Our DNA Autumn 2019

N E W S for A L U M N I

BIOLOGY NEWS | FALL 2019

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Contents Publisher School of Biological Sciences

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Direct correspondence to:

From the Director

Engaging students through the rigors of research

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Ants of the World

With new funding from the NSF, Jack Longino continues to map the world’s ants

School Director M. Denise Dearing

Faculty Spotlight

Going with the flow: John Sperry

Alumni Spotlight

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

Nikhil Bhayani (BS’98)

It Takes a Village… and a Facilities Manager With Jose Rojas’s retirement, SBS gets a new manager

Research

Jamie Gagnon wields gene-targeting scissors

Outreach

Second-graders turn recess into citizen science

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

Writer & Editor David G. Pace

Additional Contributors Paul Gabrielsen | University Marketing & Communications Matt Crawley | College of Science

On the Cover On the Cover: Zebrafish in one of the 100+ tanks in the research lab run by Jamie Gagnon, Center for Cell and Genome Sciences, Crocker Science Center, School of Biological Sciences.

The zebrafish has become increasingly popular as a model system for understanding vertebrate gene function as well for studying human genetic diseases, especially since the debut of the groundbreaking technology CRISPR-Cas9.

Photo: MattCrawley Request an e-version of OUR DNA in place of a mailed copy at development@biology.utah.edu

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FROM THE DIRECTOR

An on-going project, Biology Under Cover is the latest exhibit located in the lobby of the Aline W. Skaggs Building.

Engaging Students

Through the Rigors of Research

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ur semester began with our annual science retreat where we showcased the cutting edge research being conducted in the SBS. Eight graduate students and postdocs presented their research along with our newest faculty member, Dean Castillo (inset photo) who comes to us from Cornell. Dean is an evolutionary geneticist who works on the genetics of selection and sexually selected traits. We also hosted three distinguished speakers. Dr. Robert (Bob) Sclafani from UC Denver, this year’s Lark speaker. Dr. Ole Jensen, DDS, MS and Dr. Cynthia Sagers, Vice President for Research at Arizona State University were our Distinguished Alumni Speakers. A total of fourteen of our wonderful undergraduate scholars also presented posters of their research enabled through the largesse of our scholarship donors.

While we warmly greet new faculty this year, we also must say goodbye to plant physiologist Dr. John Sperry for his twentyeight years of service to the U. All the best, John, as you retire.

In November we celebrate the inaugural Diversity Fellows Program by hosting a dozen undergraduate students from across the country for a preview of the graduate school application process. This program gives students a chance to interact with graduate students, postdocs and faculty from the SBS and to see the wonders of Utah.

We’ve recently immortalized research in the School of Biological Sciences by rendering in metal the journal and book covers produced by our faculty. You will find these displayed in the lobby of the Aline W. Skaggs Biology Building. Each cover has a QR code linked to a description of the research and the article from the journal. Stop in and take a look!

Dean Castillo And, finally, I want say thanks again to all of our supporters.

Your financial donations, collectively, allow us to provide the hands-on training needed for our next cohort of scientists, researchers, teachers and informed citizens.

All the best for a happy 2020,

M. Densie Dearing Distinguished Professor, Director School of Biological Sciences 1

RESEARCH

Ants of the World With new funding from the NSF, Jack Longino continues to map the world’s ants

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or more than thirty years, University of Utah entomologist Jack Longino has been watching the ground. Whether he’s deep in a tropical jungle or scanning the sidewalks of a Central American city, Longino is always looking for ants.

“Ants rule!” he says.

Recently, Longino compiled those decades of work into a monograph, detailing 234 species of the ant genus Pheidole.

He’s now given names to fifty-seven of those species himself.

Longino formatted the monograph to emulate a bird guide, hoping to engage more ant fans in the work of documenting and conserving ant species.

“You can think of what I do as making a map of diversity,” Longino says. “The first step in understanding and using animals and plants is having a map of what we’ve got. I’ve dedicated my career to filling in the map.”

But he’s not stopping there. Thanks to a $1.3 million grant from the National Science Foundation, Longino and colleagues are about to embark on a project to obtain genetic information from 4,500 species of ants around the world to construct a comprehensive evolutionary tree of life for his favorite insect family.

Introducing Pheidole The ant genus Pheidole is one of the most diverse and is found throughout the world, but particularly in Central America. In 2003, famed biologist E.O. Wilson published what was then considered a comprehensive guide to Pheidole including  Jack Longino in the Danum Valley, Borneo. Photo courtesy of Jack Longino.

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more than 600 species (among them the auspiciously named Pheidole longinoi).

In his recent monograph (a single-author report focused on a highly specific subject), Longino summarized his years of searching for and cataloging ants in the wet forests of Central America. “I maintain this collection of hundreds of thousands of ants from Panama to Mexico,” he says. “You look at them and organize them and make this physical map. And it’s all here in my lab, a reflection of the diversity of a big part of the world.”

“There’s an old Chinese proverb—the beginning of truth is calling things by their right names.”

P.tsontekonwei: After the local term for the species, meaning “big head” in Nahuatl, a language in southern Mexico.

P. rima: After a character in Green Mansions by William Henry Hudson. “It’s the story of a guy in tropical Venezuela who falls in love with a wood nymph named Rima,” Longino says. “Rima lives in the treetops, and this new species of Pheidole only lives in the treetops.”

P. familiaparra: In honor of the Parra family, who aided Longino’s expedition to Costa Rica in 2015.

Ants of the World In the field, many ant species can initially look similar, he says.

“But under the scope, they look as different as giraffes and zebras and mice.” Because dozens of the ant species he had collected were not yet named, Longino set to work affixing appropriate names.

“There’s an old Chinese proverb,” he says. “The beginning of truth is calling things by their right names.”

Naming new species “Naming things is fun,” Longino says. He begins by naming species according to their physical characteristics, such as P. corniclypeus, so named for the spines projecting from the clypeus, a plate on the front of the ant’s head. Others, such as P. tikal, are named for the place where they were first found. Beyond that, Longino indulges in some creativity. Here’s a sampling: P. natalie: “After my new daughter-in-law. I’ve named an ant after every member of the family!”

Documenting the Pheidole ants of Central America is no small achievement. But there’s a big world of ants out there, and Longino’s next step is to learn about them all. In July 2019, Longino and colleagues from UC Davis, the California Academy of Sciences and North Carolina State University secured a $1.3 million grant from the National Science Foundation to fill in all the branches on the ant evolutionary tree. They’ll do this through the analysis of ultra-conserved elements (UCEs), or genetic markers that are the same in multiple species. Currently, researchers have collected UCE data for only about 13 percent of the 13,500 ant species worldwide. Longino’s effort will add data from 4,500 additional species so that the final data set will cover 96 percent of ant genera (plural of genus) and 45 percent of species.

The data will also include information on where ants live and what climates they prefer. “It’s another tool to assess how ecosystems in general are responding to habitat changes that we’re seeing in the world today,” Longino says. “We want to get a good sense of how the world’s biodiversity, the whole fabric of diversity hundreds of millions of years in the making, is being affected by what we do.”

Get to know the new species Longino named by following @LonginoJack on Twitter: A new species featured each day for fifty-seven days.

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FACULT Y SPOTLIGHT

Going with the Flow:

John Sperry

Retiring botanist studied how plant’s xylem tissue carries phenomenal amounts of water to tree leaves where it evaporates and influences regional weather patterns

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ohn Sperry grew up in Normal, Illinois, but his interest in plants–eventually their vascular function–would propel him into work that was far from standard in botany via Duke University and, eventually Harvard where he earned his PhD. At Harvard his Swiss-born mentor Martin Zimmermann was considered among the top plant physiologists in the world and a scholar whom Sperry credits with, more than anyone else, “showing him how” to do research. Even so Zimmermann strongly questioned the ability of Sperry’s proposed, novel technique to measure the blockage of vascular flow by cavitation.

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function in conducting water and dissolved nutrients upward from roots, that would become the subject of Sperry’s PhD thesis.

And it was that thesis and the questions it spawned that laid the foundation of all of the research he would do for the next thirty-plus years, including a stint as a post-doc at the University of Vermont prior to his arrival at the University of Utah in 1989.

“As humans, we are acutely aware of the importance of maintaining vascular function,” Sperry’s Research Statement reads. “To plants it is no less critical. My laboratory investigates hydro-vascular structure and function in plants in relation to their ecology, physiology, and evolution.” The scale of this function in plants is, he explains, a “phenomenal process. The sheer quantity of water moved through plants often exceeds

river flow on a watershed scale,” he explains. “The plant’s xylem tissue carries all of this water to the leaves where it evaporates and influences regional weather patterns.”

It takes “watershed scale” flow for plants to obtain carbon dioxide from the atmosphere through their open stomata. It’s counter-intuitive, but the transport is driven by negative liquid water pressure, “a remarkable fact,” says Sperry “that will always irritate physicists” who often aren’t as familiar with metastable fluids as is a plant physiologist.

Sperry and his lab study how plant form and function have evolved. To do this they have developed more efficient technologies for the larger data sets required. Sperry custom designed centrifuge rotors to quickly expose the vascular system of plants to a known negative pressure. This in turn has allowed him to create the kinds of vulnerability curves which improve prediction of plant water use and to help move his research toward macro applications in forests to predict plant responses to climate change.

What does the coordination look like between regulation of photosynthesis and environmental conditions? The answer lies in predicting what the stomata will do. Stomata are typically found in the epidermis of plant leaves. Specialized “guard cells” surround stomata and function to open and close stomatal pores, balancing the trade-off of water evaporation for required carbon dioxide.

“We … concentrate on the fundamental carbon-for-water trade-off that confronts all terrestrial plants,” continues Sperry.

“Photosynthesis requires the plant surface to be porous to carbon dioxide diffusion, but at the cost of also being porous to evaporative water loss.” Indeed, the xylem has been called “the vulnerable pipeline,” part of an elaborate system that includes “a transport system that teeters on the edge of physical possibility.”

Failed water transport, or “cavitation,” is caused by water stress or freezing. Over the years, Sperry has learned that some plants are more vulnerable to this kind of “spectacular failure” than others.

“This turns out to be part of the answer to the question of why some plants grow where they do when others cannot,” says Sperry. Vulnerability to cavitation provides the key to predicting how stomata respond to environmental cues, a missing element that Sperry and colleagues have integrated into predictive models for how plants respond to their environment.

It’s not surprising then that Sperry’s work in plant hydraulics– the water stresses and trade-offs they face–has had a profound impact on predicting how rapid environmental change will affect the future of plants and forests. This according to U ecologist and Sperry colleague William “Bill” Anderegg. Before his own appointment in Biology, Anderegg, who was studying Colorado forests, spent time in Sperry’s lab. There he learned first-hand what was confirmed later for him about Sperry’s mentoring of young researchers.

“I attended a major conference in the field recently,” says Anderegg, “where there was a ‘mentor tree’–an artistic set of wooden branches where young scientists anonymously wrote the name of someone who had changed their career…

John’s name was all over the tree and was the most frequent name by far.”

John Sperry In the middle of “everywhere,” northern British Columbia. Photo: Holly Sperry

Sperry will retire from the University of Utah in December, so it’s a time to look back on a career that started, in retrospect, as early as kindergarten in his hometown of Normal. “Of course I was also obsessed with being a truck driver,” he adds. “But I did draw lots of trees and enjoyed watching our teacher demonstrate the ascent of food coloring in the transpiration stream of a celery stalk.”

But like a true scientist he is always looking forward as well, not just finding a home for that centrifuge with the custom-made rotors, but enlisting the programming skills of undergraduate lab associate Henry Todd. Todd, together with lab mates Martin Venturas and Yujie Wang, is facilitating climate change simulations of 520 combinations of 8 species in 20 sites across the country based on six climate projections and two emissions scenarios … over 30 years.

“The sheer quantity of water moved through plants often exceeds river flow on a watershed scale.”

John Sperry will not be parsing through this kind of macro data for much longer, limiting himself to just a few more papers and farewell meetings. Retirement will allow him more time to adventure with his wife Holly in their truck camper and to be in his favorite laboratory: the outdoors. He and his canoeing buddies also look forward to expanding their summer-long explorations of northern wilderness, a place where you can travel over 600 miles under your own steam and not see another soul for a month and a half. Sperry is harking to the dictum: “no one on their death bed wishes that they had spent more time at work.”

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Undergraduate

Researchers

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ven before the Undergraduate Research Initiative in the College of Science launches early next year, undergraduates in biology, with the help of research scholarships by our esteemed donors, have already made their debut. At the School’s Retreat in August, fourteen presented their research. Here is a sampling.

Dalley Cutler Senior Dalley Cutler’s personal hero is Greta Thornburg, the young Swedish environmental activist recently invited to the United Nations to advocate for reversing man-made climate change. Along with this sixteenyear-old, and others like her, the Idaho Falls native wants to see sensible policies and actions based on scientific understanding. The same is true of his own research in the Dentinger Lab. “Many producers are either incorrectly identifying wild mushroom food products or are purposely lying about the species contained in those products,” he says. “There are no international or national regulations to protect consumers from buying and eating poisonous wild mushrooms sold on the internet as edible wild mushrooms.”

He uses metabarcoding genomic analysis techniques to identify species sold as wild mushrooms in food.

“I generated the data for this [research] poster some time ago,” he says, “but due to other obligations like class attendance and work I was unable to invest the necessary time to learn how to process and accurately analyze that data.” A scholarship provided by George R. Riser was a game-changer for him, providing time away from work obligations to write the appropriate scripts and install the right software that will streamline future projects. It has also allowed him to begin generating and processing data for his next project.

Cutler has high hopes to work in a field where he can use scientific techniques to better understand the natural world and to use that understanding to protect and conserve vulnerable ecosystems from the impacts of the climate and ecological crisis that will be occurring over the course of his life. Inspired by an out-spoken girl in pigtails from the Nordic country, he is committed as a scientist to make a difference.

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Bridget Phillips As one of the College of Science’s Ambassadors, sophomore Bridget Phillips regularly appears at College events hosting alumni and special guests, and working with faculty and staff to promote science teaching and research at the The University of Utah.

A team member in the Shapiro Lab, she studies the genetic causes and patterns of variation in domestic pigeons. “Because axial skeleton structure is highly conserved,” she says, “understanding skeletal development in pigeons can tell us about the processes that control skeletal development in other animals as well.” A little known fact about her model subjects is that pigeons provide a unique opportunity to identify specific genes involved in many morphological traits “because all 350 breeds are capable of interbreeding to generate genetic crosses.”

A Salt Lake City native, Phillips is the recipient of the Ole Jensen (BS’72) Scholarship this year. Because of the scholarship, she says, “I’ve been able to dedicate much more of my time to [research in the Lab]. I greatly appreciate and deeply value the scholarship.”

Phillip’s ambition is to attend graduate school and to continue her research in genetics. “By completing a degree in Biology and a minor in mathematics, I hope to be better equipped to study immunology through genetics and bioinformatics research.”

She is thrilled that as a first-year student at the University “I was able to start in a wonderful lab and be able to live in the Crocker Science House with other like-minded science folks.”

Anthony Khong In high school Anthony Khong discovered he had a passion for both biology and psychology. “I was at a crossroads on what to pursue until I researched the field of neuroscience and specifically neuropsychology for a class assignment,” the Salt Lake City native says. “My dream is to combine these passions into a career that keeps me coming back out of curiosity and exploration.”

Khong is jump-starting that career while working as an undergraduate in the Rose Neurobehavioral Lab run by faculty member and principal investigator Gary Rose. “The process of collecting data for this project has broadened my awareness of what the field of biology offers in disciplines greatly,” he reports.

“I was very excited to present my findings to the scientific community at the SBS Retreat last August.”

His subject for his current research involves the Bluehead Wrasse (Thalassoma bifasciatum) which uses a hierarchy system to determine the male in a population.

“The population,” says Khong “consists of a terminal phase (TP) male and initial phase (IP) females. If the TP male were to be removed from the population, the highest ‘ranking’ IP female will transition into the new TP male. IP females are ‘primed’ to become TP males based on their rank in the population hierarchy.” Remarkably, a dominant IP female can show TP-typical courtship behavior within a day after removal of the TP male. The transformation to the TP male coloration pattern (e.g., blue head), and development of testes, requires at least eight-to-ten days and appears to be androgen dependent.

Outside of the lab Anthony’s interests include graphic design and leadership studies. As recipient of a Mark Skolnick Research Scholarship, he’s a big fan of the University of Utah where academic research and extracurricular activities convene into a seamless whole.

And who is Khong’s favorite hero? At least one of them is Jackie Chan, the Hong Kong martial-artist-turned actor/director. He’s “one of my idols since he stands as a pillar in the community, helping to pave the way for Asian American representation in both pop culture and in the United States.”

From making movies with Asian casts, to touring the country for philanthropy projects, says Khong, “Jackie has shown me that I can also make a lasting impression in both my community and my field of study.”

Distinguished Alumni 2019 Cynthia Sagers (PhD’93) and Ole Jensen (BS’72)

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ALUMNI SPOTLIGHT

This is the Way My Day was Like: Nikhil Bhayani Coming Home to U Biology… and The Pie 8

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very time I come to the U with my kids,” says Nikhil K. Bhayani, MD, FIDSA (BS’98), “I take them on a reality tour. I [recently] told my youngest son, ‘Let’s retrace my footsteps when I used to go from one of the lecture halls at Presidents Circle, to the Student Union. This is the way my day was like.’”

They ended up at the Pie Pizzeria Underground, a decades-long favorite haunt of students and faculty just west of main campus on 2nd South, famous as much for its densely graffitied walls as its provocatively named specialties like “Hawaii Pie-O” and “Holy Shittake.” “It really feels like a college campus,” says Bhayani of the U. “My son tells me that he wants to get pizza here [at the Pie] every day.”

sure they’re getting the latest. In private practice you want to be at the top of your educated game. This motivates me to stay on top too.”

In his administrative role as physician advisor, Bhayani oversees all infectious disease policy-making—like the use of antibiotics, what lab teams are going to be doing—at fifteen acute care hospitals under the umbrella of the Texas Health Resources system. With a large African immigrant population Dallas/Ft. Worth, also home to a major international airport, experiences emerging infectious diseases and thus needs intense anti-microbial stewardship, including CDC protocols and cooperation with the local health department. Bhayani is at the center of these various sector components.

Though born in Virginia, Bhayani considers Salt Lake City, where he was raised, home. His parents, both originally from India, married in New York City after Bhayani’s father had finished graduate studies at the University of Rhode Island.

“I always wanted to go to medical school,” says Bhayani who graduated in 1998 with a biology major and a chemistry minor.

(His brother Mihir also graduated from the University of Utah with a degree in chemistry in 2000 and is also a medical doctor.)

While an undergraduate he worked in a bioengineering lab run by Richard Normann, and later in one of the labs at the Moran Eye Center. He recalls fondly some of his fellow Indians, in particular Rajesh, Monica and Leena Gandhi, a few years older than he, but also graduates in biology who went onto medical careers in infectious diseases and cancer.

Bhayani later attended Ross University School of Medicine in Portsmouth, Dominica, and was awarded his medical degree in 2003. In 2006 he completed medical residency training at Mercy Hospital and Medical Center in Chicago where his brother currently lives.

Nikhil and his family now live in Texas where he practices medicine at Dallas-Fort Worth Infectious Diseases, an integrated health care network comprised of physicians, hospitals, case managers, community clinics, and managed care partners.

There he also enlisted as an Infectious Diseases and Epidemiology Physician Advisor at Texas Health Resources in Arlington. In 2016, Bhayani was named Physician of the Year by the Texas Health Arlington Memorial Hospital. Not one to rest on his laurels, he was hired earlier this year as an Assistant Professor in the Department of Internal Medicine, at Texas Christian University and the University of North Texas School of Medicine where he brings his undergrad U experience full-circle by teaching pre-med-students. Especially gratifying recently was when a graduating senior, also interested in infectious diseases, came to him to ask if he could “shadow” him for four weeks for one of the student’s electives.

In clinical practice, says Bhayani, who works long-term with patients who live with HIV and other infectious diseases, “the research is always changing what we do. You have to keep up with developing trends… . We get patients who are insured, who have steady jobs and who are a little more educated, so when they read about new medications they want to make

“As you grow up and become successful, always look back and reflect how you got there and give back to the community you were nurtured in.”

It’s an intense but meaningful career, and sometimes Bhayani considers what it would be like to return more to teaching and mentoring, the kind that he feels he got at the University of Utah’s School of Biological Sciences. “My dad always said, ‘As you grow up and become successful, always look back and reflect how you got there and give back to the community you were nurtured in,” says Bhayani. Even so, he never wants entirely to give up his clinical experience at what amounts to the largest nonprofit based healthcare group in the country, second only to Intermountain Healthcare based in Salt Lake City.

“As I reflect, who I am today is thanks to my parents and the University of Utah for giving me motivation and an opportunity to pursue higher education,” says Bhayani who with his wife of eighteen years, also originally from India where her parents still live, is busy raising two sons. This while trying to keep up with following the NBA, NFL and, of course, the Utes, which he loves.

“Most of the work is done by my wife,” Bhayani concedes. He refers to her as the “pillar of the house, that “she keeps everything going. Left to me it would be like college all over again.”

Pizza anyone?

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It Takes a Village…

and a Facilities Manager José Rojas retires after two decades of service

academic units, Biology relies on Rojas and his team to be in a constant state of demolitions, bidding, implementing hazard waste abatements, and pricing and securing equipment like million-dollar microscopes, tanks, and cages, wind tunnels and centrifuges. Then there’s also that other lab: BioKids, an NAEYC accredited, year-round Early Childhood Program located at the School in Building 44.

Rojas’ work also requires an artistic side, designing exhibits like the museum-grade cabinet that now houses the gene-targeting equipment Dr. Mario Capecchi used to do his foundational research in the School of Biological Sciences which led to the good scientist’s Nobel Prize. One of his last projects was designing a display, “Biology Under Cover,” of selected journal covers over the decades by School faculty now memorialized in metal in the lobby of the Aline Wilmot Skaggs Building.

Rojas on the roof of South Biology at the regular staff BBQ, 2019.

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acilities manager at the School of Biological Sciences for 20 years, José Rojas, probably knows more about the ins-and-outs of how labs operate than most principal investigators. Like the biology subjects U biologists examine— from cone snails to mitochondria, and from mammals to the tiny round worms of C. elegans—Rojas’ work in retrofitting lab spaces requires prodding, perturbing and replicating.

Labs in the four biology buildings (Aline Skaggs, South Biology, Talmage Building and Life Sciences) are constantly in a state of flux: living organisms in their own right. With more tenure-line faculty/principal investigators than most

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Rojas’ work has not gone unnoticed: he received the prestigious District and University Staff Excellence Award in 2017. A native of Puerto Rico, he has made his home in Utah since 1983, but still returns to Florida and points beyond at least annually, bearing his signature bounty of local macaroons for the staff back at the U. He and his staff regularly host a BBQ on the roof of the South Biology building next to the expansive greenhouse.

Rojas could pretty much tell you everything that’s going on in there as well.

These are big, steel-toed boots to fill. The job requires not only a thing for materials and construction, but a good dose of management and intuiting the quirky needs of faculty/principal investigators whose labs house everything from wind tunnels to million dollar microscopes; from mice to fruit flies; and plants to mammals. Never mind the anatomy lab: one of only two labs of its kind on campus, housing full cadavers.

Under New Management: Jeff Mauger J

eff Mauger has been a part of the University of Utah community in many different roles since his arrival to Utah in the fall of 1997. Not planning to stay very long, he started out as a student, eventually receiving both a Bachelor’s and Master’s of Fine Art. His work has been shown and sold in a number of galleries and private showings throughout the years. After graduating, Jeff worked for multiple architectural firms downtown before finding himself back at the “U” working for Facility Management where he has been for the last twelve years (“Earning back my tuition,” he says).

While working towards his degrees, Jeff took a part-time job with Campus Design and Construction where he met his wife, Jenn. They currently live in Taylorsville with their two children, Alexander, eleven, and Addison, eight, both of whom are avid baseball players. Jenn and Jeff love to watch and support their children in both academics and sports.

At first blush, you might wonder how an artist ended up as the new facility manager here at the School of Biological Sciences. The job not only requires an understanding for materials and construction with a good dose of management, but also an ability with intuiting the quirky needs of faculty/ principal investigators. For this, Jeff pulls from his first degree, a BS in Landscape Architecture which he earned from West Virginia University where he gained a great understanding in project management and construction.

Combined with his love of getting to know and working with people, he hopes to create a relatively seamless transition as U Biology’s new facility manager.

Briefly Noted Sue Phillips (MS’96) is the new Director of the U.S. Geological Survey’s Forest and Rangeland Ecosystem Science Center (FRESC) in Corvallis, OR. A protégé of faculty member and former Department Chair James Ehleringer, Phillips spent several years in Moab after graduation at the USGS’s field station. “I’ve had the privilege of being a support to some amazing scientists over the years,” she says. “You don’t have to be a principal investigator after graduation; there are many gratifying jobs out there where you’re doing great science as part of a team.” She credits Ehleringer for not only saying he believes in a collaborative approach to science, but demonstrating it in his lab, one of the largest at SBS. Working as a scientist in a government agency certainly requires the collaborative skill set.

Phillips is not only a talented scientist but a marathon athlete in open water swimming. She also is proud mother of a 16-year-old daughter.

Connor Morgan (BS’19) has hung up his cap and gown, and his sojourn at the office of the Associated Students of the University of Utah where he served as president to join the campaign of former U.S. Naval Reserve officer Pete Buttigieg, the young mayor of South Bend, IN. Buttigieg, the nation’s first openly gay presidential candidate for a major party, is seeking the Democratic nomination and Morgan is there to help him win the race. Referring to his duties as student body president, he says, “I’m guessing it will be one of the best jobs I’ve ever had.” He especially enjoyed working with student leaders, administrators and faculties in a collaborative approach with many partners around the U. A Salt Lake native, Morgan is planning on attending law school.

Dr. Larry Cain (BS’93) a 6-foot-9 center who played for the Utes from 1990-93, has always been good in school and progressed through the process after being the first person from his family to graduate from college. Connections made through basketball encouraged him to reach even higher. At Utah, he wound up being the team’s starting center. After graduating he went on to graduate from the U’s Medical School. Now practicing family medicine in St. George. He’s delivered more than 2,000 babies thus far. It’s a place where he’ll likely retire: “Once that red sand gets in your toes,” he says “it’s hard to get out. You can’t shovel sunshine.”

Briefly Noted, continued page 16

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RESEARCH

Running with Scissors: Jamie Gagnon Newly-appointed Mario Capecchi Chair is using new technologies to understand how embryos develop.

genetics,” Gagnon says, “is that zebrafish are now genetically accessible model of all vertebrates, including humans which share 70 percent of genes with fish.”

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The impulse for Gagnon’s current work in vertebrate lineage and cell fate choice happened in Northern Maine, during a winter-mountaineering trip with his friend and fellow researcher Aaron McKenna whom he met while they were undergraduates at Worcester Polytechnic Institute in Massachusetts. There in the wilds, not far from Vermont where Gagnon grew up, ensued an extended conversation between the two which started to form a deeply complex but exciting research question.

“Before CRISPR,” says Gagnon whose interest early on had been more in engineering than biology, “we were all using the earlier generation of genome editing tools. Even so, we were able to determine that after making a mutation in a cell, when it divided, the change that had been made was inherited.”

“If we want to study how embryos grow, we have to do it in a living animal,” Gagnon remembers acknowledging to McKenna.

“We knew we needed to do it [research] in live animals, complete and whole. I couldn’t shut up about it for several days,” he says, smiling. “Everyone was mutating genes.” It seems that at the time, and perhaps still to this day, ‘Let’s break a gene and see if you’re right about what it does’, was pro forma.

ne could argue that the age of genomes is divided between before CRISPR-Cas9 and after CRISPR-Cas9 (commonly referred to as just “CRISPR”). As a Harvard post-doc studying the genes involved in embryo development, James (Jamie) Gagnon remembers in 2012 that “pivotal moment” when these “really nice pair of scissors now easy to make” came on the scene.

The new “scissors” rapidly scaled up genome editing, allowing researchers to more easily alter DNA sequences and modify gene function. At the time CRISPR was inspiring others to move from the research model of smaller organisms like the C. elegans, a transparent worm made up of approximately 1,000 cells, to much larger ones like zebrafish. “The power of 12

Photo: Matt Crawley

Instead, the developmental biologist (Gagnon) and the computational researcher (McKenna) decided to pick up where others had ended (and published), using technology in a creative way to mark cells with a genetic barcode that could later be used to trace the lineage of cells. The two were

suddenly using data sets of CRISPR-scissor mutations to figure out how cells actually developed in zebrafish.

In 2014 Gagnon published a paper describing how to use the “scissors” in zebrafish which then got Gagnon and McKenna thinking about using mutations to tell them how cells are related in embryos. “We were both getting married,” remembers Gagnon, who was still living in Boston at the time.

“The project evolved during regular meetings between us planning out both of our weddings.”

Once Gagnon and his wife Nikki whom he also met in Worcester arrived at the University of Utah in January 2018, Gagnon went from postdoc to principal investigator. In his lab at the Crocker Science Center’s Center for Cell and Genome Sciences, Gagnon, who is now assistant professor in the School of Biological Sciences and, as of August, the new Mario Capecchi Endowed Chair, curates 10,000 fish in 1,000 controlled tanks that are carefully labeled for experiments.

He refers to the experience of setting up a lab as launching his own start-up company, from buying DNA amplifiers that regulate temperature during cyclical programs (PCRs) to putting pipettes in the hands of students for the first time.

This past spring he also completed teaching his first section of principles of Cell Biology (Biol2020) with colleague Julie Hollien in which they taught a total of 430 undergraduates.

Still, the prevailing question for Gagnon the researcher is how does biology build an animal with millions of cells, all sharing information and all shape-shifting at the same time? And how does science then best go about studying that?

“Let’s break a gene and see if you’re right about what it does.”

How does science turn chaos and cacophony into a symphony that is the marvel of a living organism?

A symphony orchestra isn’t a bad metaphor for the edge of science that Gagnon and his lab and colleagues find themselves standing at. (It helps, perhaps, that his wife Nikki, a trained studio artist, works at the Utah Symphony | Utah Opera.) “For thirty years,” says Gagnon, people have been deciphering the genome code … one of the worst computer codes ever written.” Just how bad is bad? Imagine three billion letters in one long line with no punctuation or formatting.

Photo: Matt Crawley

Perhaps it’s the engineer in him, but to get at that unwieldy code, he sees his task as finding additional tools to regulate CRISPR activity. These tools include doing base-editing and using self-targeting guide RNAs to facilitate cells themselves making a record of what they’re doing, what they’re listening to, as it were, as they play their own “score” of development.

“We want to turn the single, really good sharp knife of CRISPR,” he explains “into a Swiss Army knife” to figure out the score of an organism’s symphonic work.

The micro-scissors of CRISPR that appear to have issued a sea change in genomic studies, he hopes, can be used to “force cells to make notes along the way” of their own developmental journey. “Every time the oboe plays,” he says, returning to the metaphor, “we want the player [the cell] to make a record and journal entry on it.”

“In early embryos, there are multiple languages or instruments being used by a finite number of cells to communicate with other cells and to build an animal,” he continues. To which language/instrument does a cell “listen” to, and what choices (expression) does it make as a result?

In a sense Jamie Gagnon is no longer just trying to “decode” the genome, but to use CRISPR to make a version, readable to humans, of what cells are doing in real time and how. In short he’s looking for the creation of a cell-generated Ninth Symphony, a complex but coordinated record of how development occurred that a Beethoven would be proud to conduct.

It may be dangerous to run with scissors, something parents routinely warn their children of, but it turns out that a really good pair of them can do more than the obvious: they can inspire other technologies that promise to bend the arc of science towards even greater aspirations.

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OUTREACH

Second-Graders Turn Recess into Citizen Science C

ertain strains of bacteria have been shown to kill deadly parasites and invite investigation for human applications. But parasites that carry deadly diseases like African sleeping sickness aren’t welcome in labs (for obvious reasons), where these investigations take place.

That’s when scientists seek out less dangerous relatives of these parasites that are nevertheless evolutionarily close to the parasites that cause human disease.

Enter the European firebug. It turns out that the insect carries a parasite called Leptomonas, but also carries a bacteria that defends them from it. What can a biologist learn about this secret weapon in firebugs that keeps them safe from parasite growth?

Well, first off you have to locate firebugs to study the phenomenon.

It turns out that Utah is one of the few places outside of Europe where one can find firebugs of the species needed for this kind of research. “It was sort of mystical,” says professor Colin Dale about the coincidence, “as if the universe were converging for us.” With the help of Christy Bills the “bug woman” at the Natural History Museum of Utah, which has a fairly comprehensive map of firebugs in Utah, Dale was able to secure a class of second-graders to help him collect the insects for his lab experiments.

At Newman Elementary School, a Title I school with a minority-majority population of mostly Latinx in the Salt Lake City section of Rose Park, enough firebugs were collected and “plated” in the lab to isolate their bacteria to see if they were making toxins that will kill parasites. “It was a great experience,” says Dale, “to go over there and to meet these children and to see them being engaged in real science. It seemed to have really stimulated them.” So much so that the class, taught by Manessa Adams, had “tons of questions,” for the principal investigator about all things bugs “as 2nd graders are wont to do,” Dale quips. (Shared stories of black widow spider bites took the fore.)

 A young student at Newman Elementary showing her Firebug discovery.

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Second graders with faculty member Colin Dale showing the container of firebugs collected during recess at Newman Elementary School in Salt Lake City.

The experience for the students was largely made possible by both Adams and Bills who, Dale says, has clearly gotten it across to them both before and after his visit “the big picture of the thing.” Science, he reminds us, is ninety percent trial and failure. Adams, he says, “inspired them that they were doing more than typical school work. More engagement like this can craft an interest to do science at an earlier age.” Adams agrees: “How neat that our little recess activity has turned into something so exciting!”

Tag-teaming of this kind can build a learning experience that is experiential. While Adams facilitated the citizen science project, Bills, a personal friend of Adams’, visited later to give them a context for the firebugs. “Kids have an intrinsic awareness and curiosity about [these things]. I love sharing bugs with kids and helping them learn more about them.”

The exercise involving symbiotic bacteria in the gut of firebugs has already come full circle for Dale whose students in Biol5960 cultured bacteria and determined that one of the specimens has anti-Leptomonas activity. “We have now sequenced the

“How neat that our little recess activity has turned into something so exciting.”

Bills supplied vials for each child to do more collecting, along with gummy worms, “because,” she says wisely, “you know, second graders!”

Bills spirited away some of the firebugs to be pinned and displayed later at the museum. Adams hopes that the whole experience will be brought full-circle by having her students visit the museum. If they do, they will see some of their own collection on public display. Bills’ intention is to return to Newman to talk to the kids about their isopod terrarium, their observations and possibly sort winter leaf litter to look for invertebrates under a microscope.

genome of that bacterium and found one anti-protozoal protein already!” he reports. Clearly, the firebug outing has impacted more than budding entomologists at Newman Elementary. “The thing I came away with from this,” concludes Dale, “is that we at our level should make more of an effort to connect with schools and the public,” with our research.

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Briefly Noted Arie Sitthichai Mobley (BS’2000) recently published a textbook for undergraduates: “Neural Stem Cells and Adult Neurogenesis.”

When she began teaching at a small liberal arts university in a department for undergraduate neuroscience, she said there were many books on stem cells, but they were either too broadly or narrowly focused, or too advanced for an undergraduate course. The lack of an appropriate textbook motivated her to write one aimed at undergraduate neuroscience students. The book is to help students appreciate the potential, and understand the limitations of stem cells, while providing a basic knowledge of stem cell physiology. Mobley graduated from South Sevier High School (Monroe, UT, near Richfield) in 1991 and, after graduating in biology, continued at the U earning a doctorate in neuroscience. She did her post doctorate at Yale and then became an assistant professor at Western New England University in Springfield, MA. After teaching for four years, she moved to Bar Harbor, Maine, where she is an associate study director at The Jackson Laboratory.

SBS is one of only a few programs which has a robust elective emphasis for undergrads in the biology of the nervous system.

J. Floyd Hatch (BS’76) is the Owner and President of Intermountain Realty Group, licensed in 1989. He worked as an oil and gas exploration geologist for several years prior to entering the real estate market. Floyd grew up in Salt Lake City and developed an affinity for hunting and fishing at an early age. He and his wife Carol, also an alum of the “U,” have five children and own a 5,000-acre ranch in Morgan County, Utah, where they built an eight-bedroom hunting lodge. Many of Floyd’s friends began as clients and he is known for checking in with them long after deals have closed. He has served on the community, state, and national level with several organizations including the Boy Scouts of America and Rotary International.

Guy G. Musser (BS’59; MS’61) passed away in October 2019 in Florida. He was the Archbold Curator Emeritus, Vertebrate Zoology, Mammology at the American Museum of Natural History where he worked beginning in 1966. Before that the Salt Lake City native worked at the University of Utah with zoologists Stephen Durrant and William Behle and had a reputation for being an exceptional field scientist and taxonomist. Musser, who earned his PhD from the University of Michigan, researched the geographic origins of murine rodents in Asia by examining the phylogenetic relationships between the rats and mice found on that continent and their IndoAustralian cousins. Robert S. Voss, from the Division in which Musser made his name at AMNH, has written that Musser’s “career began just as the influence of the New Systematics was beginning to wane.” He continues: “One of Guy’s great gifts, I think, is to be undeceived by the opinions of others and to focus on the facts.” Musser was 83.

It takes a village . . . to operate a world-class School of Biological Sciences, especially when you have more than 1,400 declared majors (the largest of any academic unit on campus). The University of Utah’s HR Division knows about village dynamics. That’s why they annually give out Staff Excellence Awards. Denise Brenes, Director of Undergraduate Advising who previously received a 2019 Academic and Student Affairs District Excellence Award was awarded in August the University Staff Excellence Award. This prestigious award program recognizes superior service and ongoing contributions by full-time staff employees. Brenes is no stranger to advising accolades.

Last year she was recipient of the Excellence in Advising Administrator Award bestowed annually by the National Academic Advising Association. NACADA is an association of professional advisors, counselors, faculty, administrators, and students working to enhance the educational development of students. All of this to say, the “Village” is in good hands.

Cecil O. Samuelson, Jr. (BS’66) worked as a professor of medicine and later dean of the school of medicine at the University of Utah before landing at Intermountain Healthcare (IHC) as a senior vice president. Later he became the 12th president of Brigham Young University. Samuelson has received numerous scholastic honors and is the author or co-author of forty-eight original publications. He also has served as a director, officer or member of several national medical and hospital organizations.

He is currently an emeritus general authority of The Church of Jesus Christ of Latter-day Saints.

Ecologist Nalini Nadkarni, a faculty member, was recently featured in “Wait, Wait . . . Don’t Tell Me!,” National Public Radio’s news quiz show. She had a nine-minute appearance live in Salt Lake City at the program’s 1,000th anniversary show. At a packed Eccles Theatre downtown she was the guest during the “Not my Job” segment in which, as host Peter Sagal intoned to the enthusiastic audience, “we ask smart people dumb questions.” Nadkarni spends so much time in the tree canopy of Central America, that she inspired a tree-top Barbie doll by Mattel, to encourage girls to gear up for scientific discovery in the tropical forests high above the forest floor. The video story appeared earlier on NPR’s “Maddie About Science” series.

Dan Fischer (BS’71) is the founder and CEO of Ultradent Products, Inc., a dental manufacturer with a thirty-year history 16

of innovation and quality. After earning his DDS from Loma Linda University in 1974 he founded Ultradent in his basement, with his children as its first employees. Considered one of Ultradent’s flagship products, Astringedent® and later Viscostat®, resulted from Fischer’s insight, determination, and willingness to work after hours— using his own blood to test his efforts—to produce exactly what he felt the market needed. Fischer also works part-time in his daughter’s dental practice, which enables him to connect with patients and practice minimally invasive dentistry—a philosophy around which Ultradent develops its products and procedures.

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Zebrafish scale on the point of a needle. Photo: Matt Crawley

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