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Bioinformatics resources should provide simple and flexible support for genomics research. A huge amount of gene mapping data, micro-array expression data, expressed sequence tags (EST), BAC sequence data and genome sequence data are already, or will soon be available for a number of livestock species. These species will have different requirements compared to typical biomedical model organisms and will need an informatics framework to deal with the data. In term of exploring complex-intertwined genomic data, the way to organize them will be addressed in this study. Therefore, we investigated two issues in this study: one is an independent informatics framework including both back end and front end; another is how an informatics framework simplifies the user interface to explore data. We have developed a fundamental informatics framework that makes it easy to organize and manipulate the complex relations between genomic data, and allow for query results to be presented via a user friendly web interface. A genome object-oriented framework (GOOF) was proposed with object-oriented Java technology and is independent of any database system. This framework seamlessly links the database system and web presentation components. The data models of GOOF collect the data relationships in order to provide users with access to relations across different types of data, meaning that users avoid constructing queries within the interface layer. Moreover, the module-based interface provided by GOOF could allow different users to access data in different interfaces and ways. In another words, GOOF not only gives a whole solution to informatics infrastructure, but also simplifies the organization of data modeling and presentation. In order to be a fast development solution, GOOF provides an automatic code engine by using meta-programming facilities in Java, which could allow users to generate a large amount of routine program codes. Moreover, the pre-built data layer in GOOF connecting with Chado simplifies the process to manage genomic data in the Chado schema. In summary, we studied the way to model genomic data into an informatics framework, a one-stop approach, to organize the data and addressed how GOOF constructs a bioinformatics infrastructure for users to access genomic data.

Bioinformatics resources should provide simple and flexible support for genomics research. A huge amount of gene mapping data, micro-array expression data, expressed sequence tags (EST), BAC sequence data and genome sequence data are already, or will soon be available for a number of livestock species. These species will have different requirements compared to typical biomedical model organisms and will need an informatics framework to deal with the data. In term of exploring complex-intertwined genomic data, the way to organize them will be addressed in this study. Therefore, we investigated two issues in this study: one is an independent informatics framework including both back end and front end; another is how an informatics framework simplifies the user interface to explore data. We have developed a fundamental informatics framework that makes it easy to organize and manipulate the complex relations between genomic data, and allow for query results to be presented via a user friendly web interface. A genome object-oriented framework (GOOF) was proposed with object-oriented Java technology and is independent of any database system. This framework seamlessly links the database system and web presentation components. The data models of GOOF collect the data relationships in order to provide users with access to relations across different types of data, meaning that users avoid constructing queries within the interface layer. Moreover, the module-based interface provided by GOOF could allow different users to access data in different interfaces and ways. In another words, GOOF not only gives a whole solution to informatics infrastructure, but also simplifies the organization of data modeling and presentation. In order to be a fast development solution, GOOF provides an automatic code engine by using meta-programming facilities in Java, which could allow users to generate a large amount of routine program codes. Moreover, the pre-built data layer in GOOF connecting with Chado simplifies the process to manage genomic data in the Chado schema. In summary, we studied the way to model genomic data into an informatics framework, a one-stop approach, to organize the data and addressed how GOOF constructs a bioinformatics infrastructure for users to access genomic data.

The effect of exogenous somatotropin (eST) on bone changes were evaluated in twenty-nine juvenile horses in race training using radiographs of the third metacarpal obtained over the course of a 128 day research project. A biodensitometer was used to measure bone density, and a micrometer was used to measure cortical bone width and medullary cavity width. Fifteen horses were given daily intramuscular injections of eST and fourteen horses were given daily intramuscular injections of sterile saline and served as the control group. By day 128, the increase in total radiographic bone aluminum equivalence (RBAE) was significantly greater in the eST horses than in the control horses. The increases in RBAE in the dorsal and the medial cortices were greater in the eST horses than in the control horses, but these differences were not significant. There was a trend for changes in the ratio of RBAE in the dorsal to palmar and in the medial to lateral cortices to be greater in the eST than in the control horses. By day 128, the increases in both the dorsal and the medial cortical bone width were significantly greater in the eST than in the control group of horses. The eST horses had a significantly greater decrease in dorsal to palmar medullary cavity width, and increase in dorsal to palmar bone diameter than the control group. A computed index of dorsal cortical bone increased significantly more in the eST than in the control group. The stresses applied to bone are greater in the dorso-medial direction in racehorses. To decrease the strain, bone must either increase in bone mineral density, cortical width, and/or bone diameter. Both the eST group and the control group did make these changes in bone over time, but the eST group more effectively remodeled and modeled bone to increase the strength of the third metacarpal than did the control group of horses. In this research project, exogenous somatotropin treatment had a positive effect on the density and geometry of the third metacarpal. These changes are believed to result in a decreased risk of bone injury to the eST treated horses.

The purpose of this study was to develop a model of post-traumatic osteoarthritis in the palmar metacarpal condyle and to evaluate the timing of the early events following impact trauma on subchondral bone and articular cartilage. In each of 12 skeletally mature horses, an impact injury was created on the palmar metacarpal condyle of one randomly chosen limb, under arthroscopic and fluoroscopic guidance. A low to moderate level of forced exercise was instituted; and horses were evaluated clinically via lameness examinations, synovial fluid analysis, and radiographs. Macroscopic examination, micro-computed tomography, and sample collection were performed following euthanasia at one month (3 horses), 4 months (4 horses), and 8-10 months (5 horses) after impact injury. There was variability in impact-lesion location, depth, and area on macroscopic inspection; histologic evaluation revealed more consistent cartilage defects due to impact injury. Cartilage degeneration, in terms of color and clarity, was observed in impacted joints. The mean sulfated glycosaminoglycan (sGAG) concentration from cartilage at the impact site was significantly lower than for a similar site in control limbs. Higher concentrations of cartilage oligomeric matrix protein (COMP) were observed in synovial fluid from impacted joints. Bone viability, as evaluated by the Alamar blue assay, was significantly decreased in impact specimens versus control specimens one month after impact injury. This impact injury model caused lesions consistent with mild focal osteoarthritis in the palmar metacarpophalangeal joint, involving cartilage more than subchondral bone. Further development is required to create a reliable and consistent model of naturally occurring post-traumatic osteoarthritis at this site. / Equine Guelph, University of Guelph