The Willamette River, one of only 14 American Heritage Rivers, flows through the most densely populated and agriculturally productive region of Oregon. Previous biological monitoring of Willamette River fish detected elevated frequencies of skeletal deformities in fish from certain areas of the lower (NP [NP], rivermile [RM] 26-55) and middle...
Mycobacterium avium is an intracellular pathogen that is associated with disseminated
infection, especially in patients with acquired immunodeficiency syndrome (AIDS). It
appears that patients with AIDS acquire M. avium mostly through the intestinal tract,
and that bacteria enter the intestinal wall at the terminal ileum. Previous studies have
found that...
Biological agents and their products commonly cause foodborne illnesses. In the United States it is estimated that there are over 76 million cases of foodborne illnesses each year, resulting in an economic loss of approximately $40 billion. These high figures demonstrate the need for bioassays that display a rapid and...
Streptococcus gordonii is a bacterial species that naturally colonizes the oral cavity of most healthy humans. It resides in the mouth as an adherent to dental surfaces and, with few exceptions, does not cause disease in individuals it inhabits. It possesses qualities that encourage its use as a vector to...
Ceratomyxa shasta is a myxozoan parasite of salmonids and requires the freshwater polychaete, Manayunkia speciosa to complete its life cycle. The parasite’s distribution is currently limited to the Pacific Northwest region of North America and has been reported to cause substantial losses of both wild and hatchery salmonids. The spatial...
The majority of our modern understanding of bacterial pathogenesis is based on the strategy that involves screening bacterial genomes for the presence of the genes encoding pathogenic factors, and analysis of these genes via forward and reverse genetics. Chlamydiae represent a unique group of pathogenic bacteria in which it is...
In this thesis, I studied the translation of dengue virus RNA using a luciferase reporter gene system in Vero cells. The dengue reporter mRNA construct, which harbors 5´-terminal viral nts and 3´-terminal nts, could be translated efficiently compared to an alpha globin reporter construct. The 5´-cap structure and 3´-untranslated region...
Francisella tularensis is a gram-negative facultative intracellular
coccobacillus that primarily infects macrophages. The causative agent of tularemia,
this bacterium is considered among the most infectious organisms known, requiring
fewer than ten organisms to cause disease. Although ubiquitous in nature,
transmission to humans is rare but can occur via insect bites,...
Standard methods of measuring fecal pollution in water do not distinguish between human and non-human sources. Molecular technology enabled the development of host-specific markers that distinguish fecal sources. Human specific PCR primers, HF183F and HF134F, were designed based on phylogenetic analyses of partial 16S rRNA gene sequences from the Bacteroidales...
Clostridium perfringens type A isolates producing enterotoxin (CPE) are an
important cause of both food poisoning (FP) and non food borne gastrointestinal
diseases (NFBGID) in both humans and animals. C. perfringens type A food
poisoning is caused by isolates carrying the CPE encoding gene (cpe) on the
chromosome while the...
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...
The ability to move towards favorable environmental conditions, called chemotaxis, is common among motile bacteria. In particular aerotaxis has been extensively studied in Escherichia coli. Three putative aer gene homologs were identified in the V. cholerae genome designated VCAer-1 (VC0512) VCAer-2 (VCA0658), and VCAer-3 (VCA0988). Deletion analyses indicated that only...
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...
Vaccinia virus is the prototypic member of the Orthopoxvirus genus. It undergoes a complex replication process where a key step in the transition from immature virion to intracellular mature virion is the cleavage of the major core protein precursors. The product of the I7L open reading frame (ORF) is a...
The Baculoviridae comprise a diverse group of occluded DNA viruses that contain large double-stranded DNA genomes of 80 - 180 kb and may encode up to 180 gene products. To understand how baculoviruses replicate and process their genomes and the gene products that are involved in these events, a series...
Chlamydiae are obligate intracellular bacteria that infect a variety of
eukaryotic hosts and affect normal host processes. Within host cells, their
developmental cycle takes place inside non-acidified vacuoles termed inclusions. An
inclusion membrane composed primarily of secreted chlamydial synthesized proteins
called Incs encloses the inclusion. At this location, Incs have...
Candidatus Pelagibacter ubique is the first cultured representative of the SAR11 clade, a clade that is found throughout the oceans and accounts for approximately 25% of all bacterial cells [1]. It has a streamlined genome that is the smallest of any known free-living organism. In this study the complete genome...
Clostridium perfringens type A isolates, an anaerobic enterotoxigenic spore forming bacterium, are the third leading cause of food-borne disease in the United States. Factors that contribute to the virulence of C. perfringens include the ability of the bacterium to form heat resistant spores and to produce an enterotoxin (CPE). Although...
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...
There have been many studies that describe the protective degradation or metabolism of potentially harmful plant toxins, such as, mimosine from Leucaena leuconcephala, pyrrolizidine alkaloids from tansy ragwort (Senecio jacobaea), oxalate and some mycotoxins by rumen microbes. There are many cases of plant-related toxicoses suffered by ruminant animals where there...
Chemical and microbial analyses were made at four seasonal intervals on soil horizons under red alder, conifers, and mixed
alder-conifers at the Cascade Head Experimental Forest, established in 1937 by the U. S. Forest Service near Otis, Oregon.
Microbial analyses showed that although plate counts of molds and bacteria fluctuated...
The F13L protein is the major envelope antigen of vaccinia virus, the prototypic member of the Orthopoxvirus genus. F13L is 372 residues in length and is essential for the formation of wrapped forms of virus. F13L contains a number of potential functional domains including a palmitylation site, a phospholipase domain...
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...
Optimum growth temperatures were determined for nine strains of Streptococcus thermophilus and ten strains of Lactobacillus bulgaricus, all commercial yogurt or yogurt
starter isolates. Optimum growth temperatures ranged from 35 C to 42 C for S.thermophilus strains, averaging 38.6. Optimum growth temperatures for L.bulgaricus strains ranged from 43 C to...
At present all vaccines for fish are primarily delivered either by injection or immersion which introduces added stress and labor. A more attractive method of vaccine delivery is oral administration using an enteric protection system, Enteric Coated Antigen Microspheres (ECAMs), which can be utilized for a variety of antigenic forms....
2,4,6-Trinitrotoluene (TNT) has been the common munitions used in the world and is an environmental contaminant that is amendable to reductive transformation reactions. The rumen is an extremely reductive environment containing diverse microbial populations. There are 21 pure culture ruminal bacteria species in culture collection, these were tested for the...
For the past twenty-seven years, Human Immunodeficiency Virus (HIV)/Acquired Immunodeficiency Syndrome (AIDS) has become a worldwide pandemic. Due to the properties of HIV, such as its fast replication rate and error-prone reverse transcriptase, researchers have been unsuccessful in finding a cure or vaccine. Researchers have, however, developed a treatment regimen...
Morphological, cultural, biochemical and serological characteristics of
33 bacterial strains, thought to be similar to Cytophaga psychrophila, the
causative agent of bacterial cold-water disease were compared. Bacterial
strains identified as C. psychrophila were obtained from diseased salmonids
collected at widely separated geographic locations, and from fish with
pathological signs different...
The purpose of this study was to characterize Cytophaga
psychrophila isolates obtained from coho fingerlings with low temperature
disease collected at selected hatcheries in Oregon. In
addition, cultures thought to be related to this bacterium were
isolated from Siletz Hatchery water, deformed juvenile and spawning
adult coho salmon, rainbow and...
A plan for the reestablishment of anadromous salmonid stocks into waters above the Pelton Round Butte Hydroelectric Project (PRB) located on the Deschutes River, Oregon has been under development since 1996. The PRB complex, starting at river kilometer (Rkm) 103, blocks the further upstream migration of anadromous salmonids into upper...
Current detection methods for bacterial contamination rely on structure based detection of proteins and nucleic acids. While these methods are easy to use and reliable, they cannot evaluate the toxicity of a sample and the potential to cause disease. Previously, erythrophore cells derived from Betta splendens had been suggested as...
Cell-based biosensors are function-based detectors that use the physiological response of a living cell to sense biologically stimulating agents. This emerging technology extends the application of current detection methods by reporting on the toxicity of a sample and the potential to cause disease. Previously, Betta splendens erythrophores have been described...
Tumor necrosis factor alpha (TNF α) and interferon gamma (IFN γ) were initially recognized as inflammatory mediators produced by immune cells in response to infectious agents or foreign material. (1,5) However, over the past decade much research in mammalian species has indicated that these proteins also play key roles in...
The immune toxicity of 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) has been studied for over 35 years, but only recently has the profound immune suppression associated with TCDD exposure been linked to induction of regulatory T cells (Tregs). The effects of TCDD are mediated through binding the aryl hydrocarbon receptor (AhR), a ligand-activated transcription...
A technique that uses hypotonic lysis of erythrocytes was optimized for the purification of leukocytes from the peripheral blood and anterior kidney (pronephros) of rainbow trout Oncorhynchus mykiss. Comparisons of initial blood dilution (1:2, 1:4, and 1:6) and the time of exposure to hypotonic conditions (10, 20, and 40 s)...
The ability of Flexibacter columnaris to attach to fish
cells was studied. Four of the five bacterial strains
tested were able to adhere to fish cells derived from four
different fish species. The attachment of these strains
in vitro required magnesium but was not affected by
increasing the incubation temperature...
Ceratomyxa shasta is a myxozoan parasite that infects salmonid fishes causing the disease ceratomyxosis that is characterized by severe hemorrhage and necrosis of the intestine and death of the fish host. Ceratomyxa shasta is endemic to the Pacific Northwestern United States and Canada, where epizootics are reported for both wild...
Relationships among myxozoan parasites of the order Multivalvulida were examined through comparative DNA sequence analysis. Members of this group of parasites is known for the damaging effects they have on their fish hosts, especially commercially important species. Most species infect muscle, where they form cysts and many release proteolytic enzymes....
The anaerobic and highly reductive conditions found in the ovine rumen are considered favorable for the degradation of the nitroaromatic explosives such as hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX). In this study, we used stable-isotope-probing to determine the bacteria responsible for the degradation of RDX in the rumen. Results indicate 10 μg mL⁻¹ (45...
Nearly 3000 juvenile Chinook (Oncorhynchus tshawytscha) and coho (O. kisutch) salmon captured in nearshore waters off the coasts of Washington and Oregon from 1999-2004 were tested for infection by Renibacterium salmoninarum, Nanophyetus salmincola, and skin metacercariae. First, three quantitative PCR primer/probe sets were compared for detection of R. salmoninarum; amplification...
The bacteriophage receptor of lactococci was found on the cell
walls. A carbohydrate analysis of the cell walls from phage-resistant
mutants of L. lactis subsp. cremoris KR with reductions in phage binding
indicated that a loss of galactose correlated with a loss in binding
and infection of all phage tested:...
Clostridium perfringens is a pathogenic anaerobic bacterium able to produce more than 17 toxins, allowing C. perfringins to cause a wide variety of diseases in humans and animals. Beside toxins production, C. perfringens able to form a highly resistance spores can survive in the environments for years. These spores are...
The myxozoan parasite of salmonids, Ceratomyxa shasta, is established throughout the Klamath River, CA-OR, with high parasite densities below the series of dams and above the dams (upper basin) in the northernmost tributary, the Williamson River (WMR). Two objectives were designed to address concerns about C. shasta effects on reintroduced...
Diseases caused by parasites are recognized as significant sources of mortality in wild fish populations. I assessed the impacts of multispecies parasitism on a threatened stock of juvenile coho salmon (Oncorhynchus kisutch). A crucial prerequisite to this research was proper identification of parasites, which can be difficult for species lacking...
Myxobolus cerebralis, a myxozoan parasite that infects almost all species of wild and cultured salmonids, was first identified in northeastern Oregon in the Lostine River in 1986. Fish that are heavily infected with M. cerebralis develop whirling disease, which was determined to be the cause of catastrophic declines in rainbow...
Cyclic nitramines released into all environmental compartments through anthropogenic activities are toxic and possibly carcinogenic and mutagenic. Soils on military ranges, located throughout the world in various climatic regions and close to human activities, are especially susceptible to cyclic nitramine contamination. The properties of soils on military ranges will directly...