Doctor of Philosophy / Department of Diagnostic Medicine/Pathobiology / Daniel U. Thomson / In current literature, there is a limited amount of large scale data available demonstrating lameness morbidity in beef cattle feedlots, the subsequent outcomes of individuals exhibiting lameness, the morbidity and mortality of various lameness diagnoses, or the effect of locomotion score at the time of first morbidity and its effect on outcome. In addition, current perceptions of lameness by feedlot industry participants are not known and a reliable locomotion scoring system fit for use in a feedlot setting has not been developed. Consequently, the objectives of this research were three-fold. First, to obtain a baseline of the perception of lameness within the feedlot industry. Second, to develop a functional locomotion scoring system for use in feedlots and to test a training program implementing this locomotion scoring system for inter-rater reliability. Third, determine the association of lameness diagnosis and locomotion score at time of initial lameness diagnosis with case outcome in feedlot cattle and provide beef cattle feedlot lameness morbidity, mortality, and realizer incidence rates due to different lameness etiologies in a large scale, multisite study. One hundred forty-seven consulting nutritionists, veterinarians, and feedlot managers participated in the feedlot cattle lameness survey. The median response of estimated lameness incidence in the feedyard was 2%, with a mode of 1% and a mean of 3.8%. Participants indicated that footrot, injury, and toe abscesses were the most common causes of lameness. A locomotion scoring system was developed to clinically assess locomotion of beef cattle. The scoring system consisted of 4 categories: normal movement (0), slightly affected gait (1), obviously shortened stride or bobbing of head (2), and reluctance to move or apply weight to the limb while walking or standing (3). A total of 50 commercial feedlot employees and agricultural students were trained to use the scoring system in either English or Spanish. The scoring system was tested for inter-rater agreement and rater agreement against a cooperative standard based on consensus score by a team of individuals involved in the development of the scoring system, which included beef cattle veterinarians and welfare experts. Intra-class correlation coefficient (ICC) and Fleiss’s kappa were used to evaluate inter-rater agreement and rater agreement against the cooperative standard. Inter-rater agreement using ICC was 0.85 (95% CI; 0.75 to 0.93) while the mean kappa value was 0.52 (moderate agreement). Rater agreement with the cooperative standard resulted in mean kappa value of 0.64 (substantial agreement). A dynamic population longitudinal study with an initial study population of 245,494 head of feedlot cattle, with 524,780 animal arrivals and 527,220 animal departures recorded over the 12-month study was conducted over a year by trained personnel in six participating feedlots located in Kansas and Nebraska. Lameness morbidity incidence was 1.04 cases per 100 animal-years; lameness mortality was 0.397 cases per 100 animal-years. Cattle locomotion score (LMS; scale of 0 to 3 at time of initial diagnosis) were LMS1(22% of lameness cases), LMS2 (31%), and LMS3(22%). 24% of the lameness cases were not assigned a locomotion score (NS). Mortality risks were greatest for LMS3 (33.0%) and NS (31.3%), and were least for LMS1 (10.0%) with LMS2 (19.1%) being intermediate (P < 0.05).

Mastitis is a syndrome manifested by mammary gland inflammation which is thought to cause between $300 and $400 million in annual losses to the Canadian Dairy Industry. Studies have indicated that <i>S. aureus</i> may cause the production of anti-inflammatory cytokines which may enhance its survival within the bovine mammary gland. However, other studies have reported differing results following S. aureus intramammary infection (IMI). This thesis tested the hypothesis that S. aureus generated anti-inflammatory cytokine responses at the site of infection. In the first objective, different S. aureus isolates were screened for their effects on cytokine production (IFN-γ, TNF-α, IL-4 and IL-10) by bovine peripheral blood mononuclear cells (PBMCs) in vitro. Nine S. aureus isolates were co-cultured with PBMCs from lactating dairy cattle. Cattle used in the study had recall immune responses to <i>S. aureus</i>. The majority (6/9) of S. aureus isolates had minor effectors on cytokine production. The three remaining isolates generated large cytokine responses with both pro-inflammatory (IFN-γ and TNF-α) and anti-inflammatory (IL-4 and IL-10) characteristics. Two of these three isolates were tested in vivo by experimentally infecting lactating ewes. Cytokine production was characterized in the teat end, the mammary parenchyma and the supramammary lymph nodes (SMLNs). One isolate generated anti-inflammatory responses <i>in vivo</i> (IL-4 and IL-10) whilst the other generated both pro-inflammatory (IFN-γ) and anti-inflammatory (IL-10) responses in vivo. Given that some studies have suggested a role of staphylococcal enterotoxin C (sec) in the generation of anti-inflammatory responses, the role of sec was also investigated using bovine PBMCs. When purified SEC protein was co-cultured with PBMCs from beef steers, anti-inflammatory cytokines were produced. However, a <i>S. aureus</i> strain which was transformed for the sec gene did not affect cytokine production when co-cultured with PBMCs from lactating dairy cattle. The results of this thesis suggest that <i>S. aureus</i> infection can cause anti-inflammatory cytokine production but the response depends on the isolate causing the infection. Furthermore, the role of sec appears to be minimal.

Mastitis is a syndrome manifested by mammary gland inflammation which is thought to cause between $300 and $400 million in annual losses to the Canadian Dairy Industry. Studies have indicated that <i>S. aureus</i> may cause the production of anti-inflammatory cytokines which may enhance its survival within the bovine mammary gland. However, other studies have reported differing results following S. aureus intramammary infection (IMI). This thesis tested the hypothesis that S. aureus generated anti-inflammatory cytokine responses at the site of infection. In the first objective, different S. aureus isolates were screened for their effects on cytokine production (IFN-γ, TNF-α, IL-4 and IL-10) by bovine peripheral blood mononuclear cells (PBMCs) in vitro. Nine S. aureus isolates were co-cultured with PBMCs from lactating dairy cattle. Cattle used in the study had recall immune responses to <i>S. aureus</i>. The majority (6/9) of S. aureus isolates had minor effectors on cytokine production. The three remaining isolates generated large cytokine responses with both pro-inflammatory (IFN-γ and TNF-α) and anti-inflammatory (IL-4 and IL-10) characteristics. Two of these three isolates were tested in vivo by experimentally infecting lactating ewes. Cytokine production was characterized in the teat end, the mammary parenchyma and the supramammary lymph nodes (SMLNs). One isolate generated anti-inflammatory responses <i>in vivo</i> (IL-4 and IL-10) whilst the other generated both pro-inflammatory (IFN-γ) and anti-inflammatory (IL-10) responses in vivo. Given that some studies have suggested a role of staphylococcal enterotoxin C (sec) in the generation of anti-inflammatory responses, the role of sec was also investigated using bovine PBMCs. When purified SEC protein was co-cultured with PBMCs from beef steers, anti-inflammatory cytokines were produced. However, a <i>S. aureus</i> strain which was transformed for the sec gene did not affect cytokine production when co-cultured with PBMCs from lactating dairy cattle. The results of this thesis suggest that <i>S. aureus</i> infection can cause anti-inflammatory cytokine production but the response depends on the isolate causing the infection. Furthermore, the role of sec appears to be minimal.

The parallel gene expression profiles of Brucella melitensis and the host have not been elaborated. In this study, I analyze and discuss the transcriptional profiles of B. melitensis invasive-associated genes, the expression profile of intracellular B. melitensis and B. melitensis-infected non-phagocytic cells in the first 12 h post-infection (PI), and the in vivo temporal global transcriptome of both B. melitensis and the infected bovine host in the first 4 h PI. The initial study found that B. melitensis at late-log phase of growth were more invasive in non-phagocytic cells than at early-log or stationary growth phase. Microarray-based studies identified 454 Brucella genes differentially expressed between the most and the least invasive growth phases. Additionally, B. melitensis strains with transposon interrupted in loci BMEII0380 (acrA) and BMEI1538 (hypothetical protein) were found to be deficient in internalization compare with the wild-type strain. A second experiment was designed with the goal of characterizing host and pathogen transcriptome in parallel. For detecting intracellular Brucella gene expression, a combined protocol consisting of a linear amplification of sense-stranded RNA biased to pathogen transcripts to the previously enriched host:pathogen RNA mixed sample, was developed. RNA samples were hybridized on human and Brucella cDNA microarrays, which analysis revealed a common down-regulation transcriptional profile at 4 h PI that was reverse at 12 h PI. The integrity of B. melitensis virB operon and the expression of host MAPK1 were confirmed as critical for early B. melitensis intracellular survival and replication in non-phagocytic cells. Finally, a temporal morphological and molecular characterization of the initial B. melitensis:bovine host interaction using a calf ileal loop model was performed. B. melitensis was isolated from intestinal Peyer’s patches as soon as 15 min and from systemic blood after 30 min postintra luminal inoculation. Microarray results revealed a common transcriptional profile in Brucella, but two different transcriptional profiles were identified in the host in the first 4 h PI. The importance of differentially expressed biological processes, pathways and individual genes in the initial Brucella pathogenesis is discussed.

Economic events may cause structural changes in markets. To know the effect of the economic event we should analyze the structural changes in the market demand and supply. The purpose of this dissertation is to analyze the effect of selected economic events on market demand and supply using econometric models. Structural changes can be modeled according to the types of changes. For an abrupt and instantaneous break, a dummy variable model can be used. For a smooth and gradual movement, proxy variables which represent the event can be applied, if we know the variables. If we don‟t know the appropriate proxy variables, a smooth transition regression model can be employed. The BSE (Bovine Spongiform Encephalopathy) outbreak in the U.S. in 2003 is assumed to make abrupt and instantaneous changes in Korean meat consumption. To analyze the effect on Korean meat consumption, the Korean demands of beef, pork, chicken, and U.S. beef are estimated using an LA/AIDS (Linear Approximate Almost Ideal Demand System) model with the dummy variable specifying the time before and after the BSE. From the results we can confirm that food safety concerns caused by the BSE case changed Korean meat consumption structure. Korean beef and U.S. beef became less elastic, and pork and chicken got more elastic to budget. Korean beef became less price elastic, but pork and U.S. beef got more price elastic. The changes of U.S. natural gas supply caused by technology development and depletion in reserves are analyzed using a smooth transition regression model. From the results, we can confirm that the productivity improvement by technology development is greater than the labor cost increase by depletion, but not greater than the capital cost increase by depletion in mid-2000s. The effects of posting the winning bid in a repeated Vickrey auction are examined using a proxy variable. By applying an unobserved effect Tobit model to the experimental auction done by Corrigan and Rousu (2006) for a candy bar, we can confirm that the changes of bidding behavior are significant, especially when the winning bid is high. By extracting the bid affiliation effects, we showed that true willingness to pay can be estimated.

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Bovine herpesvirus-1 (BoHV-1) is associated with the syndrome bovine respiratory disease, which is the major cause of morbidity and mortality within feedlots in Australia and around the world. Currently there are no vaccines that completely prevent BoHV-1 infections and viral shedding. The most efficacious vaccines used are live attenuated which have the potential to revert to wild type and cause disease. DNA vaccines are ideal vaccine candidates as they not only induce humoral and cellular immunity, they are also inexpensive and easy to produce. However, DNA vaccines although efficacious in small animal models have not yielded similar success in large animals. The inconsistent translation of DNA vaccines to large animal models, including cattle, has been associated with poor delivery of the vaccine to the nuclei of cells which is required for antigen transcription. Recently, the human herpesvirus-1 protein VP22 (hVP22) was demonstrated to exhibit the uncommon capacity to spread intercellularly from the cell of expression to the nuclei of neighbouring cells in a golgi and energy independent process. This process was very efficient with hVP22 being identified in all cells of a monolayer after transfection. hVP22 was quickly used to promote the efficiency of DNA vaccines by fusing the hVP22 gene with antigen genes in the vaccine resulting in the increased delivery of the antigenic protein to neighbouring cells. The fusion protein was subsequently degraded and presented as peptides on the cell surface in association with major histocompatibility complex (MHC) class II molecules that lead to an increase in fusion protein specific antibody production. This pathway, although successful augmenting the humoral response, did not increase the amount of antigen presented on MHC class I molecules which is essential for protection against intracellular pathogens. This thesis describes the development of a methodology whereby VP22, fused to a DNA binding protein, was hypothesised to increase the number of cells the DNA vaccine was delivered to and then to facilitate the transport of the DNA vaccine to their nuclei. A homologue of hVP22 has been identified in BoHV-1 and the capacity of the BoHV-1 protein to spread intercellularly and localise in the nuclei of cells was determined in this thesis using a novel and definitive model. Although retaining similar translocation capabilities to hVP22 the BoHV-1 VP22 homologue could not be expressed in bacteria and was subsequently not able to be used to demonstrate the proposed vaccine concept. hVP22 instead was fused to the DNA binding protein, Gal4, for bacterial expression. The purified fusion protein was demonstrated to bind not only oligonucleotides encoding the Gal4 binding sequence but also to a model DNA vaccine encoding Gal4 binding sequences in vitro. However, application of the hVP22 fusion protein:vaccine complex alone or condensed with poly-L-lysine to mammalian cells did not promote the delivery of the DNA vaccine to the nuclei of cells. As part of the DNA vaccine development for BoHV-1 the first nucleotide sequence of the Unique Short region of the Australian BoHV-1 strain V155 (8925 nucleotides) was determined. The sequence information generated permitted insights into epitopes contained within BoHV-1 antigens, particularly glycoprotein D which has been identified as the most appropriate glycoprotein for the purpose of vaccination. Furthermore, comparison of the Unique Short sequence variations between different subtypes of BoHV-1 provided molecular data that may be associated with the observed variation in virulence. Further optimisation of the methodology described in this study is required to facilitate the delivery of the DNA vaccine into cells by the VP22 fusion protein. The future development of strategies that utilise polypeptides to augment delivery of DNA vaccines into cells and then to facilitate the transport of the vaccine to the nuclei of cells, resulting in increased antigen expression, may ultimately lead to the successful application of this vaccine technology in animal models.