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Giant Poisonous Rats

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

Productivity Resources

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

NEXT-GEN ASTRONOMY


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

$602 Million in Funding

Research Funding Tops $600 Million


Two years after achieving a $500 million funding milestone and with the added boost of funding for research related to the COVID-19 pandemic, the University of Utah reports $603 million in research funding for fiscal year 2020, which ended June 30.

“We would like to express our appreciation to our donors, investors, government officials and research partners,” said Vice President for Research Andy Weyrich. “Their support drives critical research projects in medicine, technology, mental health, economic growth, social injustice, racial disparities and much more.”

The milestone comes in a fiscal year that saw the U invited to join the prestigious Association of American Universities, a group of 65 top-tier research universities in the U.S. and Canada. The U, along with Dartmouth College and the University of California, Santa Cruz, joined the AAU in 2019 as peers with the top universities in the nation.

The research funding milestone also comes amid a global pandemic and a proliferation of research related to the medical, economic and social aspects of COVID-19. Following seed grants totaling $1.3 million, funded by the Office of the Vice President for Research in partnership with the Immunology, Inflammation and Infectious Disease (3i) Initiative, U researchers in various disciplines secured additional external funding, which contributed to passing the $600 million mark.

“Our researchers are at the forefront of addressing the impact COVID-19 has on our society,” Weyrich said. “We’ve been awarded a significant number of research grants across multiple disciplines to support COVID research, including the social, psychological and economic impacts the virus has on our global community.”

 - First Published in @theU

 

 

Debate 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.

 

Equity, Diversity & Inclusion Committee

equity, diversity, and inclusion committee

 

The College of Science established an Equity, Diversity, and Inclusion committee to promote awareness and active practices to increase diversity on our campus. The committee will work as an advisory body to the College of Science Dean, while also working on initiatives to increase the diversity of students, faculty and staff at the College.

Committee members include:

Pearl Sandick, Dean’s Office (chair)
David Bowling, SBS
Shelley Minteer, Chemistry
Christel Hohenegger, Math
Tino Nyawelo, P&A
Jordan Gerton, CSME
Lindsey DeSpain, Dean’s Office/staff rep

Do you have a concern or an issue that the Equity, Diversity, & Inclusion committee should know about?

 

 

 

department committees:


 

Physics & Astronomy

Mathematics

Chemistry: Curie Club

Presidential Scholar

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

 

 


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

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
 

Student Visas

International Students


F1 Visa Update

July 14, 2020 - Update for International Students

Proposed changes in visa restrictions for international students have been rescinded, and visa qualifications will return to the standard set in the spring of 2020. International students are now able to register for classes that best suit their pathway to a degree, regardless of whether the class will be held online or in-person.

The College of Science remains committed to supporting you and helping you reach your academic goals and maintain your visa status under the current Immigration guidelines. The University of Utah continues to monitor this situation and will provide ongoing updates as new information becomes available.

I encourage you to reach out to your academic advisors or, in the case of graduate students, your department’s graduate program coordinator, with any questions or concerns that you may have.

We value the strength and diversity of our international student community, and we will continue to do whatever possible to support you during your academic career in the College of Science.

Sincerely,

 

 

 

Peter Trapa


Giant Poisonous Rats

The secret social lives of giant poisonous rats.

Read More
Beckman Scholar

Sonia Sehgal awarded prestigious Beckman Scholarship.

Read More
Frontiers of Science

The longest running lecture series at the University of Utah.

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Next-Gen Astronomy

The Sloan Digital Sky Survey is providing groundbreaking insight.

Read More
October Update

The magazine for the students, faculty, alumni and friends of the College of Science.

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$602 Million in Funding

Research funding passes $602 million for 2020.

Read More
Notebook 2020

The magazine for the students, faculty, alumni and friends of the College of Science.

Read More
Debate 2020

STEM students least likely of any subject group to vote in U.S. elections.

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Donor Recognition

Thank you for your support of our vibrant community of scientists and mathematicians.

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OurDNA Spring ’20

The Fall 2019 Issue of OurDNA Magazine.

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Jordan Herman, PhD’20

Next time you’re stuck between an intimidating toucan and a camouflaged pit viper ...

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Presidential Scholar

Pearl Sandick has been named a University of Utah Presidential Scholar.

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Rapid Response Research

Behind-the-scenes story of an NSF Rapid Response Research grant.

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A.A.U. Membership

Utah joins the prestigious Association of American Universities.

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College Rankings

U.S. News & World Report University Rankings.

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11 Billion Years

Kyle Dawson and a global consortium of astrophysicists create a 3-D map of the universe.

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Back to School

The College of Science reopening plan for fall 2020.

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HIV Microscopy

Ipsita Saha is using electron microscopy to reveal the dynamic structure in HIV.

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Masks for U

Spread the word, not the virus.

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Forest Futures

William Anderegg explains the risks of investing in forests.

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Recent Awards

We're going to need a bigger trophy room.

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Dean’s Update

Updated: June 12, 2020.

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Crab Nebula

Scientists detect Crab Nebula using innovative gamma-ray telescope.

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We Stand…

For a compassionate, equitable, and just society for all.

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Student Info

Guidelines for the Summer 2020 semester.

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Dominique Pablito

Zuni, Navajo and Comanche, student majoring in chemistry and biology.

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OurDNA Fall 19′

The 2019 Issue of Notebook Magazine.

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2020 Convocation

College of Science 2020 Convocation videos and slideshow.

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2020 Churchill Scholar

Michael Xiao brings home the U's fifth straight Churchill Scholarship.

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Karl Gordon Lark

Honoring Karl Gordon Lark, 1930-2020.

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2020 Research Scholar

Delaney Mosier receives top College of Science award.

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Students & COVID-19

Info and resources for students, including financial assistance.

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Goldwater Winner

Isaac Martin awarded prestigious Goldwater Scholarship.

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Science Podcasts

Podcast from the College of Science.

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Courtship Condos

Why is Dean Castillo managing the sexual relations of fruit flies?

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Goldwater Winner

Lydia Fries awarded prestigious Goldwater Scholarship.

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Ana Rosas

Medicine is a family tradition for the Rosas.

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Dean’s Update

The latest information for science students, faculty and staff. Updated: March 24, 2020.

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Coronavirus Research

Physicists receive NSF grant to test coronavirus particles.

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Essential Research

Essential Research Activities and the process to become essential.

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Science VS Virus

Utah scientists address the Coronavirus pandemic.

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Crocker Science Center

New era begins at the U, with the newly renovated Gary and Ann Crocker Science Center.

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Discover 2019

The 2019 Research Report for the College of Science.

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Running with Scissors

In gene-targeting, CRISPR makes a really good pair of "scissors".

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Electrochemistry

Henry S. White - A positive force in Electrochemistry.

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Commutative Algebra

Can commutative algebra help us solve real-world problems?

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Alumni Panel

Distinguished science alumni share their experiences.

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TreeTop Barbie

Nalini Nadkarni has created a "Canopy Researcher" version of the popular Barbie doll.

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Research Funding

Research funding passes $540 million for 2019.

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Fellow of the A.M.S.

Davar Khoshnevisan, named Fellow of American Mathematical Society.

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Math in Paris

I needed to take a math class, so I searched "learning abroad differential equations"

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Going with the Flow

John Sperry studies how plant hydraulics and xylem tissue influence regional weather.

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Staff: Jose Rojas

Jose Rojas probably knows more about how labs operate than most principal investigators.

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Staff: James Muller

Building better science buildings.

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Dean Peter Trapa

Peter Trapa has been named as the new Dean of the College of Science.

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Notebook 2019

The 2019 Issue of Notebook Magazine.

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Quaid Harding

From beekeeping to biology, Quaid Harding is looking for a buzz.

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Zhao Scholarship

Taylor is the first recipient of the Michael Zhao Memorial Scholarship. She’s […]

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Royal Fellow

Christopher Hacon adds another honor of a lifetime to his already stellar resume.

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Rachel Cantrell

2019 Goldwater Recipient A 2019 Goldwater Scholarship has been awarded to Rachel […]

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Leslie Sieburth: Associate Dean

The College of Science is pleased to announce the appointment of Professor Leslie […]

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Pearl Sandick: Associate Dean

The College of Science is pleased to announce the appointment of Professor Pearl […]

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Janis Louie: Associate Dean

The College of Science is pleased to announce the appointment of Professor […]

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New Physics

Pearl Sandick discusses Dark Matter and challenging the Standard Model.

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Teaching Excellence

Kelly MacArthur is recognized for her extraordinary dedication to her students.

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Staff: Mary Levine

An indispensable part of the Department of Mathematics.

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Teaching Excellence

Recognizing extraordinary skill in university teaching.

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Distinguished Research

Professor Molinero’s work is a hallmark of what research and scholarship should be about.

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Distinguished Teaching

Gernot Laicher, Professor/Lecturer in the Department of Physics & Astronomy.

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2019 Research Scholar

The College of Science Research Scholar Award is given annually to one […]

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2019 Hatch Prize

Professor Joel Harris has been awarded the 2019 Hatch Prize for outstanding teaching!

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Associate V.P. for Research

Diane Pataki is now Associate Vice President for Research at the University of Utah.

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2019 Churchill Scholar

Cameron Owen - Chemistry and physics major and student researcher.

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Insects, Bacteria & Ice

Water doesn’t always freeze at 32 degrees and other chilling facts from Valeria Molinero.

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Discover 2018

The 2018 Research Report for the College of Science.

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Student Veteran

2018-19 Student Veteran of the Year, Craig L. Hanson  “When I first […]

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AMS Fellow

Tommaso de Fernex, Ph.D. Associate Department Chair of Mathematics.

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AMS Fellow

“I was delighted to learn the news from the AMS,” said Peter Trapa.

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Plant Genomics

QUESTION: How does RNA decay contribute to gene expression?

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Breakthrough Prize

Christopher Hacon, has been interested in math for as long as he can remember.

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2018 Churchill Scholar

Scott Neville - Mathematics major and student researcher.

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Beckman Alumnae

Ming Hammond recounts her experience in the inaugural class of Beckman Scholars.

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Under Pressure

Unravelling the mystery of a fundamental property of lithium.

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2017 Churchill Scholar

Michael Zhao - Mathematics major and student researcher.

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2016 Churchill Scholar

Mackenzie Simper - Mathematics major and student researcher.

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