Breast cancer is a highly heterogeneous disease with multiple drivers and a complex regulatory network. Periostin (Postn) is a matricellular protein involved in a plethora of cancer types and other diseases. More specifically, Postn has been shown to be involved in various processes of tumor progression such as angiogenesis, cell survival, invasion, and metastasis. A high Postn level in breast cancer has been corelated with a more aggressive phenotype. Despite extensive research, it remains unclear what Postn is doing to the cancer environment and how cancer cells regulate Postn. Here, we assessed the role and regulation mechanisms of Postn in ErbB2-mediated tumorigenesis. By crossing Postn deficient animals into the oncogenic NeuNDL model of ErbB2-positive breast cancer, we have shown that Postn deletion delays tumor onset and increases overall survival by affecting proliferation and apoptosis. These tumors also showed a decrease in collagen deposition which is the proposed mechanism for its effect in vivo. Using isolated cancer cells from the Postn deficient background we assessed re-expression of Postn which had no effect on in vitro tumorigenesis processes or in vivo subcutaneous growth in immunodeficient mice. Furthermore, we established an in vitro model to study the regulation of Postn using a bovine pituitary gland derived extract as a natural repressor of Postn. Using mass spectrometry and RNA sequencing, we identified potential regulators of Postn gene expression. We also showed a cross regulation between FGFR, TGFβ and PI3K/AKT pathways to regulate Postn expression. In ErbB2-mediated murine breast cancer cells, we found that TGFβ can induce Postn expression in a SMAD-independent manner while bFGF can repress Postn expression through a PKC-dependent pathway. Postn induction and repression by TGFβ and bFGF respectively, are both dependent on PI3K/AKT signaling. Overall, these results suggest a cancer-driving function for Postn and reveal a novel mechanism for regulating Postn expression.

We study the evolution of simple cells that are equipped with a genome, a rudimentary gene regulation network at transcription level and two classes of functional genes: motion effectors allow the cell to move in response to nutrient gradients while nutrient importers are required to actually feed from the environment. The model is inspired by the protist Naegleria gruberi which can switch between a feeding and dividing amoeboid state and a mobile agellate state depending on environmental conditions. Simulation results demonstrate how selection in a variable environment affects the gene number and effciency so that the cells can rapidly switch from one expression regime to the other depending on the external conditions.

Rhodococcus, a species of bacteria commonly found in the soil, is a under-explored producer of small bioactive compounds including siderophores, pigments and antibiotics.. MTM3W5.2 is a strain of Rhodococcus that was previously discovered to produce an antibiotic-like compound that has inhibitory effects on other Rhodococcus strains, including the veterinary pathogen, R. equi. The biosynthetic gene cluster responsible for production of the antibiotic has been identified, and a small gene, BTZ20_3964 at the start of the operon is believed to be the regulator of the gene cluster. To test this, a deletion construct was created using an overlap-extension PCR method to remove most of gene 3964. The deletion construct was cloned into the plasmid pEX18Km, along with a kanamycin resistance marker. The deletion construct, pEX18Km3964AD was transformed into competent MTM3W5.2 cells for a double crossover recombination event to replace the functional gene with the deletion construct, using the KanR gene to select for the merodiploids, and the SacB gene to select for the deletion mutants after the second recombination event. The deletion mutant’s ability to produce the inhibitory compound will be determined. Production of the compound will be restored by complementing the deletion mutant with the functional gene cloned into the expression plasmid pDD57.

Coral reefs form marine-biodiversity hotspots of enormous ecological, economic, and aesthetic importance that rely energetically on a functional symbiosis between the coral animal and a photosynthetic alga. The ongoing decline of corals worldwide due to anthropogenic influences heightens the need for an experimentally tractable model system to elucidate the molecular and cellular biology underlying the symbiosis and its susceptibility or resilience to stress. The small sea anemone Aiptasia is such a model organism and the main aims of this dissertation were 1) to assemble and analyze its genome as a foundational resource for research in this area and 2) to investigate the role of miRNAs in modulating gene expression during the onset and maintenance of symbiosis. The genome analysis has revealed numerous features of interest in relation to the symbiotic lifestyle, including the evolution of transposable elements and taxonomically restricted genes, linkage of host and symbiont metabolism pathways, a novel family of putative pattern-recognition receptors that might function in host-microbe interactions and evidence for horizontal gene transfer within the animal-alga pair as well as with the associated prokaryotic microbiome. The new genomic resource was used to annotate the Aiptasia miRNA repertoire to illuminate the role of post-transcriptional regulatory mechanisms in regulating endosymbiosis. Aiptasia encodes a majority of species-specific miRNAs and first evidence is presented that even evolutionary conserved miRNAs are undergoing recent differentiations within the Aiptasia genome. The analysis of miRNA expression between different states of Symbiodinium infection further revealed that species-specific and conserved miRNAs are symbiotically regulated. In order to detect functional miRNA-mRNA interactions and to investigate the downstream effects of such miRNA action, a protocol for cross-linking immunoprecipitations of Argonaute, the central protein of the miRNA-induced silencing complex, was developed. This method identified binding sites of miRNAs on a transcriptome-wide scale and revealed target genes of symbiotically regulated miRNAs that were identified previously to be involved in the symbiosis. In summary, this dissertation provides novel insights into miRNA-mediated post-transcriptional modulation of the host transcriptome and by presenting a critically needed genomic resource, lays the foundation for the continued development of Aiptasia as a model for coral symbiosis.

Regulation of gene expression is required for embryogenesis and maintenance of the highly specialized and diverse neuron populations of the retina. Chromatin remodelling proteins control gene expression by modifying chromatin structure and are essential for many biological processes including mammalian development. The ATP-dependent chromatin remodelling protein Snf2h is highly expressed in the central nervous system, and pathogenic variants that cause neurodevelopmental abnormalities in the human population have recently been identified. This work aims to characterize the effects of Snf2h loss in the retina. Snf2h retinal conditional knockout (cKO) mice were generated using Snf2h-floxed mice and Chx10-Cre retina-specific Cre driver lines to ablate the Snf2h protein from the retina at embryonic day 10.5. Visual function was assessed via optomotor response-based testing and full-field scotopic electroretinography, and histological changes were examined via immunohistochemistry. Disease progression was tracked at one, two, three, and six months of age. Snf2h cKO mice showed a significant decline in visual function and exhibited retinal neuron loss compared to wildtype control littermates at all time points assessed. This work shows that the chromatin remodelling protein Snf2h plays an essential role in the structure and function of the retina.

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Phosphoenolpyruvate carboxykinase (Pck) catalyzes the first step of gluconeogenesis, and the gene which encodes this enzyme (pckA) is transcriptionally regulated. High pckA expression is observed in succinate-grown cells, while little expression is observed in glucose-grown cells. pckA regulatory mutants have previously been isolated (Osteras et al. 1997) and pckR, a gene encoding a Lacl-GaIR DNA-binding transcriptional regulator, has been implicated in the regulation of pckA transcription. Here we shew that pckR insertion mutations result in a dramatic decrease in pckA expression even in succinate-grown cells. We demonstrate that the previously identified rpk-9 mutation is tightly linked to pckR. The rpk-9 mutation results in constitutive pckA expression, and we show that plasmids carrying the pckR gene complement the rpk-9 mutation in glucose-grown cells. A putative Lacl-GaIR operator binding site has been identified in the pckA promoter, however no evidence of an interaction between this site and the pckR gene product could be found. / Thesis / Master of Science (MS)

This thesis is missing page 53, no other copies have this page. -Digitization Centre / Bacterial adaptation to changing conditions and to the host environment requires coordinated changes in gene expression that permit more efficient utilization of metabolites and increased survival. An important form of gene control is through the use of alternative sigma factors that direct RNA polymerase to recognize a distinct group of genes. One such sigma factor is RpoS, which is widely present in Proteobacteria including many serious human pathogens. As a key stress response regulator, RpoS plays an important role in adaptation, but its effect on virulence varies in different species. RpoS contributes to virulence through either enhancing survival against host defense systems or directly regulating expression of virulence factors in some pathogens, while RpoS is dispensable, or even inhibitory, to virulence in others. The primary objective of this study is to understand the mechanism of RpoS control in gene expression and pathogenesis of Escherichia coli. This thesis first describes the characterization of RpoS regulon in laboratory and pathogenic E. coli strains by transcriptome profiling analysis. Comparison of RpoS regulons identifies a core set of RpoS-controlled genes as well as strain-specific groups of genes, including many implicated in virulence. The contribution of RpoS to enteropathogenesis in vivo was tested using a Citrobacter rodentium (CR)mouse infection model that is commonly used to simulate E. coli infection in human intestine. Mutations in rpoS result in reduced colonization and delay in mortality, indicating RpoS is important for full virulence. Clinical and natural E. coli isolates exhibit variable abilities in stress resistance and virulence, which is partly attributable to attenuating polymorphisms of rpoS commonly found in E. coli populations. A possible mechanism responsible for the occurrence of rpoS polymorphisms in pathogenic E. coli is addressed. Using a group of representative enterohemorrhagic E. coli strains, we report that growth-enhanced mutants can be selected during growth on succinate and other poor carbon sources under both aerobic and anaerobic conditions. The majority of these mutants carry nonsense or missense mutations in rpoS. Phenotypic microarray analysis reveals that rpoS mutations result in increased utilization of 92 nitrogen and 8 carbon sources. Therefore, the occurrence of rpoS polymorphisms may increase the fitness of the population as a whole for better nutrient scavenging. In conclusion, RpoS may be viewed as a transient regulator that orchestrates the temporal expression of a large regulon for better adaptation under specific conditions including natural and host environments. Under conditions not requiring RpoS, its functions can be turned off through decreasing expression, rapid proteolysis, inhibition of RpoS activity, or selection of attenuating mutations. The final part of this thesis reviews the distinct and niche-dependent involvement of RpoS in virulence of many rpoS-bearing pathogens. - / Thesis / Doctor of Philosophy (PhD)

Juvenile hormone (JH) is an important insect hormone that controls diverse biological processes in postembryonic development and adult reproduction. JH exerts its effects through the nuclear receptor Methoprene-tolerant (MET). MET is a transcription factor of the basic helix-loop-helix (bHLH)/Per-Arnt-Sim (PAS) family. In the presence of JH, MET forms a heterodimer with its DNA-binding partner Taiman (TAI). The MET-TAI complex directly binds to the regulatory regions of some JH target genes and regulates their transcription. However many questions remain unanswered regarding the JH-regulated gene expression. The work in this report aims to determine the role of protein kinase C (PKC) in JH signaling in adult mosquitoes and to find the direct target genes of Krüppel homolog 1 (Kr-h1), a zinc finger transcription factor encoded by a JH early response gene. We discovered that PKC is an essential component of a membrane-initiated JH signaling pathway. PKC was activated by JH in a phospholipase C (PLC)-dependent manner. Inhibition of PKC activity dramatically decreased the JH-induced gene expression. RNAi experiment indicated that several PKC isoforms were involved in the JH action in adult female mosquitoes. We showed that PKC modulated the transactivation activity of MET by enhancing the binding of MET and TAI to the promoters of JH target genes. Kr-h1 is rapidly upregulated by JH in newly emerged mosquitoes. RNAi-mediated depletion of AaKr-h1 caused a substantial decrease in oviposited eggs, indicating that this protein plays an essential role in mosquito reproduction. We combined chromatin immunoprecipitation (ChIP) with cloning of the generated DNA and have identified chromatin binding sites of AaKr-h1 in Aedes aegypti. After adult emergence, binding of AaKr-h1 to its in vivo targets increased with the JH-induced increase in AaKr-h1. Interestingly, depletion of AaKr-h1 in newly emerged mosquitoes led to considerable upregulation of some AaKr-h1 target genes but downregulation of other target genes. The results suggest that AaKr-h1 acts downstream of AaMET to regulate gene expression in response to JH and that AaKr-h1 can activate or repress the expression of individual target gene. / Ph. D.