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News & Events


SRI Speaker Series Kickoff

SRI Speaker Series Kickoff Event

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UCUR – STEM Abstract Workshop

If you are interested in submitting an abstract to the Utah Conference […]

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Open to All – Business Consulting Case Competition

Gain experience, network, and explore the healthcare consulting industry Info Session Tuesday, […]

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Free Natural History Lecture Series – Tuesdays at 6:00pm

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SRI Welcome to Campus Event

Please join us on Thursday, September 8th at the Grotto outside Crocker […]

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First Week of Classes

One more week before we are back in full swing! A few […]

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SRI Team

SRI Team


Josh Steffen, Ph.D.

SRI Director; Associate Professor Lecturer

Josh Steffen, Ph.D.

SRI Director; Associate Professor Lecturer
Josh received his BA in biology and secondary education from St. Olaf College. He carried his Ph.D. and post-doctoral research at the University of Utah where he studied plant reproductive development with Gary in the lab of Gary Drews. He carried out post-doctoral research in the lab of Richard Clark where he studied natural variation in gene expression. Over the past 8 years he has held faculty positions at Colby-Sawyer College and Utah Valley University where he focussed on undergraduate education. In 2018 he accepted a position in the School of Biological Sciences at the University of Utah. Currently, Josh manages the Science Research Initiative (SRI), teaches courses associated with the SRI, and mentors multiple undergraduate research groups. Undergraduates working with Josh are using metagenomic approaches to characterize pollinator foraging behaviors, attempting to identify novel antimicrobials, and carry out genetic analysis of maize mutants.
 joshua.steffen@utah.edu

Heather Briggs, Ph.D.

SRI Associate Director; Associate Instructor

Heather Briggs, Ph.D.

SRI Associate Director; Associate Instructor
Heather completed a M.S. at the University of Michigan (Natural Resources) and a Ph.D at the University of California, Santa Cruz (Environmental Studies & Ecology and Evolutionary Biology). She went on to complete two postdoctoral positions, first at Harvard, then at UC Irvine. Heather now helps manage the SRI where she empowers students to work through hypothesis generation, experimentation, and interpretation. As an evolutionary community ecologist, Heather’s research is motivated by the desire to understand how variation in community context influences the outcome of biotic interactions. Through the exploration of the various determinants of insect behavior, plant ecology, and floral evolution, her research considers the importance of context-dependent interactions from both the plant and pollinator perspectives.
 heather.briggs@utah.edu

Ryan M. Stolley, Ph.D.

SRI Associate Director; Associate Instructor

Ryan M. Stolley, Ph.D.

SRI Associate Director; Associate Instructor
Ryan received his BS in chemistry from Fort Lewis College and Ph.D in organic chemistry from the University of Utah. He then conducted a post-doctoral appointment at Pacific Northwest National Laboratory’ Center for Molecular Electrocatalysis. After PNNL, he was a AAAS Science and Technology Policy Fellow in the US Department of Energy’s Solar Energy Technologies office. Ryan is currently an assistant research professor in the chemistry department where he works with numerous groups as a synthetic chemistry specialist, co-director of the SRI, and chairperson of the Salt Lake section of the American Chemical Society. Ryan’s research is in fundamental organic and organometallic chemistry uncovering new reaction paradigms using underexplored or entirely new functional groups, exotic ligands for rare-earth element coordination, and a variety of exotic conducting materials.
 801-581-6538
 ryan.stolley@utah.edu

Laura Rupert

SRI Project Coordinator

Laura Rupert

SRI Project Coordinator
Laura received B.S. degrees in Geography (emphasis in climate change & landscape dynamics) and Environmental Studies (emphasis in air, water and health) from the University of Utah. Her research experience includes undergraduate field work in the Fijian Islands with a focus on water quality in fresh- and saltwater systems. Within the SRI, she coordinates day-to day operations of the program and works with the goal of collaborating and communicating effectively with college leadership, faculty, students, postdocs and staff.
 L.rupert@utah.edu

SRI Fellows

 

Josh Scholl, Ph.D.

SRI Fellow

Josh Scholl, Ph.D.

SRI Fellow
Josh received his B.S. in biology from Florida Atlantic University and M.S. and Ph.D from the University of Arizona in ecology and evolutionary biology. He then worked as a postdoctoral researcher with Amy Iler at the Chicago Botanic Garden and as an adjunct lecturer at Northwestern University. Josh now works as a postdoctoral associate for the SRI. In his research, Josh is interested in understanding the strategies organisms use to cope with changing environments (e.g., urban areas and deserts) and how those strategies affect fitness and population dynamics. He also loves teaching and developing educational tools. To this end, he is a big proponent of the Ecological Society of America's SEEDS (Strategies for Ecology Education, Diversity and Sustainability) program which he enjoyed as an undergraduate member and now as a chapter advisor. To learn more about Josh and his research, education, and outreach endeavors visit https://joshuapscholl.weebly.com/.
 joshua.scholl@utah.edu

Selvi Kara, Ph.D.

SRI Fellow

Selvi Kara, Ph.D.

SRI Fellow
Selvi received her Ph. D in mathematics from Tulane University in 2017 and she held a faculty position at the University of South Alabama for 4 years after her Ph.D. Before joining the SRI as a postdoctoral fellow, she worked as a Research Associate at the University of Utah, Department of Mathematics. Selvi’s research is in commutative algebra, combinatorics, and geometry. Her research is focused on using combinatorial tools to study algebraic/geometric problems. One of her recent research interests is in higher dimensional chip-firing, a dynamical system, and she is interested in studying these systems combinatorially and algebraically. Selvi is one of the co-founders of Meet a Mathematician, a collection of short video interviews of mathematicians from historically excluded backgrounds in mathematical sciences. She is dedicated to creating and supporting spaces which center mathematicians and students from historically excluded backgrounds and amplify the historically excluded voices and their experiences in mathematical spaces.
 selvi.kara@utah.edu

Rodolfo Probst, Ph.D.

SRI Fellow

Rodolfo Probst, Ph.D.

SRI Fellow
Rodolfo received his B.Sc. in Biology at the State University of São Paulo and an M.Sc. in Systematics, Taxonomy, and Biodiversity at the University of São Paulo, both in Brazil. He recently obtained his Ph.D. at the University of Utah (Ecology, Evolutionary and Organismal Biology), where he investigated the evolution of ant-plant mutualistic interactions while working in the lab of Jack Longino. His research uses genomic tools, taxonomy, and natural history to understand ant-plant symbioses. He is led by his interest in insect evolution and his passion for tropical fieldwork, teaching the public about bugs and conservation, and exploring the outdoors. When not at the lab or collecting ants, he likes going road biking and hiking around Utah, cooking, and writing poetry.
 rodolfo.probst@utah.edu

Mikhael Semaan, Ph.D.

SRI Fellow

Mikhael Semaan, Ph.D.

SRI Fellow
Mikhael received twin BSes in Electrical Engineering and Physics from California State University, Long Beach, before continuing to the University of California, Davis for his Physics PhD. While at Davis, he taught active learning-based courses geared towards bioscience majors and cultivated a passion for scientific communication between disciplines. His research centers on how pattern and structure emerge in “complex systems:” how do we discover nature's patterns? How do we recognize a forest's structure as intricate, but a coin flip's as simple? Tackling these questions involves a combination of techniques from physics, mathematics, and computer science—applied in such seemingly unrelated areas as finance and cardiology! As an SRI Fellow, Mikhael is most excited to equip students not just with these tools but with the skills to build new ones, so that they might carry them across disciplinary boundaries throughout their chosen careers.
 m.t.semaan@utah.edu

Gennie Parkman, Ph.D.

SRI Fellow

Gennie Parkman, Ph.D.

SRI Fellow
Gennie received her BS in molecular biology from the University of Utah and went on to complete a PhD in Oncological Sciences and Master’s in Clinical Investigation. Her graduate research was focused on the PI3K>AKT cellular signaling axis in melanoma and understanding its role in melanoma initiation and progression. Her thesis was devoted to elucidating the role of this pathway in MAPK-driven melanoma as upregulation of PI3K lipid effectors contributes to current treatment primary and secondary resistance. Before joining the SRI as a postdoctoral fellow, she co-led a SRI cancer biology stream with Dr. Sheri Holmen to define critical targets in cancer that be identified as therapeutic interventions for metastatic melanoma and glioma and is enthusiastic to continue this work. In addition to her research, Gennie has served as an Adjunct Instructor at Westminster College and Utah Valley University and is committed to undergraduate science education. As an SRI fellow, Gennie is excited to not only equip students with the background necessary to identify the most crucial questions in cancer biology but also to formulate hypotheses and have the confidence to undertake the experiments necessary to answer these vital questions.
 gennie.parkman@hci.utah.edu

Austin Green, Ph.D.

SRI Fellow

Austin Green, Ph.D.

SRI Fellow
Austin Green is a postdoctoral research fellow at the University of Utah under the Science Research Initiative (SRI) and one of the leaders of Wasatch Wildlife Watch (WWW). Both the SRI and WWW are all about providing experiential and research-based learning and mentorship opportunities to undergraduate students and volunteer citizen scientists. Austin’s research goals are to help elucidate how human influence affects wildlife distribution and behavior in an effort to apply this knowledge to on-the-ground wildlife conservation. Austin is passionate about teaching and interacting with people, and he firmly believes that the best way to protect the wild lands we all love is to approach it with inclusive community engagement. He is excited to not only contribute to science and conservation on a local level, but it also help provide valuable evidence about human-wildlife interactions across the globe.
 austin.m.green@utah.edu

SRI Students

Learn By Doing in the SRI


Want to learn how to conduct research and create connections with faculty and other College of Science students? Join the Science Research Initiative (SRI)!

SRI offers College of Science students the opportunity to participate in discovery-based scientific research starting on your first day on campus, with no prior research experience required. You will gain research skills that will help you in science classes, learn with College of Science peers, and connect with faculty across the University. The SRI will jumpstart your path academic success, and give you needed skills to prepare for an internship or a career - whether that's in a research lab, an office, or one of the many other opportunities open to our graduates. Find out more below, or email us for more information.

Fall Year 1

Enroll in a 1-credit class in which you will learn about how science happens, join a community of researchers, and determine placement in a lab based on your research interests.

1
Spring Year 1

Begin the scientific journey in your selected lab. Students will engage in research activities for approximately 10 hours per week.

2
Fall Year 2

Continue in your selected stream and keep building upon your skills as a researcher. Students are given various opportunities to share research findings and mentor new students.

3
Beyond

Stay involved with the SRI community. Connect with new research and professional development opportunities in both SRI & College of Science.

4

FAQ


SRI Research Streams

SRI Research Streams


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 starting in the spring semester of SRI participation. Research can be performed for credit depending on a student's academic program, and scholarship opportunities are available.

Click on a tile to learn more about the stream.


 

CS Cancer Systems Biology
Cancer Systems Biology

Stream Leader: Dr. Fred Adler

 

SC Surface Chemistry and Catalysis
Surface Chemistry and Catalysis

Stream Leader: Dr. Scott Anderson

MB Making and Breaking Bonds
Making and Breaking Bonds

Stream Leader: Dr. 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.

To learn more about this stream, contact Prof. Armentrout at (armentrout@chem.utah.edu)

 

MS Molecular Systematics
Molecular Systematics

Stream Leaders: Dr. Bryn Dentinger/Kendra Autumn

This research program will give students the opportunity to work in the Mycology Genetics laboratory at the Natural History Museum of Utah. The data generated from this research will contribute to a project aimed at constructing the first complete molecular-based phylogeny of a newly described genus of fungi (Lanmaoa) in the mushroom forming family Boletaceae, thereby providing a baseline understanding of species diversity. Additionally, the results of this work will allow us to more precisely delineate species-level differences in a poorly studied group of economically important edible and putatively poisonous mushrooms.

Developed Skills Include: DNA extraction; PCR; DNA sequencing 

FA Flagellum Assembly in Bacteria
Flagellum Assembly in Bacteria

Stream Leader: 

The Blair lab SRI project concerns an important molecular recognition process in which a protein at the base of the bacterial flagellum, called FlhB, specifically recognizes only certain proteins in the cell and directs them to be transported through the flagellum itself, so that they can be incorporated into the growing flagellar structureThe rules that govern the recognition of appropriate cargo molecules are not understood, in spite of decades of study. Our aim is to characterize the interactions between FlhB and the various exported cargo proteins using biochemical and spectroscopic approaches.

 

Developed Skills Include: protein expression and purification; analysis of protein-protein interactions; NMR spectroscopy to characterize interactions in molecular detail

NEW STREAM COMING
NEW STREAM COMING

Stream Leader: 

PM Pollination Metagenomics
Pollination Metagenomics

Stream Leaders: Dr. Heather Briggs, 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

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 nativepollinators. Students will have the opportunity to learn basic molecular, microbiology, and field ecology research techniques.

If you would like to learn more about this Research stream please contact Joshua. Joshua.steffen@utah.edu.

BD Big Data for Climate Science
Big Data for Climate Science

Stream Leader: Dr. Tim Collins, Dr. Sara Grineski

Climate change is producing more severe heat waves, storms and floods. People’s access to protective resources, such as clean water and greenspace, is critically important in the context of climate change. Our team’s environmental justice (EJ) research has found disparities in the risks of climate change-related hazards/disasters and people’s access to protective resources, with communities of color, lower economic standing, and other socially disadvantaged statuses experiencing the greatest risks and the most limited access to resources at local, national, and international levels. Unfortunately, nearly all EJ studies rely on publicly accessible data about people, which are only available in aggregate or for coarse-scale geographic units.In this SRI stream, students will examine climate justice issues at an unprecedentedly fine scale and generate novel insights as part of our project team.

The project integrates big spatial data on climate change-related phenomena (e.g., heat, flood risk, air pollution, greenspace) with restricted-access “microdata” on the entire U.S. population, including individual people’s precise residential locations. We are conducting the project through the Wasatch Front Federal Statistical Research Data Center (WFRDC), located in the U’s Gardner Commons. Through the project, students will learn about environmental and climate justice research; master tools and techniques for integrating and analyzing spatial data from disparate sources on people and environmental conditions; acquire Special Sworn Status (SSS) to analyze the restricted-access microdata through the U.S. Census Bureau in the WFRDC; and contribute to advancing knowledge about climate justice issues. Students most likely to thrive in this stream will be interested in quantitative data analyses.

If you would like to learn more about this stream, please contact Tim Collins at tim.collins@geog.utah.edu.

CM Computation Methods for Hot Nuclear Matter
Computation Methods for Hot Nuclear Matter

Stream Leader: Dr. David Clarke

Atomic nuclei are made of nucleons, i.e. protons and neutrons. When a collection of nucleons gets extremely hot and/or dense, the nucleons melt into a plasma, the so-called quark-gluon plasma. Physicists have to research this plasma in detail in order to understand some of the hottest and densest systems in nature. Some characteristics of quark-gluon plasma can only be calculated using computational techniques. The computational technique our group employs is called lattice field theory. Lattice calculations generate random snapshots of these hot and dense systems, then perform statistical analyses on these snapshots. Generating these snapshots is highly computationally demanding, utilizing a significant fraction of the resources of the most powerful supercomputers in the world. Therefore we must always consider how to make our code more efficient.

Undergraduates working in this Stream will learn basic statistical analysis, learn how to write rudimentary scripts to analyze data, see basic ways to assess performance, and gain modest familiarity with concepts in modern physics. If they like, students will also have the opportunity to get familiar with Linux operating systems and object-oriented programming and to manage simulations on supercomputers.

If you would like to learn more about this Stream or think you might be interested in it, feel free to contact David Clarke at clarke.davida@gmail.com.

SB Social Belonging in STEM Classes
Social Belonging in STEM Classes

Stream Leaders: Dr. Gina FreyHum

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.

If you would like to know more about this stream, please contact Gina Frey at gina.frey@Utah.edu.

HW Human Wildlife Coexistence
Human Wildlife Coexistence

Stream Leader: Dr. 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 conservationIt 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.

In this stream, we will design and implement projects leveraging remote sensing trail cameras and large-scale fieldwork in both natural and urbanized landscapes, perform data analytics with Program R, develop ways to identify wildlife in photographs using artificial intelligence, and promote citizen science education and engagementThese techniques will help us answer questions with direct conservation implications, such as: How does varying levels of human disturbance affect wild mammal distribution, behavior, and community composition? What natural history and behavioral traits make species more or less susceptible to the effects of human disturbance? At what levels of human disturbance do wild mammal species begin showing behavioral responses, and how does this response vary by species? 
Learn more about this stream by contacting Austin Green (austin.m.green@utah.edu), or by checking out Wasatch Wildlife Watch.
AR Hallar Aerosol Research Team (HART)
Hallar Aerosol Research Team (HART)

Stream Leader: Dr. 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.  

Learn More: https://hart.chpc.utah.edu 




VS Viral Suppressors of RNAi
Viral Suppressors of RNAi

Stream Leader: Dr. Sarah Hansen

The Bass Lab studies Dicer, an enzyme that cleaves double-stranded RNA and is important for normal cellular function. It also plays a role in defense against viruses that we don’t fully understand. In this project we are studying viral  suppressors of RNAi (VSRs) which are a group of proteins that inhibit Dicer function and can be found in many viruses (e.g., ebola, influenza A, SARS-CoV-2, and Zika virus). The questions we want to answer include:1. How do these VSRs inhibit Dicer?2. Are they inhibiting the same Dicer function or do VSRs from different viruses act with different mechanisms?3. Are other pathways in the human innate immune response effected (e.g., RIG-I, MDA5)?These questions are explored through biochemistry and cell-based experiments. It is a great project for students who want to learn the fundamentals of biochemistry research and learn more about a university lab environment.

Undergraduate students working on this project will prepare and test one VSR of their choosing from a list of proteins/viruses we want to study. They will have the opportunity to learn basic molecular biology and biochemistry techniques. Future directions of this project include work in human cells and I am willing to teach these techniques to an interested student.

If you have any questions or want to discuss the project please contact the stream leader Dr. Sarah Hansen (sarah.hansen@biochem.utah.edu)

CB Cancer Biology
Cancer Biology

Stream Leader: Dr. 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.

CF Higher-Dimensional Chip Firing
Higher-Dimensional Chip Firing

Stream Leader: Dr. Selvi Kara

In this research stream, we will investigate unsolved mathematics problems in higher-dimensional chip firing games. These games are dynamical systems as they exhibit change over time. We will analyze their dynamics using tools from several mathematical fields such as combinatorics, linear algebra, and algebraic topology. We will start our investigation by studying various configurations of the chip-firing game and learn how to establish our findings rigorously using mathematical proofsOur goal is to prove new theorems that explain how these games behave over time. This research stream also offers opportunities to use programming languages such as Python.

If you have any questions about the stream or SRI, feel free to reach out to selvi.kara@utah.edu!

VB Vector Biology, Surveillance, and Management
Vector Biology, Surveillance, and Management

Stream Leader: SLC Mosquito Abatement 

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.

If you would like to learn more about this stream, please contact Christopher Bibbs at Chris@SLCMAD.org

SO Synthetic Organic Electrochemistry
Synthetic Organic Electrochemistry

Stream Leader:

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.
PC Investigating Potassium Channels
Investigating Potassium Channels

Stream Leader:

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.  

NN Neural Networks
Neural Networks

Stream Leader: Dr. 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.

Undergraduate students participating in this SRI stream will be introduced to machine learning and learn how machine learning tools are used in practice. Students will learn about the mathematics that forms the basis for neural networks and the optimization methods used to train them. They'll learn how to program in python and use packages such as scikit-learn and pytorch to analyze data. Working in teams, students will use neural networks to solve real-world classification problems like object recognition in images, detecting falsified financial transactions, and controlling for manufacturing defects. They'll also learn to effectively communicate and visualize results. 

FV Functional Validation of Potential Cancer Targets
Functional Validation of Potential Cancer Targets

Stream Leader: Dr. Gennie Parkman

This SRI Research Stream aims to understand more about the genetics of cancer, specifically melanoma, beginning with the effects of certain genes that are up or downregulated in BRAF mutant melanoma on proliferation, invasion, and migration in vitro. Through collaboration with the Huntsman Cancer Institute, this in vitrowork has tremendous potential to be translated into pre-clinical testing in in vivomodels.

In this research stream, we will conduct literature review and data analysis using publicly available data sets, such as the Broad Institute’s Project Achilles database, to ask “What genes may be important in melanoma?” We will then learn fundamental steps of molecular cloning in order to generate target genes and clone them into an expression vector. Then, we will produce cell lines expressing these genes and test them! Students will learn cell culture, as well as many molecular biology methods, such as mRNA and protein expression analyses, proliferation assays, etc., to functionally validate gene targets. If the results of our analyses are promising, these genes may be tested in established mouse models through collaborators at HCI.

No background is needed to work in this research stream. If you have any questions about this stream or SRI, please contact Dr. Gennie Parkman at gennie.parkman@hci.utah.edu.

DB DNA Barcoding
DNA Barcoding

Stream Leader: Dr. 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.

If you would like to learn more about this stream and the materials needed to uniquely identify species using DNA technology, please contact Rodolfo Probst at rodolfo.probst@utah.edu.

AM Ant Mutualism
Ant Mutualism

Stream Leader: Dr. Joshua Scholl

In this stream we will study the Aspen sunflower, Helianthellaquinquenervisand its ant bodyguards (shown above). We’ll ask questions like, which ant species is the best bodyguard? Do the ants increase the plant’s reproductive success (more seeds)? Do the ants stay on the plant all day/season or just during certain parts of the day/season?

As part of this project, you will get outside and learn about the wonderful world of species interactions and capture ants using our state-of-the-art ant aspirator. You will also be introduced to basic plant identification and anatomy and experimental design. In the Wasatch Mountains we’ll apply these skills to conduct ant exclusion experiments and use a variety of ecological analysis tools to evaluate hypotheses. Important transferable skills that you can gain by participating in this project include competency in the popular R software (data wrangling and visualization), public speaking, writing, wilderness safety skills, and creative problem solving.

For more information about this stream please contact Josh Scholl at joshua.scholl@utah.edu.

SE Seed Ecology
Seed Ecology

Stream Leader: Dr. Joshua Scholl

Our goal in this stream is to explore the environmental factors (e.g climate, elevation, urbanization, etc.) that drive seed ratios in seed heteromorphic species. For example, how does increased drought, a consequence of climate change, affect seed ratios? How do changes in seed ratios affect plant population growth? Seed heteromorphic species allow us to ask very exciting questions about germination ecology which in turn help us to understand and ultimately predict plant population dynamics in changing environments.

To answer these questions students will design and implement projects collecting plant species across environmental gradients (e.g. from SLC west to the Nevada border or from downtown SLC up into the mountains). We may also conduct germination and growth trials of the seeds we collect in a greenhouse. As part of this project, students will learn basic plant identification skills, plant anatomy, collect plants in the field, have the opportunity to conduct greenhouse and growth chamber experiments, and learn to use a variety of ecological analysis tools to quantitatively evaluate hypotheses. Important transferable skills that students can gain in this project include competency in the popular R software (data wrangling and data visualization), public speaking, writing, wilderness safety skills, and creative problem solving.

For more information about this stream please contact Josh Scholl at joshua.scholl@utah.edu.

CS Complex Systems
Complex Systems

Stream Leader: Dr. 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
MA Underexplored Molecular Architectures
Underexplored Molecular Architectures

Stream Leader: Dr. 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

For more information about this stream, contact Ryan Stolley at ryan.stolley@utah.edu

BN Biogeography of Nematodes
Biogeography of Nematodes

Stream Leader: Dr. 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.

If you would like to learn more about this stream, please contact Michael Werner at michael.werner@Utah.edu

UE Urban CO2 Emissions
Urban CO2 Emissions

Stream Leader: Dr. Kai Wilmot

To investigate relationships between urban CO2 emissions, population density, and a number of socioeconomic variables, we are combining satellite observations of CO2 with atmospheric modeling techniques for 113 major urban centers around the world. Ideally, our results will improve understanding of the role of cities in addressing climate change and point to possible development strategies that may be relevant to policymakers.

Over the course of the Spring 2023 and Fall 2023 semesters, undergraduates working with this project will consider and help analyze observed COdata and atmospheric transport modeling outputs for cities around the globe. Students will have the opportunity to learn basic techniques/approaches in atmospheric modeling and observation, will identify, read, and share literature related to climate change, emissions, and urbanization, and will develop preliminary skills in programing/coding.

If you are interested in this project and have further questions, please email Kai Wilmot at Kai.Wilmot@utah.edu.

PL Plant Light Sensing and Greening
Plant Light Sensing and Greening

Stream Leader: Dr. 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.

If you would like to learn more about this stream, please check more information on chanyulyoolab.org or contact Chan Yul Yoo at chanyul.yoo@utah.edu.

PI Plant Immunity and Amino Acid Metabolism
Plant Immunity and Amino Acid Metabolism

Stream Leader:

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.

If you would like to learn more about our research activities, please contact Heejin Yoo at heejin.yoo@utah.edu

NEW STREAM COMING
NEW STREAM COMING

Stream Leader:

BIOLOGY
 

CHEMISTRY
 

MATH
 

PHYSICS & ASTRONOMY

SCIENCE EDUCATION