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Dean’s Update

COVID-19 Updates


March 24, 2020

Dean Peter Trapa

Dear College of Science Community,

As we all continue to grapple with the COVID-19 pandemic, the health and safety of our students, faculty, and staff is our foremost priority. The University is carefully monitoring the situation and is posting recommendations and additional information at the University COVID-19 Central website.

The College continues to follow the University’s guidance closely.  Key points include:

All classes are being conducted in an online format. To remain up to date, students should use these tips and tools. In no circumstances will students be required to pay additional online course fees.  A Credit/No-Credit grading option has also been instituted in all undergraduate classes.

The University remains open and operational at this time, however all administrative offices in the College of Science have ceased on-site operations and moved to teleworking arrangements.  Please refer to the College of Science contact page for electronic contact information.

Please adhere closely to the University Travel Restrictions. If individual circumstances allow for it, we are strongly encouraging students to remain off-campus following these housing guidelines.   For out-of-state students: time away this semester will NOT affect the status of your residency applications.

As of Friday, March 20th, at 5pm, the College of Science is restricting research to essential operations defined as follows: caring for experimental living organisms; maintaining continuous cell lines; and maintaining equipment and reagents that will otherwise be damaged by a complete shutdown.  Principal Investigators (PIs) should carefully consider this mandate, and where a doubt exists, should discuss the options with their chair or director. Exceptions will be made for PIs whose research is directly related to COVID-19.

These measures are powerful tools to lessen the impact of a disease that has the potential to overwhelm the medical system for those who are most ill and in need of healthcare.  SVP Good’s video presentation gives an excellent overview.

Commencement and Convocation exercises have been postponed. The College of Science is tremendously proud of the accomplishments of our students.  We are in the process of formulating alternative plans to celebrate our graduates.

Most importantly, we are here to support you during this challenging time.  The situation may feel overwhelming, but through calm and careful concerted efforts — and through the very power of science itself — we will see through this crisis.   The following resources are fully operational and remain open for your use should you need them:

Looking towards the future,  the College of Science remains fully committed to fulfilling our educational and research missions.  I look forward to working with all of you to continue our outstanding tradition of scientific discovery.

 

Peter Trapa

 

 

Dean of the College of Science

 

Coronavirus Research

Coronavirus Research


One of the biggest unknowns about the coronavirus is how changing seasons will affect its spread. Physicists from the University of Utah have received the university’s first COVID-19-related grant to tackle the question.

The National Science Foundation (NSF) has awarded a Rapid Response Research (RAPID) grant to Michael Vershinin and Saveez Saffarian of the U’s Department of Physics & Astronomy to study the structure of the SARS-COV-2, the coronavirus strain at the center of the pandemic. The physicists will create individual synthetic coronavirus particles without a genome, making the virus incapable of infection or replication. The researchers will test how the structure of the coronavirus withstands changes in humidity and temperature, and under what conditions the virus falls apart.

The results will help public health officials understand how the virus behaves under various environmental conditions, including in the changing seasons and in microclimates such as air-conditioned offices.

“We’re making a faithful replica of the virus packaging that holds everything together. The idea is to figure out what makes this virus fall apart, what makes it tick, what makes it die,” said Vershinin, assistant professor of physics and astronomy and co-principal investigator of the grant. “This is not a vaccine. It’s won’t solve the crisis, but it will hopefully inform policy decisions going forward.”

The researchers searched the fully-sequenced SARS-COV-2 genome that was published in January and zeroed in on the genes responsible for the structural integrity of the virus. They are now synthesizing these genes in living cells and allowing their proteins to assemble into virus particles.

“Coronavirus spreads similarly to the influenza virus—as small mucus droplets suspended in the air. The predominate idea is that viruses lose infectivity because the particles lose structural integrity,” said Saffarian. “The physics of how the droplets evolve in different temperature and humidity conditions affect how infectious it is.”

The RAPID funding program allows NSF to quickly review proposals in response to research on urgent issues, such as global pandemics.

“This application of sophisticated physics instruments and methods to understand how the 2019 coronavirus will behave as the weather changes is a clear example of how our investment in basic research years later prepares us for a response to a crisis that impacts not only our society, but also the whole world,” said Krastan Blagoev, program director in NSF’s Division of Physics.

ONE FROM MANY

At the onset of the coronavirus, Vershinin and Saffarian dove deep into the scientific literature to learn as much as possible about corona and related viruses, such as influenza. They realized that many studies looked at the spread of influenza on an epidemiological level. There are fewer answers about how climate and specific conditions effect a single virus particle. Both researchers bring decades of experience working in the nanoscale. Vershinin lab’s specialty is using optical tweezers, a tool that enables him to probe individual molecules just a few atoms across.

“It’s often compared with the tractor beam from ‘Star Trek.’ You just use light to reach in and apply force to manipulate things,” Vershinin said.

Saffarian’s lab focuses on viruses that, like coronavirus, contain RNA strands. His lab utilizes many tools to track the behavior of individual virus particles, including HIV.

The researchers are members of the Center for Cell and Genome Sciences in the College of Science, where scientists who apply physics, chemistry and biology work alongside each other and can form collaborations rapidly—a key advantage in the fight against the virus.

“You don’t just gain the insight that you want by looking at the virus on a large scale. Looking at a single virus particle is the key to being able to tease out what’s going on,” Vershinin said. “Modern biology and biophysics allows us to ask these questions in a way we never could have before.”

Funding for this research was provided by NSF under award number PHY-2026657 for nearly $200,000.

 

by Lisa Potter

>> @theU - 03/18/2020

 

 

Essential Research

Essential Research Activities


As of March 23, 2020, only research activities that have been determined to be essential by the college dean or center/institute director, in consultation with the VPR, can be conducted on campus. Essential research activities can only be carried out by personnel that are classified as mandatory with Human Resources. These personnel, as well as their time on campus, should be kept to a minimum and laboratories and facilities must have detailed protocols in place to maintain physical distance and to protect the health and safety of research personnel and the general public. No other personnel or visitors are permitted in research buildings, laboratories, or facilities while these restrictions are in effect.

Graduate students and post-doctoral researchers should not be classified as mandatory unless their work is critical to essential research. See the Graduate School guidance for further details. We ask PIs and mentors to be extremely judicious in classifying research personnel as mandatory and to keep the health and safety of our research community and the public as their foremost consideration.

Currently, all research activities conducted by University of Utah personnel on campus, at other university properties, or at other field or remote research facilities must fall into one of the following categories:

  • Priority clinical and pre-clinical research
  • Animal care or priority animal research
  • Maintenance of other live organisms (e.g. plants, fungi, non-vertebrates) and cell cultures
  • Maintenance of equipment or experimental infrastructure that will be damaged by interruptions
  • Research functions necessary for health and safety
  • Other urgent research activities if approved by the VPR

Individual approvals of other urgent research activities must be sent to the college dean or institute/center director, who will then forward the request to the VPR if approved at the college/institute/center level.

Keep up to date on COVID-19 related Research information at research.utah.edu/coronavirus/.

If you have questions or concerns please contact the VPR office at vproffice@utah.edu.

 

 

Science VS Virus

Utah science and the Coronavirus


As COVID-19, the disease caused by the new coronavirus, spreads across the globe, University of Utah scientists are stepping up to the plate to address the numerous unanswered questions that are emerging in its wake. Sound science that informs how the novel virus came to be, how it behaves and how it spreads will be invaluable for developing and implementing strategies to defeat it.

Within a few short weeks, more than a dozen new research studies have popped up across the U—from physics to biochemistry to bioengineering—and many more are in the works.

The U’s Immunology, Inflammation, and Infectious Disease Initiative quickly assembled support for these new efforts with a virtual meeting that attracted 207 participants and funding for COVID-19 research. While projects at the U vary in approach, they share a common goal: to create a brighter future for all of us. We describe five of them here.

Do changes in temperature and humidity affect the new coronavirus?

One of the biggest unknowns about the coronavirus is how changing seasons will affect its spread. Researchers from the Department of Physics & Astronomy received grant funding to answer this question. The physicists will create individual synthetic coronavirus particles without a genome, making the virus incapable of infection or replication. The researchers will test how the structure of the coronavirus withstands changes in humidity and temperature, and under what conditions the virus falls apart.

Lead scientists: Michael Vershinin and Saveez Saffarian, Physics & Astronomy

A drug to block infection

One thing we really need is a medicine that prevents or treats COVID-19. Biochemists at U of U Health are working toward that goal by repurposing a strategy they developed against another infectious disease, HIV. Their trick is to build mirror-images of pieces of proteins, called D-peptides. These little chemicals are designed to jam the infection process and because D-peptides aren’t found in nature, they aren’t degraded by the body. This could mean that one dose could last a long time, simplifying treatment and lowering cost. Getting new drugs approved can be a lengthy process so this approach may not help with the current outbreak. That’s why the scientists are simultaneously creating a broad inhibitor that could be effective against other new coronaviruses.

Lead scientists: Debra EckertChristopher HillMichael, Kay, Biochemistry

Origins of the new coronavirus

Bats are rife with coronaviruses, most of which are likely harmless to people. Scientists have found that these viruses can exchange pieces of genetic information with each other, giving rise to viruses that cause outbreaks in humans. To find the role these exchanges may have played in the origin of SARS-CoV-2, researchers in the Department of Human Genetics are scouring the virus’ genome to find regions that have changed recently, and are determining whether genetic exchange could have empowered the virus to infect us and evade our immune defenses. Understanding how docile viruses turn deadly could one day inspire new ideas to stop them.

Lead scientists: Stephen Goldstein, Nels Elde, Human Genetics

Who should be tested for covid-19?

We are living the reality that there is a limited number of COVID-19 tests, due to international shortages of supplies to make them. In this situation, it is best to reserve testing for individuals who are most at-risk for having the disease and developing severe symptoms. But who are they? Using mathematical models of disease spread, and clinical data from those who have already been tested, infectious disease physicians are developing an online calculator. Plug in medical data and out comes a score indicating the likelihood that the patient will test positive. If the score is high, she should be tested. If the score is low, she can monitor symptoms at home (calling in if they change) potentially preserving a precious test.

Lead scientist: Daniel Leung, Infectious Disease

Planning for a better future.

If we could see that the future looks dire, we might be able to come up with ways to change it. Epidemiologists are creating models based on what is known about transmission of the new coronavirus from person-to-person and combining it with census data. The result? An indication of when the disease might enter different parts of the country and expected number of cases. With this virtual world, scientists can then determine how things might change when people take precautions like social distancing. The scientists are also developing hospital-specific scenarios to anticipate needs for beds, masks, ventilators and other precious items in limited supply. With these data, the hope is to be able to shift the future from ominous to optimistic.

Lead scientist: Lindsay Keegan, Epidemiology


 

Alex Acuna

Alex Acuna


Alexandra “Alex” Acuna doesn’t even remember her native Venezuela, as she arrived in the U.S. with her parents and two older siblings when she was just a few weeks old. She does recall as a young child huddling in a room for seven months with other families experiencing homelessness at the Road Home Shelter in Salt Lake City where her closest ally was “Mike Wazowski,” a ratty, single-eyed monster toy she hugged day and night.

Eventually, the family moved into a basement apartment with two other families before landing more permanently in government-subsidized housing. “There were a lot of points in our childhood when my siblings and I were skating on thin ice,” she says, referencing everything from food and housing insecurity to fear of deportation; from the stigma of not being part of the majority Latinx community to almost yearly changes in schools. To make matters worse, her parents separated shortly after the family’s arrival. “Survival took up all of our time,” she says.

There was one stabilizing force for the family: food and the community that comes with each cuisine. It started in their modest apartment kitchen with her mother selling empanadas, a cottage industry that grew to a full-fledged Venezuelan restaurant that, in 2014, opened in Salt Lake.

Acuna’s mother, whose college experience was derailed in Venezuela by her first pregnancy, was determined to make sure her children got to the best public schools possible. Even so, as Acuna puts it, once at the UofU she experienced what so many first-generation students do: “I had no access to people who understood the system I was trying to navigate. I didn’t know what I didn’t know. I didn’t know where to look for resources.”

The College of Science’s Access Program was a life ring. Not only did it provide Acuna a scholarship, but a first-year cohort with older students along with housing during the summer before her first year so that she could familiarize herself with campus life. Another important component of the program directed by Tanya Vickers was getting into a lab, something Acuna admits “was not even on my radar.” In Leslie Sieburth’s lab at the School of Biological Sciences Acuna became embedded in a community: “How do you bridge the gap in knowledge,” she asks, “without a network of people?” The answer is you probably don’t, especially with Acuna’s background and lack of opportunities that many college-bound students take for granted.

For three years, Acuna fought self-doubt during “the worst of times” that she was somehow an intruder, a forever-outsider who didn’t belong in a lab that, frankly, she wasn’t even sure the value of. “Tanya was a great mentor,” she says now of Vickers, acknowledging that her mentor helped her see that, while her mother needed her to work in the restaurant, Acuna needed to prioritize her education, a difficult thing to do when you’ve been a character in a shared survival narrative as intense as theirs.

Eventually, the school/work balance was struck. “My mother was never a helicopter mom. But she sees me in the trenches and can now share the glory of it with me.” (Acuna still works weekends in the restaurant, patronized by the flowering Venezuelan community and others in Utah’s capital city.)

Says Sieburth of Acuna, “Alex joined my lab with an enormous amount of raw talent. It was a pleasure to mentor her, and to help her recognize her remarkable facility for research.”

An opportunity seized soon presents other opportunities. In February 2019, Acuna was admitted to the inaugural year of the Genomics Summer Research for Minorities sponsored by the U’s medical school. Currently, she does research in the Tristani-Firouzi lab where the gene-editing and cloning of plants she was doing with Sieburth are now placed for this budding molecular biologist into a medical and physiological context. In the Tristani lab they are studying the genetic component of atrial fibrillation, one of the most common types of cardiac arrhythmia. “It’s given me power to things that I wasn’t even aware of before coming here,” says a grinning Acuna.

What’s next for Alex Acuna? “I know that I’m definitely moving on,” she says of her career as a scientist. “I’m just not clear what direction: academics or medical school.” As a paid undergraduate research assistant, though, one thing she is sure about: “I’ve found a sustainable model. These worlds–personal and professional–they could combine [after all]. They did combine. I understand my ambition, and I now have such sensitivity to activities outside of the lab.”

For Acuna and her family, who are now naturalized citizens of the U.S., their experience is not just an immigrant story of survival; it’s an incomplete narrative born in Venezuela and perpetually vectoring toward real promise.

Dalley Cutler

Dalley Cutler


Biology senior Dalley Cutler's personal hero is Greta Thunberg, the young Swedish activist invited to the United Nations to advocate for reversing man-made climate change and who was subsequently named Time Magazine's Person of the Year. Along with this sixteen-year-old, and others like her, the Idaho Falls native wants to see sensible policies and actions based on scientific understanding.

The same is true of his own research in the Dentinger lab. “Many producers are either incorrectly identifying wild mushroom food products or are purposely lying about the species contained in those food products,” he says. “There are no international or national regulations to protect consumers from buying and eating poisonous wild mushrooms sold on the internet as edible wild mushrooms.” He uses metabarcoding genomic analysis techniques to identify species sold as wild mushrooms in food products.

“I generated the data for this poster some time ago,” he says, referring to the research poster he displayed at the School of Biological Sciences' annual Retreat in August 2019.  “But due to other obligations like class attendance and work I was unable to invest the necessary time to learn how to process and accurately analyze that data.” A scholarship provided by alumni donor George R. Riser was a game-changer for him, providing time away from work obligations to write the appropriate scripts and install the right software that will streamline future projects.

The scholarship has also allowed him to begin generating and processing data for his next project.

Cutler who is graduating with his bachelor's in biology in April 2020 has high hopes to work in a field where he can use scientific techniques to better understand the natural world and to use that understanding to protect and conserve vulnerable ecosystems from the impacts of the climate and ecological crisis that will be occurring over the course of his life.

Inspired by an out-spoken girl in pig tails who was named Time Magazine's Person of the Year for 2019, he is committed as a scientist to make a difference.

Jessica Stanley

Jessica Stanley


Jessica Stanley, undergraduate research scholar in the Clayton/Bush Lab), will tell you that one of the best things about being at the University of Utah isn’t biology (although she’s definitely keen on that), but MUSS. No, that’s not a kind of hair gel, it’s an acronym for Mighty Utah Student Section.

In 2001, average student attendance at University of Utah home football games was around 500 students per game. In 2002, the Alumni Association and Department of Athletics partnered to start the Utah Football Fan Club (the current MUSS). “When I came to Utah as an assistant in 1994,“ Utah Head Football Coach Kyle Whittingham is quoted as saying, “the student section consisted of four students and a dog. And the dog was a stray.” Not so now. MUSS has grown to 6,000 members and was named the nation’s fourth best student section by NCAA.com in 2014.

Outside of rooting for her favorite football team, Stanley, who studies birds and the parasites who live on them, can get downright technical, in a biological sort of way. When asked what she’d most like someone to know about her research findings to date she reports, that “there has been no correlation found between pectinate claw prevalence and parasite abundance. However we have found a correlation between claw length and mite load.”

Okay.

A Cottonwood Heights (Utah) native, Stanley studies the function of pectinate claws on cattle egrets. “We are trying to understand the function of the claw and how it may be used for removal of ectoparasites,” she says. At the 2019 Biology Retreat and Lark Symposium, she was one of 14 undergraduate scholarship recipients who presented research posters. “Most people know that avian families use preening as an anti-parasite behavior; however, most people do not know that scratching with the foot is also an important behavior,” she explained to guests at the event. “Scratching can be used to help control parasites in regions that are not easy to preen, such as the head. The pectinate claw (comb-link serrations) can be used to aid in parasite removal.”

Still trying to envision what a pectinate claw looks like? Stanley, who is a Senior, and hopes to attend veterinary school and work with large animal exotics, can help.

More about Jessica Stanley:

How has the scholarship funded by Ryan Watts (BS'2000; Denali Therapeutics) you’ve received assisted you thus far? What would you want the donor of your scholarship to know about how valuable the scholarship has been to you?

This scholarship has given me the opportunity to build my resume while learning the valuable world of research. It has helped me to understand the correct research methods and has taught me to think outside the box. This scholarship has also made me more comfortable talking with others about their ideas and how I can include their opinions into my work.

If you had to pick one action hero, historical hero, or personal hero of yours, who would it be and why?:  

I would chose my Grandfather Norman. He has taught me that hard work and family are all you need to have a great life. You do not need material goods to make you happy. You make your own happiness in this world and nothing can stop you from being what you want to be.

Outside of research and school, what are your Interests?:  ultimate frisbee

Sahar Kanishka

Sahar Kanishka


Biology student, ACCESS member, College of Science Association for Women in STEM member, and recipient of an undergraduate research scholarship funded by alumnus, Ryan Watts (BS'2000 and founder of Denali Therapeutics), Sahar Kanishka is a force in the Utah student community.

Major: Biology
Year: Sophomore
Lab: Gagnon Lab
Hometown: Salt Lake City, Utah
Interests: Studying anatomy, swimming, watching movies, hiking

What do you love about your research?
Being able to control the temporal aspect of CRISPR genome editing would allow for editing to occur during any stage of embryonic development. We have not been able to optimize temporal control of editing with small molecule regulation, but we are testing to see if genomic editing is occurring.

Tell us something about your research:
Zebrafish are capable of rapid tissue regeneration!

Describe attending the UofU?
The ACCESS program is amazing. I love that the U is a big campus. There are so many resources for students, places to explore, and people to meet just on campus.

What are your dreams for a career, research?
In the future, I plan on attending medical school and open clinics where resources are scarce. I plan on pursuing an MBA to give me the tools in operating clinics. I also plan on continuing research throughout my career!

How have the scholarships you’ve received assisted you?
This scholarship has been very important in my academic endeavors, and being able to continue my education. I am grateful to the donors for being supportive of my research and for investing in education.

 

Leadership

Leadership


Karl Gordon Lark

Honoring Karl Gordon Lark, 1930-2020.

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Christoph Boehme

Physics & Astronomy selects Christoph Boehme as Department Chair.

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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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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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