Stream Leader: Fred Adler

Like people, the cells in our bodies change their behavior in response to their environments, an ability called plasticity. Plasticity is useful when cells need to respond to some challenge, like an injury, but can turn deadly in cancer cells that can use it escape the body's natural defenses and treatment. In this unique project, two streams will work together to study cancer cell plasticity. In the first, students will join the Judson-Torres lab and learn the cutting-edge technologies in genomics and live cell imaging needed to study plasticity in real time. In the second, students will join the Adler group to analyze, visualize and mathematically model the data, and help design the next round of experiments. The two streams will flow together as a broad river that carries a new understanding cancer cell plasticity and delivers ideas for novel treatment strategies.

Find more about Dr. Adler and their research at https://faculty.utah.edu/FREDERICK_R_ADLER  

Stream Leader: Joe Bednarek

Cryptococcus neoformans is an opportunistic fungal pathogen with global distribution. Immunocompromised populations are most at risk. Infections begin in the lungs where fungal spores are inhaled and either lie dormant or proliferate if met with an insufficient immune response. Pulmonary proliferation is followed by escape to the bloodstream and dissemination to the brain. C. neoformans in the bloodstream are poorly understood. We do not know how many fungi are there or how they disseminate. Do they travel as free fungi or do they move within ‘Trojan horse’ immune cells? We intend to answer these questions with techniques including microscopy, flow cytometry, and enzyme immunoassays.

Stream Leader: Peter Armentrout

This 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.

Recent experimental studies performed in this group include:

1. Reactions of actinides (both uranium and thorium
2. Reactions of lanthanides (of atmospheric interest to the US Air Force
3. Measurement of hydration energies of transition metal dications (solvation energies)
4. Fragmentation energies of peptides, useful information for sequencing proteins in analytical mass spectrometry

Find more about Dr. Armentrout and their research at https://chem.utah.edu/directory/armentrout/

Stream Leaders: Jessica Brown

We are exposed to fungi every time we breathe, yet the vast majority of these interactions are not harmful. Why do a small subset of fungi cause severe disease in humans? These infections are not passed person-to-person, so whatever provides the selective pressure for some fungi to cause disease must come from the fungal environmental niche. In this project, we will explore the activation of diverse stress pathways in the budding yeast Saccharomyces cerevisiae. We will test whether certain conditions can promiscuously activate multiple pathways and whether promiscuous activation facilitates the ability of fungi to infect other organisms. We will also test how stress pathways respond to extreme weather and whether heat waves, drought, etc., and whether adaptations to those events also increase fungal ability to colonize or infect animals.

Stream Leader: David Blair

Find more about Dr. Blair and their research at https://faculty.utah.edu/DAVID_F_BLAIR

Stream Leader: Christoph Bohme

Find more about Dr. Bohme and their research at https://web.physics.utah.edu/~boehmelab/

Stream Leaders: Heather Briggs, 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. 

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. 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.

Over the course of the next year undergraduates working with 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 native
pollinators. Students will have the opportunity to learn basic molecular, microbiology, and field ecology research techniques.

Find more about Dr. Briggs and Dr. Steffen at https://science.utah.edu/sri/sri-team

Stream Leader: Richard Clark

This research stream will introduce students to genetics and genomics in the context of understanding diapause in the two-spotted spider mite (scientific name: Tetranychus urticae). This mite species is a major agricultural pest, and each fall it enters diapause, a physiological state characterized by reproductive cessation in females and the accumulation of red-orange carotenoid pigments and other metabolites and proteins that allow mites to withstand the freezing temperatures and other stresses of the winter months. Students will isolate and characterize mutations that disrupt carotenoid biosynthesis and will use genomic (DNA) and/or transcriptomic (RNA) sequencing data to identify potential diapause mediators. An outcome of the research will be a better understanding of how diverse insects and mites overwinter in regions with temperate climates, and the skills that will be learned will be broadly applicable to diverse areas of modern biology of relevance to agriculture and even medicine. More generally, students will learn about plant-herbivore interactions and agriculture, and about how climate change will impact biological systems, biodiversity, and human welfare.

Stream Leader: Will Mace

The Noble Gas stream uses laboratory techniques to date groundwater and determine the recharge conditions of water as it infitrates the water table. This stream will give students access to understanding noble gas geochemistry, laboratory skills, and field work opportunities around the Wasatch Front.

Stream Leader: Allesandro Venosa

This stream will include some basics of mouse genotyping (to know if they are mutants for the gene of interest), analyzing and tabulating flow cytometry data (with appropriate training), and then performing some flow cytometry staining. Our goal is to generate mutants with impaired immune function and determine how these changes in the genetic makeup impact the inflammation resulting from ozone exposure.

Stream Leader: Kristin Johnson, Jamie Gagnon

The Gagnon lab has recently demonstrated that the small molecule gadusol acts as a sunscreen to protect zebrafish from Ultraviolet Radiation (UVR) induced DNA damage. Gadusol and the genes involved in its biosynthesis are conserved across many species, including brine shrimp. In this stream students will perform fieldwork to collect brine shrimp cysts from different regions of the Great Salt Lake. They will then raise these brine shrimp under laboratory conditions and quantify gadusol at different developmental stages. Undergrads will perform UVR treatments on brine shrimp at different developmental stages to determine if there is a correlation between UVR resistance and gadusol levels, suggesting that gadusol acts as a sunscreen in brine shrimp. In addition to developing field work and molecular and developmental biology techniques, students will also learn to read peer reviewed literature critically as well as how to design experiments with proper controls to answer research questions.

Stream Leaders: 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 that course. We have found at two different institutions, course-level belonging affects student performance in large general chemistry and introductory physics courses. Expanding upon these studies, we are interested in understanding the mechanism of how social belonging affects course performance and retention. One step in determining the mechanism is to explore the characteristics of the course that students use when describing their sense of belonging and belonging uncertainty. Our goal is to help instructors create course environments that support and encourage all students to reach their potential and continue to pursue careers in STEM or healthcare.

Undergraduates will be studying open-ended responses from the belonging surveys to determine characteristics students use to describe their course-level belonging in STEM courses. They will be developing themes or ideas from the student quotes. Qualitative research is collaborative, hence the student, while having their own project component, will be part of a qualitative-research team. You will learn about social psychology, inclusivity and equity, and qualitative-research methods.

Find more about Dr. Frey and their research at https://chem.utah.edu/directory/frey/research-group/

Stream Leader: Austin Green

Wild animals are under continuous pressure to adapt to new environments as more land surrounding protected areas is converted for human use and populations continue to grow. This highlights the importance of research that promotes human-wildlife coexistence on functional landscapes that combine both human use and conservation. It is critical that we understand how mammals occupy and navigate these functional landscapes, as they commonly function as ‘umbrella’
or ‘flagship’ species because their natural rarity and large area requirements tend to place them under threat of extinction, and their use of multiple habitats makes it possible to protect other species. One way in which mammals may occupy urbanized landscapes and avoid the human ‘super-predator’ is by altering their behavior. Specifically, mammals may adapt how they use both space and time; adjust how they interact with other species; and change where and when they feed, sleep, and reproduce. In this stream, we will investigate how human influence alters mammalian behavior and space use in an effort to inform on-the-ground conservation initiatives.

Stream Leader: Gannet Hallar

This research group makes measurements of gases and particles in the atmosphere. We then look at the chemical & physical make up of those particles and gases, which helps us understand the source location and impacts. We make these measurements at the University of Utah, where we are continuously understanding our urban environment and a mountain-top Lab in Steamboat Springs, Colorado  & in the town of Alta, which help us understand the remote environment.  

Over the course of the next year undergraduates working with on this project will gain hands-on experience with aerosol instrumentation through work with a variety of instruments in the aerosol monitoring lab on the 8th floor of the William Browning Building. Students who are interested will also have opportunities to gain field work experience through set-up and maintenance of aerosol monitoring equipment, often deployed along mountain regions. Specifically, students will study wildfire smoke, dust storms, and calibrate aerosol instrumentation.  

Find more about Dr. Hallar and their research at https://hart.chpc.utah.edu 

Stream Leader: Talia Karasov, Madelyn Allen

The Karasov Lab studies the coevolution of plants and their pathogens. Plants produce a variety of compounds to defend against pathogens and herbivores. This project specifically focuses on how bacterial pathogens have evolved to evade plant chemical defenses. The questions we wish to address include: 1. What plant compounds inhibit pathogen growth? 2. Is sensitivity to these compounds dependent on pathogen strain? 3. How have these compounds influenced pathogen evolution?

These questions will be explored through microbial experimentation and genetic analysis. It is a great project for students who wish to learn fundamental microbiology lab techniques and begin thinking about the genetics behind evolution. Undergraduate students working on this project will grow various bacterial pathogens with plant defensive compounds giving them the opportunity to learn microbiology lab techniques and statistical analysis. Future directions of this project include analyzing genetic information to better understand what genes are responsible for a given pathogen’s resistance or susceptibility to a compound.

Stream Leader: Sheri Holmen

Melanoma is the most deadly form of skin cancer resulting from abnormal growth of melanocytes, the pigment-producing cells of the skin. 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 semester, undergraduates will use SnapGene software to simulate molecular cloning. Then, they will learn to design and synthesize a target gene, construct an expression vector, transfect cells, and characterize gene expression at the protein level by western blotting. These genes will then be tested functionally using various in-vitroassays 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.

Find more about Dr. Holmen and their research at https://uofuhealth.utah.edu/huntsman/holmenlab

Stream Leaders: Marcus Mifflin, Andrew Roberts

The Roberts laboratory is motivated by the structural complexity achieved by nature to produce biologically active peptides. Our research aims to develop approaches to reproduce this complexity by constructing these structures using chemical and peptide synthesis tools. For example, lasso peptides are therapeutically relevant natural products of growing interest due to their unique three-dimensional shape that results when a circular ring becomes threaded with a linear segment that becomes locked in place by bulky groups that prevent its unthreading. To recreate these folded molecules, we are working to develop a nature-inspired approach. We first build amino acid reagents by chemical synthesis to enable reversible circularization. These reagents can then be incorporated into peptides grown on solid beads, one amino acid residue at a time, to control the order of building blocks that comprise the peptide sequence. Once built, these peptides are taken off the solid beads so they can be purified, reacted, and evaluated for their ability to fold into a lasso peptide. To guide our folding strategy, we are collaborating with the Swanson laboratory to understand and design improved lasso peptides folds using computational tools to refine the targets for evaluation. Skills developed: Fundamental laboratory skills, solid-phase peptide synthesis (SPPS), purification and analysis by high-performance liquid chromatography (HPLC), and structural analysis by mass spectrometry (MS). Scientific professional development: Critical thinking, communicating results, time management, and teamwork.

Stream Leader: Christopher Bibbs

Salt Lake City Mosquito Abatement District (SLCMAD) serves a 180 square mile region of Salt Lake City proper and the western rural expanse that approaches the Great Salt Lake. We use a complex blend of custom engineering, aviation technology, droplet physics, physiology, molecular biology, ecology, and integrated environmental sciences to serve our area. Research in mosquito control is whimsical and complex, spanning topics in community ecology, population genetics, pathology, epidemiology, and fundamental principles like mosquito behavior. As a result, we are a learning agency that tries to develop modern, environmentally conscientious, and effective means of protecting public health. Our research is balanced with routine tasks, such as field population monitoring, molecular assay of virus, and mosquito rearing for study. We use our regular program elements to gain a nuanced understanding of mosquito population dynamics and habitat exploitation and in turn fuel an everchanging portfolio of research intended to both safeguard public health and inform practices used across the nation.

Over the course of the next year undergraduates working with SLCMAD will be involved in molecular protocols, collect mosquitoes in the field, and use mosquitoes in a variety of tasks, such as pesticide sensitivity tests, virus detection,
mosquito identification, and research bioassays. Undergraduates will have the opportunity to learn basic molecular, toxicology, and field ecology techniques.

Find more about SLCMAD and their research at http://www.slcmad.org/

Stream Leader: J David Symons

Cardiovascular disease (CVD) is the leading cause of death in the United States. Aging and obesity are primary risk factors for CVD. There is an urgent need to provide meaningful research experiences to undergraduates that will encourage their participation in rigorous post-graduate training to understand the pathophysiology and treatment of CVD. Here we leverage our strengths in cardiovascular and metabolic research at the University of Utah (UU) in general, and our particular interest in the lipotoxic sphingolipid ceramide in particular. Blood and tissue ceramides are heightened by aging and/or obesity, and associate positively with the prevalence and severity of CVD. We have unparalleled tools and core facilities to discern the mechanisms whereby this lipotoxic metabolite contributes to acute ischemic stroke (Symons), chronic kidney disease (Ramkumar), and dysfunction in the heart (Boudina), endothelial cell (Chaix), and brain (Holland). In addition to completing hypothesis-driven research, each mentee will participate in a robust educational series, social activities, and present their findings locally, regionally, and / or nationally. Our mentoring team will provide clinically-relevant research experiences and encourage qualified students to consider research careers in the cardiovascular sciences.

Stream Leader: Melodie Weller

Research in the Weller Lab focuses on the intricate relationship between pathogens and the onset of autoimmune diseases, particularly Sjogren's Disease (SjD). We investigate potential pathogenic reservoirs that might contribute to the development or progression of chronic autoimmune conditions. Undergraduate students in this stream will be trained in a range of molecular biology techniques. These include RNA/DNA isolation to study the genetic material of pathogens and in vitro models, protein characterization to understand their functional roles, and in vivo and in vitro models to monitor pathogen-host interactions. Additionally, students will gain experience in immunohistochemistry, enabling detailed visualization of cellular and tissue-level responses. The research extends to informatics, where students will analyze and interpret complex datasets. Computational modeling and epidemiological analyses of global infectious disease data are integral to our approach, helping us identify and understand potential pathogenic reservoirs associated with autoimmune diseases. The lab operates with a strong emphasis on collaboration and a data-driven methodology. Together, we work to unravel the intricate associations between pathogens and the immune system, aiming to shed light on the etiology of autoimmune diseases and inform potential therapeutic strategies.

Stream Leader:  Henry White

Mission: To make synthetic organic electrochemistry mainstream through the invention of enabling, green, safe and economic new reactions, the demystification of fundamental electrochemical reactivity, vibrant partnerships with industry,
education of a diverse set of scientists and engineers, and by engaging in community-wide education and outreach. 

Our stream will work on fundamental studies of electrocatalytic systems for synthetic organic chemistry reactions where we will utilize electricity instead of dangerous and expensive reagents for important chemical reactions.

• Undergraduate researchers perform hands-on research in electroorganicsynthesis.
• Participation in the entirescientific process (literature searches, experiment design, laboratory work, analysis, and
  dissemination of results)
• Students rated the top benefits of this SRI stream as: learning laboratory skills, critical thinking, teamwork, and
  communication skills, which reflects the unique interdisciplinary and cooperative nature of the CSOE program.

Find more about Dr. White and their research at https://chem. https://chem.utah.edu/directory/white/research-group

Stream Leader: Shrinivasan "Cheenu" Raghuraman, Baldomero "Toto" Olivera 

Ion channels are proteins that are found in the cell membrane and allow the movement of ions across the membrane. They shape the physiological properties of different cell types. For example, they control the release of cytokines by immune cells, control the bioelectrical signals in neurons and cardiomyocytes which are important for cellular communication and proper functioning of the brain and the heart. All ion channels are made of multimeric subunits that assemble together to form a pore.  One of the largest and most diverse family of ion channels is the voltage-gated potassium-channel. Although there are limited number of subunits (encoded by ~70 genes), each subunit can combine in different combinations, resulting in an enormous array of homomeric and heteromeric subytpes. An example of different K-channel subtypes formed by two subunits is shown in the figure below. The function of different K-channel heteromers have remained elusive due to the lack of selective pharmacology to discriminate between the heteromers. Our lab discovered and developed conotoxins as pharmacological tools to study the properties of different K-channels. Conotoxins are used by cone snails for predatory purposes- they paralyze their prey by targeting various ion channels and receptors. In our lab, we have extracted and purified conopeptides from the venom of different cone snail species. In this project, we will use conopeptides and other marine bioactive compounds to study the properties and functions of different voltage gated K-channels. We will use a technique called two-electrode voltage clamp to study the properties of K-channels. Students will gain an understanding of different concepts from molecular biology, bioelectricity and biophysics.

(collaborative project With Wayne Potts lab) The global COVID19 pandemic has uncovered the need to understand and address the roles of immune cells in combating pathogenic attacks. While initial inflammation is essential to control invading pathogens, prolonged inflammation results in “cytokine storms” with unintended consequences and pulmonary complications. Current anti-inflammatory drugs are non-selective and are often contraindicated in patients with comorbities, highlighting the need to develop drug leads that are selective and superior to current anti-inflammatory drugs. We recently developed an in vitro drug screening platform to identify marine natural products with immunomodulatory properties and identified a library of conotoxins that modulate cytokine release. In the next phase of this project, our goal is to test these drug leads in animal models of respiratory distress. Using mice infected with influenza virus (H3N2 strain) as a model system, we will test the library of conotoxins in modulating cytokine levels. Students will be exposed to animal handling techniques, dissection skills, immunostaining and ELISA assays. In addition, students  will gain experience in testing drug leads using in vitro and in vivo assays that are essential for conducting pre-clinical trials.  

Find more about Dr. Raghuraman / Dr. Olivera and their research at https://faculty.utah.edu/SHRINIVASAN_RAGHURAMAN and https://faculty.utah.edu/BALDOMERO_M_OLIVERA

Stream Leader: Eric Schmidt

Stream Leader:

Stream Leader: Rodolfo Probst

In this stream, we will test molecular protocols for barcoding species involved in symbioses (I am an expert on mutualisms between ants & plants, groups that we have many new species to discover and several unanswered questions about their interaction) but eventually apply our protocols to any groups of interest. While participating in this stream, you will learn molecular techniques (different DNA extractions, PCR, cutting-edge genetics, bioinformatics), evolutionary thinking, and biodiversity monitoring – and on top of that, learn about symbioses! These techniques and analyses will help us recognize and catalog new species, know how they are genetically related and how their communities change over time. Plus, we will be able to understand how symbiotic organisms interact across areas (for example, Central America) and eventually conduct real-time barcoding in the field.

Find more about Dr. Probst and their research at https://science.utah.edu/sri/sri-team

Stream Leader: Robyn Brooks

In this research stream, we will learn about the tools and theory of Topological Data Analysis (TDA). Topological Data Analysis is an area of applied mathematics which uses the tools of topology and geometry to study the shape and structure of data. A fundamental hypothesis of TDA is that data come as samples from an underlying space with shape properties, and understanding that shape is important to understanding the studied phenomena. Applications of TDA include a diverse range of fields, such as cancer biology, neuroscience, image analysis, dimensionality reduction for high dimensional data, signal analysis, and feature selection, to name a few. In this stream, our goal is to do novel research in both the theory and applications of Topological Data analysis. Students will learn about Topology and Data analysis, and develop math literacy skills, such as reading, writing, and discussing quantitative topics. There will be opportunities to do research in the theory of TDA, such as developing mathematical theorems and examples in the area of computational topology, which provides the mathematical tools for the application of TDA. There will also be opportunities to create and implement algorithms in Python for the computation of mathematical invariants and statistical summaries given by TDA. Finally, there will be opportunities for collaboration with other areas of science, to pose and investigate quantitative questions in different disciplines, using TDA statistical software.

Stream Leader: Tim Tribone

SET is a fast-paced and addictive card game in which players race to find a matching collection of cards with specific properties. Lurking underneath the colors and shapes displayed on each card is surprising and sophisticated mathematics! The main goal of this stream will be to study the mathematical structure underlying the game of SET in order to answer some challenging questions about the nature of the game and its many variations. Along the way we will learn the high-powered abstract mathematics needed to study these questions. Specialized fields such as linear and abstract algebra, combinatorics, probability, and geometry will all play a role. After studying the base game, we will dive into generalizations of SET based on group theory and projective geometry. There will be unique opportunities for students to form their own research projects about SET and related games. Students who are interested in coding will be encouraged to write code to help formulate and answer interesting questions about SET.

Stream Leader: Mikhael Semaan

From the intricate highway system of human vasculature, to the large-scale geological formation of mountains, to the individual motions of atoms and molecules, and so much in between... Can we detect and describe emergent pattern and structure? How do real-world systems process information? How do they absorb and dissipate energy to function? What do they have in common? All “complex systems!”

In this stream, you will develop and apply tools to understand a “candidate system” most interesting to you, tailored to your field. You will learn and build the rest of the skills needed as part of the stream.

Topic Outline

• Nonlinear dynamics and chaos: How does simple →complex?
• Simulating and visualizing: Hidden order in chaos!
• Symbolic dynamics and measurement: Producing noisy data
• Modeling stochastic processes: From data →model
• Information theory and energy: How does the system function?
• Project outcome: apply tools to student-chosen example system (molecular motors, neuron channels, information engines, disease dynamics...)

Skills Developed Include:

• Programming literacy
• Scientific computing (Python)
• Model simulation and data genesis
• Data science / visualization and statistics
• Nonlinear dynamics and information theory

Find more about Dr. Semaan and their research at https://science.utah.edu/sri/sri-team

Stream Leader: Ben Myers

In the Myers Lab, we study how animal cells communicate with each other and how mistakes in this process drive cancer and other diseases. We recently discovered a surprising new type of intracellular signaling mechanism, and we’re excited to find out exactly how it works and what it means for the future of biology and cancer treatment. Over the course of the stream, students will help characterize a new protein-protein interaction involved in this intracellular signaling mechanism, and investigate whether similar signaling mechanisms are at play in other areas of human health and disease. The techniques employed will include: 1) bioluminescence resonance energy transfer, a powerful technique for precisely monitoring key protein-protein interactions within living cells, and 2) site-directed mutagenesis, which will gives student the ability to alter individual amino acids within a protein of interest, and then study their biological relevance. Undergraduates will learn how to perform rigorous experiments as well as how to think critically and creatively. Students will also receive one-on-one mentoring from Dr. Myers, in a lab that is recognized for the high caliber of undergraduate research and the ability of undergraduates to lead key projects and make cutting-edge discoveries.

Stream Leader: Stavros Drakos, Joe Visker

Heart failure (HF) is a condition that results from long-term, chronic damage to the heart, which eventually will lead to complete failure and increased mortality. Over the years, medical professionals have been working to better understand HF and how to promote recovery. One of these strategies is to implant a pump, called a left ventricular assist device (LVAD). The pump is inserted into the heart to help it circulate blood. The National Institutes of Health defines myocardial recovery as “the sustained normalization of structural, molecular, and hemodynamic changes sufficient to allow the explant of the LVAD (Left Ventricular Assist Device).” Put simply, myocardial recovery refers to your heart getting better after a heart attack or other damage to the heart that may occur.

Stream Leader: Ryan Stolley

This SRI stream will uncover new chemical reactions to build never-before seen arrangements of atoms and use a variety of chemical, analytical and computational tools to uncover how these new groups of atoms behave; and to expand on this capability to build ever more complex molecules. In our lab students will learn the principles of organic chemistry and chemical experimentation and the instrumental tools for us to ascertain structure and function of organic molecules.

Skills Developed Include:

• Rules of the physical world
• Basics of reaction chemistry
• Broadly applicable analysis methods
• Navigating a busy lab environment
• Project management

Find more about Dr. Stolley and their research at https://science.utah.edu/sri/sri-team

Stream Leader: Michael Werner

This Research Stream will sample nematodes from pedestrian locations on campus to exotic locations across Utah, including deserts, mountains, and the Great Salt Lake. After field collections, we will process soil samples in the laboratory, and perform molecular genotyping to identify species abundance and diversity. Then, we will use statistical and computational methods to analyze their relatedness. By studying the biogeography of nematodes in Utah, we will better understand the diversity, evolutionary history, and limits of this remarkable taxa.

Undergraduates will have the opportunity to gain experience in field work, and learn methods in molecular biology and phylogenetics. There may even be the opportunity to describe and name new species. We anticipate that student results will eventually be published in a scientific journal.

Find more about Dr. Werner and their research at https://www.werner-lab.org/

Stream Leader: Maíra Alves Constantino

This stream will investigate how mechanics of tissue can influence the development of non-malignant nevus into melanoma, the deadliest type of skin cancer. Cells can sense the physical cues of their microenvironment by means of intramembrane proteins called integrins, leading to activation of downstream signaling pathways that can alter cell proliferation, migration and differentiation. Mechanical stimuli can also affect the secretion of proteins that alter the physical properties of the microenvironment, leading to a recursive mechanobiological feedback loop. Students will analyze the mechanics of the extracellular matrix of murine melanoma at different stages of disease using microrheology, a technique that measures the mechanical properties of materials by following the trajectory of micron-sized beads.

Stream Leader: Chan Yul Yoo

Undergraduates joining our SRI research stream will grow various plant species under varying light conditions using LED light (red, far-red, blue, white light, and dark) and under various stressed conditions (drought, salinity, etc.) to understand the mechanisms by which chloroplast biogenesis is affected at the molecular and cellular levels.

Participants will learn a variety of basic molecular biology and cell biology techniques such as DNA/RNA/protein extraction, PCR, quantitative RT-PCR, DNA/protein gel electrophoresis, western blotting, and fluorescence microscopy. In addition, undergraduates will learn how to access various bioinformatics resources to search and analyze genes of interest from various organism.

Find more about Dr. Chan Yul Yoo and their research at https://www.biology.utah.edu/faculty/chan-yul-yoo/

Stream Leader: Heejin Yoo

This research team will try to elucidate the effect of individual amino acid for plant immunity especially during PCD. Additionally, we will try to do amino acid profiling using HPLC after exogenous application of specific amino acid to analyze amino acid dynamics. Combined outcomes will enhance scientific understanding of the role of amino acids for plant immunity and provide foundational knowledge to improve disease resistance of economically important crop species.

Undergraduates who register for this project will first learn basic mechanisms for plant immunity; Then, students will test the effect of exogenous application of individual amino acid for programmed cell death and elucidate underlying mechanisms using basic molecular biology technique and metabolic analysis.

Find more about Dr. Heejin Yoo and their research at https://www.hyoo-pbio.com/ or https://www.biology.utah.edu/faculty/heejin-yoo/

Stream Leader: Carsten Rott, Minjin Jeoeng

We have arrived at a special moment in time, where we can now observe the Universe in fundamentally new ways using high energy neutrinos, gamma-rays, cosmic-rays, and gravitational waves. By viewing the Universe through these cosmic messengers and in their combination an era of discoveries awaits us. The “Multi-messenger Science with IceCube” stream engages students in active research with the objective of improving the multi-messenger science capabilities of the IceCube Neutrino Observatory in Antarctica. Participants will develop an understanding about how IceCube detects neutrinos and how to correlate signs with astrophysical sources. They will learn how to program and analyze data in Python, and work on a project for characterizing the optical properties of the detector medium. Participants would gain hands-on experience with the Linux operating system, code repositories, and supercomputers widely in this research.

Stream Leaders: Luiza Aparecido, Bianca Zorger, Rebecca Senft

Our lab is currently focused on understanding how plant processes are affected by heat and drought. More specifically, we are interested in 1) investigating the competitive physiological advantages of an invasive tree species (Russian olive) under these stressors; and in 2) determining plant functional traits that enable the survival of co-occurring plant species across an elevation gradient. For project 1, undergraduate students will assist with field work at three sites across Utah by utilizing common plant physiology equipment (sap flow sensors, photosynthesis systems, etc.) This research is an integral component of the dissertation project of doctoral student Rebecca Senft, who will coordinate the project and supervise students. Additionally, there is a possibility of conducting winter research that would include a greenhouse experiment where plants will be subjected to a simulated heatwave. For project 2, students will learn a variety of experimental techniques to evaluate the physiological responses of plants to drought and heat (e.g. leaf thermotolerance, leaf water potential, leaf water uptake, curves of vulnerability, and leaf gas exchange). We will conduct this study in the Campus Arboretum and Red Butte Garden focusing on a large set of species that includes mono and dioecious species, woody and herbaceous plants, and broadleaf and conifer trees.

Stream Leader: Vikram Deshpande, Eric Montoya

Topological quantum materials are characterized by global quantities such as topological invariants rather than local details, making them extremely robust against typical materials defects and perturbations. Potential applications have been proposed in areas such as electronics, spintronics and quantum computing. However this area is still in its infancy with most ideas still untested and many more in the works. In our program, we work with a toolkit of layered materials to construct atomically-thin (“van der Waals”) heterostructures, create devices using these heterostructures and test theoretical predictions for novel phenomena based on these topological materials such as exotic superconductivity, emergent states of matter composed of fractional particles and many more.

Stream Leader: Rob Judson-Torres

Like people, the cells in our bodies change their behavior in response to their environments, an ability called plasticity. Plasticity is useful when cells need to respond to some challenge, like an injury, but can turn deadly in cancer cells that can use it escape the body's natural defenses and treatment. In this unique project, two streams will work together to study cancer cell plasticity. In the first, students will join the Judson-Torres lab and learn the cutting-edge technologies in genomics and live cell imaging needed to study plasticity in real time. In the second, students will join the Adler group to analyze, visualize and mathematically model the data, and help design the next round of experiments. The two streams will flow together as a broad river that carries a new understanding cancer cell plasticity and delivers ideas for novel treatment strategies.

Stream Leader: Cameron Metcalf, Ashwini Sri Hari

The Metcalf Lab is interested in understanding the impact of environmental pollutants on epilepsy morbidity and mortality. We propose that specific and combined pollutants worsen seizures and increase the rate of Sudden Unexpected Death in Epilepsy. We study metabolic, neuroinflammatory, and other markers to identify biochemical pathways that may contribute to the detrimental effects of pollution on the brain. Sudden Death in Epilepsy is likely due to respiratory failure, and therefore we are interested in understanding the impact of pollutants both on central breathing control (brain regulation) and pulmonary function. We use models of epilepsy, including a model of the rare epilepsy Dravet Syndrome, to understand environmental impacts on epilepsy morbidity and mortality.

Stream Leader: Marysa Lague

Plants to Planets: Exploring the Role of Land in the Global Climate System Stream lead: Dr. Marysa Lague Earth’s climate encompasses complex interactions between the atmosphere, oceans, land, and ice. Climate is critically important for life on land, with temperature, rainfall, and light controlling the distribution of vegetation across the land surface. However, vegetation also modifies the global climate system, by controlling the fluxes of water, energy, and carbon between the land and the atmosphere. Vegetation modifies temperatures by cooling the surface through transpiration (water that passes through leaves during photosynthesis), while the color and number of leaves of a plant directly impact how much sunlight is absorbed by the land surface, which impacts surface temperatures. Moreover, ~30% of anthropogenic emissions of CO2 are taken up and stored by plants on land, acting as a buffer against global warming. Using numerical models of the Earth system, we can answer questions like “how does changing what plants grow where alter climate?” In this stream, students will learn about the physics governing the complex interactions of different components of the Earth system. The climate is a fundamentally interdisciplinary complex system; to study it, we use understanding, tools, and methods from physics, applied mathematics, computer science, Earth science, biology, hydrology, oceanography, and atmospheric sciences.

Topic Outline

• Physics of the climate system

• Physics of plant-atmosphere interactions

• What is an Earth System Model?

Project outcome: run an Earth system model experiment where you change where plants grow to see how this impacts the rest of the climate system

Skills Developed Include: Programming literacy; Scientific computing and data analysis (Python); Navigation and use of high performance computing systems; Data science / visualization

Find more about Dr. Lague and their research at marysalague.com

Stream Leader:

Stream Leader: Jon Wang, Yahampath Marambe

How will climate change and human activity transform western US forests? Increasing wildfires, droughts, insect attack, and land use are threatening these ecosystems, and space technology can be used to track these dynamics at large scales. Join this stream to learn about remote sensing, fire and forest ecology, machine learning, and image analysis - including potential opportunities for field work, drone flights, and coding/programming. We will build a machine learning approach for tracking forest health and disturbance by analyzing imagery from satellites, airplanes, and drones.

Stream Leader: Sarah Hinners

Red Butte Garden is Utah’s Botanical Garden, nestled between campus and the foothills at the mouth of Red Butte Canyon. Botanical gardens perform many roles beyond just creating a beautiful garden for people to enjoy. Research and conservation work at the garden includes maintaining a seed bank of Utah native rare plant seeds, conducting horticultural trials of native and water wise species for planting in our region, supporting ecological management and restoration in our natural areas, and testing the many ways in which plants can contribute to the health and wellbeing of society. Students participating in this stream will have the opportunity to participate in and conduct research across these different areas of activity, from ex situ conservation practices (rare seed collection and seed banking), design and conduct plant trials, and collect ecological field data for restoration and monitoring projects. You’ll develop, implement, and report on your own project under the supervision of our horticultural and conservation staff.

Stream Leader: Kayleigh Mullen

A key priority of Utah’s Hogle Zoo (UHZ) is fostering a meaningful impact on the conservation of Utah wildlife. We achieve this through education, outreach and hands on work throughout the state.

The Conservation Department has several projects currently underway:

• A long term commitment to help restore the Jordan River, through community based activities including tree planting, trail clean ups, invasive species removal and pollinator garden creation.

• Wildlife monitoring through the use of trail cameras along the Jordan Rover and the surrounding watershed.

• Amphibian conservation through statewide surveys, breed and release programming, telemetry research and habitat restoration.

Students will assist in the above research gaining experience in fieldwork, public outreach and volunteer management.

Stream Leader: Clement Chow

Our lab is focused on understanding the role of genetic variation on disease outcomes. We employ quantitative and functional tools, in a variety of model organisms, to study how genetic variation impacts basic cellular traits important to human health. Our work in model organisms will help to model and inform studies of genetic variation in the human population. We hope to identify variation that can lead to more precise, personalized therapies, especially for rare disease.

Stream Leader: Kasey Cole

The use of fossil data to inform contemporary conservation is essential for sustaining biodiversity in the future. This is because as human impacts on ecosystems accelerate, there is a growing emphasis in conservation planning towards maximizing the capacity of ecosystems to respond to anticipated changes in the near future. Doing so, however, requires understanding how ecosystems responded to past changes that occurred over timescales exceeding those of direct human observation. The fossil record provides these data and documents baselines of animal communities that can be used to evaluate the impacts of historic, human-induced climate change and attest to the responses of species to ecosystem changes over geological timescales. In this stream, we study fossil animal remains recovered from Utah’s high-elevation cave deposits to establish what animal communities looked like before human-induced climate change. We then compare these past records with recent zoological survey data to evaluate whether ongoing climate change has contributed to range shifts or local extinctions, as has been predicted for the region’s montane mammals. This work is interdisciplinary and sits at the intersection of Anthropology, Ecology, Geology, and Climate and Environmental Science, and has implications for contemporary ecological restoration, conservation, and wildlife management projects. Students joining this stream will learn skills related to vertebrate osteology, climate modeling, database and museum collections management, and statistical data analysis, and will have the opportunity to develop independent research projects and present their findings to the public and other members of the scientific community.

Please reach out to the stream leader, Dr. Cole (Kasey.cole@utah.edu) to find out more about this research and opportunities for student involvement and collaboration.

Stream Leader: Rajive Ganguli, Raviteja Tatikonda

This research explores harnessing the power of modern artificial intelligence to enhance mining safety outcomes. Specifically, it investigates the use of OpenAI's GPT-3 and other generative language models for analyzing mining accident and fatality reports from the Mine Safety and Health Administration (MSHA) database. By applying natural language processing techniques like classification, summarization, and recommendation generation to mine safety narratives, this work aims to demonstrate the potential of AI to help identify risks, predict incidents, and enable targeted interventions. The overarching goal is leveraging cutting-edge AI innovations to reduce avoidable accidents and fatalities through data-driven insights and proactive safety recommendations tailored to the mining industry. This research represents an important step toward safer mines powered by artificial intelligence. Find more about Dr. Rajive Ganguli https://faculty.utah.edu/u6025759-RAJIVE_GANGULI/research/index.hml and his research group at https://mining.utah.edu/ai.sys/

Stream Leader: Kathleen Ritterbush

Stream Leader: Jay Love

Our research program is highly integrative and aims to characterize guiding principles of the evolution of life. Much is left to know about the relative weights of different evolutionary forces in the generation of biodiversity, and our coordinated research strategy seeks to quantify these weights through (1) focused, integrative study of the evolutionary patterns of birdsong, a complex behavioral trait, and (2) by comparison with viral evolutionary dynamics during large outbreaks. Rich data sources from detailed field observations, laboratory experimentation, open-access databases, and public health surveillance provide material to employ computational methods including mechanistic modeling with parameter estimation and evolutionary simulation, acoustic analysis, and novel phylogenetic tools. While students will primarily work on a project that matches their interests, the two research lines will be integrated, and researchers will work and learn together regardless of whether they are focused on viruses or our feathered friends! Participants in this research stream will develop skills in study design, data collection and analysis, phylogenetics, and computer simulation. We welcome those with unquenchable curiosity!