2024 Project Descriptions for Rogers Program

Prerequisites must be completed by the end of spring semester 2024.

Please review application instructions and download the student application.

BIOLOGY

Diversity and function of phospholipase D venom toxins in spiders
Principal investigator: Greta Binford

Spiders in the brown recluse lineage have unique toxic enzymes (SicTox) in their venoms that target membrane phospholipids. This toxin gene family has evolved different phospholipid target specificities. We are comparing the effect on insects, cells, and neurons of SicTox variants that are expressed in venom and in non-venom tissues. Our goals are to understand what this enzyme does when it is not a venom toxin, what parts of the protein are responsible for differences in activity, and how specific activities affect natural targets. This work will develop skills in phylogenetic comparative analyses, bioinformatics, cell culture, molecular biology and bioassays.

Prerequisites:
Bio 110, 201, 202 required. Successful completion of Bio 311/312, Bio 390, Bio 361, Bio 407, Bio 408 will be helpful but is not required.

Investigating how cells construct their internal compartments
Principal investigator: Greg Hermann

Lysosome related organelles (LROs) are intracellular compartments that carry out key functions within specialized animal cells. While much is known regarding the functions of LROs, for example pigment synthesis by melanosomes and blood clotting by platelet dense granules, the mechanisms involved in their initial construction and the generation and maintenance of their morphology remain poorly understood. Defects in the formation and morphology of LROs underlie a number of human genetic diseases. We have discovered and are analyzing the function of genes involved in lipid metabolism that control the formation of LROs in the model organism, Caenorhabditis elegans, whose homologues function similarly in humans. Student investigations employ a combination of genetic, molecular, and microscopy based tools.

Prerequisites:
Required course: Bio202
Desired course or courses: Bio311/312, Bio361, or Bio369

Urban Insect Ecology: ecological interactions between native and non-native species in urban community gardens
Principal investigator: Heidi Liere

Despite the overall detrimental effects of urbanization to biodiversity, there is a growing recognition of the potential value urban green-spaces for biodiversity conservation, especially for small beneficial organisms like pollinators and insect natural enemies (i.e. predatory and parasitic insects that consume crop pests). Community gardens are diverse urban green spaces where numerous native and non-native species coexist. The main objective of this project is to investigate the factors that influence the competitive and non-competitive interactions between native and non-native ladybird beetles—important pest control agents in agricultural systems. This information could help provide garden management recommendations to enhance habitat for native beneficial species.

Prerequisites:
Required: BIO 110
Preferred: BIO 335
The project will last 6 weeks from mid-May till the end of June. Exact dates to be determined.

Transcriptional regulation of pluripotency in embryonic stem cells
Principal investigator: Sharon Torigoe

Pluripotent stem cells (PSCs) hold important promise for regenerative medicine due to their capacity to differentiate into any functional cell type. The future success of generating and utilizing PSCs depends on gaining deeper understanding of the unique characteristics of PSCs. We will be investigating the mechanisms for transcriptional regulation that are necessary to maintain the functions of one type of PSC, the mouse embryonic stem cell. In particular, we will
examine how these transcriptional programs are encoded into the genome and how that information is read and interpreted by proteins.

Prerequisites:
Required: BIO110
Desired: BIO202; BIO311; BIO312

Genetic factors of drug exposure effects in Drosophila melanogaster
Principal investigator: Norma Velazquez Ulloa

Nicotine is the chemical in tobacco associated with its addictive properties. The negative consequences of developmental and adult nicotine exposure are well known, yet an effective treatment has not been developed. Additional research of the mechanisms of nicotine addiction are needed to develop new therapies. My lab has characterized developmental, neural and behavioral effects of developmental and adult nicotine exposure in Drosophila melanogaster, the common fruit fly, a proven model organism for identifying genetic mechanisms. In this project we will investigate the contribution of specific candidate genes and of specific mutations in influencing the effects of nicotine we have characterized.

Prerequisites:
BIO110, BIO202, CHEM110, CHEM120 are required.
Priority for selection will be given to students who have taken at least one of the following courses:
BIO252 and/or PSY280 and/or BIO380 and/or BIO422 and/or BIO375 and/or BIO311
Previous experience working with fruit flies also preferred
Intermediate knowledge of R preferred

Studying mechanisms of neurodegenerative disease in zebrafish
Principal investigator: Tamily Weissman-Unni

Our lab uses genetic approaches to label and visualize cells in the living zebrafish brain and study how neurons develop and function. We use fluorescence microscopy to study the zebrafish model system, because these vertebrates have a similar brain structure to humans, and they are transparent during early development. Projects focus on understanding the aggregation and function of the alpha-synuclein protein in Parkinson’s disease. Students will use microinjection techniques into fertilized zebrafish eggs, fluorescence microscopy to visualize the brain in living fish, and image processing techniques to analyze their data.

Prerequisites:
Bio 202 or equivalent; Neuroscience background and/or interest. (Additional background in cellular or molecular biology is ideal.).

CHEMISTRY

Purification and Characterization of Uromodulin’s N-glycans
Principal investigator: Jean-Philippe Gourdine

Uromodulin is the most abundant glycoprotein in the urine (~20 to 70mg excreted daily). Thirty percent of its mass comes from complex sugars (glycans). These glycans play a role in bladder microbial homeostasis against uropathogenic Escherichia coli but may also play a role in bladder bacteria metabolism. To explore this hypothesis, we will purify uromodulin, and its N-glycans, and then label them with a fluorescent tag for further bacterial growth experiments.

Prerequisites:
Required: CHEM 220 Organic Chemistry II
Preferred: CHEM 330 Structural Biochemistry
Not required but helpful (any): BIO 202 Biological Core Concepts: Mechanisms or BIO 311 Molecular Biology

Expanding the mining for genes encoding carbohydrate-active enzymes in bladder microbial genomes
Principal investigator: Jean-Philippe Gourdine

Urine is not sterile; a collection of microorganisms known as urobiome reside in the bladder. In collaboration with Dr. Lisa Karstens at Oregon Health & Science University (OHSU), we have developed a bioinformatics pipeline (Python & R), to mine bacterial genes involved in carbohydrate metabolism. New additions to the bladder bacterial genome collection have been released recently. Thus, we propose to expand the project with a larger dataset (n=1,134), encompassing microbes isolated from patients with diverse bladder disorders. This project delves deeply into data science leveraging microbial genomics and health data, will be conducted at Lewis & Clark and OHSU.

Prerequisites:
Required: DSCI-140 - DSCI-245
Preferred (any of): ECON 103, OR HEAL 200, MATH 123, MATH 255, POLS 201, PSY 200
Not required but helpful: BIO 202, CHEM330

Glyphosate (Roundup) Degradation as a form for Phosphorus Recovery
Principal investigator: Louis Kuo

Phosphonates [RP(O)(OR’)2] are used as herbicides that are ubiquitous in the environment. We recently made several molybdenum compounds and polymers that degrade the herbicide glyphosate (i.e. Roundup) under mild conditions. The products are commodity chemicals, and this transformation represents a form of phosphorus recovery which is a national priority. Experimental methods will be used to elucidate a mechanistic route with modified glyphosate molecules. A heavy reliance on multinuclear NMR (nuclear magnetic resonance) is required as well as organic and inorganic synthesis. In addition, there is “live” sample component that entails looking at glyphosate degradation in the background of a soil/clay matrix.

Prerequisites:
Chem 220 or Chem 366 (preferred).

Exploring the Structural Basis of Dynein Regulation
Principal investigator: Nikolaus Loening

Motor proteins serve a number of functions in the cell, including helping transport biological molecules (cargo) to where they belong. One such motor protein, dynein, is important for moving cargo from the periphery of cells toward the center and in human cells needs to partner with another protein (dynactin) to move cargo across long distances. The regulation of how these two proteins interact determines what, when, and where cargos are transported. In this project, we will study how the interactions between these two proteins are regulated by changes in the structure of dynein using a variety of biophysical techniques.

Prerequisites: Chem 220
Suggested Courses: Bio 312 and/or Chem 336

INTERDISCIPLINARY

Rehearsing disaster: Understanding earthquake preparedness behavior in an interactive environment
Principal investigators: Elizabeth Safran, Peter Drake, Erik Nilsen, Bryan Sebok

A devastating “megathrust” earthquake off the Pacific Northwest coast could happen at any time, and residents must learn to prepare for, survive, and thrive in the aftermath of such an event. We are developing video games to investigate their own effectiveness as risk communication tools and to elucidate what drives earthquake preparedness behavior among PNW residents ages 18-29. Student
researchers will: 1) analyze the data from an experiment conducted in spring, 2024 on players’ identification with in-game depictions of place and living circumstance; and 2) conduct an experiment on the effects of cooperation with another player on preparedness motivation.

Prerequisites:
2-4 students: PSYCH 300 ideal, other upper-level methodology courses considered.

MATHEMATICAL AND COMPUTER SCIENCE

Dependable Computing
Principal investigator: Alain Kägi

My research seeks to widen the adoption of formal methods in building reliable and trusted cyber-physical systems. Specifically, I want to establish if the field of formal verification has reached such a level of maturity as to allow one to prove an implementation of a complete cyber-physical system adheres to its specification.

As a proof of concept, I am building a networked temperature sensor using as many existing, reliable components as possible (e.g., the seL4 microkernel), building the rest from scratch using a subset of the C programming language, and using best software engineering practices (e.g., separation of concerns).

Prerequisites:
CS-172 or equivalent

Using Machine Learning to Provide Timely Feedback during Hands-on Cybersecurity Exercises
Principal investigator: Jens Mache

Computers and software are all around us, and cybersecurity is more and more important. Hands-on cybersecurity exercises have great potential, but timely feedback is needed to identify when we are heading in the wrong direction and to help us improve. The goal of this project is to apply machine learning to explore building and experimenting with a human-in-the-loop feedback system. Scenarios may include capture the flag, malware analysis and web applications.
NSF grant 2216485.

Prequisites:
CS-369, CS-211 or CS-293

PHYSICS

Lasers and electromagnets for laser cooling of atomic lithium
Principal investigator: Ben Olsen

We use light from lasers and magnetic fields to trap atoms and cool them to just above absolute zero temperatures. These cold atoms can emulate all sorts of quantum systems like superconductors or neutron stars, and we use them to learn more about many-body physics. In this project, you will help develop some tools for manipulating atoms: lasers and electromagnets. Based on existing preliminary designs, you will develop computer models of the components, simulate their properties, then fabricate and construct the devices. You will characterize their electromagnetic and optical behavior and integrate them into the apparatus.

Prerequisites:
Required: Familiarity with concepts of electricity and magnetism (Phys 142 or Phys 251)
Preferred: Experience with computer programming, optics, electronics, and laboratory measurements (Phys 201)

Integrating Imaging Physics into Undergraduate STEM Education
Principal investigator: Bethe Scalettar

Imaging is everywhere. We use our eyes to see and cameras to take pictures. Scientists use microscopes and telescopes to peer into cells and out to space. Doctors use ultrasound, X- rays, radioisotopes, and MRI to look inside our bodies. This project will generate engaging, interactive tutorials that will help the upcoming generation of scientists and non-scientists, and the general public, learn about and master the physical foundations, diagnostic and therapeutic applications, and strengths and weaknesses of key medical imaging techniques, such as ultrasound and MRI. In addition, the tutorials will enhance engagement, learning, and retention in STEM by illustrating its pivotal role in the fascinating and important fields of medical imaging and imaging science.

Prerequisites:
(a) Ability to program (experience with Python is optimal but not mandatory).
(b) Interest and willingness to master the basic physics of medical imaging techniques.
(c) Artistic skill is a bonus.