Faculty

Of Mice and Monarchs

January 20, 2022

Of Mice and Monarchs

Sara Weinstein, Postdoctoral Researcher

Monarch butterflies possess a potent chemical armor. As caterpillars, they eat plants filled with toxic cardenolides that build up in their bodies and make them unpalatable to most—but not all—predators. In central Mexico, where the largest winter monarch aggregations occur, scientists observed that rodents attack monarchs that fall to the ground. In particular, the black-eared mouse (Peromyscus melanotis) specializes in these bitter-tasting insects, eating as many as 40 per night.

In a new study, University of Utah biologists found that mice at California monarch overwintering sites can also consume monarch butterflies. Working at one of the largest monarch aggregations outside of Mexico, Pismo State Beach Monarch Butterfly Grove, the researchers discovered that the western harvest mouse (Reithrodontomys megalotis) also ate the grounded monarchs. However, with the precipitous decline in western monarch populations, this butterfly buffet may be in jeopardy.

A harvest mouse munching on a monarch.

The authors do not think that rodents are contributing to the western monarch decline, nor that the monarchs are the only thing that mice can eat. Rather, documenting this new feeding behavior is a reminder of how little we know about the interactions that may be lost as insect populations decline.

“We are in an insect apocalypse right now. There are estimates that 40% of studied invertebrate species are threatened and that over 70% of flying insect biomass is already gone. This is devastating on its own and is also going to have enormous impacts on the other organisms that feed on insects,” said Sara Weinstein, the postdoctoral researcher who led the study.

“Western monarchs and other western butterflies need conservation attention and part of that awareness-raising is illuminating the many ways these animals are interconnected to other insects, birds, mammals, as well as our human communities. This study helps us appreciate more deeply how fewer butterflies means less food for other native animals” said Emma Pelton, senior conservation biologist at the Xerces Society.

Weinstein with a lab-reared monarch.

The study published in the journal Ecology on Dec. 12, 2021.

To study mouse-monarch interactions, the researchers first trapped rodents in the grove in February 2020. The rodents were released, but their feces were kept to screen for monarch DNA—which they found in one sample. This first survey occurred in late winter as monarchs were leaving the aggregation and few remained for mice to munch. Weinstein and colleagues intended to return the following fall during peak monarch season. However, after years of decline, the western monarch population crashed.

“At a site where 100,000 butterflies used to roost, in 2020 there where were fewer than 200 monarchs. So, we had to change tactics,” Weinstein said. “We tested whether rodents would feed on the butterflies using captive-reared monarchs.”

Weinstein set up lab-reared monarch carcasses under camera traps and captured footage of wild harvest mice eating butterflies. She also caught a half dozen mice and offered them monarchs. The mice ate monarchs, typically favoring the abdomen or thorax, high-calorie parts with fewer toxins.

“Many rodent species are likely to have some resistance to cardenolides in monarchs, due to genetic changes at the site where these toxins bind,” said Weinstein. “The Pismo Grove is one of hundreds of western monarch aggregation sites, and it seems likely that, at least in the past, rodents throughout the western monarch range may have supplemented their winter diets with monarchs. If you can handle the cardenolides in a monarch, their bodies are full of fat and offer a pretty good meal.”

Animation of mouse eating a butterfly.

Mouse eating an entire monarch butterfly.

This meal will be a lot harder to find, as over 90% of western monarchs have disappeared in the last 40 years. The missing beauties will surely impact the ecosystem that depends on them for food.

Denise Dearing, Distinguished Professor at the U, was senior author of the study. Photos and animations by Sara Weinstein.

Find the study, “Harvest mice (Reithrodontomys megalotis) consume monarch butterflies (Danaus plexippus), in the journal Ecology: https://doi.org/10.1002/ecy.3607

 

by Lisa Potter, first published in @theU

 

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James Webb Space Telescope

January 4, 2022

James Webb Space Telescope

In December 2020 the James Webb Space Telescope (JWST) finally launched. The $10 billion observatory is a twenty-year joint effort of NASA, the European Space Agency, and the Canadian Space Agency, and the most powerful telescope ever developed. Its mission—peer 13.5 billion lightyears back in time to the earliest stages of the universe.

Anil Seth

JWST’s launch date was December 25 from Europe’s Spaceport in Kourou, French Guiana. Longtime fans of the telescope are celebrating it as a Christmas miracle. It was the first planned to launch in 2007, but decades of delays and false hope drove the project from its initial budget of $500 million up to its current $10 billion cost.

You can watch recorded launch video and future NASA livestreams at  https://www.nasa.gov/nasalive.

The stakes are high for Anil Seth, associate professor in the Department of Physics & Astronomy. Out of more than 1,000 proposals for observation time on the telescope, Seth’s is one of 266 that were approved. He spoke with AtTheU to talk about this cosmic milestone.

What is the James Webb Space Telescope?

It is the largest and most powerful telescope that we’ve ever sent into space—the primary mirror is about the size of a typical house. It’s really big compared to the Hubble Space Telescope, which has a primary mirror the size of a bedroom. Hubble uses the ultraviolet and visible light to create jaw-dropping images of deep space that fundamentally changed our understanding of the cosmos. JWST will be much, much, much farther away than Hubble, located almost one million miles from Earth. From there, it can detect the faintest traces of infrared light, the wavelength of light emitted by everything that produces heat.

NASA assembly, July 2017

The telescope’s primary power is to detect faint galaxies far, far away. It’ll be able to pick up the infrared light spectrum of planets, newly forming stars, black holes, and other faint objects in ways that we’ve never been able to before. Almost every astronomer is probably going to want to use JWST for something. We saw so much using the Hubble Space Telescope. With JWST, we’ll be able to see more than we can imagine. It’s very exciting.

The launch date has been pushed back several times including once this week. Is the telescope launch tricker then usual?

The size makes it really hard to launch. The telescope has three big segments—a sunshield the size of a tennis court, the house-sized primary mirror, and the secondary mirror, Right now, it’s all packaged up like a Christmas present to fit inside the rocket. After launch, the segments will begin to unfold. It’s a complicated process involving hundreds of steps that have to work perfectly. This has never been done before—one error and the whole project could fail. That’s why people are so stressed out!

Where will JWST orbit in space?

It’s going to orbit the sun almost one million miles away from Earth. It will live at what is called a Lagrange point, a location where gravity from the earth and sun are equal. And will just sit there, orbiting with the Earth around the sun. This ensures that the telescope will always point away from the sun.

Full-scale model, September 2005

Anything warm emits infrared light—stars, humans, every other thing on Earth. To make an infrared-detecting telescope, the equipment needs to be extremely cold, so its heat doesn’t interfere with infrared readings from space. That’s what the sun shield is for. The massive mylar sail will create a shadow that prevents the telescope from absorbing heat. The sunshade will begin to unfurl a week after launch, starting with 107 release mechanisms that have to fire simultaneously. The sun shield will then always be between the telescope and sun, keeping the telescope really cold. If this doesn’t happen right…it’ll be bad.

JWST’s location also provides a wide-open view for observations. The Hubble space telescope orbits the Earth just over 300 miles up, which means the planet sometimes blocks the telescope’s vision as it orbits the earth every 90 minutes. At JWST’s Lagrange position, it’s much easier to keep a single orientation in the sky for a longer time and to make observations constantly. So we’ll end up getting more data each year from JWST than from Hubble.

You will be one of the first astronomers to get observation time on the JWST. Can you tell us about your research?

I study black holes. Every black hole has stuff falling onto it that emits light. It turns out that a lot of that light gets emitted at infrared wavelengths. This telescope is much, much, more sensitive to those wavelengths than any other previous telescope. The problem is that we’ve never seen what a faint black hole looks like at these wavelengths.

The Andromeda Galaxy, approximately 2.5 million light-years from Earth.

I’m leading a project that will look at places where we know black holes exist, because we’ve measured them from the motions of the stars around them, but that are very faint. These are so much fainter than something like a quasar, which is where the black hole is devouring as much material as it can. The black holes I’m interested in are just sipping their material, and they’re much more typical of the average black hole in the universe. We’re basically looking unique signatures in this wavelength spectrum that will tip us off to a black hole is present. One of the objects we’ll focus on is the first one ever photographed.

- by Lisa Potter, first published at @theU

 

NASA J.W.S.T. VIDEO

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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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Theory Meets Intuition

December 20, 2021

Theory Meets Intuition

Will Feldman

Will Feldman, Assistant Professor of Mathematics, joined the Department of Mathematics in 2020. He studies mathematical models of physics and thinks about the things most of us take for granted, for example, fluid flow, water droplets, and flame propagation. These models are often developed by engineers or physicists using basic assumptions, but the resulting equations can be difficult or impossible to solve exactly.

“I’m interested in proving mathematically rigorous results for these models,” said Feldman. In his research, the results sometimes show the limitations of the modeling assumptions used to derive the equations. Other times, they explain the behavior of all the solutions of the equation without relying on special formulae. “And sometimes, the results are used to justify numerical computations, which are meant to approximate solutions of these equations,” he said.

One particular type of problem Feldman has studied is called “homogenization”—the study of the physical properties of complicated heterogeneous materials. The idea is to “average” or “homogenize” the complicated small-scale inhomogeneities in the material to derive simpler effective equations to describe properties at larger scales. For example, the ideas of homogenization theory can be used to study the shapes of water droplets on surfaces that have microscopic roughness, such as a plant leaf, a piece of glass, or a table top.

Water droplet on fabric.

“I like to work out these kinds of questions because I get to use both physical intuition and theoretical mathematical tools,” he said.
Feldman wasn’t always interested in mathematics. As an undergraduate, he thought he wanted to study physics or history. He started taking math classes because math was useful in studying advanced physics. “I had a lot of amazing math professors, and I started to like math a lot,” he said. “Eventually, I realized I could maybe study math and also bring in my interest in applications (especially physics). Basically, that’s how I ended up studying partial differential equations.”

Like many undergrads who study math, Feldman was worried he would need a special talent to succeed at math, but he had supportive and encouraging mentors, so he never got too discouraged. “I hope the experience of having good mentors has taught me to be a good mentor, too, and show my students I believe in them and the many interesting possibilities available in a career in or related to mathematics,” he said.

Before joining the U, Feldman received his Ph.D. from UCLA in 2015 and was an L.E. Dickson Instructor at the University of Chicago from 2015-2019. He was also a member at the Institute for Advanced Study (IAS) from 2019-2020. The IAS is one of the world’s leading centers for curiosity-driven basic research, based in Princeton, NJ.

In 2019, Feldman was awarded the John E. and Marva M. Warnock Presidential Endowed Chair for Mathematics by the University of Utah. He will hold the chair for five years and anticipates the funding will provide new and interesting directions for his research. He hopes to have a positive impact by training, mentoring, and supporting a next generation of mathematicians. “It was a great honor to be offered the Warnock Chair,” said Feldman. “I am obviously very proud to receive the award and grateful to the Warnock family and the university.”

As he moves forward in his research, he’s been thinking about problems involving interfaces in heterogeneous media. He’s also been wondering about transport equations and models of grain boundary motion in polycrystalline materials. He’s looking forward to discussions and collaborations with his colleagues in the Math Department, especially in the applied and probability groups.
Feldman and his wife are in the midst of raising two young children. He enjoys the great hiking in Utah and is looking forward to relearning how to ski and maybe starting new outdoor activities, such as climbing and biking. He enjoys cooking and has become obsessed (during the pandemic) with making a great cup of coffee.

- by Michele Swaner, first published at math.utah.edu

Warnock Presidential Endowed Chair

“A Presidential Endowed Chair at the University of Utah is one of the highest honors that we can bestow on a faculty member.” —Dean Peter Trapa

Presidential Endowed Chairs are crucial for the recruitment and retainment of the most accomplished faculty members. Through these philanthropic gifts, the faculty are able to further support their cutting-edge research and explore new areas in their field.

John E. Warnock, BS’61, MS’64, PhD’69, and Marva M. Warnock created a Presidential Endowed Chair for Faculty Development in Mathematics in 2001 through a gift of Adobe Systems stock.

For more information on a establishing a Presidential Endowed Chair, or other named gift opportunities, please contact the development team at 801-581-6958, or visit science.utah.edu/giving.

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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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The Frontier of Physics

December 20, 2021

The Frontier of Physics

The Standard Model of particle physics is the theory that explains how the most elementary particles interact with each other and combine to form composite objects, like protons and neutrons. Developed over the course of many decades, what we know as the Standard Model today was formulated nearly half a century ago and remains a focus of study for particle physicists. But by itself, the Standard Model fails to provide an explanation for many important phenomena, such as the existence of the dark matter in the universe.

The Standard Model

Today, physicists and researchers are on the frontier in the search for physics beyond the Standard Model, using connections between theoretical particle physics, cosmology, and astrophysics to help us understand the universe.

Pearl Sandick, Associate Professor of Physics and Astronomy and Associate Dean of Faculty Affairs for the College of Science, is on that frontier. As a theoretical particle physicist, she studies some of the largest and smallest things in the universe, including dark matter, which is the mysterious stuff that gravitationally binds galaxies and clusters of galaxies together.

While regular matter makes up about one-sixth of the total matter in the universe, dark matter makes up five-sixths. There are compelling arguments that dark matter might actually be a new type of elementary particle. Electrons are an example of an elementary particle—they are the most fundamental building blocks of their type and are not composed of other particles. Other examples of elementary particles include quarks, neutrinos, and photons.

In August 2019, Sandick and her colleagues hosted a workshop entitled “The Search for New Physics—Leaving No Stone Unturned,” which brought together dozens of particle physicists, astrophysicists, and cosmologists from around the world to discuss recent advances and big ideas. “It was such a vibrant environment; I think it helped us all broaden our perspectives and learn new things. Though there’s a lot going on in the meantime, we’re already excited about the prospect of hosting a second “No Stone Unturned” workshop in the new Science Building.”

Recently, Sandick has turned her attention to another cosmological phenomenon—black holes—tackling the question of how their existence affects our understanding of dark matter and other physics beyond the Standard Model.

“Some of this new research makes use of the cosmic microwave background (CMB), which is leftover radiation from the Big Bang that we can observe today,” said Sandick.

“CMB measurements can help us understand the structure and composition of the universe, including how much is made of dark matter. The CMB also can provide hints about what other particles or objects existed in the early universe.”

Before the CMB was created, the universe was very hot and very dense. In this environment, the densest places would have collapsed to become black holes. The black holes that formed in this way are called primordial black holes (PBHs), to differentiate them from black holes that form much later when stars reach the end of their lives. Heavy enough PBHs would still be around today and could make up some or all of the dark matter, providing an alternative to the idea that dark matter is a new particle. Lighter PBHs probably are not an explanation for dark matter, but they would have had an important interplay with dark matter and other new particles.

Sandick, along with a U of U postdoctoral associate, Barmak Shams Es Haghi, have been looking into the many impacts of a population of light PBHs in the early universe. Recently, they’ve completed the first precision study of some spinning PBHs in the early universe, finding that current CMB measurements from the Planck satellite (an observatory operated by the European Space Agency) and future measurements with the CMB Stage 4 experiment at the South Pole and in the Chilean desert are sensitive to many important PBH scenarios. The Planck data already point to some more and less likely possibilities, while CMB Stage 4 will be an important step forward in understanding the life and death of small black holes.

In addition to her research, Sandick is passionate about teaching, mentoring, and making science accessible and interesting. She has been recognized for her teaching and mentoring work, with a 2016 University of Utah Early Career Teaching Award and a 2020 University of Utah Distinguished Mentor Award. In 2020, she also was named a U Presidential Scholar. Women are still widely underrepresented in physics, and Sandick is actively involved in organizations that support recruitment, retention, and advancement of women physicists. She has served on the American Physical Society (APS) Committee on the Status of Women in Physics and as the Chair of the National Organizing Committee for the APS Conferences for Undergraduate Women in Physics. She is currently chair of the APS Four Corners Section, which serves approximately 1,800 members from the region. In 2011, she founded a group to support women in the Department of Physics and Astronomy and continues to serve as their faculty advisor.

She earned a Ph.D. from the University of Minnesota in 2008 and was a postdoctoral fellow at Nobel Laureate Steven Weinberg’s group (Weinberg Theory Group) at the University of Texas at Austin before moving to the University of Utah in 2011.

- by Michele Swaner, first published at physics.utah.edu

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Research Funding

December 1, 2021

Annual growth in research funding.

Research Funding Tops $640 Million

University of Utah research funding continues to grow, totaling $641 million in fiscal year 2021, which ended June 30. The total is a new record high for the U, which achieved milestones of $600 million in funding last year and $500 million three years ago.

“Despite the ongoing pandemic, U research activities continue to thrive and grow in many disciplines across campus,” says Andy Weyrich, vice president for research. “Our remarkable research community is the reason why the U is a global leader in discovery and innovation.

Research Funding Sources

Sources of Federal Research Funding.

According to the vice president for research office, federal funding is the largest source of research grants to the U, comprising 68% of funding. More than half of the federal funding (52%) came from the National Institutes of Health and 16% came from the U.S. Department of Energy.

Economic Impact

Economic impact in Utah.

Research grants were awarded to more than 1,000 principal investigators in diverse disciplines across campus. The funding supports nearly 8,000 employees and more than 4,000 trainees, including postdoctoral researchers, students and research assistants.

U research drives economic growth and development. In FY20, U research grants contributed $228 million to salaries and wages, which contributed $31 million in state and local sales taxes, according to the Kem C. Gardner Policy Institute. Since 2000, the U has launched 300 companies and more than 750 products, generating around 37,000 life science jobs.

 - First Published in @theU

 

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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

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