LETTER FROM THE DIRECTOR
One of the remarkable things about traveling is finding the unexpected, the moments that overturn our preconceptions. The surfaces of things often look only a little different from our expectations. But when we take the time to dig deeper, a new world can open up, of hidden histories of ecology, people, arts, and languages. Stranger things are often closer than we thought, and it is a special skill of the faculty in the School of Biological Sciences to discover those strange things and share the surprises with our students.
Our new faculty exemplify the surprises that lie behind the surface of living things.
When Nick Vierra looks within neurons, he finds that they do indeed talk to each other with the signals that make it possible to read this letter. But that signaling occurs through cellular structures that nobody anticipated. When Luiza Aparecido notices an urban
tree on a hot day, she sees beyond the wilted leaves to the internal struggle to stay alive in this novel environment. Or when Eleinis Ávila-Lovera looks at the green stems of plants, she doesn't just say "everyone knows that plants are green." She considers what those stems are doing.
At their best, these journeys take us outside the world of science into important, and surprising, applications. Would one expect that studying how plants use water would have allowed Jim Ehleringer to protect the financial interests of growers of the legendary Hawaiian Kona coffee? Or that Talia Backman, a graduate student in Talia Karasov’s lab, would discover that bacteria have hijacked proteins from the viruses that attack them to attack other bacteria? Or that ecologist Nalini Nadkarni's obsession with trees would lead her to climb into the world of impact investing through a new role at our Sorenson Impact Center?
One never knows what is lurking behind the surface of a new place, a corner of biology, and even one's own life. And that is precisely what education is about. Discovery happens every time we open our minds, whether in the classroom, the field or in the lab, and when the boundary between research and instruction breaks down. Preconceptions are necessary to see anything and the best scientists and students are those who use preconceptions to open themselves to surprise rather than confirming what they expect.
So it is when you go somewhere, flip over a rock, talk to a new person, or take that wrong turn. Or maybe just open up this issue of Our DNA.
Sincerely,
Director Fred Adler
RECOGNITION
SOPHIE CARON OUTSTANDING UNDERGRAD RESEARCH MENTOR AWARD
PRESIDENTIAL SCHOLAR
JAMES GAGNON EXCELLENCE IN TEACHING AND MENTORING AWARD
TALIA KARASOV AND MICHAEL WERNER
MARIO R. CAPECCHI ENDOWED CHAIRS
NALINI NADKARNI
NATIONAL GEOGRAPHIC SOCIETY, EXPLORER-AT-LARGE
NATIONAL AUDUBON SOCIETY RACHEL CARSON AWARD
OFER ROG
GENETICS SOCIETY OF AMERICA
EARLY CAREER MEDAL
ÇAĞAN ŞEKERCIOĞLU
WHITLEY FUND’S TOP 10 CONSERVATION BIOLOGISTS OF THE PAST 30 YEARS
LESLIE SIEBURTH GUTENBERG CHAIR
NATHAN PATCHEN GOLDWATER SCHOLAR
ERON POWELL COMMENCEMENT SPEAKER
PAULINA MARTINEZ KOURY (CARON LAB) NSF GRADUATE RESEARCH FELLOWSHIP
KYLE KITTELBERGER (ŞEKERCIOĞLU LAB) THE CENTER FOR LATIN
AMERICAN STUDIES TINKER FIELD RESEARCH GRANT
MATTHEW WALLER (CLAYTON/BUSH LAB)
PHYLLIS COLEY AND THOMAS A. KURSAR GRADUATE FIELD RESEARCH AWARD
HANNAH MEIER (REIMER LAB)
SHURL & KAY CURCI FOUNDATION FELLOWSHIP
MATIAS GIGLIO (OLIVERA LAB) NEURAL SYSTEMS & BEHAVIOR ADVANCED
TRAINING AWARD / MARINE BIOLOGICAL LAB
Cover: Tailocins binding to the outer cell membrane of a target, competing, bacterial strain.
Credit: Daniel Rouhani
Our DNA is the official magazine of the School of Biological Sciences, University of Utah, published in partnership with Marketing & Communications, College of Science. Associate Director of Marketing & Communications: Bianca Lyon
Writer & Editor: David Pace
Designer/Photographer: Todd Anderson
Follow us on social media @uofu_biology or UBiologySchool
Prefer only a digital version of Our DNA? Send us an email and subscribe to the SBS e-newsletter at the same time. info@biology.utah.edu
by TANYA VICKERS
FROM MULTICELLULAR ORGANISMS, LIKE US, TO SINGLECELLED BACTERIA, LIFE IS 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 graduate student completing her final year in the School of Biological Sciences, found her project and niche studying bacteria and the viruses that infect them. “I’m especially interested in how bacteria have taken this a step further,” she says, “using remnants of past viral infections as a novel defense mechanism.”
“Phage” is the word used to describe a virus that infects and threatens bacterial cells. While phages do not infect human cells, a lot can be learned from the strategies used by bacteria to survive a viral infection. Together with principal investigator and SBS Assistant Professor Talia Karasov (yes, they share the same first name), the team recently made an unexpected discovery. Karasov sums it up: “We looked in the genome [DNA of bacteria] …and learned that the bacteria had taken a phage and
repurposed it [using gene recipes from the phage] for warfare with other bacteria, now using it to kill competing bacteria.”
REPURPOSING VIRUSES
“The bacterial strains (Pseudomonas) that I am studying are essentially repurposing the viruses that infect them,” says Backman, “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.
“What we know and are learning about microbes,” continues Backman, “is considered ‘foundational or basic science,’ but it’s anything but ‘basic.’
Understanding how life works can lead to new ideas and innovations. Today, human health, and the medicines we rely on, are challenged by the failure of antibiotics, medicines critical in combating bacterial infection.” Research on bacteria, and their unique viral pathogens, might
just offer a novel solution to the antibiotic crisis.
NEW CLASS OF ANTIBIOTICS
Beyond revealing how microbial communities combat infection, compete and evolve is the adjacent opportunity and potential to discover a new class of antibiotics. “Perhaps tailocin therapy and training our cells to identify and destroy bacterial invaders by using bits and pieces from the pathogens that infect us,” Backman says, “will be the next generation in antibiotic medications.” Antibiotics have been a medical miracle since the mid-twentieth century. However, World Health Organization Assistant DirectorGeneral on Antimicrobial Resistance Hanan Balky cautions that “there is a major gap in the discovery of
Culex tarsalis.
Credit: Christopher Bibbs
antibacterial treatments and more so in the discovery of innovative treatments. This presents a serious challenge to overcoming the escalating pandemic of antimicrobial resistance and leaves every one of us increasingly vulnerable to bacterial infections, including the simplest infections.”
Basic science is paving the way for novel solutions to global challenges, like antibiotic resistance. “My research,
and ongoing efforts in labs like Dr. Karasov’s in the School of Biological Sciences,” says Backman “is at the forefront of providing insight into the mechanisms that organisms use to live, reproduce, and overcome infection.”
The future for Talia Backman who plans on graduating with her doctorate in May looks bright. “Once I finish with my PhD research next summer (2025), I look forward to
GET READY TO BE BITTEN BY THE BUG OF COMPOSITE BIOLOGY RESEARCH.
The Salt Lake City Mosquito Abatement District (SLCMAD) is a catalyst for one of the College of Science’s Science Research Initiative’s (SRI’s) student research streams.
Toxicologist and behaviorist Chris Bibbs, SLCMAD’s laboratory director and an SRI stream leader, along with others from SLCMAD, take students the distance in the fascinating world of mosquitoes as they interface with public health and environmental concerns.
SRI student and biology major
pursuing a career that will allow me to continue to do part-time research and part-time teaching. I hope to inspire students to appreciate the pursuit of knowledge and not be afraid of digging deep into the molecular mechanisms that can inform solutions to today's grand challenges.” <
For more information about this research and a video (interview with Backman) go to biology.utah.edu/news
Irvane Nelson has a personal interest in diabetes research and sugar metabolism which led him to gathering lab experience at SLCMAD… studying mosquitoes. It turns out that these seemingly unrelated fields share quite a bit of research space. By assisting Bibbs on a project looking to develop toxic sugar baits for the pests, Irvane is contributing to broader research focused on creating insecticides that are safer for our environment, all while furthering his personal interest in how living organisms respond to sugar.
As the climate warms, mosquitoes that can harbor and transmit disease will be an increasing threat. For these reasons, it’s not surprising that
SLCMAD, the Centers for Disease Control, the National Institutes of Health and others are investing more resources in mosquito research. SBS’s Neil Vickers collaborates with SLCMAD and serves on its board of trustees, offering a reciprocal opportunity to advance research and promote undergraduate research.
SLCMAD deploys every aspect of biology, ecology, chemistry, physics, and every nuance and subdiscipline to get the job of mosquito abatement done. It’s a model for targeted, realwork experience connected with academics and research, and—except for the mosquitoes—everyone, especially SRI and biology students, seems to benefit. <
THE SCHOOL OF BIOLOGICAL SCIENCES PRIDES ITSELF ON OFFERING STUDENTS OPPORTUNITIES TO ENGAGE IN RESEARCH, EARN WHILE LEARNING, AND FIND INSPIRATION IN LABS AND THE FIELD THAT INFORM ACADEMIC AND CAREER GOALS.
Here we provide a sampling of the bright, the bold and the persistent who are preparing for careers in human health.
KIMBERLY GAMARRA
“My parents are immigrants from Peru and their transition to the U.S, especially navigating healthcare, was a challenge, says Kimberly Gamarra BS’24. “I suffered from a brain tumor as a child, so a big motivation for them moving to the U.S. was to make sure I received the best treatment possible."
Gamarra was recently accepted to the U’s Spencer Fox Eccles School of Medicine. Navigating her family’s adopted home of the U.S., she began her undergraduate studies early during high school, completing concurrent enrollment classes through Salt Lake Community College (SLCC) before finishing her degree at the U.
“This whole process opened my eyes to the strengths and struggles of our current healthcare system and ways I can help make it better.”
At the U Gamarra found guidance and community through the Refugees Exploring the Foundations of Undergraduate Education In Science's (REFUGES) Bridge Program. Now administered through SLCC, REFUGES is designed to support students with tools for college and career readiness. “From the start, I've always wanted to do medicine," she reflects. “That was my goal. And so having [this] program was a huge help in acclimating to the new campus and getting to know faculty, staff, and other students.” <
~ Julia St. Andre
MIA
SHENEMAN
“I am a transfer student from Salt Lake Community College where I received my Associate of Science in Pre-Health Sciences,” says biology major Mia Sheneman. “It was much easier for me to get involved in U campus life than I had anticipated— and it’s been so rewarding doing so!”
Sheneman transferred to the U as a junior and didn’t waste any
time getting involved. She found meaningful student employment to complement her educational and career goals while also working to cover the cost of her tuition. She has worked as a learning assistant and teaching assistant in chemistry and mathematics courses as well as a clinical research assistant for the Department of Emergency Medicine and a healthcare assistant at the University of Utah Hospital. “Doubledipping” in this way helps hundreds of students supplement their income, learn, and get involved all at once.
“One important lesson that I've learned at the U is that confidence is contagious,” continues Sheneman. “As I've grown more comfortable speaking with others, leading classes, and preparing for exams, I've noticed that this attitude is reflected in others, empowering fellow students to take pride in their accomplishments.
This has helped me build strong connections within the community and reinforced the importance of uplifting others as we navigate our journeys together.”
In spring 2025 when Sheneman receives her BS in biology, she will be the first member of her family to complete a college degree.
“When you have an idea, you just have
to go for it," she says. "The biggest step to take is the first step.” <
~ Isabel DuBay
NATHAN PATCHEN
“I am passionate about improving the quality of life for patients, allowing them to lead healthier and hopefully more fulfilling lives,” says Nathan Patchen. “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.”
Patchen recalls the principal investigator of his lab assigning him to learn how to synthesize a compound they use for experiments in an effort to bring 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, he and his PI discovered the error was occurring in a step Patchen was not in control of. “We were so excited to have found the solution. After
SCIENCE FOR ALL
THE ADVANCEMENT OF CHICANOS/ HISPANICS AND NATIVE AMERICANS IN SCIENCE (SACNAS) “IS A PLACE WHERE YOU CAN GO FOR OPPORTUNITIES,” SAYS PARKER GUZMAN, SACNAS UNDERGRADUATE CHAPTER PRESIDENT AND BIOLOGY MAJOR. Since 2021, two professors have been serving as SACNAS advisors for the College of Science student community: Naina Phadnis from the SBS and Holly Sebahar from the Department of Chemistry. More recently, SACNAS captured the attention of Rodolfo Probst, who completed a PhD in biology at the U and is now a postdoctoral fellow for the College of Science’s Student Research Initiative (SRI). He offers support as an advisor and mentor.
In 2022, Probst accompanied students to Puerto Rico, where SACNAS held the National Diversity in STEM (NDiSTEM) Conference. Paying it forward, in April of 2023, Guzman and Palepoi Gilmore, a first year medical student in the Spencer Fox Eccles School of Medicine, created and hosted a local version of the NDiSTEM. Here, students could connect to other SACNAS members, network, gain access to resources, and find a place to present their research without the pressures often found in formal academic spaces.
“Sometimes,” says Guzman, “you feel pressure to perform if you're presenting, or as a student, you might feel a sense of hierarchy that is always pervasive.” At SACNAS conferences, however, there is a sense
correcting the problem, I was able to successfully produce the desired product. Better yet, the new method dropped the cost of our experiments from sixty dollars per experiment to less than a cent.”
For Patchen it was exciting that he could play such a key role in helping his lab achieve a research goal that opens realms of possibility. “It feels great to be able to contribute to something larger than myself.” <
~ Tanya Vickers
Nathan Patchen, a junior in the Honors College studying biochemistry and biology, is a 2024 Goldwater Scholarship recipient.
of community and support, alleviating that pressure. Probst concurs: “Folks are kinder and engage with purpose. The atmosphere creates that, and it’s a celebration of diversity of backgrounds, research, and ideas.” <
Another version of this story by CJ Siebeneck can be found at science.utah.edu/news
DUNE Sandworms
FACT VS FICTION WITH A U WORM WRANGLER
by LISA POTTER
FOR MICHAEL WERNER , A SCIENCE FICTION FAN AND BIOLOGIST WHOSE RESEARCH FOCUSES ON THE ROUNDWORM NEMATODE, DUNE IS PEAK ENTERTAINMENT.
Author Frank Herbert’s 1965 novel Dune and its most recent film adaptations also shaped a young Werner’s worldview.
“Science fiction allows the reader to explore different aspects of the near possible; that’s the science part, but also fantasy, and that’s the fiction part,” says Werner now an assistant professor in the U’s School of Biological Sciences. “The best science fiction writers explore the different
facets of the human condition, like love and loss and oppression and tyranny. I found these existential questions to be really inspiring when I was thinking about different career paths and made me excited to pursue science as a possible future.”
To Werner, Dune is the best example of science fiction. The story takes place thousands of years into the future in an interstellar society where a handful of noble houses control planetary fiefdoms, one of which is ordered to steward an inhospitable desert planet indigenous to the Fremen people. It is also the only place where “spice” is found, the most valuable compound in this fictional universe that extends life, enhances mental abilities, and facilitates intergalactic travel. The epic explores multiple themes and it birthed the most infamous creatures in fiction—Shai-Hulud, the massive
worms that swim through the planet’s oceans of sand and produce mélange deposits that the characters refer to as "spice".
When the first of the latest iterations of Dune movies dropped in 2021, Werner wrote about the science of sandworms and their Earthly counterparts. In March, his lab published a study about worms living in a different inhospitable place— nematodes in the Great Salt Lake. Previously, only two multicellular animals had been known to inhabit the notoriously salty ecosystem.
@theU spoke with Werner about the science behind the sandworms of Dune. “I’ve thought a lot about this because I love Dune and I love worms,” he says. <
SCIENTISTS HAVE LONG SUSPECTED NEMATODES INHABIT GREAT SALT LAKE SEDIMENTS, BUT UNTIL RECENTLY, NO ONE HAD ACTUALLY RECOVERED ANY THERE.
It took a researcher with a hammer and loads of field experience to solve the puzzle of where nematodes
exist in the lake. Along with biology professor Michael Werner, postdoctoral researcher Julie Jung announced in March that they discovered thousands of tiny worms in the lake’s microbialites, reef-like structures that cover about a fifth of the lakebed.
Initial attempts failed to find these roundworms in lakebed sediments, prompting Jung to take a hammer to
samples of microbialites where she struck biological pay dirt. Breaking up the carbonate structures yielded thousands of nematode specimens representing several species, resulting in a significant discovery and opening several new lines of inquiry into the lake’s largely hidden web of life. < ~ Brian Maffly
A longer version of this story can be found on biology.utah.edu/news
UNMASKING IMPOSTERS
HOW ISOTOPE EXPERTISE FUELED THE FIGHT AGAINST COUNTERFEIT KONA COFFEE
AS A WORLD-RENOWNED EXPERT IN STABLE ISOTOPE ANALYSIS, JIM EHLERINGER HAS MADE GROUNDBREAKING CONTRIBUTIONS TO FIELDS RANGING FROM ECOLOGY TO FORENSICS.
But it was his unique expertise that found an unexpected application in the fight to protect the reputation and livelihoods of Hawaii's Kona coffee growers.
In 2019, a class action lawsuit was filed on behalf of Kona coffee's small-scale farmers against over 20 companies accused of selling coffee falsely labeled as "Kona." At the heart of the case were several types of stable isotope and element abundance analyses performed by Ehleringer's group, which revealed a telling difference between authentic Kona beans and the impostors.
"As you go from green beans to roasted beans, you're changing the water content," explains Ehleringer.
"So I borrowed an approach from geology that instead looked at the relative concentrations of rare elements in the beans. These ratios, I found, stay constant even at roasting temperatures."
By testing coffee samples from around the world as well as over 150 from Kona farms, Ehleringer's team identified stable isotope ratios and key element ratios—such as strontium to zinc, and barium to nickel—that clearly distinguished genuine Kona coffee. "We were able to establish a fingerprint for Kona coffee," he says.
This fingerprint revealed a troubling truth: the chemical signatures associated with authentic Kona coffee were different from the samples of "Kona" coffee sold by the defendants.
"It's the characteristics of the volcanic rock that make Kona coffee elementally unique," Ehleringer explains. "Those elements and their ratios are what give it that distinct profile."
Ehleringer's simple yet powerful approach proved a game-changer.
"Other researchers have used stable isotope ratio and element abundance methods to test things like honey, oils, onions, and wine," he notes. "But in this case, it helped uncover a widespread scam that was cheating Kona's small-scale farmers out of their livelihoods."
Although some defendants contested the test results initially arguing they
had not been replicated by other laboratories, the defendants were unwilling to conduct independent analyses themselves, ultimately settling out of court. The Kona growers received a $40 million settlement, a significant sum for an industry where most farms span just five acres or less.
Since this story was first reported in the New York Times in January, the victory has turned bittersweet. The Kona growers have since approached him again, suspecting the same companies are back to their old tricks.
"I want to help them, but I can only do so through proper legal channels," Ehleringer says of the Kona farmers, still proud that his expertise could empower them to defend the authenticity of their prized product."The truth is on their side, and my research gives them the scientific tools to fight back. But the wheels of justice turn slowly."
Today, as Ehleringer has entered phased retirement, the SIRFER lab which provides stable isotope ratio analyses on both organic and inorganic samples, will be relocated to the U’s Department of Geology & Geophysics where it will remain under the direction of geologist Gabriel Bowen. <
NEW FACULTY
WHEN FACULTY FIRST ARRIVE AT THE SCHOOL OF BIOLOGICAL SCIENCES (SBS), THERE’S A LOT ON THEIR “TO-DO” LIST. IN ADDITION TO PREPARING TO TEACH CLASSES AND GETTING ASSIGNED COMMITTEES TO SIT ON, THESE RESEARCHERS SPEND MONTHS, EVEN YEARS, SETTING UP THEIR LABS, POPULATED WITH STUDENTS, STAFF AND POST-DOCTORAL RESEARCHERS. IT’S NOT UNLIKE LAUNCHING A START-UP.
GROWING STRONG
ELEINIS ÁVILALOVERA
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. This stalwart resilience fascinated Eleinis Ávila-Lovera in her undergraduate years, an interest that has guided her entire educational journey as a plant ecophysiologist. Born and raised in Venezuela, she was drawn to desert regions and has since found her way in arid Utah as an assistant professor of the SBS.
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 it continue acquiring carbon despite the lack of leaves.”
Plants such as these are the focus of Ávila-Lovera’s research, analyzing the benefits and drawbacks of stem photosynthesis in regard to drought tolerance. Taking inspiration from these adaptations, Ávila-Lovera wishes to create a classroom environment that provides students all the tools and resources they need to excel, to not just transmit information, but to provide the basis that allows them, in turn, to master and apply their newfound knowledge.
Having been encouraged to thrive by multiple mentors before her, Ávila-Lovera eagerly looks forward to providing a similar mentorship role to
her current and future students. <
~ Michael Jacobsen
GENE EXPRESSION IN NEURONS
NICHOLAS
VIERRA
“Brain neurons are highly specialized and differentiated,” says Nick Vierra, a newly arrived neurobiologist at the SBS. “They modify their function in response to experience. This is the fundamental basis of learning.” Vierra studies the cell body of neurons, a field that tends to be underrepresented in neurobiology.
We have a good understanding of how synapses work because people put in the hard and careful effort needed to make the tools to probe their biology. But this focus on synapses has caused the cell body to be overlooked. The Vierra lab is studying how protein machinery in the cell body translates signals from synapses and sends that message to the nucleus.
As a postdoctoral researcher, says Vierra, “I wanted to learn how to make and use antibodies correctly as tools. “Antibodies—proteins produced by
the immune system that attach to foreign substances in the body—can be used incorrectly and produce misleading results. When we make antibodies, we take extra steps to ensure they’re generating bona fide results.” In this way antibodies can be harnessed to make powerful probes for discovering cell biology, for example, to determine where in the cell a particular protein resides.
Not surprisingly, perhaps, making tools leads to more questions to answer. Studying the cell body of neurons uses standard cell biology techniques, like live cell imaging, light microscopy, and electrophysiology.
“One of the challenges we face is that we don’t know the identity of many of the proteins functioning in the cell body that work to decode synaptic signals,” Vierra says. “A key approach we take is to identify them via protein mass spectrometry, so we know what these proteins are. This gives us a starting point to dissect the protein complexes we think are functioning to translate synaptic signals into a form recognizable by the cell.” <
~ CJ Siebeneck
PLANT ECOLOGY
LUIZA
APARECIDO
Luiza Aparecido is a new assistant professor who studies plant physiology in response to a changing climate. Born and raised in Sao Paulo, her journey to this position at the U
is the result of a lifelong passion for plants. “Ever since I was a young kid growing up in Brazil, I've always been interested in what plants are doing. That's always gonna be where my mind goes when it comes to the type of work that I do. I love plants very much, and I know that we need them, and their role in the ecosystem is very important.”
Aparecido earned her master's degree in tropical forest science working in the Amazon rainforest and then earned her PhD at Texas A&M, followed by a postdoctoral researcher position at Arizona State University. She became fascinated by arid land ecology, a surprising contrast to her roots in the tropical rainforest.
Her current research is crucial for understanding plant responses to heat and drought stress in urban landscapes like Salt Lake City. “There's so much we don't know about these plants that are unique and have adapted to these ecosystems—how they are going to look in the future, and if they are really as resistant as people think they are.”
Looking forward, Aparecido is excited to collaborate with the community of researchers at the U and continue to explore Utah’s unique plant ecology, as well as share her love for plants with her future students. Outside of the lab, she enjoys road tripping, hiking, and spending time with her dog, “Cookie.” < ~ Julia St. Andre
FROM FOREST
CANOPY TO IMPACT INVESTING
For the past four decades, Nalini Nadkarni has ascended trees in the rainforest as well as forests in the northwest to observe the many plants, animals, and microbes that live in the upper canopy. But that is not where her efforts stop.
Reaching beyond the scientific community, biology professorturned NatGeo Explorer at Large has created science education programs for people who are incarcerated, programming for churches and synagogues, and worked with Mattel to create a set of Explorer Barbies to inspire girls to study nature. Despite the sedentary nature of trees, Nadkarni wants people to recognize the multiple ways trees enrich our lives and life on our planet.
With that same spirit of creating connections, Nadkarni recently became a Sorenson Impact Institute Senior Fellow in Residence at the U where she sees common ground and potential for complementary efforts between ecology and social impact investment. At Sorenson she is bringing her expertise, experiences, and contacts in ecology, conservation biology, and the environment to the Institute to create new pathways to connect ecological actions and programs with the power and mission of impact investment. <
HOW SYMBIOSIS HELPS DEFINE EVOLUTION
by CJ SIEBENECK
AT THE U’S SCHOOL OF BIOLOGICAL SCIENCES, THE COLIN DALE LAB, ALONG WITH SARAH BUSH AND DALE CLAYTON HAVE JOINED WITH HUMAN GENETICIST ROBERT WEISS AND COLLABORATORS FROM THE UNIVERSITY OF ILLINOIS (KEVIN JOHNSON) AND VIRGINIA COMMONWEALTH UNIVERSITY (BRET BOYD) TO EXPLOIT AN AMAZING BIOLOGICAL SYSTEM.
Their focus: to study the relative contributions of stochasticity, contingency, and determinism towards evolution.
The target subject? Bird lice! Their diets consist almost solely of feather keratin, which is deficient in B-vitamins. It’s a deficiency that symbiotic bacteria can rectify, and every bird louse has independently used this solution by “domesticating” them as B-vitamin factories. This symbiotic relationship creates an evolutionary safety net where the bacteria can afford to lose genes whose functions are complemented by their host. In a field dominated by stochastically (randomly) generated mutations, a deeper understanding begins to emerge.
“The resulting approaches are really novel and uncover striking and highly supported patterns,” says
Colin Dale, principal investigator and co-author of a paper published last summer in Nature Communications: “Stochasticity, determinism, and contingency shape genome evolution of endosymbiotic bacteria.” “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.”
The findings of this research are possible thanks to a dream-team
mitochondria or chloroplasts in plants. These have been theorized to have once been independent microbes, showing that when a larger organism can consistently supply nutrients, evolution allows the symbiont to further benefit its host. Traits like photosynthesis originated through such a process, which we can now better define.
collaboration between global field workers and, in Dale’s words, “The silicon bubble of computational biology.” Bush and Clayton, along with many other collaborators, have been collecting and studying bird lice for decades, yielding a gift to science that keeps on giving. They then pass the fruits (or lice) of their labor to graduate students like Ian James, who craft complex data analysis pipelines to obtain insight from those sets of data.
It's a growing system that has been used to answer important questions in the field of evolutionary biology, presenting implications for the evolution of structures like
“In the context of symbiosis, this system is actually really interesting because it’s so boring,” quips Dale. “The lack of variation in the underlying biology 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.” <
A longer version of this story can be found at biology.utah.edu/news.
UNLIKE HEART ATTACKS IN HUMANS, MANY ANIMALS CAN CLEAR CARDIAC SCAR TISSUE AND REGROW DAMAGED MUSCLE AS ADULTS, A TOOL SCIENTISTS ARE SEEKING TO REPLICATE TO ADVANCE TREATMENT OF CARDIAC PATIENTS.
Led by Jamie Gagnon, his team compared zebrafish, which can regenerate its heart, with medaka, which cannot. Both come from the teleost family of ray-finned fish, descended from a common ancestor. Gagnon suspects heart regeneration is an ancestral trait common to all in the family, so understanding their evolution is key. If the reason a subject would lose this advantage is found, a way to replicate it could follow.
The team used a device to injure the fish hearts in ways that mimic human heart attacks. A copper wire cryoprobe was used to make tiny incisions, then applied to the edge of the heart. Ninety-five percent of fish survive this process, allowing this regeneration to take place. After three or fourteen days, their hearts were extracted and dissolved into a single-cell solution, to be subjected to RNA sequencing
in search of markers indicating the response to the injury.
“Zebrafish have this immune response that is typical of what you might see during a viral infection, called an interferon response,” says Clayton Carey, a postdoctoral researcher and lead author of a published study in Biology Open. “That response is completely absent in medaka.”
Differences were documented in immune cell recruitment and behavior, epicardial and endothelial cell signaling, and alterations in the structure and makeup of the heart. The indication is that this regeneration is sourced in the immune system, as more macrophages (specialized immune cells), migrated to the wound site for zebrafish.
“The more we learn about how animals can regenerate tissues will help us think about our limitations, how we might engineer strategies to help us overcome them,” says Gagnon. “Our hope is that we build this knowledge base in animals that can be studied in detail, then use that knowledge to generate more focused experiments in mammals, and then maybe someday in human patients.” <
This response forms a transient scar that doesn’t calcify. “What you do with that scar is what matters,” Gagnon says. “We think the interferon response causes these macrophage cells to promote the growth of new blood vessels.” Over time new muscle replaces the damaged cardiac tissue and the heart heals.
DISTINGUISHED ALUMNI
EACH YEAR THE SCHOOL OF BIOLOGICAL SCIENCES (SBS) FIELDS NOMINATIONS FOR THE DISTINGUISHED ALUMNI AWARD. TWO ALUMNI WERE SELECTED AND WILL BE ACKNOWLEDGED DURING THE SCHOOL’S ANNUAL AWARDS CEREMONY IN 2025.
FAILURE DONE GRACEFULLY
It’s generally not a good idea (or even allowed) to take biochemistry as your first biology class. But that’s exactly what CLARISSA HENRY BS’95 did as a freshman at the U.
“[I]t was so great,” she says, “that I changed my major from Chinese to biology.”
The class Henry took was a section taught by Baldomero Olivera, the distinguished professor who still runs one of the largest labs in the SBS. But it was a team effort for this Pennsylvania native who now calls Orono, Maine her home as Professor and Director of the Graduate School of Biomedical Science and Engineering, University of Maine. She also cites David Gard and David Wolstenholme (currently both emeritus professors) as equally entertaining and inspiring lecturers.
After declaring her major in biology, Henry found a spot in the lab of Darryl Kropf, now also emeritus. “It was in his lab that I became fascinated with how cells interact with their local environment,” she says. “Over 20 years later, I’m still fascinated with how cellenvironment interactions modulate cellular health.”
Henry’s experience is a testament to the undergraduate research opportunities still available directly from the SBS faculty or through the Science Research Initiative in the College of Science. “Undergraduate research was so easy to do at Utah, and undergraduates were very valued.”
And Henry continues to pay that undergrad experience forward. Today, her lab, which primarily focuses on how signaling between muscle cells and their extracellular matrix mediates musculoskeletal development and homeostasis in zebrafish, has been home to over 50 undergraduates.
“Throughout my career, over twothirds of my publications have [had] undergraduate authors.”
Henry also directs the statewide graduate school of biomedical science and engineering program.
“I was lucky enough to have mentors
throughout my research career who encouraged me to have a growth mindset and to embrace mistakes as learning opportunities,” she says. ”It is so important in life to be able to navigate failure gracefully.” <
LARK LEGACY
In October, PAUL KEIM , one of the longest-serving postdoctoral researchers in the lab run by the late K. Gordon Lark, was tapped to present the annual Lark Lecture at the SBS Science Retreat. Keim was a natural pick for a distinguished alumni award, not only because of his work with Lark in the 80s but because of his auspicious career in The Pathogen and Microbiome Institute (PMI), an impressive cross-disciplinary research unit at Northern Arizona University where, after graduating from NAU with a BS, he returned to and has been on the faculty for the past 36 years.
PMI is closely associated with TGen North, with whom the institute shares infrastructure to maximize Arizona’s investment in science.
At the U, Keim studied everything from soybeans to kangaroo rats. “We did everything," he says about the
lab’s variety. “It’s what I call either the Lark curse or the Lark blessing… Gordon was willing to work on any interesting biological problem.”
This was before Keim found himself working in infectious diseases, in particular with the deadly bacterium anthrax and later cholera and more recently the SARS-COVID-19 coronavirus, among others. At one highly elevated juncture he would find himself on the world stage as, following the attacks on American soil September 11, 2001, letters laced with anthrax spores started showing up in people’s mail. Five individuals eventually died from it.
How the story played out during the era of the “Anthrax Letters,” the title of a recent Netflix docudrama in which Keim is prominently featured, has
Joining the Wilkes Center Climate Solutions Hackathon offered a valuable break from the routine grind of a first-year PhD student in biology.
all of the intrigue you would expect of a compressed but harrowing era starting in October 2001. It was a time when the country was rattled to the bone and saw terrorists, it seemed, around every corner—and in every letter delivered by the postal service.
It was through the use of genomic technology and evolutionary principles at PMI and TGen North that Keim and his team were able to trace the specific, professionally processed spores, used in the attacks to an American microbiologist, vaccinologist, Bruce Ivins, a professional acquaintance of Keim’s and a known expert in the handling of anthrax spores.
Keim was readying to testify in court when Ivins took his own life. “Whether or not Bruce Ivins [was the culprit]
the collaborative effort among students from various majors, urging us to tackle the issue from diverse perspectives and glean insights from each other.
Our team [currently] consists of PhD students from the School of Biological Sciences and an undergraduate premed student studying Biomedical Engineering. The education and interests of each team member provide a wealth of foundational
is still hotly debated. But the Justice Department was convinced of his guilt and they shut the whole thing down destroying all the evidence. "So all the evidence that we were analyzing, all the anthrax strains, all the letters,” he says with some disappointment if not bitterness “... it's gone.”
Being pressed into the harsh and sometimes unforgiving media light (and hype) has been a defining feature of Keim’s career, but it has always been unapologetically rooted in the ethic of scientific inquiry that relentlessly follows the facts, honors the data and reaches conclusions that counter sacred paradigms in different scientific fields. His mentor Gordon Lark would be proud. <
Our team’s final project, establishing the Wildfire Resilience Collective, ended up winning first place. However, the true highlight was
knowledge, but, most importantly, we share a common goal of utilizing our research to inform policymakers and stakeholders in shaping land use decisions.
What exactly is a hackathon? While often associated with coding challenges, its essence lies in rapidly developing solutions within a condensed time frame. Our team’s focus was far removed from coding. We aimed to grasp the impact of wildfires on community resilience and the mechanisms behind fostering such resilience. < ~Hannah Meier
Learn more about the Hackathon at wilkescenter.utah.edu
Thank you to all of our alumni and friends who contribute to the School of Biological Sciences. Your support enables us to provide exceptional education, conduct groundbreaking research, and prepare the next generation of leaders in our discipline.
To meet the tremendous demand for STEM graduates in Utah, the School of Biological Sciences' top priorities include support for undergraduate students and graduate students, some of whom you can read about in this issue of Our DNA.
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