Fall-sown barley will be increasingly important in the era of climate change due to higher yield potential and efficient use of water resources. Resistance/tolerance to biotic and abiotic stresses will be critical. Low temperature is an abiotic stress of great importance. Resistance to barley stripe rust (incited by Puccinia striifomis...
The following dissertation consists of six sections: a general introduction, three manuscripts, a general conclusion, and an overall bibliography. The three manuscripts report on: (1) identifying genetic interactions in diverse germplasm developed during introgression of a major gene conferring resistance to stem rust (Puccinia graminis f. sp. tritici), (2) mapping...
This dissertation consists of a general introduction, three manuscripts, and general conclusions. The research integrates research on (1) the effects of barley genetics and production environment on the contribution of barley to beer flavor, (2) the effects of degree of malt modification on barley contributions to beer flavor and (3)...
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Patrick M. Hayes
This dissertation consists of a general introduction, three manuscripts
This thesis consists of three manuscripts addressing separate components of barley breeding, plus an introduction and a conclusion summarizing the status of barley in the Pacific Northwest, plus the implications of the research presented in this thesis. In the first manuscript, a package written for the statistical software "R" that...
This dissertation consists of a general introduction, three research manuscripts, and general conclusions regarding the mapping of quantitative trait loci (QTLs) for sustainability traits in the Triticeae Coordinated Agricultural Project (TCAP) facultative/winter 6-rowed elite malting barley genome-wide association studies (GWAS) mapping panel, the TCAP FAC-WIN6. The first research manuscript, a...
In recent years, red raspberry production in Washington and British Columbia has been severely limited by a newly emerged virus complex that causes symptoms of crumbly fruit. The complex is comprised of three viruses: Raspberry bushy dwarf virus (RBDV), Raspberry leaf mottle virus (RLMV) and Raspberry latent virus (RpLV). Both...
The effect of anthropogenic disturbance on river systems is gaining attention, and concerns about the state of freshwater natural resources are increasing globally, as are efforts to restore habitat that has been degraded by disturbance. In rivers, non-point source pollution affects the physical characteristics of the habitat and the endemic...
As DNA sequencing technologies continue to advance, resulting in increased throughput and decreased costs, both the number of researchers utilizing these technologies and the quantity of data outputted by a single sequencing experiment will, likewise, continue to increase. Currently, DNA sequence data can be generated at a much faster rate...
The Pacific Northwest (Oregon and Washington in the United States and British Columbia in Canada) is one of the major producers of red raspberry (Rubus idaeus L.) and blueberry (Vaccinium corymbosum L.) in the world. The expansion of growing area with these crops has resulted in the emergence of new...
Northern highbush blueberry is a long-lived perennial crop that is well adapted to low soil pH conditions. The plants are often shallow rooted and absorb primarily the ammonium (NH₄) form of nitrogen (N) rather than nitrate-N (NO₃-N). Traditionally, commercial blueberry fields have been irrigated with overhead sprinklers and fertilized using...
The major components of wheat flour are keys to its functionality in processing and product quality. The major components, other than the lipids, are polymers: starch, protein, and non-starchy polysaccharides (NSP). In wheat NSP are primarily arabinoxylans (AX). These components are compartmentalized in the grain but are forced into close...
This dissertation focuses on the behavior of security returns around certain events that occurred in the Saudi stock market. In the first study, we measure and analyze the reaction of security returns around a major horizontal merger that occurred in the banking industry in Saudi Arabia. The objective of this...
During the Tropical Composition, Clouds and Climate Coupling (TC4) experiment
that occurred in July and August of 2007, extensive sampling of active convection in the
ITCZ region near Central America was performed from multiple aircraft and satellite
sensors. As part of a sampling strategy designed to study cloud processes, the...
Estimates of species' vital rates and an understanding of the factors affecting those parameters over time and space can provide crucial information for management and conservation. We used mark–recapture, reproductive output, and territory occupancy data collected during 1985–2013 to evaluate population processes of Northern Spotted Owls (Strix occidentalis caurina) in...
The promotion of democracy abroad has become a critical national security objective for the United States. Since the collapse of the Soviet Union, newly independent states have received millions in aid to facilitate their transition to democracy. A significant portion of this funding has been administered by the United States...
For over 100 years, National Parks have existed to preserve America’s natural and cultural heritage for current and future generations. As environmental pressures on wildlife and habitats have increased in recent decades, National Park lands have become important protected areas for many threatened and endangered species. Conservation and management of...
The purpose of this study was to understand the experiences of first-generation persons of color attending and persisting at a community technical college. Students of color continue to be an increasing population in our higher education system. Many of these persons of color are choosing to attend two-year institutions. A...
Changes in climate caused by increased concentrations of carbon dioxide (CO₂) in the Earth’s atmosphere have led land and ocean surface temperatures to increase by 0.85°C and sea level to increase by 19 cm relative to preindustrial times. Global climate change will lead to further alterations in mean temperature and...
The Columbia River Gillnetter is the pilot of the Lower Columbia River commercial fishing industry, keeping fishermen and the public in touch with today's important issues.
In the United States, marine debris is defined as “any persistent solid material that is manufactured or processed and directly or indirectly, intentionally or unintentionally, disposed of or abandoned into the marine environment or the Great Lakes.” Oregon State law defines marine debris similarly. Marine debris is a growing global...
Treatment of extrahepatic portosystemic shunts provides many options, including cellophane banding. These cellophane bands are secured with a ligation clip. Weck® offers two forms of these: the stainless steel Hemoclip, and the polymer Hem-o-lok. This in vitro study compares the mechanical strength of these two of types of clips by...
Environmental DNA (eDNA) is an emerging biological monitoring tool that can aid in assessing the effects of forestry and forest manufacturing activities on biota. Monitoring taxa across broad spatial and temporal scales is necessary to ensure forest management and forest manufacturing activities meet their environmental goals of maintaining biodiversity. Our...
The purpose of this thesis is to analyze an abrupt case of climate change in the past as a means to understand the mechanisms that force climate change. By looking to past analogs of climate change, we hopefully will gain an understanding of these events, which could be used to...
The federally threatened northern spotted owl (Strix occidentalis caurina) is the focus of intensive conservation efforts that have led to much forested land being reserved as habitat for the owl and associated wildlife species throughout the Pacific Northwest of the United States. Recently, however, a relatively new threat to spotted...
This study evaluated biomass production, water-use efficiency (WUE), biomass allocation, and water use characteristics of common plant species in Owens Valley, California, USA. The species studied were the grasses Distichlis spicata, Leymus triticoides, and Sporobolus airoides, the forbs Glycyrrhiza lepidota, Juncus arcticus, and Salsola tragus (annual), the desert shrubs Artemisia...
This paper details a method to compute absolute water velocity profiles from glider-based acoustic Doppler current profiler (ADCP) measurements based on the "shear method" developed for lowered ADCPs. The instrument is a 614-kHz Teledyne RDI ADCP integrated into the body of a Teledyne Webb Research Slocum Glider. Shear is calculated...
Coastal wetland plants are adapted to varying degrees of inundation. However, functional relationships between inundation and productivity are poorly characterized for most species. Determining species-specific tolerances to inundation is necessary to evaluate sea-level rise (SLR) effects on future marsh plant community composition, quantify organic matter inputs to marsh accretion, and...
A project to restore and increase the native riparian habitat on a 1½ acre site along Oak Creek will begin in spring 2013. In order to carry out long-term monitoring and evaluation of the efficacy of the restoration effort, it is necessary to know what is growing there now. To...
This classification is an update of the 2004 classification of native vegetation of Oregon by Kagan, Christy, Murray and Titus. As before, this classification lists the native plant associations known to occur in Oregon, and includes both successional and climax vegetation types that were part of the presettlement landscape of...
Manuscript I: The removal of residual casting material from gating has traditionally been performed by abrasive grinding techniques. However, high amounts of belt wear can occur when working with high strength alloys, especially those typically seen in the aerospace industry. An alternative machining process called electrochemical machining (ECM) uses electrolysis...
The capabilities of modern three-dimensional (3D) capture technology such as laser scanning and image-based 3D reconstruction are well suited to enhance the practice and research of civil engineering. However, given the often-overwhelming focus placed on the incredible capabilities of these tools and techniques, it is important to investigate the limitations...
Quaking aspen (Populus tremuloides Michx) is a species with high phenotypic plasticity and a broad distribution that, in the last decade, has experienced climate stress-induced mortality called Sudden Aspen Decline (SAD). In order to help mitigate the effects of SAD in the future, we need a better understanding of aspen’s...
In 2008, the Oregon State TRIGA® Reactor (OSTR) was converted from highly-enriched uranium (HEU) fuel lifetime improvement plan (FLIP) fuel to low-enriched uranium (LEU) fuel. This effort was driven and supported by the Department of Energy's (DoE's) Reduced Enrichment for Research and Test Reactors (RERTR) program. The basis behind the...
The existence, sources, distribution, circulation, and physicochemical nature of macroscale oceanic water bodies have long been a focus of oceanographic inquiry. Building on that work, this paper describes an objectively derived and globally comprehensive set of 37 distinct volumetric region units, called ecological marine units (EMUs). They are constructed on...
We monitored the distribution, abundance and productivity of the federally threatened Western SnowyPlover (Charadrius nivosus nivosus) along the Oregon coast from 5 April – 31 August 2016. From north to south, we surveyed and monitored plover activity at Sutton Beach, Siltcoos River estuary, the Dunes Overlook, North and South Tahkenitch...
We monitored the distribution, abundance and productivity of the federally threatened Western Snowy Plover (Charadrius nivosus nivosus) along the Oregon coast from 3 April – 11 September 2015. From north to south, we surveyed and monitored plover activity at Sutton Beach, Siltcoos River estuary, the Dunes Overlook, North and South...
The Pigeon Guillemot (Cepphus columba) is now the only species of marine bird in Prince William Sound (PWS), Alaska that is listed as "not recovering" on the Exxon Valdez Oil Spill (EVOS) Trustee Council's Injured Resources List and has shown no sign of population recovery. During the 20 years since...
Advancements in molecular biology and computer science have enabled researchers the ability to investigate the transcriptome – the quantification of an organism’s RNA transcripts in response to its environment on a system wide scale. The collective chapters of this thesis utilize high-throughput RNA sequencing, which produces hundreds of millions of...
Archaeological excavations of the Cooper's Ferry site in the Lower Salmon River Canyon, Idaho, have revealed a stratified record of cultural occupation, spanning the late Pleistocene and early Holocene periods. The purpose of this study was to contribute to the understanding of cultural adaptive strategies represented in the archaeological record...
Sea otters fulfill a keystone role in several Northeastern Pacific nearshore ecosystems. However, their influence has been absent in Oregon coastal waters since their extirpation in the 19th and early 20th century. Interest has been growing for a translocation attempt to reintroduce sea otters to Oregon from one or more...
There is an ever growing number of Latinas/os who reside and have settled permanently in rural America. Unbeknownst to most, rural Latinas/os face adversities unfamiliar to those living outside of this scope. As it stands, the barriers urban Latinas/os students face when transitioning to college has been well documented. However,...
The Lakes Basin Bibliography consists of over 600 references relating to the natural resources of Oregon’s Lakes Basin. Forty percent of the items listed are available to anyone online though not all links are persistent. The remaining sixty percent are held in at least one library either in print or...
In the midst of the sixth mass extinction, understanding wildlife disease spillover is critical to maintaining protected wildlife areas. Studying ecoimmunology and wildlife disease ecology helps to understand immune and disease traits in an ecological context, which is invaluable in preventing pathogen spillover between livestock and wildlife. To investigate this...
This thesis reports on computational research in two different areas. I first discuss the Min-protein system found within Escherichia coli. Following this I discuss an extended investigation into improving free energy functionals that are used within Classical Density Functional Theory in order to model water. Chapter 2 examines the dynamics...
This thesis proposes expanding the locations where literacy narratives are currently used as readings and as writing assignments and considering broad conceptions of the types and uses of literacy narratives read in classrooms. In particular, this thesis asserts the value of expanding the literacy narratives read beyond the current canonical...
Diversity literary awards and other sources were used to create a list of high-quality titles written by and about underrepresented groups. This list was used to assess the diversity and inclusiveness of the library collections of a land-grant university. Gaps in the collection and acquisition processes were identified and will...
During the eighteenth century, diagrams increasingly became an important aspect of scientific inquiry. Diagrams employed simplification as a strategy for representing complex information, played a role in standardizing scientific language, and served as instruments of reason to think through and communicate problems and findings in mathematics, physics, chemistry, astronomy, natural...
This document provides definitions and a general overview of streams and lakes of San Juan County (SJC) and then describes impacts to these water bodies and strategies for determining widths of buffers that protect their functions. It similarly provides definitions and a general overview of SJC upland (terrestrial) habitats, describes...
The atomic age was enacted by many scientists as a way to realize health and human rights. Human rights were conceived in this context as rights to economic development, science education, and nuclear medicine. The United States Atomic Energy Commission (AEC) acted hand in hand with UN agencies and educators...
Native America tribes and community members throughout Oregon have asserted a strong opposition to the fossil fuel industry’s attempt to expand railways, build pipelines, and construct refineries, holding facilities, and export terminals. Despite the limited presence of fossil fuel infrastructure in the state, however, the industry is actively pursuing permits...
Research Objective: Nearly 60 million people in the United States reside in a rural area. Residents in rural areas have higher rates of chronic disease, risky health behaviors, disability, infant mortality, and age-adjusted mortality than their urban counterparts. Health insurance and access to care mitigate those risks, in part because...
There are many uncertainties that complex engineered systems will face throughout their lifecycles due to changes in internal and external conditions. It is desirable for complex engineered systems to be resilient against various uncertainties. The ability to overcome such uncertainties should be embedded into the system from the beginning. However,...
In recent years, several interrelated forces—prolonged drought, growing populations, height-ened environmental protections, sustained agricultural use, and hydrologic alterations due to climate change—have increased pressure on water users in the Western United States, where the agricultural sector accounts for up to 90% of total water withdrawals. Technology im-provements developed since the...
Maintaining the sustainability of the earth’s ecosystems has attracted much attention as these ecosystems are facing more and more pressure from human activities. Machine learning can play an important role in promoting sustainability as a large amount of data is being collected from ecosystems. There are at least three important...
The anthropogenic introduction of nutrients to water bodies has been shown to alter the structure and function of natural aquatic ecosystems, yet national EPA lake and reservoir nutrient criteria remain too broad for effective regional water quality management. This study uses a reference site approach to propose numeric nutrient criteria...
Writing a program that performs well in a complex environment is a challenging task. In such problems, a method of deterministic programming combined with reinforcement learning (RL) can be helpful. However, current systems either force developers to encode knowledge in very specific forms (e.g., state-action features), or assume advanced RL...
Wheat (Triticum aestivum) is one of the world’s major staple food crops, with flour produced from starchy endosperm being used for breads, cakes, noodles and various other wheat-based foods. The unique bread making properties of wheat are primarily attributed to its gluten-forming storage proteins: gliadins and glutenins. This study investigated...
Microbial ecology has been transformed by metagenomics, the study of the genetic in-formation in entire communities of organisms. In the following we develop metagenomic tools arising from the classic Wasserstein metric as applied to questions regarding the diversity between microbial communities. We provide a novel proof of the characteriza-tion of...
Although dam construction has been an integral tool in development initiatives for nearly a century, dams can have significant negative impacts on local residents, particularly those who are permanently displaced from their homes and must be resettled elsewhere. Dams have unique impacts on indigenous peoples. As a result, many dam...
Whitebark pine (Pinus albicaulis) is an iconic North American high-elevation tree species currently threatened by climate change, mountain pine beetle, and white pine blister rust (WPBR), a lethal disease caused by the non-native fungal pathogen Cronartium ribicola. In collaboration with the USDA Forest Service Dorena Genetic Resource Center, germplasm was...
Reintroduction programs are increasingly being used to save animals from extinction and aid in their recovery. The California Condor (Gymnogyps californianus), one of the most endangered birds in the world, is a remarkable example of how reintroduction programs can help rapidly increase a species' population numbers and range following a...
Parasitic infections and immune challenges can affect host reproductive fitness and, ultimately, the evolution of host populations in a myriad of ways. The fitness implications of parasitic infections range from increased host mortality to subtle changes in reproductive investment. From alterations of behaviors, sexual signaling, and competitive ability to changes...
Since at least the 1970s, rural areas in the western United States, as elsewhere across the country and world, have been subject to social, economic, and political forces that have resulted in novel demographic and land tenure trends when compared to previous decades. Collectively, these processes of restructuring have created...
With the growth of Internet technologies, online-based foreign language curricula are being introduced at large numbers of institutions internationally. This peer-reviewed volume, geared towards a broad audience, presents innovative research on online language teaching, with chapters by highly engaged scholars and practitioners from the U.S. and Europe, with a strong...
Rhizopogon is a large genus of ectomycorrhizal (EM) fungi that grows in association with host trees of the family Pinaceae. We have conducted a series of studies investigating the ecology and evolutionary biology of the EM symbiosis shared between R. subgenus Villosuli and trees of the genus Pseudotsuga. Two members...
In this dissertation, I examine the process of building a Sámi food movement in northern Sweden. Using 15 months of ethnographic research that included observation of food events (n=100) and semi-structured interviews with food producers and activists (n=47), I describe how Sámi individuals are incorporating global food activism frameworks into...
The group of scientists that make up the Intergovernmental Panel on Climate Change found in 2007 that the warming of Earth’s climate is unequivocal and largely due to human activity. Earth’s climate has changed in the past, though the recent magnitude and pace of changes are unprecedented in human existence....
For the first time in several years, the El Niño-Southern
Oscillation did not dominate regional climate conditions
around the globe. A weak La Niña dissipated to ENSOneutral
conditions by spring, and while El Niño appeared
to be emerging during summer, this phase never fully
developed as sea surface temperatures in...
In 1746, Dr John Buchanan, a recently retired medical officer in the British Army, produced a manuscript, 'Regimental Practice, or a Short History of Diseases common to His Majesties own Royal Regiment of Horse Guards when abroad (Commonly called the Blews).' Revised almost until the time of Buchanan's death in...