chemistry

New tools for peering into cell function.

September 9, 2024

New tools for peering into cell function

Sep 9, 2024
Above: Ming Hammond, professor of chemistry. PHOTO CREDIT: Dave Titensor, University of Utah

U chemists discover how key contrast agent works, paving the way to create markers needed for correlative microscopy.

Two labs at the University of Utah’s Department of Chemistry joined forces to improve imaging tools that may soon enable scientists to better observe signaling in functioning cells and other molecular-scale processes central to life.

Rodrigo Noriega, assistant professor of chemistry and co-author of the study.

The Noriega and Hammond labs, with complementary expertise in materials chemistry and chemical biology, made critical discoveries announced this month in the Journal of the American Chemical Society that could advance this goal. Their joint project was kickstarted through a team development grant from the U College of Science and the 3i Initiative to encourage faculty with different research interests to work together on big-picture problems.

“We’re trying to develop a new kind of imaging method, a way to look into cells and be able to see both their structural features, which are really intricate, while also capturing information about their activity,” said co-author Ming Hammond, a professor of chemistry. "Current methods provide high-resolution details on cellular structure but have a challenging ‘blind spot’ when it comes to function. In this paper, we study a tool that might be applied in electron microscopy to report on structure and function at the same time.”

Biological samples often need “markers,” or molecules that are the source of detectable signals, explained co-author Rodrigo Noriega, an assistant professor of chemistry. A widely used type of markers are flavoproteins which, when photoexcited, trigger a chemical reaction that yields metal-absorbing polymer particles whose high contrast in electron microscopy is easily seen.

Scientists had long assumed that a mechanism involving singlet oxygen generation, a special kind of reactive oxygen species, was at play. However, the U team found that electron transfer between the photoexcited marker and the polymer building blocks is the main contributor to the process.

You can read the full story by Brian Maffly in @TheU.

 

Delve into the puzzle of ice crystallization and uncover its secrets.

July 8, 2024

Delve into the puzzle of ice crystallization and uncover its secrets

July 5, 2024
Above: A screen capture from a slow-motion movie covers mere nanoseconds — when water is tuned to a critical point called the liquid-liquid transition.

Making ice requires more than subzero temperatures. The unpredictable process takes microscopic scaffolding, random jiggling and often a little bit of bacteria.

We learn in grade school that water freezes at zero degrees Celsius, but that’s seldom true. In clouds, scientists have found supercooled water droplets as chilly as minus 40 C, and in a lab in 2014, they cooled water to a staggering minus 46 C before it froze. You can supercool water at home: Throw a bottle of distilled water in your freezer, and it’s unlikely to crystallize until you shake it.

Freezing usually doesn’t happen right at zero degrees for much the same reason that backyard wood piles don’t spontaneously combust. To get started, fire needs a spark. And ice needs a nucleus — a seed of ice around which more and more water molecules arrange themselves into a crystal structure.

Valeria Molinero, a physical chemist at the University of Utah, builds computer simulations of water to study ice nucleation.

The formation of these seeds is called ice nucleation. Nucleation is so slow for pure water at zero degrees that it might as well not happen at all. But in nature, impurities provide surfaces for nucleation, and these impurities can drastically change how quickly and at what temperature ice forms.

For a process that’s anything but exotic, ice nucleation remains surprisingly mysterious. Chemists can’t reliably predict the effect of a given impurity or surface, let alone design one to hinder or promote ice formation. But they’re chipping away at the problem. They’re building computer models that can accurately simulate water’s behavior, and they’re looking to nature for clues — proteins made by bacteria and fungi are the best ice makers scientists know of.

Understanding how ice forms is more than an academic exercise. Motes of material create ice seeds in clouds, which lead to most of the precipitation that falls to Earth as snow and rain. Several dry Western states use ice-nucleating materials to promote precipitation, and U.S. government agencies including the National Oceanic and Atmospheric Administration and the Air Force have experimented with ice nucleation for drought relief or as a war tactic. (Perhaps snowstorms could waylay the enemy.) And in some countries, hail-fighting planes dust clouds with silver iodide, a substance that helps small droplets to freeze, hindering the growth of large hailstones.

But there’s still much to learn. “Everyone agrees that ice forms,” said Valeria Molinero, a physical chemist at the University of Utah who builds computer simulations of water. “After that, there are questions.”

You can read the full story in Quanta magazine. Read the published research @PNAS.

Peter Armentrout Returns as Interim Chemistry Chair

June 21, 2024

Distinguished Professor Returns to Leadership

June 21, 2024
Above: Peter Armentrout (Credit: Matt Crawley)

 

Distinguished Professor of Chemistry Peter B. Armentrout has been appointed interim chair of the Department of Chemistry at the University of Utah.

Peter Armentrout. Credit: Matt Crawley

His term will commence July 1, 2024, following the completion of Matt Sigman’s term as chair which began in 2019.

Armentrout is a researcher in thermochemistry, kinetics and the dynamics of simple and complex chemical reactions. As a research professor, he invented and constructed the guided ion-beam tandem mass spectrometer, which has provided highly accurate thermodynamic measurements on a multitude of chemical species.

Upon his arrival at the U in 1987 from UC Berkeley, Armentrout was awarded a Camille and Henry Dreyfus Teacher-Scholar Grant, secured tenure the following year and, in 1989, was promoted to full professor. He has since been recognized with the University-wide Distinguished Research Award (1994) and the Buck-Whitney Award from the American Chemical Society Eastern New York Section (1993), and in 1997, the graduate students at the Ohio State University Department of Chemistry selected Professor Armentrout as their Mack Memorial Award Lecturer.

In 1998, Armentrout was promoted to Distinguished Professor of Chemistry and named Cannon Fellow in 2003, and then, in 2018, was appointed the Henry Eyring Presidential Endowed Chair. He received the Biemann Medal from the American Society of Mass Spectrometry in 2001, the Utah Award of Chemistry from the Utah Sections of the American Chemical Society in 2003, the Field and Franklin Award for Outstanding Achievement in Mass Spectrometry from the American Chemical Society in 2009, the Governor's Medal for Science and Technology Award from the State of Utah in 2010 and, the following year, the prestigious Rosenblatt Prize for Excellence from the U — the university’s highest honor awarded to a faculty member.

In 2018, Armentrout received the Ron Hites Award from the American Society of Mass Spectrometry and the John B. Fenn Award for a Distinguished Contribution in Mass Spectrometry from the American Society of Mass Spectrometry.

His teaching was recognized in 1989 with the Outstanding Undergraduate Teaching Award and in 2011 with the R. W. Parry Teaching Award, both given by the Department of Chemistry.

Armentrout has served on the editorial advisory boards of the International Journal of Mass Spectrometry, and formerly of the Journal of the American Society of Mass Spectrometry, Journal of the American Chemical Society, Journal of Physical Chemistry, Journal of Chemical Physics, Organometallics and the Journal of Cluster Science (charter member).

He is a member of the American Chemical Society, American Physical Society (fellow), American Society for Mass Spectrometry, and the American Association for the Advancement of Science (fellow). He presently has over 560 research publications that have appeared in the literature. Forty-four students have received their PhDs with Professor Armentrout.

Earlier, Armentrout served as Department Chair from 2001 to 2007. During that time, Armentrout instituted several reforms regarding parental leave and secured funding for the David M. Grant NMR Center (Gaus House) and partial funding for the Thatcher extension to the South Chemistry Building.

Armentrout says of the appointment: “I am honored to be asked to take the reins of this exceptional department for a couple more years. The research and teaching abilities and collegiality of this faculty are second to none and will enable us to collectively advance and lead within the U. I look forward to working with them as well as our supporters outside the university system in the near term.” 

"In addition to being a world-class chemist with a towering international reputation, Peter is also an exceptional teacher, mentor, and administrator,” said Peter Trapa, dean of the College of Science. “His appointment as interim chair will continue to advance Utah's Chemistry Department as one of the best in the world. I look forward to working with Peter as we continue to build on the department's strengths.”

Trapa continued, “I'm also deeply grateful to Distinguished Professor Matt Sigman for his outstanding leadership as chair over the past five years. Matt’s contributions to the department, especially his unwavering commitment to excellence, will be felt for many years to come.”

You can read a short autobiography of Peter Armentrout and his early career from 2013, here.

By David Pace

Chemist Aaron Puri Receives Simons Foundation Early Career Award

May 23, 2024

Chemist Aaron Puri Receives Simons Foundation Early Career Award

PURI RECOGNIZED FOR PIONEERING RESEARCH INTO METHANE-MITIGATING MICROBIAL ECOSYSTEMS


“I am honored to receive this award and excited to join the community of researchers supported by the Simons Foundation to answer fundamental questions about microbial ecology and evolution.” says Aaron Puri, Assistant Professor in the Department of Chemistry and the Henry Eyring Center for Cell and Genome Science and one of five awardees for 2024. The Simons Foundation Early Career Investigator in Aquatic Microbial Ecology and Evolution Award recognizes outstanding researchers in the fields of microbial ecology, microbial biogeochemistry, and microbial evolution in marine or natural freshwater systems. Its purpose is to promote the careers of investigators who contribute to understanding these areas.

Puri joined the College of Science faculty in 2019 after working as a postdoctoral fellow at the University of Washington. He earned his Ph.D. in Chemical and Systems Biology from Stanford University in 2013, and his B.S. from the University of Chicago in 2008. Puri has also received the NIH Maximizing Investigators’ Research Award and the NSF CAREER Award. 

“This award will enable our research group to work at the interface of biology and chemistry to decipher the molecular details of interactions in methane-oxidizing bacterial communities,” says Puri. His research aims to solve big problems with microscopic solutions. “These communities provide a biotic sink for the potent greenhouse gas methane, and are a useful system for understanding how bacteria interact with each other and their environment while performing critical ecosystem functions.” The Simons Award is an indicator that this is only the beginning of Puri’s research successes.

 

by Lauren Wigod

 

Goldwater Scholars 2024

April 17, 2024

Goldwater Scholars 2024

Two College of Science students awarded the prestigious Goldwater Scholarship for 2024-25

The Barry Goldwater Scholarship is a prestigious award given to undergraduate sophomores and juniors who intend to pursue research careers. Goldwater Scholars often go on to hold distinguished research and leadership positions across many disciplines. For the 2024-2025 academic year, 438 scholarships were awarded to college students across the country. At the University of Utah, two undergraduate students have earned the honor of becoming Goldwater Scholars: Muskan Walia and Nathan Patchen.

Nathen Patchen
Biochemistry

“Biochemistry was a great way for me to combine my love of biology and chemistry and understand not only how things work, but why,” says Nathan Patchen about what motivated him to pursue research in that field. Patchen was awarded the Goldwater Scholarship for his work in Yang Liu’s lab, an assistant professor of biochemistry at the Spencer Fox Eccles School of Medicine. 

Patchen describes his research as broadly being focused on DNA damage repair. He says “[w]e have access to revolutionary gene editing tools that, when used in conjunction with advanced imaging techniques, allow us to explore how cancer cells undergo DNA damage repair as never seen before. Personally, I am doing this by implementing a modified CRISPR-Cas9 that allows us to capture time-resolved images after damage and then produce data about the kinetics of repair.” 

After graduating from the U, Patchen hopes to pursue an MD/PhD to practice medicine while continuing his research on gene editing and aging. Outside of his time in the lab, he enjoys being active through swimming, biking, and running as he trains for an IRONMAN 70.3 in St. George, Utah in May. 

 

Muskan Walia
Mathematics
Philosophy

“Mathematics is at the cusp of interdisciplinary research” says Muskan Walia. During the College of Science ACCESS Scholars research program, she reflected on her academic interests and goals. She explains, "I wasn’t interested in studying any discipline in a vacuum or in isolation. Rather, I wanted to work on mathematics research that centered justice and informed public policy.”

The majority of Walia’s undergraduate research sprouted from her time in ACCESS where with the help of Fred Adler in the mathematics department at the College of Science, she began to adapt an epidemiological SIR model to predict the number of cells infected with SARS-CoV-2. Since then, she has created other models to further answer her questions about disease. These include a “... model of disease progression within an infected individual, a model of an antigen test, and a model of symptoms to evaluate how testing can be used to limit the spread of infection.”

“Ultimately, I want to lead a team that utilizes mathematical principles to tackle the most pressing social justice related questions of our time.” Walia is one of 57 awardees honored this year who intend to pursue research in mathematics or computer science. Besides innovating mathematical models, Walia enjoys spending time outside bird watching with her mom and gardening with her grandmother.

 

 

By Lauren Wigod
Science Writer Intern