The Next Antibiotic Revolution: Viruses to the Rescue

The Next Antibiotic Revolution: Viruses to the Rescue


Dec 09, 2024
Above: Talia Backman – Ph.D. student, School of Biological Sciences, shares a micrograph of tailocins.

From multicellular organisms, like us humans, to single-cell bacteria, living things are subject to attack by viruses. Plants, animals and even bacteria have evolved strategies to combat pathogens, including viruses that can threaten health and life.

Talia Backman, a University of Utah doctoral candidate wrapping up her final year in the School of Biological Sciences, found her project and niche in studying bacteria and the viruses that infect them.

She studies how bacteria create and use weapons, called “tailocins,” by repurposing genes from viruses.

“I’m especially interested in how bacteria have taken this a step further,” Backman said, “using remnants of past viral infections as a novel defense mechanism.”

“Phage” is the word that refers to the viruses that infect bacterial cells. While phages do not attack human cells, a lot can be learned from the strategies used by bacteria to survive a viral infection. Working with Talia Karasov, the principal investigator and assistant professor of biology (yes, they share the same first name), Backman recently helped make an unexpected discovery.

Repurposing viruses

“The bacterial strains (Pseudomonas) that I am studying are essentially repurposing the viruses that infect them,” Backman said, “retaining features from the infectious particles that ultimately help them to kill or co-exist with other strains of bacteria. These repurposed phage parts are called ‘tailocins.’ Understanding the role tailocins may be playing in shaping the prevalence, survival, and evolutionary success of certain bacterial strains is not well understood and is a major focus of the research in the Karasov lab.

Research on bacteria, and their unique viral pathogens, might just offer a novel solution to the antibiotic crisis. Beyond revealing how microbial communities combat infection, compete and evolve is the adjacent opportunity and potential to discover a new class of antibiotics.

Read the full article in @School of Biological Sciences.

Exploring the Vulnerabilities of Endangered Birds

Exploring the Vulnerabilities of Endangered Birds


Dec 02, 2024
Above: Kyle Kittelberger( a graduate student in the School of Biological Sciences) at a bird banding station in northeastern Turkey holding a steppe buzzard. Courtesy Kyle Kittelberger.

Looking to inform the conservation of critically endangered bird species, University of Utah biologists completed an analysis identifying traits that correlate with all 216 bird extinctions since 1500.

Species most likely to go extinct sooner were endemic to islands, lacked the ability to fly, had larger bodies and sharply angled wings, and occupied ecologically specific niches, according to research published this month.

While some of these findings mirror previous research on extinct birds, they are the first to correlate bird traits with the timing of extinctions, said lead author Kyle Kittelberger, a graduate student in the School of Biological Sciences.

“I’ve been very interested in extinctions and understanding the species that we’ve lost and trying to get a sense of how we can use the past to better inform the present and future,” said Kittelberger, who is completing his dissertation on how the bodies and wings of certain species of migratory songbirds have changed in response to climate change.

Connecting bird traits with species extinction

His team’s analysis tapped into BirdBase, a dataset of ecological traits for the world’s 11,600+ bird species compiled by U biology professor Çağan Şekercioğlu and the Biodiversity and Conservation Ecology Lab at the U. The team simultaneously analyzed a broad range of biogeographical, ecological and life history traits previously associated with extinction and extinction risk for bird species that have gone extinct as well as those that lack recent confirmed sightings and have therefore disappeared.

One in eight species is in peril

This timing coincides with the rise of scientific observation, resulting in a systematic documentation of plant and animal life. It is also the time when European exploration took off, leading to the disruption of ecosystems around the globe as a result of colonization and introduced species.

Today, 1,314 bird species are at risk of extinction, according to the IUCN Red List of Threatened Species, or about 12% of the total.

Many species, such as the ‘Akikiki (Oreomystis bairdi), endemic to the Hawaiian island of Kauai, are so rare that they are functionally extinct. Kittelberger photographed the pictured ‘Akikiki, also called Kauai’s creeper, in the Alaka‘i Wilderness Preserve in 2022, when it was believed around 70 or so remained in the wild; today, only one individual remains.

As with many other Hawaiian bird species, the main threat to the ’Akikiki comes in the form of introduced species, principally malaria-carrying mosquitoes and habitat-wrecking livestock, according to Hawaii’s Division of Forestry and Wildlife.

Read the full article by Brian Maffly in @TheU.

Climate change fueling more severe wildfires in California

Climate change fueling more
severe wildfires in California


Nov 18, 2024

Wildfires continue to damage California’s forests as human-driven climate change amplifies their impacts.

A new Environmental Research Letters study reveals that the severity of the state’s wildfires has rapidly increased over the last several decades, contributing to greater forest loss than would have been expected from past increases in burned areas.

“Fire severity increased by 30% between the 1980s and 2010s,” said Jon Wang, an assistant professor at the University of Utah School of Biological Sciences and former postdoctoral researcher at the University of California Irvine Department of Earth System Science. This means that for every acre of forest scorched by fire, the damages to mature trees are considerably higher than what occurred in the average fire several decades ago.

Jon Wang conducting field research in Norway. Photo credit: Acacia England, U.S. Forest Service

“When fire moves through an area on the forest floor, often mature trees survive and, in some situations, they may thrive from fire effects on nutrient cycling,” said study co-author James Randerson, professor in the UC Irvine Department of Earth System Science. “The new research suggests more fire is jumping into the tree crowns, causing more damage and tree mortality.”

Randerson added that wildfires also have moved into new areas with denser and more vulnerable forests. Those areas include northern mountain and coastal regions that may have been protected in the past by cooler summers and higher levels of surface moisture.

“Forest exposure has increased 41% over the past four decades, suggesting denser forests are now more vulnerable to wildfire,” said Wang, who joined the U last year and is the principal investigator for the Dynamic Carbon and Ecosystems lab.

The question Wang and his team wanted to answer was how much-rising tree cover loss in California is due to increases in total area burned, how much of the loss is due to increasing wildfire severity, and how much is due to fire moving into new areas with denser forests.

“There’s a pretty shocking map of just how much these fires have expanded into northern California forests,” Wang said. “There’s just a lot more fire in these northern forests than there used to be. Climate change allows severe fires to affect forests that once tolerated milder fires.”

Read the full article by Brian Maffly in @TheU.

New Faculty: Eleinis Ávila-Lovera

New Faculty:  Eleinis Ávila-Lovera


September 25, 2024

Above: Eleinis Ávila-Lovera

Like all living things, plants have to respond and adapt to various stressors in their environment. But unlike most living things, plants must cope with these issues while being completely immobile.

In the field.

This stalwart resilience fascinated Eleinis Ávila-Lovera in her undergraduate years, an interest that has guided her entire educational journey as a plant ecophysiologist. Drawn to the deserts of the region, she has found her way here as an assistant professor of the School of Biological Sciences

Starting in Venezuela where she was born and raised, Ávila-Lovera was inspired by her grandparents to live her life to its fullest potential. Her grandmother Leonidas Guevera de Lovera taught her to read and write at the age of four. When combined with her grandfather Luis Lovera’s work ethic setting a perfect example, Ávila-Lovera was able to adapt and thrive as efficiently as the plants she would eventually study. Guided by the insightful teaching of her undergraduate mentor Wilmer Tezera, she was quickly drawn to the arid environments of the region. It’s hard enough to weather the world while immobile, exponentially more so in the scorching heat with no water. And yet, countless plants are able to adapt and thrive in these conditions.

“There’s a particular genus called Parkinsonia (palo verde),” Ávila-Lovera explains when asked for an example, “Whose bark is completely green. It’s a drought-deciduous plant, meaning that it loses its leaves during the dry season. In a desert this could lead to zero carbon gain, yet the palo verde is still able to withstand the arid heat, because the green stem helps them continue acquiring carbon despite the lack of leaves.”

Plants such as this are the focus of Ávila-Lovera’s research. Her lab is currently working on two projects: One, led by graduate student Osedipo Adegbeyeni, is comparing the water status regulation between leaves and photosynthetic stems in desert plants. The other, led by postdoctoral researcher Oranys Marin, is studying the link between hydraulic conductivity and stem photosynthesis in desert plants. Ultimately the former project aims to decipher differences in how stems and leaves tolerate drought conditions. The latter explores the potential coordination of traits that allow better performance of plants in drought conditions.

Ávila-Lovera also currently teaches BIOL 5460, Plant Ecology in a Changing World. Taking inspiration from the adaptations she has studied, she wishes to create a classroom environment that provides students all the tools and resources they need to thrive. Being over 3,000 miles from home herself, she’s well versed in the process of learning to flourish in unfamiliar soil. She aspires not just to transmit information, but to provide the basis that allows  students to master and apply their newfound knowledge in turn.

“It’s important to remember that ecology as a science has the same rigorous background as other sciences,” Ávila-Lovera explains. “I do consider myself an environmentalist. I do not eat red meat or poultry and try to reduce my carbon footprint. But ecology itself is a science; we’re testing hypotheses, and it’s critical to approach it with the organization and structure one would expect.”

Having been allowed to thrive by multiple mentors before her, Ávila-Lovera eagerly looks forward to providing a similar mentorship role to her current and future students.

By Michael Jacobsen

You can read more about Ávila-Lovera and her study of the chromatic story of plant survival here.

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Scientists awarded 1U4U Seed Grants

scientists awarded 1U4U Seed Grants


Above: Microbiolites at Bridger Bay on the northwest corner of Antelope Island. Credit: Utah Geological Survey. Biologists Jody Reimer and Michael Werner are part of a 1U4U team that study microbiolites.

Six College of Science faculty members are members of winning teams awarded seed grants of up to $50,000 as part of the 1U4U Seed Grant Program.

Six faculty members in the College of Science are members of winning teams awarded seed grants of up to $50,000 as part of the 1U4U Seed Grant Program.

The program supports cross-campus/cross-disciplinary research teams to solve some of the greatest challenges of our local, national, and global communities. College of Science faculty among the winning teams included Jon Wang, (biology), Colleen Farmer (biology), John Lin (atmospheric sciences), Jody Reimer (biology & mathematics), Michael Werner (biology) and Qilei Zhu (chemistry).

Bonderman Field Station at Rio Mesa (Photo courtesy of Zachary Lundeen)

The theme of the 2024-2025 program was “The Future of Sustainability.” Sustainability is a foundational goal that cuts across multiple intellectual topic areas (e.g., healthcare, water, energy, wildfire, critical minerals, education, food security) and can be interpreted widely.

At the University of Utah, faculty have engaged sustainability across a wide range of domains, including but not limited to environmental, social, communal, health, economic, technical, and legal.

Some of the topics of winning projects include the impact of air quality on elite athletic performance, study of suicide behaviors, and improving health by linking silos.

“It is exciting to fund so many teams working on sustainability projects,” said Dr. Jakob Jensen, associate vice president for research at the U. “The teams are considering sustainability across a wide range of topics from forest management and urban heat islands to physical therapy and mental health. These seed projects will drive significant innovation and impact communities throughout the region.”

Winning teams with College of Science faculty include the following:

Research Team: John Pearson (medicine) & Jonathan Wang (College of Science — biology)
Application Title: Heat and Healing: The Influence of Urban Heat Islands on Postoperative Outcomes

Research Team: Colleen Farmer (College of Science — biology), Ajla Asksamija (Architecture & Planning), Zach Lundeen (Bonderman Field Station), Jorg Rugemer (Architecture & Planning), Atsushi Yamamoto (Architecture & Planning)

Research Team: John Lin (College of Science — atmospheric sciences) & Tanya Halliday (Health)
Application Title: Impact of Air Quality on Elite Athletic Performance:  from Salt Lake to Beyond

Research Team: Jody Reimer (College of Science — biology and mathematics), Brigham Daniels (Law), Beth Parker (Law), Michael Werner (College of Science — biology)
Application Title: Understanding Great Salt Lake microbialite ecology to inform sustainable water management policy

Research Team: Qilei Zhu (College of Science — chemistry) & Tao Gao (Engineering)
Application Title: Ion-Conductive Membrane-Enabled Sustainable Industrial Electrochemical Production

 

For more information about the 1U4U Seed Grants and a complete list of this year's awardees click here.

How symbiosis helps define evolution

How symbiosis helps define evolution


September 3, 2024
Above: Colin Dale

“We’re looking at how deterministic the process of evolution is,” biologist Colin Dale says. “We’ve leveraged that question in this beautiful system, where we’ve got samples that have evolved under near identical conditions in nature.”

At the School of Biological Sciences at the University of Utah, the Dale Lab, along with U biologists Sarah Bush, Dale Clayton (Clayton/Bush Lab) and Robert Weiss U Human Genetics, in addition to collaborators from the University of Illinois (Kevin Johnson) and Virginia Commonwealth University (Bret Boyd) are exploiting an amazing biological system to study the relative contributions of stochasticity, contingency and determinism to evolution.

They do this using feather-feeding lice and their symbiotic bacteria that play a critical role in supplementing their host’s overly protein-rich diet of feather keratin. Their paper “Stochasticity, determinism, and contingency shape genome evolution of endosymbiotic bacteria” published this summer in Nature Communications.

“Keratin is a protein, and animals can’t live on protein alone,” says Dale. “The bacteria are producing B vitamins that are essential for these lice. Consequently, all feather-feeding lice have bacterial symbionts.”

The Clayton/Bush lab: Bacteriocytes in the abdomen of an adult female Columbicola columbae. Red and green colors show bacterial and louse cells, respectively. The bacteriocytes form conspicuous tissues called ovarial ampullae (oa) that are associated with developing eggs (mature oocytes: mo). Inset shows vertical transmission, with bacterial cells moving from the ovarial ampulla to the posterior pole of an oocyte through follicle cells. Credit: adapted from Fukatsu et al. 2007)

These bacteria are “endosymbiotic” which means they live (obligately) within the cells or bodies of a host animal. Remarkably, these bird lice have been collected from all over the globe, yet they have independently picked up the same species of bacteria to domesticate as vitamin “factories.” Dale recalls a question posed by the famous paleontologist Stephen Jay Gould: If we could see replays of the tape of life, taking place under near-identical conditions, would the process of evolution prove to be repeatable?

“What you have to worry about with Gould’s thought experiment,” Dale states, “is that distinct environmental conditions can induce distinct selection pressures. But since these lice are ectoparasites on birds, they’re buffered against variation in the environment and have no variation in diet. So, it’s one of the best examples of an evolutionary process that has evolved repeatedly under near-identical conditions.”

Symbiotic lifestyle

Mutations are randomly or “stochastically” generated but many do not survive the test of natural selection because they negatively impact fitness. However, upon transitioning to a symbiotic lifestyle, bacteria can withstand the mutational inactivation of many genes because those gene functions are supplanted by genes in their host. In this work, Dale and colleagues found that gene losses in the bacterial symbionts follow a decision tree-like structure that results in the minimization of their gene inventory, through the removal of redundant gene functions. In simple terms, if Gene A and B have redundant functions and the bacteria lose gene A, they are forced to maintain Gene B in order to survive (or vice versa). However, the loss of gene B might then facilitate the loss of genes X, Y and Z because the functions of those genes are uniquely dependent on gene B. Thus, cascading patterns of co-dependent gene loss and retention are initiated as a consequence of distinct stochastic losses in each symbiont genome.

“That’s the beautiful outcome of this paper,” says Dale. “It provides empirical evidence for this long-term trajectory and interplay between stochasticity, contingency and evolutionary determinism.” This has implications for the evolution of mitochondria and chloroplasts, which according to the theory of endosymbiosis, are organelles that used to be independent microbes that became symbiotic with eukaryotic cells in a similar way to these bacteria and the lice.

“Those organelles started off with big gene inventories,” Dale says. “When our cells provided them with an abundance of nutrients, they minimized their functions to retain only those that proved beneficial to their hosts, encompassing photosynthesis in the case of the chloroplast and aerobic energy generation in the case of the mitochondrion.

Notably, these very important traits originated through symbiosis and defined the evolution of plants and animals on Earth.

Cutting-edge of computational biology

The Dale Lab has a substantial focus on computational genomics and data science, catalyzed in large part by a very talented graduate student, Ian James, who obtained his bachelor’s degree in biology from the U and subsequently discovered that he had a talent for computer science.  “Ian is extraordinarily creative,” says Dale. “He starts out with biological questions and crafts complex data analysis pipelines, often using machine learning approaches, to obtain answers from big sets of data, ultimately producing some really psychedelic figures.”

Graduate student Ian James engrossed in “the silicon bubble of computational biology." Credit: courtesy of Colin Dale.

In combination with collaborators in Illinois and Virginia, who also utilize cutting-edge computational techniques to understand the patterns of louse and symbiont evolution, James uses pattern recognition and association rule mining to uncover hidden relationships between variables in large datasets to detect contingency in evolution.

“The resulting approaches are really novel and uncover striking and highly supported patterns” continues Dale. “Such approaches also have great potential for understanding the etiologies of diseases such as cancer, that often arise as a consequence of gene(s) becoming damaged.”

While Dale enjoys being trapped in what he calls “the silicon bubble of computational biology,” he also recognizes that field biologists, including Bush and Clayton, play a critical role in enabling this work to come to fruition. It requires specimens collected from all over the world to provide the genetic material for the cutting-edge data science and analysis. Bush and Clayton, along with many other collaborators, have been collecting and studying bird lice for decades, yielding a gift (to science) that literally keeps on giving.

The system has been used to answer many important questions in the field of evolutionary biology and serves as a model for the understanding of co-evolutionary interactions in biology textbooks. “In this case, in the context of symbiosis, this system is actually really interesting because it’s so boring” quips Dale. “Again, it’s the lack of variation in the underlying biology that makes it an excellent candidate for this type of study. I’ve always paid attention to the aphorism stating that ‘all that glitters is not gold.’ It’s also worth noting that sometimes the gold doesn’t glitter at all.”

by CJ Siebeneck

New bioinformatics major

New bioinformatics major opens doors to thriving careers


August 28, 2024

Beginning fall 2024, the degree provides rigorous interdisciplinary training to help graduates thrive in rapidly growing sectors.

Tommaso De Fernex, Chair of the Department of Mathematics. Credit: Todd Anderson

Tommaso De Fernex, chair of the Department of Mathematics at the University of Utah, has announced a new bioinformatics bachelor's degree (BS) available beginning fall semester 2024. The degree provides rigorous interdisciplinary training to help graduates thrive in rapidly growing sectors.

At the nexus of data science and life and physical sciences, bioinformatics applies intensive computational methods to analyze and understand complex biological information related to health, biotechnology, genomics and more. Through a comprehensive curriculum, undergraduates at the U will gain expertise in a variety of areas that together form an inter-disciplinary, multi-semester laboratory with rich possibilities.

“This major represents a pivotal step in keeping our students at the forefront of biotechnology,” says De Fernex. “It embodies true interdisciplinary collaboration, drawing expertise from biology, chemistry, and computer science faculties. I'm grateful for the dedication of our faculty in developing this program and for our strong partnerships with the medical campus and Utah's thriving biotechnology sector.”

 The complexity of life

Another math professor at the U, Fred Adler, agrees. The “study of life” is decidedly complex, says Adler who has joint faculty appointments in biology and mathematics and is currently director of the U’s School of Biological Sciences. “Unraveling that complexity means combining the tools developed in the last century: ability to visualize and measure huge numbers of tiny things that used to be invisible, technology to store and analyze vast quantities of data, and the fundamental biological and mathematical knowledge to make sense of it all.”

Continues Adler: “A few years ago, we heard that biology is the science of the 21st century. But with all the excitement and innovation in AI and machine learning, it might seem that this prediction was premature. We think nothing could be further from the truth.” Clearly, with the advent of biostatistical modeling, machine learning for genetics, biological data mining, computer programming and computational techniques for biomedical research, he said, “the preeminent role of biology in the sciences” has arrived.

A busy intersection

Bioinformatics is a field that intersects virtually every STEM discipline, developing and utilizing methods and software tools for understanding biological data, especially when the data sets are large and complex. Mathematics, (including statistics), biology, chemistry, physics, computer science and programming and information engineering all constellate to analyze and interpret biological data. The subsequent process of analyzing and interpreting data is referred to as computational biology.

Historically, bioinformatics and computational biology have involved the analysis of biological data, particularly DNA, RNA, and protein sequences. The field experienced explosive growth starting in the mid-1990s, driven largely by the Human Genome Project and by rapid advances in DNA sequencing technology, including at the U.

The new bioinformatics bachelor’s degree also complements the University’s storied graduate program in biomedical informatics, run by the Department of Biomedical Informatics at the Spencer Fox School of Medicine.

High-growth career field

The field of bioinformatics is experiencing rapid growth, with the U.S. Bureau of Labor Statistics projecting a 15% increase in related jobs over the next decade, outpacing many other occupations. Graduates with a bioinformatics degree can expect to find opportunities in diverse sectors, including biotechnology, pharmaceuticals, healthcare and research institutions. The interdisciplinary nature of this degree equips students with a unique skill set that combines biological knowledge with computational expertise. This blend of skills is increasingly valuable in today's data-driven economy, opening doors to a wide range of career paths and translating into higher earning potential for bioinformatics graduates.

"Students with quantitative expertise, like that offered in the new bioinformatics degree, are in high demand in the life sciences industry," says Peter Trapa, dean of the College of Science. "Recent data on U graduates highlights strong job placement and impressive salaries for graduates with such skills. This degree is designed to prepare students for success in these thriving job markets."

What students can expect

As a bioinformatics major, a student will learn from and collaborate with faculty pushing the boundaries of genomics, systems biology, biomedical informatics and more. Other universities and colleges offer a similar degree, but advantages to the U’s bioinformatics major include the following:

  • Hands-on research experiences in a student’s first year through the College’s celebrated Science Research Initiative
  • Core mathematical foundations through the renowned Department of Mathematics
  • Access to an R1 university with nationally ranked biomedical, health sciences and genomics programs
  • Internship opportunities with industry partners
  • Advisory support and career coaching

Concludes De Fernex, “Our bioinformatics curriculum promises a challenging yet immensely rewarding journey, equipping students for high-paying careers or further advanced studies. In today's world, where science and medicine increasingly rely on big data analysis, bioinformatics stands as a frontier of discovery.”

Students can learn more about the new bioinformatics major by visiting http://math.utah.edu/bioinformatics.

By David Pace

Scientists Find Hope in Cone Snail Venom

Scientists Find Hope in Cone Snail Venom


Aug 23, 2024
Above : Ho Yan Yeung, PhD (left) and Thomas Koch, PhD (right, also an author on the study) examine a freshly-collected batch of cone snails. Image credit: Safavi Lab.

Based on work by Toto Olivera, the father of research on cone snail venom, scientists are now finding clues for how to treat diabetes and hormone disorders in a toxin from one of the most venomous animals on the planet.

An international research team led by University of Utah scientists has identified a component within the venom of a predatory marine cone snail, the geography cone, that mimics a human hormone called somatostatin, which regulates the levels of blood sugar and various hormones in the body. The hormone-like toxin’s specific, long-lasting effects, which help the snail hunt its prey, could also help scientists design better drugs for people with diabetes or hormone disorders, conditions that can be serious and sometimes fatal.

The results were published Aug. 20 in the journal Nature Communications.

A blueprint for better drugs

Somatostatin acts like a brake pedal for many processes in the human body, preventing the levels of blood sugar, various hormones, and many other important molecules from rising dangerously high. The cone snail toxin, called consomatin, works similarly, the researchers found—but consomatin is more stable and specific than the human hormone, which makes it a promising blueprint for drug design.

By measuring how consomatin interacts with somatostatin’s targets in human cells in a dish, the researchers found that consomatin interacts with one of the same proteins that somatostatin does. But while somatostatin directly interacts with several proteins, consomatin only interacts with one. This fine-tuned targeting means that the cone snail toxin affects hormone levels and blood sugar levels but not the levels of many other molecules.

In fact, the cone snail toxin is more precisely targeted than the most specific synthetic drugs designed to regulate hormone levels, such as drugs that regulate growth hormone. Such drugs are an important therapy for people whose bodies overproduce growth hormones. Consomatin’s effects on blood sugar could make it dangerous to use as a therapeutic, but by studying its structure, researchers could start to design drugs for endocrine disorders that have fewer side effects.

Consomatin is more specific than top-of-the-line synthetic drugs—and it also lasts far longer in the body than the human hormone, thanks to the inclusion of an unusual amino acid that makes it difficult to break down. This is a useful feature for pharmaceutical researchers looking for ways to make drugs that will have long-lasting benefits.

Learning from cone snails

Finding better drugs by studying deadly venoms may seem unintuitive, but Helena Safavi, associate professor of biochemistry in the U’s Spencer Fox Eccles School of Medicine and the senior author on the study, explained that the toxins’ lethality is often aided by pinpoint targeting of specific molecules in the victim’s body. That same precision can be extraordinarily useful when treating disease.

“Venomous animals have, through evolution, fine-tuned venom components to hit a particular target in the prey and disrupt it,” Safavi said. “If you take one individual component out of the venom mixture and look at how it disrupts normal physiology, that pathway is often really relevant in disease.” For medicinal chemists, “it’s a bit of a shortcut.”

Among Safavi’s coauthors are faculty from the U’s School of Biological Sciences, including Baldomero Olivera and Samuel Espino. The U has been a hotspot for research into the venom’s pharmacological properties since Olivera arrived in Utah in 1970 from his native Philippines, bringing his interest in cone snails with him.

Read the full, original story by Sophia Friesen in UofU Health.
Read about Toto Olivera’s 2022 Golden Goose Award for early research in cone snails here.

Humans of the U: Nathan Patchen

Humans of The U: Nathan Patchen


August 12, 2024

“Initially, I chose to attend the University of Utah because I heard they had an excellent biology program and many opportunities for pre-medical students. I understood that the U was a top research school, and I knew I wanted to pursue a career in the biological sciences.

In my first year, however, I had some great experiences with the university’s chemistry department and fell in love with chemistry. Since then, I have decided to double major in biochemistry and biology. My goal is to pursue an MD-PhD, so I can do both research and work with patients.

I am passionate about improving the quality of life for patients, allowing them to lead healthier and hopefully more fulfilling lives. I hope to do this by working in the field of genetics/genomics and using gene editing techniques to find new tools to combat diseases that are otherwise untreatable. Additionally, I am interested in understanding why and how we age and improving patient outcomes through this process.

These interests are reflected in the research I have been a part of on campus as an undergraduate. The prestigious research that happens at the U is one of the reasons I was drawn to the school. Though research can be frustrating, time-consuming, and tedious, I have found it to be the most enriching part of my education. The incredible opportunity to participate in the forefront of science has drastically expanded my capabilities not only as a scientist but as a person.

Recently in my lab, the principal investigator (PI) assigned me to learn how to synthesize a compound we use for our experiments in an effort to bring our costs down. It was a difficult process to optimize the protocol for our lab, but through extensive troubleshooting and consulting with other labs, I became an expert on the topic.

After months of running the process over and over again without success, my PI and I discovered the error was occurring in a step I was not in control of. We were so excited to have found the solution After correcting the problem, I was able to successfully produce the desired product. Better yet, the new method dropped the cost of our experiments from $60 per experiment to less than a cent. It is exciting that I could play such a key role in helping my lab achieve a research goal that opens realms of possibility. It feels great to be able to contribute to something larger than myself.

I have recently been recognized as a Goldwater scholar which is exciting because it is a testament to my commitment to pursue science and my desire to make an impact on the world through discovery. To me, receiving this award is a great honor, it tells me that someone believes in me, and is willing to invest in my development. It is my goal to live up to that expectation, whether it be through science, medicine, or some other field, my goal is to serve and improve the lives of others.

—Nathan Patchen, a junior in the Honors College studying biochemistry and biology and a 2024 Goldwater Scholarship recipient 

This story originally appeared in @TheU.

Fueling Utah’s Booming BioTech Sector

Fueling Utah's Booming Biotech Sector


Aug 15, 2024

Over the last few years, opening a newspaper and seeing Utah at the top of the national economic rankings has become commonplace. 

In teaching labs through the Science Research Initiative (SRI) students learn by doing, starting their first year in the College of Science.

There has been a steady stream of articles about billion-dollar valuations for Utah startups and consistently low unemployment. Amid these headlines, there is growing recognition among analysts and policymakers in Utah that the biotechnology and life science sectors are playing a significant role in that growth. A recent report from the Kem C. Gardner Policy Institute found that the industries created $8 billion in GDP in 2022, part of a total statewide economic impact of $21.6 billion. Job growth in the sector has been particularly impressive; Utah’s 5.7% annual job growth rate significantly outpaces the national average of 3.2%. Due to these steady increases, Utah now has the highest share of statewide employment among all states nationally except Massachusetts. These jobs are also high-paying positions. Wages in the sectors average $96,000, which is 48% higher than the $65,000 average in other industries.

The University of Utah and the College of Science play an important role in this booming expansion, helping supply a sizable portion of talented employees and researchers. According to National Center for Education Statistics graduation data, the U awards roughly 37% of life science-related bachelor’s degrees and 95% of graduate degrees given by schools in the Utah System of Higher Education. Graduates from the College account for nearly two-thirds of those undergraduate degrees and over one-third of the PhDs. As they build their careers, alumni have the opportunity to take principles they learn by working with award-winning faculty and then applying them in professional settings.

“Innovation in biotechnology is touching on every aspect of our lives, from climate change and agriculture to health and wellness,” says Fred Adler, professor of mathematics and current director of the School of Biological Sciences (SBS), the largest academic unit in the College. “As discovery and innovation accelerate, so do the links between basic science and applications. In the SBS, faculty are making transformative contributions to drought-resistance crops based on fundamental discoveries in genetics, testing of drug safety based on research of animal behavior, and to neuroscience through new ways of imaging cells at the finest resolution.”

EXCELLENCE IN EDUCATION

In the School of Biological Sciences, faculty are making transformative contributions to drought-resistance crops based on fundamental discoveries in genetics. Credit: Mathew Crawley

The pipeline from the classroom, and the lab, to a successful career is most fruitful when exceptional instructors and researchers provide mentorship and guidance for students. College faculty have been recognized with a range of teaching and research awards, spanning honors like the National Medal of Science (given to three faculty members from the College of Science over the years) and MacArthur Genius Grants (four recipients) to the Rosenblatt Prize, the U’s highest honor for teaching and research (11 recipients). The College has also had 15 members elected to the National Academy of Sciences, 10 of whom are still actively teaching and pursuing research. These individual honors underscore the quality of the researchers’ academic units and are reflected in their national rankings: the SBS graduate program is ranked #13 and the Department of Chemistry comes in at #18 among public universities nationwide by U.S. News & World Report.

Chemistry and biological sciences, which educate a significant number of students that join the biotech and life science sectors, are the top-ranked programs in their fields in Utah and hold top-ten rankings among both public and private schools in the West. The two units also received over $28.4 million in external research funding during fiscal year 2023. These resources provide unique opportunities for students to learn relevant science in hands-on settings and engage in transferable research skills. Considering this impressive track record, it makes sense that life science and biotechnology-related faculty continue to garner recognitions in their fields.

Take, for example, Distinguished Professor and Thatcher President Endowed Chair of Chemistry Cynthia Burrows who won the prestigious Linus Pauling Medal Award. The Burrows Lab hosts organic, biological, analytical and inorganic chemists interested in nucleic acid chemistry, DNA sequencing technology and DNA damage. The team focuses on chemical processes that result in the formation of mutations which could lead to diseases such as cancer. Studying site-specifically modified DNA and RNA strands and DNA-protein cross-linking, Burrows and her group are widely known for expanding studies on nanopore technology to detect DNA damage. Burrows’ research in altering nucleic acid composition can provide valuable information in genetic diseases as well as manipulating the function of DNA and RNA in cells.

The Caron Lab studies the mushroom body of the Drosophila (fruit fly) to better understand how brains are developed to learn.

Another U chemist, Aaron Puri, has also drawn national attention as one of five recipients of the Simons Early Career Investigator Award in Aquatic Microbial Ecology and Evolution. The award will provide $810,000 to the Puri Lab over the next three years and, according to Puri, “will enable our research group to work at the interface of biology and chemistry to decipher the molecular details of interactions in methane-oxidizing bacterial communities.” His research looks at the molecular details of interactions in these communities, aiming to solve big problems with microscopic solutions. “These communities provide a biotic sink for the potent greenhouse gas methane,” he continues, “and are a useful system for understanding how bacteria interact with each other and their environment while performing critical ecosystem functions.”

Nearby, in the Skaggs Biology Building, is the lab of Ofer Rog, who recently won an Early Career Medal from the Genetics Society of America. Rog was recognized for work visualizing meiotic exchange between “sisters,” exploring synaptonemal complex proteins and tracking single molecules. Building on this work, the Rog Lab published a study in the Proceedings of the National Academy of Sciences in December that outlined a groundbreaking way to study the synaptonemal complex. Rog explains of the complex, “You can think of it like a zipper. The axes of the chromosomes are like the two sides of your shirt. The synaptonemal complex (SC) is kind of like the teeth of the zippers that lock onto each other and can pull and align the two sides of the shirt correctly.” Rog’s team was the first to pinpoint the exact position where the SC interacts with itself to facilitate genetic exchanges. Looking forward, unlocking the SC’s role in meiosis may lead to a stronger understanding of fertility in humans.

Another esteemed faculty member in biology is Sophie Caron, a U Presidential Scholar, who uses the Drosophila mushroom body — a computational center in the fruit fly brain — as a model system to understand how brains are developed to learn. With work described as “stunning” and “breathtaking,” Caron has built an interdisciplinary research program by drawing on computational models, species-comparative studies and various anatomical and behavioral techniques to elucidate the structural, functional and evolutionary pressures that shape the mushroom body’s learning function. In addition to her research, Caron — who was also awarded an outstanding teaching and mentorship award last year— designed and teaches an extremely popular neurobiology class (BIOL 3240), a course taken by hundreds of students.

FROM THE CLASSROOM TO THE BOARDROOM

Graduates from the College of Science also play crucial roles in Utah’s burgeoning biotechnology community. Equipped with cutting-edge knowledge learned in classrooms and research labs throughout campus, these alumni are at the forefront of research and development, contributing to significant advancements in life science fields. Their expertise not only drives the success of numerous biotech companies but also attracts substantial investment to the state. By bridging academic excellence with industry needs, alumni ensure a steady pipeline of talent that sustains the growth and dynamism of Utah’s biotechnology sector.

Tom Robbins and Amy Davis of bioMérieux.

There are many examples of these types of professional outcomes. Randy Rasmussen (PhD’98 biology) and Kirk Ririe (BS’05 chemistry) were two of three co-founders of BioFire Diagnostics. The company pioneered instruments that shortened DNA analysis techniques from hours to minutes. Using this technology, they created molecular diagnostics that now simultaneously test for multiple infectious agents, allowing healthcare professionals to get quick and accurate results from onsite instruments. In 2013 BioFire was purchased by bioMérieux, a French biotech firm, for over $450 million. The company is now one of Utah’s largest life sciences employers, with over 3,400 employees throughout its six sites. While Rasmussen and Ririe have since moved on to other projects, College of Science graduates like Amy Davis (PhD’03 biology), vice president of molecular biology, and Tom Robbins (PhD’04 mathematics), vice president of software development, continue to play significant roles in the company’s work.

Some College alumni have also found ways to share their experiences with a new generation of students. Ryan Watts (BS’00 biology) discovered a passion for research while an undergraduate. After he finished his degree, he earned a PhD from Stanford University and eventually co-founded the biotech startup Denali Therapeutics, focused on defeating neurodegeneration. The company went public in December 2017, breaking that year’s record for an initial market valuation of a biotech company. Today, Denali has over 400 employees and a market cap of over $3 billion, including a growing presence in Utah. Despite his busy schedule as CEO, Watts taught a winter semester course for five years at the U which tracked the biotechnology industry and introduced biology students to processes around drug discovery, business strategy, programming and portfolio decision-making.

Another alumnus, Berton Earnshaw (PhD’07 mathematics) used his academic experience to join the founding team of Red Brain Labs in 2012. When the machine learning-focused company was acquired by Savvysherpa in 2014, Earnshaw stayed on as a principal and senior scientist. Eventually, Earnshaw became director of data science research at Recursion Pharmaceuticals, a young clinical-stage biotech and drug discovery company based in Salt Lake City. In a succession of senior roles, Earnshaw has helped guide the company’s foundational machine learning and AI development, assisting in the company’s rapid growth to over 500 employees and an international expansion. Earnshaw started teaching courses at the U on machine learning and neural networks beginning in 2018. In 2024, he accepted a role as a senior fellow with the College of Science, in part to provide an industry perspective into the dynamic world of deep learning and AI.

LOOKING FORWARD

Berton Earnshaw, Recursion.

Unwilling to rest on its laurels, the College of Science is devoting significant resources to prepare graduates for what the Utah Department of Workforce Services deems accelerating growth in the rapidly changing fields of biotech and life sciences. The Department of Mathematics, School of Biological Sciences, and Kahlert School of Computing recently announced a new undergraduate degree in bioinformatics. New faculty hires throughout the College have included individuals with expertise in areas like data science, genomics, machine learning, gene editing and next-generation imaging techniques. More undergraduate students are participating in bioscience-related research than ever, either through the celebrated Science Research Initiative or direct placements in labs throughout campus. Together, these investments help ensure that future students will be well-prepared after they enter the workforce.

The notoriety of Utah’s burgeoning biotechnology and life sciences sectors continues to be indelibly linked to the College of Science in a feedback loop that benefits the economy, the community, and the University of Utah.

by Eliot Wilcox
Operating Manager, College of Science, University of Utah

This story is featured in Synthesis, the College of Science's annual magazine.