University Archives

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Welcome to the University Archives electronic records community. The University Archives community in Scholars’ Bank is for university records in digital form. The material contained in Scholars’ Bank represents a small portion of the institutional records housed in University Archives. If you are interested in other historic or contemporary records not seen here, please contact Special Collections and University Archives at spcarref@uoregon.edu or 541-346-3068.

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Open Access
Inside Oregon Winter 2018: Priorities 101
(University Communications, 2018) Dorsch, Ed; Evano, George; Ward Leslie, Melody; St. Clair, Anthony; Dorsch, Ed
News for and about the people supporting the University of Oregon.
Open Access
Inside Oregon Summer 2017
(University Communications, 2017) Dorsch, Ed; Epifano, Melissa; Evano, George; Henderson, Bonnie; Nelson, Sharleen; O'Neil, Cheri; Dorsch, Ed
News for and about the people supporting the University of Oregon.
Open Access
Inside Oregon Summer 2015
(University Advancement, 2015) Camozzi, Rosemary; Evano, George; Graham, Jonathan; Munther, Courtney; Dorsch, Ed
News for and about the people supporting the University of Oregon.
Open Access
Leveraging Rehabilitation and Implantable Strain Sensors to Improve Bone Healing After Traumatic Femur Fractures
(University of Oregon, 2025-02-24) Williams, Kylie; Guldberg, Robert
The primary objective of this thesis was to quantify patient-specific loading and rehabilitation parameters to elucidate how specific rehabilitation conditions impact bone healing after traumatic bone injuries. Our overall hypothesis was that parameters of mechanical loading and exercise will impact bone healing. To test this hypothesis, we utilized three rehabilitation platforms that enabled investigation of distinct rehabilitation parameters. These platforms including (1) a rodent running wheel with engineered resistance brakes or on/off brakes to enable running of different intensities or durations, respectively, (2) a treadwheel with an adapted on/off brake as a scalable platform, and (3) altered treadmill with speeds conducive to rodent needs. These platforms allowed for the investigate of distinct rehabilitation platforms and their relationship to bone healing. We also used implantable wireless strain sensors that enabled real-time non-invasive monitoring of mechanical cues as a function of time, rehabilitation conditions, and healing status. In collaboration with University of Utah, we used these sensors and in vivo microCT scans to develop subject-specific finite element models to quantify niche mechanical cues during different rehabilitation conditions. We discovered that higher intensity rehabilitation, relative to rehabilitation of lower intensity, increased early-stage strain magnitudes and significantly improved bone healing, with explant femurs matching intact strength. Beyond loading magnitude, we also discovered the importance of both long term and short term on bone healing. Nonlinear multivariate analyses revealed that rehabilitation must balance activity and rest to improve bone healing, where rehabilitation with longer running distance and shorter daily rest periods resulted in 100% union after 3 mm bone injuries. These results further found that the necessary balance of rehabilitation and rest depends on subject-specific factors such as injury size since the same rehabilitation conditions resulted in only 20% union after a 2 mm bone injury but 100% nonunion after a 3 mm bone injury. Using previous studies to inform a rehabilitation regimen predicted to improve bone healing, we also found the importance of short-term rest between exercise loading bouts. Rehabilitation that involved steady-state running for 12 minutes significantly hindered bridging and bone formation compared to rehabilitation that involved intermittent rest periods between one minute running bouts. Systemic myeloid-derived cell types, previously predicted to impair bone healing, were also downregulated for rehabilitation with short-term rest periods. These results highlight rehabilitation with data-informed levels of intensity, activity, and both short and long term rest as a therapeutic to modulate early mechanical loading and the immune response to enhance bone repair.This work facilitated a deeper understanding of how specific rehabilitation parameters regulate mechanical cues and bone repair and validated an implantable sensor platform to further investigate mechanobiology. This thesis aids in the development of subject-specific rehabilitation with the novel insight into the importance of rest on bone healing. Our results challenge the fields focus on optimizing the loading magnitude to improve bone repair. In addition, this thesis provides foundational support for the commercialization of implantable sensor technologies to track implant mechanics as a noninvasive feedback of healing status and to inform personalized clinical decisions. This dissertation includes content from several published articles including Nash* et al. (2022) Connective Tissue Research; Nash* et al. (2022) Physiology in Health and Disease, Springer; Williams and Harrer et al. (2024) NPJ Regenerative Medicine; and Williams et al. (submitted 2024) Science Advances. *Publication under maiden name: Kylie Nash
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“I Don’t Know My Way Around Here Anymore”: Representations of Loss of Home in Novels and Memoirs by Contemporary East German Authors
(University of Oregon, 2025-02-24) Lehmann, Tobias; Klebes, Martin
In this dissertation, I analyze how contemporary German-language literature by authors from East Germany expresses the theme of losing one’s home. I explore whether and how they process their experiences of loss during the Wende through their writing. To achieve this, I conduct a close reading of three novels that address the loss of home following the unification of Germany: Neue Leben and Simple Storys by Ingo Schulze, and Wie es leuchtet by Thomas Brussig. Additionally, I provide necessary context by drawing upon personal narratives from two memoirs: Zonenkinder by Jana Hensel and Eisenkinder by Sabine Rennefanz.In Neue Leben, I analyze the letters of the protagonist Enrico Türmer to his sister, his friend Johann, and his fiancée Nicoletta. These letters, written in the first half of 1990, are published and annotated by an editor who pretends to be Ingo Schulze and is interested in Türmer, who has disappeared without a trace. Wie es leuchtet is based on individual plot strands developed separately from one another, which come together in a mosaic-like arrangement, creating a snapshot of German transformation. Brussig mixes fiction with actual events and individuals, bringing to life an essential part of the loss of home in Germany. In Simple Storys, 29 seemingly uncomplicated narratives reveal the collapse of an entire world in small everyday incidents. Ingo Schulze depicts the loss of his protagonists’ home, taken by surprise by world history, with precision, humor, and empathy. For Jana Hensel and Sabine Rennefanz, unification meant less a newly acquired freedom than a state of ‘metaphysical homelessness.’ In their memoirs Zonenkinder and Eisenkinder, they describe their childhood in the GDR, which was marked by uprooting and social change. The main contribution of this dissertation is to contextualize novels about the Wende and the loss of home, allowing for comparisons and highlighting intertextual references that have not been previously analyzed in this way. This dissertation contains literary representations, symbolisms, figures, and references that have not been coherently linked and conceptualized in interdisciplinary terms in previous studies.
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Dewey's Methodology
(University of Oregon, 2025-02-24) Ukai, Shunji; Pratt, Scott
This dissertation traces the development of Dewey’s methodology from the 1880s to the 1940s. The aim of the dissertation is twofold. First, it shows how traversing Dewey’s methodology indicates that the attempt to philosophize with Dewey necessarily culminates in a conception of philosophy that is against analytic philosophy and foundationalism. Second, it shows how philosophizing in Dewey’s wake irresistibly inclines toward protesting against totalitarianism for the sake of creating a more democratic culture. This dissertation achieves these aims by taking up Dewey’s major philosophical and religious predecessors in the dominant western tradition and how he moves away from them. The predecessors that I mainly take up are the following: materialism, Spinozism, Spencerism, Cartesianism, Leibnizianism, Kantianism, Christianity, and scholasticism. In the process of tracing Dewey’s engagements with these predecessors, I show how Dewey first arrives at the “psychological method,” then how he moves away from it for the sake of the “empirical method.” Essentially, Dewey abandons the “psychological method” because it reproduces the old type of philosophizing in which philosophy is taken to be a search to disclose some underlying ground. In the end of the dissertation, I return to the question of how Dewey’s methodology is against analytic philosophy and foundationalism, then to his anti-totalitarianism. Dewey’s methodology is against analytic philosophy insofar as it exhibits the same traits as the “method of intellectualism.” The methodology is against foundationalism because it reproduces the notion that the primary task of philosophy is to search out some underlying ground. Thinking with Dewey’s methodology is irresistibly anti-totalitarian because the unified empirical context that the “empirical method” ventures on to create exhibits democratic traits which are at odds with totalitarianism. I conclude this dissertation by conceptualizing the two as the tension between “democracy as a way of life” and “totalitarianism as a way of life,” and by showing that the Deweyan invitation to make the venture into experience may be reframed as an invitation to undertake “activism” against totalitarianism as a way of life.This dissertation includes previously published material.
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Thermal Comfort and Indoor Air Quality in Low Socioeconomic Status Classrooms
(University of Oregon, 2025-02-24) Coronado Cabrera, Maria; Kwok, Alison
Indoor air quality and thermal comfort influence student performance and wellbeing in schools. Most studies in this area have concentrated on measuring classroom environmental conditions and comparing them with student’s perceptions of comfort, specific academic tasks, or measures associated with health, like absenteeism. This approach, though valid, ignores the influences that modify and dictate classroom indoor conditions. For example, most adaptive opportunities (such as window operations or thermostat) are in the immediate control of the teacher, not the students. Additionally, facility maintenance and operations managers have specific policies and mandates that regulate and control the indoor environmental conditions of classrooms; many of these related to aging school facilities and limited funding. This is most pressing for schools located in disadvantaged communities, which often do not have sufficient funds to maintain or modernize their schools and may suffer more from chronic exposures to unhealthy environmental conditions. The objective of this dissertation is to characterize the environmental performance of low-socioeconomic classrooms in different contexts and investigate how teachers, facility maintenance and the classroom physical environment influence their indoor environmental conditions. The dissertation presents five chapters that investigate different aspects of indoor air quality and thermal comfort. The first chapter describes the mixed-method case study approach used in the subsequent chapters to study thermal comfort and indoor air quality in schools. The methodology aims to construct a holistic understanding of the building, occupant, and maintenance factors that influence indoor environmental quality in educational settings. The following chapters present three case studies that took place in schools in different locations in the Americas: Eugene, Oregon, Southern California, and Gran Concepción in Chile. The Oregon case study assessed the efficiency of ventilation strategies and protocols in one classroom during the COVID-19 pandemic for CO2 and particulate matter (PM2.5 and PM10) concentrations. The study found that since the outdoor air quality and temperatures were relatively ideal during the study period, occupancy levels, and teachers’ adaptive behaviors and activities were the major influences on indoor air quality. While the results are not generalizable, the case study showed that, on average, during mild weather seasons like the spring, natural ventilation could provide adequate ventilation rates for the classroom during normal use, and near optimal ventilation during emergency use, if all doors and windows remained open. The following case study investigated particulate matter concentrations (PM2.5 and PM10) in three schools in the Gran Concepción region in Chile, along with a survey of self-reported health symptoms from teachers. This area is characterized by high levels of energy poverty, so wood stoves are widely used to heat residences. In the three schools, indoor and outdoor PM2.5 and PM10 surpassed the World health Organization’s (WHO) air quality guidelines (AQG), and in some cases reached environmental emergency levels according to Chilean local regulations. Also, outdoor air pollution stemming from wood stove burning smoke and traffic didn’t appear to be an important health concern for teachers. The symptoms teachers reported more frequently matched those related to teaching in previous literature. The case study portrayed the urgency of improving IAQ in the region and showed the disconnect between air pollution concentrations and the chronic exposure concerns of teachers in a context of energy poverty. The final case study investigated the ways in which classrooms’ physical environment, teachers, and maintenance managers, influenced thermal conditions and IAQ in low socioeconomic status Southern California schools using a mixed-methods approach. The qualitative portion of the case study found that the construction of indoor environmental conditions in classrooms depended on 1) the effective communication between teachers and maintenance managers, 2) the adaptations to the classroom environment resulting from comfort, teaching and learning influences, and 3) managers’ ability to plan and execute maintenance, and respond to emergencies. These findings were complemented with the quantitative portion of the case study, where permanent classrooms of all ages and conditions outperformed portable classrooms regarding thermal comfort and ventilation. In addition, the thermal performance of classrooms directly reflected each school district’s temperature policies, and the results suggested that including controlled adaptive opportunities for teachers could be beneficial for energy efficiency and occupant comfort. The case study showed that teacher awareness, education, and training on indoor environmental quality are vital for the optimum use of building systems and the creation of ideal environmental conditions in classrooms. This dissertation includes previously published and unpublished co-authored material.
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Critique and the Ambivalence of Colonial Modernity: Towards a Postcolonial Genealogical Critique
(University of Oregon, 2025-02-24) Nobowati, Zeinab; Koopman, Colin
This dissertation develops conceptual and methodological tools from a variety of traditions, especially that of critical theory and Michel Foucault’s thought specifically, that can serve the development of a postcolonial genealogical critique, that is, a critique that rethinks the relationship between colonial history and the present and problematizes the postcolonial political order and its hold on our subjectivities. I think about Foucault’s philosophical tools as a method of analysis that is both conditioned by its colonial context and at the same time enables a certain critical interrogation of those very conditions.The first part of the dissertation develops and proposes genealogical postcolonial critique as a method for studying the normative ambivalence of colonial modernity, i.e., the entanglement of enlightenment and violence. Genealogical critique, a philosophical method of critique based on studying the history of the present and developed mainly by Nietzsche and Foucault, is an especially apt method for postcolonial critique, but I suggest that it needs to be modified due to its Eurocentric bias. The third chapter discusses the transformative work of postcolonial genealogical critique by highlighting its epistemological and affective work, as well as its practical implications for the pathologies of collective memories. The last two chapters articulate the possibilities of ethical and feminist self-transformation in postcolonial times by drawing inspiration from Foucault’s work on ethical self-practices. The fourth chapter reflects on the effects of the afterlives of colonialism in relation to the ethical self and explores the relationship between critique, ethical self-practices, and internalized oppression through an engagement with Foucault alongside Franz Fanon and Audre Lorde. The last chapter builds upon my work in the previous chapters to discuss the relevance of postcolonial genealogical critique for the study of the gendered afterlives of colonialism. More specifically, I focus on the study of gendered ideologies in post-revolutionary Iran and show how the historical lens of genealogy allows us to situate the development of gendered ideologies in the global context of colonial modernity and recognize the relationality between local political formations and transnational relations of power.
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Poetry Finding Itself: The Dialectic of Logos and Mythos
(University of Oregon, 2025-02-24) Donkin, Michael; Peppis, Paul
This dissertation critically examines the long-standing debate between prose and poetry, tracing its origins to the ancient conflict between mythos and logos. I argue that the dichotomy between prose and poetry is theoretically incoherent, a confusion that has historically obstructed a clear definition of poetry. Through a genealogical survey of lyric poetry’s evolution from ancient prayer and hymn, I demonstrate that lyric emerged as the principal poetic form in modern times due to its profound connection with mythical thought. Additionally, this work explores how the prose versus poetry debate’s incoherence has shaped modern literary theory, with a particular focus on an overlooked manifesto by Virginia Woolf, where she envisions a novel that synthesizes poetry and prose. Ultimately, I propose a definition of poetry rooted in the concept of “mythical speech,” challenging contemporary assumptions and offering a new framework for critically engaging with poetry in its diverse, ever-evolving forms.
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NEW METHODS FOR ELEMENTAL SULFUR ACTIVATION IN WATER: DEVELOPMENT OF HYDROPHOBIC SYSTEMS FOR SULFANE SULFUR UTILIZATION
(University of Oregon, 2025-02-24) Garcia, Arman; Pluth, Micha
Elemental sulfur (S8) is an underutilized source to study the role of sulfane sulfur, which primarily is a result of the low solubility of S8 in water (< 20 nM). However, a few examples in nature have demonstrated elemental sulfur can be stored within sulfur granules and hydrophobic pockets. To further understand the role and impact of S8 and sulfane sulfur related species this dissertation investigates new systems to increase the availability of S8 in water. The research presented in this dissertation is aimed to 1) develop systems to solubilize S8 in water, 2) investigate the thiol-activation of S8, and 3) further understand the rules to study S8 in water. Chapter I is a broad overview of reactive sulfur species and the role of sulfane sulfur in chemical biology. Chapter II is an initial investigation into applying surfactants to solubilize S8 in water and subsequent activity of the micelle/S8 system. Chapter III delves into applying cucurbit[n]urils (CB[n]) and develop a discreet host-guest system to solubilize, activate, and deliver S8. Chapter IV reports the development of ElliptiCB[n], a collaborative project that measures the ellipticity of solid state CB[n] hosts and host-guest complexes. This dissertation includes previously published and unpublished co-authored materials.
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Khrushchev’s Perestroika: The Sovnarkhoz Reform in Soviet Dnipropetrovs’k, 1957-1965
(University of Oregon, 2025-02-24) Ko, Kwangyeol; Hessler, Julie
This dissertation examines the 1957 Soviet economic reform that created regional economic councils, called “sovnarkhozes,” in place of central industrial ministries, many of which were simultaneously abolished. This reform represented a significant restructuring (in Russian, “perestroika”) of the system of economic management that had developed during Stalin’s First Five-Year Plan. It had both economic and political ramifications. Although the reform lasted only until 1965, its abandonment was neither inevitable nor a sign of the nonviability of the socialist economic system. Rather, it represented the potential for the Soviet system to adapt and change in light of new conditions and concerns. The Sovnarkhoz reform was not a failed reform to move toward a market economy and liberalism, as claimed in previous studies, but rather an attempt to make the planned economy more efficient and to advance Soviet society towards the communist future. The dissertation discusses the origins of the Sovnarkhoz reform in conjunction with a remarkable public discussion. Soviet people were invited to present their perspectives on the problems of the centralized system and their thoughts for reform. Although it is impossible to map the comments of the tens of millions of citizens who participated in the discussion onto the actual reform, the dissertation argues that the discussion illustrated participatory politics in the Soviet setting. A big question concerned the balance between centralized, sectoral decision-making and administration, or departmentalism, and regionalism. The dissertation argues that the seeming conflict between these two organizational principles was non-antagonistic, not a zero-sum game, and their relationship was continuously reexamined in subsequent years. Third, contrary to scholarship that holds that recentralization was already apparent in the Sovnarkhoz system as early as 1960, the dissertation shows that the personnel, structure, and work of the Sovnarkhoz continued to expand up until the dissolution of these councils. Finally, the dissertation examines the surprising role played by the Sovnarkhoz in foreign economic relations, arguing that it served as a middle ground connecting the local economy with foreign states. The dissertation rests on a vast source base, including the archives of Ukraine’s Dnipropetrovs’k Oblast’, central Soviet archives, and newspapers.
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From Data Gaps to Forest Futures: Mapping Current Conditions and Estimating Carbon Vulnerabilities in Southeast Alaska and Coastal British Columbia
(University of Oregon, 2025-02-24) Lamping, James; Lucash, Melissa
The temperate rainforests of Southeast Alaska and Coastal British Columbia are globally significant for their role in carbon storage and cycling, hosting some of the highest aboveground carbon densities in the world and large reserves of late-seral forest. Recent shifts in forest management practices have transitioned the region towards the conservation of late-seral forest, with the Tongass National Forest implementing young-growth management and British Columbia setting large areas aside for conservation. However, this region lacks estimates of forest composition and structure that are spatially complete across political boundaries. There is also uncertainty in how the interaction among young-growth management, climate change, and wind, the main driver of natural disturbance, will affect the future carbon storage capacities of these forests. The research presented is divided into three primary chapters. The first chapter utilizes a GNN modeling approach, integrating regional forest plot data with environmental predictors to estimate aboveground biomass, species-level biomass, basal area, and three other structural attributes across a vast and ecologically diverse landscape. The study identifies key environmental variables influencing forest structure and provides comprehensive maps highlighting spatial patterns of forest attributes. The second chapter focuses on the conservation of old-growth and mature forests, employing the GNN method to classify forest seral stages. It examines the distribution and extent of old growth and mature forests, contextualizing them within various protected areas and assessing their vulnerability to management policies. The third chapter models future carbon and species vulnerabilities under various scenarios of management and climate change using the LANDIS-II landscape model. Potential shifts in forest composition and carbon storage are quantified.
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Women in Local Language Media in Ghana: History, Political Economy, Content
(University of Oregon, 2025-02-24) Fofie, Ivy; Steeves, Leslie
This dissertation addressed a blind spot in feminist media history, political economy, and media women’s relationships with gender, sexuality, and media economy both historically and contemporaneously. It used multiple methods hinged on historical studies, feminist studies, and media studies, underpinned by a postcolonial and decolonial framework, to understand women’s adjudicator roles in male-dominated cultural institutions such as the media. First, it historicized local language advice show hosts who worked in media immediately before and after the liberalization of the Ghanaian airwaves and placed them within feminist media history. Then, it analyzed the content of contemporary shows through the lenses of gender and sexuality to understand their decolonial feminist praxis. Finally, it appraised the political economy of women’s media, making a case for the role of the audience in women’s social justice work in Ghana and in the global south.Findings suggest that historically, women working in advice shows, although they did not explicitly identify as feminists, espoused feminist ethos as adjudicators between state-mandated institutions and women and children. Their approach to gender and sexuality largely pre-empted a feminist decolonial future despite periods of forced heteronormative and unprogressive gender and sexuality discourse. Consequently, contemporary advice program hosts demonstrate radical feminist activism in its nuanced form, which is consistent with contemporary African feminist organizing, albeit with some problematic discourses. The study also found evidence of other mediating factors, such as age, ethnicity, and religion, that both empower and disrupt women’s activist work. Finally, the study found that women show hosts collaborate with herbal and aphrodisiac medicine advertisers to create the very problems they purport to solve and count on the revenue they generate through hyper-sexualized and over-sensational content to fund their programs and media organizations. The study, therefore, used a positive case of the role of the audience to suggest a blueprint for funding women’s media in global south contexts for maximum feminist impact. While critiquing women’s overall engagement with gender and sexuality, the research also argued that women’s media has the potential to make meaningful contributions provided they receive the right gender-sensitive training from feminist stakeholder organizations. Theoretical contributions to decolonial African feminisms are also discussed.
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Microbial and Biochemical Surveys Along the Geographical Gradient of the Oregon Coast
(University of Oregon, 2025-02-24) Habibi Soufi, Hengameh; Louca, Stilianos
To understand the factors shaping microbial assembly and community composition in intertidal sediments along the Oregon coast, we collected sediment samples from 10 cores at depths of 160–190 cm, spanning over 300 km. Using metagenomic and 16S rRNA data, we constructed functional and taxonomic profiles, revealing redundancy in functional groups but variability in taxonomic composition. Regression models using chemical data measured in lab, geographical distances, and environmental variables from public datasets failed to significantly predict taxonomic composition. However, permutation null model tests suggested that biological interactions play a significant role in driving taxonomic variation in subsurface sediments, namely through taxa excluding each other via different mechanisms.
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Fractional Topology in Hybrid Magnetic Skyrmions
(University of Oregon, 2025-02-24) Parker, William; McMorran, Benjamin
Magnetic materials were first used to record information over a century ago when Valdemar Poulsen used a magnetic wire recorder to record and play back audio in 1900. From that first device to the magnetic hard drives ubiquitous in big data centers today, there have been seemingly endless schemes for how to use magnetism to store and manipulate information. In that time, semiconductor information storage has gained dominance in consumer devices, but the relatively low cost and long lifespan of hard drives makes them the preferred choice in big data and commercial applications. However, hard drives have their own drawbacks, most notably their energy consumption - a 2016 study estimated that in 2014, U.S. data centers consumed 1.8% of total U.S. power consumption. A more recent study from the Electric Power Research Institute puts that figure at 4% of total U.S. power consumption in 2023, with generative artificial intelligence models pushing that number higher in years to come. The need for low-cost, low-energy, long-lifespan non-volatile computer memory is high and increasing. With this need comes a new candidate information carrier, the magnetic skyrmion. Magnetic skyrmions are topologically protected particle-like magnetic configurations that can be driven through a material at low current densities, making them promising for use in magnetic logic and memory devices. However, their integration into real world devices requires a better understanding of their structure and behavior, and the measurement techniques to achieve that. In this work, I lay out a theoretical framework to capture the novel topology of skyrmions in one of the most promising host systems, Fe/Gd multilayer thin films, and show how it explains their stability. I then describe novel magnetic imaging techniques, and apply them to this host system to gain a full understanding of the skyrmions within it.
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Early Life Assembly of Zebrafish (Danio rerio) Microbiomes
(University of Oregon, 2025-02-24) Smith, Caitlin; Singh, Nadia
Microbiomes can influence fish health and development and may play a role in fish evolution. How fish acquire their microbes, especially early in life, remains a fundamental question in microbial ecology. Here, I address this question using the model organism, zebrafish (Danio rerio). Zebrafish are a useful model vertebrate with which to uncover the relationships between a host and its resident microbes, and explore questions related to community assembly of the microbiome. Zebrafish develop quickly, hatching by 3 days post fertilization, and reaching sexual maturity by 75 days post fertilization. Zebrafish eggs can be sterilized to derive axenic larvae. Axenic larvae are a boon for microbiome research, since they allow researchers to study how a lack of microbiome influences larval health, or how individual members of the microbiome modulate different host responses. However, rendering these fish axenic removes the microbes that naturally colonize the eggs surfaces, erasing any contribution of the parents or the environment as source pools of microbes to the offspring. These microbes may be critical for egg survivability and larval development. In this dissertation, I explore the early-life microbiome assembly of zebrafish, beginning with the egg. In chapter 2, I review current literature on early-life assembly in fishes, drawing from research performed in other species, such as Atlantic salmon (Salmo salmar), brown trout (Salmo trutta), and lake sturgeon (Acipenser fulvescens), to inform my hypotheses regarding how the egg microbiome might be influenced by parental genetics, transmission, and developmental stage of the embryo. In chapter 3, I characterize the egg microbiome of zebrafish reared in the UO Huestis Zebrafish Facility, and address the role of parentage and embryonic development on microbiome composition. Finally, in chapter 4, I explore the roles of the parental microbiome and the environmental microbiome as sources to the egg and larval gut microbiome. The egg microbiome of zebrafish is dynamic, and composition rapidly changes between fertilization and hatching. I find that parentage and developmental stage are important drivers for microbiome assembly on zebrafish eggs. Post-hatching, the egg microbiome is also an important source to the larval gut microbiome, therefore its contributions to larval health and development cannot be ignored. I observed that the skin microbiome was a major source of microbes for both eggs and larvae, as was water collected from the crossing tanks in which the eggs were fertilized. This suggests that water may be an important medium of transmission of microbiota from parent to egg. Overall, this dissertation presents novel research characterizing the egg microbiome of zebrafish. Currently, this is an underexplored life stage with respect to microbiome assembly in this important model organism. These results have implications for future research on host-microbiome assembly and host-microbe interactions using zebrafish as a model.
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MECHANISMS OF MEMBRANE TARGETING AND ACTIVATION OF PHOSPHATIDYLINOSITOL-4-PHOSPHATE 5-KINASES (PIP5Ks)
(University of Oregon, 2025-02-24) Duewell, Benjamin; Hansen, Scott
The ability for cells to localize and activate peripheral membrane binding proteins is critical for signal transduction. Ubiquitously important in these signaling processes are phosphatidylinositol phosphate (PIP) lipids, which are dynamically phosphorylated by PIP lipid kinases on intracellular membranes. Functioning primarily at the plasma membrane, phosphatidylinositol-4-phosphate 5-kinases (PIP5K) catalyzes the phosphorylation of PI(4)P to generate most of the PI(4,5)P2 lipids found in eukaryotic plasma membrane. Recently, we determined that PIP5K displays a positive feedback loop based on membrane-mediated dimerization and cooperative binding to its product, PI(4,5)P2. In Chapter II of this dissertation, we examine how two motifs contribute to PI(4,5)P2 recognition to control membrane association and catalysis of PIP5K. Using a combination of single molecule TIRF microscopy and kinetic analysis of PI(4)P lipid phosphorylation, we map the sequence of steps that allow PIP5K to cooperatively engage PI(4,5)P2. We find that the specificity loop regulates the rate of PIP5K membrane association and helps orient the kinase to more effectively bind PI(4,5)P2 lipids. After correctly orienting on the membrane, PIP5K transitions to binding PI(4,5)P2 lipids near the active site through a motif previously referred to as the substrate or PIP binding motif (PIPBM). Our data reveals that the PIPBM has broad specificity for anionic lipids and serves a critical role in regulating membrane association in vitro and in vivo. The strength of the interaction between the PIPBM and various PIP lipids depends on both the membrane density and the extent phosphorylation on the inositol head group. Overall, our data supports a two-step membrane binding model where the specificity loop and PIPBM act in concert to help PIP5K orient and productively engage anionic lipids to drive the positive feedback during PI(4,5)P2 production. In Chapter III, we follow up on a recent study that showed PIP5K exist in a weak monomer-dimer equilibrium in solution but can shift to a dimeric state following membrane association. Dimerization potentiates PIP5K function, increasing lipid kinase activity 20-fold, providing a possible mechanism for the rapid PI(4,5)P2 generation seen during signaling events. In Chapter III we established a novel FÖrster Resonance Energy Transfer (FRET) biosensor to detect and quantify PIP5K dimerization on supported lipid bilayer technology using Total Internal Reflection Fluorescence Microscopy (TIRF-M). This FRET biosensor allows for the frequency and duration of PIP5K dimerization to be quantified with high resolution. We used this FRET biosensor to demonstrate that human PIP5K paralogs (α, β, and γ) are able to heterodimerize. Previous studies have shown that PIP4K enzymes inhibit PIP5K enzymes by an unknown mechanism. Here, we use the FRET biosensor to demonstrate the mechanism of inhibition is via blocking the dimer interface. The creation of this PIP5K dimerization FRET biosensor establishes a novel assay for examining how proteins and peptides modulate membrane-mediated dimerization of PIP5K, which will be critical for elucidating the mechanisms that control cellular PI(4,5)P2 lipid homeostasis in the future.
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Simulation of defects in molecular materials using ab initio methods
(University of Oregon, 2025-02-24) Gormley, Eoghan; Hendon, Christopher
Molecular materials such as metal-organic frameworks (MOFs) are emerging as an interesting class of materials for their wide range of applications as well as their customizability and tunability. Like other materials, the properties of molecular materials can be modified through the use of defects - however, the nature of these defects in these systems can be much more complex than in conventional materials. Because of this, modifying conventional computational methods is essential for understanding defects in these systems. This research addresses the limitations of traditional approaches by refining techniques for calculating chemical potentials and employing higher levels of theory, such as many- body perturbation theory (MBPT), to model the unique electronic structures of MOFs. These modifications attempt to account for the intricate chemical environments, large unit cells, and significant structural dynamics inherent to molecular materials. We propose that chemical potentials for defects should be calculated based on the reactions that form the defects, thereby incorporating the thermodynamics of covalent bond formation and cleavage, as opposed to referencing them to elemental phases and treating all atoms of a given species as thermodynamically equivalent. We also attempt to use MBPT to more accurately predict the electronic properties of these materials (thereby overcoming the underestimations of fundamental band gaps typical of simpler ab initio methods)which is essential to predict the stability of defects that these materials can host. Finally, a case study on Yttrium-based MOFs with HHTP linkers demonstrated the potential impact of defects and guest ions on conductivity, showcasing the practical implications of accurate defect modeling. Theoretical findings enhance the predictive power of computational methods for MOFs, informing material design and optimization for applications in catalysis, gas storage, and electronic devices. This dissertation includes previously published coauthored material.
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Fresh Quantitative Approaches for High-Throughput Characterization Using ChemFETs and Statistical Analysis
(University of Oregon, 2025-02-24) Banning, Douglas; Banning, Douglas
Anion receptors are an increasingly important area of focus in synthetic organic chemistry, especially in areas such as environmental pollution detection and remediation. Many organic anion receptors are hydrophobic, limiting their utility for direct evaluation of aqueous anion affinity. Electrochemical sensors such as chemically-sensitive field effect transistors (ChemFETs) can bridge this gap. Incorporation of anion receptors into the chemically sensitive membrane of a ChemFET can facilitate direct measurement of aqueous anion affinity of hydrophobic sensors. One key piece of information that this can elucidate is the relative affinities of anions with the host by direct comparison of detection limits for each anion. Relative ranking of anion detection limits can be compared to the Hofmeister series, especially useful for determining the placement of relatively unknown, reactive species into the Hofmeister series.Dodeca-n-butyl bambus[6]uril was used in the selective membrane of a ChemFET to produce the first reported placement of hydrosulfide in the Hofmeister series. The contribution of the binding pocket geometry on anion affinities was then explored by comparing anion detection limits of dodeca-n-butyl bambus[6]uril with dodecabenzyl bambus[6]uril. The utility of ChemFETs was then expanded to assess the anion affinity of metal organic frameworks (MOFs), to learn about the anion binding nature of a novel MOF. After studying the nature of host-guest interactions using electrochemical sensors, research efforts expanded to include a statistically-based analytical method for characterization of synthetic pathways. Design of experiments (DOE) is generally used to characterize processes, and quantify impacts of main and multi-factor interactions on desired outputs. In chemical applications, DOE can characterize syntheses, specifically the impacts of each factor (together or in isolation) on the resulting product. This information can then be used to provide optimization conditions to produce desired properties. Significantly, this evaluation technique can be applied to historical data in order to characterize reactions before running any new experiments. In this particular case, flat aluminum 13 (f-Al13) cluster was analyzed via DOE in an effort to optimize desired properties. This data was then used to provide optimization conditions for the factors of size (minimize) and polydispersity index (minimize). Two different sets of optimization conditions were used as a validation run to synthesize aluminum particles, demonstrating a drastic improvement in one of the two optimization conditions. Finally, other research efforts are examined and documented. These efforts include ChemFET characterization of anion receptors, synthetic challenges, and application of DOE to characterize and optimize reactions. Overall, this dissertation involves the coalescence of different areas of study in order to solve difficult problems.
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Understanding Spatiotemporal Variation in Plant Form-Function Relationships
(University of Oregon, 2025-02-24) Dawson, Hilary Rose; Silva, Lucas
Leaf traits represent the wide variety of leaf forms plants have evolved to maximize carbon gains over their lifetimes. Although extensive research supports the use of these physiological metrics, much variation in leaf traits remains unexplained. In this thesis, I address three influences on leaf trait variation: leaf ontogeny, environmental stress, and cross-kingdom interactions.In the first study, I use two evergreen dwarf shrubs as case studies to demonstrate that leaf traits vary depending on cohort (current year’s growth or previous year’s growth) in Vaccinium vitis-idaea and Empetrum nigrum. Despite this difference, researchers often do not specify which cohort they measured or differentiate between the cohorts. In the second study, I test how plant form and function hold in herbaceous prairie species under experimental drought conditions in a U.S. Pacific Northwest grassland. I found that plant form-function relationships were robust against drought, and leaf traits remained unchanged. In the third study, I used stable isotope tracers to determine if common mycorrhizal networks favor fungal resource acquisition at the expense of plant resource demands, or if they are passive channels through which plants regulate resource fluxes. I found that plant functional type and tissue stoichiometry were the most important predictors of interspecific resource transfer. This dissertation includes previously published and unpublished coauthored material.

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