees pull water from underground like a straw away from competitors?"

Answers to these questions have implications about how forests survive and thrive, especially during drought as the earth continues to warm globally. Tennant sees her work as multi-faceted ... and multi-disciplinary--narrative threads that tell the broader story of not only life systems, as in forests, but even larger systems, and not only ecological.

Tennant's minor in Ecology & Legacy Humanities, introduced to her by adjunct biology professor and Dean of the Honors College Sylvia Torti, extends the questions Tennant is addressing both in the field and in the lab. The intersection between biology and the humanities fosters empathy for the natural world that can inform public discourse as well as public policy that extends beyond scientific inquiry. This "leaning into the interdisciplinary," says Tennant, is what propels her learning at the University of Utah and what appears to be the foundation of an auspicious career later in forest ecology and related fields.

In the meantime Tennant pivots between a growth chamber adjacent to the SBS greenhouses and the lab downstairs. The samples she collects come from as many as thirty-five trees in various degrees of competition with each other for water. Using a Licor LI-6800 photosynthesis system which measures gas exchanges and fluorescence, she determines the flow of C02, O2 and H20 in and out of the leaf through the stomata. She and her team also conduct statistical tests using research software, initiating how the micro affects the macro of ecological systems.

A Texas native, Tennant was attracted to the U because of family in the area and, of course, the mountain environment. Along with her passion for science, she says, "they're what kept me here." Her ambition is to be a research professor someday, to "spread my knowledge and education as far as I can," and "to apply focused research to a much broader discussion."

That discussion has added to the story that Tennant is helping to author, and it seems to move with extraordinary balance and ease between more than one campus lab (she also works with SBS's Bryn Dentinger's fungi lab at the Natural History Museum of Utah), the forest field and the broad community contours represented by the humanities.

In her citation for the award, Dean Peter Trapa talked about Tennant's demonstrated "genuine wonder of the world around" her and her "thirst for knowledge." Her response to the award? "I am honored to be a woman in STEM and to follow the footsteps of other trailblazing female researchers."

 
by David Pace
 

Josh Carroll

February 23, 2021

 

Josh Carroll

Veteran To Janitor To Physicist, Via YouTube.

Josh Carroll volunteered for the U.S. Army before he finished high school. He did three tours of duty in Afghanistan. He worked as a janitor, among other jobs, between those tours. And in the library of the school he was cleaning, he found one book that rekindled his love of science and set his career on a new path.

The book?

Stephen Hawking’s A Brief History of Time.

“I began reading that every night just piece by piece, and it just slowly started to re-sink in, like just, oh my goodness, I’ve really missed this,” Carroll told me in a recent episode of the TechFirst podcast. “This is like, I love learning about it.”

That book re-opened his eyes.

And that love of learning was essential to Carroll’s path to achieving his dream.

Because Carroll had a problem. While as a kid he had always loved space and learning about the stars, he did not have the math and physics background to pursue a career studying them. Thanks to volunteering for three tours of duty, he had a 10th-grade math education and none of the prerequisites for advanced college courses in physics or astronomy. So after starting a general studies degree at New River Community College in Virginia he decided to do something radical about his passion: teach it to himself.

And, as featured by YouTube recently where I heard his story for the first time, Carroll’s teacher became videos. In a subsequent job as a security guard, online lectures in calculus and trigonometry filled the long hours between patrol rounds. Khan Academy helped, of course, and online lessons from college-prof-turned-internet-academic PatrickJMT (read Patrick: Just Math Tutorials) filled his nights.

Typically, however, as can be the case with many self-taught people, one critical thing slipped through the cracks. And it was only after he learned enough to apply for advanced studies at another university that Carroll discovered it.

“I went and applied to go to Radford University to get into their physics program and found out that I was missing the entire field, the entire course of trigonometry, which I didn’t even know … I didn’t know about it,” Carroll told me. “And so when I went to apply, they were like, ‘Oh, you didn’t take trig, you won’t be able to do our physics program.’”

That was three or four weeks before the semester started.

Carroll begged for an exception and promised to learn trigonometry in those three weeks, which the university granted. Then he crammed those weeks full of trig courses and videos, and ended up near the top of his class.

But it wasn’t without some adrenaline-pumping experiences.

“It was terrifying and exhilarating ... there were still some gaps,” Carroll says. “There was still some stuff at that time that I just didn’t know the rules, because I never had to apply them before. So it was also a lot of on-the-job training sort of a thing, where I would answer the question and then I’d ask one of my classmates, ‘Did I do this right?’ And they’d be like, ‘No, you need to do this with the sine function’ or something.’”

The result was a Bachelor of Science in physics and graduation from Radford University, and now Carroll divides his time between being a research and development engineer at Booz Allen and a master’s program in science and technology at the University of Utah that focuses on computational science and applied mathematics.

Not bad for someone working in post-school life as a janitor and security guard, and picking up a copy of A Brief History of Time by of the most famous physicists in history.

The most impressive part, of course, is the way that Carroll took control of his education and learned the knowledge that he needed on his own ... with the help of innumerable people who have shared their expertise online.

“I’m a big proponent of what I call the ‘democratization of learning,’ the decentralization of certain skill sets that you can learn, especially with computer science and coding, there’s so many things out there,” he says. “It’s a culture in computer science and coding. There’s GitHub and there’s online resources you can go to and absolutely pick skills up without the degree stamp.”

 - by John Koetsier first published by the Forbes.com

Vignesh Iyer

February 17, 2021

Vignesh Iyer

How did you become interested in math?
I’ve always gravitated toward STEM subjects even in elementary school. In college, I was exposed to various subjects but a common language each subject used was math. I’m a curious student and hungry to consume as much knowledge as possible. Math is a universal language that allows me to communicate with those in different fields and tells me how things work. Math has allowed me to explore other subjects and influences the way I interact with problems—from social sciences to applied sciences and engineering.

What kind of internship did you have while at the U? How did you get it?  What did you like about it?
At the beginning of 2020, I started interning for the Pharmacotherapy Outcomes Research Center (PORC) at the University of Utah College of Pharmacy. I applied using the College of Science internship page. I loved interning with the PORC because it allowed me to engage in computational mathematics, work in pharmacology, and interact with different data science and statistical analysis techniques. The team I worked with was performing a correlational study between medication types and bile-duct cancers. I was able to work on the entire computing and mathematics aspect of the study and learn some cool chemistry along the way. My favorite part of the internship was learning how to access databases and interpret the information using data analysis.

You finished your bachelor’s degree and are now in graduate school at the University of California, Irvine. What are you studying?
I entered UC Irvine last fall to begin my graduate studies in mathematics. Graduate school is a whole new challenge but it’s such an enjoyable challenge! My coursework has really taught me to think in new ways, and I’m able to explore new areas of mathematics. At the moment, my favorite class is abstract algebra because it’s a whole new area of math I’ve never been exposed to. I think the online learning part of graduate school has presented learning curves but they’re interesting learning curves.

I’d like to continue my graduate studies in mathematics and get a Ph.D., whether that’s returning to the U. or staying here at home in Southern California.

Is there an area of research that interests you in math? What do you like about it?
I’m interested in applied and computational mathematics. More specifically, I’m interested in applying computational mathematics to data science and machine learning. Applied and computational mathematics explores modeling and/or simulating systems using computers and various mathematical subjects, such as numerical methods, inverse problems, etc. What I like about applied and computational mathematics is that it allows me to be an all-around researcher and engage and contribute to different fields.

Long-term career plans?
After my graduate studies are completed, I’d like to pursue a career in robotics, focusing primarily on research and development in machine learning and artificial intelligence.

 - first published by the Department of Mathematics

Kyle Kazemini

February 10, 2021

Kyle Kazemini

How did you become interested in math?
I had an exceptional math teacher in high school. He had a great sense of humor and genuinely cared about all of his students. He also loved math and it was apparent in his teaching. His lessons were both fun and interesting. My enjoyment prompted me to take calculus and decide to study math further. My interest in math has only continued to grow.

How did you get your internship?
My math advisor, Angie Gardiner, told me about the College of Science Internship Program, and I applied for some positions. I was hired as a sports science intern for University of Utah Athletics. The people I worked with were great, and they all made me feel like part of the team.

My first project was to transform ForceDecks data. ForceDecks is a system for analyzing an athlete’s performance and to make assessments. The data from ForceDecks has a unique format that’s difficult to use in statistical programming languages like R and Python. My job was to develop a tool to fix this issue. I used Excel and VBA (Visual Basic for Applications) to create an automated tool for transforming the data into a user-friendly format.

My second project was to analyze the ForceDecks data. Now that it had a better format, I used R to analyze the data. The purpose of the analysis was to detect athlete asymmetries and possible injury risks. I generated statistics, tables, and plots. These projects made use of both my statistical and programming skills. I enjoyed this internship because I love applying math and computer science in interesting and impactful ways. Because of this internship, I have since become interested in quantitative medicine.

You’re involved in the Directed Reading Program. What is it? 
The Directed Reading Program is a mentoring program between graduate and undergraduate students, who work together on a reading project in mathematics. Any student can sign up for the program, regardless of their level in math. I heard about it through Math Department announcements, and I’m so happy I did. My graduate student mentor is awesome! We’ve read about differential equations and basic mathematical biology. Currently, we’re reading about partial differential equations.

What year are you?  
I’m a junior and plan on graduating in the spring of 2023. I’m taking an extra year since I’m doing a double major with computer science. My interest in computer science started when I took some CS courses as part of my math major. After learning some of the basics of CS, I began to wonder what was out there. Since then, I’ve become excited about theoretical computer science, as well as image processing and computer vision. Studying computer science has made me better at math and vice versa. Although math is the subject I love most, I think studying CS gives me a different perspective on mathematical problems. I also love learning about computing for its own sake.

What about career plans? 
I’m planning on doing a Ph.D. in math, but I’m still narrowing down my research interests. I’m deciding between pure and applied math because I enjoy things like applied mathematical biology, but I also just love math problems on their own. In addition to math bio, I’m interested in partial differential equations. I’m excited to learn about the theory behind PDEs, including real analysis, functional analysis, and Sobolev spaces.

Hobbies or interests outside of math?
I started studying Muay Thai (Thai boxing) when I was 13. Muay Thai is like kickboxing, except with elbows and knees. I was taking classes at a gym for about three years, but now I do it just for fun/exercise at home on a punching bag. I think martial arts are awesome for learning things like discipline and self-confidence.

I also love film—my favorite film is Good Will Hunting, which is pretty typical for a math nerd! I love it because it has a math genius, a great love story, and it’s about triumphing over difficult challenges. I enjoy most film genres—anything from romance to horror to documentaries.

I’m new to snowboarding, and I really like it. My favorite resort (for now) is Brighton. Currently, my favorite video game is CSGO(Counter-Strike: Global Offensive). I don’t play a lot of games because school keeps me busy, but in the past I’ve loved playing Skyrim, Call of Duty, and Halo.

I’ve wanted to build my own computer for years, and I finally did it for the first time a few months ago. I use it for school, work, and for intensive tasks that my laptop just can’t handle. Building it made me really happy!

 - first published by the Department of Mathematics

Brennan Mahoney

February 9, 2021

Brennan Mahoney

“As a child I always seemed to have an interest in animals,” says Brennan Mahoney, HBS’20, “and  originally  I wanted  to  be  a   veterinarian!”     Fate, however, would intervene for this Sandy, Utah native.

When he was ten years old Mahoney’s father had a massive heart attack in the left anterior descending artery (LAD), what’s colloquially called the “widow-maker” because when it is blocked it often results in the patient’s death. His father survived thanks to the “herculean efforts,” of the medical team.

“The work of the doctors and how they treated my family throughout the period of his recovery,” he says, “… turned my interests in biology towards its applications in the field of medicine.” Mahoney’s father would eventually receive a heart transplant nearly two years to the date of the attack, and Mahoney would later enroll in pre-med at the University of Utah where, when he’s not studying, he enjoys playing the guitar and piano, cooking, hiking, (“This is Utah, of course,” he says) … and following Ute football.

The summer after his freshman year, Mahoney worked toward his certification as a nursing assistant (CNA) so that he could start gaining clinical experience. “I worked as a home health aide in many different contexts,” he explains, “but mostly dealt with people who had neurological disorders or injuries.” It was during this time that he met a client who, prior to his injury, had worked as a researcher, and the experience pushed Mahoney to look for opportunities in a neuroscience lab. At the same time, Mahoney also worked as a tutor at West High School in Salt Lake City.

Enter Sophie Caron, professor in the School of Biological Sciences who at the time held the endowed Mario Capecchi Chair, named after Utah’s Nobel laureate who holds joint appointments in SBS and Human Genetics at the U. Caron’s lab studies multisensory integration (MI), a process by which brains integrate sensory information into a comprehensive picture of their environment.

The Caron lab, 2020

“For the study of this,” reports Mahoney who graduated with honors last summer but continues working in the Caron lab as a technician, we “used a brain area known as the mushroom body of [the fruit fly] D. melanogaster as a model.” The Caron team characterized the connection of neurons from multiple sensory modalities using a technique known as GFP reconstitution across synaptic partners or GRASP for short. “With knowledge of the patterns underlining MI, this logic could be applied to more complex brains,” says Mahoney, including, potentially, the human brain.

The research culminated in a first publication for Mahoney and his undergraduate colleague Miles Jacob, also credited as a co-author. The article, which made the cover of the journal Cell Reports highlights fundamental differences in the way associate brain centers, notably the mushroom body, integrate sensory information and converge in higher order brain centers. The findings are built  on previous work from the Caron lab that described a pathway conveying visual information from the medulla to the ventral accessary calyx of the mushroom body. “[O]ur study,” reads the article abstract, “defines a second, parallel pathway that is anatomically poised to convey information from the visual system to the dorsal accessary calyx.”

It is these kinds of scientific findings that inspire a young researcher like Brennan Mahoney to keep going. His ambition, in fact, is to apply to an MD/PhD program where he can continue in research that can help health professionals practice the good work that he witnessed first-hand when his father was singularly under their care.

"The efforts of my father's medical team allowed him to live so that he could continue to raise me and my two brothers and continue to live a happy and full life to this day. I hope to be able to help people in that same capacity, be it through direct patient care or through the findings of my future research."

The School of Biological Sciences regularly grants the Research Scholar Award to deserving undergraduate researchers like Brennan Mahoney. You can support these scholarships through a donation here.

by David Pace

Sonia Sehgal

December 1, 2020

Sonia Sehgal

 

U Biology's Sonja Sehgal accepted a Beckman Scholarship this past spring to add to the trove of awards that were already sitting on her academic “mantle” at home. Collective kudos include a Biology Research Scholars Award, a College of Science Scholarship and a Utah Flagship Scholarship.

The Beckman, however, is a step up from her other awards. It represents an unprecedented opportunity, perhaps found nowhere else, in which an undergraduate researcher can hone her craft at the bench and under extraordinary mentorship. The program is a 15-month, mentored research experience for exceptional undergraduate students in chemical and biological sciences, and Martin Horvath, associate professor in the School of Biological Sciences, will serve as her mentor. (Rory Weeks, undergraduate in the Department of Chemistry is the second U Beckman Scholar for 2020-21.) Each scholar receives a $21,000 research stipend to facilitate nine academic calendar months and two three-month summers of research experience. Recipients from around the nation participate in the prestigious Beckman Symposium each summer with one another. Their research began in June 2020 and will conclude in August 2021.

“I started out as a freshman in the ACCESS,” the biology senior explains, referring to the decades-long program hosted by the College of Science Program for Women in Math and Science. “Through this program, I was able to explore various fields in STEM which really kick-started my interest in pursuing biology! Joining the Horvath Lab further sparked my curiosity and has shown me that science goes beyond the stereotypical image of a “scientist.”

Tracking toward a career in medicine

Sonia Sehgal (undergraduate, Biology Research Scholar, Beckman Research Scholar) and Martin Horvath discuss the structure of MutY

Sonia Sehgal (undergraduate, Biology Research Scholar, Beckman Research Scholar) and Martin Horvath discuss the structure of MutY.

Sehgal is far from stereotypical, as a scientist or as an undergraduate. As a woman she knows that she’s in the minority as she works through her academic career and finally a professional career in STEM (Science Technology Engineering and Mathematics). As a complement to her academic career, the Sandy, Utah native has found a job as a University Ambassador. “The ambassadors work closely with the Office of Admissions to share our experience and bring a personal perspective to prospective U of U students,” she says. “When not giving tours or working recruitment events, we can be found having a good time with each other or,” she quips, “practicing walking backwards.”

Though Sehgal finds herself walking backwards while giving tours, she is definitely moving forward in her academic career. “I’m excited to continue doing research and I also plan on attending medical school after graduation. I want to learn about the various mechanisms that can cause diseases to present themselves in different forms across individuals. I want to use this platform to relay these findings with patients and create more representation in the field to strive for a more trusting and effective patient interaction.”

But before medical school, there’s research to be done, a focus in undergraduate education in the SBS that has arguably become the School’s signature.  “In the Horvath lab,” Sehgal explains about her work, “MUTYH is a DNA repair enzyme commonly related to diseases like cancer. I am currently finding the role of different biological probes to see how they can affect the activity of this enzyme. Learning more about regulating the activity of MUTYH will allow us to create better drug-targeting systems for cancer in the future.” What most people, even the scientifically-inclined, may not know about the model subject Sehgal is studying is that the MutY enzyme can be found in almost every living organism, yet there is still a lot we don’t know about it.

Hangin' out.

That’s something that inspires rather than discourages Sehgal who will graduate with her BS in 2021. With the help of the Beckman Scholarship, the mentorship of Horvath and the broad view of higher education she gets by being an ambassador, Sehgal finds her future as she tracks toward a career in medicine, promising. And true of all of accomplished undergraduate researchers of Sehgal’s stripe, she is poised for far more awards, and accomplishments.

“The Beckman experience has been going well,” she reports. “Because of the COVID-19 pandemic, the first stage has been virtual. I have been working on coding and molecular docking. However, I look forward to getting into the lab next semester and start testing!” Of Sehgal Horvath adds, "Sonia has a gift for finding a simple clear question to address in her science. She will go far. I feel really lucky to have had the chance to work with her these past years."

Asked what her interests and “likes” she doesn’t stray very far from her time in the lab. She likes rock climbing, dogs … and getting positive results for polymerase chain reaction (PCR), a method widely used to rapidly make millions to billions of copies of a specific DNA sample.

It’s the sort of thrill that allows a budding scientist, like Sonia Sehgal, to take a very small sample of DNA and amplify it to a large enough amount to study in detail.

Beckman Abstract

  • "Finding the role of biological probes on MUTYH activity,"(S. Sehgal)
    DNA damage is implicated in many cancers, such as colorectal cancer. One form of this damage occurs when guanine becomes oxidized to form 8-oxoguanine (OG). MUTYH is a base excision repair (BER) enzyme in humans that excises adenine (A) at OG:A lesions in DNA and thus prevents mutations that may arise after rounds of replication. Interestingly, both inhibition and overactivation of MUTYH can contribute to cancer-causing activity. In this project, MUTYH will be studied through computational modeling and an activity assay to find biological probes that can bind to the protein and affect its function. These probes can later be tested in animal models and may serve as the foundation for anticancer drug discovery. In addition, through analyzing the effect of biological probes on this enzyme, the BER pathway and the dual role of MUTYH in preventing and causing cancer can be further understood. Use of these probes to control MUTYH activity and BER overall can aid with creating more efficient drug targeting systems for cancer treatment in the future.

 

 

by David Pace