ourdna-spring20 | College of Science

Forest Futures

June 22, 2020

Given the tremendous ability of forests to absorb carbon dioxide from the atmosphere, some governments are counting on planted forests as offsets for greenhouse gas emissions—a sort of climate investment. But as with any investment, it’s important to understand the risks. If a forest goes bust, researchers say, much of that stored carbon could go up in smoke.

In a paper published in Science, University of Utah biologist William Anderegg and his colleagues say that forests can be best deployed in the fight against climate change with a proper understanding of the risks to that forest that climate change itself imposes. “As long as this is done wisely and based on the best available science, that’s fantastic,” Anderegg says. “But there hasn’t been adequate attention to the risks of climate change to forests right now.”

Meeting of Minds

William Anderegg

In 2019, Anderegg, a recipient of the Packard Fellowship for Science and Engineering from the David and Lucile Packard Foundation, convened a workshop in Salt Lake City to gather some of the foremost experts on climate change risks to forests. The diverse group represented various disciplines: law, economics, science and public policy, among others. “This was designed to bring some of the people who had thought about this the most together and to start talking and come up with a roadmap,” Anderegg says.

This paper, part of that roadmap, calls attention to the risks forests face from myriad consequences of rising global temperatures, including fire, drought, insect damage and human disturbance—a call to action, Anderegg says, to bridge the divide between the data and models produced by scientists and the actions taken by policymakers.

Accumulating Risk

Forests absorb a significant amount of the carbon dioxide that’s emitted into the atmosphere—just under a third, Anderegg says. “And this sponge for CO₂ is incredibly valuable to us.”

Because of this, governments in many countries are looking to “forest-based natural climate solutions” that include preventing deforestation, managing natural forests and reforesting. Forests could be some of the more cost-effective climate mitigation strategies, with co-benefits for biodiversity, conservation and local communities.

But built into this strategy is the idea that forests are able to store carbon relatively “permanently”, or on the time scales of 50 to 100 years—or longer. Such permanence is not always a given. “There’s a very real chance that many of those forest projects could go up in flames or to bugs or drought stress or hurricanes in the coming decades,” Anderegg says.

Forests have long been vulnerable to all of those factors, and have been able to recover from them when they are episodic or come one at a time. But the risks connected with climate change, including drought and fire, increase over time. Multiple threats at once, or insufficient time for forests to recover from those threats, can kill the trees, release the carbon, and undermine the entire premise of forest-based natural climate solutions.

“Without good science to tell us what those risks are,” Anderegg says, “we’re flying blind and not making the best policy decisions.”

Mitigating Risk

In the paper, Anderegg and his colleagues encourage scientists to focus increased attention on assessing forest climate risks and share the best of their data and predictive models with policymakers so that climate strategies including forests can have the best long-term impact. For example, he says, the climate risk computer models scientists use are detailed and cutting-edge, but aren’t widely used outside the scientific community. So, policy decisions can rely on science that may be decades old.

“There are at least two key things you can do with this information,” Anderegg says. The first is to optimize investment in forests and minimize risks. “Science can guide and inform where we ought to be investing to achieve different climate aims and avoid risks.”

The second, he says, is to mitigate risks through forest management. “If we’re worried about fire as a major risk in a certain area, we can start to think about what are the management tools that make a forest more resilient to that disturbance.” More research, he says, is needed in this field, and he and his colleagues plan to work toward answering those questions.

“We view this paper as an urgent call to both policymakers and the scientific community,” Anderegg says, “to study this more, and improve in sharing tools and information across different groups.” Read the full paper @ sciencemag.org

Karl Gordon Lark

April 22, 2020

photo by Ben Okun

Karl Gordon Lark, Distinguished Professor Emeritus at the University of Utah, passed away on April 10, 2020, after a seven-year battle with cancer. A renowned geneticist, Lark uncovered fundamental aspects of DNA replication and genetics across many systems, from bacteria to soybeans to dogs. He came to the U in 1970 as the biology department’s inaugural chair with a vision—to build a research and teaching powerhouse in the desert. In just six years he recruited 17 faculty members from all biological disciplines, establishing an institution of scientific excellence.

“Today, the tremendous impact of Gordon’s vision and leadership are felt in the School of Biological Sciences, across campus and throughout the state of Utah,” said Denise Dearing, director of the school. “Gordon was responsible for the expansion of molecular biology—a new field in those days—across the U. He will be dearly missed.”

“The [University of Utah’s] nascent research community, in every field from molecular biology to community ecology, was built by Lark in creative, often wildly unconventional small steps,” wrote Baldomero “Toto” Olivera, Distinguished Professor of Biological Sciences, in an unpublished essay for the Annual Reviews of Pharmacology and Toxicology.Olivera conducts world-renowned research on cone snail venom and pain management, and was recruited by Lark. “It is his guidance that makes me feel unconstrained in exploring unusual solutions to seemingly intractable problems.”

Lark was preceded in death by his first wife, Cynthia (née Thompson). He is survived by his four children, Clovis, Ellen, Suzanna and Caroline and his granddaughter, Willow. He is also survived by his second wife, Antje Curry, his stepdaughter, Tara, and her two children, Liam and Briar.

A life of inquiry

Curiosity and coincidence guided Lark’s lifelong pursuit of discovery. He was born on Dec. 13, 1930, in West Lafayette, Indiana, into a household that valued intellect. His father was physics chair at Purdue University and his mother was an artist and psychiatrist. Lark was precocious in his academic pursuits and enrolled at the University of Chicago a year after World War II ended at the age of 15. There, he met Leo Szilard, regarded as the father of the Manhattan Project but who had turned his attention from nuclear reactions to the newly emerging field of the molecular basis of life. Szilard suggested that Lark spend the summer at Cold Spring Harbor, a famous laboratory that helped develop the field of molecular biology. There, Lark met Mark Adams, a scientist from New York University who would become Lark’s mentor.

Adams studied phages, which are viruses that invade bacterial cells and take over various host functions to propagate themselves. He not only inspired Lark’s love of research, but also taught him how to organize effective undergraduate science education. In the fall, Lark returned to Chicago to complete his degree and had his first eureka moment—he discovered reversible changes in the physical structure of phage proteins. It would be about four more years before the field generally accepted that molecules could change a protein’s shape.

“To this day, I think it’s one of the best pieces of science I’ve ever done,” Lark reflected in comments to the U’s American West Center. “It was the bringing together of physics and chemistry and biology into one moment. I didn’t think of it that way at the time, but from then on I was hooked!”

Lark returned to Cold Spring Harbor in the summer of 1950 to work with Adams, and there he met his future wife and scientific collaborator, Cynthia. Lark completed his doctorate at NYU, spent two years as a postdoc at the Statens Serum Institut in Copenhagen, Denmark, and one year at the University of Geneva. On subsequent return visits, he met Costa Georgopoulos, a biochemist who discovered a new class of proteins called chaperones. More than 20 years after they first met, Georgopoulos would move to the Department of Biochemistry at the U.

“Gordon and I shared many old friends and colorful memories from our times in Switzerland,” Georgopoulos remembered. “Gordon’s nickname in the lab was ‘double-decker’ because his plentiful, high-rising hair resembled a double-decker bus.”

In 1956, Lark accepted a position at St. Louis University Medical School. Here, Lark had what he called his second epiphany—an experiment to show that in the absence of protein synthesis, replication of DNA stopped at a particular point on the bacterial chromosome. The experiment set the course of his research for the next two decades. In 1963, the Larks moved on to the physics department at Kansas State University where they focused their research on the process of DNA replication in bacteria. They pioneered how to measure the point when DNA begins replicating, how to track the progression of replication in living cells and developed the technique of measuring the size of cells before they begin to replicate. In 1965, the American Association for Microbiology honored Lark with the Ely Lilly Award, given each year to recognize landmark research in microbial physiology.

Building scientific and teaching excellence in Utah

In 1970, the U’s Robert Vickery recruited Lark to build a powerful new biology department in what would become the School of Biological Sciences in 2014. And build he did. During his time as chair from 1970-77, he hired 17 new tenure-track faculty, including Mario Capecchi who would subsequently become a Nobel Prize laureate, Raymond Gesteland and Ray White, who went on to establish new departments in the School of Medicine.

“As chair, Gordon was an unusually skilled administrator, combining a rare insight into the environment that different members of faculty and staff needed to succeed and the energy to provide it,” said Capecchi. “I was attracted to the young Utah biology department in part by Gordon’s support of long-term studies aimed at significant problems, but without the promise of immediately publishable results, quite different from the ‘publish-or-perish’ policies imposed at many other places.”

Lark also impressed the importance of teaching to the biology faculty, both by personal example and with innovative programs. In the department’s very early days, he hired one of the world’s most charismatic young science personalities, David Suzuki, as a visiting scholar to teach the introductory course in genetics. He implemented video recordings of well-taught introductory courses so they could be offered more frequently to more students. For several years as chair, he funded an annual program in which a prominent faculty member from outside the College of Science taught a course in their own area, designed for biology students.

“During Gordon’s final years after retirement and while battling cancer, he voluntarily and unpaid taught an Honors course for a general student audience. With biographical and autobiographical readings, he introduced the human sides of pioneers in the exciting advances of 20th century physics and chemistry, several of whom Gordon had known personally,” said Larry Okun, professor emeritus of biology. “He taught that course right through 2019, his own last fall semester.”

In Utah, the Larks turned their attention from bacteria to plant cells and tissues, particularly soybeans, for the next decade. In the early 1990s, disaster and serendipity struck—the Lark lab was destroyed while the building was under renovation. After a year of trying to salvage their work, they switched to studying whole soybean plants in agricultural fields, focusing on the genetics underlying certain traits, such as the ability of the crop to adapt to different climates. Overall, their laboratory identified genes that increased the yield of soybeans by 10%.

In 1996, tragedy and serendipity struck again. The Lark’s Portuguese water dog, Georgie, had died of an autoimmune anemia disease. Heartbroken, the Larks connected to a dog breeder, Karen Miller, to buy another puppy. When the time came, Miller gave Lark the $1,500 dog for free hoping to guilt him into studying the breed’s genetics.

It worked. Miller coordinated with Portuguese water dog owners from around the country to send Lark blood samples and X-rays of their pets. What became known as “The Georgie Project,” eventually identified genes that determine the size and shape of the head, thickness of the thigh bone, shape of the pelvis and characteristics of the lower foreleg.

A legacy that spans generations

Lark formally retired from the U as a Distinguished Professor in 1999, but his legacy in biology reaches beyond his direct collaborators. The next generation of biologists also feels his influence.

“The magnitude of Gordon’s accomplishments is hard to really capture in today’s world,” said David Grunwald, professor of human genetics at the U’s School of Medicine. “Individuals can have a big effect on an institution. They can either set a precedent that honors creativity, respect and excellence, or they can make everyone feel like a cog in a machine. Gordon built a place that engendered creativity.”

The K. Gordon Lark Fund was established in 2018 by the School of Biological Sciences in anticipation of growing it to a fully endowed-chair in his name. To honor his memory, donors can make gifts to the endowment here.

Courtship Condos

April 8, 2020

Dean Castillo

Playing to the ethic of pursuing pure science, new faculty member Dean Castillo is driven by research questions not necessarily the research organism. While working on his bachelor’s and even before that while growing up in rural northern California, he worked with “tons of different organisms,” he says, including fungi. So it wasn’t difficult for him as a geneticist to move from his earlier subjects such as tomatoes and nematodes at Indiana University, where he earned his PhD, to fruit flies (Drosophilia) during his postdoc at Cornell and now at the University of Utah.

The question for Castillo was the same: how do natural and sexual selection shape mating interactions and behaviors, species interactions, and ultimately speciation?

The focus of Castillo, a recent faculty arrival at the School of Biological Sciences, remains evolutionary interactions between organisms, whether in “fruit” or the flies that feed on the yeast of that fruit. Genes determine behavior, and in the case of the fruit fly the female can mate with more than one male and store different sperm in different organ “storage areas” before determining which sperm will be used. How does that anatomically happen and what genes are motivating the female to determine which sperm is used?

Drosophilia - Fruit Flies

“Why does one female mate but another doesn’t?” he further asks. Once his lab determines how and where sperm from two different males is being stored in one female they will pursue other areas of inquiry: finding the genes that control female choice in the brain and, instead of pollen competition from his tomato days, it’s now sperm competition.

The equipment Castillo uses for his research includes one centimeter-high glass “condos” for the tiny flies with removable “gates.” From cotton-topped vials where the flies live on a bed of molasses and yeast, the researcher inserts a female in one side of a bifurcated chamber and a male in the other. Once the researcher lifts the gate between the sides, they can observe the eternal mating behavior of the two sexes on the micro level.

Behavior is only part of the Castillo lab’s integrative approach which combines these condo experiments with population and molecular genetics to understand the genetic basis of sexual behaviors. The approach is also designed to explore the reduction or cessation of reproduction between members of different species. (Think of crossing a horse and a donkey to produce a mule, which is sterile). Comparative genomics can help track this “reproductive isolation,” as it is termed, across the tree of life.

Drosophilia - Fruit Flies

“By studying the mechanistic and genetic links between sexual selection and reproductive isolation we can determine the influence of these forces on generating biodiversity,” says Castillo, sitting in the adjacent office to his lab on the fourth floor of the Aline W. Skaggs biology building. The almost feral view out his windows eastward to the Wasatch is a reminder of one of the big attractions to taking a position at the University of Utah: its stunning setting and, perhaps more importantly, its accessibility to wild nature. In fact, the flies that Castillo studies are easily found in the area, including in American Fork Canyon and Zions National Park. His wife Deidra, who with Dean also earned her PhD from Indiana University at Bloomington, begins her research soon in the Vickers lab one floor down. It turns out that there is overlap between her research in plant-insect interactions and Vickers’ research in moth olfaction and neuroethology.

Managing courtship condos to get at basic biology questions like how genes control behavior can seem random, even mercurial. This is especially true when compared to the careful planning required to procure one’s own family when both parents are academics. (The Castillos have three children, including a one-year-old.) It turns out that their first child was born during qualifying exams. Later, number two entered the scene while they were both defending their theses, the third during their postdocs prior to their move to Utah.

Dean Castillo with a few thousand research subjects.

For the time being, the five Castillos will be staying put except, perhaps, for combining science with mountain and high-desert camping trips looking for fruit flies.

Ana Rosas

April 3, 2020

Every student’s story is one-of-a-kind, and Ana Rosas’ is no exception.

Rosas’ desire to become a doctor was deeply personal. She recalls her grandmother dying just one month after being diagnosed with untreatable and advanced liver cancer. “During my grieving, I thought about what, if anything, could have been done to prolong” her grandmother’s life. Was the late diagnosis due to her grandmother’s Hispanic heritage? Her community’s mistrust of physicians? Socio-economic barriers? “Though I was provided with encouragements,” she wrote in her recent application to medical school, including from select teachers at local Cottonwood High School, “I was also independently driven to learn and become equipped with tools needed to one day give back to my community.”

Ana arrived as a one-year-old in the United States with her mother and aunt, both of whom had been doctors in their native Colombia. But neither woman was eligible to practice medicine in the U.S. Instead, these two single mothers focused on raising their children. Being in a country that unexpectedly eliminated her career did not keep Ana's mother from sharing her expertise. Rosas remembers her mother conducting a hands-on anatomy class with a pig's head on the dining room table, even introducing surgical procedures.

At the University of Utah as a biology major intent on going to medical school, Rosas quickly realized that she didn’t have the same resources or opportunities, finding that she was on her own to navigate, for example, finding a lab to do research. She didn’t know anyone in the health sciences. Seventy emails later she landed in Dr. Albert Park’s lab at Primary Children’s Hospital in Salt Lake City where she worked with her team to better remove laryngeal cysts in infants. The learning curve was steep: literature reviews, in-text citations, and continually managing her share of “imposter syndrome” that started as early as high school where she was a minority. Her work with Park resulted in her presenting a poster at a national Otolaryngology meeting and a first authorship in a related prestigious international journal. “I have not had many undergraduates achieve so much in such a short time,” Park says of Rosas.

Now a senior at the School of Biological Sciences, Rosas has been busy working in not one but two labs. With Kelly Hughes she works with bacteria, specifically Salmonella, and focuses on identifying the secretion signal for a regulatory protein that is required for proper flagellar formation. “I mutagenize the protein,” she says, “by incorporating random amino acid substitutions at each amino acid position of the protein.” Along the way she looks for colonies that are defective. “This way I can send those colonies for sequencing and obtain data that can tell what amino acids are essential for the proper secretion of the protein” under study.

Her second lab experience with Robert C. Welsh in the School of Medicine's Department of Psychiatry brings Rosas' career ambitions back full circle to her heritage and her desire to give back to her community, which is often under-served by the medical profession and under-represented in institutions of higher learning. Using imaging equipment, she and her colleagues are developing a diagnostic and prognostic tool to determine where ALS (Alzheimer’s) patients are in the progression of the disease. Related to that is lab work of another kind. In the “engagement studio” at University Neuropsychiatric Institute (UNI) she is gathering feedback from minority groups to see what obstacles—from language barriers to mistrust of medical authorities–impact their participation in research. “We want to figure out what researchers can do to encourage their cooperation,” she says.

At the same time, while demonstrating that she’s not only successfully balancing on that once precipitous learning curve, Rosas has demonstrated that she’s clearly ahead of it. Currently she is treasurer of the InSTEM group on campus and has helped initiate the new Health Sciences LEAP program which does science outreach in high schools. “I want to help minorities like me,” says Rosas, “better navigate college for the first few years.” Tanya Vickers who directs the ACCESS program for the College of Science, is most certain she will do exactly that, referring to Rosas as a “remarkable young woman.”

Rosas has indeed come a long way from anatomy lessons on her mother’s kitchen table. Applying to medical schools has provided the chance to reflect on her journey and, considering the barriers and uncertainty she first felt, that journey has proven to be an auspicious one.

by David G. Pace

Alex Acuna

March 20, 2020

Alexandra “Alex” Acuna doesn’t even remember her native Venezuela, as she arrived in the U.S. with her parents and two older siblings when she was just a few weeks old. She does recall as a young child huddling in a room for seven months with other families experiencing homelessness at the Road Home Shelter in Salt Lake City where her closest ally was “Mike Wazowski,” a ratty, single-eyed monster toy she hugged day and night.

Eventually, the family moved into a basement apartment with two other families before landing more permanently in government-subsidized housing. “There were a lot of points in our childhood when my siblings and I were skating on thin ice,” she says, referencing everything from food and housing insecurity to fear of deportation; from the stigma of not being part of the majority Latinx community to almost yearly changes in schools. To make matters worse, her parents separated shortly after the family’s arrival. “Survival took up all of our time,” she says.

There was one stabilizing force for the family: food and the community that comes with each cuisine. It started in their modest apartment kitchen with her mother selling empanadas, a cottage industry that grew to a full-fledged Venezuelan restaurant that, in 2014, opened in Salt Lake.

Acuna’s mother, whose college experience was derailed in Venezuela by her first pregnancy, was determined to make sure her children got to the best public schools possible. Even so, as Acuna puts it, once at the UofU she experienced what so many first-generation students do: “I had no access to people who understood the system I was trying to navigate. I didn’t know what I didn’t know. I didn’t know where to look for resources.”

The College of Science’s Access Program was a life ring. Not only did it provide Acuna a scholarship, but a first-year cohort with older students along with housing during the summer before her first year so that she could familiarize herself with campus life. Another important component of the program directed by Tanya Vickers was getting into a lab, something Acuna admits “was not even on my radar.” In Leslie Sieburth’s lab at the School of Biological Sciences Acuna became embedded in a community: “How do you bridge the gap in knowledge,” she asks, “without a network of people?” The answer is you probably don’t, especially with Acuna’s background and lack of opportunities that many college-bound students take for granted.

For three years, Acuna fought self-doubt during “the worst of times” that she was somehow an intruder, a forever-outsider who didn’t belong in a lab that, frankly, she wasn’t even sure the value of. “Tanya was a great mentor,” she says now of Vickers, acknowledging that her mentor helped her see that, while her mother needed her to work in the restaurant, Acuna needed to prioritize her education, a difficult thing to do when you’ve been a character in a shared survival narrative as intense as theirs.

Eventually, the school/work balance was struck. “My mother was never a helicopter mom. But she sees me in the trenches and can now share the glory of it with me.” (Acuna still works weekends in the restaurant, patronized by the flowering Venezuelan community and others in Utah’s capital city.)

Says Sieburth of Acuna, “Alex joined my lab with an enormous amount of raw talent. It was a pleasure to mentor her, and to help her recognize her remarkable facility for research.”

An opportunity seized soon presents other opportunities. In February 2019, Acuna was admitted to the inaugural year of the Genomics Summer Research for Minorities sponsored by the U’s medical school. Currently, she does research in the Tristani-Firouzi lab where the gene-editing and cloning of plants she was doing with Sieburth are now placed for this budding molecular biologist into a medical and physiological context. In the Tristani lab they are studying the genetic component of atrial fibrillation, one of the most common types of cardiac arrhythmia. “It’s given me power to things that I wasn’t even aware of before coming here,” says a grinning Acuna.

What’s next for Alex Acuna? “I know that I’m definitely moving on,” she says of her career as a scientist. “I’m just not clear what direction: academics or medical school.” As a paid undergraduate research assistant, though, one thing she is sure about: “I’ve found a sustainable model. These worlds–personal and professional–they could combine [after all]. They did combine. I understand my ambition, and I now have such sensitivity to activities outside of the lab.”

For Acuna and her family, who are now naturalized citizens of the U.S., their experience is not just an immigrant story of survival; it’s an incomplete narrative born in Venezuela and perpetually vectoring toward real promise.