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Opportunities in Science at Lewis & Clark

2020 Project Descriptions for Rogers Program

February 13, 2020

  • 2020 Rogers

Prerequisites must be completed by the end of spring semester 2020.

Please review application instructions and forms here.



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

Spiders in the brown recluse lineage have toxic enzymes in their venoms that target membrane phospholipids. Within the context of venom expression, the SicTox gene family lineage has evolved to have different phospholipid target specificities. We are analyzing diverse members of this gene family to infer the patterns and processes of molecular evolution of these enzymes. With these data we are inferring molecular determinants of specificity, and the functional consequences of specificity for prey capture. This work will develop skills in phylogenetic comparative analyses, bioinformatics, molecular biology and a suite of bioassays.

Bio 141, 151, 200 (or 110, 201, 202); Successful completion of Bio311/312 will be helpful.

Investigating how cells construct their organelles
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, molecular, and microscopy based tools.

Required course: Bio110 (or Bio151 or Bio200)
Desired course: Bio202 (or Bio200), Bio311/312, or Bio361

Regeneration and diversity in an old growth Pacific Northwest forest
Principal investigator: Margaret Metz

Student researchers will census a network of seed traps and seedling monitoring plots to understand the role of regeneration dynamics in the maintenance of diversity an old growth Pacific NW forest. Students will collect fallen leaf and seed material for sorting and identification to species, measure plant performance, the biotic neighborhood, and the abiotic environment to understand how many factors contribute to seedling recruitment and survival. The project will involve residence at a forest service site near Carson, WA several weeks, long days in the field carrying gear and working off-trail, and many hours spent on detail-oriented plant identification and data collection.

Course prerequisites:
BIO 141, BIO 110/201, or equivalent. BIO 223/323 or 335 preferred.

Other criteria:
Wilderness First Aid certification or willingness to obtain (wilderness first responder certification preferred); valid driver’s license and insurance if driving personal vehicle to research site.

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, attention to detail, the ability to work as part of a team. Housing will be provided during the days of the week/internship when fieldwork is active, but is a forest service house with bunkrooms shared with our and other research teams. The interpersonal skills needed to work and live closely with other team members and maintain positive team dynamics is crucial.
Availability- Students must be available June 1 through July 11 (6 weeks) with possible extensions to July 25.

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: BIO110 (or BIO151)
Desired: BIO202 (or BIO200); BIO311/312

Zebrafish neuroscience research

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: 1) measuring rates of neuron production in the developing brain; and 2) understanding the 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.

Bio 151, 202, or equivalent; Neuroscience background and/or interest. (Additional background
in cellular or molecular biology is ideal.)

Purification and Functional Specificity of 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. Venomous mixtures contain several gene families that express proteins which are biologically relevant. We are interested in how specific venom proteins from Sicariid spiders – Loxosceles and Sicarius - act to disrupt cellular structures, particularly phospholipids within the plasma membrane. This work applies molecular biology, cellular biology, and biochemistry to analyze the effects of venomous components on cells of select model organisms.

Bio200; Bio311/312 is preferred



Study of Protein-Capped Gold and Silver Nanoparticles in Wastewater Treatment
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 fare in the wastewater treatment process and interact with the natural environment. This project will examine the stability of gold and silver nanoparticles capped with bovine serum albumin under a variety of environmental and treatment conditions using UV-vis spectroscopy, dynamic light scattering, and transmission electron microscopy techniques.

Chem 120 or previous chemistry research experience

Development of a Self-Healing Stent
Principal investigator: Casey Jones

This project seeks to attach molecules similar to resveratrol, a compound found in red wine, to metal cardiovascular stents. Stents are delivered to patients with coronary artery disease, but often fail from improper healing. Our lab has established in vitro that resveratrol improves release of a compound responsible for cardiovascular healing. Now we are seeking to test molecules structurally similar to resveratrol. To accomplish this goal, we will (1) attach resveratrol analogues to metal surfaces, (2) characterize the release of these molecules in solution, and (3) evaluate the response of endothelial cells to the modified surfaces.

Organic chemistry (Chem 220)


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

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. This summer we will: 1. Conduct, and analyze results from, an experiment on knowledge acquisition via video games vs. web-based media; and 2. develop a game for a future experiment investigating effects of identification with place and/or living circumstances on preparedness-related outcomes.

4 students: CS 488 and experience with Unity game development platform ideal; CS 172 at minimum.
2 students: PSYCH 300 ideal, other upper-level methodology courses considered



Cybersecurity Analysis Scenarios
Principal investigator: Jens Mache

Cybersecurity analysis is of growing importance due to our increasing reliance on computers and networks. Current security scenarios typically lack interactive, experiential components and configuration flexibility. This project extends previous research and seeks to develop 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.

Desired “Computer and Network Security” and/or CS-293 “Networks and Web Development”;


Quantum chromodynamics
Principal investigator: Mohamed Anber

Quantum chromodynamics (QCD) is the theory that governs the strong nuclear force. The strong coupling nature of QCD is one of the most difficult problems in physics. This research aims to use new numerical/analytical techniques to shed light on some aspects of QCD.

Students should have strong mathematical and/or coding abilities. They also should be independent.


Rubidium Stabilized Optical Frequency Combs
Principal investigator: Andrew Funk

An optical frequency comb is a light field that consists of many different well defined and discrete optical frequencies (colors of light) where the different frequencies have a uniform spacing in terms of their frequency in analogy to the teeth of a regular hair-comb. Optical frequency combs have applications in quantum computing, precision measurements of fundamental physical constants, and even measurement of general relativistic effects. We will continue previous work on a homebuilt fiber laser and stabilizing it with rubidium vapor cells and diode lasers.

Physics 152 or equivalent. Preferred skills/experience: Experience with optics and lasers.
Experience programming in LabView. Experience in analog circuit design, analysis, and measurement.

Investigations into the Acoustics of the Mandolin
Principal investigator: Stephen 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.

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.


Identifying the effect of worldview threat from racial passing on the efficiency of cardiac function in adult humans
Principal investigator: Diana Leonard

Racial passing occurs when a person presents as a race other than their own. However, this act likely disrupts prevailing societal norms. In this study, student researchers will measure physiological reactions of adult human participants as they judge various behaviors. We expect participants to show less efficient cardiac performance while reading about racial passing (versus control behaviors), a threat effect that will be greater when passing is depicted as intentional. Participants’ own colorblind ideology endorsement will correlate with physiological threat and subsequent derogation of racial passers. These results will support our model of racial passing as a worldview threat.

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

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