Date of Award


Document Type


Degree Name

Doctor of Philosophy (PhD)


Animal Nutrition and Food Science

First Advisor

David E. Kerr


Mastitis represents a major issue within the dairy industry responsible for economic loss via decreased animal productivity and associated veterinary costs. Currently, there is a push to identify a phenotypic innate immune response that will yield dairy cows with an enhanced resistance to mastitis. Bovine dermal fibroblasts were used as a cell model to measure the response of individuals to Gram-negative bacterial stimuli through the TLR4 signaling pathway. Fibroblast cultures were isolated from 15 dairy heifers at 5, 11, and 16 months of age in order to determine the variability in responsiveness to LPS as well as to monitor the development of the innate immune response in calves. These individuals displayed a large range in response to LPS as measured by IL-8 production. In addition, response within individuals increased dramatically with age.

To determine the cause behind this, DNA methylation was investigated as a potential player in the variation in response described both within an individual over time as well as across individuals. Fibroblast exposure to 5-aza-2'-deoxycytidine, a DNA demethylating agent, increased the cellular response to LPS, but more so in cultures that had previously displayed low responding phenotypes. This suggested that DNA methylation acted as an inhibitor of the innate immune response, and may be responsible for some degree of the variation seen in the LPS response. To determine the effect of epigenetic factors on this response, microarray analysis was conducted on RNA isolated from cells either having been epigenetically modified (DNA demethylation and histone hyperacetylation) or without undergoing any epigenetic treatment. This analysis identified 1,758 genes with altered expression due to epigenetic modification.

To focus on DNA methylation's role, methylated CpG island recovery assay (MIRA-Seq) libraries were created from fibroblasts to investigate differential methylation from a group of the same individuals sampled at 5 and 16 months of age. In addition, transcriptomic data were generated by RNA-Seq from fibroblasts collected from the young and older samples and exposed to LPS for 0, 2, and 8 hours to characterize age-associated changes in the innate immune response. Cultures from older animals were much more responsive to LPS as indicated by greater expression of IL-8, IL-6, TNF-α, and CCL20 at various times in response to LPS. TLR4 and CD14 were more highly expressed in older cultures, suggesting these fibroblasts are more able to detect the presence of LPS. Analysis of the bovine fibroblast methylome revealed methylation with remarkable stability except for 20 regions along the genome undergoing major shifts due to age. Similar data were collected from fibroblasts isolated from different individuals displaying either a low or high responding phenotype resulting in 843 regions with differential methylation between groups. This suggests that DNA methylation may be playing a role in both the age-dependent and between animal differential responses to LPS, and also gives the first in depth look at the bovine fibroblast methylome and its stability over time.



Number of Pages

194 p.