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Opportunities in Science at Lewis & Clark

2018 Project Descriptions for Rogers Program

February 07, 2018

Prerequisites must be completed by the end of spring semester 2018. 

Please review application instructions and forms here.



1. Investigating how cell-type specific compartments are constructed
Principal Investigator: Greg Hermann

Lysosome related organelles (LROs) are cellular compartments that carry out key functions within particular cells of an organism. 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 construction remain poorly understood. Defects in these processes underlie a number of human genetic diseases. We are discovering and analyzing the function of genes controlling the formation of LROs in the model organism, Caenorhabditis elegans, whose homologues function similarly in humans. Student investigations use a combination of genetic and microscopy based tools.

Required course: Bio151 or AP equivalent
Desired course: Bio200, Bio311/312, or Bio361


2. Seedling dynamics and maintenance of diversity in an old growth forest
Principal Investigator: Margaret Metz

Student researchers will census a network of seedling monitoring plots and seed traps in the Wind River Experimental Forest to assess the interactions between native trees and oomycete pathogens to understand how diversity is maintained in an old growth coniferous forest. Oomycetes, or water molds, are highly destructive fungus-like plant pathogens, best known for damage to agricultural crops. Native oomycetes are abundant in forested systems, yet their role in driving the dynamics or diversity of forests is unknown. The project will involve residence at a forest service research station and long days in the field (at a beautiful corner of the world). [Note, this is a 6-week internship]

Course prerequisites: BIO 141 or equivalent. BIO 223 or 335 preferred.

Wilderness First Aid certification or willingness to obtain (wilderness first responder certification preferred); valid driver’s license
Fieldwork will entail long days with repetitive, detailed measurements, strenuous hiking, and the ability to lift and hike with heavy backpacks on uneven terrain. Experience working in rugged field conditions, and/or orienting in the back country will be very useful, as will a positive attitude, enthusiasm for learning, the ability to work as part of a team, and the interpersonal skills needed to work and live closely with other team members.


3. 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.

Required: BIO151 or equivalent
Desired: BIO200, BIO311/312


4. Mapping neuronal development using multicolor imaging in Brainbow zebrafish
Principal Investigator: Tamily Weissman

Brain function relies upon the precise organization of neural circuits. The majority of neurons are born during early brain development, but there are questions regarding how neuronal production is regulated. Our lab uses a multicolor fluorescence labeling approach (“Brainbow”) to label neurons in many different colors within the living zebrafish brain. Students will use embryonic microinjection techniques, express fluorescent proteins in zebrafish larvae, and use fluorescence microscopy to visualize dividing cells in vivo (in living fish). Some positions will focus on generating digital media for an interactive, Brainbow-focused website. Please note interest in application.

Prerequisites: Bio 151 or equivalent; Neuroscience background and/or interest. (Bio 200 and/or additional background in cellular or molecular biology is ideal.)


5. Zebrafish to study cellular mechanisms of Parkinson’s Disease
Principal Investigator: Tamily Weissman

Parkinson’s Disease involves the abnormal aggregation of a protein called alpha-synuclein. Zebrafish is a useful model system for studying Parkinson’s Disease because: 1) human forms of alpha-synuclein are readily expressed in zebrafish; and 2) the developing zebrafish is optically transparent, allowing clear visualization of expressed proteins. Students will use embryonic microinjection techniques, express fluorescent proteins in zebrafish larvae, and use fluorescence microscopy to visualize neurons and their connections in vivo. Our investigations will focus on the role of alpha-synuclein aggregation in disease. Some positions will focus on generating digital media for an interactive, Brainbow-focused website. Please note interest in application.

Prerequisites: Bio 151 or equivalent; Neuroscience background and/or interest. (Bio 200 and/or additional background in cellular or molecular biology is ideal.)


6. Cellular Effects of Toxic Spider Venom Proteins on Model Organisms
Principal Investigator: Pamela Zobel-Thropp

Venoms are complex cocktails of proteins and peptides that have evolved over millions of years, primarily to immobilize prey. Multiple gene families produce venomous mixtures that are of biological interest. Some proteins have variable expression patterns and functional activity within, and among, different species. We are interested in how specific venom proteins act to disrupt cellular structures. This work applies molecular biology, cellular biology, and biochemistry to analyze the cytotoxic effects of venomous components on cells of select model organisms.

Prerequisites: Successful completion of Bio311/312 or Bio361 is preferred


7. Identification of genes and neural circuits underlying the effects of nicotine exposure during development
Principal Investigator: Norma Velazquez Ulloa

Nicotine is the chemical in tobacco associated to addiction, yet little is known about the changes nicotine causes that produce addiction. My lab uses Drosophila, the common fruit fly, to discover the mechanisms for nicotine’s effects. Students working in this project will expose flies to nicotine, dissect brains, stain them, and use fluorescence and confocal microscopy to characterize nicotine’s effects on neurotransmitters and on proteins associated to nicotine metabolism. Students will also use molecular biology to identify genes involved in nicotine’s effects.

Prerequisites: BIO151 or experience handling fruit flies and BIO200.



8. Kinetic Study of Gold and Silver Nanoparticle Interactions in Aqueous Environments
Principal Investigator: Anne Bentley

Gold nanoparticles have the potential to be used in disease diagnosis, imaging, and treatment, and silver nanoparticles have antibacterial properties that have already found use in consumer products. While it is inevitable that increased medicinal and consumer use will result in these nanoparticles being introduced to the environment, little is known about how gold and silver nanoparticles will interact with the natural environment and with each other if co-released. This project will examine the stability of gold and silver nanoparticles under a variety of environmental conditions using UV-vis spectroscopy, dynamic light scattering, and transmission electron microscopy techniques.

Prerequisites: Chem 120 or previous chemistry research experience


9. Development of an immobilized ruthenium (III) chloride catalyst
Principal Investigator: Casey Jones

Ruthenium (III) chloride is a catalyst currently being used for the synthesis of pharmaceuticals and other compounds. However, ruthenium is also a toxic element for the human body and there are strict limits set on the amount of ruthenium that is found in pharmaceuticals. This project seeks to attach ruthenium chloride to the surface of aluminum metal so that it can (1) catalyze the desired reaction, (2) without leaching into the product, and (3) can be easily removed and reused in additional reactions. Students will explore and learn surface modifications and characterization, organic and organometallic chemistry, and green chemistry.

Prerequisites: Organic Chemistry (Chem 220)


10. Designing a Self-healing Stent
Principal Investigator: Casey Jones

This project seeks to attach resveratrol, a compound found in red wine, to metal cardiovascular stents. Stents are used in patients with coronary artery disease, but often fail from improper healing. Resveratrol has been shown to have the potential to improve cardiovascular healing. Our hypothesis is that a stent releasing resveratrol or analogues will improve healing, leading to device success with less risk to patients. To accomplish this goal, we will (1) optimize the attachment of resveratrol and analogues to metal surfaces, (2) characterize the release of these molecules, and (3) evaluate the response of endothelial cells to the surfaces.

Prerequisites: Organic Chemistry (Chem 220)


11. Oxidative Degradation of Organophosphate Neurotoxins: Mechanistic Investigation
Principal Investigator: Louis Kuo

Sulfur-containing organophosphates are used as neurotoxic pesticides that are ubiquitous in the environment. We recently discovered several molybdenum oxo-peroxo compounds that oxidatively degrade these pesticides under mild conditions and converts to value-added commodity chemicals; this represents a form of phosphorus recovery. Experimental and computational methods will be used to to elucidate a mechanistic route, and this begins with understanding the active species in solution that degrades these pesticides. Specifically, the project seeks to confirm the role/presence of hydroxyl, perhydroxyl radicals with luminescence and HPLC methods. Alternatively, we will also pursue a molybdenum-peroxide route with solution models of the oxo-peroxo compounds.

Chem 366 (Preferred)
Chem 220 (Absolutely required)


12. Fundamental Investigation of Sulfide Oxidation by New Molybdenum(VI) Catalysts
Principal Investigator: Louis Kuo

Sulfide oxidation has benefits for petroleum desulfurization and in organic synthesis.  This project examines the mechanism of sulfide oxidation by two new molybdenum(VI) dioxo complexes that are robust and ideal catalysts; they are air stable, easily synthesized and readily tracked with NMR spectroscopy.  This proposal seeks to find structure-activity relationships for the molybdenum catalyst, and elucidate how the dioxo functionality is activated by H 2 O 2 for sulfide oxidation. The summer project entails kinetics (tracked by 1 H NMR) which will inform the design of practical molybdenum catalysts that oxidize sulfides for petroleum oil refining and for catalytic organic synthesis.

Chem 366 (optional)
Chem 220 (required)



13. The spatial distribution of clouds from infrared sky images
Principal Investigator: Jessica Kleiss

Recent news reports announced that 2017 was the second hottest year on record since 1880. However, the magnitude, location, and timing of changes in temperature and rainfall at different places on the planet depend on feedback cycles in the climate system. The cloud feedback is one of the least understood feedbacks in our current climate, and projected changes in our future climate are even more uncertain. Improving our current models of cloud cover requires improved observations of clouds in the climate system.

This research projects is directed at shallow cumulus clouds, which are difficult to routinely observe and are therefore important to accurately model.  This involves integrating measurements from multiple instruments including ground based and satellite observations. In particular, a new ground based visible and infrared all-sky camera ( has yet to be fully utilized to report on the temperatures of shallow cumulus clouds, and how cloud temperature relates to their diurnal variations in cloud base height and size (vertical and horizontal). This project will involve valuable image analysis of a new data set, and is a great opportunity to contribute meaningfully to the research community. You will apply and improve your geometry skills, develop data science and scripting skills, and gain insight into earth science.

Preferred prerequisites: GEOL-170.



14. Cloud identification from sky images using Machine Learning techniques.
Principal Investigators: Jessica Kleiss and Peter Drake (co-investigators)

Historically, clouds were observed from were previously gathered at individual weather stations on an hourly or daily basis. Atmospheric science now benefits from a massive amount of data from continuously operational ground instruments and satellite observations. How can we sift through all this data to find meaningful patterns and information?  This project aims to use a machine learning approach to improve our existing capability to identify cloudy and clear regions in digital images of the sky. We will improve upon an existing research design framework using a deep convolutional neural network. Can a computer match your eye’s ability to identify clouds in the sky? Come and find out for yourself!

Required: CS 172.
Desired: CS 369, a GEOL course.


15. Rehearsing disaster: Promoting earthquake preparedness through video game research
Principal Investigator: Liz Safran, Erik Nilsen, Peter Drake

A devastating “megathrust” earthquake off the Pacific Northwest coast could happen at any time. Residents must learn to prepare for, survive, and thrive in the aftermath of such an event, as emergency responders will be overwhelmed and essential services may be unavailable for many weeks. We plan to create a video roleplaying game to interactively educate young (ages 19-26) PNW residents. This game will also serve as a research tool to investigate its own effectiveness, examining how character power (high or low) and identity (similar to or different from the player) affect learning, co-operation, and self-efficacy.

CS 488 ideal; CS 172 at minimum
ENVS 220 or PSYCH 300



16. Adaptive Sampling Designs in Clinical Trials
Principal Investigator: Yung-Pin Chen

The main purpose of randomization in a clinical trial is to prevent selection bias and to provide a basis for valid statistical inference. However, a sampling design with complete randomization could result in severely disproportionate assignments to treatments, which may seriously affect the efficiencies of statistical procedures in use. Clinicians can be caught between the need for both randomness and balance. One goal of this project is to explore various adaptive sampling designs that achieve balance in treatment assignments while remaining sufficient random. In particular, we will study the trade-offs between randomness and balance under various adaptive sampling designs.

Prerequisites: Students are expected to have some knowledge of basic probability and statistics. Computer skills (experiences in Mathematica or R) are a plus.


17. Capture-the- Flag Challenges that Enhance Cybersecurity Analysis Skills
Principal Investigator: Jens Mache

Cybersecurity analysis skills are of growing importance due to our increasing reliance on computers and networks. Current security exercises typically lack interactive, experiential components and configuration flexibility. This project seeks to develop a series of configurable cybersecurity scenarios, the infrastructure necessary for running them, and documentation that explains security implications. Scenarios may include capture the flag, web applications, malware analysis, data science, firewalls, buffer overflows, recover the network and intrusion detection.

Prerequisites: CS-311 Computer and Network Security and/or CS-293/393 Networks and Web Development


18. 3-orbifolds and their Laplace spectra
Principal Investigator: Liz Stanhope

Looking at a tree outside the window, or the building next door, we see our local spatial universe is modeled well by 3-dimensional Euclidean geometry. We will examine other three-dimensional spaces. For example, the set of all points in Euclidean 4-space that are equidistant from the origin form a curved 3-space called the 3-sphere. Wonderful existing theorems tie the resonance frequencies of smooth 3-dimensional objects to the topological and geometric properties of that object. The focus of this project is to examine the extent to which previous results extend to a special class of non-smooth 3 dimensional objects called 3-orbifolds.

Prerequisites: Math 215, Math 225, Math 305, if possible Math 421 & 442



19. Compactified QCD
Principal Investigator: Mohamed Anber

The strong nuclear force (quantum chromodynamics or QCD) is responsible for confining the quarks inside the nucleons. However, we still do not fully understand why confinement happens, thanks to the complexity of the mathematics that describes this force. One of the ways to simplify the mathematical description is to compactify one of the spatial dimensions over a circle. This enables us to analytically compute various physical observables that are otherwise very complicated to compute. The purpose of this project is to study aspects of compactified QCD.

Prerequisites: Physics 252 Thermal and Statistical Mechanics + strong analytical and programming skills


20. Electromagnetically induced transparency in rubidium vapor with transverse magnetic fields.
Principal Investigator: Andrew Funk

Electromagnetically induced transparency (EIT) is a quantum mechanical optical effect where a normally opaque material (i.e. absorbs “signal” light) becomes transparent when “control” light is shone onto the material. This project will investigate how the sensitivity of the EIT effect in rubidium vapor to small magnetic fields (1-10 pT – one million times smaller than the Earth’s magnetic field) affects the fluctuation properties of the laser light used for the signal and control fields. This would have applications in magnetometry as well as longer term implications for fields such as quantum information and time/frequency metrology.

No prerequisites, but preference will be given to students who have completed Physics.


21. Investigations into the Acoustics of the Mandolin
Principal Investigator: Steve Tufte

We continue a broad-based experimental study of the acoustics of the mandolin. We will further investigate the complex coupling of the motions of the doubled strings using high-speed video and the musical implications of these interactions will be elucidated. Measurements of the sound spectrum and bridge impedance combine to characterize the transfer of mechanical energy from string motions through the bridge to the motions of the instrument body that ultimately produce sound. Experiments to understand in detail the connection between the mechanical properties of the bridge and the resulting sound spectrum aim to identify potential improvements in bridge design. Details of the resulting body motions, the modes of vibration, will be studied using holographic interferometry.

Prerequisites: Preference for students equipped with skills learned in Physics 201: Experimental Methods in the Physical Sciences
Other useful experience: computer skills, optics, differential equations, Physics 451.



22. Group-based Emotions as Mechanisms of Competitive Victimhood
Principal Investigator: Diana J. Leonard

Competitive Victimhood (CV) occurs when individuals attempt to establish that their group (e.g., “Americans”) has suffered more than an adversarial group. Our past work suggests that when this serves to rehabilitate the group’s moral image (i.e., “we have done bad things but we have suffered), it alleviates moral emotions like shame, which then paves the way for renewed intergroup violence. The current project uses experimental procedures with online samples to examine the emotional reactions and consequences of CV when its function is toward other outcomes, such as garnering sympathy or recruiting allies in a dangerous conflict.

Prerequisites: Psy 200 (Stats) and 300 (Research Methods) are highly recommended; Psy 260 (Social Psychology) is preferred.


23. The Use of Tangible Technology to Teach Kids Coding Concepts
Principal Investigator: Erik Nilsen

This project extends previous research on the benefits of combining digital and tangible technology to enhance creativity in young children. Two versions of an iPad app (Scratch Jr) will be evaluated to for effectiveness in teaching 7 - 10 year olds fundamental computer programming concepts including iteration, sequencing, looping, code reuse, forecasting and debugging. The main difference in the versions is whether the coding is accomplished entirely on the ipad screen or with physically manipulable (tangible) coding blocks that interact with the app. Along with running the study, students will help design a museum exhibit at OMSI highlighting the research.

Prerequisites: This can be met through coursework (Psy 300 or CS 171/172) or other experience.


24. Exploring the Event-Related Potential, Behavioral, and Cognitive Correlates of Food Cue Processing, Craving, and Food Consumption in Healthy Young Adults
Principal Investigator: Todd D. Watson, PhD

We will use event-related potentials (a noninvasive measure of brain function) to index cortical responses to distracting high- and low-calorie food cues, and will determine if the magnitude of food-related brain responses predicts young adults’ eating habits, food craving, and snack food consumption. This study will extend the literature by delineating the neural correlates of early attentional processes that may be important in cue-induced food craving, relating these effects to both potentially unhealthy and healthy “real world” eating behaviors, and increasing our knowledge on how individual differences in craving can modulate neural responses to appetitive cues.

Prerequisites: It is highly preferred (but not required) that undergraduate students have previous experience with human electrophysiology and/or cognitive testing in a laboratory setting. It is also highly preferred that students have had coursework in statistics, research methods, and neuroscience.


For more information:

Amy Timmins
Administrative Specialist I