Anadromous Oncorhynchus mykiss (steelhead) express diverse migratory behaviors and life history strategies. Adult migration timing diversity within steelhead is often categorized into divergent early- and late-migration phenotypes. On the Rogue River in Oregon, adult steelhead return from the ocean during distinct early-summer, late-summer, and winter runs. Additionally, some juvenile steelhead...
Breast cancer is the leading cancer in women with an estimated 13% of women in the United States developing a form of invasive breast cancer in her lifetime. The survival rate is estimated to be 85%, but the American Cancer Society estimates that early detection of breast cancer in the...
Urban stormwater runoff with a high impervious area can significantly impact pollution concentrations of receiving water bodies. The use of low impact development (LID), which mimics the hydrological properties of the site before development, has been studied in an increasing number of studies, and the available database has shown to...
Hydrological and biogeochemical processes occurring throughout a watershed are typically reflected in stream water chemistry, including in coastal watersheds. While Oregon Coast Range streams have been studied in the past, there is a dearth of knowledge in terms of seasonal temporal trends and spatial variability that this study seeks to...
Prior research has demonstrated that unique and salient objects in a visual display may capture an individual’s attention. However, researchers have shown that some individuals, such as those with video game experience, are better at resisting salient-driven capture compared to others (Chisholm et al., 2010). The first manuscript presented in...
Magmatic-hydrothermal ore deposits are giant geochemical anomalies in the earth’s crust most often generated by normal magmatic terrestrial processes. They are often associated with oxidized and hydrous intermediate to highly evolved magmas that have concentrated metals and have the necessary components to efficiently extract and transport them as ascending magmatic-hydrothermal...
The distribution of mobile marine predators often reflects underlying dynamic ecological processes. The geographical focus of this PhD is the South Taranaki Bight (STB) of New Zealand, where wind-driven coastal upwelling generates productivity and prey to support a blue whale foraging ground. The STB is also New Zealand’s most industrial...
Lone Lake is an approximately ninety acre lake in Langley, WA on Whidbey Island. Since 2008, Lone Lake has experienced a number of harmful cyanobacterial blooms (cyanoHABs). Since 2016, however, the intensity of these cyanoHABs have impacted both ecosystem functions and human activities in the watershed. In June of 2020,...
This study examines dissolved rhenium (Re) as a function of water runoff using river samples from two contrasting watersheds, the Eel and Umpqua Rivers in the Pacific Northwest, USA. These watersheds share many key characteristics in terms of size, discharge, climate, and vegetation, but they have a 10-fold difference in...
Melanocytes are dendritic, pigment-producing cells located in the skin and are responsible for its protection against the deleterious effects of solar ultraviolet radiation (UVR), which include DNA damage and elevated reactive oxygen species (ROS). They do so by synthesizing photoprotective melanin pigments and distributing them to adjacent skin cells (e.g.,...
The pozzolanic reactivity test (PRT) is used to quantify the pozzolanic reactivity of supplementary cementitious materials (SCMs). The PRT computes reactivity by measuring heat release (Q) and calcium hydroxide (CH) consumption, as interpreted using thermodynamic modeling. The robustness of PRT is examined by experimentally varying CH-to-SCM ratio, solution-to-solid ratio, sulfate...
Converting energy from ocean waves is a challenging area for control theory application because of the nonlinear dynamics in various time scales. Generally, wave energy converter (WEC) control is applied in order to maximize power absorption, in the most common wave conditions, and subject to the devices’ physical constraints. Commonly,...
Survival of ecological systems pivot on critical moments. In the arid John Day Basin of Eastern Oregon, extensive restoration of the stream and floodplain focused on supporting salmon has been ongoing for the past 20 years, but recurring short periods of extreme temperature increase and low flows result in mortality...
Passive acoustic monitoring is a valuable tool for observing the status of marine environments. Comparisons of underwater soundscapes over temporal and spatial scales can provide data to inform marine conservation efforts, including protection of threatened and endangered species. This dissertation utilizes passive acoustic data collected via a broadly spaced array...
The commercial groundfish fishing industry and groundfish research have a long concurrent history of activity on the Oregon continental margin. Within the non-whiting groundfish fishery, the target species are primarily flatfishes, sablefish, lingcod, and rockfishes, though landings of each have fluctuated over time. Recent work shows that over the past...
Household food availability is comprised of both food purchases and foods obtained from alternative sources, like social networks, community services, and household food production. While the food available at home is associated with eating behaviors, diet quality, and health outcomes of children and adults, the literature on food acquisition of...
Forest Vegetation Management (VM) is an important tool used in the Pacific Northwest (PNW) for reforestation. It has been well documented that VM increases seedling survival and crop tree volume growth. What is less understood, is how altering the plant community and successional trajectory affects the way the ecosystem uses...
Racehorses are elite athletes that undergo repetitive stresses from jogging, cantering, and galloping exercises, and there is significant evidence that the majority of racehorse musculoskeletal injuries are due to repetitive stress or overuse. Musculoskeletal injuries have negative consequences on the racing industry through the loss of use or death of...
Wheat (Tritium aestivum) is an extremely important crop worldwide. It accounts for almost one quarter of the calories consumed each day by more than one third of the world’s population, and is grown over more land area than any other crop. Wheat breeding programs constantly strive to increase or maintain...
Cnidarians and their symbiotic dinoflagellates form a productive mutualism that shapes marine environments. In this symbiosis, dinoflagellate species from the family Symbiodiniacea reside within cnidarian host gastrodermal cells and provide the host with photosynthetically fixed carbon in exchange for host metabolites. This nutritional exchange allows both partners to thrive in...
Classic biological control can be a powerful option for those tasked with managing biological invasions; however, some biocontrol releases lead to non-target attack – feeding, damage or development on species other than the target species. The cinnabar moth, Tyria jacobaeae L. (Lepidoptera: Erebidae) was introduced to Western Oregon as a...
Soil moisture strongly affects the balance between nitrification, denitrification and N2O reduction and therefore the nitrogen (N) efficiency and N losses in agricultural systems. In rice systems, there is a need to improve alternative water management practices, which are designed to save water and reduce methane emissions but may increase...
Watermelon (Citrullus lanatus) is rich in lycopene and citrulline and has high phenolic content and antioxidant capacity. Previous studies demonstrate the health benefits of watermelon intake on improved blood pressure regulation along with others. Similarly, cherries, raspberries, walnuts and green tea are rich in anthocyanins, polyphenols, and polyunsaturated fatty acids...
The buildup of reactive oxygen species (ROS) and reactive nitrogen and oxygen species (RNS) is known as oxidative stress. Oxidative stress results in a wide variety of modification to biological macromolecules including nucleic acids, lipids, and proteins. For at least 30 years it has been known that high levels of...
Anammox (anaerobic ammonium oxidation) bacteria are capable of providing low-cost nitrogen removal for numerous types of wastewaters. However, low growth rates cause long startup-times and inhibition by oxygen and metabolic substrates necessitate close process control to maintain performance. Incorporation of Simultaneous Anammox and Denitrification (SAD) into constructed wetlands could provide...
Private set intersection (PSI) allows two parties, who each hold a set of items, to compute the intersection of those sets without revealing anything about other items. Recent advances in PSI have significantly improved its performance for the case of semi-honest security, making semi-honest PSI a practical alternative to insecure...
Continental flood basalts represent short-lived but immense blasts of mafic magma to the continental crust. The youngest and smallest continental flood basalt worldwide, the Columbia River Basalt, initiated with the eruption of the most mafic member, the Steens Basalt (~16.9 Ma). The Steens Basalt is exposed in southeast Oregon, southwest...
Modification of microbial electrolysis cells (MECs) by altering the sizes of the anode and the cathode, or their interaction with the liquid stream affects the performance of the MEC, but it remains difficult to quantify how much each change will contribute to the overall performance. Through this study, a method...
The U.S. Pacific Northwest is home to one of the most extreme wave climates in the world with waves of 10 m in height arriving to the coast approximately each year. With an average water temperature of 12℃, the beaches in the region are too cold to go on a...
Methane is a product of biogeochemical processes which respond to changes in climate. The history of atmospheric methane is recorded by ice cores providing insight into past changes in these biogeochemical processes. This dissertation is comprised of three studies which focus on centennial- and millenial-scale variability of methane from ice...
Fungi play critical roles in ecosystem processes and interact with plant communities in mutualistic, pathogenic, and commensal ways. Fungal communities are thought to be influenced by both associated tree communities and soil properties. However, the relative importance of the biotic and abiotic drivers of soil fungal community structure and diversity...
Internal curing is a term used to describe a process in which curing water is provided to a concrete mixture from inside the mixture. Internal curing water has typically been provided in North America mixtures by using prewetted porous materials, like fine lightweight aggregate (FLWA). Alternative materials, such as superabsorbent...
Monitoring marine ambient sound using standardized methods supports assessments of ocean sound levels across widespread ecosystems. This thesis quantifies differences among coastal and deep-water marine soundscapes in the Atlantic and Pacific oceans. The sources of sound in a soundscape are compartmentalized into three components and compared over time and among...
The Toba Caldera Complex is the youngest resurgent caldera in the last 100 kyrs, formed from four overlapping eruptions starting 1.2 Myrs ago. The last caldera-forming eruption, the Youngest Toba Tuff eruption, occurred ~74 kyrs ago, emitting 2800 km3 of ash and pumice into the atmosphere and forming the caldera...
Porous carbon is indispensable in modern technology applications. It is used for energy storage, gas separation, water purification, catalyst support, and chromatography. The diversity of its applications stems from its unique properties, including high specific surface area, tunable pore volume, and chemical stability. Specifically, the large surface area provides high...
Cobalt germanides have been widely studied as semiconductor contact materials, but recent theoretical studies suggest that they may also be excellent catalysts for methane steam reforming with stabilities and activities comparable to noble metal catalysts. In order to study the catalytic activity of cobalt germanides, it is critical to first...
Solid solutions based on the perovskite ferroelectrics Bi₀.₅Na₀.₅TiO₃ (BNT) and Bi₀.₅K₀.₅TiO₃ (BKT) might someday replace current Pb-based ferroelectric and piezoelectric devices. This is one goal of the Restrictions on Hazardous Substances (RoHS) guidelines seeking to limit Pb in consumer devices. Although the Bi-based ferroelectrics are well suited to the task...
Software testing is a very important task during software development and it can be used to improve the quality and reliability of the software system. One potential way to reduce the cost and increase the efficiency of software testing is to generate test data automatically. Search-based approaches successfully generate unit...
Historically, the difficulty of obtaining pure cultures of abundant marine
microbial plankton has an obstacle to reconstructing the underlying
mechanisms of biogeochemistry in the ocean. While a number of dominant
marine species from the ocean surface have been cultured, the dominant
microbial plankton of the dark ocean proved far more...
Changes in environmental conditions in marine ecosystems could directly or indirectly influence distribution, abundance, settlement, and size at settlement of flatfish. Understanding species-specific and age-specific responses to environmental variability is important for managing commercially important flatfish stocks. Slope-spawning flatfish whose offspring rely on extensive drift from the slope (spawning) to...
Linking marine epizootics to a specific aetiology is notoriously difficult. Recent diagnostic successes show that marine disease diagnosis requires both modern, cutting-edge technology (e.g. metagenomics, quantitative realtime PCR) and more classic methods (e.g. transect surveys, histopathology and cell culture). Here, we discuss how this combination of traditional and modern approaches...
Understanding seasonal migration and localized persistence of populations is critical for effective species harvest and conservation management. Pacific salmon (genus Oncorhynchus) forecasting models predict stock composition, abundance, and distribution during annual assessments of proposed fisheries impacts. Most models, however, fail to account for the influence of biophysical factors on year-to-year...
Surface water and groundwater interactions are a key component in the functioning of stream ecosystems. Exchange of water between the stream and the hyporheic zone creates habitat for aquatic organisms and serves as a control for stream biogeochemical, thermal, and flow processes. This study takes a multi-method field-based approach to...
Cells represent microcosms of spatial and temporal structural organization, with the achievement of internal spatial organization relying upon a collection of macromolecular motor complexes to transport and localize components throughout the cell. Cytoplasmic dynein is one such motor complex, and is the principal ATP-dependent motor for retrograde transport along microtubules...
One of the important ‘hallmarks’ of cancer is angiogenesis, which is the process of formation of new blood vessels that are necessary for tumor expansion, invasion and metastasis. Under normal physiological conditions, angiogenesis is well balanced and controlled by endogenous proangiogenic factors and antiangiogenic factors. However, factors produced by cancer...
This thesis describes an investigation of the molecular basis of the substrate specificity and catalytic mechanism of a unique pseudoglycosyltransferase (PsGT) enzyme, VldE. PsGTs are a newly discovered group of glycosyltransferase (GT)-like proteins that catalyze the transfer of a pseudosugar to an acceptor molecule via a C-N bond formation. This...
Re-introduction of large wood for expanding hydraulic variability is an increasingly common practice, yet it is not yet known what elements of hydraulic variability are most beneficial to fish. In an experiment designed to emphasize the minimization of energy expenditure through controlled predation and drift, we investigated whether juvenile coho,...
The level of reactive oxygen species (ROS) is tightly regulated in biological systems as overproduction can lead to oxidative stress and result in a number of diseases. Due to its negative effects, antioxidants are studied and used against ROS in medicine, pharmaceuticals and therapeutics. Because of issues with the uptake...