2023 Project Descriptions for Rogers Program
Summer science research
Prerequisites must be completed by the end of spring semester 2023.
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 toxin gene family has evolved to have different phospholipid target specificities. We are comparing the effect on cells 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 insect cells. This work will develop skills in phylogenetic comparative analyses, bioinformatics, molecular biology and bioassays.
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 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 remain poorly understood. Defects in the formation of LROs underlie a number of human genetic diseases. We are discovering and 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.
Required course: Bio110
Desired course or courses: Bio202, 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, 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.
BIO 110/201. BIO 323 or 335 preferred.
Wilderness First Aid certification (wilderness first responder certification preferred) or willingness to complete certification this spring. Valid driver’s license and insurance for driving personal vehicle to research site (if driving).
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. The other skills can be taught if this sort of work is a new experience!
Students should be available approx. May 30-July 7, 2022 (6-week internship); shifts of this calendar, including 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, and are subject to change if conditions change.
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.
Desired: BIO202 (or BIO200); BIO311/312
Genetic factors of drug exposure effects in Drosophila melanogaster
Principal investigator: Norma Velazquez Ulloa
Long-term nicotine exposure, whether during development or in adult organisms, has deleterious consequences. My lab has characterized specific developmental, neural and behavioral effects of these two types of exposure in Drosophila melanogaster, the common fruit fly, and a proven model organism for identifying genetic mechanisms for diseases. In this project we will investigate the contribution of specific candidate genes and of specific mutations in influencing the effects of nicotine we have characterized. This is a 5-week project.
Minimum requirements: BIO110 and BIO202.
Other qualifications (one of more of the following): BIO252 or PSY280, BIO422, MATH255, BIO361, BIO311, BIO312, BIO352, familiarity with R, previous experience working with flies.
Neural development and 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 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.
Bio 202 or equivalent; Neuroscience background and/or interest. (Additional background in cellular or molecular biology is ideal.). CS background also fruitful.
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 octahedra, cubes, and rhombic dodecahedra 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 transmission and scanning electron microscopy techniques.
Glyphosate (Roundup) Degradation as a form for Phosphorus Recovery
Principal investigator: Louis Kuo
Phosphonates [RP(O)(OR’)2] are used as herbicides that are ubiquitous in the environment. We recently made several molybdenum compounds and polymers that degrade the herbicide glyphosate (i.e. Roundup) under mild conditions. The products are commodity chemicals, and this transformation represents a form of phosphorus recovery which is a national priority. Experimental methods will be used to elucidate a mechanistic route with modified glyphosate molecules. A heavy reliance on multinuclear NMR (nuclear magnetic resonance) is required as well as organic and inorganic synthesis. In addition, there is a biochemical and electrochemical component that entails concentrating the dissolved phosphate products for precipitation into commodity phosphate fertilizers.
Chem 220 or Chem 366 (preferred). Will have to supervise high school student(s).
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 cargos 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 220
Suggested Courses: Bio 312 and/or Chem 336
Urban Air Quality: Sources and Effects
Principal investigator: Jessica Kleiss
Recent widespread forest fires have increased public awareness of air quality, including the sources of air pollution, behavioral change, and health impacts. How is air quality perceived, as a result of the smell and taste of the air itself, media communication, and social cues? Which air pollutants pose a health risk to humans and nonhumans, and what are the spatial, temporal, and technological challenges of measuring them? This six-week research project will primarily focus on research design development: a survey of the literature, use and deployment of air quality sensors, meetings with specialists, and development of research questions and methodology.
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. Programmers will polish and playtest a game under development and begin designing the next one. Experimenters will conduct focus groups, design a survey, and launch an experiment that incorporates the game.
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
Principal investigator: Alain Kägi
My research seeks to widen the adoption of formal methods in building reliable and trusted distributed computing system components. Specifically, I want to establish if the field of formal verification has reached a level of maturity allowing us to answer the following two questions about a non-trivial distributed system component:
- Prove that its implementation adheres to its specification (functional correctness), and
- Prove that its specification satisfies desirable properties (e.g., confidentiality).
As a proof of concept, I am building a temperature sensor on a single-board computer applying rigorously standard software engineering practice of separation of concerns.
CS-172 or equivalent
Using Reinforcement Learning to Give Rapid Feedback during Hands-on Cybersecurity Exercises
Principal investigator: Jens Mache
Computers and software are all around us, and the importance of cybersecurity education is growing. 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 to explore building (and experimenting with) a semi-automated human-in-the-loop feedback system. Scenarios may include capture the flag, malware analysis and web applications.
CS-369, CS-211 or CS-293
Colorblind ideology moderates worldview threat from racial passing behavior.
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 experiment, student researchers will study reactions of adult human participants as they judge various behaviors. Participants will read messages refuting a colorblind ideological approach to intergroup relations (versus a neutral, control message). We predict that those in the experimental group will rate racial passers more favorably and show less cognitive depletion compared to participants in the control group. In the control group, participants’ own colorblind ideology endorsement will correlate with cognitive depletion 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.
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 and mathematical modeling to form a more cohesive physical picture of how cells swim. This is a half-time project – please consult with Dr. Bae about scheduling options.
Physics 251 (or 142) and math 225 are prerequisites. Experience working in a chemistry or biology lab is desired.