Ole Jensen, BS’72

On the surface, Ole Jensen’s start as an undergraduate biology major, angling for medical school, didn’t appear particularly auspicious. His one claim to fame was that as an undergraduate the Salt Lake native was tapped to be a “calf sitter,” which meant that he would sit all night with young bovine used in experiments and monitor their heart rates. The calves were a critical part of the University’s artificial organ program which would eventually produce the world’s first artificial heart in the 1980s.

Not bad for a Utah boy who, when he wasn’t fishing with his Norwegian-born father on the Provo River and elsewhere, spent much of his early life collecting what would become one of the largest insect collections in the state.

It was a heady time to be studying biology at the U. Department Chair Gordon Lark was bringing in guest lecturers and expanding the faculty at a prodigious rate, including micro-biologist Mario Capecchi who would eventually be awarded the Nobel Prize for his work in genetics. Jensen recalls his time in the early seventies as an undergraduate at the U. One day, he says, anatomy professor Stephen Durrant “threw out twenty animal bones spread over a long table and asked the students to identify […them] as part of the midterm exam.” It turned out that the students, who in class had been studying strictly land mammals, got very few correct answers. “One bone that very much perplexed me that I remember to this day,” Jensen continues, “was half of a frontal bone with an ovoid depression. It was from a dolphin: the depression access for the spout!” Needless to say, it was “a particular shock” to find a marine mammal bone in the pile, but it was an experience that Jensen still recalls with some exhilaration.

After graduating from dental school at Northwest University, Jensen continued to Michigan to study oral surgery and, as a post doc, anesthesia, which would eventually lead to a Master’s degree in anesthesiology before returning to the west where he set up practice in Denver. There he plied his trade, as both a science and an art, for the next 38 years. But research has continued to braid its way through his entire professional life—a continuous thread that has kept him at the forefront of the fast-moving field of oral and maxillofacial surgery in which technology, the life sciences and medicine converge. As with many oral surgeons, Jensen performed four-on-one implant operations, which combine bridgework with a maximum of four implants per each of the crescent arrangements or arches.

Eventually, he modified the procedure so that it was less invasive and more intuitive, underscored by his determination to see the implant not as an analogue to a tooth (or teeth) but as a function of bio-mechanical forces, mathematically determined. Eventually he would join forces with business partners to found Clear Choice Dental Implants. “Basically, for five years I wanted to die,” Jensen says of the start-up which now has forty clinics across the nation. The company nearly failed three times, including during the recession of 2008. “I wanted to practice . . . business with integrity, and to be doing things in the best interests of the patients. It’s hard to do that with this kind of work where it’s not too costly and not too difficult for doctors to perform.” In a recent DentalTown podcast, Jensen explains, “If you have a business that is related to dental implants, you’re not going to do stuff that will put the business at risk."

"So this has a business, scientific, and a clinical basis of validity," he says ". . . [and] we stand by the way we treat our edentulous patients… .” Of course success is never final. With his rigorous research background and his bias for asking lots of questions, this time about biofilm, the pervasive glue-like matrix that grows virtually everywhere and can lead to complications in bio-medical work, Jensen took on yet another professional challenge. In September he was hired as Chief Medical Officer for Israel-based NOBIO, helping to create products through Nano-technology in which particles with superior micro-biotic activities are baked into the product to prevent bacteria from growing on surgically implanted devices.

Jensen’s research questions, especially as they’ve related to medicine, have been open ones. “Almost everything I’ve done is in surgery,” he says. “Now I’m doing a project with computers,” referring to his latest adventure. Inspired by the training of pilots who learn to fly by logging many hours in flight simulators, Jensen and his team at Massachusetts General Hospital in Boston are developing a program for surgical simulations.

Dalley Cutler

Dalley Cutler


Biology senior Dalley Cutler's personal hero is Greta Thunberg, the young Swedish activist invited to the United Nations to advocate for reversing man-made climate change and who was subsequently named Time Magazine's Person of the Year. Along with this sixteen-year-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 food 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 products.

“I generated the data for this poster some time ago,” he says, referring to the research poster he displayed at the School of Biological Sciences' annual Retreat in August 2019.  “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 alumni donor 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.

The scholarship has also allowed him to begin generating and processing data for his next project.

Cutler who is graduating with his bachelor's in biology in April 2020 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 pig tails who was named Time Magazine's Person of the Year for 2019, he is committed as a scientist to make a difference.

Running with Scissors

Jamie Gagnon

One 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.

“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.”

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

Zebrafish Research subjects

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.

“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.

Zebrafish Scale

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.

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?

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.

The Gagnon Lab

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.”

Illustration by The Gagnon Lab

“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.

 

by David Pace

- First Published in OurDNA Magazine, Fall 2019

Going with the Flow

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

John 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.

It was the ultimate success of that technique and new discoveries of how vascular tissues, or xylem in particular, 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 30+ 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 CO2 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 CO2 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.”

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.

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."

- First Published in OurDNA Magazine, Fall 2019

Staff: Jose Rojas

Facilities manager at the School of Biological Sciences for 20 years, Jose 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 tiny round worms of C. elegans—Rojas’s work in retrofitting lab spaces requires prodding, perturbing and replicating.

Labs in the four biology buildings (Aline Skaggs [ASB], 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 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, and 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. Currently Rojas is 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’ 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 project 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’ work has not gone unnoticed: in 2017 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. At first blush you might wonder how an artist ended up as the new facilities manager here at the School of Biological Sciences. 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.

Bridget Phillips

As one of the University of Utah 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 works studying the genetic causes and patterns of variation in the axial skeleton of 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 Salt Lake native, Bridget is the recipient of the Ole Jensen Scholarship this year. Because of the scholarship, she says, "I’ve been able to dedicate much more of my time to [research in the Shapiro Lab]. I greatly appreciate and deeply value the scholarship."

Dr. Jensen (BS'72), co-founder of ClearChoice Dental Implant Centers, established an endowment for undergraduate research at the School just last year. He will be at the Retreat this year to receive the 2019 Distinguished Alumni Award.

Bridget'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."

Favorite Thing About the UofU:
"I was able to start in a wonderful lab as a first-year and be able to live in Crocker Science House with other like-minded science folks."

Hero:
Thomas Hunt Morgan, who was able to show that chromosomes have a role in heredity.

Little Known Fact:
"Because all 350 breeds are capable of interbreeding to generate genetic crosses, pigeons provide a unique opportunity to identify specific genes involved in many morphological traits."