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N E W S for A L U M N I

BIOLOGY NEWS  |  SPRING 2021

V R A N A T O M Y    |    P L A N T P A N D E M I C S    |    B U S I N E S S O F B E E S


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Contents 1 2 4 8 9 10 12

From the Co-Directors

Some Sunshine at the End of a Tough Year!

Mitigating Plant Pandemics

Talia Karasov on the Impact of Plant Immune Diversity on Pathogen Evolution and Spread

Retiring Faculty

Birdsong and Tree Top Barbie

Outreach

Bee Campus USA

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Publisher University of Utah School of Biological Sciences 257 S 1400 E, 201B Salt Lake City, UT 84112-0840

School Directors Leslie Sieburth Neil Vickers

Writer & Editor David G. Pace

Alumni Relations  |  Development Committee

Distinguished Alumni Awardees

Nalini Nadkarni Çağan Şekercioğlu Neil Vickers

Pedagogy

On the Cover

Reshma Shetty and T. Mitchell Aide

Dissecting an Alligator—Virtually

Tributes

Remembering SBS Catalyst Gordon Lark In Memoriam: Friedrich Bonhoeffer

Stay connected Visit, respond, subscribe, donate: www.Biology.utah.edu

Genetically, Arabidopsis populations are largely resistant to being overtaken by single strain outbreaks of the bacterial pathogen Pseudomonas syringae. Both plant (pictured here) and pathogen (detail of which is pictured on the back cover) are the subject models of the Karasov lab and inform the development and deployment of pathogen-resistant crop varieties to address global food insecurity. Photo by Matt Crawley Back cover micro photo by Birgit Schröppel and Sonja Kersten at the Natural and Medical Sciences Institute at the University of Tuebingen and Max Planck Institute for Developmental Biology, respectively Request an e-version of OUR DNA in place of a mailed copy at development@biology.utah.edu

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FROM THE DIRECTORS

Some Sunshine at the End of a Tough Year!

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t has been a strange year to be at the University. Usually a bustling hub of activity, the last fourteen months have seen the campus become serenely quiet. Few students walking from class to class, only occasional sightings of colleagues in the hallways, deserted coffee carts. For many there have been tragic losses and difficult challenges. With the help of a generous donor who provided matching funds, our alumni, faculty and staff raised a significant amount of emergency funding to support students who were struggling to make ends meet and continue their education during the pandemic. We are truly grateful to all those who donated.

The end of the academic year saw the clouds lift a little, allowing a bit of sunlight to shine through. Although much of the School of Biological Sciences undergraduate teaching occurred online this past year with the notable exception of several laboratory classes that were run in-person, we were able to celebrate the graduation of College of Science degree recipients with a convocation ceremony held in the spectacular setting of Rice-Eccles stadium. Students were safely arrayed in seats on the turf with parents and supporters cheering from the stands! It was a beautiful day and a fitting way to send off our graduates at the end of this unusually taxing year. At the conclusion of the ceremony, many students spontaneously tossed their caps in the air—a great memory. In the afternoon, we honored our SBS advanced doctoral degree recipients with an in-person hooding ceremony. Academic regalia hails back to clothing worn by clergy from the 11th and 12th centuries. Hoods were worn by monks to keep warm in the cold monastical libraries where they studied, copied and preserved the record of written knowledge. Over time the hoods were embellished with colors and came to signify that the recipient had made original contributions to knowledge. It was a great pleasure to personally recognize each of our graduates. Although the past year has been very demanding for everyone, you’d have to admit that it’s been a fascinating

year to be a biologist— witnessing what we study and learn both in the classroom and research laboratories emerging from the pages and taking on a very real form. Understanding epidemiology, the biology of viruses, how messenger RNA vaccines are made and Co-Directors Leslie Sieburth and Neil Vickers work, natural selection and the emergence of new variants, statistics–experiments–trials–control groups and evaluating data have all been at the forefront of understanding and beating back the pandemic. We hope you enjoy this issue of Our DNA in which we feature Assistant Professor Talia Karasov—a new faculty member who works on the interactions between microbes and their plant hosts. We also celebrate the retirements of two of our esteemed colleagues, Professors Nalini Nadkarni and Franz Goller. In addition, we recognize our 2021 Distinguished Alumni award recipients, Dr. Reshma Shetty and Dr. Mitchell Aide. We hope that by the next time we pen our Directors’ message a new normal will have emerged and many of the familiar aspects of university life will have returned. Meanwhile, have a terrific and safe summer.

Neil J. Vickers  |  Leslie E. Sieburth Professors and Co-Directors School of Biological Sciences

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RESEARCH

Mitigating

Plant Pandemics I

t’s not easy for anyone to navigate the pandemic these days, let alone a 5.7 earthquake and then hurricane-force winds that uprooted thousands of trees in Salt Lake Valley.

Harder still when you’ve been tapped in Germany to be a new faculty member in the School of Biological Sciences… and you have a lab to launch. Such was the case last year when Talia Karasov, an evolutionary geneticist who studies plant-microbe interactions at the Max Planck Institute in Tuebingen Germany, found herself on an airplane headed to Salt Lake City. She is part of a recent innovative hiring cluster at the University of Utah in which multiple, related academic units come together to hire researchers who study related topics in evolutionary biology.

For Karasov, “going boldly where no one has gone before” is decidedly earthbound. 2

Karasov made it safely, masked and sociallydistanced, to Utah and began setting up her lab—similar to launching a startup. It’s been a whirlwind execution. Fortunately, her dog “Laika,” named after another famous traveling dog (the first to orbit earth… on the Russians’ Sputnik), has been there all along as a steadying force. Traversing new frontiers is in the family, apparently. For Karasov, though, “going boldly where no one has gone before” is decidedly earthbound… through flora and its pathogens. Plant pathogens pose a huge problem for food security around the globe. Annually, plant pests—including microbes and insects—are responsible for 20–40% loss in agricultural yield. Decades of research on pathogen resistance has led to great success in identifying, developing and deploying pathogen-resistant crop varieties. Unfortunately, pathogens often evolve quickly to overcome these resistance traits. A common pattern has emerged in which a single genotype of pathogen evolves to circumvent resistance, and spreads widely to other populations and then globally. Once the pathogen evolves to circumvent resistance, the cycle begins anew. It’s hard if not impossible to keep up with these arms races in various cash crops, especially when the cycle of resistance/counter-resistance can happen within a few years. This boom-bust cycle may not be inevitable, however. Indeed, anecdotal evidence from wild plant systems suggests that many (if not most) wild plants are less likely to suffer epidemics. In her research of plant-pathogen interactions Karasov studies non-agricultural plant systems to understand which factors


are important for preventing outbreaks. Substantial evidence points to the role of diversity—genetic and environmental—in keeping plants healthy. It has been widely hypothesized that genetic diversity in plants, or the lack thereof, plays a central role in plant-pathogen epidemics. In modern agriculture, we often plant single genotypes of crops across large areas. This low genetic diversity sets up a perfect environment for a pathogen to invade and spread widely. In contrast, wild plants differ between individuals in their immune systems, and a pathogen that can infect one plant in a population may not find success in the neighboring plant that encodes a different immune complement. Karasov’s work seeks to explicitly determine the impact of plant immune diversity on pathogen evolution and spread. “How are pathogens evolving and spreading in wild, heterogeneous populations?” is a central query propelling Karasov’s research. She begins asking this question by

performing field surveys to assess the abundance and genotypes of pathogens infecting wild populations. Once she has determined which microbes are colonizing a host, she uses comparative and population genomics analyses to determine which plant and microbial genes are evolving in response to one another. These coevolutionary analyses pinpoint the molecular mechanisms that plants use to resist pathogens and that pathogens use to infect plants. During her post-doc studies at Max Planck she and her team sought to learn about pathogen adaptation to a diverse host by studying wild populations of the model plant Arabidopsis thaliana. Karasov found that Arabidopsis populations were largely resistant to being overtaken by single strain outbreaks of the bacterial pathogen Pseudomonas syringae. Genetic diversity in Arabidopsis populations seems to have forced the diversification of the pathogen population, and has prevented any one pathogen from causing widespread disease. This research also identified numerous rapidly evolving genes in the pathogen populations that may be evolving in response to changes in the host populations.

“How are pathogens evolving and spreading in wild, heterogeneous populations?” Through this interdisciplinary work that synthesizes field work with comparative genomics, microbiology and molecular biology Karasov and her colleagues are starting to get a picture of which genes and environmental factors are important for preventing pathogen spread. It’s the sort of question embedded in host-pathogen evolution and the maintenance of genetic diversity that will certainly inspire inquiries here in Salt Lake City and to possible solutions to the fast turn-around cycle of defense-counter-defense in crop yields essential to our own survival as a species. Meanwhile, since arriving in the Beehive State, Karasov has been joined by another four-legged friend, a cattle dog adopted here in Utah, and together they have successfully made a home despite the epidemio-, geo- and meteorological challenges they’ve faced.

 Karasov masked with Laika at the airport on their way to Utah

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FACULT Y

Photo by Skyler Ewing on Pexels

Swan Song

for Birdsong Retiring Faculty: Franz Goller

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hy do birds sing? This is an age-old question, and answers have been proposed by everyone from Artistotle and Aristophanes to David Attenborough and the late poet Maya Angelo, but just as interesting as the “why do birds sing?” is the “how do they do it?” Dr. Franz Goller, who is retiring from the School of Biological Sciences after twentythree years, has made significant advances to our understanding of how birds sing. His work has elucidated the mechanisms of neuromuscular coordination of the various systems involved in birdsong production, systems that are analogous in interesting ways to human speech. Walking into Franz’s lab in 2002, I was, of course, first struck by the musicality of the space. There were scarlet-beaked zebra finches hopping on and off their perches. Starlings, robins, white-crowned sparrows, and yellow-headed blackbirds, and around all of these birds were curious scientists trying to listen in (so to speak) for a deeper understanding of how these birds produced sounds. Franz was asking questions such as: How do birds learn to sing? Why do different species 4

By Sylvia Torti

generate such different ranges of sound features? What aspects of song are difficult to produce and make individual birds into vocal athletes? Do individual birds’ individualistic skill sets and weaknesses appear in their song performance? And perhaps most startling, Why do birds silently sing in their dreams? Pursuit of these questions led Franz frequently from his lab and into the outdoors. He established collaborative friendships with colleagues in the US, Europe, and South America and travelled in pursuit of birds that allowed him to address his ever increasing number of questions. What I found so rare was that Franz opened his lab, and shared his love of birds, birdsong, and scientific exploration (as well as good coffee) not only with students, budding scientists, and colleagues, but also artists and writers. I was a fortunate recipient of his openness and patience, which resulted in my novel Cages (Schaffner Press 2017), a fictional story that takes place largely inside a birdsong laboratory. Franz also collaborated with Krista Caballero and Frank Ekeberg (a visual artist and sound artist, respectively) on their Birding the Future series entitled Lab Birds (https://www.birdingthefuture.net/lab). This willingness to engage other disciplines and to take the time to enter into protracted, often difficult conversations around


communication, the limits to scientific inquiry, and ethical questions is part of what makes Franz so unique. Franz’s scientific contributions are many and broad. Early on, using the first-ever fiber optic visualization of the syrinx, he showed direct evidence for the mechanism of sound generation by the syrinx. He then made major contributions to our understanding of how peripheral mechanisms (muscles and nerves that drive the entire sound system from the brain to the air sacs to the beaks) contribute to sound production. Perhaps his most lasting impact from this work on peripheral mechanisms is the utility of this information to those who study the brain, behavior and evolutionary significance of communication behavior. His contributions played a central role in understanding vocal performance in these other disciplines, specifically animal behavior, tradeoffs or cost of song, sexual selection and evolutionary trends in different groups of birds in terms of acoustic features (by syrinx structure) important for vocal performance. Franz is always looking for new ways to ask questions about song and most recently, he has been investigating how sleep may be involved in song-like activation (and memory) in the brain. Originally from the Tyrolian region of Austria, Franz received his undergraduate and MSc. degrees from the University of Innsbruck. He then came to the US for his doctorate (University of Notre Dame) and post-doctoral work (Indiana University). He joined the University of Utah’s Department of Biology, now the School of Biologial Sciences, in 1998. Over the course of his career, he received millions of dollars in research funds to support his work as well as that of nine graduate students and six post-doctoral fellows. Graduate students across campus sought out Franz to serve on their theses committees for his attentiveness to their work, his creative input and his showing up for meetings on time! For these traits, he was often asked to serve on committees in areas well outside of his expertise, spanning neuroscience, behavior and physiology of vertebrates, neuroethology and thermoregulation in insects, etc. In the last five years alone, he served on twenty PhD committees. Franz is also a well-loved professor who was extraordinarily generous with his time. He taught courses in SBS that ranged from large courses (Evolution and Diversity of Life) to specialized physiology courses (Comparative, Environmental and Human Physiology) to Honors courses (Science and Storytelling) to field courses (Natural History of the Colorado Plateau where students not only raved about the science experience, but the daily meals cooked by Franz). The School of Biological Sciences thanks Franz for his contributions and wishes him the best in his upcoming years as Emeritus Professor of Biology.

Diversity Fellows Program

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he second annual Diversity Fellows Program took place virtually in November 2020. The initiative supports undergraduates who are applying to Biology graduate programs, identify with axes of diversity which have been historically excluded from STEM, and who aim to enter a biology grad program within the next one-to-three years. Participants who identify with marginalized communities are especially encouraged to apply.

The School of Biological Sciences aims to build a more equitable community where people of color, LGBTQ+ individuals, undocumented, and first-generation students are welcome and valued in scientific research. At the virtual workshop, seventeen Diversity Fellows worked on aspects of their applications to biology graduate programs and/or secured resources to support their STEM careers. “Because we went completely virtual last year,” says Andy Sposato who with Thien Vu—both SBS graduate students—organized the event, “it was important to us to develop some video materials for participants to view prior to the live workshop day. Basically, we used a flipped classroom approach.” Workshop components included reviews of personal statement drafts submitted by fellows, virtually live Q&A panels and video interviews with University organizations offering resources. Also included were an application workshop and a virtual poster session where fellows could ask more questions, learn about current research in SBS, and network with each other using the social platform Gather Town. Fellows “Zoomed in” from Utah, California, Texas, Colorado, New York, Washington, Rhode Island, Pennsylvania, Canada and Ecuador. An alumni from the 2019 Diversity Fellows Group, Hannah Young (they/them). who is now a graduate student at SBS, paid it forward by volunteering this year and said, “I couldn’t be more excited to pursue my graduate education here!” For this and other work in equity, diversity and inclusion (EDI) at SBS, Sposato and Vu were recognized during the SBS awards ceremony in April for their contributions to increased EDI in the School.

Syliva Torti is Dean of the University of Utah Honors College, SBS adjunct Professor, and alumna of the School (PhD’98). She is the author of two novels, including Cages, winner of the 2016 Nicholas Schaffner Award for Music in Literature. 5


FACULT Y

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r. Nalini Nadkarni has a busy brain. I should know; I’ve been married to her for nearly forty years. She can be described as (in no particular order): a taxi driver, surveyor, hitch hiker, pioneering canopy researcher, forest ecologist, mother, TED talk giver, science and art mixer, teacher, science-to-incarcerated promoter, solo hiker, Canopy Barbie creator, science and religion cross-linker, disturbance and recovery specialist, nationally-recognized public speaker, nature fashionwear designer, woodworker, and overall inspiration to the world.

She is a seriously creative individual, charismatic, with an intense desire to communicate science to non-traditional audiences. Nalini was one of the first people, and certainly the first woman, to use mountain climbing gear to scale towering forest trees. As she sat in her leafy empyrean, the masses of epiphytes (canopy-dwelling plants) that cloaked branches captured her imagination, launching a decades-long research program on the roles of epiphytes in forest ecosystems.

Bucking Groove Formation Dr. Nalini Nadkarni Retires… whatever that means By John “Jack” Longino SBS Professor of Biology

She taught me those ropes—literally—and I spent many hours in treetops with Nalini, absorbing the sights, sounds, smells, and feel of the canopy. At the time, others using ropes to gain canopy access were mostly brawny guys, with an “only the bravest and toughest” ethos. Nalini was the opposite. “With the right equipment, your grandmother can do this,” she has said more than once. She was selfless in promoting tree climbing, teaching hundreds of people how to get on that rope and inch-worm up to the canopy. Academia encourages groove formation, in which you carve out a novel intellectual groove for yourself, and you continually mine that groove for new knowledge. That has its place and value, but Nalini is a professional groove-hopper. She started her career at a major research university, winning accolades as a preeminent ecosystem ecologist. But the era encouraged groove formation above all else and was not supportive of women who wanted children—or of faculty who saw science as being for those outside as well as inside the ivory tower. This prompted her stint as Director of Research at a botanical garden in Florida, followed by a long career at The Evergreen State College in Washington State. This was the ideal crucible for a groove hopper. A small liberal arts college, Evergreen had a radical agenda: no grades, no faculty rank, no departments, and, as a core principle, interdisciplinarity. She and I split one position there, allowing us time not only to teach but to develop our research and to raise our two children. It was at Evergreen that Nalini’s creativity was given free reign. While maintaining an active research program, she constantly

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spun out cool projects: Legislators Aloft, teaching Washington State legislators how to climb trees and consider forest biodiversity as a value to protect; and Canopy Confluences, camping out with a mixed group of scientists, musicians, artists, and writers—getting them all into the canopy to create art, music, and poetry that might raise awareness about the importance of trees in those who gravitate toward the arts. It was at Evergreen that she became interested in bringing science and nature to people other than her own tribe. She began giving sermons to religious groups, not as scienceversus-religion, but science and religion, studying how the values of trees are expressed in holy scriptures of the world’s major religions. She began working with the incarcerated, developing the Sustainability in Prisons Project. Prisons and jails became sites for not only science lectures but for sustainability research and the rearing of endangered species by incarcerated men, women, and youth. Her office walls became cluttered with national awards. After ninteen years even Evergreen was becoming a groove, and she was approached by the University of Utah to run a new Center for Science and Math Education (CSME). Our children were fledged, and we decided to groove-hop again. Utah recruited us both and we joined the Department of Biology, now the School of Biological Sciences, in 2011. Nalini came knowing there would be challenges, reentering the culture of a large research university, and… in a place with so few trees! Times have changed since her stint at an R1 university in the 1980s. At the U she found a welcoming faculty, collegiality, and institutional goals of greater inclusivity and interdisciplinarity. During her time in Utah, Nalini has continued her research on canopy ecological interactions. She has also blazed a path in science outreach and communication, both locally and nationally. She taught courses and coordinated workshops in effective science communication. She continued her focus on the incarcerated, with the Initiative to bring Science Programs to the Incarcerated (INSPIRE) in Utah. She brought her science training to bear in quantitative studies of prison environments, showing that nature imagery reduces rates of violence in prisons. She has engaged scientists with youth in custody of the juvenile justice system with her STEM Community Alliance Program (STEMCAP). She has mapped trees on church grounds. She has arranged for the Tabernacle Choir at Temple Square to sing nature-oriented hymns to the annual meeting of the Ecological Society of America that was to be held in Salt Lake City (alas, nixed by the pandemic). She learned how to use a lathe to make wooden bowls, a new connection to her beloved trees. So what is retirement for Nalini? She has always been strongly allergic to academic politics, administrative burdens, and anything that smacks of routine (except perhaps her breakfast of one boiled egg and a piece of toast). Retirement for Nalini will be a time to focus on some of her favorite projects, but also a time of reflection and prospection. Who knows what will happen next. I’ve never been disappointed.

In Memoriam:

Friedrich Bonhoeffer F

riedrich Bonhoeffer, Director at the Max Planck Institute for Developmental Biology, passed away on January 29, 2021 in Tübingen, Germany; he was a renowned scientist whose pioneering research revealed how axons find their targets during development, recognized by the 2020 Gruber Prize for Neuroscience (jointly with Corey Goodman and Marc Tessier-Lavigne). Bonhoeffer came to spend a sabbatical with Gordon Lark in 1972 at the newly-formed Department of Biology and made seminal contributions towards establishing Molecular Biology at Utah. Earlier in his career, he had an enormous impact in the field of DNA replication, by isolating the first temperature-sensitive mutants in DNA replication; one of these stopped DNA replication immediately (the gene was later shown to encode the DNA polymerase present at the replication fork). The DNA replication mutants that Bonhoeffer isolated were essential to defining the replication complex. He remained closely associated with molecular biologists at Utah in the 1970s (including the Lark, Wechsler, Olivera and Greenlee laboratories). After Bonhoeffer switched his research focus to neurodevelopment, several graduate students and faculty members from Utah trained in his laboratory, including the late Chi-bin Chien and Rolf Karlstrom, a Biology PhD student with Mike Bastiani, who became Chair of the Biology Department at the University of Massachusetts, Amherst. 7


OUTREACH

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he buzz around campus is that the University of Utah has become certified as an affiliate of the Bee Campus USA, a Xerces Society program designed to marshal the strengths of educational campuses for the benefit of pollinators. The U joins many other cities and campuses across the country united in improving their landscapes for pollinators.

The U and SBS in particular know a thing or two about the science of beekeeping. SBS’s Amy Sibul, the U’s Bee Campus USA committee chair, says a group of dedicated students, faculty, and staff have implemented multiple pollinator-friendly initiatives at the institution since 2012. “We have been working to build bee-friendly habitat and raise awareness about pollinator conservation on campus and beyond for years. We’re so happy that the University of Utah is recognized for this work and can serve as a role model for including pollinators in the planning of urban spaces and infrastructure. It is essential that humans pay attention to these vital insects as we look to the future. They are an integral part of food webs and ecosystem functioning in both urban and wild spaces.” The backbone of the U Bee Campus USA Committee is the Beekeepers’ Association, for which Sibul serves as the faculty advisor. This student organization maintains honeybee hives on campus and hosts pollinator awareness events, public school classroom visits, and lectures on campus to educate people about the importance of bees and other pollinators. A pollinator Conservation Garden was completed on campus in 2019. In addition to the SBS’s Community Engaged Learning program, multiple other campus partners have provided support in the Bee Campus USA designation, including the Office of Sustainability. The U is lucky—it has an affiliated botanical garden, Red Butte Garden, which has incorporated multiple pollinator-friendly spaces and awareness campaigns into their efforts. The U also has an affiliated natural history museum, which maintains an extensive insect collection managed by Bee Campus USA Committee member Christy Bills, and leads multiple insect-oriented outreach events for the public. Utah is a bee biodiversity hotspot, with over 1,100 species of bees identified in the state. A new U Bee Campus website will include information about these important insects, and will also include a list of native pollinator-friendly plants, simple landscaping techniques to provide habitat for them, and links to current pollinator awareness events and active research at the U. A version of this e-article first appeared in @theU. 8


ALUMNI

2021 Distinguished Alumni T

he Alumni Relations and Development committee at SBS has announced the recipients of the annual Distinguished Alumni Awards. This is the first year that SBS is honoring a lab alumni, Reshma Shetty, who graduated in computer science at the U in 2002 but was a lab member in the Olivera lab at the SBS. She attributes her time with faculty member/PI Baldomero “Toto” Olivera as a formative experience in propelling her into co-founding in 2008 Gingko Bioworks in Boston. She has been active in the field of synthetic biology for over a decade. In 2008 Forbes magazine named Shetty one of eight people “Inventing the Future,” and in 2011 Fast Company named her one of 100 Most Creative People in Business. She was a guest of the College of Science’s ACCESS program in 2019 where she spoke with undergraduates in STEM on women in the field and the challenges of creating a start-up. T. Mitchell Aide received his PhD in 1989 while a member of Phyllis “Lissy” Coley’s lab and has been a professor at the

University of Puerto Rico since 1992. As a successful academic he has dedicated himself to training Latin American scientists and started a company to monitor biodiversity through the use of a sophisticated platform to collect acoustic data in the wild. His efforts have significantly impacted conservation in the tropics. Aide’s PhD work included a single-authored publication in Nature, demonstrating that the synchrony of production of young leaves for a community of tropical trees may have evolved as an adaptation to reduce herbivory by insects. A Fulbright and Smithsonian post-doctoral fellow, he has since published more than 140 peer-reviewed articles and mentored scores of students and post-docs, a service that has had profound impacts on education and conservation in Latin America. Both Aide and Shetty were acknowledged at the SBS’s annual awards ceremony, this year virtual on ZOOM, April 28, 2021.

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PEDAGOGY

Anatomy in Virtual Reality The U’s first off-site virtual reality (VR) lab for students

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or some classes, Zoom just doesn’t cut it. Students enrolled in labs typically work in close proximity and share the specimens they are dissecting. That’s why—while COVID-19 precautions are still in place—SBS’s Colleen Farmer, PhD, will teach her biology students in the virtual world.

The J. Willard Marriott Library, in partnership with Teaching and Learning Technologies (TLT) and the School of Biological Sciences at the University of Utah, have designed and built the U’s first off-site virtual reality (VR) laboratory for student use. Farmer is teaching the course Biology 3665: Form, Function and Adaptation of Animals. Her students are using VR kits produced by the library and TLT to dissect the specimens they’re studying throughout the semester. “In this particular class, students are looking at form and function in vertebrates,” said Farmer. “It’s so exciting to be using virtual reality to really make this an active learning experience, especially at this unique time when safety is of the utmost concern.” What Farmer is talking about isn’t something that is easily described or illustrated in photographs or video. “You really have to be looking through the headset to see the kind of extraordinary learning that goes on here,” said Farmer. “For example, when we dissect a dogfish in a traditional lab, there’s really only room for one person to be doing the dissecting while the other students huddle around to see what’s happening. Using the VR dissecting technique, every student has their own dogfish and they’re able to work with 10

By Heidi Brett

the specimen as long as they need—removing various organs, examining the vascular system and so on.” “Being able to use accelerometers and virtual reality headsets to learn has been very neat,” said Russell Belt, a student in Farmer’s class. “Not only are we able to collaborate on virtual projects in real time, but I have been able to meet new people during the COVID pandemic as a result. That has proved very valuable in bolstering my educational experience at the University of Utah.” Another powerful aspect of this approach is the use of a “multiplayer” platform where all of the students can be in the same virtual space with the instructor, seeing each other as a virtual head with a name displayed and sets of hands (wands) and talking with each other in real time. The students can “walk” around in the space to see the anatomy from different points of view and the instructor can use a laser pointer to draw attention to particular features. Students have the benefit of the student-student interactions of a regular classroom from the safety of their own home. “We have made a few changes to the laptop specs to support the memory needed for this robust software,” said Tony Sams, new media projects specialist. “At the end of the day, we’ll have 40 laptop/headset packages for students to check out. These systems will take their learning to a whole new level.” Funding for this project was provided by the CARES Act through the Utah Education Network. A version of this article first appeared in @theU.


Briefly Noted Mary C. Beckerle, chief executive officer and director, Huntsman Cancer Institute (HCI); and distinguished professor of biology and associate vice president for cancer affairs at the U was elected to the National Academy of Science in April. “I have the best job in the world,” she says, and whether it’s meeting with clinicians and donors, developing financial sustainability, or building relationships and teams, she’s working to turn ideas into action and meaningful progress. “We are at the most exciting time in history when it comes to the ability of scientific knowledge to improve health.” And while she’s had to reduce the time she spends in the lab to dedicate more time to leading HCI, she’s not slowing down when it comes to saving lives.

Two SBS faculty members, Sophie Caron and William Anderegg, have received the National Science Foundation’s most prestigious award for early-career faculty. The Faculty Early Career Development award provides recipients with five years of funding to help them lay the foundation for their future research.

In a Journal of Mammology paper, Sara Weinstein, lead author and post doc researcher in the Dearing lab found that the African crested rat is the only mammal known to sequester plant toxins for chemical defense. The team also uncovered an unexpected social life— the rats appear to be monogamous and may even form small family units with their offspring. The research was picked up broadly by the national and international press, intrigued by the existence of giant poisonous rats.

Distinguished Professor Denise Dearing was selected to receive a Humboldt Research Award, conferred in recognition of the awardee’s entire academic record to date. Award winners are invited to carry out research projects of their own choice in cooperation with specialist colleagues in Germany.

A new Capsicum (Solanaceae) species from the Andean-Amazonian Piedmont has been found and named. With her co-authors, SBS’s Lynn Bohs, also known as “Doctor Pepper,” announced the good news in a recently published paper which appeared in PhytoKeys. The chili pepper genus includes five species cultivated worldwide as vegetables, spices, and medicines.

In a new paper from Richard Clark’s lab, analysis of the smallest known arthropod genome reveals a mechanism for genome reduction that appears to be driven by a specialized ecological interaction with plants. The article, in e-Life with SBS alumnus Robert Greenhalgh (PhD’18) as lead author, was selected as an editors’ choice by Science.

BioUtah’s 2020 Utah Life Sciences’ Executive of the Year award went to SBS alumnus Randy Rasmussen, PhD’98 “for his vision in founding and building a successful global diagnostic company to revolutionize testing for infectious disease.” Rasmussen is co-founder of BioFire Diagnostics in Salt Lake City.

In March, Ofer Rog’s lab announced its first two publications. The lab studies the synaptonemal complex (SC), a conserved structure that underlies chromosome-wide behaviors during sexual reproduction. The SC has been observed in almost all eukaryotes— from yeast to worms to humans. One paper appeared in Current Biology and the other in PLOS-Genetics.

Briefly Noted, continued on page 13

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Probably Gordon’s most lasting contributions are the intangible benefits of the interactive research-oriented community that he created. One specific event stands out to me. Gordon encouraged meetings that would showcase diverse research and facilitate new interactions across broad fields of biology. These regularly featured outside speakers, as well as research groups from elsewhere within the University. At a 1978 Research Retreat at Alta Lodge, Mark Skolnick, in the Utah Department of Biophysics, Ron Davis from Stanford (whom Gordon had tried to recruit to Utah a few years earlier) and David Botstein from MIT, were invited. Mark Skolnick trained in human genetics with Luca Cavalli-Sforza. Gordon recognized his unique creativity and had urged the Department of Biophysics to recruit him. Mark was trying to meet the challenge of mapping human disease genes, but it was unclear how this could be achieved. Type II restriction enzymes had only recently been discovered, and cloning technology was in its infancy.

Remembering

K. Gordon Lark (1930-2020)

By Baldomero “Toto” Olivera

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his year is the 50th anniversary of the Biology Department, with Gordon Lark newly recruited to be the first Chair. Last December, Gordon would have celebrated his 90th birthday, but he passed away in April 2020. Here I recount an event that embodies Gordon’s singular vision.

After becoming Chair, Gordon’s restless intellect led him to broadly explore all areas of biology to define where groundbreaking discoveries could be made. He generated novel ideas with the most creative experts he could find, and these deep intellectual engagements resulted in close friendships. These included eminent biologists in very different fields, such as Robert MacArthur, then at Princeton, and Martin Heisenberg at the University of Würzburg. I can still remember Gordon being shaken and intensely emotional when MacArthur passed away. Gordon supported everything that enhanced research and unfailingly mentored younger faculty. He was driven to create an intellectual community of top-line researchers in Biological Science at Utah, which required sustained effort, a clear vision and a sense of purpose, talents that Gordon certainly had. This led to both tangible and intangible benefits that have had a long-lasting impact. Many of these research programs that were established at Utah have garnered both national and international recognition, including the Nobel Prize to Mario Capecchi. Elsewhere, Mario Capecchi and Elaine Ostrander (Gordon’s close collaborator with whom he established the field of dog genetics) have paid tribute to Gordon’s groundbreaking research. 12

Informal interactions at this retreat culminated in a remarkable closing lunch exchange. At the end of the first day of the conference, graduate students gathered at the bar. These were the first recruited to the department, including Kirk Thomas, Bob Smith and Mark Manning. Mark Skolnick’s students had presented their work on human disease genes, including hemochromatosis and breast cancer. Mark approached the graduate students at the bar and asked what work Ron Davis did. Kirk and Bob explained what restriction enzymes were and how Ron had used these to clone genes. They described how mutations at a restriction site might be detected. This set the stage for the lunch the following day; a discussion of human disease genes such as those that caused breast cancer and hemochromatosis became the focus of a lively discussion between John Roth, David Botstein, Ron Davis and Mark Skolnick. There was an “epiphany moment” where the idea of using restriction enzyme polymorphisms to map genes emerged. Everyone present at that table or listening close by who heard the conversation remembers the palpable excitement when the potential of a connection between restriction enzymes and mapping human disease genes was fully grasped. In retrospect, the scientific consequences of that retreat lunch were extraordinary. This triggered a successful effort to recruit Ray White, leading to establishing the research institute in the Department of Human Genetics focused on mapping human disease genes. This Institute attracted many outstanding young researchers to Utah. A paper describing the basic idea was published, including Ron, David, Mark and Ray White as authors. Within a year, Mark Skolnick’s lab had identified their first restriction enzyme polymorphism; the definitive identification of the breast cancer genes by Mark’s group at Myriad Genetics, an event commented on by the New York Times can be traced back directly to that meeting. This was just one of the notable scientific achievements that would not have happened without the intellectual community that Gordon worked tirelessly to achieve. No matter what he was doing, Gordon valued—and the scientific community benefitted and continues to benefit from—creative thinking. Acknowledgements: I thank Kirk Thomas, Sandy Parkinson and Kevin Chas for helping me reconstruct events from long ago and for their editorial comments.


Briefly Noted continued Post-retirement in 1997, Emeritus Professor Del Wiens and his wife Carol were sailing around the home islands of Japan when their boat was boarded by heavily-armed Russian sailors. Apparently, the couple had inadvertently entered Russian territorial waters. Released after four hours, Wiens reported later to SBS on the episode saying, “we could take some satisfaction in knowing that we were likely the only American sailboat ever to be escorted by a Russian warship!”

In July 2020 the National Geographic Society designated Distinguished Professor Phyllis (Lissy) Coley a National Geographic Explorer. Coley is now SBS Distinguished Professor Emeritus. SBS’s Coley-Kursar Endowment celebrates the legacy of ecological research and graduate student training by Coley and the late Dr. Thomas Kursar. Funds support students conducting field studies.

Nitin Phadnis and his colleagues won a 2020 Editors’ Choice Award for an outstanding population and evolutionary genetics article published in Genetics. The article was titled “Extensive Recombination Suppression and Epistatic Selection Causes Chromosome-Wide Differentiation of a Selfish Sex Chromosome in Drosophila pseudoobscura.”

Alumna Michele Lefebvre, PhD’05 is employed in Hilo on the big island of Hawaii as an environmental impact assessment specialist and project manager for Stantec, an international professional services company in the design and consulting industry. She coordinates baseline surveys, including biological and cultural inventories and works with stakeholders.

Post Doctoral fellow Elena Boer (Shapiro lab) won the Developmental Biology Outstanding Paper Award for her manuscript “Pigeon foot feathering reveals conserved limb identity networks” from the journal Developmental Biology. The prize was designed to promote the work of early career researchers who have published in the journal.

Led by SBS’s William Anderegg, researchers found that human-caused climate change played a significant role in pollen season lengthening and a partial role in pollen amount increasing. Their research is published in PNAS. The paper, released in February, was broadly reported in the commercial press. In November, Anderegg was also tapped to present at the celebrated Frontiers of Science Lecture series, held virtually. The U’s Academic Affairs office awarded a 2020 On-line Excellence Faculty Award to Naina Phadnis, assistant professor and assistant undergraduate director of SBS. She developed and taught the school’s first online/hybrid biology course in 2016. Last spring, Phadnis ran a workshop for her colleagues and consulted one-on-one to help others make the transition.

Alumnus Steve Mimnaugh, MD BS’73 recently retired as an ER physician in Salt Lake City. He is a founding member of the beloved Disgusting Brothers Band as well as ‘SPLORE, a nonprofit dedicated to getting folks with disabilities out into white water rafting and other outdoor sports. A newlywed, he is busy writing a book about his time in the ER, informed by evolutionary theory.

Thure Cerling, with joint appointments in SBS and the department of Geology and Geophysics where he is also chair, was awarded a Geochemistry Fellows Honor by the Geochemical Society and the European Association of Geochemistry. The honor is bestowed upon outstanding scientists who have, over some years, made a major contribution to the field. With SBS Distinguished Professor Jim Ehleringer, Cerling is deeply involved in Stable Isotope studies and for twenty years ran the international summer IsoCamp at the U.

Are you an alumni? Share with us updates on your career and/or personal life. Send your news with a headshot of yourself to development@biology.utah.edu

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hank you for taking the time to look through the official magazine of the School of Biological Sciences. With the warmer weather and vaccines now available, there’s a lot of optimism about how the University of Utah and SBS will engage our students and get research labs fully up to speed in the coming months. We want to thank you for maintaining your support during these past months which have proven trying for all of us. Our alumni and our friends play a critical role in supporting our initiatives which are focused on SBS undergraduates and graduates who are busy in labs and in the field asking questions, finding answers and then applying basic science discoveries to benefit society. We hope that you will consider a gift as we approach the end of the academic year when students are gathering for graduation and gauging their own experience at U Biology and the U and how they can continue as part of our community.

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A scanning electron microscope image of Pseudomonas colonizing Arabidopsis thaliana plant leaves, the plant-host subject model of the Karasov lab.

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Neil J. Vickers       Leslie E. Sieburth Professors and Co-Directors School of Biological Sciences

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Our DNA, Spring 2021 Issue  

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