Faculty

Karl Schwede

December 10, 2020

Fellow of the American Mathematical Society

Professor Karl Schwede in the U’s Department of Mathematics has been named a member of the 2021 Class of Fellows of the American Mathematical Society (AMS). The Society recognizes members who have made outstanding contributions to the creation, exposition, advancement, communication and utilization of mathematics. Schwede joins 14 other professors in the department who were previously named fellows by the AMS.

“It’s an honor to be named as a fellow of the American Mathematical Society, and I’m grateful for the recognition of my peers in the profession,” said Schwede.

Schwede received his undergraduate degree in mathematics from Whitman College and a Ph.D. in mathematics from the University of Washington. Math was originally third on his list of interests in college, but as he took more advanced math courses, his focus changed to mathematics.

Schwede does basic research in mathematics, studying algebra, geometry and particularly singularities. Much of his work is in the setting of modular arithmetic (also known as clock arithmetic), the same setting as much of our modern communication systems. For example, 5 hours after 10 is 3 or 5+10 = 3. “In this area, I have primarily studied singularities of geometric shapes by algebraic means,” said Schwede. Recently, he has begun working in mixed characteristic, which connects the positive characteristic of clock arithmetic with classical (5+10 = 15) geometric worlds.

He joined the U’s Math Department in 2014 as an associate professor and became a professor in 2018. Last spring, Schwede received a Simons Fellows Award in Mathematics from the Simons Foundation.

 

by Michelle Swaner, originally published in @theU

Giant Poisonous Rats

December 9, 2020

The secret social lives of giant poisonous rats.

The African crested rat (Lophiomys imhausi) is hardly the continent’s most fearsome-looking creature—the rabbit-sized rodent resembles a gray puffball crossed with a skunk—yet its fur is packed with a poison so lethal it can fell an elephant and just a few milligrams can kill a human. In a Journal of Mammology paper published today, Smithsonian Conservation Biology Institute, University of Utah and National Museums of Kenya researchers found the African crested rat is the only mammal known to sequester plant toxins for chemical defense and uncovered an unexpected social life—the rats appear to be monogamous and may even form small family units with their offspring.

Sara B. Weinstein and Katrina Nyawira.

“It’s considered a ‘black box’ of a rodent,” said Sara Weinstein, lead author and Smithsonian-Mpala postdoctoral fellow  and postdoctoral researcher at the University of Utah. “We initially wanted to confirm the toxin sequestration behavior was real and along the way discovered something completely unknown about social behavior. Our findings have conservation implications for this mysterious and elusive rat.”

People in East Africa have long suspected the rat to be poisonous. A 2011 paper proposed these large rodents sequester toxins from the poison arrow tree (Acokanthera schimperi). A source of traditional arrow poisons, Acokanthera contains cardenolides, compounds similar to those found in monarch butterflies, cane toads and some human heart medications. Cardenolides, particularly the ones in Acokanthera, are highly toxic to most animals.

“The initial 2011 study observed this behavior in only a single individual. A main goal of our study was to determine how common this exceptional behavior was,” said co-author Denise Dearing from the University of Utah.

When threatened, the African crested rat lives up to its name and erects a crest of hair on its back to reveal a warning on its flanks—black and white stripes running from neck-to-tail on each side of its body. The 2011 study hypothesized that the rats chew the Acokanthera bark and lick the plant toxins into specialized hairs at the center of these stripes.

In the new study, researchers trapped 25 African crested rats, the largest sample size of the species ever trapped. Using motion-activated cameras, they documented nearly 1,000 hours of rat behavior. For the first time, they recorded multiple rats sequestering Acokanthera toxins and discovered many traits that suggest they are social, and likely monogamous.

“Everyone thought it was a solitary animal. I’ve been researching this rat for more than ten years, so you would expect there to be fewer surprises,” said Bernard Agwanda, curator of Mammals at the Museums of Kenya, co-author of this study and the 2011 paper. “This can carry over into conservation policy.”

A rich social life

As a postdoctoral fellow at the Mpala Research Centre, Weinstein first searched for the rats with camera traps, but found that they rarely triggered the cameras. Weinstein was then joined by Katrina Nyawira, the paper’s second author and now a graduate student at Oxford Brookes University. Together, they spent months experimenting with live traps to capture the elusive rodents.

“We talked to rangers and ranchers to ask whether they’d seen anything.” said Nyawira. Eventually they figured out that loading the traps with smelly foods like fish, peanut butter and vanilla, did the trick. “Out of 30 traps, we finally got two animals. That was a win. This thing is really rare.”

Those two animals changed the course of the study. They first caught an individual female, then caught a male at the same site two days later.

The African crested rat.

“We put these two rats together in the enclosure and they started purring and grooming each other. Which was a big surprise, since everyone we talked to thought that they were solitary,” Weinstein said. “I realized that we had a chance to study their social interactions.”

Weinstein and Nyawira transformed an abandoned cow shed into a research station, constructing stalls equipped with ladders and nest boxes to simulate their habitat in tree cavities. They placed cameras in strategic spots of each pen and then analyzed every second of their footage, tracking the total activity, movement and feeding behavior. The aim was to build a baseline of normal behavior before testing whether behavior changed after the rats chewed the toxin cardenolides from the poison arrow tree.

“They’re herbivores, essentially rat-shaped little cows,” Weinstein said. “They spend a lot of time eating, but we also see them walk around, mate, groom, climb up the walls, sleep in the nest box.”

The footage and behavioral observations strongly support a monogamous lifestyle. They share many of the traits common among monogamous animals: large size, a long life span and a slow reproductive rate. Additionally, the researchers trapped a few large juveniles in the same location as adult pairs, suggesting that offspring spend an extended period of time with their parents. In the pens, the paired rats spent more than half of their time near each other, and frequently followed each other around. The researchers also recorded special squeaks, purrs and other communicative noises making up a wide vocal repertoire. Further behavioral studies and field observation would uncover more insights into their reproductive and family life.

After the researchers established a baseline of behavior, they offered rats branches from the poison arrow tree. Although rats did not sequester every time the plant was offered, 10 rats did at least once. They chewed it, mixed it with spit, and licked and chewed it into their specialized hairs. Exposure to the Acokanthera toxins did not alter rat behavior, and neither did eating milkweed, the same cardenolide-enriched plant used as chemical defense by monarch butterflies. Combined, these observations suggest that crested rats are uniquely resistant to these toxins.

“Most people think that it was a myth because of the potency of the tree,” said Nyawira. “But we caught it on video! It was very crazy.”

The rats were selective about using Acokanthera cardenolides, suggesting that rats may be picky about their toxin source, or that anointed toxins remain potent on the fur a long time, just like traditional arrow poisons from the same source.

African crested rat conservation

The African crested rat is listed as IUCN species of least concern, but there’s little actual data on the animals. Agwanda has studied African crested rats for more than a decade—and sees indications that they’re in trouble.

“We don’t have accurate numbers, but we have inferences. There was a time in Nairobi when cars would hit them and there was roadkill everywhere,” said Agwanda, who continues to monitor the populations. “Now encountering them is difficult. Our trapping rate is low. Their population is declining.”

The research team is planning future studies to better understand their physiology and behavior. “We are particularly interested in exploring the genetic mechanisms that allow the crested rats and their parasites to withstand the toxic cardenolides” said co-author Jesús Maldonado of the Smithsonian Conservation Biology Institute and Weinstein’s Smithsonian-Mpala Postdoctoral fellowship co-advisor.

“We are looking at a broad range of questions influenced by habitat change. Humans have cleared forests to make farms and roads. We need to understand how that impacts their survival,” Agwanda said. Additionally, Agwanda is building an exhibit at the Museums of Kenya to raise awareness about this unique poisonous animal.

About the Smithsonian’s National Zoo and Conservation Biology Institute

The Smithsonian’s National Zoo and Conservation Biology Institute leads the Smithsonian’s global effort to save species, better understand ecosystems and train future generations of conservationists. As Washington, D.C.’s favorite destination for families, the Zoo connects visitors to amazing animals and the people working to save them. In Front Royal, Virginia, across the United States and in more than 30 countries worldwide, Smithsonian Conservation Biology Institute scientists and animal care experts tackle some of today’s most complex conservation challenges by applying and sharing what they learn about animal behavior and reproduction, ecology, genetics, migration and conservation sustainability to save wildlife and habitats. Follow the Zoo on Facebook, Twitter and Instagram.

About the National Museums of Kenya

National Museums of Kenya (NMK) is a state corporation established by an Act of Parliament, the Museums and Heritage Act 2006. NMK is a multi-disciplinary institution whose role is to collect, preserve, study, document and present Kenya’s past and present cultural and natural heritage. This is for the purposes of enhancing knowledge, appreciation, respect and sustainable utilization of these resources for the benefit of Kenya and the world, for now and posterity. NMK’s mutual concern for the welfare of mankind and the conservation of the biological diversity of the East African region and that of the entire planet demands success in such efforts. In addition, NMK manages many Regional Museums, Sites and Monuments of national and international importance alongside priceless collections of Kenya’s living cultural and natural heritage. As an institution that must respond to the growing needs of the society, NMK is striving to contribute in a unique way to the task of national development.

Media Contacts

Sara Weinsteinpostdoctoral researcher at the University of Utah; postdoctoral fellow at the Smithsonian-Mpala

Denise Dearingdistinguished professor and director, School of Biological Sciences

Lisa Potterresearch/science communications specialist, University of Utah Communications
Office: 801-585-3093 Mobile: 949-533-7899 

Adapted from a release by the Carnegie Observatories. Also published in @theU

A Catalyst for Safety

December 8, 2020

A Catalyst for Safety

In June 2019, a chemical spill in a Department of Chemistry laboratory led to a full department shutdown until a comprehensive safety assessment could be completed. Within days, most laboratories re-opened. Within weeks, the department had put into motion an unprecedented safety makeover in partnership with the Office of Environmental Health and Safety (EHS) and the College of Science. Since then, the college and EHS have enacted creative solutions to rebuild a culture of lab safety from the ground up—and it has paid dividends in implementing safeguards related to COVID-19.

Tommy Primo

“Everyone from the department level up to the President’s Office has made significant changes to how the U regulates laboratory safety,” said Peter Trapa, dean of the College of Science. “By the time COVID-19 hit, we had the right infrastructure, the right coordination between EHS and our own folks, so that we could quickly lead out in the COVID era.”

Committed committees

Matthew Sigman

At the time of the spill, the U’s laboratory safety culture had been through a series of internal and external audits, including one by the Utah State Legislature. The reports identified crucial gaps in safety and made recommendations for improvement. The U has made significant progress addressing these recommendations, including establishing and expanding the number and authority of college and departmental-level safety committees. Within the College of Science, the Departments of Chemistry, Mathematics, Physics & Astronomy and the School of Biological Sciences all have committees made up of staff and faculty who performed routine lab inspections and reported violations. The previous safety system’s structure allowed some violations to remain unresolved. Now, the committees are empowered to recommend how violations get addressed. They’ve also expanded their scope to include postdocs and graduate students who can make suggestions for outdated practices or areas that need attention. In the coming weeks, safety committees will be required in all University colleges.

“To change the safety culture, there has to be the motivation, and it has to be a grassroots effort,” said Matthew Sigman, Peter J. Christine S. Stang Presidential Endowed Chair of Chemistry. “This is a success because it’s collaborative, it’s conversational, and it’s pragmatic. It’s about building relationships and getting buy-in from the top down.”

Sarah Morris-Benavides

In January, EHS and the College of Science jointly hired Sarah Morris-Benavides as the first associate director of safety for the College. Morris-Benavides facilitates communication between researchers, and helps translate regulatory protocols between the college and EHS. She also heads the College of Science’s safety committee that is made up of the department committee chairs. She and the committees have worked closely to ensure that classes and research are conducted safely in light of the coronavirus restrictions.

“I can’t tell you how valuable they’ve been,” said Morris-Benavides of the response to COVID-19. “We had a great benefit that these committees were already established and in place.”

Every month, the college safety committee meets to discuss each department’s safety protocols. “We have the ability to say, ‘Well, here’s something that they’re doing in biology. Does that make sense for physics?” she said. “Chemistry learned a lot from their amazing safety turnaround, and they’ve shared their best practices. It all benefits every department.”

Precipitating solutions

Selma Kadic

The U overhauled the previous laboratory safety system by restructuring EHS directly under the Vice President for Research Office, and Frederick Monette became its new director. This helped rebuild trust between the EHS and researchers, who had historically been at odds.

“Fred Monette was all in right away. His willingness to sit down with people, listen to their concerns, and back it up financially meant a lot to the people in the department,” said Holly Sebahar, professor of chemistry who was the chair of the chemistry safety committee at the time of the shutdown.

Safety violations can be complicated; some are easy fixes, such as ensuring lab members wear proper PPE, but other issues are expensive, such as electrical or ventilation upgrades within older buildings. Traditionally, the burden of arranging infrastructure upgrades and their cost often fell solely on the principal investigator (PI) of the laboratory in question.

Angus Wu

To change that, EHS and the College of Science lobbied for an infrastructure improvement project to fund overdue, expensive safety upgrades in College of Science buildings, many of which were identified as deficiencies during the chemistry shutdown. The resulting $1 million capital improvement project will address electrical upgrades, seismic bracing, and ventilation improvements in several buildings, beginning in January 2021. Addressing these deficiencies in one comprehensive project will be much quicker, more economical, and result in less disruption to laboratory operations compared with the past approach of fixing each issues one by one at the request of individual laboratories.

Working with the College of Science, the VPR Office facilitated the purchase of 20 new refrigerator/freezers rated for storage of flammable chemicals to replace units that failed to meet regulatory requirements, sharing the cost 50/50 with the PIs. These initiatives demonstrated the administration’s commitment to promoting a culture of safety across the university.

From the ground up

As another example of a changed safety culture, the Department of Chemistry aims to incorporate safety in all aspects of academic life. Every speaker, seminar and many group meetings now incorporate a ‘safety moment,’ with each presenter asked to share an example of a safety incident and how they addressed it.

Shelley Minteer

“We have upwards of 30 or 40 external visitors a year. That’s a lot of safety moments. They’ll walk through that experience, then walk through the lab procedures to fix the problem,” Sigman said. “It’s a lessons learned, but also it’s an open conversation. We want to have the lowest risk, but we know when you sign up to be a chemist, you have the danger. Even when you cross the t’s, dot the i’s, something can happen.”

The collaborations go beyond the science—last year, EHS, the College of Science and the College of Mines and Earth Sciences co-hosted a two-day lab safety symposium with speakers and training sessions that addressed all types of issues, from chemical storage to creating effective safety committees. More than 400 staff, students and faculty attended the mandatory event to emphasize that every individual is responsible to making their environment safe. The U is applying that same philosophy for COVID-19.

“As we started going through the safety culture changes, we realized that it’s not that students or post docs or faculty won’t follow safety protocols, they will, if they know where they are, if they can find the paperwork,” said Shelley Minteer, associate chair for faculty for the Department of Chemistry and COVID-19 coordinator for the department. “We learned a lot from the safety ramp up. We need clear guidelines and good communication. We’ve been applying those same principles to COVID.”

 

by Lisa Potter - first published in @theU

 

Productivity Resources

November 10, 2020

Productivity resources

Stay safe. stay healthy. Stay connected.

The Covid-19 pandemic has taken a toll across university campuses. Below are some tips to help manage stress and focus on staying productive while working remotely.

  1. Take care of yourself. 
  2. Learn a new skill or technique: Invest time in broadening your research focus.
  3. Revisit a long forgotten project: Do you have publishable results that have been on the shelf?
  4. Promote your work online: Update your website or FAR.
  5. Create a graphical abstract of your research: Use this on your website; share it with your departments’ development team.
  6. Apply for funding: Check out the Faculty Funding Opportunities emails from the CoS.  
  7. Think about your career plans: Write a plan for yourself.
  8. Conduct informational interviews: Meet on Zoom to brainstorm about new research directions.
  9. Be nice to your fellow humans: Check in with your research group and colleagues.  Offer encouragement and celebrate accomplishments.
  10. Do fun stuff: Fun projects, fun brainstorming, add fun to your personal life (while staying safe, of course)!

*Adapted from AAAS: Advice for working from home during COVID-19 (Bodewits, 2020).

  • Three questions to ask yourself each day:
    • What choices am I making about the things I have control over?  If you’re feeling overwhelmed, consider what choices you can make about the information you receive and whether that information is serving you well.
    • What do I need, physically, intellectually, emotionally?  Do this at the beginning of the day. Use this self-dialog to build your schedule.
    • What is good right now?  Identifying positive things helps control fear and panic, allowing you to better focus on the tasks at hand. 
  • NCFDD Resources: COVID-19
  • Core Curriculum  Note that for each webinar, you can navigate to the “Resources” tab, where you will find a summary and discussion questions.  Some webinars also feature templates and examples for further reading.

*Adapted from the National Center for Faculty Development and Diversity (NCFDD). The UofU is an NCFDD institutional member, so access to these resources is free.  To create your account, choose “Become a member” in the upper right corner of the page, and choose our institution from the drop down menu.  Then “Activate your membership” to create your own account using your email address.

 

 

Next-Gen Astronomy

November 3, 2020

 

Gail Zasowski

Next-gen astronomical survey makes its first observations.

The Sloan Digital Sky Survey’s fifth generation collected its very first observations of the cosmos at 1:47 a.m. on October 24, 2020. As the world’s first all-sky time-domain spectroscopic survey, SDSS-V will provide groundbreaking insight into the formation and evolution of galaxies—like our own Milky Way—and of the supermassive black holes that lurk at their centers.

Funded primarily by member institutions, along with grants from the Alfred P. Sloan Foundation, the U.S. National Science Foundation, and the Heising-Simons Foundation, SDSS-V will focus on three primary areas of investigation, each exploring different aspects of the cosmos using different spectroscopic tools. Together these three project pillars—called “Mappers”—will observe more than six million objects in the sky, and monitor changes in more than a million of those objects over time.

The survey’s Local Volume Mapper will enhance our understanding of galaxy formation and evolution by probing the interactions between the stars that make up galaxies and the interstellar gas and dust that is dispersed between them. The Milky Way Mapper will reveal the physics of stars in our Milky Way, the diverse architectures of its star and planetary systems, and the chemical enrichment of our galaxy since the early universe. The Black Hole Mapper will measure masses and growth over cosmic time of the supermassive black holes that reside in the hearts of galaxies, and of the smaller black holes left behind when stars die.

“We are thrilled to start taking the first data for two of our three Mappers,” added SDSS-V spokesperson Gail Zasowski, an assistant professor in the University of Utah’s Department of Physics & Astronomy. “These early observations are already important for a wide range of science goals. Even these first targets provide data for studies ranging from mapping the inner regions of supermassive black holes and searching for exotic multiple-black hole systems, to studying nearby stars and their dead cores, to tracing the chemistry of potential planet-hosting stars across the Milky Way.”

A sampling of data from the first SDSS-V observations. Center: The telescope’s field-of-view, with the full Moon shown for scale. SDSS-V simultaneously observes 500 targets at a time within a circle of this size. Left: the optical-light spectrum of a quasar, a supermassive black hole at the center of a distant galaxy, which is surrounded by a disk of hot, glowing gas. The purple blob is an SDSS image of the light from this disk, the width of a human hair as seen from about 21 meters (63 feet) away. Right: The image and spectrum of a white dwarf –the left-behind core of a low-mass star (like the Sun) after the end of its life.

The newly-launched SDSS-V will continue the path-breaking tradition set by the survey’s previous generations, with a focus on the ever-changing night sky and the physical processes that drive these changes, from flickers and flares of supermassive black holes to the back-and-forth shifts of stars being orbited by distant worlds. SDSS-V will provide the spectroscopic backbone needed to achieve the full science potential of satellites like NASA’s TESS, ESA’s Gaia, and the latest all-sky X-ray mission, eROSITA.

As an international consortium, SDSS has always relied heavily on phone and digital communication. But adapting to exclusively virtual communication tactics since the beginning of the COVID-19 pandemic was a challenge, along with tracking global supply chains and laboratory availability at various university partners as they shifted in and out of lockdown during the final ramp-up to the survey’s start. Particularly inspiring were the project’s expert observing staff, who worked in even-greater-than-usual isolation to shut down, and then reopen, the survey’s mountain-top observatories.

“In a year when humanity has been challenged across the globe, I am so proud of the worldwide SDSS team for demonstrating—every day—the very best of human creativity, ingenuity, improvisation, and resilience.” said SDSS-V director Juna Kollmeier, of the Carnegie Observatories. “It has been a challenging period for SDSS and the world, but I’m happy to report that the pandemic may have slowed us, but it has not stopped us.”

Anil Seth


The University of Utah will actually operate as the data reduction center for SDSS-V, supported by the U’s Center for High Performance Computing. Joel Brownstein, a research associate professor in the Department of Physics & Astronomy, is the head of data management and archiving for SDSS-V. “As we see the first observations streaming to Utah from the mountain observatories, we are just starting to grasp the amazing potential of this ambitious data set. We are fully and proudly committed to making our results more accessible to the larger community by introducing new tools that enable a dynamic, user-driven experience.”

SDSS-V will operate out of both Apache Point Observatory in New Mexico, home of the survey’s original 2.5-meter telescope, and Carnegie’s Las Campanas Observatory in Chile, where it uses the 2.5-meter du Pont telescope.

SDSS-V’s first observations were taken in New Mexico with existing SDSS instruments, in a necessary change of plans due to the pandemic. As laboratories and workshops around the world navigate safe reopening, SDSS-V’s own suite of new innovative hardware is on the horizon—in particular, systems of automated robots to aim the fiber optic cables used to collect the light from the night sky. These robots will be installed at both observatories over the next year. New spectrographs and telescopes are also being constructed to enable the Local Volume Mapper observations.

Dr. Anil Seth, the University of Utah’s representative on the Advisory Council that oversees SDSS’s operations, highlighted the impact of the project’s open data policies and worldwide collaboration. “SDSS’s 20-year legacy has touched nearly every astronomer in the world by this point. It has become the go-to reference for astronomy textbooks on galaxies, made the most precise measurements of how our Universe is expanding, and showed us how powerful shared data can be. I look forward to see what new results SDSS V will reveal!”

For more information, please see the SDSS-V’s website at www.sdss5.org.

Adapted from a release by the Carnegie Observatories. Also published in @theU

Debate 2020

September 29, 2020

Election 2020

On October 7, the University of Utah is hosting the 2020 Vice Presidential Debate.

"Civic engagement is a core value of our nation and, as we host the 2020 Vice Presidential debate, Utah students will be able to learn about the political process and experience firsthand how being involved matters." —Ruth V. Watkins, President of the University of Utah

 

Let your voice be heard. VOTE!

Voting may not seem important to science majors and faculty, but participation is incredibly important. A voice for science in federal, state, and local politics provides a crucial point of view for our world. Much of the funding decisions that support scientific research and discovery occurs on the federal level, so what happens in Washington, D.C. impacts our College of Science community.

STEM students least likely to vote.

A Tufts University survey of university students across the US reports that STEM students are the least likely of any subject group to vote. In 2016, the humanities turnout was 53%. The STEM turnout was 43%. The Union of Concerned Scientists provides students with voter registration information and trains scientists for involvement in policy and advocacy.

 

The Condorcet Paradox

Looking for a scientific perspective on our electoral process? Learn how mathematical analysis makes a difference in the political process through this video of Professor Tom Alberts explaining the Condorcet Paradox.

 

Presidential Scholar

August 24, 2020

Presidential Scholar

Pearl Sandick

Pearl Sandick one of Four U Presidential Scholars named.

Four faculty members—a pharmacologist, a political scientist, an engineer, and a physicist—have been named Presidential Scholars at the University of Utah.

The award recognizes the extraordinary academic accomplishments and promise of mid-career faculty, providing them with financial support to advance their teaching and research work.

The 2020 recipients are: Marco Bortolato, associate professor in the Department of Pharmacology and Toxicology in the College of Pharmacy; Jim Curry, associate professor and director of graduate studies for the Department of Political Science in the College of Social and Behavioral Science; Masood Parvania, associate professor and associate chair in the Department of Electrical and Computer Engineering in the College of Engineering; and Pearl Sandick, associate professor in the Department of Physics and Astronomy and associate dean of the College of Science.

“These scholars represent the exceptional research and scholarship of mid-career faculty at the University of Utah,” said Dan Reed, senior vice president for Academic Affairs. “They each are outstanding scholars and teachers in their fields of specialty. Their scholarship is what makes the U such a vibrant and exciting intellectual environment.”

Presidential scholars are selected each year, and the recipients receive $10,000 in annual funding for three years. The program is made possible by a generous donor who is interested in fostering the success of mid-career faculty.

Pearl Sandick

Pearl Sandick, a theoretical particle physicist and associate professor in the Department of Physics and Astronomy, studies explanations for dark matter in the universe—one of the most important puzzles in modern physics.“I love that my work involves thinking of new explanations for dark matter, checking that they’re viable given everything we know from past experiments and observations, and proposing new ways to better understand what dark matter is,” she said. “I find this type of creative work and problem solving to be really fun on a day-to-day basis, and the bigger picture — what we’ve learned about the Universe and how it came to look the way it does — is just awe-inspiring.”

She has given a TEDx talk and been interviewed on National Public Radio’s Science Friday. Sandick is passionate about teaching, mentoring students and making science accessible and interesting to non-scientists. In addition to the Presidential Scholar award, she has received the U’s Early Career Teaching Award and Distinguished Mentor Award.

“One of the great joys of working at the U is our commitment to engaging students at all levels in research,” Sandick said, “and I’ve been thrilled to work with amazing undergraduate and graduate students.”

by Rebecca Walsh first published in @theU

11 Billion Years

August 5, 2020

 

 

Professor Kyle Dawson

11 billion years of history in one map: Astrophysicists reveal largest 3D model of the universe ever created.

(CNN) A global consortium of astrophysicists have created the world's largest three-dimensional map of the universe, a project 20 years in the making that researchers say helps better explain the history of the cosmos.

The Sloan Digital Sky Survey (SDSS), a project involving hundreds of scientists at dozens of institutions worldwide, collected decades of data and mapped the universe with telescopes. With these measurements, spanning more than 2 million galaxies and quasars formed over 11 billion years, scientists can now better understand how the universe developed.

Image courtesy of SDSS

"We know both the ancient history of the Universe and its recent expansion history fairly well, but there's a troublesome gap in the middle 11 billion years," cosmologist Kyle Dawson of the University of Utah, who led the team that announced the SDSS findings on Sunday. "For five years, we have worked to fill in that gap, and we are using that information to provide some of the most substantial advances in cosmology in the last decade," Dawson said in a statement.

Here's how it works: the map revealed the early materials that "define the structure in the Universe, starting from the time when the Universe was only about 300,000 years old." Researchers used the map to measure patterns and signals from different galaxies, and figure out how fast the universe was expanding at different points of history. Looking back in space allows for a look back in time.

"These studies allow us to connect all these measurements into a complete story of the expansion of the Universe," said Will Percival of the University of Waterloo in the statement.

The team also identified "a mysterious invisible component of the Universe called 'dark energy,'" which caused the universe's expansion to start accelerating about six billion years ago. Since then, the universe has only continued to expand "faster and faster," the statement said.

Image courtesy of SDSS

There are still many unanswered questions about dark energy -- it's "extremely difficult to reconcile with our current understanding of particle physics" -- but this puzzle will be left to future projects and researchers, said the statement.

Their findings also "revealed cracks in this picture of the Universe," the statement said. There were discrepancies between researchers' measurements and collected data, and their tools are so precise that it's unlikely to be error or chance. Instead, there might be new and exciting explanations behind the strange numbers, like the possibility that "a previously-unknown form of matter or energy from the early Universe might have left a trace on our history."

The SDSS is "nowhere near done with its mission to map the Universe," it said in the statement. "The SDSS team is busy building the hardware to start this new phase (of mapping stars and black holes) and is looking forward to the new discoveries of the next 20 years."

 

Adapted from a release by Jordan Raddick, SDSS public information officer
Also published in @theU, Spectrum Magazine, CNN, Forbes, and more.

 

HIV Microscopy

July 20, 2020

HIV Microscopy

Ipsita Saha, graduate research assistant

Pioneering method reveals dynamic structure in HIV.

Viruses are scary. They invade our cells like invisible armies, and each type brings its own strategy of attack. While viruses devastate communities of humans and animals, scientists scramble to fight back. Many utilize electron microscopy, a tool that can “see” what individual molecules in the virus are doing. Yet even the most sophisticated technology requires that the sample be frozen and immobilized to get the highest resolution.

Now, physicists from the University of Utah have pioneered a way of imaging virus-like particles in real time, at room temperature, with impressive resolution. In a new study, the method reveals that the lattice, which forms the major structural component of the human immunodeficiency virus (HIV), is dynamic. The discovery of a diffusing lattice made from Gag and GagPol proteins, long considered to be completely static, opens up potential new therapies.

When HIV particles bud from an infected cell, the viruses experience a lag time before they become infectious. Protease, an enzyme that is embedded as a half-molecule in GagPol proteins, must bond to other similar molecules in a process called dimerization. This triggers the viral maturation that leads to infectious particles. No one knows how these half protease molecules find each other and dimerize, but it may have to do with the rearrangement of the lattice formed by Gag and GagPol proteins that lay just inside of the viral envelope. Gag is the major structural protein and has been shown to be enough to assemble virus-like particles. Gag molecules form a lattice hexagonal structure that intertwines with itself with miniscule gaps interspersed. The new method showed that the Gag protein lattice is not a static one.

The Saffarian Lab in the Crocker Science Center

“This method is one step ahead by using microscopy that traditionally only gives static information. In addition to new microscopy methods, we used a mathematical model and biochemical experiments to verify the lattice dynamics,” said lead author Ipsita Saha, graduate research assistant at the U’s Department of Physics & Astronomy. “Apart from the virus, a major implication of the method is that you can see how molecules move around in a cell. You can study any biomedical structure with this.”

The paper published in Biophysical Journal on June 26, 2020.

Mapping a nanomachine.

The scientists weren’t looking for dynamic structures at first—they just wanted to study the Gag protein lattice. Saha led the two year effort to “hack” microscopy techniques to be able to study virus particles at room temperature to observe their behavior in real life. The scale of the virus is miniscule — about 120 nanometers in diameter—so Saha used interferometric photoactivated localization microscopy (iPALM).

First, Saha tagged the Gag with a fluorescent protein called Dendra2 and produced virus-like particles of the resulting Gag-Dendra2 proteins. These virus-like particles are the same as HIV particles, but made only of the Gag-Dendra2 protein lattice structure. Saha showed that the resulting Gag-Dendra2 proteins assembled the virus-like particles the same way as virus-like particle made up regular Gag proteins. The fluorescent attachment allowed iPALM to image the particle with a 10 nanometer resolution. The scientists found that each immobilized virus-like particle incorporated 1400 to 2400 Gag-Dendra2 proteins arranged in a hexagonal lattice. When they used the iPALM data to reconstruct a time-lapse image of the lattice, it appeared that the lattice of Gag-Dendra2 were not static over time. To make sure, they independently verified it in two ways: mathematically and biochemically.

80 nm sections of cells (2020 Biphys Journal) - Saha & Saffarian

Initially, they divided up the protein lattice into uniform separate segments. Using a correlation analysis, they tested how each segment correlated with itself over time, from 10 to 100 seconds. If each segment continued to correlate with itself, the proteins were stationary. If they lost correlation, the proteins had diffused. They found that over time, the proteins were quite dynamic.

The second way they verified the dynamic lattice was biochemically. For this experiment, they created virus-like particles whose lattice consisted of 80% of Gag wild type proteins, 10% of Gag tagged with SNAP, and 10% of gag tagged with Halo. SNAP and Halo are proteins that can bind a linker which binds them together forever. The idea was to identify whether the molecules in the protein lattice stayed stationary, or if they migrated positions.

Rendering of Gag molecules proteins diffusing across a virus-like particle - Dave Meikle/Saffarian Lab

“The Gag-proteins assemble themselves randomly. The SNAP and Halo molecules could be anywhere within the lattice—some may be close to one another, and some will be far away,” Saha said. “If the lattice changes, there’s a chance that the molecules come close to one another.”

Saha introduced a molecule called Haxs8 into the virus-like particles. Haxs8 is a dimerizer—a molecule that covalently binds SNAP and Halo proteins when they are within binding radius of one another. If SNAP or Halo molecules move next to each other, they’ll produce a dimerized complex. She tracked these dimerized complex concentrations over time. If the concentration changed, it would indicate that new pairs of molecules found each other. If the concentration decreased, it would indicate the proteins broke apart. Either way, it would indicate that movement had taken place. They found that over time, the percentage of the dimerized complex increased; HALO and SNAP Gag proteins were moving all over the lattice and coming together over time.

A new tool to study viruses.

This is the first study to show that the protein lattice structure of an enveloped virus is dynamic. This new tool will be important to better understand the changes that occur within the lattice as new virus particles go from immaturity to dangerously infectious.

Saveez Saffarian and Ipsita Saha

“What are the molecular mechanisms that lead to infection? It opens up a new line of study,” said Saha. “If you can figure out that process, maybe you can do something to prevent them from finding each other, like a type of drug that would stop the virus in its tracks.”

Saveez Saffarian, professor in the Department of Physics & Astronomy at the U, was senior author on the paper.

 

by Lisa Potter first published in @theU

Also published in Eurekalert
 

Forest Futures

June 22, 2020

Forest Futures

Know the risks of investing in forests.

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

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

Meeting of Minds

William Anderegg

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

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

Accumulating Risk

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

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

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

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

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

Mitigating Risk

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

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

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

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

 

 

by Paul Gabrielsen first published in @theU