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Skeletal muscles are involved in numerous processes including postural maintenance, locomotion, ventilation of lungs and protection of the bones and viscera. Muscle also plays important roles in chronic diseases including sarcopenia, cachexia, insulin resistance and diabetes. The major component of muscle is the constituent muscle fibres. Muscle fibre cross-sectional area (CSA), fibre number, and proportion of fibre types are important determinants of muscle function, overall metabolism and the quality and quantity of meat in livestock. Genetic variation plays a substantial role in the variation observed in fibre traits. The underlying pathways and genes remain poorly understood; therefore a greater understanding can potentially lead to treatments of disease. The aim of this thesis was to gain a deeper understanding of the genetic mechanisms which underlie variation in the number, CSA and type of muscle fibres. Linkage analysis of soleus fibre properties was performed in an F2 intercross, and refined in the F34 intercross of two strains selected for high and low bodyweight, LG/J and SM/J respectively. Quantitative trait loci (QTL) were then integrated with LG/J and SM/J muscle transcriptome data to identify candidate genes. Genome-wide association analysis identified 6 QTL affecting properties of muscle fibres. Transcriptome analysis indicated a number of differentially expressed candidate genes within the QTL; Ppp1r16b, Gm826, Chd6, Alad, Akap2, E130308A19Rik, Gm9174 and Hdhd3. Functional testing of a mouse Chd6 knockout 5 model confirmed no involvement in fibre properties and has therefore been discounted from the candidate genes. The genetic mechanisms accounting for the differing fibre properties in the LG/J and SM/J strains have been elucidated in greater detail. Integration of QTL mapping and transcriptome data led to a manageable number of candidate genes which could underlie the effects of the QTL via differential expression or coding sequence differences. Available knockout models will facilitate validation of the candidate genes.

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A dissertation submitted to the Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, in fulfillment of the requirements for the degree in Master of Science (Medicine) in the Division of Human Genetics / Epigenetic mechanisms regulate gene expression, a particularly important activity during foetal development. DNA methylation contained within promoter and regulatory intergenic regions influence gene activity. In utero alcohol exposure as a result of maternal consumption during pregnancy has been associated with disruption of foetal DNA methylation and gene expression, leading to neurological dysfunction, growth retardation and facial anomalies. While similar phenotypes in offspring have been associated with chronic preconception paternal alcohol exposure, the mechanisms underlying these effects remain largely unexplored. This study aimed to: (1) validate significant changes in sperm DNA methylation in a list of ten candidate genes in male mice chronically exposed for ten weeks to ethanol (n=10) compared to a calorie-equivalent sucrose solution (n=10); (2) validate significant changes in gene expression in candidate genes in the brain, liver and placenta of E16.5 embryos sired by ethanol (n=24) compared to sucrose (n=24) treated male mice; (3) quantify DNA methylation changes in candidate genes in the three embryonic tissues. (4) Lastly, previously generated microarray data were reanalysed using bioinformatics tools to generate a top ranked candidate differentially expressed gene list that was used to identify and analyse biological functions or pathways significantly over represented among these genes using PANTHER and DAVID. This study was unable to provide validation for most of the significant differences observed in the sperm DNA methylome in the original study, most likely because of the low sperm DNA concentration. Significant methylation differences were however observed at individual CpG sites in three candidate genes (Igf1r, Odc1, Depdc1b) in specific tissues of embryos sired by ethanol-exposed males relative to embryos sired by sucrose-treated males. There was concordance in the direction of altered gene expression between the cases and controls using the microarray and real-time PCR approaches for two genes in the brain (Grm7 and Zfp317), three genes in the liver (Igf1r, Vwf and Depdc1b) and one gene in the placenta vii (Vwf). However, none of the candidate genes selected for validation showed statistically significant changes. This may be a result of the modest fold changes observed in the microarray experiment that as shown in many cases, often do not replicate. The remainder of the genes showed no changes in expression in the test embryos relative to the control. The functional enrichment analysis revealed biological processes that were over represented in the brain and liver indicating that they may be more vulnerable to the effects of alcohol, compared to the placenta. Overall, the study could not provide a statistically significant correlation between methylation changes in the sperm that were inherited by the offspring which subsequently dysregulated gene expression in the embryo. However, as trends toward significance and significant DNA methylation changes were observed in the embryonic tissues, this study supports the idea that preconception paternal alcohol exposure can induce epigenetic alterations in a locus and organ specific manner within offspring. / MT2016

Thesis (M.A.)--Boston University / PLEASE NOTE: Boston University Libraries did not receive an Authorization To Manage form for this thesis or dissertation. It is therefore not openly accessible, though it may be available by request. If you are the author or principal advisor of this work and would like to request open access for it, please contact us at open-help@bu.edu. Thank you. / The gene Myh9 encodes non-muscle myosin heavy chain I lA, an essential podocyte cytoskeleton structural protein. Abnormalities in the MYH9 gene are associated with chronic kidney disease (common in people of African ancestry) and rare hereditary autosomal dominant syndromes. In the current study, preexisting heterozygous Myh9 knockout mice aged 9 and 17 months were investigated to assess the biological role of the gene Myh9 product, non-muscle myosin IIA, in kidney structure and function. The objective was to determine the effects of potentially decreased expression of Myh9 genetic alteration and the role of Myh9 in the pathogenesis of chronic kidney disease (especially focal segmental glomerulosclerosis), and to develop a model to further study Myh9- related kidney disorders. Our results demonstrated that deletion of one allele of Myh9 in 129/Sv mice had no effect on the kidney structure compared with wildtype mice despite a significant decrease in expression of Myh9 in the heterozygous mice. / 2031-01-01

The Endoplasmic Reticulum (ER) is a net-like intracellular organelle where protein is folded, matures, and is transported. When cellular stressful circumstances affect the ER, unfolded proteins are stacked in the ER lumen. This cellular stress is called ER stress. To defeat ER stress, cells have a defensive mechanism called the Unfolded Protein Response (UPR). Many chronic diseases such as obesity and type 2 diabetes or neurodegenerative disease such as Alzheimer’s disease have recently been linked to ER stress. Exercise has a significant effect on ameliorating the development of these chronic diseases or neurodegenerative diseases. However, no studies have assessed the effect of exercise on UPR activity in the brain. So this study was mainly focused on identifying how voluntary running wheel exercise affects the UPR in the brain of C57BL/6 mice exposed to a variety of dietary conditions of differing levels of dietary fat and different periods of feeding. As an exercise protocol, access to a voluntary running wheel for 3 weeks was used and running mice were grouped depending on their level of running activity. Using real-time PCR and western blotting, UPR-related gene/protein expression (XBP1, ATF6, eIF2α, and GRP78) was assessed in different brain regions. Exercise had a significant effect on up-regulating UPR activity in the brain of mice fed low fat diet (LFD) or high fat diet (HFD) for 3 weeks or 3 months. These effects were time and brain region dependent. However, the effect of exercise on up-regulating UPR disappeared in mice fed very high fat diet (VHFD) for 4 months. In addition to assessing UPR activity, the possibility that exercise-induced UPR activation was associated with activation of apoptosis was investigated. Apoptotic signaling was not affected by exercise. Trophic factors are activated by exercise and are known to be linked to UPR activity. The possibility that IGF-1, one such trophic factor, was responsible for exercise-induced UPR up-regulation without activating apoptosis was studied. The results showed that IGF-1 was not responsible for exercise-related activation of the UPR in the brain. The chemical chaperone 4-phenylbutyric acid (PBA) was given to mice to reduce ER stress and the effect of exercise on the UPR of the brain was studied. PBA had a tendency to lower ER stress in the hypothalamus. In this condition, exercise had a significant effect to decrease UPR activity. In conclusion, voluntary exercise activates the UPR in several brain regions of mice exposed to high-fat diet for up-to 3 months without activating apoptotic signaling. Only long-term exposure to dietary fat increased the brain UPR. It is possible that this exercise-induced UPR activation without apoptosis may contribute to the protective effect of exercise on brain health. (134 pages)