SRI Research Streams - Spring 2022

College of Science faculty are engaged in research across disciplines. SRI scholars will have the opportunity to interact with faculty and determine which research stream best meets their interests during the spring semester of SRI participation. Research can be performed for credit, and scholarship opportunities are available.

Click on a tile to learn more about the stream.


PN Pollinator Networks
Pollinator Networks

Stream Leader: Dr. Heather Briggs

SG Seed Genetics
Seed Genetics

Stream Leader: Dr. Gary Drews

Seeds directly or indirectly produce 50% of the calories provided in the human diet.  In cereal grains, such as maize (corn) many of the calories are stored in a tissue called endosperm. Research in the Drews lab focuses on understanding the molecular mechanisms regulating endosperm development.  Using reverse genetic approaches in maize, the Drews lab has identified a collection of genes that are turned on in tissues that play essential roles during normal seed development.

The Drews lab research stream will focus on using genetic approaches to understand the function of the genes turned on in endosperm.  As a first step, the Drews lab has generated mutations in a series of genes of interest using the CRISPR Cas9 systems.  Initial analysis suggests that mutating single genes fails to reveal the function of genes of interest.  Students working with professor Drews will be involved in identifying and characterizing plants with multiple genes removed (double mutants).  Preliminary results suggest that eliminating redundant gene products results in profound seed developmental defects.

While working with professor Drews you will be introduced to the biology of plant reproduction and seed development, and modern approaches to genetics.  Undergraduate researchers will be taught a variety of key molecular biology research skills including, but not limited to, DNA extraction methods, PCR, and electrophoresis, and will be taught common computational approaches for evaluating DNA sequences.

AC Ant Cultivated Fungi
Ant Cultivated Fungi

Stream Leader: Dr. Bryn Dentinger/Kendra Autumn

Attine ants are fungus farmers who feed, weed, and eat their crop. There are two types of attine ants that each farm a different kind of fungus. Both fungi are found exclusively under agriculture by attines, but have close free-living relatives. The close evolutionary relationships of ant-cultivated fungi and their free-living relatives provide an opportunity for insight into the evolution of ant fungal crops and their association with their farmers. In particular, I am investigating defensive compounds produced by ant-farmed fungi. I hypothesize that the farmed fungi will possess a different complement of defensive compound-producing genes than their free-living relatives, due to the role of many defensive compounds in making fungi unpalatable to invertebrates, as well as evidence of reduction of defensive compounds in human-farmed crop plants. Students will contribute toward this effort by helping to sequence museum specimens of free-living relatives of the ant-cultivated fungi, and will learn DNA extraction, PCR, and DNA sequence analysis in the process.

EN Evolution of Neural Circuits
Evolution of Neural Circuits

Stream Leader: Dr. Sophie Caron and Chelsea Gosney

An organism must adapt to its environment to ensure the survival of the next generation. The ways in which neural circuits evolve to different environments is largely unknown. To understand how the brain changes in response to varying ecologies, we use the Drosophila olfactory circuit as a model. In this stream, students will have the opportunity to determine which odors are important for species with vastly different ecologies. Students will be working with four species of Drosophila: D. melanogaster and D. simulans, which can be found worldwide, and D. pseudoobscura and D. persimilis, which are native to the American West. Students will test which odors are important to stimulate egg laying between the varying species to begin to identify which pathways within the olfactory circuit are under higher selection.

DT Diagnostic Technologies, ARUP
Diagnostic Technologies, ARUP

Stream Leaders: TBD

The ARUP research stream will provide novice students with introductions to fundamental scientific principles in the context of clinically relevant diagnostic technologies. Students will be introduced to diagnostic assays, the dynamics of clinical testing, the process of developing and comparing new diagnostic technologies, and receive introductions to the challenges of interpreting data resulting from testing assays.  The ARUP research stream will provide students the unique opportunity of shared mentorship by both ARUP and SRI-associated research staff and faculty.

CB Cancer Biology
Cancer Biology

Stream Leaders: Gennie Parkman and Dr. Sheri Holmen

Melanoma is the most deadly form of skin cancer resulting from the abnormal growth of melanocytes, which are the pigment-producing cells of the skin. Despite novel therapies that have greatly advanced the landscape of melanoma treatments, once distant metastases are evident, patient prognosis is still quite dismal. Interestingly, Utah has the highest rate of melanoma per capita, thus making it an especially relevant cancer to study here. Utah’s melanoma rate has more than doubled in the past 17 years. Furthermore, according to Cancer Stats and Figures 2020, melanoma is the 5th most common cancer for males and the 6th most common cancer for females. To develop new treatments for melanoma, we must first understand more about the genetics of this heterogeneous disease.

Multiple screening efforts have led to the discovery of new genes that may be responsible for the initiation or progression of melanoma. However, these genes need to be functionally tested before we are able to truly understand their impact on this disease. Our research will employ molecular cloning methods to study these novel genes and their impact on cellular signaling pathways. Over the course of a year, undergraduates will learn to design and synthesize a target gene, construct an expression vector, transfect cells with the transgene, and characterize it at the mRNA and protein expression levels by RT-PCR and western blotting. These will then be tested functionally using various in vitro assays to gain an understanding of the gene’s effect on melanoma cell proliferation, invasion, and migration. By achieving a better understanding of the role of target genes and their contribution to melanoma, we will be able to identify therapeutic targets that may advance the outcome of melanoma therapies.

PM Pollen Metagenomics
Pollen Metagenomics

Stream Leader: Dr. Joshua Steffen

Utah is home to an astonishing diversity of native bee species.  Recent estimates suggest that over 900 bee species call Utah home including more than 100 at Red Butte Garden alone.  Compared with honey bees, relatively little is known about the vast majority of these native bee species.  To support native bees, and the plant species they pollinate, we need to gain a better understanding of their basic biology.

Most research describing the foraging behavior of bee species uses approaches that are quite labor-intensive or require specialized expertise.  We are developing and testing molecular approaches that allow us to more efficiently categorize the pollen, microbes, and fungi collected and distributed by pollinators.  Our research group will be employing a molecular approach called DNA metabarcoding to assay foraging behavior.  DNA metabarcoding has the potential to reveal all the species in an environmental sample based upon the DNA sequences that are present in that sample.  Over the course of the next year, undergraduates working on this project will test molecular protocols, collect native pollinators in the field, and use bioinformatic tools to provide accurate descriptions of the foraging behavior of native pollinators.  By gaining a nuanced understanding of foraging behavior we will be able to better inform practices used to support the health and diversity of plants and pollinators in native ecosystems.

UM Underexplored Molecular Architectures
Underexplored Molecular Architectures

Stream Leader: Dr. Ryan Stolley

Our lab focuses on developing new organic chemical reactions that have heretofore been ignored or alluded synthesis. In our lab you will get training on working in a synthetic chemistry laboratory, working with general and advanced analysis instruments, and building the knowledge base of fundamental organic Chemistry.

EC Electrosynthetic Chemistry
Electrosynthetic Chemistry

Stream Leaders: Dr. Shelley Minteer and Dr. Henry White

Chemists and engineers strive to develop safe, efficient, and environmentally sustainable chemical synthesis for the production of high-value molecules, such as those used in medical applications. Advances by electrochemists have demonstrated remarkable new means for improving product selectivity under mild reaction conditions. Unexplored realms of chemical synthesis are now attainable using electrons at the primary reactant.

Supported by the National Science Foundation Center for Chemical Innovation (Links to an external site.), chemists at the University of Utah and across the country are embarking on a collaborative project to employ the extensive knowledge of electrochemists, materials scientists, and physical chemists in using electrons to make new molecules.  The overarching goal is to deploy this exciting new knowledge to advance chemical synthesis.

Undergraduates participating in this SRI project will demonstrate how using electrons as reactants can make pharmaceutical synthesis greener, safer, and environmentally friendly. Students will work towards learning advanced electrochemical methods for carrying out chemical transformations.  Working as a team, they will participate in designing a research plan for developing a general electrochemical route for introducing chemical functionality into molecules, and then demonstrate the general application of their method in the chemical syntheses of a series of molecules.

The project will provide students with a working knowledge of many aspects of organic preparatory chemistry, the physical chemistry of electron-transfer reactions, catalysis, materials chemistry, and quantitative analytical measurements, providing a foundation for future advanced research in all areas of chemistry.  Biweekly meetings of the entire team with the project leaders (Profs. Minteer and White) will focus on discussion of individual student results and the overall progress of the team.

CM Crystallography and Molecular Structure
Crystallography and Molecular Structure

Stream Leader: Dr. Ryan Vanderlinden

The crystallographic X-ray lab collaborates with labs across campus to determine the three-dimensional molecular structure of their novel molecules. The method we use for molecular structure determination is called X-ray crystallography. When an intense x-ray beam is passed through a singular crystal a diffraction pattern can be collected that contains information about the relative position of the atoms that make up the crystal from which a structure can be derived. The information gathered from the structure determination is used for compound identification or to understand the structure-function relationship. An undergraduate research student that joins the Crystallographic X-ray Lab can expect to learn the fundamentals of x-ray crystallography: grow crystals, collect x-ray diffraction data, process data, solve structures and build models.

MB Making and Breaking Bonds
Making and Breaking Bonds

Stream Leader: Dr. Peter Armentrout

My group is focused on measuring thermodynamic information although we obtain kinetic and often dynamic information about chemical reactions as well. Using an instrument called a guided ion beam tandem mass spectrometer (GIBMS), We examine how reactions of cations and molecules change as a function of the available kinetic (sometimes electronic) energy. When the reaction is endothermic (requiring extra energy), we can measure a threshold for the process, which directly provides the thermodynamic information of interest. We have applied this technique to a range of systems, simple atom + diatom reactions (most recently of lanthanide and actinide elements), hydration of metal ions, up to fragmentation of small biomolecules.

SB Sense of Belonging in STEM Classes
Sense of Belonging in STEM Classes

Stream Leader: Dr. Gina Frey

Students in introductory STEM courses often have concerns about whether they will be academically successful in large university courses, but many have an additional concern that maybe “people like me don’t belong in this course.” This concern is called belonging uncertainty and is related to the insecurity someone feels because of their identities.

In our group, we are studying the effect that course-level student belonging has on student performance and retention in the course. We have found at two different institutions, course-level belonging affects student performance in large general chemistry courses. We are also finding a similar effect in introductory physics. To better understand these effects and what we as instructors can do to create a more inclusive classroom, our group is interested in understanding the mechanism of how social belonging affects course performance and retention.

S Spintronics

Stream Leader Dr. Christoph Boehme

The research of the Department of Physics & Astronomy's spin electronics group is focused on the study of spin-selection rules on electronic transitions in condensed matter. Spin-selection rules are quantum mechanical processes that allow the spin of electrons to govern the probability of electronic transitions such as spatial changes, i.e. electric current, or energetic changes, i.e. optical emissions. The electron spin is what gives an electron its magnetic moment. Thus, our work explores the connection between magnetic and electric properties of materials and the this could lead to new electronic (actually spintronic) devices applications such as spin-based quantum sensors and quantum memory.

MM Mathematical Modeling and Pandemics
Mathematical Modeling and Pandemics

Stream Leader: Dr. Fred Adler

In addition to disrupting about every aspect of normal life, the COVID-19 epidemic has brought unprecedented attention to the importance of mathematical modeling and data analysis. The tools needed to understand and predict this epidemic run the gamut from differential equations and large simulations, with methods coming from statistics and applied mathematics. Data are noisy and complicated, and raise many questions about the challenges of counting cases, tracking their sources, understanding viral spread, and quantifying stresses on the health care system and the economy.

We will access the vast quantity of available data, and use them to study the spread and genetics of this virus. Recent studies have shown that the spike protein, that lives on the outside of the virus and is critical for it to enter cells, has mutated in ways that might affect its ability to infect people.

Our SRI team will take an interdisciplinary approach to this aspect of the pandemic. Students will learn the skills needed to download and visualize genetic data using R and python, link these data with fundamental mathematical models of epidemiology, evolution, and the physics of viral entry. Working in teams, we'll investigate hypotheses about the causes consequences of viral evolution, and learn to effectively communicate and display these results to audiences ranging from scientists and decision-makers to the general public.

ML Machine Learning Using Neural Networks
Machine Learning Using Neural Networks

Stream Leader: Braxton Osting

The abundance of data created in science, engineering, business, and everyday human activity is simply staggering. This data is often complex and high-dimensional, taking the form of video or time-dependent sensor data. Machine learning methods allow us to understand such data, automatically identifying patterns and making important data-driven decisions without human intervention. Machine learning methods have found a wide variety of applications, including providing new scientific insights and the development of self-driving cars.

One machine learning method in particular, neural networks, has emerged as the preeminent tool for the supervised learning tasks of regression and classification. Loosely modeled after the human brain and the basis for deep learning, Neural Networks use composition to develop complex representations of data. In recent years, researchers using Neural Networks have made tremendous breakthroughs in topics as varied as image processing, natural language processing, and playing board games such as Go.

VS Viral Suppressors of RNA Silencing
Viral Suppressors of RNA Silencing

Stream Leader: Dr. Sarah Hansen

RNA sensing and RNA interference (RNAi) are essential mechanisms for antiviral defense in many organisms. RIG-I and other RIG-I-like helicases are a family of enzymes that can detect (RIG-I, MDA-5) or cleave (Dicer) “non-self” double-stranded RNA (dsRNA) such as dsRNA from a viral genome. Additionally, these helicases initiate a larger immune response from the cell. To combat these types of antiviral defenses, some viruses evolved to encode viral suppressors of RNA silencing (VSRs).  The mechanism by which VSRs target different components of the RNA silencing pathways is poorly understood. The goal of this project is to study a known VSR protein from Nodamura virus. Students will work with this protein and potential targets (RIG-I, MDA-5, LGP2, and Dicer) in vitro to determine how this VSR inhibits the RNA sensing pathway in human cells.

This project will allow students to work in a biochemistry laboratory where they will get to learn:

1) to clone, purify, and do experiments with proteins and RNA in vitro

2) to work with human and bacterial cells

3) to perform in vitro experiments, and collect and analyze results from those experiments

4) skills related to scientific writing and communication

Additionally, students will be immersed in the Bass Lab, including group meetings and sub-group meetings with Prof. Bass, so they can learn about graduate-level research conducted in the field of protein-RNA biochemistry.