2025 Project Descriptions for the Rogers Program

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 toxingene 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 the causes and consequences of among-individual behavioral differences in wild mice
Principal Investigator: Tracy Burkhard

“Personality” influences decisions in animals, and differences in behavior can have important consequences. For example, bolder animals might venture further from their burrows. While this might help them expand their territory, it might also expose them to predators. Why don’t all animals behave alike? How do these differences impact an animal’s success? This work addresses these questions in wild mice. Three positions: 1) stable isotope analysis (lab-based); 2) mouse trapping and fieldwork; 3) developing and/or building innovative behavioral tools (e.g., coding, Raspberry Pi, RFID arrays, PVC apparati, etc). One student may act in multiple positions if interested and qualified.

Prerequisites:
For all positions: Preference given to students demonstrating competencies or interests in one or more of these areas. There will be minimal supervision at times; thus, successful candidates will be self-motivated, independent, and problem solvers. Because of the highly interdisciplinary nature of the project, strong interpersonal skills are required.

1) Stable isotope analysis (wet lab)

Required: Any upper or lower division course in chemistry, biochemistry, molecular biology, developmental biology, neuroscience (or equivalent) with significant wet lab or previous relevant research experience.

Preference will be given to students interested in analyzing the isotope data, with coursework in biostatistics and experience coding in R required. Project will last 6 weeks from mid-May until the end of June with exact dates to be determined.

2) Mouse sampling and trapping (fieldwork)

Preferred: Animal Behavior, Mammalogy, Ecology, Vertebrate Zoology.

Required: Any upper division course in Ecology or Evolution with lab or previous relevant research experience.

Willingness to work full days under exposure, outdoor conditions (e.g., humid, muddy, buggy, rainy…). Will involve daily hiking in Tryon in addition to data collection, entering, and analysis. Attention to detail and a positive attitude are essential. Must be able to carry 20-30 pounds of field equipment and be up-to-date on tetanus shots. Preference given to students with own vehicle, though candidates without cars will still be seriously considered.

3) Developing innovative behavioral tools

Preferred: Relevant courses in computer science, computational biology, physics, biomechanics, etc. Experience working with any of the following: programming in python, Raspberry Pi, video recording, AI data processing, soldering, apparatus designing and building, 3D printing, camera traps, security cameras.

Required: Interest in troubleshooting and designing new tools to suit biological contexts. Students interested in applications of computer science, data science, physics, engineering, or other relevant discipline tobiological questions particularly encouraged to apply. Students will work with staff and faculty in Physics and Computer Science and with Dr. Burkhard in Biology. Note that the successful candidate may not be one formally trained in physics or computer science (but instead may have formal or informal experience with construction, crafting, etc). Project will last 6 weeks from mid-May until the end of June with exact dates to be determined.

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

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

Urban agroecosystems are diverse habitats where numerous beneficial insect species coexist. This includes ladybird beetles, which provide important pest control services. Even though non-native species are abundant in our area, they have co-existed for years with native species. However, we don’t know if this coexistence will continue under climate change. The main objective of this project is to investigate competitive interactions between native and non-native ladybird beetles at different temperature regimes. This will help us understand how these important predator communities and their pest control services will shift under climate change and may lead to gardening practices recommendations to mitigate the effect of temperature extremes on beneficial insects in urban areas.

Prerequisites:
Required: BIO 110
Preferred: BIO 335, BIO 490 (Agroecology)
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

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

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 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.).

Noble Metal Nanoparticle Shape Control
Principal Investigator: Anne Bentley

Tiny crystals of noble metals (gold, silver, platinum, and others) display their crystalline surfaces (or facets) to the surrounding environment, and the chemical behavior of different crystal facets can vary significantly. Students working on this project will synthesize gold cubes and then use electrochemistry and electroless oxidation / reduction approaches to deposit silver and other noble metals. Students will gain experience in nanoparticle synthesis, UV-vis spectroscopy, dynamic light scattering, and scanning electron microscopy.

Prerequisites:
Chem 120

Expression and characterization of two GH38 from the bladder bacteria Lactobacillus crispatus
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 with glycosyl hydrolases (GH) such as GH18, GH85, GH38, GH92, and GH125. Only ten bacterial GH38 have been characterized so far. We recently obtained expression vectors of these two GH38 from Lactobacillus crispatus UMB0054, a bladder bacteria associated with health. This project focuses on expressing and purifying these GH38 from L. crisaptus UMB0054 (transformation, protein expression affinity chromatography with Nickel-NTA). The purified enzymes’s activities will be assessed with biochemical assays with uromodulin.

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

Monitoring the growth of commensal bladder bacteria on host glycoproteins
Principal investigator: Jean-Philippe Gourdine

Our previous bioinformatical data suggested that bacteria such as Bifidobacterium longum have the genetic capacity to de-mannosylate glycoproteins in healthy female bladders. Our preliminary data showed that purified uromodulin (UMOD), the most abundant glycoprotein in the urine (~20 to 70 mg excreted daily) can be degraded by commercially available probiotics Bifidobacterium longum subsp longum 35624. In this project, we will test the demannosylation of UMOD with bladder bacteria isolated from the healthy female bladder Streptococcus oralis subsp. dentisani, Streptococcus mitis UMB1341, Bifidobacterium longum UMB0788 (by culturomics and glycomics (lectin-blot) gifts from our collaborator Dr. Alan Wolfe Lab.

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

Urban Oak Woodland Regeneration in the Santa Monica Mountains of Los Angeles, CA
Principal Investigator: Alana Rader

This research examines forest regenerating following wildfire in oak woodlands of the Santa Monica Mountains, Los Angeles. Satellite derived data on fire dynamics and canopy coverage will be evaluated alongside biophysical measurements from oak trees in long-term monitoring plots to characterize patterns of oak tree regeneration. Together, the monitoring plots are unique as they have all experienced at least one instance of fire from either the Woolsey (2018), Malibu (2024), or the most recent Palisades (2025) fires. Research findings will support early implementation and planning oak woodland restoration and provide foundation for monitoring ecosystem services provided by regenerating oak trees.

Prerequisites:
Familiarity and comfort using excel is a requirement.
Previous experience using R Statistical Software is an asset but not required.
Introductory data science, coding, and/or biology courses will be an asset, but are not required.
The project will last for 6 weeks starting June 2 – exact dates are to be determined.

Limiting Behavior of Discrete Stochastic Processes: Random Walk and the Moran Process
Principal Investigator: Yung-Pin Chen

A discrete dynamical system can be described by a set of difference equations, and a continuous dynamical system can be described by a set of differential equations. In this project, we will investigate whether a set of difference equations can approach a set of differential equations under proper rescaling of time and space. We will look at one dimensional and higher-dimensional random walks. In particular, we will study a stochastic process proposed by Patrick Moran in 1958 for modeling genetic drift. Under the Moran process, there is a finite population of a constant size of organisms, and the organisms can be classified into two different types. At each time, an organism is selected at random to reproduce and an organism is selected at random to perish, so that the population size is kept constant throughout the process.

Prerequisites:
Students should have some basic knowledge of axiomatic probability theory, linear algebra, discrete mathematics, and statistics. Programming skills (experiences in Mathematica, Python, or R) are desired.

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

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, small language models and reinforcement learning to explore building and experimenting with a human-in-the-loop hint system. Scenarios may include capture the flag, malware analysis and web applications. NSF grant 2216485.

Prerequisites:
CS-369 and (CS-211 or CS-293) 

The dynamics of micro-swimmers: correlating optical force measurements with high-speed video microscopy of swimming algae.
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 is a prerequisite.
• 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)

Exploring Executive Functioning, Resilience, and Heart-Rate Variability: A “Sidewalk Neuroscience” Study
Principal investigator: Todd Watson

We will use low-cost/open access research tools to extend the literature on cognitive abilities, personality traits, and autonomic nervous system function that may buffer the effects of long-lasting stressors such as the COVID-19 pandemic or climate change. Specifically, we will explore interrelationships between elements of executive functioning (control processes that help regulate cognition and behavior), trait and state aspects of psychological resilience (the ability to bounce back from negative life events), and heart-rate variability (a measure of brain-heart interactions), and determine if these variables predict young adults’ recent and long-term stress levels.

Prerequisites:
This project is designed to give an introductory research opportunity to inexperienced students. As such, there are no specific prerequisites other than enthusiasm and basic relevant coursework (e.g. introductory social science, life science, or statistics/data science classes).