2026 Project Descriptions for the Rogers Program

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 courses: Bio311/312, Bio361, or Bio369

Transcriptional regulation in embryonic stem cells
Principal investigator: Sharon Torigoe

During development, multicellular organisms develop from a single cell, which repeatedly duplicates to generate trillions of cells. While these cells are genetically identical, these cells differentiate into a multitude of distinct tissues and cell-types, each with unique functions, raising questions about how gene expression is regulated in development. In the Torigoe lab, we investigate mechanisms for transcription regulation, which underlie cell-type-specific gene expression. We are currently focused on pluripotent stem cells, which represented the earliest stages of mammalian development. In particular, we study how transcriptional programs are encoded into the genome and how that information is interpreted by proteins.

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

Effect of developmental nicotine exposure on the embryo, larvae and adult female of D. melanogaster.
Principal investigator: Norma Velazquez Ulloa

Tobacco and nicotine-laced product use remain a public health concern across the world. Such exposure has documented deleterious effects for the mothers and their offspring. In my lab, we have established that developmental nicotine exposure has some similar effects in the progeny of exposed flies, to those seem in other organisms, including humans. However, to date, we have not studied whether the exposed parental female flies are affected by the nicotine exposure, nor characterized the developmental effects of nicotine at the embryo nor the larval stage. This research will fill that gap.

Prerequisites:
Required: Bio110, Bio202, and at least 1 Bio lab course completed by summer of 2026.

Preferred: Bio110 taken with me and/or Bio380 and/or fruit fly experience. In addition, one or more of the following courses: Bio252 or Psy280, Neurobiology, Physiology, Cell Biology, Molecular Biology, Structural Biochemistry, Drugs & Behavior, Math255, familiarity with R and willingness to learn more, interest or familiarity with Python. Fine motor skills.

 

Studying Parkinson’s disease mechanisms in zebrafish
Principal investigator: Tamily Weissman-Unni

Our lab uses genetic approaches to label and visualize cells in the living zebrafish brain and study mechanisms of protein aggregation related to neurodegenerative disease. We use fluorescence microscopy to visualize the living zebrafish nervous system, because these vertebrates have a similar brain structure to humans, and they are transparent during early development. Projects focus on testing whether genetic mutations affect alpha-synuclein protein aggregation and function. Students will use microinjection techniques into fertilized zebrafish eggs, fluorescence microscopy to visualize the nervous system 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, CS is helpful.).

Eaters or Lovers? Deciphering the Urobiome’s behavior toward Uromodulin
Principal investigator: Jean-Philippe Gourdine

Our lab is interested in the metabolism of bladder bacteria toward host complex sugars (glycans). Our data suggest that Bifidobacterium longum can digest Uromodulin (UMOD), the most abundant glycoproteins in the urine. Our preliminary data suggests that some members of the urobiome can only bind to UMOD while other can digest UMOD. This project focuses on further the identification of urinary bacteria with UMOD-digesting capacity (eaters) versus binding capacity (binders), using techniques such binding test and bacterial culture on UMOD and 16SrRNA metagenomics.

Prerequisites:

CHEM 330 Structural Biochemistry or CHEM 336 Biochemistry Laboratory

CHEM 210 Organic Chemistry I or CHEM 220 Organic Chemistry II

BIO 110 Biological BIO 120

 

Characterization of Bacterial Glycoside Hydrolases from the female Urobiome
Principal investigator: Jean-Philippe Gourdine

Our lab is interested in the metabolism of bladder bacteria toward host complex sugars (glycans). Our bioinformatical data suggest that in the healthy female bladder bacteria such as Bifidobacterium longum and Lactobacillus crispatus UMB0054, have the genetic capacity to de-mannosylate glycoproteins such as UMOD with glycosyl hydrolases (GHs) such as GH18, GH85, GH38, GH92, and GH125. In the CHEM336 lab, we are currently cloning many GHs and expressing them. This project focuses on further characterizations of selected GHs (protein expression affinity chromatography with Nickel-NTA, enzymes’ activities assays with uromodulin and other substrates).

Prerequisites:

CHEM 330 Structural Biochemistry or CHEM 336 Biochemistry Laboratory

CHEM 210 Organic Chemistry I or CHEM 220 Organic Chemistry II

BIO 202 Biological Core Concepts: Mechanisms or BIO 311 Molecular Biology

Synthesis of glyphosate derivatives for the study of Roundup degradation
Principal investigator: Louis Kuo

This chemical investigation studies the fundamental chemistry of glyphosate (Roundup®) degradation by a soil mineral that:

• elucidates the fate of a widely-used herbicide impacting human and environmental health.
• uses mechanistic investigations towards understanding glyphosate degradation by manganese oxide which is a model for the soil mineral birnessite
• is novel because it uses discrete manganese coordination complexes to model various manganese binding modes to glyphosate that mimic the interactions with manganese oxide.
• is transformative because the investigation uses classical coordination chemistry strategies with esterified glyphosate derivatives, some of which have herbicidal activity.

Prerequisites:

Chem 220 and chem 366

The Schrodinger operator on orbifolds
Principal investigator: Liz Stanhope

The Schrodinger operator is the differential operator associated to the celebrated Schrodinger equation of quantum mechanics. It can be expressed as the sum ∆ + f where ∆ is the Laplace operator and f is a potential function. The Laplace operator is associated to how waves or heat spread through an object. A potential function controls the motion of quantum particles. Similar to the harmonics of a string, on suitable spaces the Schrodinger operator has an infinite list of characteristic numbers called its spectrum. This project explores how results about this spectrum extend to a particular class of singular spaces called orbifolds..

Prerequisites: familiarity with manifolds and differential operators as developed in Math 305 and
Math 442, for example

Accessible Game Development
Principal investigator: Peter Drake

Video games are enjoyed by billions of players worldwide, but many players and developers are excluded by sensory, motor, cognitive, and other disabilities. How can we make games accessible to such players and developers? In this new project, we will review the literature, learn game development tools, produce some simple games and assess their accessibility, build connections to the accessibility and game development communities, and form plans for a longer-term “computing for good” project on this topic.

Prerequisites: 

Required: CS 172 Computer Science II or equivalent; some experience playing video games.

Desired: Experience with a game engine such as Godot (which we will use), Unity, or Unreal Engine; broad knowledge of gaming genres and conventions; additional programming courses or experience; experience with or knowledge of accessible gaming

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 have implemented a high-performance, minimal networking stack from scratch. This year I plan to develop an abstract specification of a generic networking stack and prove my implementation matches the abstraction specification using an interactive theorem prover (i.e., Isabelle/HOL).

Prerequisites:
CS 172 or equivalent, desired skills: discrete mathematics

Exploring AI and Human-in-the-Loop for Hands-on Exercises and Hint Generation in Cybersecurity
Principal investigator: Jens Mache

How to improve cybersecurity? We will focus on hands-on exercises and hint generation. We will explore advantages and disadvantages of AI, retrieval augmented generation (RAG), agents, small language models, reinforcement learning and human-in-the-loop. Research questions include 1. How can language models be augmented with specific information retrieval in order to limit and focus the response? 2. How can human-in-the-loop be used both as a safeguard and to scale?

Prerequisites:
Required: CS-171
Preferred: CS-211, CS-495

Cybersecurity Clinic
Principal investigator: Jens Mache

In cybersecurity clinics, students gain hands-on experience while strengthening the digital defenses of infrastructure, nonprofits and other under-resourced community organizations. MIT, UC Berkeley, and others co-founded the Consortium of Cybersecurity Clinics, a forum to share best practices for how to launch and operate cybersecurity clinics. For adoption at Lewis & Clark, we are exploring, testing and refining coursework and materials for audit, risk assessment, incident response, penetration testing, awareness training, settings and improvement plans.

Prerequisites:
CS-111 or CS-211

The dynamics of micro-swimmers
Principal investigator: Albert Bae

The microbial universe contains rich interactions between physical, chemical and biological phenomena. At these small scales, we can use optical tweezers which use light (photons) to push and pull objects to probe the piconewton scale forces used in locomotion, thereby gaining insight into the dynamics of how cells transport themselves from one place to another. This project aims to integrate optical-tweezer based force measurements with high-speed microscopy imaging to form a more cohesive physical picture of how cells swim.

Prerequisites:

• Physics 251 and math 225 are prerequisites.
• Experience working in a chemistry or biology lab is desired but not required.

 

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)

Tactical Frivolity and Collective Action in Portland Oregon ICE Protests
Principal investigator: Diana Leonard

This study explores participants’ experiences with playful protest tactics during ICE OUT demonstrations in Portland, Oregon. We will conduct semi-structured interviews to assess how participants employed humorous, artistic, or theatrical elements in their protest activities (i.e., “tactical frivolity”), what influenced their decision to use these approaches, and their perceived effectiveness in managing reactions from various audiences—including law enforcement, fellow protesters, counter protesters, and the media. Finally, the interview will explore participants’ likelihood of using similar tactics in future protests. Since most research on collective action (e.g., protest) focuses on the role of anger, this project will expand our understanding of the emotional dimensions of protest tactics.

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

Exploring the Psychophysiological and Cognitive Correlates of Resilience in Young Adults in the Post-COVID Era
Principal investigator: Todd Watson

We will examine cognitive, psychological, and physiological traits that may buffer the effects of stressors on young adults. In an ongoing study, we will parse how executive functioning (control processes that regulate cognition and behavior), aspects of psychological resilience (the ability to bounce back from negative life events), and heart-rate variability (a measure of brain-heart interactions) relate to long-term stress levels. Separately, we will begin a new project exploring relationships between inhibitory cognitive control (the ability to suppress incorrect responses or actions), resilience, HRV, and participants’ experiences with the psychosocial and/or health-related burdens of the COVID-19 pandemic.

Prerequisites:
Previous psychology or neuroscience research experience is preferred, but there are no specific prerequisites other than enthusiasm and basic relevant coursework (e.g. introductory social science, life science, or statistics/data science classes). This project is open to all students from all majors.