Our DNA: The School of Biological Sciences, Fall 2020

Çağan

Zooming in on the SBS

We have found 2020 to be one of the most peculiar and worrying years in living memory. The COVID-19 pandemic has been the overarching story—a global calamity that seems likely to continue playing out over the next year. In Salt Lake City, we had an earthquake in March and in September a two-day windstorm of epic proportions that uprooted thousands of trees citywide. In spite of these epidemio-, geo-, and meteoro-logical challenges, the School of Biological Sciences is positively Zooming ahead.

At the end of June, we celebrated the conclusion of Denise Dearing’s term as SBS Director spanning a full six years. We are truly grateful for the many ways that Denise advanced our School. With her departure, two of us—Leslie Sieburth and Neil Vickers—were appointed as Co-Directors. As one of our colleagues observed—it will take the two of us to fill Denise’s shoes.

We were so happy that some of you attended our annual retreat in August! At this event, we welcomed two new faculty members, Talia Karasov and Michael Werner, and also nineteen new graduate students. Talia is an evolutionary geneticist who studies plant-microbe interactions and Michael (profiled in this newsletter) works on phenotypic plasticity in nematodes. We also recognize the retirements of two of our esteemed colleagues, Distinguished Professor Phyllis Coley and Professor Gary Drews (also profiled here). They both still have active research programs, so we are not saying goodbye to them. We offer our congratulations and thanks for their many years of outstanding contributions to our School.

With altered schedules and hygiene routines to keep students, faculty and staff safe, we consider ourselves fortunate to be

able to maintain focus on our research, teaching and training missions. For the most part, lab groups have been able to return to work. We have made significant changes to our undergraduate classes with many now taking place over Zoom. However, in-person laboratory sections are running for some of our classes so that students can still take advantage of highly-valued experiential learning environments. Fortunately, our warm and dry fall has allowed several of our field-based courses to maintain a full slate of outdoor activities.

We are deeply appreciative of all our supporters during these turbulent times. Budget cuts as a result of the pandemic’s economic impact mean that your donations are more important than ever and help to maintain support for students and other critical aspects of our mission.

With our best wishes that you all stay safe and healthy in 2021.

The Nature of Nurture

For years after the discovery of the double-helix molecule DNA most biologists assumed that DNA was the sole hereditary molecule, i.e. the only molecule that contains information which can be passed on to the next generation. While DNA is indeed the molecular carrier of hereditary information, lower or higher expression of genes in that database can be affected by the environment wherein an organism exists.

As a PhD candidate at the University of Chicago, new Assistant Professor Michael S. Werner first studied differentiation of stem cells and leukemia cells determined by differences in gene expression. Some of the factors that affect gene expression to keep genetically identical cells distinct from each other (e.g. a kidney cell vs. a heart cell) are chemical modifications

to chromatin–the assemblage of DNA and proteins that constitute the physiological form of heritable information.

“Some of these modifications,” says Werner, “can be copied through cell division—effectively providing an additional form of heritable information, providing long term changes to gene expression well beyond the initial inductive signal…that results in the stable development of divergent cells, tissues, and ultimately organs.” These mechanisms which do not involve an underlining change in DNA sequence are referred to as epigenetic

As a post-doctoral fellow at the Max Planck Institute, Werner expanded this inquiry to the study of alternative organismal characteristics. The sets of observable characteristics of an individual resulting from the interaction of its genotype with the environment is known as a phenotype, and the ability to form different phenotypes in response to different environments is referred to as phenotypic plasticity. What Werner finds

most intriguing, and is the major focus of his laboratory, is the potential link between the epigenetic chromatin modifications that provide for alternative cell types, and the unknown molecular mechanisms that provide for alternative organismal phenotypes.

There was another reason Werner took the leap from studying cells to plasticity in organismal phenotypes. “We’ve learned a lot about the mechanisms that provide cellular plasticity, and I think the time is now ripe to expand the scope of some of our questions,” he says. For example, “What are the proximate molecular mechanisms that transmit environmental information into physiological, behavior, and morphological changes at the organismal level?” The implications of this research, according to Werner, may also inform medical scientists who continue to investigate environmental influence on health and well-being, such as “learning, immunity, and the effects of diet and exercise.”

For Werner, the ideal organism subject model would become Pristionchus pacificus, a nematode similar in characteristics to its more famous cousin C. elegans. But depending on conditions it experiences as a juvenile, Pristionchus develops either a narrow mouth, or a wide mouth with an additional “tooth,” the latter of which is useful for killing competitors and expanding the organism’s dietary range. What provides this trait plasticity, and causes the switch in juveniles from the development of a narrow to a wide mouth?

The hypothesis that Werner is tracking down is that they are the same mechanisms that provide cellular plasticity and differentiation he studied in human cell lines as a PhD candidate in Chicago. “The ability to use a genetic model organism like a nematode provides an incredible advantage to study phenotypic plasticity, which has historically been studied in fascinating, yet less experimentally tractable organisms like butterflies, ants, crustaceans, and of course, humans.”

Today, Werner and his lab grow worms in different environmental conditions, switching them from plates to liquid culture in a flask. Depending on how developed each organism is when the switch is made determines which mouth form emerges. This would suggest that there is “memory” of their previous environment. His task is to find which epigenetic mechanisms maintain a record of environmental exposure, which genes are responding to the environment, and when.

After identifying the causative molecular mechanisms, Werner intends to see how “conserved” and general they are, and how chromatin and plasticity have shaped ecological strategies and evolutionary variation. When he’s not publishing his findings in journals like Nature Structural and Molecular Biology

and Genome Research, Werner and his lab spend a good deal of their time grinding up biological material, biochemical fractionation and sequencing before going “under the ‘scope.” If you were to ask him what kind of biologist he is, he side-steps firewall divisions, preferring to think of himself as just “a biologist.”

In an age when the life sciences has become more and more specialized, Werner is committed to the idea of research that is cross-disciplinary, which was one of the reasons he found the University of Utah’s School of Biological Sciences an attractive home for his work, and conducive to his scientific imagination. “Biology is no longer a young field,” he says, “as it was in the second half of the 20th century,” during the heyday of molecular biology when the focus was on the huge questions like “what is the molecule of hereditary information, and how does it copy itself?” While there are still important questions delving deeper into each subfield of biology, Werner believes that now the big questions are at the nexus of fields that have been historically separated from each other, “There are still fundamental questions at the interface of molecular biology, ecology, and evolution, and all of these areas can learn from each other.”

Needless to say, Werner is an advocate for integrative biology, both for its power to move science forward, and for its ability to make basic science relatable. It’s a reflection of these disparate but connected fields of study maturing, says Werner. A related concern is that in this era when basic science as a discipline is somewhat contested by the public, and even some governments and political figures, laser-focused myopia risks science losing the general interest of the public, and public funding. Paradoxically perhaps, inter-disciplinary studies not only bridge specialized fields but broaden the meanings, implications and perspectives for public consumption. Not to mention the applications basic science regularly funds through its model of open inquiry.

Meanwhile, Werner is settling into his new digs in the Aline W. Skaggs Biology Building. A native of Florida, he grew up straddling an ethnic divide (His mother is Cuban, his father Anglo) in which the play of nature vs. nurture was in high relief. As an undergraduate at Stetson University, a small liberal arts school, he toyed with a pre-med emphasis. But the fire for research would emerge later, during a nine-week stint doing an NSF-funded research experience undergraduate (REU) program at The University of Notre Dame. The experience fueled his desire to pursue graduate school in nearby Chicago where he met Talia, another new Assistant Professor in the School of Biological Sciences this year. After their PhDs the two of them found Germany and the Max Planck Institute to be “the perfect opportunity” to live abroad while each connecting to research programs that fit their intellectual curiosities.

Exploring environmentally-induced phenotypes in nematodes will continue to animate Michael Werner for the time being, as he always appreciated the idea that we are not genetically predetermined from birth, but rather have environmental influence over our lives. You can expect this forever biologist, fiercely committed to work that transcends academic silos, to look up regularly from his microscope at the broader contours of life and its ways and means, which is his ultimate, big-picture model system.

Calling all e-Birders

Quechua

Monte Neate-Clegg (Şekercioğlu lab) says that community science bird data shows different trends in bird populations than professional bird surveys do, especially in developing countries. Researchers look for trends to know whether the number of individuals in a species is increasing, stable or decreasing—with the latter as a warning sign that the species is in trouble. His results are published in Biological Conservation. More observations are needed, he and his colleagues say, both by birders and professionals.

“We hope that this study will encourage birdwatchers to be more conscientious in their recording,” says Neate-Clegg “to think of these data not just as a personal record but as contributing to a wider cause.”

Birding is a long tradition, but as paper guidebooks and life lists have given way to digital records and mobile apps, birders have become more connected, compiling their data into near-real-time global snapshots of where and when birders are seeing species.

In the study, published in Biological Conservation, Neate-Clegg, a PhD candidate and lead author, accessed data from eBird, said to be the world’s largest biodiversity-related community science project with more than 100 million bird sightings contributed each year. Birders submit

sightings and checklists to eBird, which reaches out to birding experts when a sighting seems out of the ordinary.

Downloading and analyzing eBird data is not an Excel-scale task. The U’s Center for High Performance Computing assisted in processing the data, which includes more than 800 million records. Using observations from the past twenty years, NeateClegg and his fellow ornithologists further filtered the data to focus on the best-quality observations and to match the list of species with those reported by BirdLife International, an independent global partnership of conservation organizations.

Only a little more than a third of the species displayed trends that agreed between the two data sources. Unfortunately, that’s not much better than would have been expected by chance.

Filling the data gaps

Part of the disagreement is due to the different experiences of birdwatching in the tropics as compared to the U.S. Some results of the study were encouraging, though.

As in an earlier study conducted by now alumnus Joshua “JJ” Horns (PhD’19), Neate-Clegg’s study shows that the rate of agreement with BirdLife trends for a species increases as the number of eBird checklists for that species increases. “This suggests that our accuracy will increase as more people gather data in the tropics,” he says. “It would be great to get to the point where we can successfully leverage what will soon exceed 1 billion bird records to estimate population trends.”

Keep watching and listing

With a need for more quality data, Neate-Clegg encourages eBirders to include as much additional information in their checklists as possible. For example, he says, eBirders have the option of recording all species seen or counts

of every species, as well as associated metadata such as the duration of the birdwatching period and the distance traveled.

“All of these data are important for maximizing the number of checklists we can use while controlling for variation in effort,” he says.

Birding in many different places, and not just hotspots with high species numbers, is also important. “You should be birding everywhere you go,” Çağan Şekercioğlu, principal investigator of the lab and co-author of the research says, “which also has the personal satisfaction of being a pioneer as you are adding data from places with little or no bird data.” (Şekercioğlu is currently ranked fifth in the world for spotting more than 8,000 bird species—more than 76% of all the species that eBirders have ever reported.)

In other words, keep watching the skies. And the trees. And the wetlands. Birders’ efforts do not go unnoticed. “The centurieslong symbiosis between birdwatchers and ornithologists is the best example of the collaboration of community scientists, professional scientists and conservationists,” Şekercioğlu says, who with Neate-Clegg expresses gratitude to all those organizations and birders who collect data.

Birder? Join this cause at ebird.org and at inaturalist.org A different version of this article first appeared in @AtTheU.

“You should be birding everywhere you go.”

Retiring Faculty The Inner/Outer Game of Plants

To know Tom and Lissy is to know that their research is and has been highly personal. And their ambitions would naturally extend to beyond field research to economic opportunity for their friends and associates in Central America, linking even to social justice. Their concern about forest destruction and the peoples who live in those sites has led to bioprospecting. “We used our curiosity-driven (basic) research to create ways to have benefits from intact forests via drug discovery.” Young, expanding tropical leaves invest fifty percent of their dry weight in hundreds of chemicals. “We thought they could be an undiscovered source of pharmaceutical medicines.”

Ecologist Lissy Coley

“I first stepped foot in a tropical rainforest in 1975 and have been back every year doing research on how plants defend themselves against getting eaten by insects,” says Phyllis “Lissy” Coley who retired this year from the School of Biological Sciences. The pandemic has prevented her from heading south this time around, but in fact the rainforest has been a second home. With the late Tom Kursar, her partner-in-life and in work, they blended her training in ecology and his in biophysics to work in multiple countries in both the African Congo and the Amazon as well as in Panama, Borneo and Malaysia.

“Our work has focused on why the tropics are so diverse,” she continues. “How can 650 tree species--more than in all of North America--live together in a single hectare of tropical forest?” Another question related to the first includes what drives speciation. “We have shown that the arms race with insect herbivores leads to extraordinarily rapid evolution of a battery of plant defenses, particularly chemical toxins, such that a given species of herbivore has evolved counter adaptations that allow it to feed on only plant species with similar defenses.”

It turns out that plant species with different defenses do not share herbivores and therefore can co-exist, promoting high local diversity. The concept that the high biodiversity of tropical forests is due to these antagonistic interactions is now widely accepted.

The duo set the project up in Panama, with the majority of the work being done by local scientists. It has resulted in fifteen million dollars of seed money to Panama. Their discoveries have led to promising patents, research experiences for hundreds of students and the creation of more jobs than the country’s ubiquitous and potentially destructive logging. Furthermore the project has established the island of Coiba as a protected World Heritage Site and created a new voice of Panamanian scientists helping to shape government policy and appreciation of their natural treasures.

While Coley has retired from teaching, her lab and its research continues at the School. “I think one of the unifying principles that made our department interesting to me,” she concludes, “is that many faculty were interested at some level in evolution.” The late K. Gordon Lark, department chair in the 70s, was the impetus for that. “Whether we’re talking about molecular or ecological systems, evolutionary/ecological interactions shape all of that. This has been an important unifier of research interest in the School.” Along with recent hires of outstanding young faculty researchers, which she hopes will continue, this “unifier” has helped keep such a large academic unit intact. “It has been sort of the glue.”

As Tom and Lissy have always cared deeply about graduate students, the Coley/Kursar Endowment was established in 2018 to fund graduate student field research in Ecology, Evolution and Organismal Biology. You can make a donation or set up a planned-giving vehicle to further this important work in the School of Biological Sciences at www.biology.utah.edu/ CrimsonLaureate.php

Geneticist Gary Drews

“I wanted to get a more precise understanding of what happens to the plant, in a more controlled way, to grow plants and to subject them to drought stress and water deficiency,” says Gary Drews who as of August 15 has retired from the School of Biological Sciences after 26 years. Originally his model subject in the lab was Arabidopsis before he transitioned to Zea mays or maize (corn) about ten years ago. A geneticist, Drews’ research interest has stemmed in large part from a global concern: the critical need based on world population growth to increase food production in the next thirty years by a whopping 70 percent according to the United Nations Food and Agriculture Organization.

There are multiple drivers for that statistic. “The two big ones,” he says, are the world’s population growth and predictions on the increase in meat and dairy consumption because of greater affluence. “As countries become more prosperous,” he explains, “poor countries move from grain consumption to consuming more meat and dairy.” The example he gives is of China, one of the most populous nations in the world which is rapidly moving toward more of a meat and dairy diet which requires a greater yield of sustainable plant sources, especially grain like corn.

There are 50,000 edible plant species. Of those, Drews explains, only a few hundred currently contribute to human food supplies. And of those few hundred, only fifteen species provide 90 percent of human food/energy. Finally, of those fifteen, just three--rice, wheat and corn--provide 60 percent of human food consumption.

To improve food crop yields to meet a burgeoning demand, a researcher needs to know how stressors are negatively impacting plants. In terms of corn, the major causes of crop losses include drought, heat, excess moisture (flooding), frost/ freeze, wind, disease and insects. The biggest stressor by far is drought, resulting in well over 50 percent of losses.

Some of Drews’ SBS colleagues working in plant biology are focused more on insect/plant interactions such as Lissy Coley (see companion article), while others focus on the macro systems of the ecological sciences such as stressors caused by, among others, global warming. But Drews’ work takes place on the whole organism/physiological level, in the lab… or more precisely in the greenhouse, a collective of glass-enclosed bays on the roof of the South Biology building at the School of Biological Sciences.

There, at a controlled level, he stresses his subject model in various ways to see how it changes genetically. “Our lab studies the molecular genetics of seed development,” says Drews. “Our current focus is on development of the endosperm, an important component of the seed because it provides nutrients and developmental signals to the embryo during seed development.” Endosperm is an important source of food, feed, and industrial raw materials, he explains, noting that approximately two-thirds of caloric intake for humans are derived from endosperm.

This studying of the genetic changes of drought stress is preliminary to the broader, food-production task at hand. “You

can’t fix something until you understand how it works,” he says. “The first phase is to understand what happens to the plant when the plant is subjected to stress, along the way. Only then can you identify what you can do to alleviate it a little or a lot.”

While he is officially retired, Drews’ lab will continue its work for the time being, meeting its funding obligations from the National Science Foundation which has provided grants for the lab for the past 25 years. No longer in the classroom, Drews will have time to do more snowshoeing and hiking—pandemic permitting. At Alta resort in Little Cottonwood Canyon, he has regularly met up with biology faculty for Sunday skiing outings. He also spends time flying off to Washington DC where his wife Janet Shaw, a former SBS faculty member who now keeps a lab in the U of U’s Department of Biochemistry in the medical school, is currently working for the Howard Hughes Medical Institute as a grantor.

As former chair of the SBS Greenhouse Committee, Gary Drews has long advocated for improvements for the glass bays that are critical to the controlled environments necessary for plant biology, both on the genetic level as well as the ecological. Currently, the School has prioritized the greenhouse, long underwritten by donors to the School’s research operations, by setting up feasibility studies for its improvement and/or replacement.

It’s the legacy of Gary Drews’ work that will inspire, in part, the continuance of plant biology at the U, foundational to the School’s origins.

“You can’t fix something until you understand how it works.”

Clifford Stocks

CEO of OncoResponse

In these uncertain times when “the new normal” of our lives has yet to emerge, SBS alumnus Clifford Stocks (BS’80) opens a window to fresh air on the COVID-19 pandemic. That updraft comes from his scientific orientation and is underscored by his enduring ambition to use his training in biology and beyond to elevate the health of his fellow humans.

“At the end of the day the COVID-19 pandemic is a blip,” he reminds us. “Yes, it caused and will cause many premature deaths and a disruption of lifestyle, and in many cases irreversible economic burden. However, the biomedical complex in the world has become so sophisticated we will have treatment solutions and a vaccine in short order.” He continues on the updraft with a coda: “And the world will go on as before, but hopefully this pandemic will help people remember that life can be fleeting and to stop and think about what is important

An alumnus on our singular time, a perspective rooted in valuing not only science but the inviolable drive of people to persevere

to them. And to let those close to them know they are loved.”

It’s a take on this singular time that the world desperately needs right now, a perspective rooted in valuing not only science but the inviolable drive of people to persevere and to assemble ourselves into the collaborative army of our common humanity.

Stocks knows something about perseverance in both the clinical realm and in that of business. Raised in Wyoming before arriving in Salt Lake City, he wrestled in high school and received a scholarship to the University of Utah. “I wrestled four years under coach Marvin Hess,” he says. “This was the only way I could afford to attend college.”

His memories of the U include warm summer nights, trips to the desert—”the heavy focus on the outdoors and exploring the beauty and wonder of Utah”–epitomized by the slickrock country of Moab where Stocks was born. And his time studying biology gave him the opportunity to learn a range of topics in the biological sciences and to determine that he would “dedicate my life’s work toward applying biology to help humankind.”

Not surprisingly, that dedication settled in Stocks largely because of important mentors while at the School of Biological Sciences, including Dr. Mario Capecchi, who would later be awarded the Nobel Prize, and whose biochemistry class “inspired in me a love and respect for the power of molecular biology.”

Dr. Robert Vickery, now SBS professor emeritus, was another formative figure for the budding scientist. He “taught evolution and cemented for me the importance of recognizing natural selection processes in many biological systems,” says Stocks, “including the ability of cancer to form resistance and the power of differentiation in the immune system to combat infection, disease and neoplasms.”

But it was during his senior year as research technician in the laboratory of Seth Pincus, MD in the Department of Immunology at the U’s Medical Center that the young researcher found a home in science. Stocks stayed on there for four years following his graduation from the U in 1980.

After earning an MBA at the University of Chicago where he also did research in molecular genetics and cell biology, Stocks transitioned from the bench to the business side of biotech when he landed his dream position and stayed for 15 years at ICOS Corporation (before it was acquired in 2007 by Lilly

and Company). Following other professional stops Stocks founded Seattle-based biotech company OncoResponse, and as CEO has narrowed his broad range of research interests to immuno-oncology. The company currently has several antibodies directed at modulating immunosuppression of the tumor microenvironment in pre-clinical development and is working toward increasing immunotherapy offerings and improving the lives of cancer patients.

“I have always loved rivers and mountains,” says the former wrestler and kayaker, turning to his life outside the world of the lab and of business. “During the ‘80s and ‘90s I was part of a world class whitewater kayaking team that conquered several first descents of rivers in North and South America. Today Stocks is an avid fly fisherman which keeps him near rivers in the mountains. Along with his wife of 25 years, Renee, and their five children they remain focused on academics, athletics and the outdoors.

“Life and career are a journey so make sure to enjoy it and do not let obstacles weigh you down,” he advises. “Oh, and wear your mask to protect others from the spread of COVID-19, and expect others to do same, to protect you and your loved ones.”

The pandemic may be a “blip,” in the organic scheme of things, but it is also, potentially, a transformative opening for inquiry, discovery and resolution. It is an opportunity for all of us, especially, perhaps, for those at the forefront of public health and in the science-inflected imaginations of those like Clifford Stocks.

Visit science.utah.edu for other alumni spotlights in celebration of the College of Science’s 50th anniversary this year.

“Life and career are a journey so make sure to enjoy it and do not let obstacles weigh you down.”

For undergraduates, the opportunity to share their work during a poster symposium is a powerful learning experience that mirrors professional science conferences and a career in research. The challenge of continuing that opportunity in the time of the COVID-19 pandemic was not lost on the School of Biological Sciences’ (SBS) Tanya Vickers. In addition to teaching in the SBS, Tanya is the Director of ACCESS, a College of Science program which provides freshmen and transfer students a supportive path into STEM degrees and careers.

Science is about preparing the next generation of innovators, explorers, and connoisseurs of curiosity. In the spring of 2020, I was motivated to find a way to preserve the longstanding tradition of hosting an ACCESS research symposium and provide talented first-year student scientists a venue to showcase their experiments in spite of the unique challenges presented by COVID. Just six weeks before the event, I decided to develop and launch a novel virtual research symposium to ensure ACCESS students could still present projects they’d invested so much in during their first year at the U. Despite the considerable challenge, it was also an opportunity to pursue and explore innovative approaches to hosting a research symposium virtually that, if not for COVID-19, would be stagnant in its delivery.

It’s been six months since the virtual symposium and I am still surprised by its success. The merits and results of the platform challenged the notion that in-person is best. Data from the spring 2020 ACCESS Virtual Research Symposium revealed the platform garnered 6,000 page views in a mere three days, and upwards of 500 guests attended student scientists’ live Zoom presentations, including Q and A sessions. In contrast, the in-person symposia typically only yielded about 200 guests each year. The virtual platform is a model that continues to be used in various applications for ACCESS. It has also been the foundation for other similar conference outings at the University of Utah, such as the first ever virtual SBS Science Retreat in August of this year.

Together Apart

A virtual symposium elevates learning during COVID

How a novel virtual symposium was realized in just six weeks’ time involved many moving parts, departmental support and cross-campus collaborations. My experience teaching and using Canvas, a learning management system in place at many universities, including the U, shaped the content, and with the collaboration and support of Micah Murdock, Associate Director of Teaching and Learning Technologists (TLT), a novel virtual research symposium was fully realized.

“Nearly all other events were cancelled,” said Sahana Kargi, Math major. “I was surprised [Tanya] had scheduled a meeting with us. When we spoke, she was so excited about the virtual symposium and I was just as excited by the end of it!”

The platform was a lofty goal that required three defining features: a webpage for students to introduce their project, a message board for peers, guests, and mentors to pose questions, and a live Zoom presentation with question and answer. Each student’s personal web-page featured their research poster, a three-minute video summary of their project, and a personal

bio. These elements provided guests with project introductions analogous to an in-person symposium, but without any time constraints. Thus, questions and comments could be primed for using one, or both, forum tools—the student scientist’s discussion board, or the thirty-minute Zoom live session scheduled on the last day. The dividends of the new symposium approach are sometimes hidden.

Tessa McNamee found the symposium critical to illuminating holes in her understanding. “I realized that the communication aspect to science was a side I had never given much thought to, and the experience [made me appreciate] my professors and other professionals who are able to clearly articulate difficult concepts.”

We wanted to build a tool with the future, as well as other disciplines and applications, in mind. In just a matter of months,

this new tool has been adapted and repurposed for different uses campus-wide. Most recently, it was chosen to serve as the cornerstone of a novel College of Science high school outreach program called Science Now. The spectrum and variety of applications the platform has already been used for, including connecting U students with non-student and nonUniversity populations, demonstrates its utility and potential.

Novel educational tools and teaching strategies are emerging across campus and around the world as we learn how to be “together apart.” The virtual symposium platform, like most projects, has been successful because we were able to quickly leverage existing tools like Canvas, and with the collaboration and support of Micah Murdock, Associate Director of the U’s Teaching and Learning Technologists (TLT) and Samantha Shaw, College of Science Program Manager. The rigor, flexibility and permanent nature of the platform will undoubtedly remain in use, even long after social distancing is a thing of the past and campuses are bustling once again.

In our darkest hours, we find a space for new forms of unity and growth, and can challenge ourselves to create and expand. As a species and as scientists, we always look forward to new ideas and what can be done. COVID has been undeniably difficult for everyone, but the development of new platforms and technologies…show that we can still be together while we are apart, and sometimes, when we are forced to make changes to long-held traditions the outcome reveals hidden opportunities to go beyond finding an equivalent, and make what we thought was “best,” even better.

In addition to the technical help I would like to recognize the thirty-five ACCESS students, and their faculty mentors, for their willingness to adapt and produce the required materials, and most of all, for believing in the vision and potential of a virtual research symposium.

“The symposium being virtual allowed me to interact with people who may not have been able to attend the in-person event. My high school Chemistry teacher was able to visit during my [Zoom] live poster presentation.”

—Tayla Chiang, Biology major

“The nature of a virtual symposium also means that we will have our own 2020 symposium online for years to come, … something we can look back on and be proud of the effort we all put in.”

—Emma Kerr, Physics major

Jordan Herman, PhD

Few encounter a fer-de-lance snake and walk away unscathed.

While working in Costa Rica recent School of Biological Sciences (SBS), graduate Jordan Herman (PhD’20) moved closer to observe a toucan dismembering the green iguana it was having for lunch. When the bird took off and dropped half of it, Herman picked up the iguana’s tail and realized she had nearly stepped on the coiled and camouflaged pit viper at her feet. As the bird returned to finish its meal, Herman stood still, suddenly stuck between an intimidating toucan and the venomous snake. She escaped the dangerous situation by offering up the tail and backing away slowly.

For Herman, this moment earned her “a new appreciation for how cool and terrifying nature can be.”

Herman originally came to the SBS graduate program in 2014 from the University of Minnesota—Twin Cities. Her research has been focused on the fitness consequences that mockingbirds experience when they are co-exploited, how the co-occurring parasites interact with each other, and the roles that host defenses play in these species interactions.

A postdoctoral fellow in the Clayton-Bush lab, Herman thrives in the outdoors and has always been captivated by birds. While working as a field assistant in the Galapagos Islands off the coast of Ecuador, she became hooked on parasitic nest flies and their endemic bird hosts. This interest, in turn, brought her to Argentina, where she worked on the effects of parasitic nest flies and brood-parasitic cowbirds on their shared host, the chalk-browed mockingbird.

Her passion for the outdoors extends to her adopted home of Utah. When she isn’t backpacking all over the Intermountain West, you can find her spending time in her Salt Lake City garden with her four chickens—Dotty, Penguin, Mungo, and Jerry. Currently, she and her partner Joey have also been treating themselves to sushi takeout from Sapa, a local Asian fusion restaurant where, she says, “you can still order mussel shooters!”

Outside of her research, Herman has also made a lasting impact in SBS where she is grounded in a close-knit community of biologists with wide-ranging research interests. As a mentor, she has soared by offering strong support and advice to those around her. “Jordan’s unwavering sense of self allows her to be a generous mentor,” explains fellow graduate student, Maggie Doolin (Dearing lab), “and one of the most consistent sources of truth and support I’ve encountered anywhere throughout my life. She is one-of-a-kind,” continues Doolin, “and I’m lucky to have had her welcome me to the SBS grad program for all things life and science.” When asked what the best advice Herman herself has received in graduate school, she replies, “Publish early!” You can find Herman’s publications in journals like Ecology and the Journal of Avian Biology.

Clearly an expert in field research, Herman uses her knowledge to give back to her community. “Given the amount of field research, field courses, and outdoor recreation that happens in SBS, our community has a major need for wilderness preparedness,” she says. This need gave rise to Herman’s involvement in developing the biennial subsidized Wilderness First Aid course which is available to students, faculty, and staff in the SBS. A future goal is to expand this program to more personnel across the College of Science.

Jordan Herman, PhD, is truly a force of nature. Next time you’re stuck between an intimidating toucan and a camouflaged pit viper, remember to ask yourself, WWJHD?: What would Jordan Herman do? The School of Biological Sciences is indebted to Jordan Herman. She will always have a place here among the wide variety of birds and lifelong friends nestled at the base of the Wasatch Mountains.

Anna Vickrey, PhD

Anna Vickrey, who graduated from the School of Biological Sciences with a PhD in 2020, has always been fascinated with domestication.

Her interest includes both the process and the “products,” which include the plants and animals important to our lives and history as humans. “I became really interested in the morphological diversity present both in domestic breeds and natural species by going to a lot of dog shows,” she says.

The Salt Lake City native also had chickens and pigeons growing up, and spent time around wild bird species. “My mom ‘rehabbed’ wild birds out of our house,” she reports. As an undergrad at the University of Utah, she became curious about how diversity is generated at the genetic level. “Naïvely, I was wondering if differences in morphology are generated by ‘coding’ or ‘regulatory’ changes to genes. In reality,” she admits, “it’s more complicated than that!” Fortunately for her, this was one of the questions that Professor Mike Shapiro was asking in his pigeon lab, which she was able to join and where she continued working through her graduation last spring.

Vickrey keeps pigeons as pets, mostly American Show Racer and Archangel breeds, so the model subject of her research for the past several years is one in which she’s had a longstanding interest. While in the Shapiro lab, she studied wing color patterns in domestic pigeons. “Even though we know that color patterns are really important for animals in the wild for things like camouflage and mate choice, there’s still a lot that’s not known about how patterns are generated at the genetic and molecular level,” she says. “I also work on head crests, a type of ornamental feather structure—sort of a fancy feather-do— that are present in lots of pigeon breeds and wild bird species.”

For each of these projects, she and her team learned some surprising things about the genes that cause these traits. For example, pigeons with a wing color pattern called “barless” also can have vision defects that are called “foggy vision” by pigeon breeders. “The gene that we found is associated with the barless color pattern is known to cause hereditary blindness in humans when the gene is mutated.” And while the researchers didn’t expect to discover this connection, foggy vision in barless pigeons is caused by eye defects that are similar to humans with this type of hereditary blindness.

Staggeringly, there are over 300 breeds of domestic rock pigeon. Similar to dogs, these breeds can look extremely different from one another (think of the difference between a Chihuahua and a Great Dane) even though they’re all the same species. Also, the pigeons all over a typical city like Salt Lake are “ferals,” she explains, meaning they’ve descended from the same domestic species.

The School of Biological Sciences houses research on a huge diversity of topics. “As an undergrad and then a grad student I’ve always felt very lucky to have exposure to such diversity— everything from crystallography and protein biochemistry to rainforest ecology!” she says. Now with her PhD, it’s clear to Vickrey that it’s important to be a lifelong learner. Even while currently finishing up the projects in the Shapiro lab, “we’re starting to get some really cool results looking at the bright red skin around the eyes.”

In turns out that the color may be another trait that was hybridized into domestic pigeons from the African speckled pigeon. She and her colleagues will also be kept busy during the next few months looking for modifier genes that control head crest size.

And what are her plans long-term? “I want to stay on a career path that allows me to continue to communicate science while keeping me connected to science. I’m really interested in genetic counseling but I’m also looking at a science policy fellowship.”

Amy Davis, PhD’03

“I enjoy learning about how infectious diseases have shaped human history because I find it inspiring to frame my current work in a broad historical context.”

Senior Director, Biochemistry Research & Innovation at Utah-based BioFire Diagnostics, LLC, Davis says she was “fortunate to be born into a world with antibiotics and large-scale vaccine production,” while reminding us that “these tools in humanity’s struggle against microbial pathogens have only been around for the last 70-80 years.”

With her work at BioFire whose systems have become the new standard for syndromic infectious disease diagnostics, what she calls her “obsession” with the history of medical science could not have converged at a more timely, and daunting, time. The coronavirus pandemic in the United States is currently emerging in a scorching third wave, and there is a herculean effort underway to bring a vaccine to market. This, of course, will require accelerated and accurate diagnostics, something BioFire’s co-founder Randy Rasmussen, also a PhD alumnus (’98) from the School of Biological Sciences, recently reiterated during a virtual COVID Salon sponsored by SBS in May of this year.

Davis, who earned her BS in biology with honors from Penn State, followed by a year as a Fulbright Scholar, recalls what first drew her to graduate school at the SBS. It was the “fabulous faculty, collaborative culture,” and, of course, the spectacular mountain setting. “My graduate education at the University of Utah taught me how to think critically, work diligently, shake off setbacks, and thrive on the pursuit of understanding,” she says. “I loved everything from the journal clubs to late nights in a quiet lab dissecting tetrads to ‘TA-ing’ for Joe Dickinson’s Genetics course to planning the next experiment.”

She remembers that seeing the mitochondrial net phenotype for the first time in a yeast mutant she had isolated in a genetic screen was “pretty exciting!” She also remembers fondly Professor Janet Shaw. While studying the molecular mechanisms of mitochondrial dynamics in Shaw’s lab, Davis was taught by her “amazing mentor and friend…how to ask the right questions, how to write, how to present, and how to balance.”

That training, experience and mentoring have served Davis well. Following her graduation from SBS, she did a post-doc on the other side of the Rockies--at the University of Colorado, Boulder. There she was at the bench researching the biology of the yeast telomerase RNA, an essential core component of the telomerase ribonucleoprotein (RNP) enzyme that synthesizes telomeric sequences onto chromosome ends.

The call of the Wasatch Front, however, as well as that of the U’s Brain Institute, propelled Davis in 2007 back to Salt Lake City where she was manager and then associate director at the Institute for a total of six years. Following that she moved to the U’s Medical School for a two-year stint to help establish a research program development office.

A career in what’s been called “The Century of Biology,” especially as it relates to health, can take one on a circuitous route. Davis’ has been no exception. After spending 20 years in academic environments, Davis made the leap to work in industry. At BioFire she learned to work with dozens of complementary teams to translate research ideas in robust clinical diagnostic tools. To broaden her experience in the biotech space, Davis accepted a role at the start up IDbyDNA

as VP of Operations. The company, also located in the U’s Research Park with BioFire, works in metagenomics technology to simultaneously profile tens of thousands of microorganisms and pathogens in any sample.

Emblematic of the extraordinary synergy Research Park was designed for, companies like BioFire and the newer IDbyDNA create opportunities for not only advancing medical technology but the careers of many University of Utah alumni. Davis later returned to BioFire as a Senior Director in research and development, where she is enjoying applying the perspective gained from operations roles to early-stage innovation projects.

To date, no other company has FDA-cleared and CE-IVD (European Union-cleared) marked assays for more pathogens than BioFire. Again, the timing of the company’s ascendancy has proven auspicious.

“As we are learning from COVID,” says Davis, “emerging pathogens (and emerging antimicrobial resistance of old pathogens) can challenge societies in significant ways. …The more we learn about the patterns of infectious diseases and human efforts to understand and combat their microscopic agents, the better we can prepare for present and future threats.”

While COVID has focused global attention on the threat of emerging viral respiratory pathogens, she says she hopes that this “reality check bolsters efforts to combat emerging antimicrobial resistance in pathogens that have been with us for centuries.”

Meanwhile, Davis continually returns to her passion for the history of medicine. She finds that her reading deeply informs her intense career at BioFire, providing perspective, inspiration and context for their work. And what exactly is on her bedside reading stand? The Mosquito by Timothy C. Winegard; the portentous sounding Superbugs: The Race to Stop an Epidemic by Matt McCarthy; and Microbe Hunters by Paul de Kruif.

From these historical tomes she is happy to base her advice to new graduates of the School of Biological Sciences, particularly telling during this pandemic time: “Take the long view and train for a career that will fulfill you ten, twenty, thirty, forty years from now.”

Visit science.utah.edu for other alumni spotlights in celebration of the College of Science’s 50th anniversary this year.

“Take the long view and train for a career that will fulfill you ten, twenty, thirty, forty years from now.”

Briefly Noted

Professor Dave Bowling was awarded a Faculty Research Award in April at the first virtual commencement in the history of the U of U. Faculty awards range from distinguished teaching to faculty service, and from community engaged teaching to bestowing distinguished professorship status. Even a high school teacher is recognized each year. This year biology teacher Robert Durham (East High School in Salt Lake City) received acknowledgment. The Bowling lab, an affiliate with the Global Change and Sustainability Center, studies how environmental and climate change affect the carbon and water cycles of forests, grasslands, and shrublands of the mountain West.

Maria-Jose Endara received an award from The World Academy of Sciences (TWAS-UNESCO) which is the most prestigious recognition granted to young scientists from developing nations who have made outstanding contributions to the international advancement of science. She is the first woman and third scientist from Ecuador to have received this award, and to recognize this honor, the Ecuadorian Congress presented her with the Pedro Vicente Maldonado Medal. Endara received her PhD in 2015 from the Coley-Kursar lab, and has continued to collaborate with Lissy Coley on the ecology and evolution of tropical trees. This past August, Endara was one of two post-docs to present her research during the annual SBS Science Retreat. She presented via Zoom from Ecuador.

Professor Michael D. Shapiro has been named the James E. Talmage Presidential Endowed Chair in Biology. The appointment is for a 5-year nonrenewable term ending June 30, 2025. Shapiro (PhD 2001, Harvard University) joined the Department of Biology (now SBS) as an Assistant Professor in 2006 and has developed an international reputation for his exciting and original research in the fields of Evolutionary Developmental Biology (“Evo-Devo”) and Evolutionary Genetics. His early work on the evolution of morphological diversity in stickleback fishes is highly respected and his group is responsible for many significant advances in this area of inquiry. After arriving in Utah, he developed an entirely new line of research aimed at identifying the

genetic changes responsible for morphological variation in domesticated pigeons. Shapiro has served as a Division Leader of the SBS since the school was formed in 2018 and prior to that as an elected member of the Executive Committee. The Endowed Chair is named after James E. Talmage (1862–1933), a scientist, leader in the Church of Jesus Christ of Latter-day Saints and early president of the University of Utah.

A Beckman Scholarship was awarded to SBS’s Sonia Sehgal. The Program is a 15-month mentored research experience for exceptional undergraduate students in chemical and biological sciences. Associate Professor Martin Horvath will serve as her mentor. Each scholar receives a $21,000 research stipend to facilitate nine academic calendar months and two three-month summers of research experience. The students will also participate in the prestigious Beckman Symposium each summer with other Beckman Scholars from around the nation. Their research will begin in June 2020 and conclude in August 2021.

Graduate student and Stringfellow Scholarship Recipient Jinzhi Li (Caron lab) is lead author of a notable cover article published in the journal Cell Reports: “Visual Input into the Drosophila melanogaster Mushroom Body.” The research highlights fundamental differences in the way associative brain centers integrate sensory information. Undergraduate researchers Brennan Mahoney and Miles Jacob (the latter of whom is a recipient of an SBS Research Scholar Award) are co-authors of the article along with PI Sophie Caron. The Drosophila melanogaster mushroom body—an associative center—is an ideal system to investigate how different sensory channels converge in higher order brain centers. “Together,” reads the abstract “with previous work that described a pathway conveying visual information from the medulla to the ventral accessory calyx of the mushroom body, our study defines a second, parallel pathway that is anatomically poised to convey information from the visual system to the dorsal accessory calyx.”

Scholarships such as those noted above are funded by alumni and friends. We thank all of our donors for their support.

Visit science.utah.edu for long-form alumni spotlights in celebration of the College of Science’s 50th anniversary this year.

Crimson Laureate Society School of Biological Sciences

NOVEMBER 2019 TO NOVEMBER 2020

Donors Over

$29,999

Batubay Hamit Ozkan

Donors Over

$9,999

John Marcell Davis, MD

Naomi C. Franklin

George R. Riser

Jon Seger, PhD and Victoria J. Rowntree

Roger L. Aamodt, PhD

Albert G. and Christine M. Anderson, PhD

Richard and Shirley Behrendt

L. Beth Blattenberger

Thure E. Cerling, PhD and Mahala Kephart

Stephen L. and Nicola Dahl, PharmD

James K. and J. Linda Detling, PhD

James R. and Edna M. Ehleringer, PhD

Briant J. and Glenna R. Farnsworth

Donald H. Feener Jr., PhD

Joseph and Mya Fullmer, PhD, MD

Apple Gaffney

David P. Goldenberg, PhD

Tulle Hazelrigg

James Madison E. Hunt, MD

Donors Over $4999

Dennis M. and Jean C. Bramble

Sue M. Durrant, PhD

Donors Over $999

Gregory Acland

Michael J. Bastiani, PhD and Denise Dearing, PhD

Lane C. and Paula W. Childs, MD

George C. and Lisbeth L. Elliott, PhD

Mark T. and Brenda Nielsen

Constantine P. Georgopoulos, PhD and Deborah Ang, PhD

Darren W. Housel, MD

Kristin Erickson Levinson

Dennis L. and Patricia A. Lombardi, MD

Donors $50 to $999

Aaron Paul and Chantel Lucile Jenkins

Roydon O. and Paula F. Julander, PhD

Daniel V. Kinikini, MD

Elizabeth Marie Kralik

Robert O. and Judy R. Kron

Sally L. Kursar

Samantha Ann Marshall, MD

Jed B. and Kathryn G. Marti, PhD

Jeffrey Masters, PhD

William E. Miller Jr., MD

Steve Mimnaugh, MD

William L. and Jane Ehardt Moore, PhD

Christopher P. Murdock

Larry Okun

Philip Paradis

James E. and Margaret A. Parry, PhD

Erik Mathias and Nan Jorgensen, PhD

Edward A. Meenen

Frank G. and Sharon R. Meyer

Stanley A. and Jane S. Mulaik, PhD

Burak Over George G. and Linda A. Seifert

William B. and Vivien G. Terzaghi, PhD

Neil & Tanya M. Vickers, PhD Doju Yoshikami, PhD

Clark B. and Sherrie W. Rampton

Gary L. and Norma D. Ranck, PhD

Lee K. and Dawn L. Roberts, PhD

Robert B. Roemer, PhD and L. Irene Terry

Douglas Samuel and Jeannie M. Prince, USN

Robert Anselmo Sclafani and Christine M. Roberts

Patricia Sharkey

Stewart Shuman

Glade V. Sorensen

Michael and Ruth C. Stevens, MD

Thomas E. Tomasi, PhD

John F. Unguren, DDS

Kevin Wendell and Filinita Tupou Nemelka

Richard J. and Shelly A. Williams, MD, FACS

The Crimson Laureate Society

As you can see from reading through this issue of Our DNA, the School of Biological Sciences is open for business during the pandemic and is, in fact, innovating how we deliver services and carry out our research in ways that would not have happened without the emergence of COVID-19. A good example of this is the story in this issue about Tanya Vickers’ development of a new platform for online workshop and symposium hosting that is now being used by many other departments and academic units at the University of Utah.

Even so, we have many students, particularly undergraduates, who are attempting to weather financial hardship. For this reason the College of Science, which is celebrating its 50th anniversary this year, is asking our devoted friends, alumni and past donors to help us reach biology’s match by an

anonymous alumni donor of $10,000 for the College’s Student Emergency Fund.

All donations will go directly toward the support of biology students who have lost jobs, are struggling to pay tuition, or who need extra monetary support during this singular time.

Thank you for your generosity. Your gift will help ensure the School’s success through the success of our students.