Since a NanoSIMS high-resolution secondary ion mass spectrometry instrument was first used for cosmochemistry investigations over a decade ago, both interest in NanoSIMS and the number of instruments available have significantly increased. However, SIMS comes with a set of challenges that are of both technical and conceptual nature, particularly for...
This study sought to ascertain the degree to which the night sky of Corvallis is affected by light pollution by determining the limiting visual magnitude. Defined as the brightness of the dimmest star that can be seen with the averted naked eye, the limiting visual magnitude establishes a quantitative standard...
One of the tasks of image processing systems is to characterize images by thinning, or skeletonizing techniques. The standard method, based on a disk growing technique, often results in disconnected skeletons. Since the standard technique is based on a square grid system, the disk shape is also square. The. purpose...
Intertidal herbivores, such as isopods, help regulate and contribute to nutrient cycling and organic carbon flow through the trophic levels in estuaries and coastal ecosystems. Though much is known about the microbiomes of macrophyte leaves that serve as the primary food source for isopods, and (to a lesser extent) the...
The objective of this study was to determine if supplementing linoleic or α-linolenic acids, and timing of supplementation around AI will alter supplemental intake, ADG, and serum progesterone (P4), cholesterol, and triglyceride concentrations in replacement Angus crossbred heifers. In yr 1, 54 heifers, stratified by age, were assigned to: barley...
The combined activities of diverse heterotrophic marine microorganisms significantly shape global biogeochemical cycles, but models of these activities are currently limited to aggregate microbial community processes, and it remains unclear how community structure and the functional roles of specific microbial taxa should be integrated into these models. Therefore, understanding the...
Italian ryegrass growth and production from
positionally selective applications and sublethal rates of a
nonselective herbicide were compared to growth and
production when treated with diuron applied preemergence as
a broadcast treatment and safened by activated carbon
applied over the crop row. In the positionally selective
treatments, herbicide spray was...
Vibrio bacteria are commonly found in freshwater, marine, and estuarine environments. Members of this genus can exist in commensal relationships with marine animals or as planktonic bacteria, however, they are well known for their roles as pathogens towards humans and animals. In this dissertation, I investigated aspects of host-bacteria relationships...
Feeding conjugated linoleic acids (CLA) improves reproductive performance in dairy cows; however, the molecular mechanisms by which CLA improves reproduction are not well understood. Therefore, we evaluated whether the CLA isomers, trans-10, cis-12 CLA and cis-9, trans-11 CLA altered synthesis of steroidogenic hormones in bovine luteal cells by measuring concentrations...
Purebred Jersey steers are often overlooked for beef production due to the perceived poor growth and production. Currently dairy persons marketing their steer offspring are receiving minimal compensation due to lack of demand by beef feeders and a saturated veal market. Twenty purebred Jersey steers were used to evaluate lifetime...
Biotic and abiotic processes at continent-ocean interfaces cycle a disproportionate mass of carbon and nutrients relative to their global surface area, and microbial activity is a principal determinant of organic and inorganic matter flux in these transition zones. Most studies using modern high-throughput ‘omics techniques to link microorganisms with costal...
Seagrasses and coral reefs play important roles in nutrient cycling, coastal protection, and maintaining marine biodiversity. However, these coastal marine organisms are declining globally due to anthropogenic stressors, such as rising ocean temperatures, ocean acidification, and eutrophication. These organisms live in close association with their microbiomes, which can be beneficial...
The Warm Springs Reservation is located in central Oregon. Livestock production consists of beef (commercial with an Angus, Horned Hereford base) and roping (Corriente and Longhorn) cattle and horses that forage most of the year on the open range within reservation boundaries. Forage consists of annual and perennial grasses and...
Antarctic Ice Sheet mass balance and, hence, sea level change is affected by the floating extensions of outlet glaciers and ice streams that take up about 44% of the coastline (Drewry et al., 1982) and are referred to as "ice shelves". Ice sheet mass loss accelerates when these ice shelves...
Thermohaline interleaving is an important mechanism for laterally fluxing salt, heat, and nutrients between oceanic water masses. Interleaving is driven by a release of potential energy resulting from the vastly differing diffusivities of heat and salt in seawater. The flows are composed of stacked intrusions that flux more buoyant and...
The relative accuracy of solutions to chaotic systems was examined using the Lorenz
system as a case study. The classical fourth order Runge-Kutta method was employed to
generate solutions using various step sizes, and the resultant solutions were compared. A
second set of solutions was then computed using one of...
The increasing level of complexity in systems creates a growing challenge
for engineers to design safe and reliable systems. The growing complexity can
lead to possible moments when situations occur that were unanticipated or were
not known that they could occur by designers and leave the system in an
undesirable...
Aquaculture is increasingly important for the future supply of fish because of steadily increasing demand while supply from fisheries is stagnating. In the EU aquaculture production has grown strongly in some countries, such as Spain and Greece, but was flat at a low level in others, such as in Germany,...
An analysis was conducted to determine the effects of nonlinearity in
the one dimensional Navier-Stokes equation describing a viscous fluid flow.
An attempt was made to numerically determine the effect of temperature
variance on the fluid, either by varying the constant viscosity factor in the
energy dissipative term in the...
Slugs are common pests of grass seed fields in western Oregon and the current focus of repeated, and often unsuccessful, efforts by growers to control them using molluscicides. Here we document rapid loss of molluscicidal bait pellets to earthworms and the resulting adverse effects on slug control. Three years of...
The fish of Suttle Lake, Oregon, have been found to harbor
an acanthocephalan parasite, which lives attached to the mucosa of
the intestine. Between July 1961 and January 1963, several hundred of
these fish were exarnined and nearly every one was infected
with this parasite, which was identified as Neochinorhynchus...
The Willamette Valley, bounded on the west by the Coast Range and on the east by the Cascade Mountains, is the largest river valley completely confined to Oregon. The fertile valley soils combined with a temperate, marine climate create ideal agronomic conditions for seed production. Historically, seed cropping systems in...
In order to understand the ability of Detroit Reservoir’s recurring cyanobacterial bloom to produce toxins, and determine the genetic similarity of the bloom from year to year, environmental samples were taken from the Detroit Reservoir bloom biomass in the summers of 2017 and 2018. DNA from these samples was sequenced,...
Limnology is undergoing a transition to high-throughput -omic analysis of freshwater
bacterial communities. An important first step in making the transition is to
characterize several genomes that can be used as references to guide metagenome
assembly and analysis. Here I characterize four new freshwater cyanobacterial
genomes, a pair of lake...
The advent of improved DNA sequencing technologies has allowed the analysis of various microbial communities. Bloom-forming freshwater cyanobacteria can produce toxins and taste-and-odor compounds that can negatively affect drinking water supplies. Here, I have employed second- and third-generation sequencing technologies to characterize bloom-forming freshwater cyanobacterial genomes and their associated heterotrophic...
Infrared radiometers, photographs, and a multispectral
scanner were used in a remote sensing study of the ocean off
Oregon during the summer of 1969. Upwelling appeared on
infrared temperature maps as a zone of cold water along the
coast and Columbia River water appeared as a warm water
"plume". Sharp...
Forest harvest persists as one of the most globally important industries, and crucially provides raw wood products for both building and fuel materials. Mechanistically complex abiotic and biotic processes curb ecosystem recovery following timber harvest and it is of great importance to understand the effects of this practice on biogeochemical...
The lagoons spanning Alaska’s Beaufort Sea coast provide a unique habitat for arctic wildlife. These lagoons and the food webs they support face extreme seasonality with nine months of ice cover followed by a spring thaw that pulses a large amount of freshwater and nutrients into the lagoons. Bacteria link...
Igneous oceanic crust encompasses ~60% of Earth’s surface and is composed of basalt glass and mafic, ultramafic, and felsic minerals. A vast marine aquifer lies within the crust, exchanging geochemically altered fluids with seawater from the overlying ocean at ridge crests, flanks, seamounts, and outcrops where permeable crust is exposed....
In a process called quorum sensing (QS), the bacterial pathogen Pseudomonas aeruginosa uses small diffusible signals to coordinate cooperative behaviors via secreted “public goods”. Under QS-dependent growth conditions, social cheaters arise with mutations in lasR, the gene for the primary QS signal receptor. These cheaters do not produce public goods....
Nitrification is the process within the global Nitrogen Cycle where ammonia (NH3) is oxidized to nitrate (NO₃⁻) and can be carried out by two distinct groups of bacteria. The ammonia-oxidizing bacteria (AOB) first oxidize NH₃ to nitrite (NO₂⁻), and second, the nitrite-oxidizing bacteria (NOB) oxidize NO₂⁻ to NO₃⁻. In aerobic...
Diatoms play a major role in ocean biogeochemical cycles and are important tools in bioengineering for natural products and nanotechnology. Diatoms and other algae growing at varying resource-limited growth rates allocate carbon to different metabolic pathways to optimize growth; however, the molecular mechanisms controlling these pathway gating strategies are not...
This study evaluated the influence of cattle stocking density on botanical composition of diet, diet preference, and cattle performance on the Zumwalt Prairie in Northeastern Oregon. In each of two years, 192 cow-calf pairs (549.27 kg, BCS = 4.89) and 48 yearling heifers (383.34 kg, BCS = 5.02) were stratified...
The Willamette Valley, bounded on the west by the Coast Range and on the east by the Cascade Mountains, is the largest river valley completely confined to Oregon. The fertile valley soils combined with a temperate, marine climate create ideal agronomic conditions for seed production. Historically, seed cropping systems in...
A method for predicting oceanic productivity from remotely sensed diffuse attenuation (488 nm) and
surface chlorophyll concentration is presented. The method uses a climatological approach which consists
of applying a set of regressions for each region and season to yield the depth of the chlorophyll maximum,
the exponential slope of...
Proteinaceous compounds are abundant forms of organic nitrogen in soil and aquatic ecosystems, and the rate of protein depolymerization, which is accomplished by a diverse range of microbial secreted peptidases, often limits nitrogen turnover in the environment. To determine if the distribution of secreted peptidases reflects the ecological and evolutionary...
High-speed intercity passenger rail projects are very complex and require many years of planning and environmental activities before construction can begin. Given the complexity of planning and environmental reviews associated with high-speed intercity passenger rail corridor planning, a systematic approach for high-level screening of various alternative routings for proposed high-speed...
A group of 75 children from 3 to 5 years old from the earliest stages of a Spanish school were the target
of an experimental test focused on the consequences of providing information about safety and fisheries
sustainability on their preferences when choosing between different seafood presentations and labels.
Both...
Understanding the mechanism of resistance, relative fitness and competitiveness of herbicide resistant biotypes is important to predict population dynamics and to establish resistance management strategies. This study was conducted to determine the level of resistance to acetolactate synthase (ALS) inhibitors and the mechanism of resistance of ALS-inhibitor resistant downy brome...
The complex, dynamic nature of microbial communities in both natural and engineered environments complicates the work of scientists and engineers who wish to channel microbial interactions for societal good. The successful management of these communities towards engineering goals is dependent on developing predictive linkages between community structure and functional outputs....
In Oregon perennial and annual grass seed cropping systems conservation management practices and their impacts on soil health and soil microbial community is not well understood. There is strong motivation to employ conservation tillage and other conservation practices to curb atmospheric carbon levels and improve soil health. However, the few...
Precise in situ measurement of the spectral absorption and scattering coefficients in several regions has revealed patterns in the distribution of the inherent optical properties on spatial scales that were previously unobtainable. The precision of the measurements was found to be consistent and unbiased across a variety of oceanic regimes...
The growing population of Oregon’s Willamette River Basin places an increasing demand on the basin’s surface waters. Watershed-scale research addressing spatial trends of dissolved nitrogen (DN) and its relationship with landuse and soil N dynamics, such as N mineralization, is sparse in the Willamette Basin. I measured DN along 124...
On coral reefs, disturbances rarely occur in isolation. Global stressors such as increasing seawater temperature often coincide with local stressors like nutrient pollution. In the face of increasing anthropogenic stress, corals can function as environmental sentinels, although little is known about how multiple stressors interact to disrupt their associated bacterial...
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,...
Cell-cell communication in bacteria is understood to facilitate the coordination of population-wide cooperative behavior in the form of concerted gene expression. The opportunistic pathogen Pseudomonas aeruginosa uses such a communication mechanism to regulate a large group of genes important to virulence strategies in this bacterium. This general mechanism of communication...
The potential impact of chemical contaminants and conservation practices on amphibians in agricultural landscapes is a key research topic globally. Amphibians represent a common group in many freshwater systems and are currently experiencing worldwide population declines. Global amphibian declines may be attributed to a number of causes, including habitat loss,...
Oligotrophic bacteria are adapted to low nutrient concentrations. As most of the ocean is oligotrophic (low in nutrients), oligotrophic bacteria thrive in the ocean and make up the majority of planktonic cells. Because of this, oligotrophs are crucial to oceanic nutrient cycles. However, marine oligotrophic bacteria are dwarfed by their...
Our objectives were to determine 1) the concentration of prostaglandin
F2α (PGF2α) in whole and extended bovine semen, 2) if concentrations of
prostaglandins in extended bovine semen are correlated to fertility, and 3) if PGF2α
administered at the time of artificial insemination would improve conception rate.
Concentration of PGF2α tended...
Pharmacokinetics (PK) is the study of the transit of drug into, within and removal from the body to reveal how the body acts on a drug when it is taken. There are four major areas in PK: absorption, distribution, metabolism and elimination. Pharmacokinetics research can be separated into two areas:...
Basal melting of ice shelves around Antarctica contributes to formation of Antarctic Bottom Water and can affect global sea level by altering the offshore flow of grounded ice streams and glaciers. Tides influence ice shelf basal melt rate (w(b)) by contributing to ocean mixing and mean circulation as well as...
At a time of rapid global change, a socio-ecological system (SES) approach can provide a framework through which to quantify and communicate the risks and uncertainties of coupled human-natural systems. Islands, and tropical coral reef islands in particular, can be excellent models for SES research since they may be considered...
The myeloid-specific transcription factor, CCAAT/enhancer-binding protein epsilon (C/EBPε) is a critical mediator of myelopoiesis. Mutation of this gene is responsible for neutrophil-specific granule deficiency in humans, a condition that confers susceptibility to Staphylococcus aureus infection. We found that C/EBPε-deficient mice are severely affected by infection with S. aureus, and C/EBPε...
The Chloroflexi CL500-11 clade contributes a large proportion of the bacterial biomass in the oxygenated hypolimnia of deep lakes worldwide, including the world's largest freshwater system, the Laurentian Great Lakes. Traits that allow CL500-11 to thrive and its biogeochemical role in these environments are currently unknown. Here, we found that...
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. Mueller,b Edna Chiang,a James R. Liebig,c Henry A. Vanderploegc
Department of Ecology and Evolutionary
Agricultural practices, including tillage, fertilization, and residue management, can affect surface runoff, soil erosion, and nutrient cycling. These processes, in turn, may adversely affect (1) quality of aquatic resources as habitat for amphibians, fish, and invertebrates, (2) costs of treating surface and ground water to meet drinking water standards, and...
Background:
Very few closed genomes of the cyanobacteria that commonly produce toxic blooms in lakes and reservoirs are available, limiting our understanding of the properties of these organisms. A new anatoxin-a-producing member of the Nostocaceae, Anabaena sp. WA102, was isolated from a freshwater lake in Washington State, USA, in 2013...
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Very few closed genomes of the cyanobacteria that commonly produce toxic blooms in lakes and reservoirs are available, limiting our understanding of the properties of these organisms. A new anatoxin-a-producing member of the Nostocaceae, Anabaena sp. WA102, was isolated from a freshwater lake in Washington State, USA, in 2013...
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Nathan M. Brown1, Ryan S. Mueller1, Jonathan W. Shepardson1, Zachary C. Landry1, Jeffrey T. Morré2
Background:
Very few closed genomes of the cyanobacteria that commonly produce toxic blooms in lakes and reservoirs are available, limiting our understanding of the properties of these organisms. A new anatoxin-a-producing member of the Nostocaceae, Anabaena sp. WA102, was isolated from a freshwater lake in Washington State, USA, in 2013...
In response to genotoxic stress, ATR and ATM kinases phosphorylate H2A in fungi and H2AX in animals on a C-terminal serine.
The resulting modified histone, called γH2A, recruits chromatin-binding proteins that stabilize stalled replication forks or promote
DNA double-strand-break repair. To identify genomic loci that might be prone to replication...
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While there has been growing interest in the gut microbiome in recent years, it remains unclear whether closely related species and strains have similar or distinct functional roles and if organisms capable of both aerobic and anaerobic growth do so simultaneously. To investigate these questions, we implemented a high-throughput mass...
Assessment of beef cow energy balance
and efficiency in grazing-extensive rangelands has
occurred on a nominal basis over short time intervals and
has not accounted for the complexity of metabolic and
digestive responses; behavioral adaptations to climatic,
terrain, and vegetation variables; and documentation of
the effects of nutrient form and...
In response to genotoxic stress, ATR and ATM kinases phosphorylate H2A in fungi and H2AX in animals on a C-terminal serine.
The resulting modified histone, called γH2A, recruits chromatin-binding proteins that stabilize stalled replication forks or promote
DNA double-strand-break repair. To identify genomic loci that might be prone to replication...
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., Mueller, C. V., Friedman, S., Freitag, M., & Lewis, Z. A.
(2014). Heterochromatin controls γH2A
Toxin production by cyanobacterial harmful algal blooms (cyanoHABs) in freshwater systems has lasting ecological and human impacts. Nutrients, light availability, hydrology, and microbial community composition impact the frequency and intensity of toxic cyanoHABs. Climate change will exacerbate toxic cyanoHABs, making real time and predictive monitoring a vital tool for managing...
Marine sediments are vast sources and reservoirs of methane, a potent greenhouse gas. Most of this methane is anaerobically oxidized by archaea before it can reach the overlying ocean, though the efficiency of this process often depends on methane fluxes and mechanisms of fluid transport. Anaerobic methanotrophic archaea, or ANME,...
Stony corals are the ecosystem engineers of the vital, dynamic, and complex marine ecosystem known as coral reefs. Globally, coral reefs are undergoing degradation from multiple anthropogenic stressors. Coral reef organism holobionts, or the host along with its microbial components, are key to reef ecosystem success and functioning. Marine microbes...
California brome (Bromus carinatus Hook & Arn), is
considered an important weed infesting wheat and grass seed
fields in the Willamette Valley of Oregon. Field and
greenhouse experiments were conducted to study some
biological aspects to develop more efficient management
strategies.
A field experiment was conducted to determine the
effect...
Pseudomonas aeruginosa is a ubiquitous environmental microbe, opportunistic pathogen, and a highly social organism. P. aeruginosa utilizes a wide array of cooperative behaviors to adapt to the environmental conditions around it. These behaviors include quorum sensing (QS), a form a cell-to-cell signaling that coordinates the expression of secreted products in...
Internal waves and tides are a dominant source of current variability, and they are intermittent and hard to predict. Internal waves can have significant variability in alongshore structure. However, previous studies on internal waves have focused primarily on their cross-shore structure and propagation. For example, while alongshore-propagating superinertial internal tides...
The phylum Cnidaria contains three main branches: Anthozoa (corals, sea anemones) Medusozoa (jellyfish, hydra), and Endocnidozoa. This latter branch is characterized by parasitism and contains the microscopic fish-parasites Myxozoa. Myxozoa are highly simplified, consisting of only a few cell types, however they have retained the nematocyst stinging cells and complex...
In the spring of 1992 an optical closure experiment was conducted at Lake
Pend Oreille, Idaho. A primary objective of the experiment was to compare techniques
for the measurement of the spectral absorption coefficient and other inherent optical
properties of natural waters. Daily averages of absorption coefficients measured using
six...
Growth and replacement patterns of four successionally important
species occurring on Douglas fir clear-cuts were investigated
from September 1964 to June 1967. The study was carried out
on the Marys Peak watershed located near Corvallis, Oregon.
Species used in the study include Holcus lanatus, Senecio
jacobaea, Lotus crassifolius var. subglaber,...
A vegetation study was made of four coastal marshes near Juneau,
Alaska. Results confirmed earlier studies' findings in southeast
Alaska that communities or assemblages of species can be identified
but from marsh to marsh these assemblages appear to have no consistent
relationship to each other or to environmental "factors" such...
Distribution of lichens was studied at seven coastal dune sites in
Oregon. Lichens were sampled in the dry stable, dry meadow,
meadow, rush meadow, marsh, shrub and forest deflation plain communities.
Observations were made of the standing water in the marsh
community. Quantitative measurements were made of the percent
organic...
Mg batteries have potential advantages in terms of safety, cost, and reliability
over existing battery technologies, but their practical implementations are hindered
by the lack of amenable high-voltage cathode materials. The development
of cathode materials is complicated by limited understandings of the unique
divalent Mg²⁺ ion electrochemistry and the interaction/transportation...
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combined with the use of stable
cathode current collectors such as Mo and W. [ 8 ]
The second major
We present the first successful ⁸¹Kr-Kr radiometric dating of ancient polar ice. Krypton was extracted from the air bubbles in four ~350 kg polar ice samples from Taylor Glacier in the McMurdo Dry Valleys, Antarctica, and dated using Atom Trap Trace Analysis (ATTA). The ⁸¹Kr radiometric ages agree with independent...
This thesis presents an experimental study of radial porosity in a manually filled cylindrical container with glass spheres. The symmetric distribution of bead diameter allowed for normalization of container properties and porosity models. The aspect ratio of the container was approximately 3.9, with tube-to-particle-diameter ratio λ ≈ 24.6 and height-to-particle-diameter...
Background: High birthweight is an established risk factor for childhood leukaemia.
Its association with other childhood cancers is less clear, with studies hampered by low
case numbers. Methods: We used two large independent datasets to explore risk associations between
birthweight and all subtypes of childhood cancer. Data for 16 554...
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Mueller,7
Colleen C McLaughlin,8 Peggy Reynolds,9 Tim J Vincent,4
Julie Von Behren9 and Logan G
Several methods for estimation of the potential
shelf-life of pasteurized fluid milk products were evaluated
for their efficacy in this investigation. These methods
were evaluated and compared to sensory, biochemical and
bacteriological indices through a series of experiments
conducted on different brands of commercially pasteurized
fluid milk. The methods evaluated...