Bioremediation in the vadose zone is unpredictable because of poor understanding of factors influencing microbial growth in this environment. A lab-scale experimental system was developed to examine, noninvasively, interactions between microbial growth, water flow, and solute transport in unsaturated porous media. Measurements of microbial colonization, and its impact on hydrology,...
Few studies have directly compared denitrifying community composition and activities in soils by coupling molecular-genetic techniques and traditional measures of denitnfication. I investigated communities of denitrifying bacteria from adjacent meadow and forest soils in the Cascade Mountains, Oregon. A key gene in the denitrification pathway, N₂O reductase (nosZ), served as...
Cometabolic biodegradation processes are potentially useful for the
bioremediation of hazardous waste sites. In this study the potential application of phenol-oxidizing
and nitrifying bacteria as "priming biocatalysts" was examined in the
degradation of polycyclic aromatic hydrocarbons (PAHs), aryl ethers, and aromatic
ethers. We observed that a phenol-oxidizing Pseudomonas strain cometabolically...
It has been held that heuristic training alone is not enough for developing one's mathematical thinking. One missing component is a mathematical point of view. Many educational researchers have proposed problem-based curricula to improve students' views of mathematical thinking. The present study reports findings regarding effects of a problem-based calculus...
My research has focused on understanding N and C cycling in soils at small scales. Isotope dilution methods commonly used to estimate gross rates of soil chemical transformations assume homogeneous distribution of label. I explored the effects of diffusion limitations on isotope dilution experiments in soil aggregates using spherical diffusion-reaction...
There is growing public concern about the high proportion of saturated fatty acids in milk fat; however, feed intake, energy partitioning toward milk synthesis, and milk fat concentrations can decrease when cows are fed high concentrations of unsaturated lipids. The objective of this study was to identify the optimal rate...
Uptake and cycling of nitrogen (N) in mature trees are not well understood.
Fertilizer-N uptake, partitioning, and use-efficiency were studied in standard strain
'Topred Delicious' and spur strain 'Redspur Delicious' mature apple trees {Malus
domestica Borck) on 'Malling 7A' (M.7A) rootstocks. The treatments consisted of a
ground application in spring,...
The black vine weevil (BVW), Otiorhynchus sulcatus (F.) (Coleoptera:
Curculionidae) is a persistent pest of nursery operations in the United States,
feeding on over 140 species of plants. The goals of this research were to 1) assess
the behavioral response of BVW to a commonly employed insecticide bifenthrin
(Talstar 0.2G®)...
This dissertation explores the physiology and gene expression of the ammonia-oxidizing bacterium Nitrosomonas europaea in surface-associated bacterial communities, or biofilms. Biofilms of N. europaea were cultivated in drip flow reactors for several weeks and gene expression microarrays were used to detect 240 genes differentially expressed between the mature biofilms and...
This study examined fish movements and assemblage dynamics in the Wenaha, Grande Ronde, Snake river system of northeast Oregon and southeast Washington. I investigated the role of fish movement in the dynamics of stream fish assemblages and evaluated relationships between species movement, assemblage structure, and the heterogeneity of habitat at...
Cereal and commercial grass-seed straws are abundant plant biomass materials that are currently being considered for application in industrial processes aimed at the production of biofuels, biomaterials, and biochemicals. The carbohydrate fraction of these straws is of particular interest in this context due to its chemical functionality and relative ease...
Although the biology of Bradyrhizobium has been studied for almost
one hundred years, virtually nothing is known about the ecology and genetic
variation in natural soil populations of this genus. The majority of
information has been obtained from studies of one species, Bradyrhizobium
japonicum, and the diversity within soil populations...
The aerobic transformation of TCE and cis-DCE by a tetrabutoxysilane-grown microorganism (Vancheeswaran et al., 1999) led to the investigation of novel substrates, including benzyl alcohol, for promoting cometabolism. The culture grew on carboxylic compounds and alcohols, but did not grow on formate, methanol, methane, propane, butane, ethylene, benzene, toluene, or...
This thesis explores the factors limiting the alkene substrate range of the vinyl chloride (VC)-utilizing bacteria, and describes a method for measuring VC transformation in situ. Vinyl fluoride (VF) was evaluated as a surrogate for monitoring aerobic VC-transformation utilizing three isolates, Mycobacterium EE13a, Mycobacterium JS60 and Nocardioides JS614. JS614 grew...
Optimization programming techniques were applied to
develop the least cost formulations for Pacific whiting
surimi-based seafood (PWSBS). To develop the quality
constraint functions, texture and color of whiting surimi
gels were determined by torsion test and colorimeter,
respectively. Whiting surimi gels were produced by heating
at 90°C for 15 min....
Radish anthocyanin extract has potential as a natural colorant because of
its pigment stability and attractive red hue. Presence of undesirable aroma
compounds could limit its applications in foods. The pungent principle of
radish, 4-methylthio-3-butenyl isothiocyanate (MTBI), is produced
enzymatically upon cell injury from its glucosinolate precursor, 4-methylthio-3-butenyl glucosinolate (MTBG),...
The evolutionary relationship between Frankia and actinorhizal plants was evaluated
by reconstructing molecular phylogenetic trees from nifH, 16S rDNA, and rbcL
nucleotide sequences. Subgroupings in Frankia phylogenetic trees reconstructed from
nifH and from 16S rDNA sequences were consistent in terms of plant origins of Frankia
strains. Although the branching order...
The vascular system transports components essential to the survival of the individual and acts as a barrier to substances that may injure the organism. Atherosclerosis is a dynamic, lesion producing disease of the arterial system that compromises the functioning of the organ by occlusive and thrombogenic processes. This investigation was...
Mat-forming ectomycorrhizal (EcM) fungi represent a prevalent constituent of many temperate forest ecosystems and create dramatic changes in soil structure and chemistry. EcM mat soil have been shown to have increased microbial respiration rates and have been hypothesized to harbor unique assemblages of fungi and bacteria. The objectives of this...
Vaccinia virus (VV) is a large double-stranded DNA virus that is a prototypic member of the orthopoxvirus family. Previous works has showed that three of the major structural proteins found within the mature VV virion core 4a, 4b, and 25K are produced from higher molecular weight precursors at late times...
A major factor in the ability of Pseudomonas fluorescens Pf-5 to act as a biological control agent is its production of antibiotics, including pyoluteorin (PLT), 2,4-diacetylphloroglucinol (2,4-DAPG) and pyrrolnitrin (PRN). The data provided in this thesis demonstrate that the presence of any of these antibiotics in the extracellular milieu affects...
Natural disturbances and human activities can alter the benthic composition of coral reefs and other marine ecosystems. Reef fishes that associate with particular structures on the sea floor, such as coral heads, may be vulnerable to perturbations of those habitats. The spread of a newly discovered crustose alga (Ramicrusta sp.)...
In recent years considerable interest has been shown in the diversity of ammonia-oxidizing bacteria in soil communities. The majority of the research has been carried out in Northern Europe where soils have received high atmospheric inputs of nitrogen over the past two centuries. In contrast, although much work has been...
Symbiosis is the close and protracted interaction between organisms. The molecular interactions that occur during symbiosis are complex with multiple barriers that must be overcome. Many Gram-negative, host-associated bacteria use a type III secretion system to mediate associations with their eukaryotic hosts. This secretion system is a specialized apparatus for...
Graduate teaching assistants (GTAs) from science, technology, engineering, and mathematics (STEM) are important in the teaching of undergraduate students (Golde & Dore, 2001). However, they are often poorly prepared for teaching (Luft, Kurdziel, Roehrig, & Turner, 2004). This dissertation addresses teaching effectiveness in three related manuscripts:
1. A position paper...
The chemolithoautotrophic nitrite oxidizing bacteria (NOB) participate in the
biogeochemical cycling of nitrogen by catalyzing and conserving energy from the
oxidation of nitrite (NO₂-) to nitrate (NO₃-) via a nitrite oxidoreductase (NXR). The
main objective of this work was to comparatively annotate and analyze the genome
sequences of Nitrobacter winogradskyi...
The regulation of monooxygenase enzymes has been demonstrated in bacteria that grow on methane and long chain-length alkanes (>C10). Less is known about monooxygenase regulation in short chain alkane oxidizing bacteria that grow on intermediate chain-length alkanes C2-C10. This dissertation focuses on the regulation of butane monooxygenase (BMO) expression and...
Research suggests that long-term participation in professional development is critical in helping teachers meet the increasing demands of reform efforts and changing practice (Gallucci, 2003; Darling-Hammond, 1995; Little, 1993). Understanding the influence that participation in a community of teachers as a community of practice may have on teachers’ professional growth...
Aquatic fecal contamination from non-point sources impairs environmental health and serves as a vehicle for transmission of waterborne disease, resulting in economic losses worldwide. Accurate methods of diagnosing fecal pollution and its source are needed to prevent human exposure, remediate pollution, and reduce economic impacts. In order to obtain this...
Sulfur is one of the six elements required during the early stages of the evolution of life, and enzymes involved in sulfur transfer and oxidation are increasingly being recognized as potential drug targets for antimicrobials as well as for therapies for cancer, neurodegenerative and inflammatory diseases. Bacteria are able to...
The auxin-resistant diageotropica (dgt) mutant of tomato (Lycopersicon esculentum Mill.) has a pleiotropic phenotype including a lack of lateral roots and reduced gravitropic response, apical dominance, vascular development, and fruit growth. The dgt mutation reduces the auxin sensitivity of only a subset of auxin responses while levels, metabolism, and transport...
Kernel hardness (KHA) is a major factor determining break flour yield (BFY) and end-use quality of common wheat (Triticum aestivum L.). Within the soft wheat class, genotypes with consistently softer grains than common soft wheat are considered to be 'extra-soft'. In addition, 'extra-soft' wheats have greater BFY than common soft...
The main purpose of this study was to investigate and describe strategies that Thai ninth grade students use to solve algebra word problems. The second purpose of this study was to investigate teachers' instruction during word problem solving lessons. Three mathematics teachers and one of each of their classes participated...
The Pacific Northwest has a relatively low diversity of primary freshwater fishes with most of the endemism and diversity in the Columbia River and Klamath River. However, the Oregon Coastal Subprovince defined as the coastal rivers from Miami River in the north to Sixes River in the south, has a...
Graphium sp., a eukaryotic alkanotroph, is able to oxidize small-molecular weight gaseous n-alkanes, diethyl ether and the branched ether, methyl tert butyl ether
(MTBE). However, information regarding the biochemistry of fungal-mediated alkane and ether metabolism is limited, and questions regarding the identity of alkane oxidation catalysts and the genetic underpinnings...
As people learn new concepts, they experience a process termed conceptual change. There are several theories that attempt to explain conceptual change, and this paper uses the framework theory to explain how students learn mechanics of materials. Semi-structured interviews with ninety students were qualitatively analyzed for this research in an...
This study outlines a procedure to review and identify the current forest management situation and techniques employed on
the Alsea District of the Siuslaw National Forest (SNF) in
Western Oregon and compare them to the situation and techniques
employed on the Bimbo-Lobaye Forest District (BLFD) in the
Central African Republic...
Prior to 2005, ammonia oxidation, the first step of nitrification, was thought mediated mainly by ammonia-oxidizing bacteria (AOB). However, the discovery of Thaumarchaeota carrying the genes coding for the ammonia monooxygenase (AMO) enzyme led to the discovery that ammonia-oxidizing archaea (AOA) also contribute to nitrification. Despite the uptick in studies...
Ectomycorrhizal fungi (EmF) form symbioses with trees. These symbioses profoundly influence forest ecology. Certain EmF form specialized profusions of hyphae, known as ectomycorrhizal fungal mats (mats) which are visible to the naked eye, alter forest soil biogeochemistry, substantially contribute to soil microbial biomass/respiration and support unique microbial communities. Piloderma and...
This study presents a mooring analysis of the Ocean Sentinel buoy, which is a mobile test platform for Wave Energy Converters. The Ocean Sentinel is owned and operated by the Northwest National Marine Renewable Energy Center (NNMREC) at Oregon State University (OSU). The study involved a field observation as well...
The quality and availability of forage fishes and invertebrates can affect the behavior and productivity of predators that rely on these resources. This study measures the proximate composition of forage fishes and invertebrates from the southeastern Bering Sea to estimate prey energy density (quality) using a method that is ecologically...
An analytical algorithm to formulate a sparser set of adjacency constraints than the conventional algorithm is proposed. Utilizing matrix algebra applied to an adjacency matrix, constraints are systematically and efficiently derived by the proposed algorithm. The proposed algorithm is proved to provide a true set of adjacency constraints in the...
Mount Hood National Forest provides opportunities for many forms of outdoor recreation. Recreationists spend money to pursue outdoor activities on public lands such as national forests and national parks. The purpose of this study was to measure the economic contribution of national forest visitor expenditures on the local economy of...
Within the past two decades, the rise of nanotechnology has provided various technological and industrial sectors with avenues for significant growth and improvements to existing practices. With the inherent qualities which make materials on the nanoscale unique in behavior and function, there are limitless applications of nanotechnology. One of the...
In this thesis, the effectiveness of the 100 percent + XX percent seismic response directional combination rule available in codes and standards is evaluated using simulated nonlinear seismic response of two existing multi-story reinforced concrete plan-irregular buildings. The 5-story and 8-story buildings were designed according to the 1975 seismic codes...
Rip currents pose a serious danger to visitors of bathing beaches; they are also an important process in surf zone circulation. Haller et al. [2014] demonstrated that shore-based X-band radar can be used to compliment in situ measurements of rip currents. However, little is known of the underlying radar imaging...
The present study was a part of a larger research project
investigating the relationships between perceived clothing
deprivation and selected social-psychological, socio-economic,
and social participation variables among high school students.
The purpose of the present study was to investigate the
effects of clothing values and selected demographic
characteristics on perceived...
Landslides are an insidious natural hazard, which can result in significant damage to public infrastructure. Limited monitoring tools are available, particularly tools suitable for use in forested environments. These tools often only allow a few locations across the slide to be monitored. Terrestrial Laser Scanning (TLS) shows promise as a...
Dried cattail and bulrush plant pieces in mesh bags were incubated in the
constructed wetland treating Pope & Talbot pulp mill effluent. Two ponds
planted with each species and two depth ranges in each pond were chosen, to
determine decomposition rates. Bags were withdrawn and analyzed at five time
points...
Temperature influences the incidence of chemically induced cancer in fish,
with warmer temperatures being associated with higher cancer incidence. The
mechanisms of temperature-modulated chemical carcinogenesis in fish, however,
have not been described in detail. Therefore, one primary objective of this study
was increased understanding of how temperature-modulated genotoxicity of 7,12-...
In host-associated microbiomes, the mechanisms that regulate community composition or the principles that govern dynamics remain far from clear. However, understanding how the structure of microbial communities shift as the system moves away from a healthy state is critical to assessing disease progression and to formulate any potential mitigation strategy....
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...
Abstract Valleys of headwater channels in the Oregon Coast Range impound significant amounts of sediment, with the majority of deposits originating as debris flows. Headwater valleys function as transitional sedimentary reservoirs linking hillslope sources in active orogens to sinks in sedimentary basins, yet the residence time of deposits in the...
Modern geospatial data are frequently represented in some type of three-dimensional (3D) coordinate system, for example geodetic latitude, longitude, and ellipsoid height (φ, λ, h) derived from Global Navigation Satellite Systems (GNSS). But for engineering and surveying work, φ, λ, h coordinates are usually converted to a topocentric system consisting...
Host-parasite interactions between the pathogen, Sphaerulina musiva, and its host, Populus spp., were examined in a series of studies. In the first study, variation in resistance of Populus nigra from 7 locations in Europe was differentiated based on the parameters cankers per cm and disease severity score. The analysis evaluated...
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...
Landslides are a pervasive hazard that can result in substantial damage to properties and loss of life throughout the world. To understand the nature and scope of the hazard, landslide hazard mapping has been an area of intense research by identifying areas most susceptible to landslides in order to mitigate...
Genomic instability underlies diseases of unregulated cell growth that result in
cancers and developmental abnormalities in humans. Similar genome destabilizing
mechanisms are used to create genetic variety in crops for use in breeding and trait
development. Errors that occur during DNA replication may cause mutations if
they are not corrected...
The seasonal distribution of bioavailable organochiorine contaminants in surface
water and the potential environmental factors influencing their bioavailability were
evaluated. The study was carried at the lower Willamette River at Portland Harbor, Oregon
where surface water runoff varied according to season. Bioavailable water concentrations of
DDTs and PCBs were determined...
School counseling site supervisors provide a critical contribution to the professional
development of master's program school counseling interns; however, their training
needs remain unidentified in the literature. To that end, the purpose of this quantitative
study was to explore the training needs of site supervisors of master's program school
counseling...
In order to produce infectious virus progeny, vaccinia virus (VV)
undergoes morphogenic proteolysis to regulate the structural rearrangements of
virus particles. Several of the major structural precursor proteins of VV are
cleaved at a conserved Ala-Gly-X (where X is any amino acid) motif by the VV
I7L core protein proteinase...
Summer drought is a major factor limiting the regrowth of perennial ryegrass seed crops. This phase of crop development has a strong influence on seed yield because most of the tillers that contribute towards next season's seed crop are produced or regrown during this period. In recent years many seed...