Faculty

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

Physics Innovation

August 26, 2021

Yue Zhao receives Physics Innovation Award

Yue Zhao, assistant professor in the Department of Physics & Astronomy, has received a Gordon and Betty Moore Foundation Fundamental Physics Innovation Award, in association with the American Physical Society. This award supports extended visits between researchers to learn, develop, and share techniques or scientific approaches.

The goal of the award is to stimulate ideas on innovative ways in which emerging technologies can be used to address pressing problems in the physics of fundamental particles and interactions. The rapid developments in quantum-sensing technologies keep pushing the limits of the precision frontier, and some of them provide ideal platforms to search for dark matter candidates.

“The award will allow me to collaborate with experimentalists,” said Zhao, “and investigate the possibilities of applying these fascinating technologies to search for dark matter candidates, especially in the ultralight mass regime, such as axions and dark photons. This award provides travel support for me to visit these experimental labs in order to exchange ideas and gain a more comprehensive understanding about the experimental setup.” He plans to visit a lab at Nanjing University in China.

Particle physics is a discipline within the field that studies the nature of the smallest detectable particles that make up matter and radiation. The Standard Model is the theory that explains what these particles are and how they interact with each other. It was developed by scientists during the 1970s. While the Standard Model explains a lot about the laws of physics, it isn’t able to explain all phenomena, including dark matter.

Zhao studied advanced physics at Peking University and moved to Rutgers University to pursue a Ph.D. He joined the University of Utah in July 2018.

 

By Michele Swaner, first published @ physics.utah.edu

William D. Ohlsen

August 26, 2021

In Memoriam: Emeritus Professor William D. Ohlsen

Emeritus Professor William David Ohlsen died peacefully at his home in Salt Lake City on August 9, 2021, following a diagnosis of pancreatic cancer. He joined the University of Utah faculty in 1961, where he spent 36 years teaching physics and mentoring graduate students. We will miss him.

His research at the U involved the study of defects and dopants in crystalline and amorphous semiconducting solids. Amorphous silicon, crystalline III-V semiconductors, and chalcogenides were the subjects of other investigations.

Bill was born June 8, 1932 in Evanston, Illinois, to Wilma and Edward Ohlsen and grew up in Ames, Iowa.

Bill graduated from Iowa State University in 1954 with a B.S. in Physics and received a Ph.D. in Physics from Cornell University in 1961.

Bill was introduced to the love of his life, Ruth Bradford, in 1955 by Ruth's sister Nancy. Following months of exchanging letters and phone calls, they met for the first time in person on January 1, 1956. They spent a total of four days in each other's presence before marrying on June 16, 1956 in a double wedding ceremony with Nancy and John Clark, Bill's boyhood neighbor and lifelong friend.

Bill was an enthusiastic traveler, visiting twenty-two countries over the course of his life, including two sabbatical trips to Germany. An avid lover of the outdoors, Bill enjoyed skiing, hiking, biking, fishing, hunting, camping, backpacking, and running. At home, he enjoyed classical music, a good book, a good basketball game, and a good beer. He also loved puzzles and games, including chess, sudoku, and the Wall Street Journal Saturday crossword.

He is survived by his wife, Ruth Bradford Ohlsen; three daughters, Diane Ohlsen Guest, Patricia Ohlsen Horton, and Lynn Ohlsen Craig; nine grandchildren; seven great-grandchildren; and his sister, Anita Wald Tuttle.

Bill cared deeply about the environment and lived his principles. For example, he walked or rode his bike to work every day of his life, composted, recycled, participated in highway trash collections, and chose to avoid air travel to the extent possible. Bill will be remembered by all who knew him for his humility, generosity, wisdom, and kindness.

In lieu of flowers, donations can be made to Save Our Canyons. Visit http://saveourcanyons.org for more information.

 

Adapted from The Salt Lake Tribune by Michele Swaner, first published @ physics.utah.edu

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

Chemistry in Pictures

July 13, 2021

Chemistry in Pictures

Throughout spring semester 2021, students in chemistry professor Tom Richmond’s Integrated Chemistry for Health Sciences course have been taking pictures of chemistry in the world around them. From using shaving cream as sunburn relief to the thermodynamics of digestion, the students have put into pictures the principles they’ve learned in class. Now one of those pictures, documenting a home chemistry experiment by pre-nursing student Ashlee Taft Nelson, is published in the magazine Chemical and Engineering News.

“The Chemistry in Pictures project helped me see that chemistry, as a whole, is so much broader than just a list of elements,” Nelson says. “It is found in every part of life that helps defines processes of growth and change.”

The photo shows two eggs that have been soaked in different solutions to illustrate how fluid moves through a membrane. An egg sans shell soaked in water will swell, since the concentration of water inside the egg is less than outside and the water moves through the membrane to balance things out. An egg soaked in corn syrup will shrink, though, since there’s more water inside the egg than in the corn syrup.

Developed during the COVID-19 pandemic, the Chemistry in Pictures assignment helps students drawing insightful connections between the concepts they learned in class and their everyday lives and fulfill the learning objectives of a chemistry education. Publication of Nelson’s photo is, Richmond hopes, the first of many opportunities to share his students’ insights with the world.

See other examples of: blood testing, protein denaturation and other student projects.

Developing the assignment

For years, Richmond has been asking his introductory chemistry students to create and solve chemistry problems that mattered to them, in part to hone their science communication skills.

“Altering this basic format by adding a picture that they have taken with their cellphone has proven to be an effective way for students to personalize their learning and works well for a generation of students who live on social media,” he says. “It also prompts them to more directly see the relevance of chemistry in their lives whether in the kitchen, at work or at play.”

During the COVID-19 pandemic, Chemistry in Pictures proved useful in checking in on students’ learning while access to the laboratories was limited. Richmond and veteran TA Lizabeth Cowgill realized that the assignment could do even more.

“We realized this assignment could serve as a new curriculum tool that would not only serve as an artifact regarding student understanding but could also contribute to changing a student’s attitude toward the subject of chemistry,” says Cowgill, now a graduate student in the College of Pharmacy.

Mark St. André, Associate Dean in the U’s Office of Learning Outcomes Assessment says he works with a lot of departments to tailor assignments to meet university learning objectives. Chemistry in Pictures, he says, is unique.

“It makes sense what he’s trying to do,” St. André says. “He’s trying to get them to think with a different side of their brain by representing the problem using pictures. I’m not anywhere close to a brain expert, but common sense would tell us that activating the creativity you need to build a picture is likely to help you think about the issue differently and probably increase your understanding of it.”

Bringing chemistry into focus

The Integrated Chemistry for Health Sciences course is for pre-nursing students and others heading into healthcare fields. Understanding the chemistry behind why a patient is ill is vital, says Mardie Clayton, professor of nursing.

“Basic principles of chemistry transcend human physiology and pathophysiology, enabling students to understand how the body works normally and abnormally,” she says, with the photo of fluid moving in and out of the eggs as a good example. “Understanding the movement of fluids is vital to understanding cellular function and to the management of associated diseases such as heart disease.”

Richmond says that the Chemistry in Pictures experience also teaches students to observe and interpret chemical phenomena. “The ability to communicate scientific concepts – whether to patients or peers – is certainly needed to address many critical issues in our society at large,” he says.

Watching the flashbulb light up

Cowgill gathered feedback on Chemistry in Pictures as the class progressed. The students thoroughly enjoyed the creative freedom of the assignment, she says.

One student said: “If I could change one thing about these assignments it would be to have them more frequently. Chemistry in Pictures assignments helped me apply chemistry to everyday things in my life. It forced me to have to think in a different way and ask how and why questions. It was one of the most beneficial assignments for me personally because it felt interactive even despite being online.”

Students completed five Chemistry in Pictures assignments over the course of the semester, totaling nearly 700 among the entire class. Cowgill says that while the first two assignments showed solid understanding of content, the creativity and real-life application began to shine through starting at the third assignment.

“It was like a lightbulb had gone on in all 135 students!” she says. “I started to see experimental design and treatment, adventure and risk taking, research incorporation, friends and family involvement and engagement, but most importantly, spark.” The students, she says, were starting to go above and beyond the expectations of the assignment. And the spark was never lost.

“I saw their minds challenging their own comprehension and understanding and read the excitement when, say, their proposed experiment went as planned,” she says. “These students blew me away—absolute brilliance.”

Lasting memories of a first exposure

In response to an open call by Chemical and Engineering News for chemistry-related photos, Richmond sent in Nelson’s “egg-sample” image. It was published in the May 13 edition of the magazine, which is read by more than 150,000 chemistry professionals.

“Before taking Integrated Chemistry for Health Sciences, I saw chemistry as a math-based science using the list of elements found on the periodic table as variables,” Nelson says. “This project taught me to see that applications of chemistry are everywhere and to be a better observer of my environment.”

“I have been impressed with creativity and level of detail that many students exhibited in this project and suspect that their creations will be one of the lasting memories of their first exposure to chemistry,” Richmond says. “Perhaps it is not surprising that this ‘cell phone’ generation of students became adept at photographically documenting chemistry in their lives. We now often see pictures in lab reports in more advanced courses and even graduate research presentations in the department.”

Cowgill says that the assignment allows students to act as their own instructors. “It not only provides them complete creative freedom but keeps their learning unrestricted, boundless, free,” she says. “This assignment protects the most sacred component of learning: self. It is through assignments like Chemistry in Pictures where you can see raw and unedited active learning, application and educational growth tangibly.”

 

By Paul Gabrielsen, first 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

NSF CAREER Award

June 7, 2021

NSF CAREER Award

Priyam Patel receives National Science Foundation CAREER Award.

Priyam Patel, assistant professor of mathematics at the U, has received a National Science Foundation CAREER Award. The National Science Foundation's CAREER Award is the most prestigious NSF award for faculty members early in their careers as researchers and educators. It recognizes junior faculty members who successfully integrate education and research within their organizations. The award comes with a federal grant for research and education activities for five consecutive years.

Priyam Patel

“I'm thrilled to receive the award, and I'm very excited to have the ability to pursue the research and educational projects the grant will afford,” said Patel. “The award also recognizes the support the Math Department and the University of Utah provide to faculty.”

Patel works in geometry and topology. The two areas differ in that geometry focuses on rigid objects where there is a notion of distance, while topological objects are much more fluid. In her research, Patel’s goals are to study and understand curves on surfaces, symmetries of surfaces, and objects called hyperbolic manifolds and their finite covering spaces. Topology and geometry are used in a variety of fields, including data analysis, neuroscience, and facial recognition technology. Patel’s research doesn’t focus on these applications directly since she works in pure mathematics.

She is currently working on problems concerning groups of symmetries of certain surfaces. Specifically, she has been studying the mapping class groups of infinite-type surfaces, which is a new and quickly growing field of topology. “It’s quite exciting to be at the forefront of it. I would like to tackle some of the biggest open problems in this area in the next few years, such as producing a Nielsen-Thurston type classification for infinite-type surfaces,” she said. She is also interested in the work of Ian Agol, professor of mathematics at Berkeley, who won a Breakthrough Prize in 2012 for solving an open problem in low-dimensional topology. Patel would like to build on Agol’s work in proving a quantitative version of his results. Other areas she’d like to explore are the combinatorics of 3-manifolds and the theory of translation surfaces.

Patel joined the Math Department in 2019.

by Michele Swaner, first published @ math.utah.edu

Mysteries of the Universe

June 4, 2021

Mysteries of the universe

Utah researchers join project to unlock enigma of 'dark energy'

Researchers from the University of Utah are joining forces with others for a universal five-year project that seeks to map the universe and gain insights into the mysteries of dark energy.

In a culture where science fiction reigns as one of the most popular genres for movies and television, the terms "dark matter" and "dark energy" likely convey a sense of foreboding to many.

But they got their label simply because scientists know so little about them, said Angela Berti, a U. postdoctoral researcher working on the project.

"You hear 'dark matter, dark energy' kind of thrown out there, and to the extent that you've kind of read popular science news, you might be aware that the astronomy community and the physics community knows that there's some additional mass out there in the universe," she said.

In the last 20 years, researchers discovered that the universe continues expanding at an increasingly rapid rate, which is considered "strange and unusual," according to Berti.

"We don't really have a great explanation for it. So the placeholder, we call it dark energy, something that's causing the universe to expand faster and faster," she said.

The Dark Energy Spectroscopic Instrument, also known as DESI, in Tucson, Arizona, will collect data on the light from more than 30 million galaxies and other distant objects, which researchers will use to make a 3D map of the universe. DESI captures spectra, which are elements of light that correspond to the colors of the rainbow. Spectras split light into wavelengths, or redshifts, which researchers measure to find the distance to a galaxy or far-off object in space.

The project launched officially in mid-May after years of preparation. About 50 universities are participating in the U.S. and around the world.

With millions of galaxies to map, the researchers will use an algorithm to find the best estimate for distances between objects. Berti's role includes checking data on sample subsets of individual galaxies and spectra to make sure the algorithm data aligns. She will help find objects for which the algorithm is less effective in estimating distances, so researchers can improve the system.

"It's kind of cool because the reason it's really useful is when you have millions and millions of galaxies, you can't do that process by hand for every single one," Berti said.

She's also testing alternative modeling techniques for measuring redshifts.

DESI is the largest project so far to measure "very precisely the expansion rate of the universe, basically to just measure more precisely the rate at which it's expanding, and the rate at which the expansion might be changing," Berti said.

It will measure galaxies in one-third of the entire sky, she said.

The researchers don't know what they'll discover. But to make progress in understanding why the universe is expanding faster and faster, they need to measure that expansion as precisely as possible.

She said the project seeks to indirectly unravel some of the mysteries surrounding dark energy, which like dark matter, has eluded scientists for many years.

"The frustration and the foreboding comes from the fact that we haven't yet figured out what it is. It doesn't mean that we won't figure it out, and it doesn't mean that our current science is wrong, it just means that our current understanding is incomplete. And that's frustrating. ... They're two big, pressing mysteries that are yet uncracked," Berti said.

The project will "help us understand the properties of this unexplained phenomena better, and the more we understand the details about what's going on, the better chance we have of coming up with a theory that we can test," she said.

 

By Ashley Imlay, first published in KSL.com

Let’s Get Kraken

May 10, 2021

the sigman Group launches open-access tool for chemists

An open-access tool for chemists that promises to save time and money in the discovery of chemical reactions has been launched this week by the research group of Distinguished Professor Matt Sigman of the University of Utah Department of Chemistry and the Matter group of professor Alán Aspuru-Guzik at the University of Toronto.

Kraken—created in a collaboration between the Matter lab, the Sigman group, IBM Research and AstraZeneca—is a library of virtual, machine-learning calculated organic compounds, roughly 300 thousand of them, with 190 descriptors each.

“This collaborative project changes how researchers will approach reaction optimization both in industry and academics,” Sigman says. “It will provide unforeseen opportunities to investigate new reactions while also the ability to know why the reactions work.”

“The world has no time for science as usual,” says Aspuru-Guzik, “Neither for science done in a silo. This is a collaborative effort to accelerate catalysis science that involves a very exciting team from academia and industry.”

“It takes a long time, a lot of money and a whole lot of human resources to discover, develop and understand new catalysts and chemical reactions,” says co-lead author and Banting Fellow Dr. Gabriel dos Passos Gomes. “These are some of the tools that allow molecular scientists to precisely develop materials and drugs, from the plastics in your smartphone to the probes that allowed for humanity to achieve the COVID-19 vaccines at an unforeseen pace. This work shows how machine learning can change the field.”

When developing a transition-metal catalyzed chemical reaction, a chemist must find a suitable combination of metal and ligand. Despite the innovations in computer-optimized ligand design led by the Sigman group, ligands would typically be identified by trial and error in the lab. With kraken, chemists will eventually have a vast data-rich collection at their fingertips, reducing the number of trials necessary to achieve optimal results.

The Kraken library features organophosphorus ligands, what Tobias Gensch—one of the co-lead authors of this work—recalls as “some of the most prevalent ligands in homogeneous catalysis.”

“We worked extremely hard to make this not only open and available to the community, but as convenient and easy to use as we possibly could,” says Gomes, who worked with graduate student Theophile Gaudin in the development of the web application. “With that in mind, we created a web app where users can search for ligands and their properties in a straightforward manner.”

The team also notes that while 330,000 compounds will be available at launch, a bigger-scale library of over 190 million ligands will be made available in the future. In comparison, similar libraries have been limited to compounds in the hundreds with far fewer properties.

“This is very exciting as it shows the potential of AI for scientific research,” says Aspuru-Guzik. “In this context, the University of Toronto has launched a global initiative called the Acceleration Consortium which hopes to bring academia, government, and industry together to tackle AI-driven materials discovery. It is exciting to have Professor Matthew Sigman on board with the consortium and seeing results of this collaborative work come to fruition.”

Kraken can be freely accessed here. The preprint describing how the dataset was elaborated and how the tool can be used for reaction optimization can be accessed at ChemRxiv.

Story originally published in @theU