VPRI Undergraduate Fellowship Recipients
Faculty Mentor: Melissa Graboyes
Project Title: Oregon’s Response to COVID-19: Approaches and Outcomes to Social Distancing and Testing
Odalis Aguilar Aguilar
Faculty Mentor: Julie Weise
Project Title: Promesas Ingenuas/False Promises
Faculty Mentor: Melissa Graboyes
Project Title: 100 Years of Malaria in Zanzibar, East Africa
Faculty Mentor: David Garcia
Project Title: Hunting for prions: Using inheritance patterns in yeast cells to attribute epigenetic states to prion proteins
Faculty Mentor: Melissa Baese-Berk
Project Title: Influence of Listener Ideology on Perception of Non-Native Speech Intensity
Faculty Mentor: Ben Farr
Project Title: Improving accuracy in LIGO’s parameter estimation software
Faculty Mentor: Melissa Baese-Berk
Project Title: Effect of hesitation sound phonetic quality on perception of language fluency
Faculty Mentor: Laura Jeanty
Project Title: Supersymmetric Long Lived Particle Search
Faculty Mentor: Julie Weise
Project Title: Cultural Transitions: Language and Identity in Post WW-II Spanish migrants
Faculty Mentor: Amanda Cook
Project Title: Rational Design of Molecular Nickel Catalysts for Remote Hydrofunctionalization Applications
Faculty Mentor: Melissa Baese-Berk
Project Title: The Role of Semantic Predictability in Adaptation to Non-Native Speech
Major: Communication Disorders and Sciences
Faculty Mentor: Stephanie De Anda
Project Title: Language Dominance in Bilingual Spanish-English Children
Major: International Studies & Mathematics
Faculty Mentor: Clare Evans
Project Title: The Correlation Between Stigma Stemming from HIV and Antiretroviral Packaging: Design Recommendations for Introducing Discrete Packaging for Adolescents in Kenya
Faculty Mentor: Santiago Jaramillo
Project Title: Neural and behavioral assays for studying predictive coding in the mouse brain
Major: Human Physiology and Biology
Faculty Mentor: Ashley Walker
Project Title: Robo4 Project
Major: Computer and Information Science
Faculty Mentor: David Garcia
Project Title: Identifying New RNA-regulating Prions in Yeast
Faculty Mentor: Eric Selker
Project Title: Differentiation between PRC2 and H3K27 Methylation in Repression
Major: Human Physiology
Faculty Mentor: Elinor Sullivan
Project Title: The Influence of Maternal Fatty Acids and in Utero Inflammation on Child Behavior
Major: Cultural Anthropology
Faculty Mentor: Ana-Maurine Lara
Project Title:Navigating the Intersections of Political and Sexual Identity: Ethnographic Interviews among Queer Muslims in Oregon
Major: Human Physiology
Faculty Mentor: John Halliwill
Project Title: The Effect of pH on Histamine Release
Faculty Mentor: Scott Stewart
Project Title: Characterizing the role of Dach during bony ray branching in the zebrafish caudal fin skeleton
Major: Linguistics, Japanese
Faculty Mentor: Kaori Idemaru
Project Title: Acoustic Sources of Accent in Second Language Japanese Speech
Faculty Mentor: Edward Rubin and Melissa Graboyes
Project Title: The Effects of Abstinence-Only Funding on Teen Pregnancy and STD Rates
Faculty Mentor: Philip Washbourne
Project Title:The Influence of Sensory Systems in Social Behavior of Zebrafish
Major: Computer Science
Faculty Mentor: Ramakrishnan Durairajan
Project Title: New Capabilities for Self-Driving Networks
Faculty Mentor: Eric Selker
Project Title: Dissecting The Role Cohesin Plays in Influencing the Structure of the Genome in Neurospora crassa
Faculty Mentor: Melissa Graboyes
Project Title: “I Don’t Have Deaths on my Conscience”: Perspectives of Intravenous Drug Users on a Peer-Delivered Naloxone Program in Eugene, Oregon
Abstract: The United States is in the midst of an epidemic of overdose deaths. In response, harm reduction programs commonly distribute the opioid antagonist naloxone directly to drug users so that they can act as first responders to overdose. When injected, naloxone reverses respiratory depression and can save the life of a person overdosing on opioids. As evidence for the effectiveness of these programs at reducing deaths continues to be collected, little research has been conducted into the impact of serving in this role on drug users themselves. To better understand the lived experiences of drug users with naloxone, semi-structured interviews were conducted with seventeen syringe exchange participants who currently carry naloxone. Interviews revealed that carrying and using naloxone is empowering for many drug users, because it contrasts with the powerlessness they may feel in other aspects of their lives. Peer administrators use naloxone in a way that reinforces the community of care among drug users. This aligns with the goals of harm reduction programs, which seek to empower drug users to make choices to improve their lives, without abstinence as the ultimate goal. Future programs distributing naloxone to drug users should be aware of it’s potential not only to save lives, but to increase drug users’ selfconfidence and strengthen the network of overdose care in their communities.
Faculty Mentor: Dasa Zeithamova
Project Title: Behavioral and Neural Predictors of Individual Differences in Concept Generalization
Abstract: Concept learning involves linking related pieces of information to a shared label, like learning that furry creatures that bark are called ‘dogs.’ People vary is how well they learn concepts and apply them to new situations (generalization). What factors drive these individual differences? In the present study, we tested whether stable aspects of intelligence or transient activations in the brain best predicted concept generalization abilities. To measure aspects of intelligence, subjects underwent an assessment that included measures of working memory, processing speed, perceptual reasoning, and verbal comprehension, which could be combined into an overall IQ. Subjects also completed a concept generalization task while undergoing fMRI, allowing us to measure activations in brain regions that are part of the explicit rule-learning system (hippocampus, prefrontal cortex) or part of an implicit system that learns without awareness (caudate, posterior visual cortex). To elucidate the shared or dissociable roles of behavioral and neural predictors in concept generalization, we tested the relationship between accuracy in concept generalization and individual differences in measures of intelligence and activation in each brain region of interest. Behaviorally, we found that overall IQ, but not its subcomponents, predicted concept generalization abilities. Neurally, we found that only the activation in the hippocampus predicted concept generalization abilities. Finally, we found that IQ and hippocampal activation each predicted concept generalization above-and-beyond each other. These results show dissociable contributions of behavioral and neural predictors of concept generalization, suggesting that both stable cognitive abilities and transient brain states influence the ability to learn new concepts.
Faculty Mentor: James Hutchison
Project Title: The Development of a System to Determine the Size Dependence of In2O3 Nanocatalysts on CO2 Reduction
Abstract: The increase of carbon dioxide in the atmosphere has caused irreversible environmental effects, so reduction of this atmospheric carbon dioxide is necessary to prevent further environmental damage. Nano-catalysts are a promising new avenue in green chemistry as their small size and large surface area allows for less material usage as well as potentially superior chemical properties compared to their bulk counterparts. Bulk In2O3 has basis as a promising carbon dioxide reduction catalyst due to it being a poor hydrogen evolution reaction catalyst. Thus, In2O3 nanoparticles could be promising in carbon dioxide reduction.
By molecularly linking In2O3 nanoparticles to a boron doped diamond electrode via a molecular linker, the size dependence of In2O3 nanoparticles on the reduction of carbon dioxide can be determined. To enable this size dependence testing, a system to test this size dependence is developed and assembled. This system consists of In2O3 nanoparticles bound to a boron doped diamond electrode via an amine terminated carbon chain electrodeposited onto the boron doped diamond. It is hypothesized that smaller In2O3 nanoparticles will be more efficient carbon dioxide catalysts due to their increased surface area to volume ratio that promote a larger amount of active sites.Knowledge of the carbon dioxide reduction activity of a size range of In2O3 fills in a piece of the puzzle of about how to eliminate atmospheric carbon dioxide and reduce climate change effects.
Major: Human Physiology and Spanish
Faculty Mentor: Christopher Minson
Project Title: Hemodynamics of Post-Exercise and Post-Passive Heat Stress Recovery
Abstract: Recent research suggests that individuals exposed to heat stress chronically (e.g. sauna users) enjoy similar benefits as chronic exercisers. Many of exercise’s benefits are facilitated during the recovery phase, or the period of time following the cessation of exercise. By studying the cardiovascular responses during the recovery period following both heat stress and exercise, we can further explore clinically-relevant applications of heat therapy. This study seeks to compare the acute physiology of the recovery periods following exercise and hot water immersion (HWI). METHODS: 9 subjects (4 F, 5 M, age 22.4 ± 2.4 years) in random order exercised for 60 minutes at 60% VO2 peak and were immersed in 40.5oC water for 60 minutes on separate days. Measurements were made at baseline, during the interventions, and for 60 minute recovery period following both interventions. Heart rate, blood pressure, core temperature, and subjective measures were recorded every five minutes. Cardiac output, femoral and brachial artery hemodynamics were assessed using Doppler ultrasonography every 20 minutes. Skin blood flow was measured continuously during recovery. RESULTS: Brachial artery antegrade shear rate increased during HWI to a greater extent than exercise (p0.06). Skin blood flow following hot water immersion was significantly greater than that of post-exercise for the first 35 minutes of recovery (p<0.028). DISCUSSION: Many of the changes seen during the post-exercise recovery period that lead to beneficial cardiovascular adaptation are also seen during the post-immersion recovery period, suggesting hot water immersion may improve cardiovascular health.
Major: Human Physiology
Faculty Mentor: Ashley Walker
Project Title: The Effect of Pyridoxamine on Ages and Aortic Wall Structure
Abstract: Aging leads to arterial stiffening, likely due to increased advanced glycation end products (AGEs), oxidative stress, and collagen, which contribute to vascular dysfunction. Pyridoxamine, a form of vitamin B6, prevents age-related arterial stiffening. We hypothesized that pyridoxamine treatment will prevent AGEs formation in aged mouse aortas, while not affecting aortic wall structure.
Eight aged C57BL6 mice (18 mo) were treated with pyridoxamine in their water for six months and compared with eight vehicle control old mice (normal drinking water, 18 mo) and 6 untreated young mice (6 mo). Histological samples were collected. Aorta samples were quantified for AGEs via immunofluorescence. Aorta samples were also stained with Verheoff-Van Gieson and wall area was measured.
Young mice trended toward fewer AGEs than old control mice in the aorta (0.01 ± 0.003 vs 0.1 ± 0.05 AU), but the pyridoxamine treated animals were not different than old control or young mice (0.05 ± 0.02; p=0.11). The overall thickness of the aortic wall was unchanged between young, old treated, and old control subjects (area: 25840 ± 3388μm^2 vs. 34617 ± 5232μm^2 vs. 34165 ± 3377μm^2; p=0.3). Treatment did not change adventitial thickness between young, old control, and old treated groups (area: 21352 ± 2695μm^2 vs. 26102 ± 5006μm^2 vs. 30099 ± 4587μm^2; p=0.4).
These results indicate pyridoxamine treatment does not prevent the formation of AGEs or change the wall structure of the aorta in aged mice. Further studies are needed to identify the mechanism by which pyridoxamine prevents age-related arterial stiffening.
Major: Art and Art History
Faculty Mentor: Kristen Seaman
Project Title: Phrasikleia Kore: Alternative Roles for Female Viewership
Abstract: This research offers a new interpretation of the Archaic Athenian funerary monument to Phrasikleia by studying it in terms of female viewership. The monument is a “kore,” or standing female figure. It is well adorned, painted, and carved in marble with a short inscription on its base that informs the viewer that the young woman Phrasikleia died prior to marriage. It hails from pre-democratic sixth-century B.C.E. Attica (the area surrounding Athens) and is one of the most complete extant monuments of its type, having been buried shortly following its creation. However, while the sculpture and inscription have been used in many generalizing or comparative essays on such korai, Phrasikleia’s monument itself has not been given full scholarly attention. It is typically read in terms of elite male viewership, which closes many avenues of exploring the sculpture and its meaning for different audiences contemporary to it. Most readings of Phrasikleia’s kore discredit any alterity that she might represent, and instead see the work as fitting most norms for the sculptural type. My research analyzes its sculpting techniques, iconography, historical context, and viewership, and it reconstructs different ancient responses to the monument. The research will consist of exploring how the monument could have been read by some viewers as representative of a more ambivalent stance toward marriage as the only identity-making status for a Greek woman in the Archaic age, reconstructing female viewership of multiple class strata, and studying the nuances of the monument’s thematic conflation of marriage and death. I expect for my conclusions to use evidence from the monument itself, its find spot, ancient literature, and modern scholarship in order to construct a nuanced, feminine-centric study of the work.
Faculty Mentor: Andy Marcus & Peter von Hippel
Project Title: Investigating Gp32 Binding Behavior on Single-Stranded DNA With Different Polarity And Length Using Microsecond Resolution smFRET Measurements
Abstract: The single-stranded (ss)DNA binding protein (gp32) of bacteriophage T4 plays a central role in regulating the functions and integration of the helicase, polymerase and primase components of the T4 DNA replication system. The T4 replication system serves as an excellent model for higher organisms as it contains all the essential components for DNA replication. This project aims to investigate how polarity and length of the ssDNA affect gp32 DNA binding. We perform microseconds resolution single-molecule FRET (smFRET) measurements on four primer templates of 14-15 base pairs and different polarities. Data are analyzed using both second- and fourth- order time correlation functions. At the current stage of this project, our results indicate at least three different conformational stages for gp32 binding. Further analysis is required to compare if and how gp32 dimer bind differently on the different constructs.
Faculty Mentor: Matt Barber
Project Title: Host-microbe evolutionary antagonism in primates: HopQ’s role as a bacterial adhesin targeting CEACAM1
Abstract: How animals and microbes interact with each other can mean the difference between harmonious coexistence and deadly infection. These interactions create the potential for evolutionary conflict between host and microbial proteins which can contribute to antagonistic evolution of host and microbial genomes. Specific adhesion to host tissue cells is often a necessary first step in bacterial pathogenesis; “adhesins” are proteins on bacterial surfaces that mediate host cell adhesion and subsequently, invasion and infection. The N-domain of human carcinoembryonic antigen-related cell adhesion molecule 1 (CEACAM1), a host protein that modulates cell adhesion and other cell processes, is targeted and exploited by various human-associated bacterial adhesins. The Barber Lab at the University of Oregon has recently discovered that primate CEACAM proteins are rapidly evolving, suggesting an evolutionary ‘arms race’ with the bacterial proteins that target them. One such adhesin is HopQ of Helicobacter pylori. H. pylori is a bacterium that colonizes the stomach of ~50% of the human population worldwide and is the major causative agent for stomach ulcers and gastric cancer. It remains unclear how genetic diversity among adhesins such as HopQ impacts host specificity. We tested our hypothesis that HopQ will bind differentially to various primate CEACAM1 proteins by performing pull-down assays and western blots with H. pylori and recombinant, GFP-tagged, CEACAM1 N domains from a panel of primates. Interestingly, we found that HopQ binds to the N domains of human, chimp, and gorilla CEACAM1. We also found multiple sites of positive selection on HopQ that contact rapidly evolving sites in CEACAM1 lending support to a potential evolutionary ‘arms race’ between the two. These findings are directly applicable to human health, as the host specificity of a pathogen can determine what species are more susceptible to reverse zoonosis, the transfer of a disease-causing agent from humans to animals.
Faculty Mentor: Matt Smear
Project Title: Odor Concentration Change Sensing in Mice
Abstract: Our brains are constantly tracking dynamic sensory information from our environment. Exactly how the brain computes sensory input over time is not fully understood. The mouse olfactory system provides a great model to study stimuli changes over time because mice utilize odor concentration changes for olfactory navigation. It is not understood how mice optimize sensory information for spatial navigation.
One of the mechanisms guiding odor localization involves changes in odor concentration (ΔC). The ability to track odor concentration gradients is critical for vertebrates like the mouse for survival.
Previous work in the Smear lab has revealed a population of neurons in the olfactory bulb that respond to dynamic stimuli changes. The neural activity in this population of neurons was sensitive to concentration changes in odor.
The brain somehow maintains a neural representation of odor across sniffs, and this is the behavior I want to observe. A behavioral representation of these ΔC neurons had previously not been studied before. By investigating ΔC tracking behaviors in mice, my goal is to relate the neural activity we see in this neuronal population with a behavioral representation in mice and increase our understanding of sensory optimization.
Faculty Mentor: Michael Harms
Project Title: Thermodynamic and structural determination of metal and peptide binding to the human S100A9 protein.
Abstract: The human S100A9 protein is an important macromolecule found in large quantities in human neutrophils and at sites of inflammation. S100A9 has many functions including killing bacteria and turning on inflammation. It has been identified as a drug target to treat inflammatory disorders such as arthritis, but the mechanisms by which it achieves its diverse functions are poorly understood. In this study we investigated how S100A9 binds to two different types of targets as part of its biological function: 1) metals (which it sequesters to kill bacteria) and 2) innate immune receptors (which turn on inflammation). We measured binding interactions using isothermal titration calorimetry (ITC) and changes in protein structure using nuclear magnetic resonance spectroscopy (NMR). For the first project, we measured calcium and zinc binding to S100A9 by ITC and observed a large structural change in the protein by NMR. For the second project we measured binding of S100A9 to six peptides from the innate immune receptor TLR4. Only two peptides showed binding by ITC but three showed changes in structure by NMR indicating binding. We are further investigating where these peptides bind S100A9 by NMR. These studies show that S100A9 binds both calcium and zinc and that these metals bind cooperatively together. The peptide experiments showed that the peptides bind weakly to S100A9, which implies that binding may require a larger interface of TLR4. Determining how S100A9 performs these different functions is crucial to determining its role in disease states and what functions are involved.
Major: Math and Computer Science
Faculty Mentor: Ram Durairajan
Project Title: Improving Measurement Accuracy in Containers Through Trace-based Network Stack Latency Monitoring
Presentations associated with this research:
2019 Applied Networking Research Workshop
Abstract: Container systems (e.g., Docker) provide a well-defined, lightweight, and versatile foundation to streamline the process of tool deployment, to provide a consistent and repeatable experimental interface, and to leverage data centers in the global cloud infrastructure as measurement vantage points. However, the virtual network devices commonly used to connect containers to the Internet are known to impose latency overheads which distort the values reported by measurement tools running inside containers. In this study, we develop a tool called MACE to measure the latency overhead of virtual network devices as used by Docker containers. MACE is implemented as a Linux kernel module using the trace event subsystem to hook into key points along the network stack code path. Using CloudLab, we evaluate MACE by comparing ping round trip time (RTT) measurements emitted from a slim-ping container to the ones emitted using the same tool running in the bare metal machine under varying traffic loads. Our evaluation shows that the MACE-adjusted RTT measurements are within 20 microseconds of the bare metal ping RTTs on average while incurring less than 25 microseconds RTT perturbation. We also compare RTT perturbation incurred by MACE with perturbation incurred by the ftrace kernel tracing system and provide a perturbation breakdown for the various components of MACE to focus future development.
Major: Environmental Science
Faculty Mentor: Matthew Polizzotto
Project Title: Arsenic and Fluoride Contamination Analysis of Agricultural Topsoil in Guanajuato, Mexico
Abstract: Groundwater from Guanajuato, Mexico’s Independence Basin has recently been documented to contain elevated levels of arsenic (As) and fluoride (F) from past volcanic activity within the region. Guanajuato’s groundwater poses a potential health risk to residents that utilize the groundwater as drinking water, resulting in chronic exposure to toxic levels of As and F. Although contaminated groundwater is extensively used for irrigation, it remains unclear as to whether contaminants are accumulating in agricultural soils and threatening the quality of crops. Therefore, the primary objective of this work was to understand the scale of contaminant accumulation within the region’s topsoil. To do this, we analyzed fifteen batch soil samples from four farms within Guanajuato using inductively coupled plasma mass spectrometry (ICP-MS) for initial levels of arsenic in topsoil, then analyzed sixteen soil core samples from three farms using a fluoride ion selective electrode to form depth profiles for F accumulation within topsoil. We found that As in agricultural topsoil is currently below the EPA standard of 0.39 parts per million (ppm) for arsenic contamination in soils, ranging from 0.018 ppm to 0.059 ppm. Ongoing work is seeking to define the loading limits of As and F, which influences how much As and F the soil can retain. Ultimately, understanding how As and F accumulate within the region’s agricultural topsoil contributes towards creating a management plan in regards to how much and for how long local farmers can irrigate with contaminated groundwater before As and F levels in topsoil become potentially hazardous.
Fiona De Los Rios-McCutcheon
Major: Geography and Political Science
Faculty Mentor: Laura Pulido
Project Title: Environmental Narratives of Othering: Comparing English and Spanish Language Coverage of Air Pollution in Mexico
Abstract: The central question of my research project is: How do English and Spanish-language U.S. newspapers compare in their coverage of air pollution in Mexico? This research will be the basis for my undergraduate thesis for the Clark Honors College. I will be building off of research that Dr. Laura Pulido has already conducted on English-language coverage. I have drawn from existing scholarship in several subject areas for the literature review, including political ecology, U.S.-Mexico relations, media representation, and environmental history. Examination of media representation of environmental issues typically focuses on how well or accurately media portrays pressing environmental issues, while political ecologists evaluate the substantive efficacy of environmental policy and legislation. Studies related to environmental racism illustrate how global climate change and environmental degradation disproportionately affect communities of color. Very little literature covers how media engage in racial othering from an environmental perspective. This research will depend on a multidisciplinary approach for a thorough understanding of where environmental and racial narratives converge. I hope my research will contribute to a growing trend in academia and activism toward intersectionality. Dr. Pulido’s research suggests that English-language news coverage has engaged in the racial othering of Mexicans through the lens of environmental degradation. For comparison, I will be looking at La Opinión, which is the largest Spanish-language newspaper in the United States. I anticipate that La Opinión’s coverage will not engage in that same othering because of the large Mexican and Latinx community in Los Angeles, where the newspaper is based, and because most of the journalists writing for the paper are Mexican themselves. This research is important in the context of the Trump administration’s censorship of environmental issues and othering of marginalized people, particularly Mexicans. It is also essential to challenge dominant narratives that perpetuate harmful attitudes and to generate new narratives.
Major: General Social Sciences and Sociology
Faculty Mentor: Debra Thompson
Project Title: Racialized and Gendered Justice in the Criminal Court System
Abstract: Criminal courts facilitate mass incarceration and the disproportionate incarceration of people of color, especially Black people, and Black men in particular. While other research has been done around this topic, this study offers insight into how exactly this is produced in the courtroom specifically. This study sought to observe (1) the potential use of coded language in the courtroom as a proponent of mass incarceration, (2) the reproduction of race and gender-based biases in the criminal justice system, and (3) the role of the courts in both mass incarceration, and the disproportionate representation within the incarcerated population. This study employed an observational research approach which included the accumulation of both quantitative and qualitative data by recording the race and gender of main courtroom actors, every reference to race, gender, and/or class made in the courtroom, and a brief overview of each case in order to contextualize this information. The types of cases observed during this project include: Attempted Robbery, Burglary, Child Endangerment, Possession of a Controlled Substance with Intent to Sell, Robbery, and Theft (including Vehicle Theft). This study found that defendants for these cases were disproportionately Black and Latinx men, while the other main courtroom actors were disproportionately White, with all categories other than prosecutors also being disproportionately men. The structural dependency on police within the courtroom resulted in the court legitimizing all police discretion with no interrogation of bias. When defendants and their legal representation attempted to discuss any identity-based bias of the criminal justice system before a jury trial, this attempt was stopped by the judge. This study concluded that in order to produce justice, anti-racism must be made a genuine priority of the criminal justice system.
Faculty Mentor: Diana Libuda
Project Title: Characterizing Early DNA Break Repair in C. Elegans
Abstract: Accurate chromosome segregation is critical for the formation of viable gametes by the specialized cell division of meiosis. During meiosis, programmed double strand DNA breaks (DSBs) are formed and repaired by recombination mechanisms to maintain genomic integrity and to promote proper chromosome segregation. In order to better understand early repair dynamics of DSBs, we intended to devise a strain via CRISPR with an early repair phenotype closer to wildtype phenotype for future live imaging experiments. In past experiments, endogenously tagged GFP::RAD-51 mutants were utilized, but strayed from the usual wildtype phenotype. RAD-51 is a conserved recombinase that indicates an early repair stage of DSBs and is required for all meiotic recombination events. Using immunofluorescence, DSBs display distinct early repair dynamics through differential RAD-51 foci, leading to the hypothesis that these distinct dynamics indicate different DSB repair outcomes. Using the C. elegans model, we found that endogenously tagged GFP::RAD-51 mutants did not show a more wildtype RAD-51 foci phenotype after inheriting two copies of wildtype RAD-51 compared to worms that did not inherit the duplication. We also found that there is a significant difference between RAD-51 foci in early pachytene and late pachytene, the former having larger volumes and stronger intensities, representing interhomolog repair outcomes. In addition, interhomolog crossover repair outcomes show smaller, dimmer foci than do noncrossover outcomes. This indicates differential DSB end-resectioning between different stages within meiosis and between different repair outcomes.
Faculty Mentor: Shannon Boettcher
Project Title: Energetic Loss From the Use of Hole Scavengers to Measure Photoelectrochemical Cell Efficiency Limits
Abstract: Photoelectrochemical cells, which split water into hydrogen, a clean fuel, and oxygen, have shown great potential for efficiently storing solar energy. In these cells, the oxygen evolution half reaction (OER) limits the efficiency of the entire solar water splitting process. Therefore, accurate OER efficiency measurements are critical in evaluating electrode catalyst materials. Currently efficiency is measured using solution species known as hole scavengers. These species are assumed to collect all photogenerated holes, and thus indicate the energy conversion efficiency of the system. However, preliminary data gathered in the Boettcher Lab suggest that this assumption does not hold true for an entire class of OER catalysts, including two promising catalysts, NiOOH and FeOOH, because of their “conductivity switching” behavior. The purpose of my project is to show that hole scavengers introduce energetic losses in these electrodes, and to quantify these losses to provide a method for the accurate evaluation of OER catalysts.
Using a Dual Working Electrode (DWE) technique, I will take in situ electrical measurements to isolate electronic properties of the catalyst from those of the semiconductor on model photoanodes. I expect to find that hole scavengers hold surface catalysts, such as Ni, in their reduced state, thus creating an extraction barrier for holes generated in the semiconductor, and lowering the efficiency of the electrochemical cell. DWE data will be collected on two model systems: n-Si and Fe2O3 coated with impermeable and permeable catalysts, respectively. Finally, simultaneous mathematical modeling of these systems (via a Gummel iteration in Python 3.6) will provide a way to calculate the maximum efficiency for a photoanode sans extraction barrier. I expect that success in this project will provide a widely-adopted method for measuring the efficiency of photoelectrochemical half-cells that will accelerate the development of efficient solar water-splitting devices.
Major: Art & Technology
Faculty Mentor: Colin Ives
Project Title: The Body Electronic: Exploring the Permeability of the Self in the Age of Wearable Computing
Abstract: Steve Mann once said that the “goal of wearable computing is to position or contextualize the computer in such a way that the human and computer are inextricably intertwined.” My project will engage with the entanglement of body and technology through the production of a series of wearable computing accessories that explore the permeability of the self and the computer in the age of the internet. Specifically, I will ask 1) How has the development of portable computing and ubiquitous internet softened the borders of self-identity? 2) To what degree must technology interact with the physical body to become a meaningful part of it? 3) Since we use these technologies as extensions of ourselves, how does our engagement with them—both in their design and use—impart agency onto the technology itself?
My research and practice contributes to the quickly-growing field of human-computer interaction design. Though rapid innovation in the tech sector has produced incredible breakthroughs in computing, there is a need for alternative perspectives from outside the discipline; as technology becomes part of our very identities we must engage it with a critical and humanitarian eye. Visual arts practice is the ideal methodology for this engagement because the artist participates in every step of the design, execution, and communication of their work, allowing for a self-reflective analysis of the decisions and methodologies that contribute to the production of objects. This project will result in three end products: a collection of wearable computing objects, a production journal documenting my design and fabrication process, and a final manuscript detailing my findings for dissemination. My research-based practice will provide insight into human engagement with technological tools and will inspire discussion about the conception of self and the place of visual arts in the high-tech future.
Major: Physics and Chemistry
Faculty Mentor: David Johnson
Project Title: Elucidating the effects of nanoarchitecture on weak localization in (SnSe)m[TiSe2]2
Publications related to this research project:
Abstract: Single layer thick two-dimensional materials and stacks of different 2D materials (heterostructures) have caused much excitement in the materials community because they display properties not found in the corresponding bulk materials that can be optimized for applications such as energy storage and conversion. Understanding how the different 2D layers interact to produce emergent material properties is crucial for designing new materials. I propose to investigate these interlayer interactions by systematically varying the nanoarchitecture and observing the effects. Specifically, I propose to measure how the properties of compounds ([SnSe]1+Î´)m(TiSe2)2 vary as m is systematically increased, comparing my results to those found in the ([SnSe]1+Î´)m(TiSe2) system. The Johnson lab has demonstrated an extraordinary ability to control nanoarchitecture in heterostructures allowing for such systematic studies of properties as a function of nanoarchitecture. ([SnSe]1+Î´)(TiSe2) has a temperature dependent resistivity that indicates metallic behavior, but displays an upturn in the resistivity at low temperatures not found in the bulk constituents. A quantum mechanical effect known as weak localization, caused by electron-electron correlations, has been proposed to explain this upturn. The single conducting TiSe2 layer in ([SnSe]1+Î´)(TiSe2) is hypothesized to enhance electron-electron correlations. Preliminary work on the ([SnSe]1+Î´)m(TiSe2) system has shown that both the total resistivity and the magnitude of the resistivity upturn increase significantly from m=1 to m=2 and subsequently decreases as m is increased further. The thicker SnSe layers may change the properties due to increased charge transfer with the TiSe2 or change the extent of electron-electron correlation. Doubling the TiSe2 thickness is hypothesized to reduce electron-electron correlation, decreasing the magnitude of the resistivity upturn. Understanding how nanoarchitecture influences weak localization may provide insight about the physics behind the effect and inform on how to optimize this type of material for an application.
Major: Biology (neuroscience emphasis)
Faculty Mentor: Caitlin Fausey
Project Title: How Object Frequency Distribution Affects Early Word Learning
Abstract: Babies babble at 6 months, speak their first words at 1 year, and experience a rapid increase in vocabulary for object nouns around 2 years. Infants learn language for concrete objects before abstract concepts and there is a positive correlation between first learned nouns and the most frequently appearing objects in babies’ daily lives. However, exactly how infants acquire language remains a mystery to developmental psychologists and neuroscientists alike. Within this topic are two pressing questions: 1) How do infants acquire language from their everyday environments and experiences? 2) Is there an ideal approach to teaching infants new words? The sequential attention theory proposes that inductive category learning occurs via a series of comparisons between current and previous objects, drawing on similarities and differences between the two in sequence. Training learners with different object sequences alters attention and learning outcomes. Many studies teach children about objects using sequences comprised of equal numbers of each object. However, recent data suggest that this uniform distribution differs significantly from infants’ real experiences. Headcamera data, which recorded infants’ everyday visual experiences at home, reveal that most objects show up in skewed distributions, with some objects appearing much more frequently than others. My project asks: What kind of object frequency distribution is optimal for early word learning? With in-lab experiments I will compare word-learning outcomes under uniform object distribution against more realistic object distribution sequences. I will teach two-year-olds names of novel objects in three conditions: 1) uniform, 2) moderately skewed and 3) highly skewed object distribution. I expect that skewed training, which better models real-life experiences, will lead to better object name learning than the uniform training. The study’s findings will not only contribute to understanding how infants learn new words, but also has implications for general linguistic development and language teaching mechanisms.
Faculty Mentor: Adam Miller
Project Title: The genetic basis of the first connections of the brain
Abstract: There are an estimated 100 billion neurons in the human brain, equal to the number of stars in our galaxy. Nervous system function emerges from connections, or synapses, between these neurons, which can be either electrical or chemical. The synapses create a wired circuit analogous to a computer chip, but rather than being manufactured, the connections emerge over a prolonged period of development directed by an organism’s genetic code. Formation of the first synapses is critical to normal circuit wiring, as it lays the foundation upon which mature circuits are built. Past research has shown that these first synapses are electrical but it is unknown which genes are responsible for these connections and drive the continued development of these networks. This project aims to identify the genes required for the first synapses and investigate their roles from a genetic, neural circuit, and behavioral standpoint. This will provide a critical understanding of nervous system wiring, as genetic defects that alter normal circuit wiring have been linked to neurodevelopmental disorders such as autism and schizophrenia.
To explore the genes responsible for electrical synapses, we will examine the first spinal cord circuits that form in zebrafish. These neural networks provide advantages in studying synapse formation because they form within 24 hours post fertilization (hpf) in an externally developing embryo, use electrical synapses, are visualizable at the levels of neurons, circuit function, and behavior, and are genetically accessible. We have identified several genes-of-interest that may play a role in forming the first synapses and will examine when, where, and how these genes control the formation of the first synapses, analyzing them for neural network or behavioral changes. With this approach, we can identify the genes responsible for the first synapses formed in the brain and understand how these synapses impact early circuit wiring.
Faculty Mentor: Kevin Hatfield and Jennifer O’Neal
Project Title: Inter-tribal Dynamics of the Confederated Tribes of the Warm Springs and Grande Ronde Reservations
Abstract: In 2016, Northern Paiute tribal elder Myra Johnson Orange stated, “Before the coming of the white man, there were peaceful feelings among the tribes that are now, what I call, inter-tribal racism.” Myra’s statement seamlessly captures the central research question I am pursuing, comprised of two interconnected components. The first part examines how Oregon’s tribal history of the Western Valley and the Eastern region, specifically historical tribal animosities and alliances, has shaped and characterized contemporary inter-tribal dynamics on the Warm Springs and Grande Ronde Reservations. The second part explores what these contemporary inter-tribal dynamics look like in regards to cultural fusion, tribal and inter-tribal identity, cultural politics, and inter-tribal discrimination.
There currently exists little academic or historical research that specifically examines the cultural inter-tribal dynamics of either the Warm Springs Confederation or the Grande Ronde Confederation. With the creation of the Indian Reservation System, historically hostile tribes are forced to live together as one representative sovereign nation. The dominant discourse assumes that inter-tribal dynamics are characterized by a notion of unity and a semblance of tribal equality. However, this widespread assumption fails to recognize the individuality of each tribe and tribal member and inherently limits equal tribal representation on a political, social, and cultural level.
In an attempt to gain an exclusively Native perspective, I plan to conduct my research using a methodology of oral history within a framework of decolonization. Ultimately, my research will be discussed in a comparative framework, examining similarities and differences in both the tribal history and contemporary inter-tribal dynamics of the Warm Springs and Grande Ronde Reservations. I anticipate that the different geographic locations of each Reservation and the various levels of historical tribal engagement with the Bureau of Indian Affairs will indicate some degree of existing inter-tribal prejudice, discrimination, and racism in both communities.
Major: Earth Sciences (geophysics) and Applied Math
Faculty Mentor: Amanda Thomas
Project Title: Variation in Seismic-wave Attenuation along the Cascadia Subduction Zone Determined from Tectonic Tremor
Presentations related to this research project:
– American Geophysical Union
Abstract: Many subduction zones worldwide are known to host devastating large earthquakes, such as the 2011 M9 Tohoku-Oki earthquake. In addition to fast, seismic slip many subduction zones also host slow, largely aseismic slip. These “slow earthquakes” occur on timescales of weeks to months and are often accompanied by a weak seismic signal known as “tectonic tremor,” or simply “tremor.” Tremor behaves differently than regular earthquakes in that it is comprised of many small earthquakes that radiate low-frequency seismic energy and originate at the plate interface downdip of where large earthquakes typically occur. This behavior is thought to reflect variation in frictional properties, effective stress, or both in between the aseismic and seismic sections of the seismogenic zone (area capable of generating earthquakes). Seismic-wave attenuation is a parameter that quantifies the decrease in amplitude of seismic waves as a function of distance from the earthquake source. Estimates of attenuation are commonly used in ground-motion prediction equations (GMPEs) that quantify ground motion during an earthquake. Because tremor occurs frequently when compared to regular earthquakes in Cascadia, it presents an opportunity to better define attenuation parameters used for GMPEs in earthquake engineering. Our goal is to quantify seismic wave attenuation in Cascadia and determine its spatial variations using tectonic tremor. By inverting tremor ground motion data for the attenuation parameter, we can analyze if and how the results vary spatially in Cascadia and attempt to relate these variations to lithology and/or other physical properties. Changes in seismic-wave attenuation along the Cascadia Subduction Zone could result in significantly different ground motions in the event of a very large earthquake, hence quantifying attenuation may help to better estimate the severity of shaking in densely populated metropolitan areas such as Vancouver, Seattle and Portland.
Major: Cellular, Molecular, and Developmental Biology
Faculty Mentor: Karen Guillemin
Project Title: Determining the Fitness Advantage Conferred by Anti-inflammatory Gene Expression to Commensal Bacteria
Abstract: Commensal bacteria can signal to reduce or prevent immune responses that, when overactive, can cause chronic diseases like inflammatory bowel disease (IBD), attributing them a critical role in maintaining host health. People suffering from diseases like IBD have fewer commensal bacterial species known to reduce intestinal inflammation, while healthy individuals contain commensals that do provide this service. The host clearly benefits from reduced inflammation, however the potential evolutionary benefits to the bacteria are not known. Understanding why bacteria carry genes to reduce host inflammation may allow us to promote their inclusion in the microbial communities of patients with diseases like IBD. Afford
The Guillemin laboratory discovered that the zebrafish commensal bacteria Aeromonas secretes a protein, named IRP, that lowers the intestinal innate immune response. I previously investigated the benefits of IRP to Aeromonas and demonstrated that mutant Aeromonas lacking IRP (dIRP) suffers a colonization defect in monoassociations compared to wild type. Monoassociations are colonization by a single bacterial isolate and are artificial environments; I expect the defect to be worse in the context of a complex microbiota. Given this observable defect in dIRP, I am now asking whether I can rescue dIRP colonization by mimicking the effect of IRP in the host. The conditions I will test are: (1) bacterial genetic complementation, (2) introduction of exogenous IRP, and (3) a transgenic zebrafish mutant lacking intestinal inflammation. If immune modulation by IRP is a mechanism evolved by Aeromonas that allows it to thrive in the host, then reduced immune response should promote successful dIRP colonization. An understanding of the benefits of an anti-inflammatory function to commensal bacteria will allow us to manipulate microbial communities such that they foster bacteria with health promoting qualities.
Major: Physics and Mathematics
Faculty Mentor: Eric Torrence
Project Title: Search for Di-Higgs Resonance at the ATLAS Experiment
Abstract: In 2012, the Higgs boson, which explains how elementary particles acquire mass, was discovered with mass 125 GeV at the Large Hadron Collider. Still, the question remains whether there is only one Higgs boson, or several, which combine to explain the masses we observe in nature. Our research will study how a heavier Higgs boson could be found in the ATLAS data at the LHC. By the pure Standard Model phenomenon, we expect to find production of two discovered Higgs bosons from the tri-linear Higgs coupling. However, the rate at which this will happen is far below what we will be able to see for many years at the LHC.
The discovered Higgs boson can decay to different pairs of particles, and the rate is expected to be proportional to the mass of the decay particle involved. In fact, the most likely decay channel is H->bb at 33%, and the second most likely channel is H->WW at 25%. Therefore, HH->bbbb decay is the most possible, but HH->bbWW decay is chosen due to the presence of other irrelevant yet similar decays (backgrounds) in the two-b channel. Consequently, two W bosons could decay into two quarks, one lepton and its neutrino. The performance of identifying HH->bbWW events for large heavy Higgs mass will be studied specifically by using newly developed boosted object tagging. From the detector we would observe collimated jets from quarks such as b quarks merging into a single jet. By applying the relativistic kinematics theory and reducing some major backgrounds, we will be able to make the distribution plot along the mass energy. Our expectation is to see a bump on top of the distribution indicating the new physics particle that we are searching for.
Major: English and Journalism
Faculty Mentor: Barbara Mossberg
Project Title: Beyond Muses: Feminism and Gender in Modern Irish Literature (1880 – Present) from Augusta Gregory to Eavan Boland
Presentations related to this research project:
Sigma Tau Delta International English Honor Society – 1st Place Award in Essay Contest
Abstract: In the largely male-dominated Irish literary arts scene, the role of women has historically been confined to muses for men’s work. (Examples include James Joyce’s usage of his wife Nora as inspiration for Ulysses and Pulitzer Prize-winning poet Paul Muldoon’s treatment of his former partner Mary Farl Powers in his poem “Incantata.”) However, there is a critical mass of female-identifying Irish writers through whom one can trace matrilineal literary influence, from contemporary writers including Mary Lavin, Edna O’Brien, and Eavan Boland back to their modern predecessors, such as Lady Augusta Gregory. Gregory composed numerous works for the theatrical companies she co-founded in the late nineteenth century, in itself a feat for a woman at the time, and presents a complex figure to explore through a contemporary feminist context. Her creative work includes the sonnets A Woman’s Love Poems, which serves as a counterpoint to contemporary writer Eavan Boland’s poetry collections Domestic Violence and Against Love Poetry. Another significant contemporary feminist writer is Edna O’Brien, a trailblazer in writing about female sexuality, abortion, and the prevalence of Irish feminine iconography. Furthermore, her writing took place alongside real events such as the 1971 Contraceptive Train protest, in which women traveled to Belfast to purchase contraception despite Irish laws prohibiting birth control. My research begins by establishing an academic foundation from critical and historical works, then expands to archival research at University College of Dublin and University College Cork, and also incorporates interviews with Irish scholars. My research intends to establish that today’s female Irish writers produce significant models of female consciousness, and are the natural evolution of what is actually a long tradition of meritorious female Irish writers, thus bringing their history back into the light for new criticism, and creating a more complex understanding of modern Irish literature as a whole.
Faculty Mentor: Mark Carey
Project Title: Colonial-Environmental Narrative of the Great Basin in the 19th Century
Abstract: Between 1810 and 1820, Early Euro-American explorers of the Great Basin dismissed the region as “Snake Country,”—a lifeless area that could serve only as an over-land passage to the Pacific Ocean. Numerous and diverse indigenous tribes lived and thrived in the Great Basin, such as the Paiute, Shoshone, and Bannock. However the Euro-Americans’ descriptions grouped all of these tribes into the single category of “Snake Indians,” calling the Northern Paiute and other peoples, “the most miserable of the human race.” By the mid 1850s, the perspective of the white settlers had shifted: the Great Basin was referred to as a “fertile valley” while the Northern Paiute and other peoples had become a “savage,” warrior tribe. Historians have noted both the shift in the environmental narrative and the colonial narrative of the Great Basin region. However, they have only discussed these separately disallowing a cohesive understanding of the development of colonial thought. My research differs by viewing these constructions as a singular, intersecting narrative, which I refer to as the “colonial-environmental narrative.” I argue that understanding colonial thought in this way is imperative because the conceptions of the environment and people were ideologically inseparable and the intersection of narratives was vital to justifying the colonial project. Further, I hypothesize that the shift in narrative was a major factor for the Snake War in the mid 19th century. My research will primarily focus on the Northern Great Basin region and Northern Paiute people, because of my access to resources on this topic. Using diaries, letters, and paintings of early explorers and settlers, I track the change from approximately 1810 to 1875, which covers the beginning of Euro-American exploration to the dissolution of the Malheur Reservation in Southeast Oregon.
Major: International Studies
Faculty Mentor: Kevin Hatfield
Project Title: Genocide and the Northern Paiute: A History of Colonization, Dehumanization, and Extermination
Abstract: The Northern Paiutes, an American Indian tribe from Central and Eastern Oregon, experienced a significant reduction in their population at the hands of white settlers and the Oregon and federal governments over the course of the 19th century. Those who were left of the Northern Paiute population by the late 19th-20th century were subjected to cultural genocide in the form of severe assimilationist policies and economic subjugation through the reservation system. And yet, this is not a history that is widely studied, written about, or taught in schools in Oregon or around the country. My research will explore the Northern Paiutes in the context of settler colonialism in the 19th century in order to make the case that as occurrences of mass murder carried out by the state of Oregon and the federal government, the Northern Paiute were the victims of genocide. Current research into the subject has briefly referred to the Northern Paiutes as victims of genocide, but has yet to explore the relationship between settler colonialism and genocide in the region, as well as present a succinct argument to support the claim that genocide was committed. My research will show that frameworks for the analysis and identification of genocide drafted to address 20th and 21st century war crimes, such as the 8 Stages of Genocide, will prove that the Northern Paiutes were the victims of genocide at the hands of the Oregon and US governments.
Major: International Studies and Spanish
Faculty Mentor: Dan Tichenor
Project Title: Mexican Drug War: Displacement and Human Rights Affects on Guatemalan Refugees
Abstract: How does the current largest armed conflict of the Western Hemisphere, the Mexican Drug War, affect the displacement of Guatemalans and the treatment of their human rights? With a net-zero migration of Mexican nationals between the United States and Mexico since the end of the Great Recession in 2009 as well as the incorporation of Mexico into U.S. economics and politics through the North American Trade Agreement of 1994, Mexico has transformed from a state of origin to a “transit state” for Central American migrants. As a “transit state,” Mexico serves as a geographical bridge between the developed and the developing regions of the Americas, and so has replicated the restrictive immigration laws of the United States (as exemplified in the militarization of the southern border with Guatemala). While the violence of the drug wars spans across Mexico, Central and South America, it is complicity funded by the purchasing demand from United States. I expect results displaying the role of the United States indirectly facilitating violence against refugees as they are displaced by the Drug War and also restricted from asylum. My research will show original insight to the roles and responsibilities of both the Mexican and United States government to create suggested solutions for the regional conflict. From geopolitical and anthropological contexts, I plan to analyze the relationships between political, cultural and territorial conflicts regarding the Mexican Drug War as well as the cause of displacement and violations of human rights of migrants. My research will incorporate archival analysis, ethnographic observation, and interviews with political officials, journalists, lawyers, human rights and migrant advocacy organizations as well as migrants and refugees themselves. This research will be conducted in northern Guatemala, the southern border of Mexico, the capital in Mexico City, and locally in Portland and Eugene, where many Guatemalan refugees are currently seeking asylum.
Drew Jordan McLaughlin
Faculty Mentor: Melissa Baese-Berk
Project Title: Individual Differences in Perception of Variation in Speech
Presentations related to this research project:
Northwest Phonetics and Phonology Conference
Acoustical Society of America Conference
Abstract: Speech perception is a complex process due to widespread variability among speakers, and under adverse conditions it becomes even more challenging. Previous research of speech perception in adverse conditions has assumed that degraded speech is processed similarly whether it is caused by the environment (i.e., noise) or caused by the speaker (i.e., accent or disorder). However, recent research has indicated that this may not be the case and suggests that the perception of speech presented in an environmentally-based degradation requires different or additional cognitive processes than talker-based degradation. The goal of this project is to determine whether a listener’s ability to perceive speech in adverse conditions is a general process or whether listeners use different cognitive processes to overcome talker-based degradation and environmentally-based degradation in speech perception.
To answer this question, we will examine the ability to perceive speech in each adverse condition and compare this to participants’ cognitive abilities (such as vocabulary, inhibition, and working memory). Talker-based degradations will be tested using Mandarin-accented speech and dysarthric-accented speech (which each deviate from standard speech in different manners), and environmental degradation will be tested using energetic masking and informational masking. Cognitive skills (i.e., inhibition and working memory) will be measured using a number of standard tests.
We ask whether an individual’s ability to perceive specific types of speech degradation is correlated with their ability to perceive other types of speech degradation, and how perception in each condition correlates with other cognitive skills. It is possible that environmentally-based degradations will correlate with different or additional cognitive-linguistic skills than talker-based degradations. Determining whether certain cognitive abilities are linked to different types of speech degradation will be an important step toward understanding speech perception in adverse conditions as a whole.
Major: Anthropology and Romance Languages
Faculty Mentor: Carol Silverman
Project Title: Before the Spectacle: Shaping Gender and Class Identity in Beirut’s Beauty Salons
Abstract: Scholars have coined Beirut, Lebanon the trendsetting beauty city of the Middle East. Striking evidence for this includes 2007 National Bank of Lebanon billboards advertising plastic surgery loans and longs line of women waiting outside beauty salons every weekend. While previous studies of the Middle Eastern beauty industry have focused on the westernization of aesthetic models, my proposed ethnography explores the formation and interpretation of local beauty ideals in Beiruti salons and how they affect gender and class identity. To complement my salon research, I will also explore how these ideals are performed in spaces such as clubs, bars and cafés.
Specifically, I investigate 1) How do women mediate, choose, judge or reject models from local and global media? How do local models of beauty differ from global models? 2) What role do salon workers play in constructing local notions of beauty? 3) How do beauty ideals/treatments operate as mediums of social distinction among different classes of women? For example, which types of treatments access upward mobility and why? 4) How do these ideals function as instruments of women’s subordination, on the one hand, or resistance to inequality, on the other? How can beauty regimes be oppressive and/or empowering? 5) How do sites such as clubs, bars and cafés both influence and reflect ideals constructed in beauty salons?
Fieldwork will take place in two salons and five public entertainment venues located in differing socioeconomic areas of Beirut. I expect to reveal that beauty ideals/treatments operate as vehicles of social distinction and trigger competition for upward mobility amongst middle and upper class women. Beauty treatments may also foster solidarity among women; on the other hand, women may scrutinize each other. Finally, I hypothesize that in the parameters of Beirut’s male dominated society, beautification may be a strategic path to women’s emancipation.
Major: Environmental Science and Biology
Faculty Mentor: Matt Streisfeld
Project Title: Genetic architecture of local adaptation and reproductive isolation in Mimulus aurantiacus
Abstract: How do new species form in the face of ongoing gene flow? This question, which was first asked by Darwin, is still a topic of considerable debate among biologists. Recently, theoretical and field studies have shown that genetic architecture— the underlying genetic basis of a phenotypic trait, including the number of genes effecting the trait, their effect size, linkage, pleiotropy, and epistasis—is key to preventing the breakup of locally adapted traits. Traits controlled by a single gene of large effect are highly visible to natural selection, so are more likely to become differentiated than traits controlled by many genes of small effect. Additionally, adaptation usually involves many traits. If these different traits are controlled by the same sets of genes, gene flow between divergent populations will not be able to break them apart, maximizing reproductive isolation. Thus, theory predicts that isolating barriers are most effective if they have a simple genetic basis and are controlled by loci in the same genomic regions.
To test this hypothesis, I will use Quantitative Trait Locus (QTL) mapping to determine the genetic architecture of floral and vegetative trait divergence between red- and yellow-flowered ecotypes of Mimulus aurantiacus. These ecotypes are differentiated by pollinator preference but maintain ongoing gene flow. I will address the following questions: Are the phenotypic differences between the ecotypes due to a few loci of large effect or many loci of small effect? Do QTLs for divergent floral and vegetative traits overlap in one or a few genomic regions, or are they spread throughout the genome? By revealing the genetic basis of adaptation in M. aurantiacus, the results of this research will provide insight into the early stages of speciation by natural selection, contributing to understanding the effect of genetic architecture in the formation of new species.
Faculty Mentor: William Cresko
Project Title: The Genomic Architecture of Adaptive Divergence in G. aculeatus
Abstract: Adaptation generates biological diversity and has an important role in the origin of species. Understanding the genetics of this process is thus central to the field of evolutionary biology. Traditionally, adaptation has been thought to proceed through the accumulation of many mutations over time; however, recent studies of organisms which adapt extremely rapidly to new environments indicate the presence of other sources of adaptive variation. Populations of closely-related species often hybridize; if these species have adapted to different environments, hybridization can be detrimental because of its potential to erase the differentiation that suited each species to its environment. If, however, these species have adapted to similar environments, hybridization could bring new, favorable genes into a population, promoting further adaptation. My work in the Cresko Lab seeks to address where adaptive variation comes from, and how it is maintained, by investigating how hybridization affects the organization of the genome as the whole. Previously, I have studied hybridization between divergent populations of the threespine stickleback fish (Gasterosteus aculeatus) adapted to very different environments. I found that when divergent genomes are combined in a hybrid, mechanisms exist which resist the homogenization of genes and help maintain adaptive gene combinations. This summer, I will perform whole-genome sequencing of the ninespine stickleback (Pungitius pungitius), a relative of G. aculeatus. These species diverged some fifteen million years ago, but preliminary analysis of both genomes indicates that there may have been more recent genetic transfer between them, providing a source of adaptive variation to both species of stickleback. Using molecular biology, next-generation sequencing, and bioinformatic analyses, I expect to find regions of the threespine and ninespine genomes with evidence of recent genetic exchange, supporting the hypothesis that interbreeding between these species has facilitated adaptation.
Justine Vanloan Nguyen
Major: Human Physiology
Faculty Mentor: Kryn Stankunas
Project Title: VEGF Signaling Contributions to Heart Ventricle Development
Abstract: Cardiomyopathies are congenital heart diseases that affect the heart musculature. This leads to inefficiencies that cause the heart to become weaker and pump less blood efficiently. The purpose of my research is to study the developmental programs that underlie ventricular trabeculation and the role vascular endothelial growth factor (VEGF) plays in regulating this process. VEGF plays a distinct role in direct signaling of angiogenesis, the growth of blood vessels along with the cardiac muscle formation and trabeculation in the ventricles. If the pathway for the development of trabeculation in the heart is understood, then in a disease state, the knowledge of the gene pathways could lead to determining appropriate remedies.
During mouse embryogenesis, the cardiovascular system, one of the first major systems to develop, begins to form around embryonic 7.5 days (E7.5). It has to undergo drastic remodeling to meet increasing metabolic demands of the growing embryo and create a system that can efficiently transport blood throughout the organism. The muscular trabeculae, which are fingerlike projections, begin to develop at around E9.0.
In order to study trabecular development, pregnant mice are dissected when the embryos are between E9.0-E10.5 depending on the research question. Embryos are isolated and processed so that their hearts are examined through various cellular biology techniques. A highly specific small molecule inhibitor, Cabozantinib is used in order to inhibit VEGF signaling, thus disrupting the formation of the trabeculae. A VEGF inhibited sample can then be compared to an untreated wildtype sample to compare the differences in the trabeculation development.
Currently, there are two possible hypotheses that could explain VEGF signaling and its role in trabecular development. One hypothesis is that VEGF signaling is directly turning on a gene that directs VEGF signaling while the other hypothesis is that the two cell types (endocardial and myocardial cells) are directly interacting with each other due to VEGF signaling to turn on the development pathways for trabeculae.
Faculty Mentor: Anca Cristea
Project Title: Localized Economic Impacts of Immigration on the West Coast
Abstract: This project will use U.S. Census, Bureau of Labor Statistics, and Migration Policy Institute data to examine the impacts of immigration on urban labor markets on the West Coast. I will look at George Borjas’ negative selection theory, the idea that immigrants originating from developing countries migrate because they are unskilled, uneducated and unable to find economic success in their home countries, and contrast that with Daniel Chiquiar’s and Gordon H. Hanson’s 2002 findings that immigrants from developing countries actually tend to be middle or upper class immigrants with the skills and resources to navigate the immigration process. Breaking up labor markets into “skilled” labor and “unskilled” labor (based on factors like levels of education and training), I will investigate the correlations between the number of immigrants as a percentage of the local population and the local skilled and unskilled wages. I will also examine the correlation between immigrant population shares and other local economic outcomes such as local unemployment, product specialization and the regional composition of particular industries. In theory, an increase in the number of skilled workers in an area will lead to relatively lower wages for skilled workers and higher levels of production of goods requiring skilled labor. Theory also predicts that an influx of unskilled labor leads to similar effects on the unskilled labor market. Using the methods outlined below, I will test these theories in urban markets along the West Coast in an attempt to establish a causal relationship between immigrants’ size and demographic characteristics and their local economic impact.
Major: Physics and Mathematics
Faculty Mentor: Greg Bothun
Project Title: Wavelet Analysis of the PNI Climate Index
Abstract: The purpose of this project is twofold: to characterize the dominant climate cycles in the PNI and NEI climate indices, and to investigate the usefulness of various wavelets and transform algorithms for analyzing climate data. There are various packages available for wavelet transforms, but in order to determine the potential differences between wavelet bases and transform algorithms we will develop our own code.
One of the main issues with climate related data sets (and a large variety of other sampled data sets) is that they are extremely noisy. Typically, signal processing methods utilize Fourier analysis to determine periodic behavior. The low signal-to-noise ratio of climate data confounds standard Fourier methods, so alternate signal processing methods are required. Additionally, we are interested in the time coordinates of features of the original data, information which is lost in the Fourier transform. Wavelet transforms preserve the time domain features of the data, while also providing information related to the periodicity and amplitude of the data. Furthermore, wavelet transforms are well suited for detecting signals in noisy data.
While wavelet transforms have been applied to many different climate data sets, they have not been applied to the climate indices. The climate index is formed from sets of weighted data to provide a measure of the climate of a region. Climate data analysis typically involves direct analysis of highly volatile temperature or rainfall data, so application of wavelet analysis to the climate index may provide additional insight to overall regional behavior. We expect to be able to determine the dominant climate cycles in both indices and observe how they shift over the last century. If we find new cycles, further research can be done to determine their driving mechanisms. Finally, we hope to determine differences between applications of different wavelets and transform algorithms.
Sally Elizabeth Claridge
Faculty Mentor: Patrick Phillips
Project Title: Genomic Analysis of the Chronic Heat Stress Resistance Phenotype in Caenorhabditis remanei
Abstract: Organisms experience a wide range of stressful environments throughout their lifetime. These may originate from nutritional deficits or abiotic stressors such as acute heat, oxidative, or osmotic stress. Understanding the genetic architecture of stress response is important because it helps researchers evaluate how a phenotype of interest may respond to selection. Current research has found that stressful conditions of varying temporality and severity induce diverse physiologic changes in animals that promote cell protection and preservation, which reduces the metabolic cost to the organisms, decelerates aging, and extends lifespan. Obtaining a better understanding of how the genetics of a complex trait evolve under environmental stress could help elucidate how these gene regulation networks function as a whole and how their interactions over time affect phenotypic expression. Because stress response pathways have been linked to aging and homology exists between them and human disease pathways, determining these relationships could greatly benefit and advance research into human aging, neurodegeneration, and cancer. The goal of this research is to dissect the genetic basis of chronic heat stress, a model complex trait, in Caenorhabditis remanei. A population of C. remanei will be experimentally evolved in a chronic heat stress environment alongside a control population. Survival and fecundity data from both populations will be collected to serve as an estimate for the strength of selection in the heat stress population. Additionally, the survival and fecundity of evolved populations will be compared at higher temperatures to assess how the nematodes’ heat tolerance might have changed under selection pressure. Genomic changes in the descendant line that lead to adaptation are expected, and whole genome sequencing data from both the ancestral and descendant populations will be compared on a locus-by-locus basis, which will allow for the identification of regions under selection via allelic frequency statistics.
Faculty Mentor: Ramesh Jasti
Project Title: Carbon Nanohoops as New Bioimaging Probes
Abstract: Carbon nanohoops, are short slices of armchair carbon nanotubes that consists of benzene rings connected in a para-position to form a macrocycle. One of the many unique nanohoop properties being studied in depth in the Jasti laboratory is the ability to tune the fluorescence emission wavelength by changing nanohoop size. During my summer research I will attempt to study these unique properties in a cellular environment. This aim will be accomplished through the functionalization of the nanohoops to improve the solubility in aqueous solution and also to target them to specific areas of the cell. Carbon nanotube toxicity is a highly debated topic so this study may provide some insight into that topic as well.
The target molecules will be prepared using nanohoop synthetic pathways developed in the Jasti laboratory, while incorporating a novel benzylic azide as a functional handle. From here, a “click” reaction will be utilized to attach different alkyne substituents onto the carbon nanohoop. Initially, I will use β-D-lactose to functionalize the nanohoop structure. β-D-Lactose, a sugar derivative, is known to target specific areas in a cell, and thus we can track this localization using the nanohoop fluorescence.
In addition, the cytotoxicity and activity of these nanohoops and functionalized nanohoops will be studied. The fluorescence of the carbon nanohoops will allow us to visualize them in the cell and gain an understanding of the cytotoxicity of small slices of carbon nanotubes , which has not been studied before. My work and results will also be summarized in meetings with the Jasti and Pluth laboratories, and hopefully in future publications and presentations in conferences.