Explore the SRI

At many universities undergraduates have the opportunity to engage in scientific research only in their junior or senior years. Yet successful scientists all have the same core attributes—curiosity, communication skills and a willingness to learn interdisciplinary techniques— traits that many students already possess as freshmen. In 2020, College of Science will the give hundreds of undergraduates the opportunity to contribute to real research projects the year that they step onto campus.

The Science Research Initiative (SRI) is a team-based program that will connect students to discovery-based research early in their education to gain valuable scientific skills. The vision is to provide an opportunity to do research for any incoming student in the College of Science. Additionally, the cohort model makes research opportunities more equitable for students from all backgrounds.

The initiative is self-sustaining by design with experienced students tasked with training incoming freshman—a model that could allow hundreds of students to contribute to a principal investigator’s research for decades. The initiative has support from the university, the state, and industry partners who see the benefit of producing students who are ready to thrive in Utah’s STEM workforce.

“Research opportunities for undergraduates are transformative experiences. The problem that the college has historically faced is that there are many more science majors than there are openings in faculty research laboratories. The SRI solves that problem by scaling up the model of one-on-one faculty mentorship in the framework of vertically integrated research streams,” said Peter Trapa, Dean of the College of Science.

The SRI aims to give 500 undergraduates per year the opportunity to contribute to scientific discoveries, just like Bridget Phillips, a Crocker Science House Scholar and sophomore biology major with a math minor, had this summer.

Phillips was working in biologist Mike Shapiro’s Pigeon Genetics Lab writing code for a project looking for genes that determine the birds’ eye color. She was mining mountains of data searching for a quantitative trait locus (QTL) peak.

She was comparing the genotypes of two groups of pigeons with different eye colors. Because pigeons breeds are the same species, their genetics should look identical except for the gene locus underpinning eye color.

“I got a QTL peak that showed where the gene might be,” she said, smiling. “It was nice. I impressed the postdocs.”

Phillips has been working in Shapiro’s lab since her freshman year. She is an alum of ACCESS, a program where rising freshman in STEM disciplines join a cohort of like-minded undergrads ahead of their first semester in college. ACCESS facilitated her placement in the lab where she found her passion—coding and genetics, two things she never knew existed in a one career.

“Starting in a lab as a freshman is so useful, but the fear is that you don’t know what you’re doing. But you learn the skills really quickly,” Phillips said. “The earlier you can start, the better. If you find out your freshman year that you don’t like research, that’s good to know. If you like research, like I do, then you know what to aim for.”

The college based the SRI on a similar program at the University of Texas-Austin that impressed Henry White, Distinguished Professor of Chemistry and former dean of the college who championed the initiative during his tenure. Since starting the program 20 years ago, UT-Austin has increased enrollment and improved student success, particularly among those from underrepresented groups in STEM fields.

“Students from families who’ve been going to college for generations come to campus recognizing that research opportunities are just as important as the classes themselves,” said White. “This program is meant to promote students who haven’t had the opportunity to be involved in research. We hope to introduce underrepresented, first-generation students to research opportunities, enriching their experience at the U.”

During the first semester, a cohort of students will take a research course to learn basic lab techniques that will replace a traditional prerequisite class. The second semester, the students begin work in a lab led by a principal investigator. They continue the research for their third and fourth semesters, and train an incoming cohort to create a “steady-state” model. During their third year, the students can do an internship or work on an individual project that resembles a more traditional undergraduate lab experience. The college aims to have different streams of research in data science, molecular biology and many disciplines across the College of Science.

In January 2020, a small pilot cohort began the SRI journey. White, Shelley Minteer, professor of chemistry, Markus Babst, professor of biology, and Braxton Osting, professor of mathematics, have committed to developing initial projects. The goal is to eventually have 500 freshmen, sophomores and transfer students participate every year.

SRI brings benefits beyond campus Others outside the university see benefits beyond student success. Funding has come from many sources, including corporate, foundation and individual gifts and workforce development funds from the Utah State Legislature. ARUP Laboratories, a national pathology lab, research facility and a nonprofit enterprise of the University of Utah, and BioFire, a medical diagnostics company, are sponsoring SRI because they view the partnership as mutually beneficial.

“We are constantly looking for well-qualified people to work in labs. It’s a career that’s understaffed—graduates have no problem finding a job, but there’s not a good awareness of this as a possible career path,” said Sherrie Perkins, CEO of ARUP Laboratories and professor of pathology at the U School of Medicine. “We’re so pleased to be a part of this exciting new program and to continue the pipeline of excellent students coming out of the university that we employ.”

Research opportunities indeed open many doors, agreed Rachel Cantrell, a senior chemistry major and Goldwater Scholarship recipient. Also an ACCESS alum, Cantrell has worked in Ryan Looper’s organic synthesis lab since her freshman year. At the time, she thought she wanted to be a pharmacist. Instead, she fell in love with research.

She is developing a scaffold for new antibiotic candidates, a crucial field of inquiry as bacteria are constantly building resistance to current antibiotics. Cantrell’s molecule is modeled after a natural product that kills both bacteria and human cells. Her project focuses on modifying the molecule so that it will only kill the bacteria and leave human cells alone. She plans to pursue a PhD after graduating this year. Beyond the research, the community and networking aspects of ACCESS made a big impact on her life.

“I met a lot of great people there that I’m still friends with. I got to meet faculty and was selected for a scholarship to study in Germany—the community aspect was huge,” she said. To undergrads thinking about whether they want to work in a lab, Cantrell has this advice, “You have to give it a chance. I worked as a pharmacy technician for a while, but I loved being in the lab more. Check out what you like. It can open some huge doors.” The new SRI aims to do just that.

 

 

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 - First Published in Discover Magazine, Fall 2019

Welcome Class of 2019

Welcome Class of 2019

Welcome to the Crimson Laureate Society.

In recognition of your dedication to the College of Science, every member of the Class of 2019 will be an honorary member of the Crimson Laureate Society during the upcoming year.

Our members are advocates for science, making their voices heard as we work with legislators to create new science programs in Utah. We encourage all alumni and friends of science to join today.

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

Insects, Bacteria & Ice

Contrary to what you may have been taught, water doesn’t always freeze to ice at 32 degrees F (zero degrees C). Knowing, or controlling, at what temperature water will freeze (starting with a process called nucleation) is critically important to answering questions such as whether or not there will be enough snow on the ski slopes or whether or not it will rain tomorrow.

Nature has come up with ways to control the formation of ice, though, and in a paper published in the Journal of the American Chemical Society University of Utah professor Valeria Molinero and her colleagues show how key proteins produced in bacteria and insects can either promote or inhibit the formation of ice, based on their length and their ability to team up to form large ice-binding surfaces. The results have wide application, particularly in understanding precipitation in clouds.

“We’re now able to predict the temperature at which the bacterium is going to nucleate ice depending on how many ice-nucleating proteins it has,” Molinero says, “and we’re able to predict the temperature at which the antifreeze proteins, which are very small and typically don’t work at very low temperatures, can nucleate ice.”

What is ice nucleation?
It’s long been known that life likes to mess with ice. Insects, fish and plants all produce various forms of antifreeze proteins to help them survive in below-freezing conditions. And plant pathogens, particularly the bacterium Pseudomonas syringae, employ proteins that promote the formation of ice to induce damage in their hosts. Before we can talk about how these proteins work, though, we need a quick refresher on how ice freezes.

Pure water, with no impurities, won’t freeze until it reaches -35 degrees C (-31 degrees F). That’s the temperature at which the water molecules will spontaneously arrange into a crystal lattice and start to recruit other molecules to join in. To start the freezing process at warmer temperatures, however, water molecules need something to hold on to, like a speck of dust, soot or other impurity, on which it can start building its crystal lattice. This is the process called nucleation.

Ice-nucleating proteins, such as those in Ps. syringae, bind to nascent ice crystallites in such a way as to reduce the energy cost of additional freezing. They can also aggregate together to further enhance their nucleating power. “It is a lot of group work!” Molinero says.

These proteins can be so efficient that they can nucleate ice at temperatures as warm as -2 degrees C (29 degrees F). Ice-nucleating proteins are already being put to use at ski resorts, with Colorado-based Snomax International marketing an additive containing Ps. syringae that gives snowmaking machines a boost.

Antifreeze proteins, however, also bind to ice, but force it to develop a curved surface that discourages additional freezing and requires much colder temperatures for ice to grow. Also, antifreeze proteins don’t aggregate together. “They have evolved to be loners, as their job is to find ice and stick to it,” Molinero says.

All of this was previously known, including the fact that antifreeze proteins were relatively small and ice-nucleating proteins were relatively large. What wasn’t known, though, was how the sizes and aggregating behaviors of the proteins affected the temperature of ice nucleation. That’s the question Molinero and her team set out to answer.

A “single bullet”
Molinero and graduate students Yuqing Qiu and Arpa Hudait conducted molecular simulations of protein interactions with water molecules to see how they affected the temperature of ice nucleation. Antifreeze and ice-nucleating proteins, Molinero says, bind to ice with nearly equal strength.

“Nature is using a single bullet in terms of interactions to address two completely different problems,” she says. “And the way it has resolved between antifreeze or ice nucleation is by changing the size of the proteins and their ability to team up to form larger ice-binding surfaces.”

Antifreeze proteins, they found, nucleated at just above -35 degrees C, which matched experimental data. Lengthening the simulated proteins increased the nucleation temperature, which plateaued after a certain length. The simulations predicted that further assembling around 35 bacterial proteins into larger domains was key to reach the ice-nucleating performance of Ps. syringae, with a nucleation temperature of -2 degrees C (29 degrees F).

“Now we can design new proteins or synthetic materials that nucleate ice at a specific temperature,” Molinero says.

Why it matters
The implications of such a finding extend all the way to the future of water on Earth.

Precipitation begins as ice, which nucleates and grows until it’s heavy enough to precipitate. At high altitudes where it’s colder, soot and dust can do the job of triggering nucleation. But at lower altitudes, it’s not dust that triggers nucleation—it’s bacteria.

Yes, the same proteins in Ps. syringae that aid snowmaking at ski resorts also aid ice formation at warmer temperatures, allowing low-altitude clouds to precipitate. In a warming climate, Molinero’s findings can help climate modelers better understand the conditions of cloud formation and precipitation and forecast how warming will affect the amount of ice nucleation and precipitation in the future.

“The ability to predict whether the clouds are going to freeze or not is super important in climate models, because ice formation determines precipitation and also the ratio of solar energy absorbed and reflected by our atmosphere,” Molinero says. “The challenge to predict whether ice is going to nucleate or not in clouds is a major limitation the predictive ability of weather and climate models.”

At a much smaller scale, however, the antifreeze and ice-nucleating proteins can be employed together in a fine-tuned ice dance: Some insects use antifreeze proteins to protect themselves down to around -8 degrees C (18 degrees F), but then employ ice-nucleating proteins at lower temperatures to contain ice growth before it gets out of hand.

“The big picture is that we now understand how proteins use their size and aggregation to modulate how much they can nucleate ice,” Molinero says. “I think that this is quite powerful.”

Find the full study here.