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Opportunities in Science at Lewis & Clark

2019 Project Descriptions for Rogers Program

February 15, 2019

  • Rogers 2019

Prerequisites must be completed by the end of spring semester 2019. 

Please review application instructions and forms here.

 

BIOLOGY

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.

Prerequisites: 
Bio 141, 151, 200; 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.

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

 

How seedling functional traits interact with environmental conditions to maintain forest diversity in an Amazonian rainforest
Principal investigator: Margaret Metz

Many hypotheses about tropical forest diversity invoke processes that occur at the seed and seedling stage, such that regeneration dynamics are thought to create the template for future diversity of the forest canopy. Each hypothesis suggests predictions for particular patterns of growth and mortality which can be tested with empirical data. Student interns will visit Ecuador as part of a long-term study of the ecological mechanisms that influence the dynamics of tree seedlings in ways that promote or maintain tropical forest diversity. Interns will participate in an annual seedling census, collect seedling functional trait data, quantify light availability above monitoring plots, and work on data analysis upon return to Lewis & Clark. 

Prerequisites:

  • Course prerequisites: BIO 141 or equivalent. BIO 223 or 335 preferred.
  • Spanish proficiency (fluency, preferred: Bio 201 minimum, 202 or higher preferred)
  • Interns will be expected to take detail-oriented data in Spanish and work closely with Spanish-speaking collaborators.
  • Valid passport; availability to travel in May immediately following semester’s end.
  • Willingness to work under humid, muddy, buggy conditions with long days of strenuous hiking in a remote location with little to no communication to the outside world. Ability to remain focused on high quality, detail-oriented data throughout. Experience working in rugged field conditions or traveling in remote locations will be very useful, as will a positive attitude, attention to detail, 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 while far from home.
 
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 for several weeks, long days in the field (at a beautiful corner of the world), and many hours spent sorting small leaves and plant materials.

Prerequisites:

  • 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, attention to detail, the ability to work as part of a team, and the interpersonal skills needed to work and live closely with other team members.
 
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: BIO151 or equivalent
Desired: BIO200, BIO311/312

 

Identifying genes that mediate the effects of developmental nicotine exposure
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 use molecular biology to identify genes involved in nicotine’s effects. Students will also expose flies to nicotine and test them on behavioral assays. They will also dissect brains, stain them, and use fluorescence and confocal microscopy to determine expression of the genes involved in nicotine’s effects.

Prerequisites:

  • BIO151 or experience handling fruit flies and BIO200.
  • It is recommended that students have also taken one or more of the following courses: Intro to Neuroscience or Brain and Behavior, Neurobiology, Human Genes and Disease, Cell Biology, Molecular Biology, Biochem Lab, Animal Behavior, Comparative Physiology.
 
Investigating the role of thrombospondin in Drosophila synaptogenesis at the neuromuscular junction and its role in locomotion.
Principal investigator: Norma Velazquez Ulloa

Proteins of the extracellular matrix are important for nervous system and muscle development. Thrombospondins are glycoproteins that can interact with molecules in the extracellular matrix and also with proteins on the surface of cells. In mammals, thrombospondins have been shown to play a role in synapse formation in the central nervous system. In the lab, we are testing if thrombospondin has a role in synapse formation at the neuromuscular junction and on locomotor behavior in Drosophila melanogaster. This research will expand our knowledge about extracellular matrix proteins on synapse formation in the peripheral nervous system and on behavior.

Prerequisites:

  • BIO151 or experience handling fruit flies and BIO200.
  • It is recommended that students have also taken one or more of the following courses: Intro to Neuroscience or Brain and Behavior, Neurobiology, Physics, Math, Computer Science or have a background in robotics or engineering. 
 
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.

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

 
Cellular Effects 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.

Prerequisites:
Bio141, 151, 200; Bio311/312 is preferred

 

CHEMISTRY

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 

 
Chemical Archaeology in Mallorca, Spain
Principal investigator: Julio de Paula

This project continues a collaboration with Ronda Bard and Valerie Walters, of the University of Portland, and Miguel Ángel Cau Ontiveros, of the University of Barcelona, on the analysis of artifacts recovered from the ruins of the ancient Roman city of Pollentia, in present-day Alcúdia, Spain. We are also studying paintings from the 15th century AD in the museum at the Church of Saint James in Alcúdia. A Lewis & Clark undergraduate will be involved in both excavation of the site and analysis of artifacts and paintings. The main analytical techniques are Raman, X-ray fluorescence, ultraviolet and infrared reflectance spectroscopies.

Prerequisites:
At least one year of Chemistry is required (CHEM110-120, or CHEM210-220, or their equivalents.) 

 
Real world applications of zirconium vapor deposition
Principal investigator: Casey Jones

This project will explore interesting applications of surface modification of metal and/or polymer surfaces to design and test new materials. Two specific applications of interest in the upcoming summer are (1) design of a positively charged surface for the removal of negatively charged dyes and pollutants from waste water and (2) design of a novel surface modification to improve the quality of wine stored in stainless steel tanks. Students will learn surface modification and characterization techniques as well as test the feasibility of their functional materials.

Prerequisites:
Chem 120 

 
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:
Chem 220 

 
The Structural Basis of Phosphorylation on Dynein Regulation
Principal investigator: Nikolaus Loening

Cytoplasmic dynein is a 1.6 MDa motor protein complex that takes part in positioning organelles, assembling centrosomes, and transporting cargo in cells. One components of this complex, dynein intermediate chain (IC), is involved in interacting with non-dynein binding partners that regulate dynein’s cargo-binding activities and motility. The goal of this project is to use a number of biophysical approaches (NMR, CD, ITC, etc.) to help elucidate the structural basis for how phosphorylation modulates IC’s preference for its binding partners, even though the site of phosphorylation is outside of the binding site.

Prerequisites:

  • Biochemistry/molecular biology lab experience preferred…particularly experience with generating and working with single-celled organisms and protein samples (such as Bio 312 and Chem 336)
  • Coursework in biochemistry/molecular biology preferred (such as Bio 200, Chem 330, and Bio 311)
 
Organophosphate toxin degradation by molybdenum complexes
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 degrade pesticides/herbicides under mild conditions to produces value-added commodity chemicals; this represents a form of phosphorus recovery which is a national priority. Experimental methods will be used to elucidate a mechanistic route that begins with unequivocal identification of active species and intermediates in pesticide/herbicide degradation. Specifically, the project seeks to confirm key organo-immine intermediates in glyphosate degradation and their subsequent fate under aqueous oxidative conditions. A heavy reliance on multinuclear NMR (nuclear magnetic resonance) is required.

Prerequisites:
Chem 220 or Chem 366 (preferred) 

 
Sulfide oxidation by molybdenum catalysts
Principal investigator: Louis Kuo

Sulfide oxidation (R2S -> R2S(=O)) is key in the desulfurization chemistry of fossil fuels. Sulfur remediation from fossil fuels reduces acid rain production which results from petroleum combustion. To this end, we recently discovered several molybdenum oxo-peroxo compounds that carry out this oxidation under mild conditions. The sulfide- containing targets are models of thiophenes (sulfide organics) produced as byproducts in petroleum refining. Both experimental and computational methods will be used to elucidate a mechanistic route that informs the design of better reagents for sulfur oxidation that includes polymer-supported molybdenum complexes that have operational advantages of heterogeneous catalysis.

Prerequisites:
Chem 220 or Chem 366 (preferred)

 

INTERDISCIPLINARY

Machine Learning approach to multi-instrument observations
Principal investigators: Peter Drake and Jessica Kleiss

Clouds play a pivotal role in projections of climate change: cloud feedbacks have the potential to either enhance or diminish the expected global warming. Many ground-based and satellite sensors observe the amount and type of clouds present, yet all of them have different sensitivity to different cloud types, different vertical ranges, and different sources of error. This project aims to use a machine learning approach to combine different cloud sensors to produce a “best estimate” cloud observation that maximizes the strengths of available sensors. If you enjoy coding, working with data, and thinking about the natural world, this project is for you!

Prerequisites:
Previous experience with neural networks, such as CS 369 AI & Machine Learning, strongly preferred.
GEOL-170 preferred.

 
Rehearsing disaster: Understanding earthquake preparedness behavior using video games
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. analyze results from a previous experiment on how avatar features and resource richness affect preparedness-related outcomes; and 2. develop a game and a control condition for an experiment on knowledge acquisition via video games vs. web-based media.

Prerequisites:

2 students: CS 488 and experience with Unity game development platform ideal; CS 172 at minimum.

2 students: PSYCH 300

 

MATHEMATICAL AND COMPUTER SCIENCE 

Hitting Times of Random Walks on Graphs
Principal investigator: Yung-Pin Chen

A random walk is a stochastic process modeling the paths of randomly moving objects or values of quantities varying with uncertainty. Geometrically, random movements can take place in various spaces including the real line, the plane, a higher-dimensional Euclidean space, curved surfaces, or even simple sets with an algebraic structure likes groups, finite or infinite. Probabilistically, random movements can have independent increments, reinforced steps, or self-avoiding paths. In this project, we will survey the theory of random walks in a general space. In particular, we will focus on the study of hitting times of random walks on various graphs. We will compute the expected hitting times, analyze the eigen-systems of the Markov chains representing the random walks, and investigate how the geometries may impact on the hitting times.

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

 
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.

Prerequisites:
Required: CS-211 “Computer and Network Security” and/or CS-293 “Networks and Web Development”;

Desired: CS-369

 
Spectral problems
Principal investigator: Liz Stanhope

What do the resonance frequencies of an object tell us about the object?  Can we hear how many holes an object has?  Can we hear if it is twisted up? Can we hear its dimension?  The list of resonance frequencies of an object is called its spectrum.  So all of these questions are “spectral problems.”  Depending on the background and interest of the students involved in the project, we will study spectral problems in one of two possible settings.  The first setting is in graph theory – the study of the spectral properties of a class of graphs that relate closely to the theory of Markov Chains. The ideas involved in this study have applications in computer science.  The second setting is in differential geometry – the study of the spectral properties of a class of three-dimensional objects.  The ideas in this project are more closely tied to physics.  Essential to both projects are creativity, hard work, and a love for conjectures and proofs.

Prerequisites:
Recommended courses:  Math 215 and Math 225 (no required courses)

 

PHYSICS

Rubidium Stabilized Optical Frequency Comb
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 construct an optical frequency comb using a homebuilt fiber laser and stabilize the comb using rubidium vapor cells and diode lasers.

Prerequisites:
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: 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.

 

PSYCHOLOGY

Colorblind Ideology Moderates Psychophysiological Responses to Racial Passing
Principal investigator: Diana J. Leonard

Racial passing – presenting oneself as a race other than one’s own – is often viewed negatively (Dawkins, 2012). Our lab has previously shown that colorblind ideology contributes to moral condemnation of racial passers. In the current study, researchers will measure psychophysiological threat via blood pressure and heart rate variability. We expect that participants contemplating racial passing will experience greater threat after being primed with colorblind ideology compared to a contrasting prime in which group differences are embraced (multiculturalism). Psychophysiological reactivity will in turn predict negative evaluations of racial passers, supporting our model of racial passing as a form of worldview threat.

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

 
Teaching kids coding by blending digital and tangible technology
Principal investigator: Erik Nilsen

This project extends previous research on the benefits of combining digital and tangible technology to introduce computer programming concepts to young children. Four versions of a robotic programming environment called “Bee Bots” will be evaluated for effectiveness in teaching 4 – 9 year olds fundamental computer programming concepts including iteration, sequencing, looping and debugging. The main difference among the versions is whether the inputs and outputs are implemented using a graphical interface or with physically manipulable (tangible) controls on a robot. This research will be done in collaboration with a local science museum (OMSI).

Prerequisites:
None 

 
Spontaneous Eye Blink Rate Correlates of Attentional Control Over Food Cues
Principal investigator: Todd D. Watson

We will explore if spontaneous eye blink rates (EBR; a correlate of central dopaminergic activity in the brain) predict cognitive/behavioral responses to food cues, eating habits, and snack food consumption in healthy young adults. Separately, we will explore if variations in instructions alter EBR during cognitive task performance. This study will extend the literature by further delineating the neural correlates of attentional control processes that may be important in cue-induced food craving and relating these effects to both potentially unhealthy and healthy “real world” eating behaviors, as well as by exploring broader methodological issues in human electrophysiological research.

Prerequisites:
It is highly preferred (but not required) that students have previous experience with human electrophysiology, cognitive task development, and/or basic programming skills.

For more information:

Amy Timmins
Administrative Specialist I
timmins@lclark.edu