February 08, 2022

2022 Project Descriptions for Rogers Program

Summer science research

Prerequisites must be completed by the end of spring semester 2022.

Please review application instructions and download the student application.

BIOLOGY

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.

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 how cells construct their organelles
Principal investigator: Greg Hermann

Lysosome related organelles (LROs) are cellular 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 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: Bio110
Desired course or courses: Bio202, Bio311/312, and/or Bio361

Using Living Collections to Understand Trait Variation and Plasticity
Principal investigator: Randall Long

Botanic gardens and arboreta provide a unique opportunity to study trait variation and plasticity in long lived species. Many of these organizations have the same species, planted across large environmental gradients; effectively establishing common gardens. They also have detailed records and staff that are knowledgeable about the collections and local conditions. The main goal of the project is to explore how growth and trait expression is influenced by distribution. We predict that species will have the highest success in gardens within their current ranges and species occupying large environmental niches will perform well in a large range of conditions.

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


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) or willingness to complete certification this spring. 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. The other skills can be taught if this sort of work is a new experience!
   Students should be available May 23-July 1, 2022 (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.


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

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.

Prerequisites:
Bio 202 or equivalent; Neuroscience background and/or interest. (Additional background in cellular or molecular biology is ideal.). CS background also fruitful.

 

CHEMISTRY

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

This project, a collaboration with Valerie Walters (University of Portland) and Miguel Ángel Cau Ontiveros (University of Barcelona), involves excavation of the ancient Roman city of Pollentia, in present-day Alcúdia, Spain, and spectroscopic analysis of paintings from the 15th century AD in the museum at the Church of Saint James. The research period is five weeks, from the end of June, 2022, to the end of August, 2022. At this stage of the pandemic there is no guarantee that we will be allowed to work in Spain. If the trip is cancelled, alternatives to field work can be discussed.

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

Fundamental studies on organosulfur oxidation for environmental remediation by molybdenum catalysts and tungsten 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 and tungsten 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. Experimental 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.

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 the synthesis of molybdenum coordination complexes.

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 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 120
Suggested Courses: Bio 312 and/or Chem 336


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. 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 on the significance of in-game identification with place and living circumstance for preparedness motivation.

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

 

MATHEMATICAL AND COMPUTER SCIENCE

Dependable Computing
Principal investigator: Alain Kägi

We seek to widen the adoption of formal methods in building reliable and trusted distributed computing system components. Specifically we 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.

Most of the research in computing security deals with detecting flaws in existing software or detecting attacks in our infrastructure. While it is important to spend resources on these “defensive” initiatives, we think it is also critical to look at the feasibility of more “offensive” strategies such as writing flawless software. It is considered much easier to find one flaw in our computing systems than to prove the absence of any flaws, but the rewards are great.

Prerequisites:
CS-172 or equivalent

 

Using Reinforcement Learning to Give Rapid Feedback during Hands-on Cybersecurity Exercises
Principal investigator: Jens Mache

Computers and software are everywhere, and the importance of cybersecurity education is growing. Hands-on cybersecurity exercises have great potential, but we need rapid feedback 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.

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

PSYCHOLOGY

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 study, student researchers will study reactions of adult human participants as they judge various behaviors. We expect participants to show greater cognitive depletion after reading about racial passing (versus control behaviors). Participants’ own colorblind ideology endorsement will correlate with cognitive depletion and subsequent derogation of racial passers, whereas their own racial essentialist beliefs will not. These results will support our model of racial passing as a worldview threat.

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

 

Exploring Dual Mechanisms of Cognitive Control, Resilience, and Empathy in the Context of the COVID-19 Pandemic
Principal investigator: Todd Watson

We will extend the literature on cognitive and personality traits that may serve as buffers against the negative psychological effects of the COVID-19 pandemic and other stressors. Using remote/online data collection techniques, we will attempt to dissociate two distinct mechanisms of cognitive control (processes relating to the ability to modulate goal-directed thoughts and actions). In addition, we will explore potential interrelationships between cognitive control, resilience (a trait relating to overcoming or bouncing back from negative life events), empathy (the tendency to compassionately infer others’ emotions), and individual differences in perceived stress levels during the pandemic. This position is 0.5 FTE.

Prerequisites:
Students should have basic training in research design and statistics (e.g. introductory science or social science methods or lab classes). It is preferred–but not required–that students have previous experience with cognitive or neuropsychological testing, computerized experimental task development/programming, data cleaning/management, and online research.