Foot and Mouth Disease (FMD) could have a significant impact on the U.S. agriculture industry and the welfare of U.S. producers and U.S. consumers. In order to address the potential impact from animal disease outbreaks, this project is designed to utilize a combined epidemic and economic modeling framework to evaluate animal disease management strategies which can be used to reduce the potential losses in an unusual event such as FMD outbreaks. In this study, we compare the welfare changes among three different parties with different strategies using, 1) ANOVA analysis; 2) cost benefit analysis; and 3) Risk Aversion Coefficient (RAC) analysis. Four types of index feedlots are selected in the study including, Feedlot Type 1 (> 50,000 heads of animals), Feedlot Type 4 (backgrounder feedlot), Large Beef Grazing (>100 heads of animals), and Backyard (<10 heads of animals). Results suggest that early detection of FMD events has the advantage in reducing risk as shown in the epidemiological impacts. Enhanced surveillance is found to be a preferred mitigation strategy for U.S. consumers in the scenario of smaller feedlot disease introductions (e.g. Large Beef Grazing and Backyard) and for U.S. producers in the larger feedlot disease introduction scenarios (e.g. Feedlot Type 1 and Feedlot Type 4). Adequate vaccination is not cost effective when seeking to minimize average loss but becomes a preferred strategy when the risk aversion rises. Risk modeling with stochastic programming adopted in this study also confirms the importance of incorporating risk evaluation into decision making process. It offers another option for us to evaluate the mitigation strategies. Two portfolio models are adopted in this study including, E-V model (mean variance portfolio choice model) and Unified model. The results show that the preference for control strategies depends on risk attitude. Early detection proves to be preferable for U.S. consumers and is also preferred by U.S. processors and producers as Risk Aversion Parameters (RAP) rises. Adequate vaccination strategy can benefit U.S. consumers but does not give U.S. processors a better outcome. Adequate vaccination provides a better choice for U.S. producers when the RAP rises. Enhanced surveillance is preferred for U.S. consumers. For U.S. processors, enhanced surveillance does not give a better risk/return outcome. U.S. producers are likely to switch their preferences from regular surveillance to enhanced surveillance as their RAP rises.

published_or_final_version / Zoology / Master / Master of Philosophy

Foot and mouth disease (FMD) is regarded as one of the greatest biological threats to the U.S. livestock industry because of its potential to cause catastrophic economic damages and massive livestock depopulation. Current U.S. contingency plans call for "stamping out" of FMD. An integral component of a "stamping out" policy is movement restrictions. The main purpose for movement restrictions is to stop the spread of disease, but they also disrupt the agribusiness sector. Welfare slaughter, the depopulation of healthy quarantined animals, is a possibility if movement restrictions are kept in place for prolonged periods of time. Many studies have analyzed the economic consequences of alternative mitigation strategies, but generally these studies have ignored the costs that might arise because of movement restrictions affecting uninfected premises located within the quarantine zone. Ultimately this study seeks to improve preparedness in the event of a FMD outbreak. It does this by developing information for those formulating plans on the costs associated with movement restrictions regarding quarantined, uninfected large feedlots located in the Texas High Plains Region. To accomplish this objective two strategies were compared: an unrestricted feed strategy, where feed is allowed to be brought onto uninfected premises and finished cattle are sold; and a welfare slaughter strategy, where feed isn't allowed to be brought onto the uninfected premises so animals are depopulated. In addition, seasonal differences in total costs were examined. This study expanded on the High Plains Study conducted by M. Ward, L. Highfield, P. Vongseng, and M. Garner by using their epidemiological data combined with a cost accounting framework to estimate the total cost of each strategy. This study examined direct disease management costs (indemnity payments, feed costs, marketing costs, surveillance costs, cleaning and disinfecting costs, appraisal cost, euthanasia costs, and disposal costs). Overall, the unrestricted feed strategy was less expensive than the welfare slaughter strategy, costing on average $22.6 million compared to $48.5 million, respectively. Disease outbreak timing did impact the overall cost of both strategies. The results suggest the policy makers should strongly consider creating movement policies that address feed supply and finished cattle movement for uninfected large feedlots in prolonged quarantine zones; as such policies appear to reduce outbreak related costs for stakeholder and the U.S. government.

No description available.

Thesis (MSc (Veterinary Tropical Diseases))--University of Pretoria, 2008. / Includes bibliographical references. Also available in print format.

Thesis (Ph. D.)--University of Hong Kong, 2005. / Title proper from title frame. Also available in printed format.

No description available.

No description available.

Structural biology forms the basis of all functions in an organism from how enzymes work to how a cell is assembled. In silico structural biology has been a rather isolated domain due to the perceived difficulty of working with the tools. This work focused on constructing a web-based Functional Genomics Information Management System (FunGIMS) that will provide biologists access to the most commonly used structural biology tools without the need to learn program or operating specific syntax. The system was designed using a Model-View-Controller architecture which is easy to maintain and expand. It is Python-based with various other technologies incorporated. The specific focus of this work was the Structural module which allows a user to work with protein structures. The database behind the system is based on a modified version of the Macromolecular Structure Database from the EBI. The Structural module provides functionality to explore protein structures at each level of complexity through an easy-to-use interface. The module also provides some analysis tools which allows the user to identify features on a protein sequence as well as to identify unknown protein sequences. Another vital functionality allows the users to build protein models. The user can choose between building models online on downloading a generated script. Similar script generation utilities are provided for mutation modeling and molecular dynamics. A search functionality was also provided which allows the user to search for a keyword in the database. The system was used on three examples in Foot-and-Mouth Disease Virus (FMDV). In the first case, several FMDV proteomes were reannotated and compared to elucidate any functional differences between them. The second case involved the modeling of two FMDV proteins involved in replication, 3C and 3D. Variation between the several different strains were mapped to the structures to understand how variation affects enzymes structure. The last example involved capsid protein stability differences between two subtypes. Models were built and molecular dynamics simulations were run to determine at which protein structure level stability was influenced by the differences between the subtypes. This work provides an important introductory tool for biologists to structural biology. / Thesis (PhD)--University of Pretoria, 2009. / Biochemistry / unrestricted

Foot-and-mouth disease (FMD) virus causes a highly contagious, economically important disease of cloven-hoofed animals, including livestock animals such as cattle and swine. In South Africa, the disease is controlled primarily through prophylactic vaccination and strict animal movement control. To control effectively the spread of FMD, it has become increasingly more important to develop diagnostic tests that can differentiate FMDV-infected animals from those that have been vaccinated. Currently, the detection of antibodies to nonstructural proteins, especially the 3ABC nonstructural polypeptide, is considered to be the most reliable method to distinguish virus-infected from vaccinated animals. Towards the development of such a serological test, the primary aim of this investigation was to express the 3ABC nonstructural polypeptide of the SAT2 type FMD virus ZIM/7/83 in both a prokaryotic and eukaryotic expression system in order for the recombinant protein to be used as a diagnostic antigen. The nucleotide sequence of the 3ABC-encoding region of SAT2/ZIM/7/83 was determined, the amino acid sequence deduced and subsequently compared to corresponding sequences of other virus isolates representing all seven FMDV serotypes. Phylogenetic analysis revealed that the 3ABC polypeptide of the SAT serotypes, which are mostly restricted to sub-Saharan Africa, clustered separately from the euroasiatic FMDV serotypes (types A, O, C and Asia1). Amino acid sequence alignments also indicated considerable variation in the 3A, 3B and 3C proteins between the SAT and euroasiatic types located mainly in previously identified epitope-containing regions. These results suggest that the sensitivity and specificity of diagnostic tests based on the 3ABC nonstructural polypeptide of the European FMDV types may be compromised when applied to the African sub-continent. Therefore, a SAT-specific diagnostic assay is required to distinguish virus-infected from vaccinated animals. The 3ABC-encoding region of SAT2/ZIM/7/83 was subsequently expressed in Escherichia coli as a glutathione S-transferase (GST) fusion protein using the bacterial expression vector pGEX-2T, and in Spodoptera frugiperda insect cells using the BAC-to-BACTM baculovirus expression system. Although high-level expression of the recombinant GST-3ABC protein was obtained, the GST-3ABC protein was insoluble and could not be purified by glutathione affinity chromatography. Therefore, the recombinant GST-3ABC fusion protein was purified from reverse-stained SDS-polyacrylamide gels and shown to be immunoreactive in Western blot analysis using an FMDV-specific serum. Expression of the 3ABC polypeptide in insect cells infected with a recombinant bacmid yielded soluble recombinant protein, but the level of expression was lower compared to that obtained in E. coli. In addition, Western blot analysis of cell extracts prepared from recombinant bacmid-infected cells revealed the presence of three immunoreactive proteins of 47, 25 and 18 kDa. These correspond with the size of the FMDV proteins 3ABC, 3AB and 3A, respectively, suggesting that the 3C protease was responsible for proteolytic cleavage of the 3ABC polypeptide. Based on the results obtained, the bacmid expression system appears to be more suitable for the production of the 3ABC polypeptide. / Dissertation (MSc)--University of Pretoria, 2008. / Microbiology and Plant Pathology / unrestricted