bio-news

Biological Data

December 20, 2021

The Science of Biological Data

Fred Adler

In an age when cross-disciplinary collaboration has become a buzzterm, especially in academia, Fred Adler puts his mathematical models where his mouth is. Multi-disciplinary work—in which academic silos are breached in the search for truth—is the hallmark of what Adler, who has a joint appointment in mathematics and biology, does.

His is the kind of work that will be supported by the new science building recently announced by the College of Science, dedicated to applied and multi-disciplinary work, and where most STEM students at the U will eventually find themselves for a time.

As Director of the Center for Quantitative Biology, Adler and his team have applied their data-driven tool kit to everything from viruses to animal behavior, and from biodiversity to infectious diseases. Who else can claim a lab’s subject models as varied as aphid-tending ants, hantavirus, and the Southern Right Whale off the coast of Argentina?

Math in Nature

The Adler group’s approach to research is driven by basic questions about how biology works. To bring together several threads of research, the lab began a study of rhinoviruses, the most common cause of the common cold, and how they routinely and rapidly change. The study uses mathematical models based on known interactions in the immune system and genetic sequences. “We hope to build detailed evolutionary models of this rapidly change set of viruses,” Adler reports.

He and his team are now looking at cancer in humans. There are, of course, hypotheses of how cancer takes over cells in the body and grows. But too many of these hypotheses are based on assumptions that cells behave as they do with complete information and clever plans for the future instead of the confusing world of a real tissue.

“However useful some of these [current] models are,” says Adler, “they are not based on a realistic assumption.” In fact, a prime contribution of the mathematical modeler is “to make sense of things from the perspective of what you’re modeling.” What access to information does the cell or organism have, is a central, guiding question.

Muskan Walia and Emerson Arehart

Part of how cancer behaviors may be better scientifically “unpacked” is through game theory but expanded over time and space and placed in a context of incomplete information between constituent parts.

Mathematical models, or more accurately, an ensemble of models later aggregated like political polls or weather models to predict the future, may be the answer. “We usually don’t get a simple smoking gun,” says Adler referring to complicated questions in biology, whether developmental, behavioral-ecological, immuno- or micro-biological. “With nine or ten big mathematical models running all the time you have a [more robust] hypothesis,” he says.

“All thinking is done using modeling,” Adler reminds us, “whether it’s through language or, in my case, mathematics.” The strength of the latter is that when mathematical modeling is added to the classical biologist’s models, it is “perfectly explicit about its assumptions. When you do the math right (and we always do), the logic leading from assumptions to conclusions is airtight ‘true.’”

This is important because a mathematical argument can’t be controverted. “If conclusions in biological research are wrong, it’s the assumptions that are wrong,” and the researcher can then pivot on those assumptions.

Modeling of this kind, of course, has proven helpful, most recently, in the study of Sars-CoV-19, the virus that has propelled the world into a pandemic. The coronavirus does not operate in isolation, but with other components through the human immune system.

This kind of work is animated not just by its predictive character using statistics—as in the case of artificial intelligence or machine learning (“We aren’t all cyborgs, yet,” Adler says)—but, it is predictive in a mechanistic sense in that it cares deeply about the more nuanced and open-ended “how,” the foundation of the scientific method.

Adler started out at Harvard as a pure mathematician, but by the time he arrived at Cornell University as a graduate student, he had discovered that he really enjoyed talking and collaborating with biologists. Stanford-based Deborah Gordon, a renowned expert on ants, which as he puts it, “achieve a lot of stuff fairly robustly through simple rules,” was one of them. He also found himself with David Winkler in upstate New York in a bird blind and observing the breeding and offspring-raising behaviors of tree swallows. The complicated models he built based on that research were never published, but Adler was hooked on life sciences.

Whether it’s modeling the lungs of cystic fibrosis patients looking for a transplant, determining that the changesnin Covid-19 are driven not just by mutations in the virus but adaptations of human immune response, or other “bench to bedside” medical science, Fred Adler has found a home in the mechanistic aspects, the “how,” of basic science.

How to synthesize his research over the past thirty years is the next big question. For now he will continue with modeling biological systems, their signaling networks based on the body’s own network of “trust” between components, and determining how those systems are corrupted… and maybe how to fix them.

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Space Plants

December 20, 2021

The Future of Space travel

Ming Hammond

For humanity to push the boundaries of space exploration, we’re going to need plants to come along for the ride. Not just spinach or potatoes, though—plants can do so much more than just feed us.

“There’s a lot of promise, potential and hope that we can use the tools developed in synthetic biology to solve problems.” says Chemistry Professor Ming Hammond, “not just that you would find in space, but where you have extreme limitation of resources.”

A synthetic garden.

Synthetic biology is a field that engineers biological systems. In this case, the team is looking at plants as potential bio-factories. Every organism naturally produces countless proteins as part of its biological function, so why not engineer a plant to produce, say, a needed medication or a polymer that could be useful in future long-term space exploration missions?

“The benefit is that you can take seeds with you,” Hammond said. “They’re very lightweight. They grow and gain biomass using the CO2 that we breathe out. And if those plants can produce proteins on demand—we know that plants are able to produce anti-viral and anti-cancer antibodies on a large scale.”

LED lights and USB camera.

Synthetic biology is already established on Earth. But translating that same technology to spaceflight requires different considerations. Hammond and her team encountered many of these constraints when adapting their experiment to operate within the small (10cm by 10cm) CubeSat enclosure.

For spaceflight, the team decided to engineer plants to change color as they produced the target protein, and monitor the progress with a camera. It’s an elegant and innovative solution, based on a previously published method, but adapted for the constraints of a cube in space.

Final assembly.

“We had to take something that worked beautifully in the most carefully controlled conditions,” Hammond said, “and get it to work under very harsh and challenging conditions inside the plant cube.”

The plant cube was designed with the forward vision of preparing for plant growth studies on the moon, and is a technology development step towards that goal.

The entire experiment took 10 days and appeared to show successful protein production. The results from the team, including collaborators from NASA Ames and International Space University, were published this year.

10x10cm experiment enclosure.

It takes a lot of time and effort to put equipment in space, and Hammond appreciates the many hours of work that the team has put in. “We are a small but dedicated group of volunteers,” she said. “People worked nonstop to fix last-minute things that came up before launch. I’m just really proud of the effort everyone’s put in.”

SpaceX Falcon 9 rocket.

Hammond and her family traveled to the NASA Kennedy Space Center to watch the Dec. 5, 2019 launch of her experiment, which was nestled within a SpaceX Falcon 9 rocket on a resupply mission to the International Space Station.

“At the launch of my experiment, we had a chance to see Bob Behnken and Doug Hurley, the two astronauts that flew the first manned SpaceX flight on May 30, 2020,” she said. “It was an amazing opportunity to share the launch with my son, (6 years old at the time), and other family members. Of all the things I’ve done in science this, for them, is the one that probably inspires the most interest and awe.”

By Paul Gabrielsen

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Fabulous Fungi

October 27, 2021

Just below the surface of our world lies the vast, unexplored world of fungi. There are an estimated 5.1 million species of fungi weaved into the soil, water and other living organisms that inhabit our planet. Of those five million species, we’ve identified just over 70,000.

Despite being just beneath (and sometimes on) our fingertips, the fungal world remains more mysterious than the ocean. However, one small, but growing group of scientists is looking to change that. Collecting, identifying and researching, mycologists stand on the frontier of the unique, unexplored world of fungi, but so far, universities have done a terrible job of facilitating that science.

What is Mycology?

Mycology is the study of fungi, their relationships to each other and other organisms and their biological and chemical composition. Those fungi include mycelium, the mass of interwoven hyphae that forms the underlying structure of the fungus, like the root systems of plants. More commonly thought of as representatives of the fungal world are mushrooms, which are simply the meaty, fruiting bodies of the fungus.

To learn more about mycology, I spoke with the University of Utah’s only resident mycologist, [and associate professor of the School of Biological Sciences] Bryn Dentinger. As a field of study, mycology remains far younger than almost every other science. Dentinger noted that “it wasn’t until the 1970s that fungi even got their own kingdom. We’re so far behind other groups of organisms in terms of their baseline documentation that one of our main activities is still just getting out and documenting what’s out in the world.”

There are millions of unidentified fungi, and very few mycologists to find them. Still, even with the very limited knowledge of fungi that we have, some people, who Dentinger calls “mycoevangelists” think that fungi have the potential to solve many of our biggest problems.

Can Fungi Save the World?

Well, maybe.

While further research is necessary to understand whether mushrooms can be used to treat mental and physical health conditions, fungi are already helping us combat the effects of the climate crisis. Dentinger is “excited about some of the products that are being promoted, like the company Ecovative, that’s producing Styrofoam alternatives.”

Ecovative’s line of mycelium products also includes environmentally friendly skincare products, gloves, footwear, backpacks and plant-based meat. With just Ecovative’s products, mycelium already offers alternatives to single-use plastics, fast fashion and animal agriculture, some of the biggest contributors to the climate crisis. Luckily, some of those products are catching on.

Dell famously piloted mycelium packaging back in 2011. Earlier this year, Adidas released a concept shoe made of mycelium-based leather. Hopefully, they’ll continue to grow in popularity as they become more economically viable, and businesses are held to higher environmental standards.

Fungi have the potential to help us mitigate climate change, but they also will help us become more resilient to it. After the 2019 wildfires in California, the Fire Remediation Action Coalition used oyster mushrooms to divert dangerous runoff from sensitive waterways. Wildfires in the west will only worsen, but we can avoid some of their most dangerous effects with fungi.

Worsening wildfire seasons in Utah are, predominantly, due to the longer, drier summers. Drier seasons bring longer droughts, straining the desert’s limited water supply. Currently, the vast majority of Utah’s water is used for agriculture. Mushrooms, which can grow almost anywhere, use far less water than animal agriculture, especially when they’re grown indoors.

If we introduce more locally grown mushrooms in our diets, our food systems will be more resilient to drought and extreme weather events.

Mycology in Academia

Despite all this important work being done by mycologists, Dentinger finds that, at universities, “we often have to pretend to be something else. So, we masquerade ourselves as ecologists, or molecular biologists or geneticists, but really we study fungi.”

Mycologists have a difficult time collaborating with others to go out and identify organisms, especially if they are the sole professional in their department. And, because so many other fields of study have moved on “from having to document their organisms, there’s virtually no funding for that kind of research.”

With all these structural disadvantages to conducting mycological research, we’re at risk of letting the field of mycology fall even further behind. More than just neglected, Dentinger has found that mycologists often face active hostility towards their discipline. Other scientists “look at us and they’re like, ‘What are you doing? It’s not even science.’ I’ve been charged with that.”

Bryn Dentinger, far right, with his team in the field. Top photo: Curator Bryn Dentinger’s daughter Iona (6 yrs) holding a large (1 lb, 14 oz.) porcini mushroom collected high in the Uinta Mountains in late July, 2021. ©Bryn Dentinger

Still, Dentinger has forged ahead and has started teaching the first mycology class ever offered at the U. “It’s a 5000-level course, but I would say it functions as an Intro to Mycology course because it has to.” Even seniors studying biology at the U have functionally no understanding of fungi. Without students that have a firm grasp of mycology, and no other mycologists working at the U, there’s nobody at the U for Dentinger to even just “go have a conversation with.”

In this current form of mycology in academia, mycologists are isolated, unable to get funding and misunderstood by other scientists at the university. Dentinger finds it “hard to be the only one here,” which makes sense because scientific progress relies so heavily on collaboration. With more mycologists on staff, they would be able to achieve more than the sum of their individual contributions.

Like the objects of their study, mycologists are misunderstood and hard to find. Yet, the organisms they’ve dedicated their lives to have the potential to be an integral part of combating climate change and making us more climate-resilient.

Rather than continue to neglect such an important field, the U should actively look to become a leader in mycology. Dentinger lamented that he would “love to see a center for mycology at a university, but [it] just doesn’t exist. It never has.” Well, maybe it’s about time that it does.

By Will Shadley

This article first appeared in the Utah Daily Chronicle. You can read about another celebrated fungi expert, SBS alumna HBS’94 Kathleen Treseder,  here. 

Darwin’s Pigeon “Enigma”

September 22, 2021

Darwin’s short-beak enigma

Charles Darwin was obsessed with domestic pigeons. He thought they held the secrets of selection in their beaks. Free from the bonds of natural selection, the 350-plus breeds of domestic pigeons have beaks of all shapes and sizes within a single species (Columba livia). The most striking are beaks so short that they sometimes prevent parents from feeding their own young. Centuries of interbreeding taught early pigeon fanciers that beak length was likely regulated by just a few heritable factors. Yet modern geneticists have failed to solve Darwin’s mystery by pinpointing the molecular machinery controlling short beaks—until now.

In a new study, biologists from the University of Utah discovered that a mutation in the ROR2 gene is linked to beak size reduction in numerous breeds of domestic pigeons. Surprisingly, mutations in ROR2 also underlie a human disorder called Robinow syndrome.

“Some of the most striking characteristics of Robinow syndrome are the facial features, which include a broad, prominent forehead and a short, wide nose and mouth, and are reminiscent of the short-beak phenotype in pigeons,” said Elena Boer, lead author of the paper who completed the research as a postdoctoral fellow at the U and is now a clinical variant scientist at ARUP Laboratories. “It makes sense from a developmental standpoint, because we know that the ROR2 signaling pathway plays an important role in vertebrate craniofacial development.”

The paper published in the journal Current Biology on Sept. 21, 2021.

Mapping genes and skulls

Two domestic pigeon breeds photos facing each other, the left one has a very short beak, big black eye, white feathers on the head with a crest sticking up. The right pigeon has gray brown feathers on the head with a red eye ball, and a beak that's about twice as long as the other birds.

PHOTO CREDIT: Sydney Stringham

Old German Owl (left) and Racing Homer (right) domestic pigeon breeds.

The researchers bred two pigeons with short and medium beaks—the medium-beaked male was a Racing Homer, a bird bred for speed with a beak length similar to the ancestral rock pigeon. The small-beaked female was an Old German Owl, a fancy pigeon breed that has a little, squat beak.

“Breeders selected this beak purely for aesthetics to the point that it’s detrimental—it would never appear in nature. So, domestic pigeons are a huge advantage for finding genes responsible for size differences,” said Michael Shapiro, the James E. Talmage Presidential Endowed Chair in Biology at the U and senior author of the paper. “One of Darwin’s big arguments was that natural selection and artificial selection are variations of the same process. Pigeon beak sizes were instrumental in figuring out how that works.”

The short- and medium-beaked parents produced an initial F1 brood of children with intermediate-length beaks. When the biologists mated the F1 birds to one another, the resulting F2 grandchildren had beaks ranging from big to little, and all sizes in between. To quantify the variation, Boer measured beak size and shape in the 145 F2 individuals using micro-CT scans generated at the University of Utah Preclinical Imaging Core Facility. 

“The cool thing about this method is that it allows us to look at size and shape of the entire skull, and it turns out that it’s not just beak length that differs—the braincase changes shape at the same time,” Boer said. “These analyses demonstrated that beak variation within the F2 population was due to actual differences in beak length and not variation in overall skull or body size.”

An animation of the skulls of birds showing the variety of beak lengths from short to long.

PHOTO CREDIT: Elena Boer

High-resolution scans of the grandchildren of the Racing Homer and German Owl cross. The animation shows the variety of beak lengths from shortest to longest.

Next, the researchers compared the pigeons’ genomes. First, using a technique called quantitative trait loci (QTL) mapping, they identified DNA sequence variants scattered throughout the genome, and then looked to see if those mutations appeared in the F2 grandkids’ chromosomes.

“The grandkids with small beaks had the same piece of chromosome as their grandparent with the small beak, which told us that piece of chromosome has something to do with small beaks,” said Shapiro. “And it was on the sex chromosome, which classical genetic experiments had suggested, so we got excited.”

The team then compared the entire genome sequences of many different pigeon breeds; 56 pigeons from 31 short-beaked breeds and 121 pigeons from 58 medium- or long-beaked breeds. The analysis showed that all individuals with small beaks had the same DNA sequence in an area of the genome that contains the ROR2 gene.

“The fact that we got the same strong signal from two independent approaches was really exciting and provided an additional level of evidence that the ROR2 locus is involved,” said Boer.

The authors speculate that the short-beak mutation causes the ROR2 protein to fold in a new way, but the team plans to do functional experiments to figure out how the mutation impacts craniofacial development.

Headshots of domestic pigeon breeds. The left four have short beaks, the right four have medium or long beaks.

PHOTO CREDIT: Thomas Hellmann, adapted from Boer et al. (2021) Current Biology

Representative images of individuals representing short beak (left four birds) and medium or long beak (right four birds) pigeon breeds (image credit: Thomas Hellmann). Short beak pigeons, from left to right: English Short Face Tumbler, African Owl, Oriental Frill, Budapest Tumbler. (B) Medium/long beak pigeons, from left to right: West of England, Cauchois, Scandaroon, Show King. The short-beak birds all had the same ROR2 mutation.

Pigeon enthusiasts

The lure of the domestic pigeon that mesmerized Darwin is still captivating the curious to this day. Many of the blood samples that the research team used for genome sequencing were donated from members of the Utah Pigeon Club and National Pigeon Association, groups of pigeon enthusiasts who continue to breed pigeons and participate in competitions to show off the striking variation among breeds.

“Every paper our lab has published in the last 10 years has relied on their samples in some way,” said Shapiro. “We couldn’t have done this without the pigeon breeding community."

 

by Lisa Potter - originally published in @theU

Be the Light

August 16, 2021

Be the light in your community

On July 14-16, 2021, students of the American Indian Services (AIS) Pre-Freshman Engineering Program (AIS PREP) came to the University of Utah to celebrate the completion of their 2021 AIS PREP, co-hosted by the College of Science. AIS PREP is a free program for Native American students to take advanced science, technology, engineering and mathematics (STEM) courses for six weeks for three consecutive summers. At the end of the program, the students earn scholarships to any higher education institution that they choose and continue to receive financial assistance. The 2021 AIS PREP group included 113 students from different Native American tribes: Navajo (Diné), Hopi, Oglala Sioux (Lakota), Shoshone/Bannock, Zuni, Crow, Paiute, and Cheyenne. AIS PREP is focused on making the curriculum culturally sensitive to the Native American students they serve. They bring a unique opportunity to keep the students close to their homes.

“We’re the only non-profit that has taken on such a big program like this. Some of these tribal communities are in rural areas—resources are scarce,” said Meredith Little Lam, project and program manager at AIS and AIS scholarship alumnus. “The whole point of AIS PREP is that we want to make sure we give our Native American students STEM resources that will allow them to succeed in high school.”

The students traveled to the U on July 14 to stay in campus dorms, meet PREP students from other AIS PREP sites, and hear presentations from U staff and College of Science faculty to celebrate the completion of the program. The week ended with a keynote address from the architect, inventor and entrepreneur Alice Min Soo Chun, during which she shared her inspiring story of changing the world by inventing a durable, portable, collapsible solar light.

“These students come from some of the poorest reservations in the United States. This really is a trip of a lifetime for them,” said Little Lam, “Some come from areas where there’s no running water, no electricity. We live in the United States and it’s just appalling that we can’t figure out ways to help these communities. And so, I think that this is a proactive way of getting these students involved in STEM to let them know, ‘You can change your tribal communities. You have it within yourself to be that leader.’”

“The College of Science is honored to have taken part in celebrating this incredible accomplishment of completing AIS PREP,” said Cassie Slattery, director of special projects of the college. “We would be lucky to have any one of these exceptional students pursue science here at the U.”

Anyone can be a scientist


On Thursday, the students learned about a diverse array of topics from speakers, including Donna Eldridge (Navajo/Diné), program manager of Tribal outreach for Health Equity, Diversity, & Inclusion, Amy Sibul of the School of Biological Sciences, Paul Ricketts of the South Physics Observatory, Julie Callahan (Little Shell Tribe of Chippewa) of ASPIRE, and Kyle Ethelbah (Western Apache), director of the U’s TRIO programs. One of the day’s highlights was an explosive presentation from chemist Ryan Stolley. He threw balls of fire, inhaled sulfur hexafluoride to give himself a funny low voice, and had the students freeze flowers with liquid nitrogen and smash them to bits. In between the chemistry magic, Stolley shared his personal story.

“I was a Native American student, of the Choctaw Nation of Oklahoma. When I was young, school was not my focus—I was just getting into trouble. But I got a lucky break and met some chemists who really changed my life,” said Stolley. “Native students are severely underrepresented in STEM disciplines. I love any opportunity to show them that it’s possible to pursue science. I mean, I’m covered in tattoos. Anybody can be a scientist. You just have to be curious.”

Stolley spoke to the students about attending Fort Lewis College, a university in Colorado that offers free tuition to Native American students. He received a doctoral degree in organic chemistry from the U and was a postdoctoral research assistant at the Pacific Northwest National Laboratory. He returned to Salt Lake City as a research assistant professor first in the Department of Chemistry and now in the College of Science, as well as part owner of a local chemical company.

“Part of what my company does is to make products that help clean contaminants out of water across the Colorado Plateau, especially on Tribal lands,” Stolley said, “I want to get these students thinking about how we can take our science and turn it around to help our Native communities.”

Creating positive memories on campus is part of how AIS PREP helps plant the seed to pursue higher education.

“We’re excited to be partnering with the U and having the ability to connect these students with faculty and current student volunteers who are Native American so that they can instill in their minds that it’s not an impossible dream,” said Little Lam. “Maybe they’ll be teachers and maybe they’ll be researchers, but wherever they may be, they can contribute to their Tribal communities. AIS doesn’t just stop with them after they graduate. We give them financial resources, but also say, ‘Hey, we’re here for you. Even after you finish this program.’”

A problem is an opportunity in disguise

This is the first year that AIS invited a keynote speaker to address the students during their program completion celebration. For Little Lam, Alice Min Soo Chun was the perfect choice. Chun, founder and CEO of Solight Designs, Inc. invented the Solar Puff, a portable, collapsible, self-inflating light powered by the sun. Little Lam met Chun while at Navajo Strong, through which Chun donated Solar Puff lights to families on the Navajo Nation without access to electricity.

“Every problem is an opportunity in disguise,” Chun, who is also a professor at Columbia University, told the AIS PREP graduates. “By doing research and observing, anybody can do this.”

Chun’s passion for solar energy began when her son was diagnosed with asthma, a condition that was aggravated by New York City’s poor air quality. Chun was inspired to find energy solutions that would reduce air pollution and its impacts on respiratory health. She realized that her son’s respiratory issues were global; without access to electricity, millions of people are forced to burn kerosene lanterns for lighting that produce noxious fumes. She saw a need for solar lights that were durable and collapsible, but the only ones available had to be inflated, leaving users vulnerable to bacterial infections. So, she invented a foldable design that drew from her childhood.

“I’m Korean. When I was a little girl, my mother taught me origami when I was young. Origami is an incredibly powerful tool,” she said. “Paper on its own can’t stand up. Fold it once, you have a corner, you have structure.”

Through the “Give a Light” program, Solight Designs has supplied Solar Puffs to Haiti, Puerto Rico, The Florida Keys, Ghana, Ecuador, Miami and more after natural disasters left people without power. During her keynote address, Chun passed out Solar Puff lights to everyone in attendance and turned off the lights. Everyone switched on their solar lanterns, eliciting ooo’s and aww’s. The lights illuminated the entire auditorium, demonstrating the invention’s power.

“I used to get beat up a lot for looking different. So, I became a fighter—not with my fists, but with the light of my heart and mind. You are all light warriors,” Chun said. “My hope is that you leave understanding how powerful you are and that you have the ability to change the world.”

by Lisa Potter - originally published in @theU

Birds of the Philippines

June 16, 2021

What factors put Philippine birds at risk of extinction?

The lush forests and more than 7,000 islands of the Philippines hold a rich diversity of life, with 258 bird species who live nowhere but the Philippine archipelago. A new study from University of Utah researchers suggests that, due to deforestation and habitat degradation, more bird species may be endangered than previously thought—including species that may not have been discovered yet. The study is published in Frontiers in Ecology and Evolution.

“Our study provides a roadmap for not only which species may warrant heightened conservation attention,” says Kyle Kittelberger, a doctoral student in the University of Utah School of Biological Sciences. “But which traits a species may have that can help inform if it may likely be more at risk of extinction.”

Birds of the Philippines

Phillippine Frogmouth

Located in Southeast Asia, the Philippines is considered a global biodiversity hotspot and one of the most biodiverse countries in the world, hosting nearly 600 bird species. A high proportion of the wildlife is endemic to the country, meaning that it is found nowhere else. The Philippines also hosts some of the highest richness of species recently identified as distinct from other closely related species, showing that scientists still have much to learn about the Philippine ecosystems.

Within the last decade the number of endemic species has risen from 172 to 258. This increase of 86 endemic species is more than all the endemic bird species in China (67) or India (75) and more than any country in South America or Africa.

Çağan Şekercioğlu, an associate professor in the School of Biological Sciences who has done ornithological field work in over 90 countries on all continents cannot forget his first visit to the islands.

“When I first visited the Philippines in 2008, I was awestruck by the diversity and especially the endemism of its avifauna but also greatly depressed by the rapid loss of habitat,” he says. Excursions into the field took hours due to extensive deforestation. “While looking for rare forest birds in the lowlands of Mindanao, we were literally trying to keep ahead of the loggers that were cutting down century-old rainforest trees within a couple hundred meters of us,” he adds. Despite that, in 13 days he saw 161 bird species he had never seen before—and still has 163 bird species to go.

Deforestation, habitat degradation and wildlife exploitation, however, threaten that biodiversity. Southeast Asia, the authors write, is forecast to lose over a third of its biodiversity over the next century. The Philippines in particular ranks eighth in the world for the number of globally threatened bird species.

“There is a pressing need to assess what traits make some species more at risk of extinction than others and to use this understanding to help inform conservation efforts,” Kittelberger says.

Traits of threatened birds

To understand the status of Philippine birds, the researchers first determined the bird traits most predictive of extinction risk by correlating bird species’ ecological and life-history traits, including body mass, diet, elevation range, and clutch size (the number of eggs laid in a nesting season) with their conservation status. A species endemic to the Philippines was significantly more likely to face an extinction risk, they found. Narrow elevation ranges, dependence on forests and high body mass also put birds at risk for extinction.

Philippine Serpent-eagle

Then the researchers turned around and evaluated Philippine birds’ expected conservation status using those traits, comparing predicted conservation status with the IUCN Red List conservation designations. They found that 84 species were predicted to be in worse shape than their Red List designation, with 14 species predicted to be globally threatened (i.e. vulnerable, endangered, or critically endangered) that aren’t currently classified as such.

“We predicted that the Philippine Serpent-eagle and Writhed Hornbill, two species that are not currently recognized as being globally threatened, are respectively endangered and critically endangered,” Kittelberger says. “We also predicted that the Palawan Peacock-pheasant, Calayan Rail and Philippine Eagle-owl, three species currently recognized internationally as being vulnerable, are likely endangered species. All these birds, therefore, warrant heightened conservation attention as they may be more threatened than currently believed.”

Lost before they’re found

Among the 84 species predicted to be more threatened, 12 were recently recognized as separate species, and three of those were predicted to be “vulnerable.”

Palawan Peacock-pheasant

“The Philippines have a very high level of endemism and it is currently estimated that there are twice as many bird species in the Philippines that have not yet been split and officially recognized, so there is a real risk of losing species before they are described,” Kittelberger says.

Kittelberger says that their research can be applied broadly to assess the conservation status of birds throughout the region.

“The most important thing that the Philippines can do to protect birds,” Kittelberger says, “is to address the high levels of deforestation, habitat degradation, and wildlife exploitation, and to increase land protection for wildlife and increase funding for conservation efforts.”

Find the full study at https://www.frontiersin.org/articles/10.3389/fevo.2021.664764/full 

Co-authors also include Montague H. C. Neate-Clegg, J. David Blount and Çağan Şekercioğlu of the U’s School of Biological Sciences, Mary Rose C. Posa of the California Botanic Garden and John McLaughlin of the University of California, Santa Barbara. The study was supported by the Christensen Fund.

 

By Paul Gabrielsen, first published in @theU

Todd B. Alder

June 9, 2021

Todd Alder

Todd B. Alder contracted COVID-19 early on in the pandemic and today still suffers from residual effects. But being just a “long hauler” as opposed to the alternative is what he calls being “lucky.” Says Alder, “Like many of us (I am guessing), this virus has disrupted my life with family and friends, my law practice, and my ability to travel. But on the plus side, I am really enjoying the Zoom calls where I am wearing a dress shirt and tie on top and something very questionable on the bottom.”

It's a scenario of late that many of us find ourselves experiencing (working on Zoom, not necessarily being pant-less), but the light touch that this biologist-turned-patent-attorney has towards not only the pandemic but work and life itself is evident. And so is his generosity. In April Alder was a featured alum in the School of Biological Sciences’ BioLuminaries speaker series (on Zoom, of course). As a registered patent attorney and partner at Thorpe North and Western (TNW) in Sandy, Alder illuminated the circuitous path one can take as a biology student toward fulfillment and job security… not to mention the love of chihuahuas.

More on that later.

The Road Less Traveled

Alder points to his PhD advisor, SBS’s Gary Rose, as the mentor who gave him “great direction over the years, particularly when I was stuck.” At the time Rose’s lab primarily focused on the neurophysiology of electrosensory systems in electric fish. Alder took an alternate path to study neuronal mechanisms underlying temporal processing in the auditory midbrain, a subject related to Rose’s PhD dissertation from a decade earlier. It was Rose’s broad way of thinking about science, research and the labyrinth that is life and career that still benefits Alder today.

“My dissertation was very broad over some fairly diverse scientific disciplines. This would not have been possible without Gary's early influence in teaching that young graduate student to not only see the world in a different way, but to approach problems and question them in a different way as well. I will always be grateful to Gary for helping me to see that there are no isolated questions or problems in science, but that everything has a much broader context and, as Robert Frost wrote, ‘that has made all the difference.’"

That difference played out while Alder was at the U in a remarkably refreshing and surprising way. “I was recording from a neuron in the midbrain of an anuran amphibian,” he explains, “and I thought of a test to further understand how these particular neurons worked.” Normally, neurons are not held in a stable state long enough for the kind of procedure Alder was planning. “But I stopped the program that was making the frog calls and quickly wrote a section of code so the program could do the test.”

It was that recompiling of the code—and a few crossed fingers—that led to a startling discovery. Once he turned the equipment back on the neuron in question was still there. From that test Alder showed that the generally accepted theory explaining how a neuron differentiates between high and low pulse rates was wrong. It turns out that neurons do not accomplish this differentiation though energy integration. Instead, Alder found that neurons were actually counting the number of pulses that occur within the range of pulse rates to which the neuron is tuned.

“That was one of the most exciting days of my life,” Alder says, “and I have always been amazed that those very complex questions were answered with [a] test performed on one neuron (it was repeated of course).” Alder graduated from SBS with his PhD in 2000.

Tripping the Patent Fantastic

Over the course of seven years, the mixture of biology, neurophysiology, molecular biology, etc. actually led to a degree in law which in turn opened up many opportunities for Alder to work with some very diverse and fascinating technologies. Enter his work in patent law following a clerkship at TNW beginning in 2002.

A Utah native, Alder hasn’t moved far geographically (he still lives in Utah and received all three of his degrees, including his law degree, from the U). But career-wise and developmentally it has been a galactic trip. For this reason he is quick to remind up-and-coming biologists at the U that education is not, and should never have been, about getting a job. “If you really contemplate the principles you are learning and integrate them into your life, it will change you and the way you think. To me, that is worth so much more than what type of job your degree can get you.”

About dogs … and a bear

Perhaps because of his wide-ranging academic, research and now patent career, Alder’s interests, like his dissertation, are broad and diverse. He loves to rock hound, watch horror movies, study theoretical physics and philosophy, collect old books, and “seriously mess with door-to-door sales people.” (Hopefully, while masked.) “Oh, and I once goosed a black bear in the wild, which made him terribly grumpy. But that is a story for a different day... .”

Which brings us to another enduring interest of Todd Alder’s and that is his love of chihuahuas. One advantage of working from home non-stop, quarantined from everyone else, is that your pets become a fixture, a pain and, if cuddly enough, a kind of accessory for that dress shirt above that questionable garment immediately below.

You can watch a recording of the BioLuminaries lecture by Todd Alder and co-presenter Heng Xie (PhD’04) on SBS’s YouTube Channel here.

 

By David Pace

Are you a Science Alumni? Connect with us today!

Nikhil Bhayani

June 2, 2021

Nikhil Bhayani

“Every 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.”

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 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.

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?

In May 2021, after months of battling the COVID-19 pandemic, Bhayani was selected as Top Physician of the Year by the International Association of Top Professionals (IAOTP) for his outstanding leadership and commitment to the healthcare industry.

 

by David Pace

Are you a Science Alumni? Connect with us today!

Diana Montgomery

May 17, 2021

Diana Montgomery

“Perhaps my favorite experience at the University of Utah is when I started working in a biology lab for the first time and realizing I fit in and enjoyed the work and the people there,” says Diana Montgomery, BS’87 in Biology. “It certainly helped to solidify my career choice.”

While at the U, Diana worked in Allen Edmundson’s crystallography lab on Wakara Way. In addition to learning practical skills, Diana was included in the research publication, titled “A mild method for the preparation of disulfide-linked hybrids of immunoglobulin light chains” in 1987. The journal was Molecular Immunology. (Read the paper here.)

Shortly thereafter, Diana graduated from the U and moved to Baltimore, Maryland, to begin graduate school at Johns Hopkins University. Her advisor was Ernesto Freire, a well-known expert in biological thermodynamics. Diana completed a doctorate degree in Biology/Biophysics from Johns Hopkins in 1994 and conducted postdoctoral work at Northwestern University in the lab of Richard Morimoto and at the University of Massachusetts in the lab of Lila Gierasch.

Diana is now a Principal Scientist in the department of Pharmacokinetics, Pharmacodynamics, and Drug Metabolism at Merck, in Pennsylvania. She focuses on developing therapeutic proteins as new drugs, two of which are now FDA-approved products, tildrakizumab and bezlotoxumab.

Tildrakizumab (brand name Ilumya) is approved for the treatment of adult patients with moderate-to-severe plaque psoriasis in the United States and Europe. Tildrakizumab is a monoclonal antibody that selectively binds to the p19 subunit of IL-23 and inhibits its interaction with the IL-23 receptor. IL-23 is a naturally occurring cytokine that is involved in inflammatory and immune responses.

Bezlotoxumab (brand name Zinplava) is a monoclonal antibody designed for the prevention of recurrence of Clostridium difficile infections, which can be life-threatening. Bezlotoxumab works by binding to a specific toxin produced by the Clostridium difficile bacteria and neutralizes the toxin’s effects.

Merck is a multinational company and one of the largest pharmaceutical companies in the world, employing some 74,000 people. In 2020 alone, Merck invested $13.6 billion in drug research and development.

Diana has 24 research publications with nearly 1,400 citations to her credit. Her recent work has focused on describing the effects of immunogenicity on therapeutic proteins. One liability of protein-based therapeutics is their tendency to elicit an unwanted immune response against themselves. One of the manifestations of such an immune response is the activation of B cells, which produce anti-drug antibodies that bind to therapeutic protein drugs and can reduce a drug’s therapeutic effects or be associated with safety issues. Therefore, an important part of therapeutic protein drug development is to characterize the tendency of a drug to elicit anti-drug antibodies and any potential effects on clinical pharmacokinetics, efficacy, and safety.

Reflecting back to her childhood, Diana recalls several key moments that motivated her to study science.

“My father was a mining engineer. He did some geology education while we were hiking, like what type of rocks were on the trail and how to recognize fool’s gold,” says Diana. “When we went camping, he’d explain the Pythagorean theorem with the triangles of the tent. It made math and science familiar to me.”

In high school, Diana developed an interest in molecular biology and biochemistry. She then chose to attend the University of Utah because it was a reputable research university which was close to home. (Diana grew up in Tooele, Utah, about 30 miles from the U.) Diana received an Honors at Entrance scholarship to begin her studies at the U, based on her achievements in high school.

“At the U, several classes in the Department of Biology (now School of Biological Sciences) were designed to encourage students to make and test hypotheses. This form of experimental-based learning was both effective and highly enjoyable,” said Diana.

“Professors like Gordon Lark and John Roth were fantastic. They made their lectures interesting and taught us how to think like a scientist and how to do science in the laboratory. I was lucky to be a part of that, but at the time didn’t realize it was so rare. I believe it is important for students to get a feel for doing science in introductory classes like these, rather than being exposed to it for the first time in graduate school. By the end of my undergraduate years, I was hooked on the scientific paradigm of hypothesis, design, experiment, and interpret. I have the U to thank for that.”

Diana and her husband, Hwa-ping (Ed) Feng have two children, Ellen and Nathan. Diana particularly enjoys gardening and reading. She also volunteers at a local food pantry and at animal-adoption clinics.

The College of Science and its four academic departments – Biological Sciences, Chemistry, Mathematics, Physics & Astronomy – now graduate more than 650 students each year. We are proud of our many alumni who live and work all around the world. Please share your stories with us!

Are you a Science Alumni? Connect with us today!