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.

Cette étude vise à caractériser le «crampage», une entité relativement nouvelle dans l’industrie ovine au Québec. Les signes cliniques se manifestent au pas, par une hyperflexion (hanche, grasset, jarret), d’un ou des deux membres pelviens. Cinq agneaux naturellement affectés et cinq agneaux appariés cliniquement normaux ont été soumis à des examens physique, neurologique et orthopédique, à des techniques d’imagerie avancée (tomodensitométrie, résonance magnétique), à des tests électrodiagnostiques (électromyogramme, vitesses de conduction nerveuse motrice et sensitive) puis à une nécropsie. Des hématologies, biochimies ainsi que des analyses du liquide céphalorachidien ont également été réalisées. Les résultats ont été comparés entre les groupes (affectés/cliniquement normaux). Il a été constaté à la tomodensitométrie que la surface du canal vertébral mesurée au niveau de la deuxième vertèbre lombaire était inférieure dans le groupe des agneaux affectés (p=0.045). Aucune répercussion n’a été constatée sur le segment de moelle épinière correspondant. La racine S2, quant à elle, était plus grêle dans le groupe des agneaux affectés (p=0.01). À l’issue de cette étude, une cause orthopédique, musculaire ou neurologique consécutive à une lésion structurale de la moelle épinière a été écartée. Il pourrait s‘agir d’une atteinte sensitive de la racine S2 altérant la sensation dans le membre affecté, toutefois, une anomalie fonctionnelle cérébrale ou de la moelle épinière dans le renflement lombaire, est également à considérer. Sans anomalie musculaire, l’appellation «crampage» est inexacte. Nous proposons de la remplacer par des termes plus descriptifs comme «syndrome d’hyperflexion» ou «high stepping gait». / This study aims to characterize "crampage" [cramping] a relatively new condition in the sheep industry in Quebec. This condition is easily recognized by the particular gait displayed by affected sheep, characterized by a hyperflexion (hip, stifle, hock) of one or both pelvic limbs while walking. Five naturally-affected and 5 clinically normal lambs, matched by age and weight, were subjected to physical, neurological and orthopedic examinations followed by advanced imaging (CT, MRI), and electrodiagnostic testing (electromyogram, motor and sensory nerve conduction velocities). Complete blood count, serum biochemistries and cerebrospinal fluid analysis were also performed. At the study’s completion, the lambs were humanely euthanazied and necropsied. The cross-sectional area of the vertebral canal on CT images, at the level of the second lumbar vertebra, was smaller in the affected group compared to clinically normal lambs (p = 0.045). No associated change was observed in the corresponding spinal cord segment. In addition, the S2 nerve root was narrower in the affected group (p = 0.01). This study excludes a musculoskeletal origin for this problem. A spinal cord lesion was also excluded as an etiology for this condition. A sensory impairment of the S2 nerve root, altering the sensation of the affected limb, may serve as the underlying cause. A cerebral or a functional abnormality in the lumbar intumescence could also be considered. Without an obvious muscular abnormality, the lay term "crampage" is inaccurate. We propose more descriptive terminology, such as "hyperflexion syndrome" or "high stepping gait".

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.

Aflatoxin M1 (AFM1) is frequently found in milk and dairy products. It is a metabolite formed in cows from aflatoxin B1 (AFB1), contained in animal feeds. In cheese production AFM1 distributes between curds and whey. In this study, cows were fed 64 µg/AFB1/d for the high treatment, and 5 µg/AFB1/d for the low treatment, to obtain milk contaminated with AFM1 over the 0.5 µg/L and under 0.05 µg/L restrictions, respectively. Cheese was manufactured with milk contaminated with AFM1 at 0.8 and 0.03 ìg/kg by the higher and lower treatment, respectively. Two commercial cheeses were elaborated: a hard-aged cheese (cheddar cheese) and soft high moisture cheese (fresco cheese) to evaluate whether the cheese type had any impact on AFM1 analysis. AFM1 was extracted from cheese using immunoaffinity columns. Analyses were carried out by using high pressure liquid chromatography (HPLC) as the reference method and fluorometry as a method of validation. Analysis was by 2-way fixed factor analyses. AFM1 was detected in all samples by both methods of analysis. There were no detectable statistical differences between cheese types (P>0.05). AFM1 content was significantly different between the high and low concentration of AFB1 used to make the cheese type (P<0.01). Our regression model shows a linear relationship between fluorometry and HPLC methods; R2 = 0.9141 from cheddar cheese and R2 = 0.9141 from fresco cheese. There were no statistical differences between methods of analysis (P>0.05). Carryover of AFM1 in cheese detected by fluorometry in cheddar cheese was 163% and 80% for high and low treatments, respectively, and in fresco cheese was 119 and 133 for high and low treatments, respectively. These carryovers are below that reported in the literature. Results suggest that fluorometry is a simple and reliable AFM1 detection method for screening samples of complex matrices such as cheese.

L’endométrite est une maladie affectant les performances en reproduction chez la vache laitière. Elle est définie par la présence d’inflammation excessive au niveau de l’utérus durant la période post-partum. Le traitement antibiotique sous forme d’infusion intra-utérine est l’une des approches curatives les plus utilisées et améliore les performances de reproduction subséquentes. Considérant les enjeux modernes en lien avec l’antibiorésistance et la réduction de l’utilisation d’antibiotiques en productions animales, il est justifiable de remettre en question l’utilisation d’une méthode diagnostique de l’endométrite basée uniquement sur la présence d’inflammation en vue de déterminer si un traitement antibiotique doit être utilisé. En ce sens, l’objectif principal de ce projet de recherche était de valider l’exactitude des résultats de milieux de culture bactériologique utilisés à la ferme (Tri-plate et Petrifilm) en se basant sur ceux obtenus en laboratoire diagnostique. Un objectif secondaire était de vérifier la concordance entre les résultats bactériens de laboratoire et ceux cytologiques. Pour ce faire, une étude observationnelle transversale a été réalisée au sein de deux troupeaux laitiers commerciaux faisant partie de la clientèle de la Clinique ambulatoire bovine de la Faculté de médecine vétérinaire de l’Université de Montréal. Un total de 189 vaches en période post-partum (30 à 43 jours de lactation) ont été enrôlées de façon systématique afin de recueillir 2 échantillons utérins à partir de cytobrosses lors d’un même examen. La première cytobrosse était utilisée pour inoculer directement le milieu de culture Tri-plate et ensuite être envoyée au laboratoire du Service diagnostic de la FMV de l’Université de Montréal pour culture bactérienne aérobique. La seconde cytobrosse était utilisée pour l’analyse cytologique (proportion de cellules polymorphonucléaires; PMNL), puis était diluée dans 1 ml de solution saline pour inoculer le milieu Petrifilm. Après une période d’incubation de 24h, le décompte de colonies était fait pour chaque milieu de culture. À partir de ces données, les analyses statistiques ont été complétées dans le but d’optimiser la sommation de sensibilité et spécificité (Se+Sp) des deux milieux de culture en fonction des résultats du laboratoire de référence. Pour le milieu Tri-plate, le seuil de ˃ 90 colonies a permis d’obtenir la Se+Sp maximale, soit 167,7. Pour le milieu Petrifilm, le seuil de ˃100 colonies a donné la Se+Sp maximale, soit 129. En ce qui concerne la concordance entre le diagnostic cytologique et bactériologique, les résultats de notre projet montrent que 64,3% des vaches positives au niveau cytologique (˃6% PMNL) se sont avérées négatives à la culture bactérienne, démontrant un manque de concordance. En conclusion, les résultats de notre étude supportent la faisabilité et le potentiel de la culture bactérienne d’échantillons de l’endomètre à la ferme. Notre projet met également en évidence que l’utilisation d’un dépistage cytologique de l’endométrite afin d’utiliser un traitement antibiotique puisse causer un manque d’optimisation dans l’efficacité des traitements. Il semble donc pertinent que d’autres projets soient complétés afin d’approfondir le dépistage bactériologique de l’endométrite et d’analyser le potentiel diagnostique de celui-ci. / Endometritis is a disease affecting reproductive performance in dairy cows. It is defined by the presence of excessive inflammation in the uterine body during the postpartum period. From a curative point of view, the use of antibiotic treatment in the form of intrauterine infusion is one of the most widely used methods which has a beneficial effect on subsequent reproductive performance in positive cases of endometritis. Considering the modern issues concerning the use of antibiotics in animal production, the use of a diagnostic method based on the presence of inflammation in order to administer antibiotic treatment is questionable. In that sense, the main objective of this research project was to validate the accuracy of the results of bacteriological culture medium used on the farm (Tri-plate and Petrifilm) based on the ones from diagnosis laboratory. A secondary objective was to verify the concordance between the bacterial and cytological results. To do this, a cross-sectional observational study was set up within two commercial dairy herds followed by the bovine outpatient clinic of the Faculty of Veterinary Medicine of the Université de Montréal. A total of 189 cows in the postpartum period (30 to 43 days in milk) were systematically enrolled in order to collect 2 uterine samples from cytobrush during the same examination. The first cytobrush was used to directly inoculate the Tri-plate medium and then be sent to the reference laboratory (Diagnostic service of the FVM of the Université de Montréal) for aerobic bacterial analysis. The second cytobrush was initially used to make a microscopic smear for cytological analysis (polymorphonuclear cell proportion (PMNL)) and subsequently diluted in 1 ml of saline to inoculate the Petrifilm medium. After an incubation period of 24 hours, the colony count was made for each culture medium. From these data, statistical analyses were completed in order to optimize the summation of sensitivity and specificity (Se + Sp) of the two culture medium according to the results of the reference laboratory. For the Tri-plate medium, the cutoff of ˃ 90 colonies resulted in the maximum Se + Sp, which was 167.7. For the Petrifilm medium, the threshold of ˃100 colonies gave the maximum Se + Sp, which was 129. Regarding the concordance between the cytological and bacterial diagnosis, the results of our project show that 64.3% of cows positive for cytological criteria (˃6% PMNL) were found to be negative from a bacterial point of view. In conclusion, this study shows that Tri-plate and Petrifilm medium used on-farms were best to reproduce the results obtained by laboratory analysis using 90 and 100 colony threshold respectively. Our results also support a lack of agreement between cytological and bacterial diagnosis. It therefore seems relevant that other projects are completed in order to deepen the bacterial screening for endometritis and to analyze its diagnostic potential.

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.