SRI Stories: Bones of the Past

April 22, 2024

SRI Stories: Bones of The Past Teach Us About The Present

April 22, 2024

Animal bones found in Utah’s caves are being used to study the impact of climate change on current animal communities. “I like to think of it as just one big puzzle,” Kasey Cole, Science Research Initiative (SRI) post-doctoral researcher and stream leader, states. “We can look at past records of animals and compare them to modern records of animals in that same area.”

Kasey has always been interested in studying the past. Originally from California, she graduated from California State University, Fullerton with a degree in anthropology. “I started as a history major,” Kasey says. “But I took an archaeology course, just as a general education requirement, and realized I can incorporate science and a more hands-on approach to learning about the past.” She then received her master’s from California State University, Chico, before coming to the University of Utah to get her PhD.

Left to right: Randall Irmis, NHMU’s curator of paleontology, Dr. Tyler Faith, NHMU’s chief curator, and caver Tom Evans examine and collect mammal bones on the floor of Tubafore Cave. Credit: Colin Stern

“My advisor, Jack Broughton, is a wonderful archaeologist, and he specializes in zooarchaeology of western North America, the exact thing I wanted to do,” says Kasey. “The anthropology program is unified by an evolutionary and ecological theoretical perspective, which is something I wanted to pursue more. I liked the connection with biology and the connection with ecology, so that’s what got me hooked. With my background in zooarchaeology, I study environmental change in the past.” Her expertise also includes paleoecology and she works as a research affiliate for the Natural History Museum of Utah (NHMU) and the Department of Anthropology. The Utah Cave Paleo project started when citizen cavers began noticing bones at the bottom of caves they were exploring.

Enter Tyler Faith, chief curator and Randy Irmis, curator of paleontology at NHMU. They were interested in the findings and have since collected many bones from caves throughout Utah over the past four years. Last year, Kasey was brought in because of her expertise in North American fauna in order to identify and research the bones.

“At the time, I was one of Tyler Faith’s graduate students,” says Kasey. “He brought me into this project — perfect for a postdoc,” and she has been studying the bones from these Utah caves ever since.

The collaboration between the NHMU, SRI, and local cavers made this research possible, which is providing a glimpse into the past. The bones range in age, from only a few weeks old to hundreds of years old. In terms of archaeology, the caves are a gold mine, allowing researchers to understand animal communities before anthropogenic climate change. The data from the bones are then compared to current animal communities to see how they are affected by climate change.

Kaedan O’Brien, lead author of published findings from Utah caves, and anthropology Ph.D. candidate at the U, holds up a mummified wood rat at an undisclosed cave in the House Range of western Utah. Credit: Randy Irmis

“I use the term paleoecologist,” says Kasey when describing herself. “I study old environments. And the way I do that is by studying animal bones from either archaeological or paleontological contexts. I then use those animals to help me reconstruct what the environment looked like.”

Kasey’s research is interdisciplinary, involving biology, ecology, anthropology, chemistry, climate science, among others. By studying past environments through animal bones, Cole can ask questions about the climate and geologic record and even questions about human behavior.

Some of the insights provided by this research include records of the now-extinct Southern Rocky Mountain Wolf, from bones recovered in a cave in the Uinta Mountain range. These wolves went extinct in the early 1900s, and records of them are rare because of how quickly they disappeared due to eradication by humans.

The cave bones also indicate the presence of wolverines, animals that are extremely rare in Utah, with only eight confirmed sightings in Utah since the 1970s. However, bones in these caves imply resident populations of the animal.

Kasey Cole posing next to special exhibit at the Natural History Musem of Utah.

The project is beginning to expand out of the Wasatch and Uinta and into other mountain ranges such as Utah’s House Range located in Millard County. Within some of these caves, the remains of bighorn sheep are being discovered, which is fascinating since there is no historical or modern record of them in the region.

The SRI students in Kasey’s lab not only assisted with this research, but they get to explore their own individual research projects.

“It’s associated with the stream, but they’re focused on questions they’re asking,” says Cole about student activities. “The students all learn the process of identifying bones, but at the end of the semester, I want them all to have an individual project idea, so they can conduct that research the next semester. All of these research projects have transferable skills that pre-med students or other students can take with them.”

Kasey is involved with SRI because she’s passionate about teaching, and SRI is a great place for students to learn research skills and gain access to research opportunities. “The thing that brings me the most joy is talking to students and teaching them,” she says. “Also breaking down these antiquated barriers for people in science and giving people opportunities.”

Kasey Cole’s research is currently on display at the Natural History Museum of Utah in a special exhibit which opened April 1 and will be on display until early September.

By CJ Siebeneck

SRI Stories is a series by the College of Science intended to share transformative experiences from students, alums, postdocs and faculty of the Science Research Initiative. To read more stories, visit the SRI Stories page.

Cool Science: Monitoring earthquakes in Utah

April 22, 2024

Monitoring these continual motions and shifts are the University of Utah Seismograph Stations. These stations, situated throughout Utah and surrounding states, pick up and report on regional earthquakes. With this data, scientists at the university are able to develop a better understanding of earthquakes in our area. This can then help reduce the risk from earthquakes in Utah thanks to their research, education, and public service.

Director Keith Koper shares more about the Seismograph Stations and the important work they are doing in this interview on KCPW's Cool Science Radio.

More information can be found at https://quake.utah.edu

The collapse and subsequent explosion of a massive star: B.O.A.T.

April 19, 2024

Tanmoy Laskar, assistant professor, Department of Physics & Astronomy, University of Utah

The team discovered the explosion, or supernova, using NASA’s James Webb Space Telescope (JWST).

While this discovery solves one mystery, another mystery deepens. The researchers speculated that evidence of heavy elements, such as platinum and gold, might reside within the newly uncovered supernova. The extensive search, however, did not find the signature that accompanies such elements. The origin of heavy elements in the universe continues to remain as one of astronomy’s biggest open questions.

Tanmoy Laskar, coauthor on the study that published in Nature Astronomy on April 12, spoke with AtTheU about why GRB 221009A was the B.O.A.T.

We have seen gamma-ray bursts before, but this one was so bright that its light blinded our gamma-ray telescopes in space and even shook the Earth’s upper atmosphere! Several dedicated people worked very hard to reconstruct the original gamma-ray signal and found that this gamma-ray burst was by far the brightest of all time (B.O.A.T) we have ever recorded. It has been exciting to study the B.O.A.T. over the last couple of years to try to figure two big mysteries: What kind of star is responsible for this powerful light display, and what produces the heavy elements in the universe?

How can finding a supernova help in solving these mysteries?

There are two theories to what makes these powerful, gamma-ray bursts—one is the collapse of massive stars at the ends of their lives (which also results in an explosion of the star as a supernova), and the other is a merger of two neutron stars, which are dense remnants of dead stars. We looked for the signature of a supernova, which would definitively tell us which theory was responsible for the B.O.A.T. explosion.

The other reason we wanted to search for the supernova was to solve the mystery of what produces heavy metals. Supernovae are factories that manufacture many elements in the universe—could a supernova powerful enough to create the gamma-ray burst also produce heavy elements in the explosion, like platinum and gold?

Read the entire interview conducted by Lisa Potter in AtTheU.

Regenerating damaged heart tissue. Sound Fishy? (It is)

April 18, 2024

Clayton Carey, a postdoctoral researcher in the Gagnon lab and lead author on the new study. Credit here and above: Brian Maffly

A heart attack will leave a permanent scar on a human heart, yet other animals, including some fish and amphibians, can clear cardiac scar tissue and regrow damaged muscle as adults.

Scientists have sought to figure out how special power works in hopes of advancing medical treatments for human cardiac patients, but the great physiological differences between fish and mammals make such inquiries difficult.

So University of Utah biologists, led by assistant professor Jamie Gagnon, tackled the problem by comparing two fish species: zebrafish, which can regenerate its heart, and medaka, which cannot.

A tale of two fish

The team identified a few possible explanations, mostly associated with the immune system, for how zebrafish fix cardiac tissue, according to newly published research.

“We thought by comparing these two fish that have similar heart morphology and live in similar habitats, we could have a better chance of actually finding what the main differences are,” said Clayton Carey, a postdoctoral researcher in the Gagnon lab and lead author on the new study.

Gagnon’s team wasn’t able to solve the mystery—yet—but their study shed new light on the molecular and cellular mechanisms at play in zebrafish’s heart regeneration.

“It told us these two hearts that look very similar are actually very different,” Gagnon said.

Both members of the teleost family of ray-finned fish, zebrafish (Danio rerio) and medaka (Oryzias latipes) descended from a common ancestor that lived millions of years ago. Both are about 1.5 inches long, inhabit freshwater and are equipped with two-chamber hearts. Medaka are native to Japan and zebrafish are native to the Ganges River basin.

According to the study, the existence of non-regenerating fish presents an opportunity to contrast the differing responses to injury to identify the cellular features unique to regenerating species. Gagnon suspects heart regeneration is an ancestral trait common to all teleosts.

Understanding the evolutionary path that led to the loss of this ability in some teleost species could offer parallel insights into why mammals cannot regenerate as adults.

With their distinctive horizontal stripes, zebrafish have long been popular as pets in the United States. In the 1970s zebrafish were embraced by biologists as a model organism for studying embryonic development of vertebrates.

Scientists like zebrafish because they can be propagated by the thousands quickly in labs, are easy to study and proved to be extremely hardy.

Read the full story by Brian Maffly in @The U.

Gentrification drives patterns of alpha and beta diversity in cities

April 18, 2024

Over the past two decades, a return of investment and development to once-neglected neighborhoods has meant a significant increase in spending on restoring parks, planting trees and converting power and sewer easements into publicly accessible greenspaces.

That trend — sometimes called “green gentrification” — tended to raise property values, helping to price out many neighborhoods’ original inhabitants. That led to an obvious question: What had those changes done to local animal populations, and what might that say about the changing dynamics of how nature functions in American cities?

This requires a staggeringly complicated analysis, and a new study published earlier this week in Proceedings of the National Academy of Sciences (PNAS), a vast and diverse array of data includes nearly 200,000 days of camera trap surveillance, taken over three years across almost 1,000 sites in 23 U.S. cities each with a unique mammal population, pattern of urban development and interaction between the two.

Austin Green, PhD

Some of that data have been accumulated by conservation ecologist Austin Green, a post-doctoral researcher and Human/Wildlife Coexistence stream leader in the acclaimed Science Research Initiative (SRI) at the College of Science. Leveraging the citizen science movement in the intermountain region, Green and his SRI team played a critical role in assembling a cohesive, detailed data-driven narrative of how gentrification — when lower-income people are forced out from American neighborhoods — the animal populations in the areas they’re leaving behind shift toward local species less typically associated with city environments. In turn, this phenomenon adds to the larger conversation in the U.S. about the reach and complexity of racial inequity.

Green's research is part of a monumental effort to collect and interpret data that have global implications about how humans and wildlife co-exist, especially in this case, as it relates to the continuing gentrification of cities, where more than 58 percent of the world population lives. Informed by Green's work in the SRI program combined with that of many others', scientific breakthroughs, as illustrated in the PNAS study, can directly influence conservation and adaptive management strategies.

Students in this particular stream at the U learn about wildlife ecology and conservation, as well as how to conduct ecological fieldwork, design complex studies of animal behavior and human-wildlife coexistence, curate and format large scale-datasets, and conduct advanced statistical analysis.

You can read the full article by SAUL ELBEIN in The Hill about this fascinating research and its findings published in PNAS here.

Metallurgical Engineering and IperionX Unveil New Research Facility

April 17, 2024

Following the 10-year, $10 million research agreement announced earlier this year between the University of Utah’s Department of Materials Science and Engineering and Charlotte-based IperionX, the two partners, along with college and university leadership, celebrated the opening of a new state-of-the-art additive manufacturing research center on campus in the William Browning Building. The lab, which houses cutting-edge 3D titanium printing machines, will serve as a hub for the collaboration between Metallurgical Engineering Professor Zak Fang's powder metallurgy research team and IperionX as they work to advance metallurgical technologies for producing primary metals focused on titanium.

The opening of the lab, named the Titanium Additive Manufacturing Research Center, creates new opportunities for U students to gain hands-on experience with cutting-edge materials science and engineering technologies. The partnership aims to inspire the next generation of metallurgical innovators, equipping them with the skills and experience needed to pioneer breakthroughs in sustainable metal production and processing.

IperionX CEO Taso Arima.
Banner photo: Ribbon cutting, led by Provost Mitzi Montoya and IperionX CEO Taso Arima.

"This new lab represents the tangible fruits of our partnership with IperionX and underscores our shared commitment to developing transformative solutions for the energy and transportation sectors," said Fang, the lead researcher on the project. "By combining our academic expertise in materials science and engineering with IperionX's industry know-how and resources, we are poised to make significant strides in areas like additive manufacturing of titanium alloys and recycling of critical minerals."

IperionX’s role as a leader in sustainable titanium production is a key component of this collaborative research effort. The North Carolina-based company has patented technologies aimed at recycling the valuable metal at a lower cost and with reduced environmental impact compared to traditional methods.

“IperionX is excited to continue its extensive collaboration with the University of Utah and Dr. Zak Fang,” said IperionX CEO Taso Arima. “It all started here at the University of Utah, with Dr. Fang’s innovation and his vision for manufacturing and re-shoring low-cost, high performance titanium metal in America. The Titanium Additive Manufacturing Research Center will allow us to continue to rapidly innovate, and we believe this center and continued work with Dr. Fang and his research team will assist to attract students to materials science and engineering — because this is what drives innovation for the critical technologies needed for the U.S. and society as a whole.”

"This academic-industry partnership of the Fang Lab and IperionX exemplifies the College of Science’s innovative bench-to-application research to meet the needs of our energy future," said Peter Trapa, Dean of the College of Science. "By supporting cutting-edge research that addresses real-world challenges, we are cultivating the next generation of scientific leaders and driving economic growth in Utah."

Joint efforts with industry partners have been part of the U's remarkable research growth over the past decade. In fiscal year 2023, university research funding reached a landmark $768 million, nearly doubling its support in the last ten years. As the U continues to work towards a goal of $1 billion in research funding, its leadership views industry collaboration as a vehicle to accelerate discovery and translate research into real-world applications.

“Collaborations like this one are virtuous cycles,” said Richard Brown, H. E. Thomas Presidential Endowed Dean of the John and Marcia Price College of Engineering. “Cutting-edge research and industry supporting one another is the backbone of a growing innovation economy.”

Goldwater Scholars 2024

April 17, 2024

Two College of Science students awarded the prestigious Goldwater Scholarship for 2024-25

The Barry Goldwater Scholarship is a prestigious award given to undergraduate sophomores and juniors who intend to pursue research careers. Goldwater Scholars often go on to hold distinguished research and leadership positions across many disciplines. For the 2024-2025 academic year, 438 scholarships were awarded to college students across the country. At the University of Utah, two undergraduate students have earned the honor of becoming Goldwater Scholars: Muskan Walia and Nathan Patchen.

Nathen Patchen
Biochemistry

“Biochemistry was a great way for me to combine my love of biology and chemistry and understand not only how things work, but why,” says Nathan Patchen about what motivated him to pursue research in that field. Patchen was awarded the Goldwater Scholarship for his work in Yang Liu’s lab, an assistant professor of biochemistry at the Spencer Fox Eccles School of Medicine.

Patchen describes his research as broadly being focused on DNA damage repair. He says “[w]e have access to revolutionary gene editing tools that, when used in conjunction with advanced imaging techniques, allow us to explore how cancer cells undergo DNA damage repair as never seen before. Personally, I am doing this by implementing a modified CRISPR-Cas9 that allows us to capture time-resolved images after damage and then produce data about the kinetics of repair.”

After graduating from the U, Patchen hopes to pursue an MD/PhD to practice medicine while continuing his research on gene editing and aging. Outside of his time in the lab, he enjoys being active through swimming, biking, and running as he trains for an IRONMAN 70.3 in St. George, Utah in May.

Muskan Walia
Mathematics
Philosophy

“Mathematics is at the cusp of interdisciplinary research” says Muskan Walia. During the College of Science ACCESS Scholars research program, she reflected on her academic interests and goals. She explains, "I wasn’t interested in studying any discipline in a vacuum or in isolation. Rather, I wanted to work on mathematics research that centered justice and informed public policy.”

The majority of Walia’s undergraduate research sprouted from her time in ACCESS where with the help of Fred Adler in the mathematics department at the College of Science, she began to adapt an epidemiological SIR model to predict the number of cells infected with SARS-CoV-2. Since then, she has created other models to further answer her questions about disease. These include a “... model of disease progression within an infected individual, a model of an antigen test, and a model of symptoms to evaluate how testing can be used to limit the spread of infection.”

“Ultimately, I want to lead a team that utilizes mathematical principles to tackle the most pressing social justice related questions of our time.” Walia is one of 57 awardees honored this year who intend to pursue research in mathematics or computer science. Besides innovating mathematical models, Walia enjoys spending time outside bird watching with her mom and gardening with her grandmother.

By Lauren Wigod
Science Writer Intern

Utah Refugee Teens Build Cosmic Ray Detectors

April 12, 2024

On April 9, 2024, a community of refugee students and their families, scientists, educators and policymakers will celebrate an event three years in the making—the installation of five cosmic ray detectors atop the Department of Workforce Services Refugee Services Office (also known as the Utah Refugee Center) in downtown Salt Lake City. The detectors, which measure echoes of cosmic particles bombarding Earth’s atmosphere, were built by nearly 60 participants in a program called “Investigating the Development of STEM-Positive Identities of Refugee Teens in a Physics Out of School Time Experience (InSPIRE)”, which brings science research—in this case particle physics—to teenagers and contributes to a worldwide effort to measure cosmic ray activity on Earth.

“Refugee youth often encounter many challenges related to STEM, including restricted exposure to STEM education, language barriers, cultural adjustments and a history of interrupted schooling, resulting in a low rate of high school completion and college matriculation among refugee students,” said Tino Nyawelo, principal investigator of InSPIRE and professor of physics and astronomy at the U. “The project conducts research to better understand these challenges and how to best broaden access to and engagement in STEM for refugee youth and other historically disenfranchised populations.”

Tino Nyawelo kicks off the cosmic ray detector installation celebration at the Utah Refugee Services Center on April 9, 2024. (Photo: Todd Anderson)

InSPIRE brings together the University of Utah, Utah State University, Utah Department of Workforce Services Refugee Services Office, as well as the Dutch National Institute for Subatomic Physics (Nikhef) in Amsterdam, to involve teens in real science. Data from the students’ cosmic rays detectors helps us understand the origins of the universe. The celebration is on Tuesday, April 9, at 1:30 p.m. at the Refugee Services Office at 150 N. 1950 W., Salt Lake City, UT 84116. A short ceremony will include speakers from the U, USU and the Refugee Services Office, and two student-participants will be available with research posters to talk about their cosmic ray detection projects.

Funded by a $1.1 million grant from the U.S. National Science Foundation in 2020, InSPIRE explores how refugee teenagers identify with STEM subjects while they participate in a cosmic ray detector-building and research project. Fifty-seven refugee teens spent one-to two-days a week for nearly three years building the detectors while learning the principles of particle physics and computer programming. The students designed their own research projects, posing questions such as whether the moon impacts cosmic rays. While some participants focused on the detectors, others focused on crafting short films on their fellow students’ research journeys. These students are working on a documentary, in partnership with the ArtsBridge America program at the U’s College of Fine Arts.

Neriman (left) and Lina Al Samaray with a poster of their research project, Effect of the Moon on Cosmic Ray Detectors. The high highschoolers used data from existing HiSPARC detectors to investigate whether the moon’s position from the horizon impacted the rate of cosmic rays hitting Earth’s surface.(Photo: Lisa Potter)

InSPIRE is embedded within Refugees Exploring the Foundations of Undergraduate Education In Science (REFUGES), an after school program that Nyawelo founded to support refugee youth in Utah’s school system, who are placed in grade levels corresponding to their ages despite going long periods without formal education. The U’s Center for Science and Mathematics Education (CSME) has housed the REFUGES program since 2012, where it has expanded to include non-refugee students who are underrepresented in STEM fields. Since then, REFUGES has worked closely with the state of Utah’s Department of Workforce Services Refugee Services Office, which serves as a critical link to the refugee community by coordinating comprehensive services to refugees resettled in our state.

“For the past 12 years, the Refugee Services Office has collaborated with the REFUGES program to identify refugee students and their families who need academic assistance and support. Participation in REFUGES keeps these students engaged in their community while also promoting their access to educational opportunities,” said Mario Kligago, director of the Utah RSO. “It’s amazing—what started as a small project funded by a Refugee Services Office grant has grown into a multi-million dollar endeavor backed by national organizations.”

The detector technology is adapted from HiSPARC (High School Project on Astrophysics Research with Cosmics), a collaboration between science institutions that started in the Netherlands, aimed at improving high schoolers’ interest in particle physics. There are now more than 140 student-built detectors on buildings in the Netherlands, Namibia, and the United Kingdom that upload their data 24/7 to publicly available databases. Nikhef in Amsterdam coordinated the project from 2003-2023 and created the initial worldwide network of cosmic ray detection data. Starting in 2024, data on extensive cosmic air showers and the digital HiSPARC infrastructure will be hosted and maintained by the U’s Center for High Performance Computing (CHPC), led by professor Nyawelo.

Read the full article in @TheU.

Watch below the video of the cosmic ray detector deployment in Salt Lake City facilitated by Tino Nyawelo through his REFUGES and INSPIRE programs.

2024 Class of SIAM Fellows: Aaron L. Fogelson

April 5, 2024

This year's 26 esteemed fellows were nominated in recognition of their outstanding research and service to the community. Through their various contributions, SIAM Fellows form a crucial group of individuals helping to advance the fields of applied mathematics, computational science, and data science.

A professor of mathematics at the U, Fogelson, who lists his research interests as mathematical physiology, modeling of blood clotting, gels and viscoelastic fluids and numerical solution of partial differential equations (PDEs), is being recognized by SIAM for his pioneering work on mathematical modeling and numerical methods for platelet aggregation and blood clotting.

"Clotting is an extremely complex process with physical, chemical, and cell biological components which is essential to maintaining the integrity of our circulatory system," he writes on his faculty profile. "When it malfunctions the consequences can be dire, including heart attack and stroke. Clotting is subject to intense research by laboratory and medical scientists but its complexity makes it very difficult to think through how it works or to make predictions about how well medical interventions to treat clotting problems will work. That is where mathematics and the work I do comes in."

On his lab's website, Fogelson writes, "Because transmural pressure differences vary greatly in the circulatory system and because blood flowing at different speeds through vessels of widely varying diameter leads to great variation in shear stress, the challenges of forming a blood clot to stop the outflow of blood differ substantially in different vascular beds. The system that has evolved to cope with these disparate challenges involves the aggregation of cells (platelets) and the formation of fibrous protein gel (fibrin). In addition, there is a complex, powerful, and tightly regulated enzyme network (the coagulation system) involving reactions on the surfaces of activated platelets, that leads to production of an enzyme, thrombin, that is key both in activating platelets so they can cohere to one another and in forming the protein fibrin from which the fibrin mesh is constructed."

40 Years of Modeling Clotting

The Fogelson research group has been developing models of many of the disparate aspects of blood clotting for close to 40 years. "We have built and analyzed models based on PDEs, ODEs [ordinary differential equations], or SDEs [stochastic differential equations] and, as needed, we have developed novel numerical methods with which to study the PDE-based models," writes Fogelson.

Projects of current interest in this research space includes, first, developing ODE-based compartment models of platelet deposition and coagulation under flow that treat developing thrombi as porous materials and which can track resulting flow, the growth of aggregates, and the biochemistry of platelet signaling and coagulation from the initiation of clot formation through vessel occlusion. The goal is a high-throughput simulation tool that will allow extensive investigation of model behavior as model parameters and other inputs are varied to reflect different physiological situations and disease states.

A second project of interest is integrating the Fogelson lab's models of fibrin polymerization with models of platelet deposition and coagulation under flow during arterial thrombosis, to produce a more comprehensive model of the clot formation process.

Fogelson has been a faculty member at the U since 1986 after earning his PhD at the Courant Institute of Mathematical Sciences of New York University and working as a post doctoral researcher at first the University of California, Berkeley and then the Courant Institute. In addition to his faculty position in the U's Department of Mathematics, he is adjunct professor of biomedical engineering, and was Associate Dean for Research of the College of Science in the period 2014-17. His research has been supported by the National Science Foundation and/or the National Institutes of Health continuously since 1982.

Read about all 26 SIAM fellows announced here.