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Breaking the Rules: Post-Translational Modifications and Proteome Dynamics During Anoxia
No full textMost organisms are ill-equipped to survive anoxia, but some organisms have developed molecular strategies to mitigate the cellular stressors associated with a lack of oxygen. While it is established that anoxic survival is contingent on metabolic suppression, it is unclear what mechanisms support this change in gene expression. Gene expression is regulated by a variety of mechanisms within the cell, including alteration of chromatin structure through histone modifications and protein modifications which contribute to the ever-changing proteomic landscape of the cell. Protein modifications such as ubiquitylation can lead to the degradation of proteins, while modifications to transcription factors can change the relative abundance of proteins within the cell by upregulating or downregulating transcription. These mechanisms can be influenced by extracellular stimuli, allowing them to modulate the cellular phenotypes in response to environmental stressors. Embryos of the annual killifish Austrofundulus limnaeus have the greatest tolerance to anoxia of all vertebrates, making them the ideal model to study the cellular mechanisms necessary for anoxia tolerance. Understanding how epigenetic modification of histones may regulate gene expression may provide insight into how A. limnaeus cells utilize specific biological pathways to successfully survive and recover from anoxia.
Quantitative label-free mass spectrometry-based proteomics was used to quantify histone isoform abundance and histone post-translational modifications in developing embryos exposed to anoxia, and in an anoxia-tolerant cell line (PSU-AL-WS40NE) isolated from embryos of A. limnaeus. The proteomic landscape of WS40NE cells was profiled in response to anoxia and recovery from anoxia. Given the extreme nature of anoxic assault, I hypothesized that the epigenetic landscape and the proteome would be statistically significantly modified in response to anoxia. Subsequently, we expected statistically significant changes in protein abundance as a consequence of depressed cellular metabolism. In particular, I expected a downregulation of proteins that could trigger aberrant responses (e.g. dysregulated mitosis) and thus promote survival of anoxic stress.
My research found WS40NE cells experience drastic changes to the proteome during both anoxia and anoxic recovery, suggesting that gene expression is being altered at both the epigenetic and the proteomic level. Surprisingly, the histone global landscape of A. limnaeus embryos did not change in response to 24 hours of anoxia. This may be due to a need for epigenetic stability during embryonic development. Additionally, resolution at the cellular level is not possible with this type of analysis, as such work represents an aggregate of cell types. However, the histone landscape statistically significantly changed both globally and in a residue-specific manner in WS40NE cells exposed to changing oxygen availability. Both histone isoform abundance and histone post-translational modifications were differentially expressed during anoxia and aerobic recovery, suggesting that these histone post-translational modifications may be at least partially responsible for the alterations in the proteomic landscape. This research provides a foundation to understand the epigenetic and proteomic changes that may be key mechanisms of anoxia tolerance in this species, and may provide insights into how nontolerant species could be altered to survive anoxia
Urban Oregon Ash - Inventory and plan development in the face of Emerald ash borer
No full textThe invasive beetle, Emerald ash borer (EAB) was first detected in Oregon within an urban area of Washington County in 2022. The spread of this beetle has already begun to take its toll on its preferred host tree, ash (Fraxinus spp.). Though there are many species of ash throughout the urban area, Oregon only has one native ash tree, Oregon ash (F. latifiolia) which is highly associated with stream corridors and wetland habitats. Along our streams Oregon ash helps provide soil infiltration, streambank stabilization, stream shade, and other critical ecosystem services throughout private and public lands alike.
As EAB spreads it will kill much, if not all Oregon ash trees, which can grow to be over 100-feet tall when fully mature. Dead and weakened trees can pose severe social, economic, and environmental risks and impacts posing challenges with nearby homes, roads, and other infrastructure. EAB impacts coupled with other urban stressors including higher temperatures, drought, and soil compaction make for a complex and challenging dilemma resulting in significant economic burden to individual residents and government entities.
This presentation shares an Ash tree inventory and management plan development tool specifically for use in urban forested natural areas. These tools were created to help engage a variety of urban communities and municipalities for a proactive response to EAB, saving time and money. The sooner urban areas can complete an ash inventory, the sooner long-term management plans can be implemented, public health can be ensured, and economic savings can be realized
A 14-Year Content Analysis of School-Family Partnership Publications in Counseling: Trends, Gaps, and Future Directions
Get PDFThis content analysis examined 55 articles on school-family-community partnerships published in counseling journals between 2010 and 2024, identifying trends in publication type, methodology, and population focus. Most articles (54.54%) were conceptual, with Professional School Counseling leading in publication volume. Limited empirical research and a lack of focus on diverse populations were noted, with only 18.18% addressing racial minorities (primarily Latino and African American) and 5.45% focusing on rural communities. Four primary strategies for strengthening partnerships emerged: Inclusivity, Leadership and Empowerment, Equity-Focused, and Consistent Communication—each aligning with the school counselor’s roles in fostering collaborative, equitable partnerships. Recommendations emphasize a need for empirical validation of these strategies, especially for underrepresented populations, and training to enhance counselor self-efficacy and cultural competence. This study highlights opportunities to advance evidence- based practices in school-family partnerships within the counseling field
Data for: Forest Fires Increase Vulnerability to Midwinter Rain-on-Snow Snowmelt in the Western Oregon Cascades
No full textForest fires and rain-on-snow events in the seasonal snow zone of the Pacific Northwest are increasing in frequency and magnitude, yet the combined impacts of these events on snowpack and water resources remain poorly understood. We show that forest fires doubled midwinter snowmelt proportions in 2023 and 2024 compared to unburned reference sites in the western Oregon Cascades. Data from snow monitoring and micrometeorological stations installed across an elevational gradient revealed increased snowpack vulnerability during midwinter rain-on-snow events, particularly at mid elevations, where rain-on-snow induced snowmelt accounted for 23% more of total annual melt than at unburned sites. Enhanced net snowpack energy, dominated by longwave radiation at lower and mid elevations, indicates minimal buffering capacity of these already vulnerable snowpacks in high biomass burned forests to increasingly common rain-on-snow events. These findings underscore critical challenges for water managers balancing flood preparation and snowmelt-dependent water storage in a warming climate
Charging Ahead: Prioritizing Renewable Energy for Electric Minibuses in the Philippines
Get PDFThis study evaluates the environmental and economic impacts of transitioning to electric minibuses (e-jeepneys) in the informal transportation sector of the Philippines. Using a comprehensive model that simulates different e-jeepney uptake scenarios and electricity grid configurations, we analyze carbon emissions and energy costs. Data from the 2023 energy grid and vehicle emission standards are utilized to assess various grid scenarios, including net-zero and natural gas options. Our findings reveal that a 10% increase in e-jeepney uptake results in significant reductions in both carbon emissions (36 gCO2/km) and energy costs (0.70 PHP/km) when paired with a decarbonized grid. The study underscores the synergistic benefits of combining e-jeepney adoption with grid decarbonization and suggests that policymakers should pursue integrated strategies to maximize environmental and economic gains
Layout-Aware Quantum Circuitry and Algorithmic Extensions to Grover\u27s Algorithm
Get PDFLov K. Grover introduced, in 1996, Grover\u27s algorithm as a quantum search algorithm to find all solutions for quantum oracles representing classical problems. My research observed that the Grover diffusion operator of Grover\u27s algorithm gives wrong solutions when Boolean oracles are designed in some logical structures. Therefore, I invented the new controlled-diffusion operator for Boolean oracles as a new approach for Grover\u27s algorithm that always correctly solves the problem of Grover\u27s algorithm.
Another important problem in quantum computing is designing reliable and cost-effective quantum gates using reversible binary logic. In classical logic design, the stage of logic design can be separated from the stage of mapping topological circuits to geometrical architecture. In contrast to classical logic design, the stages of quantum circuit design are not separable.
For practical quantum applications, a quantum circuit is realized (transpiled) into the layout of a real quantum device. For a real quantum device, two factors affect the cost-effective transpilation: the utilization of supported (native) gates and the geometrical connectivity pattern of n neighboring physical qubits, where native gates ensure cost-effective transpilation and n ≥ 2. In this dissertation, I introduced two new approaches to leverage these two factors for real IBM quantum devices. The first approach initializes the uniform distribution for all qubits using IBM native √X gates, instead of using the conventional Hadamard gates, which are IBM non-native gates producing cost-expensive transpilation. The second approach geometrically constructs generic and cost-effective quantum gates using IBM native gates. In literature the Bloch sphere is used as a visualization tool for a quantum gate, which is initially designed using unitary matrices computations. In contrast, I introduced the Bloch sphere approach (BSA) as a geometrical design tool to design a quantum gate using the Bloch sphere, which leads to fewer unitary matrices computations.
I employed the BSA to design various generic and cost-effective quantum gates and libraries based on the layouts of IBM quantum devices. Using the BSA, I invented two quantum libraries to investigate the trade-off between scalability and reliability, for the purpose of how the input qubits of a quantum gate are routed into the layout of an IBM quantum device and how many ancilla qubits are utilized.
Experimentally, for the same layout of an IBM quantum device, I prove that the transpiled quantum circuits of oracles utilizing my two approaches always have lower quantum costs and shorter depths than those of the transpiled quantum circuits of the same oracles utilizing IBM non-native gates.
In conclusion, my dissertation helps to design correct and more efficient Grover\u27s algorithm and other algorithms (especially oracular search algorithms), using my invented controlled-diffusion operator and my introduced two gate-design approaches
Special Delivery: Special District Use of Collaboration to Solve Challenges
Get PDFAs the special district sector continues to increase in number across the U.S., understanding their role in public governance increases in value both to practitioners and academia alike. The state of the academic literature on special districts does not yet reflect the large size and importance of the sector and has been severely limited by available data, mainly coming from the U.S. Census Bureau. Existing research has focused on broad descriptions of the field of special districts, some studies focus on policy and political effects; but scant research analyzes behavior within and among special districts, particularly with their public entity partners.
This research aims to answer the question: When do special districts seek collaborative solutions to solve challenges? This research uses Qualitative Comparative Analysis to inductively and deductively explore the causes of special district collaboration across six descriptive case studies. For each case, a set of conditions was identified that resulted in a stable, public-to-public collaboration.
Each set of conditions was then compared and distilled down into three sets of minimized conditions producing the outcome. The QCA sufficient condition equations were influenced by the district’s size or scope--the larger districts had unique issues and condition equations affecting collaborative behaviors. The scope of each of the six districts, in terms of its budget, staffing, customers, and acreage, naturally divided into three categories, setting the stage for a proposed scope-based typology of districts. This research also contributes to the body of knowledge about special districts by contributing six qualitative case studies which supplements the sometimes problematic data available from the U.S. Census Bureau
Inciting Action by Analyzing Pachirat
Get PDFThe book Every Twelve Seconds: Industrialized Slaughter and the Politics of Sight by Timothy Pachirat explores “the politics of sight”, or the intentional invisibilizing or transparentizing of repugnant acts in order to encourage or limit them, through the case study of a beef slaughter house in Omaha, NE. While also utilizing the politics of sight, Pachirat hopes for great political and social change concerning the immoral acts that happen at meat plants through a radical act of transparency: a narrative ethnography. Writers with similar goals of great change in social and political issues can make use of Pachirat’s techniques, which this article explains and summarizes. His style of writing hopes not to just spread awareness but incite action. After analyzing Pachirat’s book, four helpful tips were gathered: 1) conveying an objective tone through storytelling can better persuade readers by presenting as unbiased; 2) evidence and writing structure can be most effective when the writer sticks to their strengths by reflexively drawing on their background; 3) writers need to assess the restrictions they are under and the audience they wish to reach when effectively inciting a population to action; and 4) transparency can incite great social and political change, but to maximize its effectiveness writers must work within larger discussions to practice storytelling which is thoughtfully done and context-specific to each cause. By understanding these techniques, writers can enter larger discussions of writing as activism, encourage dialogue of multiple political and social issues, and hopefully incite change through action
Advances in Theory and Computational Methods for Next-Generation Thermoelectric Materials
Get PDFThis is a review of theoretical and methodological development over the past decade pertaining to computational characterization of thermoelectric materials from first principles. Primary focus is on electronic and thermal transport in solids. Particular attention is given to the relationships between the various methods in terms of the theoretical hierarchy as well as the tradeoff of physical accuracy and computational efficiency of each. Further covered are up-and-coming methods for modeling defect formation and dopability, keys to realizing a material\u27s thermoelectric potential. We present and discuss all these methods in close connection with parallel developments in high-throughput infrastructure and code implementation that enable large-scale computing and materials screening. In all, it is demonstrated that advances in computational tools are now ripe for efficient and accurate targeting of the needles in the haystack, which are “next-generation” thermoelectric materials
Faculty Senate Monthly Packet March 2025
Get PDFThe March monthly packet includes the agenda, appendices, and the Faculty Senate minutes and attachments given for the meeting held March 3, 2025