miRNAs are short, non-coding RNA molecules that regulate gene expression posttranscriptionally through inhibition of translation and/or mRNA degradation. Mammalian development is a complex series of developmental transitions, which relies on accurate spatial and temporal regulation of gene expression and we are interested in the role that miRNAs may play in these developmental transitions. An initial objective was to establish which, if any, miRNAs were dynamically regulated in a cell model of an early developmental transition, and to establish whether differential expression of any particular miRNA played a functional role in this developmental process. Having established a role for specific miRNAs, further objectives were to assess the reliability of current miRNA-mRNA target identification procedures and to assess the general role of miRNAs in cellular differentiation. In order to explore the roles of miRNAs during an early developmental transition, an embryonic stem (ES) cell model of trophectoderm differentiation was used. In this model system the expression of the key ES cell regulatory gene, Oct4, can be conditionally repressed, which induces the ES cells to differentiate down the trophectoderm lineage. The expression of microRNAs was profiled in this model system by cloning and sequencing of small RNAs. This approach identified miRNAs that were dynamically regulated during differentiation. The expression patterns of differentially regulated miRNAs were confirmed by miRNA northern analysis. The miRNA profiling data showed that mmu-miR-294 and mmu-mir-295 are expressed at similar levels in ES cells and differentiated cells, which disagrees with previous reports that these miRNAs are ES cell specific. Several of the miRNAs with higher expression levels in differentiated cells are encoded within a placental-enriched polycomb group gene, Sfmbt2, suggesting an important role for these miRNAs in extraembryonic development. One of the miRNAs that was expressed at higher levels in ES cells than in differentiated cells, mmu-miR-92a, was shown to play a role in regulation of cell proliferation. Three current methods of identifying miRNA targets were assessed. A sequencebased method using the web-based utility miRecords, which amalgamates results from numerous target prediction databases, was used to generate lists of potential targets of the Sfmbt2 miRNA cluster and of mmu-miR-92a. Amalgamating results from multiple target prediction programs may improve the likelihood that the predicted targets are real. Exemplifying this, the single mmu-miR-92a target that was predicted by six different target prediction programs had been previously experimentally verified. An experimental method of identifying direct miRNA targets, PAR-CLIP, was investigated but proved technically limiting for routine use in the laboratory. A proteome-based experimental method for identifying potential miRNA targets, called SILAC, was successfully used to identify proteins that were differentially expressed in the cell model of trophectoderm differentiation. Differential expression of two of these proteins, CTBP2 and CKB, was confirmed by western analysis. miRecords was then used to assess whether the differentially expressed proteins were likely to be targets of the differentially expressed miRNAs that had been identified in the miRNA profiling analysis. The general role of miRNAs in cell differentiation was investigated using a cell line that does not express miRNAs. This ES cell line is deficient for the miRNAprocessing enzyme DGCR8, which results in loss of expression of mature miRNAs in these cells. Compared to wild type ES cells, miRNA-deficient ES cells expressed normal levels of the ES cell marker genes Oct4 and Sox2 but elevated levels of Nanog. In contrast to wild type ES cells, miRNA-deficient ES cells did not upregulate the mesoderm marker gene Brachyury during embryoid body differentiation and showed reduced upregulation of the endoderm marker gene Gata6. These findings suggest that miRNAs are not required for maintenance of pluripotency, but are essential for proper ES cell differentiation. The results presented in this thesis show that miRNAs are dynamically expressed during a mammalian developmental transition and are involved in regulating early developmental processes. We believe that miRNAs act as an additional level of genetic regulation to ensure canalisation during embryonic development.

Instructive signals, whether external or internal, play critical roles in regulating the developmental potency or ability to self-renew of stem cells. External signals may range from secreted growth factors to extracellular matrix proteins found in the stem cell niche. Internal signals include activated signalling cascades and the eventual transcriptional mechanisms they initiate. In either fashion, stem cells are regulated in a complex temporal and context specific manner in order to maintain or maximise their unique characteristics. Previous experiments suggest that Wnt3a plays a role in maintaining the pluripotent state of mouse embryonic stem (mES) cells. However, in the absence of leukemia inhibitory factor (LIF), Wnt signalling is unable to maintain ES cells in the undifferentiated state. This implies that maintaining the pluripotent state of mES cells is not the primary function of canonical Wnt signalling. To further characterize the role of Wnt3a in pluripotency and lineage specification undifferentiated and differentiated mES cells were induced with Wnt3a. Wnt3a induced the formation of a metastable primitive endoderm state and upon subsequent differentiation, the induction of large quantities of visceral endoderm. Furthermore, we determined that the ability of Wnt3a to induce a metastable primitive endoderm state was mediated by the T-box transcription factor Tbx3. Our data demonstrates a novel role for Wnt3a in promoting the interconversion of undifferentiated mES cells into a pluripotent primitive endoderm state. Aging of skeletal muscle tissue is accompanied by fibrosis, atrophy and remodeling all of which negatively affect muscle performance. Whether this reduction in skeletal muscle competency is directly attributed to a resident adult stem cell population called satellite cells remains largely unknown. Here, we undertook an investigation into how age affects the transcriptional profile of satellite cells and their repopulating ability following transplantation. We determined that as satellite cells age, both their regenerative capacity and ability to colonize the satellite cell niche is reduced. Additionally, we identified satellite cell specific transcriptional profiles that differed with respect to age. Therefore, we conclude that intrinsic factors are an important determinant of satellite cell regenerative capacity during the aging process.

Embryonic stem cells (ESCs) possess hypo-immunogenic properties and have the capacity to modulate allogeneic immune response. ESCs have been shown to reduce immune activation in response to third party antigen presenting cells (APCs) in vitro and have the capacity to promote allograft survival in vivo. Clinical use of live ESCs to treat immunological disorders, however, risks teratoma or ectopic tissue formation. Accordingly, the way lab is studying the immune modulatory potentials of ESC-derived factors and recently, found that dendritic cells (DCs) treated with human ESC extracts are poor stimulators of purified allogeneic T cells compared to those DCs treated with vehicle or fibroblast extracts. In the present study, I found that ESC-derived extracts directly inhibit T cell proliferation and suppress their activation without inducing cell death. Furthermore, ESC extracts are able to suppress Th1 polarization while increasing the numbers of Foxp3+ CD4+ CD25+ regulatory T cells. Moreover, I found that a protein called Milk fat globule-EGF factor 8 (MFG-E8) appears to be highly expressed in ESCs. Importantly, neutralizing MFG-E8 substantially abrogated the immune suppressive effects of ESC extracts on T cell activation. These findings lead to future studies to further define specific immunomodulatory factors derived from ESCs for potential applications.

SirT1 is a class III histone deacetylase that has beneficial roles in various diseases related to aging such as cancer, diabetes and neurodegenerative disease. Resveratrol is a natural compound that mimics most of the beneficial effects attributed to SirT1. Resveratrol has toxicity towards cancer cells and has been reported to be a direct activator of SirT1. Interestingly, SirT1 over-expression has also been reported to be toxic. We set out to determine if resveratrol toxicity is mediated through activation of SirT1. We have assessed resveratrol toxicity in embryonic stem cells and mouse embryonic fibroblast (MEFs) across different SirT1 genotypes. Our data indicates that SirT1 is not implicated in resveratrol toxicity in either normal or transformed MEFs. Thus, resveratrol toxicity does not appear to be mediated by SirT1.

The in-vitro culture of human embryonic stem and keratinocyte cells has great potential to revolutionise the therapeutics industry. Indeed it is hoped that these cells will provide a superior alternative to current tissue and organ transplantation. However, both of these cell types require animal and/or donor products for their successful maintenance in-vitro. This requirement results in a significant risk of cross contamination from the animal or donor products to either the primary keratinocyte or hES cells. These potentially transplantable cells therefore need to be cultured in an environment free from animal or donor products to remove the risk of contamination to the patient. The ideal growth conditions must comprise of two attributes; firstly they must be free from animal or donor products, and secondly the culture system must be fully defined. Recently, it was discovered that an extra-cellular matrix protein, vitronectin, could be used in conjunction with growth factors and growth factor-binding proteins (VN:GF combination), to promote enhanced cell migration and growth through the co-activation of integrin and growth factor receptors. Given that growth factors and serum are clearly important in supporting the in-vitro cultivation of mammalian cells, and that vitronectin is an abundant protein in serum, I hypothesised that these VN:GF combinations could be translated into a serum-free medium that would support the serial propagation and self renewal of primary keratinocytes and hES cells. As reported in this thesis I have developed a defined, serum-free media for the culture of these cells that incorporates the VN:GF combinations. While the two media differ slightly in their compositions, both support the serial, undifferentiated expansion of their respective cells types. Together, this represents a significant advance that will ultimately facilitate the therapeutic use of these cells. However, the in-vitro expansion of these cells in these new media still required the presence of a feeder cell layer. In view of this I aimed to explore the in-vitro micro-environment of primary keratinocytes using a novel proteomic approach in an attempt to find candidate factors that could be used in conjunction with the VN:GF media to replace both serum and the feeder cells. The proteomic approach adopted examined the secretion of proteins into the defined, minimal protein content VN:GF media when the feeder cells were cultured alone, as well as in co-culture with primary keratinocytes. This strategy allowed assessment of proteins/factors that are secreted in response to both autocrine and paracrine cellular interactions and revealed a number of candidate factors that warrant further investigation. Ultimately this proteomic information and the associated new insights into the keratinocyte in-vitro culture microenvironment may lead to the development of a culture system for these cells that is not reliant on either a feeder cell layer or serum for their successful propagation. Moreover, it is likely that this will also be relevant to the feeder cell-free propagation of hES cells. This has obvious advantages for the culture of primary keratinocytes and hES cells in that it will allow a safe defined culture system for the undifferentiated propagation of these cells. This will facilitate the generation of cells and tissues free from xenogeneic and allogeneic contaminants, thus ensuring any therapeutics developed from these cell types are approved for therapeutic applications and importantly, will minimise risks to patients.

Bibliography: leaves 113-126. / v, 126, [113] leaves, [10] leaves of plates : ill. ; 30 cm. / Title page, contents and abstract only. The complete thesis in print form is available from the University Library. / Studies the biological significance of the mouse Listone variant H2A.Z. Describes the isolation and characterisation of H2A.Z genomic clones from different mouse genomic libraries; H2A.Z gene targeting in mouse E14 embryonic stem cells; and an attempt to generatae ES cell lines and mice which lack the functional H2A.Z protein to investigate H2A.Z function in vitro and in vivo. / Thesis (Ph.D.)--University of Adelaide, Dept. of Biochemistry, 1995?

Thesis (Ph. D.)--Northeastern University, 2008. / Title from title page (viewed March 3, 2009). Graduate School of Arts and Sciences, Dept. of Biology. Includes bibliographical references (p. 172-190).

Thesis (LLM)-University of Pretoria, 2006. / Summary in English and Afrikaans. Includes bibliographical references. Mode of access: World Wide Web.

Thesis (M.A.)--Indiana University, 2008. / Includes vita. Department of Philosophy, Indiana University-Purdue University Indianapolis (IUPUI). Includes bibliographical references (leaves 48-51).

Thesis (M. S.)--Biomedical Engineering, Georgia Institute of Technology, 2008. / Committee Chair: Wang, Yadong; Committee Member: Philip Santangelo; Committee Member: Ravi Bellamkonda