Master of Science / Department of Animal Sciences and Industry / J. Ernest Minton / Enteric pathogens are responsible for major economic losses in the swine industry. In the U.S., Salmonella enterica subspecies enterica serovar Typhimurium (ST) and serovar Choleraesuis (SC) account for essentially all cases of salmonellosis in swine. Previous studies documented that oral ST eroded growth and produced unmistakable changes in the endocrine stress and somatotropic axis of young growing pigs. However, these effects occurred in the absence of elevated systemic inflammatory cytokines that were previously thought to accompany disease-associated growth retardation. In the current study, it was hypothesized that SC would produce very different systemic inflammatory cytokine responses compared to ST given the likelihood of SC to produce systemic disease in pigs. Weaned pigs were housed two per pen with free access to feed and water during a 14 d experiment. On d 0, pigs were fed either 108 CFU SC or 108 ST, and bacteria were re-fed twice weekly through the course of the experiment. Control pigs were fed dough without bacteria. Serum was collected on d 0, 7, and 14 for determination of tumor necrosis factor alpha (TNFα), interleukin-1beta (IL-1β), and insulin-like growth factor-I (IGF-I) were determined. Rectal temperatures (RT) were monitored daily beginning 2 d prior to challenge with bacteria and until 7 d following the first bacterial feeding. Pigs were weighed initially, and at the conclusion of the study. Daily body weight gain was reduced by 25.4% in pigs fed SC (P<.0001) compared to control, while growth was similar between control pigs and those fed ST. Pigs fed SC had increased RT beginning on d 2 and continuing though d 7 (P < 0.05) with the greatest elevation spike on d 3 (P < 0.001) when compared to controls. On d 7, pigs fed SC had reduced IGF-I when compared to both control (P < 0.01) and ST pigs (P = 0.01). Despite the obvious febrile response, and the reductions in body weight gain and serum IGF-I, circulating TNFα and IL-1β were not affected by treatment. It was concluded that elevated TNFα and IL-1β are not obligatory correlates of SC-induced pathology and growth retardation in weaned pigs.

Master of Science / Department of Animal Sciences and Industry / Barry J. Bradford / The prevalence of fatty liver in transition dairy cattle has been reported to be as high as 50%. There are a few reliable on-farm diagnostic tools and even fewer methods to effectively prevent fatty liver. Non-alcoholic steatohepatitis, an advanced form of non-alcoholic fatty liver in humans, is accurately diagnosed with a commercial blood test that detects plasma cytokeratin-18 (CK18) fragments released during hepatocyte apoptosis. A study was performed using 89 Holstein cows in early lactation to determine if CK18 could serve as a novel indicator of liver triglyceride (TG) content. Although no previous work has been done with CK18 in bovine plasma, our results indicated that CK18 fragments were present in plasma. However, CK18 concentrations did not correlate with liver TG content or other measures of liver function, suggesting it is not a reliable diagnostic tool. Nevertheless, based on liver TG, plasma non-esterified fatty acid (NEFA), and plasma β-hydroxybutyric acid (BHBA) concentrations, this sample population as a whole was not suffering from severe metabolic problems or fatty liver, making it possible that plasma CK18 fragments are elevated only in the most extreme cases. Currently, there is no widely-adopted preventative strategy for fatty liver. A second study was performed to evaluate if encapsulated niacin (EN) could prevent liver TG accumulation during the transition period. Twenty-four primiparous (n=9) and multiparous (n=13) cows were randomly assigned to receive 0 or 24 g of dietary EN, beginning 3 weeks prior to expected calving until 21 days postpartum. Feeding EN did not influence liver TG content, but decreased plasma NEFA concentrations, suggesting inhibition of lipolysis. Multiparous EN cows also experienced depressed dry matter intake (DMI) in the 4 days prior to calving. However, even when EN reduced DMI, plasma NEFA was still suppressed. A novel finding was the prolonged clearance of caffeine in plasma on day 7 postpartum in EN-treated animals. In contrast to other studies, this dose and delivery method of EN did not result in an increase in plasma NEFA after EN treatment ended. These research projects determined that plasma CK18 is likely not a useful diagnostic tool for mild to moderate bovine fatty liver and that feeding EN can inhibit lipolysis but may influence DMI as well. This is one of the first studies into the metabolic effects of feeding EN, and further research is needed in this field.

Doctor of Philosophy / Department of Animal Sciences and Industry / J. Ernest Minton / The three experiments described below offer support of immune function by the swine gastrointestinal epithelium. Experiment one evaluated mediators that regulate the movement of macrophages (macrophage migration inhibitory factor; MIF), neutrophils (interleukin 8; IL8), dendritic cells (CC chemokine ligand 20; CCL20) and epithelial remodeling (osteopontin; OPN) in pigs challenged with Salmonella enterica serovar Typhimurium (ST) or Choleraesuis (SC). The proximal ileum had greater IL8 expression than the distal ileum (P < 0.05), and ST increased CCL20 (P < 0.05). In vitro, MIF, IL8, CCL20 and OPN mRNA expression induced by lipopolysaccharide (LPS), ST or SC using pig jejunal epithelial cells (IPEC-J2) resulted in increased IL8 secretion, and increased IL8 and CCL20 mRNA by ST and SC (P < 0.05). Experiment two evaluated how Lactobacillus reuteri (LR) and Bacillus licheniformis (BL) differed from ST or SC in their ability to regulate, stimulate, or modify IL8, CCL20, and tumor necrosis factor α (TNFα) in IPEC-J2 cells. ST stimulated an increase in IL8 secretion, with increases in IL8 mRNA (P < 0.05). BL increased IL8 mRNA (P < 0.0001). CCL20 mRNA was upregulated by ST (P < 0.05) and BL (P < 0.05). Only ST increased TNFα mRNA (P < 0.05). Another objective evaluated whether pre-exposure of IPEC-J2 cells to LR or BL modified ST induced IL8 secretion. IL8 secretion was increased by ST (P < 0.0001), and reduced by LR (P < 0.05). Only the BL/ST co-treated wells blunted basolateral IL8 secretion (P < 0.0001). Experiment three characterized the swine CCL20 mRNA sequence and evaluated tissue expression. Cloning of CCL20 from the porcine jejunum predicted a 97 amino acid peptide. All healthy tissues expressed CCL20 mRNA. In animals challenged with Salmonella spp., SC increased spleen and liver CCL20 expression. The data demonstrate that invasive bacterial pathogens in the pig gastrointestinal tract trigger upregulation of selected proinflammatory mediators; Salmonella spp. elicited differing patterns of activation in vitro and in vivo; IPEC-J2 cells increased IL-8 secretion in response to ST and BL, but not LR, while ST stimulated secretion was inhibited basolaterally by BL pre-exposure; and numerous porcine tissues are prominent sources CCL20.

Master of Agribusiness / Department of Agricultural Economics / Ted C. Schroeder / For the industry to be able to produce a higher performing and consistent quality product, evaluation of performance and information needs to be collected and available for producers to make more informed beef cattle production management decisions. In recent history, the cattle industry has taken on the complex job of maintaining and recording performance records through programs and efforts such as breed association data bases, and herd health data bases. The constant evaluation of performance and genetic records has supplied producers with data resulting in performance, maternal and carcass statistical records such as Expected Progeny Differences (EPDs). Additionally, developing technology is helping the industry through selection and decision tools such as Carcass DNA marker identification. This study evaluates how the selection tools of EPDs and DNA affect the value of Gelbvieh / Balancer bulls at auction. Data collected for this study is from various Gelbvieh / Balancer bull sales throughout Nebraska in the spring of 2008. Variables evaluated in the study were data and information provided to potential buyers before the auctions to be able to observe how this information affected the value of the purchased bull for each buyer. Variables evaluated were Igenity Profile Carcass DNA values of Ribeye Area, Marbling, and Tenderness. Additionally, Performance EPDs of Calving Ease Direct, Birth Weight, Weaning Weight, Yearling Weight, Ribeye Area, and Marbling were evaluated. The only actual measurement observed was Scrotal Circumference. The hedonic models developed for this study suggest that the selected bull data provided to potential buyers before sale are not the only significant determinants affecting price. Statistical measurements and technologies developing the industry are having a profound and positive effect on production and as selection tools however, are not the only potential variables affecting the value of a sire at auction. Other possible variables effecting auction value can also include evaluation of phenotype, pedigree, and buyer benefits. The data and variables evaluated in the study should still be used as valuable additions to other selection tools and observations when selecting a future beef sire.

Master of Science / Department of Statistics / Suzanne Dubnicka / In animal science, challenge model studies often produce longitudinal data. Many times the lognormal distribution is useful in modeling the data at each time point. Escherichia coli O157 (E. coli O157) studies measure and record the concentration of colonies of the bacteria. There are times when the concentration of colonies present is too low, falling below a limit of detection. In these cases a zero is recorded for the concentration. Researchers employ a method of enrichment to determine if E. coli O157 was truly not present. This enrichment process searches for bacteria colony concentrations a second time to confirm or refute the previous measurement. If enrichment comes back without evidence of any bacteria colonies present, a zero remains as the observed concentration. If enrichment comes back with presence of bacteria colonies, a minimum value is imputed for the concentration. At the conclusion of the study the data are log10-transformed. One problem with the transformation is that the log of zero is mathematically undefined, so any observed concentrations still recorded as a zero after enrichment can not be log-transformed. Current practice carries the zero value from the lognormal data to the normal data. The purpose of this report is to evaluate methods for handling missing data due to a limit of detection and to provide results for various analyses of the longitudinal data. Multiple methods of imputing a value for the missing data are compared. Each method is analyzed by fitting three different models using SAS. To determine which method is most accurately explaining the data, a simulation study was conducted.

Doctor of Philosophy / Department of Diagnostic Medicine/Pathobiology / Steven S. Dritz / Vaccination against porcine circovirus type 2 (PCV2) has become a standard practice to improve pig mortality and growth rate in PCV2-affected herds. Unfortunately, there has been little field-based research evaluating factors which affect circovirus vaccination. The focus of this research was on potential vaccination-affecting factors such as age, dosing strategy, pig genetic makeup, and interaction with other vaccines. A total of 6,275 pigs were used to determine factors which affect circovirus vaccination and the effects of vaccination on average daily gain (ADG), immune responses, and viral circulation under field conditions. In the first study evaluating circovirus vaccination effects on PCV2 antibody titer, regardless of age and dose administration protocol, pigs vaccinated with a 2-dose circovirus vaccine had increased (P ≤ 0.008) antibody titers compared with non-vaccinates. In a second study, dosing strategy failed (P = 0.31) to affect antibody titers. However, product and time after vaccination did affect (P = 0.005) antibody titers. In another 130-d study across the nursery and finishing phases, pigs vaccinated with a 2-dose circovirus vaccine had decreased (P < 0.001) serum PCV2 viral load compared with non-vaccinates and ADG of vaccinates was better than non-vaccinates. However, the effect was more pronounced (vaccination-by-genetic interaction, P ≤ 0.05) in Duroc-based compared to Pietrain-based pigs. In a study limited to the nursery phase, vaccination for PCV2 and Mycoplasma hyopneumoniae independently reduced ADG and consumption, but the effect was product-dependent. In a 155-d study across the nursery and finishing phases, vaccination with a 2-dose, 2-vaccine program for PCV2 and Mycoplasma hyopneumoniae decreased (P < 0.001) nursery ADG but tended to increase (P = 0.06) finishing ADG compared to a 1-dose, 2-vaccine program, with no difference (P = 0.66) observed between final pig weights. Finally, circovirus vaccination affected PCV2-circulation in high-health research herds but not in a commercial herd where PCV2 DNA was detected in the environment. These results indicate that finishing performance was improved by a 2-dose circovirus vaccine; however, nursery performance was negatively affected by the same product. Circovirus vaccination responses of growth, viral load, and antibody titer were affected by pig genetic makeup, product, and PCV2-exposure status.

Master of Science / Department of Computing and Information Sciences / William H. Hsu / In addition to named entities such as persons, locations, organizations, and quantities which convey factual information, there are other entities and attributes that relate identifiable objects in the text and can provide valuable additional information. In the field of epizootics, these include specific properties of diseases such as their name, location, species affected, and current confirmation status. These are important for compiling the spatial and temporal statistics and other information needed to track diseases, leading to applications such as detection and prevention of bioterrorism. Toward this objective, we present a system (Rule Based Event Extraction System in Epizootic Domains) that can be used for extracting the infectious disease outbreaks from the unstructured data automatically by using the concept of pattern matching. In addition to extracting events, the components of this system can help provide structured and summarized data that can be used to differentiate confirmed events from suspected events, answer questions regarding when and where the disease was prevalent develop a model for predicting future disease outbreaks, and support visualization using interfaces such as Google Maps. While developing this system, we consider the research issues that include document relevance classification, entity extraction, recognizing the outbreak events in the disease domain and to support the visualization for events. We present a sentence-based event extraction approach for extracting the outbreak events from epizootic domain that has tasks such as extracting the events such as the disease name, location, species, confirmation status, and date; classifying the events into two categories of confirmation status- confirmed or suspected. The present approach shows how confirmation status is important in extracting the disease based events from unstructured data and a pyramid approach using reference summaries is used for evaluating the extracted events.

Master of Science / Department of Animal Sciences and Industry / Terry A. Houser / Two experiments were completed as a part of this study. The objective of the first experiment was to determine the differences in chemical characteristics of trimmings from hot processed and traditionally processed cull meat goats. Crossbred cull doe goats (n=18) were assigned to one of 3 kills days with 6 replications per day. The sides of each goat were randomly assigned to hot processed (HP) or traditionally processed (TP). HP sides were fabricated within 2 h of slaughter, ground with 2% salt and dry ice and then held at 2oC for 24h. TP sides were chilled at 2oC for 24 h prior to fabrication and grinding. After sampling, 2% salt was added to remaining trim yielding 2 treatments: traditionally processed with no salt added (TPNS) and traditionally processed with salt added (TPS). As expected, the HP treatment had a higher (P<0.0001) ultimate pH than TP and a higher water holding capacity (WHC) than TPS (P<0.002) and TPNS (P<0.001) treatments. HP and TPNS had significantly higher (P<0.0007 and P<0.0003, respectively) percent moisture than TPS. Percent fat was similar (P>0.19) for all treatments. However, TPNS had more protein (P<0.0001) than either the HP or TPS treatments. HP and TPS had decreasing L* values until d 6 when values increased significantly while TPNS decreased steadily by day. HP and TPS differed significantly from TPNS until d 6 when no significant differences were seen. For all treatments, a* values showed decreasing values until d 6. For all treatments, b* values increased until d 5. The objective of the second experiment was to investigate the viability of composting as a means for disposing of goat tissues resulting from the slaughter and fabrication process. By-products from the slaughter of cull meat goats (n=18) were assigned to 3 treatment piles: bones, offal + head (OH), and whole (bones, skull, and offal). Bones and OH piles increased in temperature, with peaks at wk 7 and wk 9, while whole piles had elevated temperatures from wk 5 to wk 9. Bone piles had statistically lower temperatures through wk 3, but were not statistically different than other treatments through the duration of the study. Whole piles had higher (P<0.0001) temperatures over the 8 wk composting period than OH and bone piles. Bone decomposition progressed over 90 d; at d 60, bones in whole piles had greater (P<0.05) decomposition than in bone piles. Similarly, skulls decomposition increased over the 90 d period. At d 60 and 90, skulls in whole piles had greater (P<0.05) decomposition than skulls in OH piles.

Master of Science / Department of Animal Sciences and Industry / Duane L. Davis / Intestinal absorption of colostral leukocytes (CL), peripheral blood mononuclear cells (PBMC), and porcine umbilical cord matrix stem cells (PUC) was analyzed in neonatal pigs. Maternal CL have previously been demonstrated in pigs, and maternal PBMC have been observed in calves to enter neonatal circulation after ingestion. PUC are primitive stem cells that are easily isolated from Wharton's jelly of the porcine umbilical cord. These cells do not have an immunogenic effect on the host upon initial transplantation. The general characteristics of PUC may allow them to serve as a delivery system to the neonate. Cellular migration through the duodenum, jejunum, and ileum was assessed using confocal microscopy. In vitro experiments utilized an organ explant culture system to determine the trafficking of labeled cells. Small-intestine tissue was collected from stillborn and sacrificed neonates. All three cell types (CL, PBMC, and PUC) were detected below the luminal surface, after 72 h of culture with media, and regardless of whether explants were from stillborns or live-born pigs. In vivo trafficking was assessed using neonatal pigs that were fed PBMC isolated from their mother or PUC from an unrelated pig. The effect of prior exposure to 25% acellular colostrum (AC) in medium was evaluated for both cell types. Piglets were euthanized 8 h or 24 h post feeding and sections of the small intestine collected. Both PBMC and PUC were found in all intestinal samples. Exposure to AC had no detected effect on the ability of either cell type to attach and migrate into the tissue. Labeled PUC were detected on the surface of the epithelium and in the lamina propria 8 h post treatment. PBMC were observed on the surface of the epithelium, in the lamina propria, and superficial submucosa 8 h following ingestion. In neonates sacrificed 24 h post treatment, both PUC and PBMC were observed on the surface of the epithelium, in the lamina propria, superficial submucosa, and deep submucosa of the small intestine. PUC and PBMC were noted at the apex, intermediate between the apex and the base, or at the base of the villus.

Doctor of Philosophy / Department of Diagnostic Medicine/Pathobiology / Tiruvoor G. Nagaraja / Escherichia coli O157 is a major foodborne pathogen. The bovine gut is the primary reservoir and the organism is shed in the feces, which serves as the major source of contamination. The objectives of our research on E. coli O157 were to 1) determine prevalence and characterize presence in the rectoanal mucosa of cattle, 2) rationalize preferential prevalence in the hindgut, 3) evaluate fecal prevalence and concentration in relation to carcass contamination 4) determine the efficacy of preharvest intervention strategies to reduce fecal prevalence and/or concentration in cattle. We determined that E. coli O157 isolated from the rectoanal mucosa were similar to fecal isolates. We evaluated methods of enumeration in cattle feces to identify fecal samples with > 10[superscript3] and 10[superscript4] CFU of E. coli O157/g. We observed that prevalence of E. coli O157 on carcasses was correlated with high-shedders. We identified gluconic acid as a substrate which stimulates growth of E. coli O157 in fermentations with ruminal microbial or fecal microbial inocula from cattle. This may explain the preference to persist or colonize the hindgut because gluconic acid is a component of colonic mucin. Additionally, we evaluated the effects of cattle diets (two grain types and two grain processing methods), which present different amounts of fermentable starch to the hindgut, on prevalence of E. coli O157. Dry-rolled grain-based diets reduced prevalence of E. coli O157, possibly because of increased flow of starch to the hindgut. Competitive exclusion cultures of E. coli in in vitro fermentations reduced E. coli O157 in ruminal microbial inoculum, but in fecal microbial inoculum cultures were only efficacious when gluconic acid also was added. Lastly, we evaluated a vaccine which targeted the siderophore receptor/porin proteins of E. coli O157. The vaccine reduced prevalence, the total number of days cattle tested positive, and the total number of days cattle were identified as high-shedders of E. coli O157. In summary, our research adds further knowledge to the literature about E. coli O157 in the hindgut, provides methods to identify high-shedding animals, demonstrates the importance of high-shedding animals, and offers information about potential preharvest interventions.