February 12, 2021

2021 Project Descriptions for Rogers Program

Summer science research

Prerequisites must be completed by the end of spring semester 2021.

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 (or 110, 201, 202); uccessful completion of Bio Bio311/312, Bio 390, Bio 361, Bio 407, Bio 408 will be helpful but is not required.


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: BIO110
Desired: BIO202 (or BIO200); Bio361; or Bio369


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, for several weeks of long days of fieldwork carrying gear and working off-trail, and many hours spent on detail-oriented plant identification and data collection.

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

Other criteria:
    Wilderness First Aid certification (wilderness first responder certification preferred); valid driver’s license and insurance for 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. The interpersonal skills needed to work and live closely with other team members and maintain positive team dynamics is crucial.
    Students must be available May 24-July 2, 2021 (6-week internship); extensions through July may be possible.
    Living and working together to complete the fieldwork will require agreement to follow COVID precautions that protect the entire team, including other collaborators that may also be at the site. These precautions include Forest Service regulations, campus policies, and any other arrangements required by the primary investigators on the project. If a COVID-safe agreement can be made, housing may be provided during the days of the week/internship when fieldwork is active (likely to be a Forest Service house with bunkrooms shared with our and other research teams). At this point, there is no guarantee we will be able to proceed with this forest research experience.


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

 

The genetic mechanisms of nicotine and ethanol cross-tolerance in D. melanogaster.
Principal investigator: Norma Velazquez Ulloa

Nicotine and ethanol are prevalent drugs of abuse across the world. Epidemiological studies demonstrate a correlation in the use of these drugs. However, many studies about drugs of abuse focus on a single drug. Drosophila melanogaster has been validated as a model organism for the study of both, ethanol and nicotine. We want to use this model system to elucidate the genetic mechanisms of cross-tolerance between these drugs. This is a phenomenon in which previous chronic exposure to one drug renders the organism less susceptible to the effects of the other drug. We have candidate genes to test this summer.

Experience with D. melanogaster, microscopy, dissections, molecular biology, chemistry and biochemistry, steady hands, attention to detail, organization skills, ability to multitask, basic knowledge of R and statistics. BIO202 required. Course work in neuroscience (Intro to Neuroscience or Neurobiology or Brain and Behavior) or biochemistry (Structure Biochem or Metabolic Biochem or Neurochemistry or Biochem Lab) would be a plus.

The role of thrombospondin in normal development of the neuromuscular junction in Drosophila melanogaster.
Principal Investigator: Norma Velazquez Ulloa

The neuromuscular junction (NMJ) is the structure where neurons connect with muscles. This connection elicits muscle contraction, which is the basis of movement. Normal development of the NMJ is crucial for normal locomotion. Thrombospondin is a protein that play a role in establishing connections between neurons in the brain, but its role at the NMJ has not been studied. We have been investigating the role of thrombospondin at the NMJ, and our preliminary data suggests that this protein is important for NMJ development and normal locomotion. Further investigation is needed to validate our results.

Experience with D. melanogaster, microscopy, dissections, steady hands, attention to detail, organization skills, ability to multitask, basic knowledge of R and statistics, course work in neuroscience (Intro to Neuroscience, Neurobiology, Brain and Behavior) or Comparative Physiology would be a plus.


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 patterns of neuron production in the developing brain; and/or 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, 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.

Prerequisites:
Bio200; Bio311/312 is preferred

 

CHEMISTRY

Open Circuit Potential Oscillations as a Probe of Localized Corrosion of Zero Valent Iron
Principal investigator: Barb Balko

Iron corrodes in the environment when its oxidation is coupled to the reduction of another species. One way to follow the corrosion is to monitor open circuit potential (VOC), the potential at which the oxidation and reduction currents are balanced. Under certain conditions, it has been found that VOC oscillates as the iron cycles between corrosion and passivation. This cycling has implications for the success of iron permeable reactive barriers (used to remediate contaminants) and the integrity of iron-containing materials. The focus of this project is to characterize these oscillations and determine how they are affected by various experimental parameters.

Prerequisites:
CHEM 310

 

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.

Prerequisites:
Chem 120

 

Fundamental studies on organosulfur oxidation for environmental remediation by molybdenum catalysts
Principal investigator: Louis Kuo

Sulfide oxidation 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)

 

Glyphosate toxin degradation by molybdenum Complexes
Principal investigator: Louis Kuo

Phosphates are used as neurotoxic pesticides that are ubiquitous in the environment. We recently discovered several molybdenum oxo-peroxo compounds that degrade the herbicide glyphosate (i.e. Roundup) 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 identification of active species and intermediates in glyphosate degradation. Specifically, the project seeks to confirm key organo-immine intermediates in this degradation and their subsequent fate under aqueous oxidative conditions. A heavy reliance on multinuclear NMR (nuclear magnetic resonance) is required as well as possibly computation modeling.

Prerequisites:
Chem 220 or Chem 366 (preferred)

 

Exploring the Structural Basis of Dynein Regulation
Principal investigator: Nikolaus Loening

Motor proteins serve a number of functions in the cell, including helping transport biological molecules (cargo) to where they belong. One such motor protein, dynein, is important for moving cargo from the periphery of cells toward the center and in human cells needs to partner with another protein (dynactin) to move cargo across long distances. The regulation of how these two proteins interact determines what, when, and where cargo are transported. In this project, we will study how the interactions between these two proteins are regulated by changes in the structure of dynein using a variety of biophysical techniques.

Prerequisites:
Chem 120


INTERDISCIPLINARY

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

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. Finish conducting, 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.

Prerequisites:
Up to 4 students: CS 488 and experience with Unity game development platform ideal. Experience with this project a plus. CS 172 at minimum.
Up to 2 students: PSYCH 300 ideal, other upper-level methodology courses considered.

 

MATHEMATICAL AND COMPUTER SCIENCE

Removing Barriers to Cybersecurity Exercise Customization
Principal investigator: Jens Mache

Networked computers are everywhere, and the importance of cybersecurity is growing. This project explores how to remove barriers to cybersecurity exercise customization. This project extends previous research and explores ideas how to create an exercise builder (XBuilder) which includes a translator from a JSON description to scripts in Terraform and bash that create and configure Docker containers. Scenarios may include capture the flag, malware analysis and web applications.

Prerequisites:
CS-211, CS-293 or CS-369


PHYSICS

Deep learning phase transitions in quantum chromodynamics
Principal investigator: Mohamed Anber

In this project we aim to use machine learning/neural networks to probe thermal phase transition in quantum chromodynamics (QCD), the strong nuclear force. We map QCD to an X-Y spin model with discrete-symmetry-preserving perturbations and use convolutional neural network to analyze the system.

Prerequisites:
Strong experience in coding with a high level of independence. Prerequisite is that you are taking/already took Physics 252 (statistical mechanics).

 

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.

Prerequisites:
Preference for students equipped with skills learned in Physics 201: Experimental Methods in the Physical Sciences


PSYCHOLOGY

The Role of Inclusive Pedagogy in STEM Educational Games
Principal investigator: Diana Leonard

Educational Games is a novel approach to curriculum that emphasizes active learning through immersive experiences (Bowman, 2014; Dumit 2017), but which often lacks an inclusive pedagogical framework. This omission is especially likely in STEM classes which do not include culture, power, and identity in their core learning outcomes but which touch on these themes unintentionally. This project will use an online survey methodology to identify opportunities and threats to equity and inclusion that may arise from implementing educational games in a STEM curriculum with varying amounts of instructional support (Hogan & Pressley, 1997) and self-reflection (LaVaque-Manty & Evans, 2013).

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

 

Exploring the Relationship Between Trait Resilience, Cognitive Control, Eating Habits, and Stress During the COVID-19 Pandemic
Principal investigator: Todd Watson

This study will extend the literature on the psychological effects of the COVID-19 pandemic on college-aged adults. Specifically, we will explore the relationship between cognitive control and trait resilience (a personality dimension that helps people overcome or bounce back from negative life events). We will also explore if these variables predict individual differences in perceived stress levels during the pandemic, potentially unhealthy eating habits, and higher levels of attentional reactivity to food cues. Data collection for this project will be remote/online.

Prerequisites:
It is preferred (but not required) that students have previous experience with cognitive or neuropsychological testing, computerized experimental task development/programming, and online research.