The bottleneck in the turnover of soil organic matter (SOM) is the conversion of large molecular compounds into smaller compounds that can be transported through a cell membrane of a microbe for processing. Once inside the cell, organic compounds can be converted into biomass or be respired. The microbial depolymerization...
The goals of this experiment highlighted in this poster were to find a suitable extractant to extract protein adsorbed onto iron oxide minerals and to determine whether those minerals can modify protein. Data obtained from this experiment provides crucial background information to study the effects hydrogen peroxide has on protein...
Molecular dynamics simulations, conventional and metadynamics, were performed to determine the interaction of model protein Gb1 over kaolinite (001), Na⁺-montmorillonite (001), Ca²⁺-montmorillonite (001), goethite (100), and Na⁺-birnessite (001) mineral surfaces. Gb1, a small (56 residue) protein with a well-characterized solution-state nuclear magnetic resonance (NMR) structure and having α-helix, 4-fold β-sheet,...
Full Text:
,1 StephanyS. Chacon,2 Nikolla P. Qafoku,3 Nancy M. Washton,1
Markus Kleber2,4
1Environmental
The ability of plants and microorganisms to take up organic nitrogen in the form of free amino acids and oligopeptides has received increasing attention over the last two decades, yet the mechanisms for the formation of such compounds in soil environments remain poorly understood. We used Nuclear Magnetic Resonance (NMR)...
Full Text:
:
implications for a mechanism to supply soil biota
with oligopeptides.
Patrick N. Reardon
b*
, StephanyS
The ability of plants and microorganisms to take up organic nitrogen in the form of free amino acids and oligopeptides has received increasing attention over the last two decades, yet the mechanisms for the formation of such compounds in soil environments remain poorly understood. We used Nuclear Magnetic Resonance (NMR)...
Full Text:
: Implications
for a Mechanism to Supply Soil Biota with Oligopeptides
Patrick N. Reardon,*,‡ StephanyS. Chacon
Molecular dynamics simulations, conventional and metadynamics, were performed to determine the interaction of model protein Gb1 over kaolinite (001), Na⁺-montmorillonite (001), Ca²⁺-montmorillonite (001), goethite (100), and Na⁺-birnessite (001) mineral surfaces. Gb1, a small (56 residue) protein with a well-characterized solution-state nuclear magnetic resonance (NMR) structure and having α-helix, 4-fold β-sheet,...
Full Text:
Andersen,*,† Patrick N. Reardon,† StephanyS. Chacon,§ Nikolla P. Qafoku,‡ Nancy M. Washton,†
and Markus
Molecular dynamics simulations, conventional and metadynamics, were performed to determine the interaction of model protein Gb1 over kaolinite (001), Na⁺-montmorillonite (001), Ca²⁺-montmorillonite (001), goethite (100), and Na⁺-birnessite (001) mineral surfaces. Gb1, a small (56 residue) protein with a well-characterized solution-state nuclear magnetic resonance (NMR) structure and having α-helix, 4-fold β-sheet,...
The ability of plants and microorganisms to take up organic nitrogen in the form of free amino acids and oligopeptides has received increasing attention over the last two decades, yet the mechanisms for the formation of such compounds in soil environments remain poorly understood. We used Nuclear Magnetic Resonance (NMR)...
Soil is a complex living system with high heterogeneity, which makes locating soil map boundaries a challenge. In traditional soil survey, the placement of soil map boundaries relies largely (at least initially) on identifying the soil-forming factors of biota and topographic relief through stereo aerial photo pairs. Future soil survey...
Andic soils (aka Andisols) have unique properties that are important to society. For soil scientists, the genesis and taxonomy of Andisols is often confused because they can form in both volcanic and non-volcanic material. This dissertation seeks to address such confusion by looking at andic soil development in the Cascade...
This dissertation reports on four related, though separate projects. The first project details the process of carrying out a digitally augmented soil mapping (DSM) effort alongside an ongoing survey in Oregon's Ochoco National Forest (ONF) using a Random Forest algorithm. The second chapter describes a initial soil survey in Oregon's...
Nursery and greenhouse products are economically important agricultural commodities for Oregon and Washington. Nursery crops including tree seedlings can be damaged or killed by soilborne plant pathogens, which can be challenging to manage because of their persistence in soil and limited options for control. Soil solarization is a pre-planting soil...
What historical and political reality is reflected in the novels Gringo viejo and La frontera de cristal? What is revealed when the characters, plot, and setting of the novels are analyzed against research of the context of U.S.-Mexico relations? We begin to explore these questions by studying three periods crucial...
As the number of weather stations declines globally, ensuring that meteorological monitoring networks efficiently and effectively monitor weather variables becomes increasingly important. Multi-variable weather sensors are becoming more widely available and make monitoring weather phenomena more economical. However, when seeking an optimal spatial distribution of these stations, choosing an objective...
The objective of this thesis was to investigate the use of the Jacobian Free Newton Krylov Method (JFNK) with physics based preconditioning for solving coupled radiative transport and material energy balance. Modeling of these physics is important in inertial confinement fusion and other high energy density systems. In this thesis,...
Soil nitrogen exists largely as organic matter, including plant liter, dead animal matter, and microbial necromass. About 90% of soil organic nitrogen is proteinaceous material that is too large for plants and microorganisms to assimilate directly. Protein depolymerization therefore plays a critical role in mobilizing this organic source of nitrogen,...
Agricultural and companion animals are integral to our way of life as they provide us with nourishment, financial resources, transportation, and companionship. However, pets, managed animals in the agricultural industry, as well as wild populations of food animals are all subject to health and mortality risks. The gut microbiome is...
The immune system is a complex network of cellular processes working in harmony to guard us against pathogenic attack. Of utmost importance is the ability of the immune system to discriminate between “self” and “non-self” and diseased versus healthy. Recognition of antigens complexed to major histocompatibility complex (MHC) molecules is...
Although it is generally assumed that the intensifying abiotic environment is the primary effect of drought on aquatic organisms, drought-induced top predator extinctions may be an important underlying mechanism. I used manipulative experiments to disentangle the impacts of drying and top predator extinctions on arid-land aquatic invertebrate communities. I then...
A growing body of work reveals that animal-mediated pollination is negatively affected by anthropogenic disturbance. Landscape-scale disturbance results in two often inter-related processes: (1) habitat loss, and (2) disruptions of habitat configuration (i.e. fragmentation). Understanding the relative effects of such processes is critical in designing effective management strategies to limit...
This dissertation investigated potential ecological limitations to seedling regeneration in young, seasonally dry, evergreen forest restoration plantations in northern Thailand. We explored whether recruitment of colonizing tree species in the restoration plantations can be attributed to seed dispersal mode (i.e. abiotic or animal dispersal) and seed size. We did this...
This is a Ph.D. dissertation for a study conducted at OSU/Horticulture. The main objective of this study was dissecting the genetic background for white mold resistance in common (snap) bean. Tow main approaches were followed to achieve the goal. The first approach was using the classical quantitative trait loci (QTL)...
Global biodiversity decline is primarily driven by habitat loss. Deforestation, the primary driver of terrestrial habitat loss, is increasing worldwide, with the most significant impact in the world biodiversity hotspots. Sadly, specific knowledge of such impacts in biodiversity-rich but data-poor countries are still unknown, and many national and regional narratives...
Carbon sequestration in tropical secondary forests growing in all climates must be quantified to understand their potential role in adaptation and mitigation strategies of global climate change. Total aboveground biomass (TAGB), soil carbon, and total ecosystem carbon (TEC) were measured in 54 secondary forests growing along a broad bioclimatic gradient...
Understanding the processes controlling organic matter (OM) stocks in upland soils, and the ability to management them, is crucial for maintaining soil fertility and carbon (C) storage as well as projecting change with time. OM inputs are balanced by the mineralization (oxidation) rate, with the difference determining whether the system...
Dust deposition provides rock-derived nutrients such as phosphorus (P) to terrestrial ecosystems. Over pedogenic timescales, as bedrock sources of P are depleted, dust sources of P may support productivity in certain ecosystems, but controls on the spatial variability of dust in montane forested systems are largely unknown. Here, we use...
Loss of native vegetation cover is thought to be a major driver of declines in pollination success worldwide. However, it is not well known whether reducing the fragmentation of remaining vegetation can ameliorate these negative effects. We tested the independent effects of composition vs. configuration on the reproductive success of...
STEMRUST_G, a simulation model for epidemics of stem rust in perennial ryegrass grown to maturity as a seed crop, was validated for use as a heuristic tool and as a decision aid for disease management with fungicides. Multistage validation had been used in model creation by incorporating previously validated submodels...
Cervical cancer is the fourth most common cancer in women worldwide with human papillomavirus (HPV) being the main cause of the disease. Currently available treatment methods are limited and emphasize the need for discovery of new therapies that improve patient outcome. Chromosomal amplifications have been identified as a source of...
This review briefly addresses what has been learned about resistance durability in recent years, as well as the questions that still remain. Molecular analyses of major gene interactions have potential to contribute to both breeding for resistance and improved understanding of virulence impacts on pathogen fitness. Though the molecular basis...
Soils contain the largest pool of carbon that is actively cycling on human timescales, leading many to view soils as a natural climate solution with multiple co-benefits. The field of soil science is rapidly evolving, but without a unified understanding of soil carbon dynamics. This dissertation leverages two distinct long-term...
This capstone project is expected to be published by United States Department of Agriculture Animal and Plant Health Inspection Service Wildlife Services (USDA APHIS WS) as part of a technical series guide available to the public through the website (https://www.aphis.usda.gov/aphis/ourfocus/wildlifedamage/sa_reports/ct_wildlife+damage+management+technical+series). USDA APHIS WS is responsible for mitigating human-wildlife conflict and...
Results are provided that highlight the effect of interfacial discontinuities in the
diffusion coefficient on the behavior of certain basic functionals of the diffusion, such
as local times and occupation times, extending previous results in [2, 3] on the behavior
of first passage times. The main goal is to obtain...
Green bean flavor has been studied since the 1960’s to better understand Blue Lake flavor in processed green beans in Oregon. Research by Stevens and colleagues showed that Blue Lake flavor could be reconstituted in a bland bean by adding 0.4ppm of 1-octen-3-ol and 1.6ppm of 3-hexen-1-ol. These two volatile...
The formation of 3-hydroxy-N-nitrosopyrrolidine from decarboxylation
of 4-hydroxy-N-nitrosoproline was demonstrated in model
heating system designed to simulate the conditions of frying bacon.
The identification of the nitrosamine was achieved by comparison of
its TLC R [subscript f] value, gas chromatographic retention time, and mass
spectral fragmentation pattern with those of...
PN junctions in nanoscale materials are of interest for a range of technologies including photodetectors, solar cells, and light-emitting diodes. However, Schottky barriers at the interface between metal contacts and the nanomaterial are often unavoidable. The effect of metal-semiconductor interfaces on the behavior of nanoscale diodes must be understood, both...
Approximately 2700 years ago, Greek settlers from the Northwestern Peloponnese region of Achaea emigrated to the central coast of Southern Italy along the Gulf of Taranto. The city they founded, Metapontum, served as an important center for Magna Graecia, the lands on the Southern Italic peninsula wholly populated by Hellenic...
Recently, there has been an increasing interest among researchers on efficiency in fisheries. They have not just been focused on the analysis of the efficiency itself but also for other purposes as measures of capacity utilisation. However, often, efficiency analyses do not offer clear results regarding the sources of the...
Deeply weathered soils in tropical rainforests and savannas are classified as Ferralsols according to the World References Bases for Soil Resources (WRB). Ferralsols are most nearly akin to the Oxisols order defined in the US Soil Taxonomy. The acidity, low cation exchange capacity, and strong phosphorus retention by the oxidic...
This study evaluated effects of Positive Action, a school-based social-emotional and character development (SECD) intervention, on indicators of positive youth development (PYD) among a sample of low-income, ethnic minority youth attending 14 urban schools. The study used a matched-pair, cluster-randomized controlled design at the school level. A multiple-measure self-report protocol...
Gut microbiota plays an essential role in health and diseases, a fact already established. With the explosive increase in obesity and its main complication, Type 2 Diabetes Mellitus (T2D), there is an immediate need for novel methods of diagnosis, prevention and treatment of these conditions. In the last one and...
Leads are long fractures wide enough for a ship to travel through the ice pack. Sea ice acts as a barrier between the ocean and the atmosphere, whereas leads allow the transfer of heat and moisture between the two. Leads play a role for marine mammals and are hunting grounds...
Phenolic acids, flavanols, flavonols and stilbenes (PAFFS) were isolated from whole grapes, juice, or pomace and purified using enzymatic hydrolysis. Only anthocyanin mono-glucosides and a few of the oligomers from
Cynthiana grape (Vitis aestivalis) were analysed. Flavonoid-anthocyanin mono-glucosides (FA) were isolated using methanol/0.1% hydrochloric acid extraction. In addition, crude extractions...
Grazing on the mountainous forested ranges of the Camp Creek
Unit, Malhuer National Forest, was typified by irregular distribution
of free-ranging cattle. A combination of management and physical,
topographic constraints caused cattle to concentrate on the riparian
zone early in the grazing season in 1977 and 1978. A large percentage...
A trial was conducted May 1 to September 4, 1989 at the Eastern
Oregon Agricultural Research Center (EOARC) Burns, OR to examine the
effects of strip or continuous grazing management on the diet and
performance of steers grazing native flood meadows. The objective was
to determine if strip grazing would...
The Common Core State Standards for Mathematical Practice (SMPs) describe ways of thinking and doing mathematics that parallels how mathematicians engage with mathematics (National Governors Association for Best Practices, 2010). These standards reflect a broader goal in K-12 mathematics education focused on moving beyond K-12 learners acquiring knowledge of mathematical...
This study will use a COSMED K5 portable metabolic unit to expand on the limited knowledge of the energy demands of top rope rock climbing. Participants will be experienced, consistent rock climbers. Two route difficulties (5.8 and 5.10) will be analyzed using a repeated measures randomized design to determine differences...
The infection biology of Mycobacterium avium subsp. paratuberculosis has recently crystallized, with added details surrounding intestinal invasion. The involvement of pathogen-derived effector proteins such as the major membrane protein, oxidoreductase, and fibronectin attachment proteins have been uncovered. Mutations constructed in this pathogen have also shed light on genes needed for...