<p>Abstract</p><p>Listeria monocytogenes is a gram-positive soil saprophytic bacterium that is capable of causing fatal infection in humans. The main virulence regulator PrfA, a member of the Crp/FNR family of transcriptional regulators, activates the expression of essential proteins required for host cell invasion and cell-to-cell spread. The mechanism of PrfA activation and the identity of its small molecule coactivator have remained a mystery for more than 20 years, but it is hypothesized that PrfA shares mechanistic similarity to the E. coli cAMP binding protein, Crp. Crp activates gene expression by binding cAMP, increasing the DNA binding affinity of the protein and causing a significant DNA bend that facilitates RNA polymerase binding and downstream gene activation. Our data suggests PrfA activates virulence protein expression through a mechanism distinct from the canonical Crp activation mechanism that involves a combination of cysteine residue reduction and glutathione (GSH) binding. </p><p>Listeria lacking glutathione synthase (ΔgshF) is avirulent in mice; however virulence is rescued when the bacterium expresses the constitutively active PrfA mutant G145S. Interestingly, Listeria expressing a PrfA mutant in which its four cysteines are mutated to alanine (Quad PrfA), demonstrate a 30-fold decrease in virulence. The Quad and ΔgshF double mutant strains are avirulent. DNA-binding affinity, measured through fluorescence polarization assays, indicate reduction of the cysteine side chains is sufficient to allow PrfA to binds its physiological promoters Phly and PactA with low nanomolar affinity. Oxidized PrfA binds the promoters poorly. </p><p>Unexpectedly, Quad also binds promoter DNA with nanomolar affinity, suggesting that the cysteines play a role in transcription efficiency in addition to DNA binding. Both PrfA and Quad bind GSH at physiologically relevant and comparable affinities, however GSH did not affect DNA binding in either case. Thermal denaturation assays suggest that Quad and wild-type PrfA differ structurally upon binding GSH, which supports the in vivo difference in infection between the regulator and its mutant. </p><p>Structures of PrfA in complex with cognate DNA, determined through X-ray crystallography, further support the disparity between PrfA and Crp activation mechanisms as two structures of reduced PrfA bound to Phly (PrfA-Phly30 and PrfA-Phly24) suggest the DNA adopts a less bent DNA conformation when compared to Crp-cAMP- DNA. The structure of Quad-Phly30 confirms the DNA-binding data as the protein-DNA complex adopts the same overall conformation as PrfA-Phly. </p><p>From these results, we hypothesize a two-step activation mechanism wherein PrfA, oxidized upon cell entry and unable to bind DNA, is reduced upon its intracellular release and binds DNA, causing a slight bend in the promoter and small increase in transcription of PrfA-regulated genes. The structures of PrfA-Phly30 and PrfA-Phly24 likely visualize this intermediate complex. Increasing concentrations of GSH shift the protein to a (PrfA-GSH)-DNA complex which is fully active transcriptionally and is hypothesized to resemble closely the transcriptionally active structure of the cAMP-(Crp)-DNA complex. Thermal denaturation results suggest Quad PrfA is deficient in this second step, which explains the decrease in virulence and implicates the cysteine residues as critical for transcription efficiency. Further structural and biochemical studies are on-going to clarify this mechanism of activation.</p> / Dissertation

This study examined the role of <I>PYKI </I>coding sequences in the expression of <I>PYK1::lacZ </I>gene fusions in <I>Saccharomyces cerevisiae. </I>Further aims were to examine the effects of the vector system upon the mRNA levels from these gene fusions the effect that these gene fusions have upon the yeast cell in general. Analysis of the <I>PYK1::lacZ </I>gene fusions revealed that <I>PYK1 </I>coding sequences were responsible for elevating mRNA levels. This elevation was not due to a single element within the coding region of the <I>PYK1 </I>gene as had been previously proposed (Purvis <I>et al.,</I> 1987a; Lithgow, 1989). Models for the stimulatory action of the <I>PYK1 </I>coding region upon the transcription of the <I>PYK1::lacZ</I> gene fusion were presented. <I>PYKI </I>coding region fragments in the <I>PYK1::lacZ</I> gene fusions stabilized the mRNA, but the data presented here were not consistent with a stability element within the <I>PYK1 </I>coding region. An alternative model was presented whereby the translation rate of the mRNA can influence its decay. The effect of expression of these gene fusions upon the yeast cell in general was monitored by examining the mRNA level of two chromosomal loci, <I>PYK1 </I>and <I>PGK1, </I>and by measuring the generation time. In contrast to previous findings, <I>PYK1 </I>and <I>PGK1 </I>mRNA levels were found not to change and so it was concluded that expression of these gene fusions had no general effect upon transcription or mRNA decay. However expression of these gene fusions did lead to an increase in generation time, and it was proposed that this might be due to a general effect upon translation brought about by a reduction in the intracellular pools of tRNAs for non-preferred codons.

Music has always played a large role in human life. The technology behind the art has progressed and grown over time in many areas, for instance the instruments themselves, the recording equipment used in studios, and the reproduction through digital signal processing. One facet of music that has seen very little attention over time is the ability to transcribe audio files into musical notation. In this thesis, a method of multipitch analysis is used to track multiple simultaneous notes through time in an audio music file. The analysis method is based on autocorrelation and a specialized peak pruning method to identify only the fundamental frequencies present at any single moment in the sequence. A sliding Hamming window is used to step through the input sound file and track through time. Results show the tracking of nontrivial musical patterns over two octaves in range and varying tempos.

Artemisinin, produced by the plant Artemisia annua, is a sesquiterpene anti-malarial therapeutic. Due to the medicinal relevance of this plant product, there is significant interest in understanding how the biosynthetic pathway is regulated at several key steps. The objective of this study is to examine several factors known to influence artemisinin yields to determine if those effects are occurring at the transcriptional level of the biosynthetic pathway. Artemisinin content has been shown to increase as the plant shifts from vegetative growth to reproductive, flowering growth. To test whether there is a corresponding increase in terpenoid gene expression during the shift to reproductive growth, levels of mRNA of terpenoid genes were measured during flowering budding and full flowering and compared to those measured during vegetative growth. Results indicate that in response to the photoperiod signal to shift to reproductive growth, early cytosolic pathway genes were highly upregulated, while there was no change in early plastidic pathway genes. Late pathway genes specific to artemisinin synthesis were upregulated >6-fold. Furthermore, glucose has also been shown to stimulate artemisinin production compared to sucrose. To test whether glucose is acting as signal to increase terpenoid gene expression, levels of mRNA of terpenoid genes were measured in glucose- and fructose-treated seedlings and compared to those in sucrose-treated seedlings. Results indicate that in response to treatment with glucose, compared with sucrose, early pathway genes in both compartments were initially upregulated. Transcript levels subsequently decreased to levels similar to those in sucrose-treated seedlings. ADS was upregulated by glucose, compared with sucrose, reaching a peak at day 7. Finally, coordinate control of sterol and sesquiterpene synthesis at a critical branch-point in the terpenoid biosynthetic pathway has been demonstrated. To test whether amorpha-4,11-diene synthase (ADS) and squalene sythase (SQS) are coordinately regulated, levels of mRNA of those two genes were measured and compared in both experimental conditions. Results indicate that under the conditions used in this study, ADS and SQS did not show coordinate regulation. This study was the first to demonstrate that: 1. terpenoid genes relating to artemisinin biosynthesis are regulated at the level of transcript accumulation as the plant shifts from vegetative to reproductive growth; 2. glucose is acting as a signal in artemisinin biosynthesis by upregulating transcript levels for several terpenoid genes.

Johannes Brahms’s Sonata No. 2, Opus 99 is considered an important work of the cello repertoire. With the lack of Romantic-era transcriptions, specifically Brahms, the purpose of this project was to create a new transcription to add to the alto saxophone repertoire. The paper examines Brahms’s own transcription of Sonata Nos. 1 and 2, Opus 120 as an example of a clarinet to viola transcription. Additionally, the paper discusses in detail the necessary changes to the music, as well as offering technical suggestions for the issues encountered when transcribing from a stringed to a wind instrument. The paper concludes with a complete transcription of Brahms’s Sonata No. 2, Opus 99 for alto saxophone and piano.

在中樞神經系統的發育過程中，神經幹細胞會先經歷神經發生 (neuro¬genesis)產生神經元，然後再通過神經膠質細胞發生 (gliogenesis)製造神經膠質細胞。這個時間順序是所有神經幹細胞分化過程中的固定模式。 Sox9是屬於一類具有 HMG (high mobility group)特徵性結構域的轉錄因子家族。以往轉基因小鼠研究證明， Sox9在脊髓和視網膜神經建構過程中，是引發神經膠質細胞新生程式的決定性主控基因。但是在小腦發育過程中，製造神經膠質細胞的調節機制仍未被界定。 / 在小鼠小腦發育過程中，室區 (ventricular zone)的神經祖細胞豐富表達 Sox9基因。因此，本實驗試圖利用條件基因剔除技術，研究 Sox9基因在小腦形成過程中的功能。結果顯示， Sox9基因在小腦被剔除後會導致包括蒲金耶氏細胞 (Purkinje cells)及 γ-氨基丁酸能中間神經元 (GABAergic interneurons)等室區衍生神經元大幅增加。與此同時，一些神經膠質細胞標記的表達亦受到影響。值得留意的是這些缺陷表型在胚胎發育後期才發生，與神經膠質細胞發生開始的時間框架一致。由於神經元和神經膠質細胞都是於共同的神經祖細胞池分化而成， Sox9基因的失活顯然影響了祖細胞池由製造神經元切換到神經膠質細胞生成的過程。進一步的微陣列基因晶片及半定量 RT-PCR分析顯示，數個參與細胞增殖、分化及細胞命運決定的基因表達量在 Sox9轉基因小鼠小腦中起了明顯的變化，而這些基因很可能與 Sox9共同調控神經膠質細胞發生的始初過程。 / 另一方面，我利用條件性 Sox9高效表達的小鼠作為動物模型及分析其表徵,希望更全面地了解 Sox9在小腦發育過程中的角色。於胚胎發育期間， Sox9基因高效表達並沒有擾亂小腦的發育；但由產後第 15周起，在小腦中持續性的 Sox9基因異位表達卻導致小鼠出現明顯的運動協調及身體平衡能力缺失。從 24 周 Sox9高效表達小鼠小腦組織分析顯示，其小腦中的貝格曼神經膠質細胞 (Bergmann glia)和蒲金耶氏細胞均出現缺陷表型，而這兩類細胞的異常變化很可能是導致條件性 Sox9高效表達小鼠運動協調缺失的主因。 / 在探究 Sox9如何調節小腦發育的同時，我發現負責分泌腦脊液及形成血腦屏障的脈絡叢 (choroid plexus)亦發生異常變化。初步分析顯示， Sox9的失活導致脈絡叢上皮細胞的凋亡率上升，而這亦解釋了為何顱內出血的情況在 Sox9基因剔除小鼠中較常見。 / 總括而言，這項研究的結果顯示 Sox9在小鼠小腦發育過程中扮演決定神經祖細胞命運的角色，在中樞神經系統發育中起著守恒的作用。而 Sox9基因的高效表達則會造成成年小鼠的運動功能障礙。此外，Sox9亦可能通過調控脈絡叢的發育和功能，以維持血腦屏障的完整性。我們需要更深入及全面的研究以了解 Sox9在小鼠小腦和脈絡叢發育中的作用及其分子機制。 / In the developing central nervous system (CNS), neural stem cells undergo a stereotypic pattern of temporal differentiation characterized by an initial wave of neurogenesis which then ceases to give way for a subsequent period of gliogenesis. Sox9 belongs to the highly conserved family of high mobility group (HMG) transcription factors, and has been shown to be the master regulator mediating the switch to the gliogenic program in several neuronal tissues including the spinal cord and the retina. While in the cerebellum, genetic control of such a developmental interval has remained poorly defined. / In the developing cerebellum, Sox9 is expressed abundantly in neural progenitors of the ventricular zone (VZ). Here, I analyzed cerebellar development of mice in which Sox9 is specifically inactivated in the cerebellum by the Cre/loxp recombination system. These mice exhibited an increased number of neuronal phenotypes, including the Purkinje cells (PCs) and GABAergic interneurons, while the expressions of several glial markers are compromised. These phenotypes occur only at late embryonic stage, a time frame which is consistent with the initiation of gliogenesis. Because neurons and glia share a common origin, the ablation of Sox9 apparently causes the progenitor pool to continue to produce neurons instead of switching to generate glial cells. Subsequent microarray and semi-quantitative RT-PCR analyses identified expression level changes in genes that have been previously implied in regulating cell fate decision and cell proliferation during development, which may possibly function in collaboration with Sox9 during the initiation of gliogenesis. / On the other hand, to comprehensively interrogate the role of Sox9 in cerebellar development, a conditional Sox9 overexpression mutant was characterized. While the ectopic expression of Sox9 did not perturb cerebellar development during embryogenesis, the continued aberrant expression of Sox9 in the cerebellum led to noticeable locomotor deficits in adult mice from 15 weeks onwards. Histological examinations at 24 weeks revealed abnormalities in both the Bergmann glia and PCs, which possibly accounted for the motor defects observed in the mutant mice. / In the course of studying the role of Sox9 in cerebellar development, noticeable abnormalities were also observed in the choroid plexus (ChP), a neurovascular tissue responsible in setting up the blood-brain barrier. Initial analysis showed that the ablation of Sox9 induced apoptosis in the ChP epithelium, which possibly explained the higher frequency of intracranial hemorrhage observed in the mutant. / In summary, the findings from this study suggest that Sox9 plays a conserved role in the developing CNS as a key molecular component in determining the neuron-glial fate choice during cerebellar development, while the ectopic expression of Sox9 could induce locomotor dysfunction in adult mice. In addition, Sox9 may also contribute to the maintenance of vascular integrity by regulating ChP development and functionality. More comprehensive investigation is required to understand the molecular mechanisms of Sox9 action during mouse cerebellar and ChP development. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Leung, Kit Ying Crystal. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2012. / Includes bibliographical references (leaves 166-184). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Abstracts also in Chinese. / Chapter Declaration --- p.i / Chapter Abstract --- p.iii / Chapter Abstract in Chinese --- p.v / Chapter Acknowledgements --- p.vii / Chapter Table of Contents --- p.ix / Chapter List of Figures --- p.xiii / Chapter List of Tables --- p.xv / Chapter List of Abbreviations --- p.xvi / Chapter CHAPTER 1 --- General Introduction / Chapter 1.1 --- Preface: The developing central nervous system - Why it matters --- p.1 / Chapter 1.2 --- Development of the Mammalian Central Nervous System: An Overview --- p.3 / Chapter 1.2.1 --- Neural induction, neurulation and the formation of the neural tube --- p.3 / Chapter 1.2.2 --- Regionalization of the rostral neural tube and formation of brain vesicles --- p.4 / Chapter 1.3 --- The Cerebellum --- p.7 / Chapter 1.3.1 --- Functions of the cerebellum --- p.7 / Chapter 1.3.2 --- Disorders of the cerebellum --- p.8 / Chapter 1.3.3 --- Gross anatomy and organization of the cerebellum --- p.11 / Chapter 1.3.4 --- Cellular constituents of the cerebellum - diversity and biochemistry --- p.15 / Chapter 1.3.5 --- Neuronal circuitry of the mature cerebellum --- p.16 / Chapter 1.4 --- Development of the Cerebellum --- p.20 / Chapter 1.4.1 --- Overview of mouse early cerebellar development --- p.20 / Chapter 1.4.2 --- Germinal matrices of the cerebellar primordium --- p.22 / Chapter 1.4.3 --- Timeline of the birth of cerebellar neurons and glial cells --- p.25 / Chapter 1.4.4 --- Postnatal development of the cerebellum --- p.27 / Chapter 1.4.5 --- Genetic regulation of cerebellar development --- p.30 / Chapter 1.5 --- SOX9 and the SOX Family of Transcription Factors --- p.33 / Chapter 1.5.1 --- SOX9 as a transcription factor --- p.33 / Chapter 1.5.2 --- Molecular regulation of SOX9 action --- p.36 / Chapter 1.5.3 --- SOX9 in development and disease --- p.38 / Chapter 1.6 --- Scope of the Thesis --- p.45 / Chapter CHAPTER 2 --- Characterization of a Mouse Model with Sox9 Conditional Knockout / Chapter 2.1 --- Chapter Summary --- p.47 / Chapter 2.2 --- Introduction --- p.49 / Chapter 2.3 --- Materials and Methods --- p.54 / Chapter 2.3.1 --- Animal husbandry --- p.54 / Chapter 2.3.2 --- Breeding strategy for the generation of Sox9 conditional knockout mutants --- p.54 / Chapter 2.3.3 --- DNA extraction and genotyping --- p.55 / Chapter 2.3.4 --- Histological examination of the cerebellum --- p.57 / Chapter 2.3.5 --- β-Galactosidase staining of embryos --- p.59 / Chapter 2.3.6 --- Microarray analysis --- p.59 / Chapter 2.3.7 --- Validation of microarray data by semi-quantitative RT-PCR --- p.60 / Chapter 2.3.8 --- In situ hybridization --- p.61 / Chapter 2.3.9 --- Image acquisition and photo editing --- p.65 / Chapter 2.3.10 --- Statistical analysis --- p.66 / Chapter 2.4 --- Results -- Part I: En1[superscript Cre]- driven Sox9 Conditional Knockout --- p.67 / Chapter 2.4.1 --- Expression of Sox9 during mouse embryonic development --- p.67 / Chapter 2.4.2 --- Effective ablation of Sox9 in the cerebellum of En1[superscript Cre/]⁺; Sox9[superscript fx/fx] mutant --- p.68 / Chapter 2.4.3 --- Deficiency of Sox9 did not cause cerebellar developmental abnormalities in the Sox9 CKO mutants --- p.71 / Chapter 2.5 --- Results -- Part II: Pax2[superscript Cre]-driven Sox9 Conditional Knockout --- p.76 / Chapter 2.5.1 --- Effective ablation of Sox9 in the cerebellum of Pax2[superscript Cre/]⁺; Sox9[superscript fx/fx] mutant --- p.76 / Chapter 2.5.2 --- Sox9 deletion resulted in cerebellar malformation at late embryonic stage --- p.78 / Chapter 2.5.3 --- Loss of Sox9 caused an increased neuronal production from the ventricular zone of the Pax2[superscript Cre/]⁺; Sox9[superscript fx/fx] mutant --- p.80 / Chapter 2.5.4 --- Sox9 deletion did not alter rhombic lip-derived neurons --- p.84 / Chapter 2.5.5 --- Expression of glial markers were compromised in the Sox9 CKO mutant at late embryonic stages --- p.84 / Chapter 2.5.6 --- Comparison of cerebellar gene expression profiles between the Sox9 CKO mutant and control --- p.90 / Chapter 2.5.7 --- Expression analysis of the proto-oncogene transcription factor Prdm16 in the mouse brain --- p.93 / Chapter 2.6 --- Results -- Part III: Sox9 and the Development of the Choroid Plexus --- p.95 / Chapter 2.6.1 --- Partial loss of Sox9 in the Pax2[superscript Cre]; Sox9[superscript fx/fx] CKO mutant induced choroid plexus abnormalities and increased susceptibility to intracranial hemorrhage --- p.95 / Chapter 2.6.2 --- The mutant choroid plexus was non-cancerous --- p.98 / Chapter 2.6.3 --- Increased apoptosis in the Sox9 CKO mutant choroid plexus --- p.100 / Chapter 2.7 --- Discussion --- p.102 / Chapter 2.7.1 --- Sox9 plays an essential role in determining the neuron-glial fate choice in the developing cerebellum --- p.102 / Chapter 2.7.2 --- Potential influence of genetic background on Sox9 CKO mutant phenotypes --- p.104 / Chapter 2.7.3 --- Prdm16 as a potential candidate in a Sox9-dependent transcriptional regulatory cascade during the initiation of gliogenesis --- p.105 / Chapter 2.7.4 --- Sox9 may be important in choroid plexus development --- p.107 / Chapter 2.7.5 --- Chapter conclusion --- p.108 / Chapter CHAPTER 3 --- Characterization of a Mouse Model with Sox9 Conditional Overexpression / Chapter 3.1 --- Chapter Summary --- p.116 / Chapter 3.2 --- Introduction --- p.118 / Chapter 3.3 --- Materials and Methods --- p.120 / Chapter 3.3.1 --- Animal husbandry --- p.120 / Chapter 3.3.2 --- Breeding strategy for the generation of Sox9 overexpression mutants --- p.120 / Chapter 3.3.3 --- Genotyping --- p.120 / Chapter 3.3.4 --- Histological examination of the cerebellum --- p.121 / Chapter 3.3.5 --- Behavioral tests --- p.122 / Chapter 3.3.6 --- Image and video acquisition --- p.123 / Chapter 3.3.7 --- Video processing --- p.124 / Chapter 3.3.8 --- Statistical analysis --- p.124 / Chapter 3.4 --- Results --- p.125 / Chapter 3.4.1 --- Sox9 was overexpressed in only a subset of cells in the mutant cerebellum --- p.125 / Chapter 3.4.2 --- Overexpression of Sox9 did not cause developmental abnormalities in the cerebellum of En1[superscript Cre/]⁺; Z/Sox9 mutant embryos --- p.127 / Chapter 3.4.3 --- En1[superscript Cre/]⁺; Z/Sox9 mutants manifested locomotion deficits during adulthood --- p.132 / Chapter 3.4.4 --- Abnormal Purkinje cell dendritic arborization and Bergmann glial scaffold in adult En1[superscript Cre/]⁺; Z/Sox9 mutants --- p.138 / Chapter 3.5 --- Discussion and Chapter Conclusion --- p.143 / Chapter CHAPTER 4 --- General Discussion, Future Works and Conclusions / Chapter 4.1 --- An Evolutionary Conserved Role of Sox9 in Determining the Neuron-glial Fate Choice during Vertebrate CNS Development --- p.147 / Chapter 4.2 --- Prdm16 may be important in the transcriptional cascade during the initiation of gliogenesis in mouse cerebellar development --- p.148 / Chapter 4.3 --- A Potential Neuroprotective Role of Sox9 in the Adult Cerebellum --- p.149 / Chapter 4.4 --- Future Works --- p.150 / Chapter 4.4.1 --- Dissecting the dual roles for Sox9 in neural stem cell maintenance and gliogenesis --- p.150 / Chapter 4.4.2 --- The contribution of glutamate toxicity to the cerebellar phenotypes observed in the Sox9 CKO mutant --- p.152 / Chapter 4.4.3 --- The involvement of Prdm16 and Notch signaling in cerebellar development --- p.153 / Chapter 4.4.4 --- The molecular mechanism of Sox9-dependent neurodegenerative phenotypes in the conditional overexpression mutant --- p.153 / Chapter 4.4.5 --- The importance of Sox9 in choroid plexus development --- p.154 / Chapter 4.4.6 --- Improving the specificity of Cre deleter mouse lines --- p.155 / Chapter 4.5 --- Conclusions --- p.155 / APPENDIX / Chapter I. --- Microarray Data --- p.157 / Chapter II. --- References --- p.166

The genes of eukaryotes exist as DNA-RNA-protein complexes known as chromatin. The structure of chromatin fluctuates to allow controlled access to genetic information while maintaining its important packaging function. Recent improvements in optics, image acquisition electronics, and live imaging techniques, as well as the introduction of fluorescent fusion proteins, have made it possible to use fluorescence light microscopy to study the dynamic nature of chromatin compaction in cells. Here we report the application of advanced fluorescence microscopy to characterize the effects of transcription on chromatin compaction in living yeast cells. Repressor protein-GFP fusion proteins which recognize specific operator sequences were used to fluorescently tag specific gene loci, and an OMX fluorescence light microscope was then used to track their positions in three dimensions. It was determined that image acquisition with the OMX microscope is rapid enough to track fluorescently tagged genomic loci in live yeast cells in 3D, and that it does so with a root mean squared (RMS) measurement error of 162 nanometers (nm). It was also determined that the OMX microscope can distinguish between strains with fluorescent spots separated by 40 or 70 kb genomic distances. Additionally, it was found that chromatin compaction of a 15 kb gene driven by the Gal1 promoter is correlated with the carbon source on which the cells are fed, and that three different carbon sources produce three different transcription-dependent chromatin structures. Reversible changes in end-to-end distance of ~500 nm within two seconds were detected in the induced strain. These findings indicate that improvements in light microscopy enable chromatin to be studied in living cells on a scale not previously possible.

The overall goal of my work has been to gain a better understanding of Axenfeld-Rieger Syndrome (ARS), a human autosomal dominantly inherited mal-development of the anterior segment of the eye that is associated with glaucoma. By studying rare genetic causes of this complex disease we are gaining insight into the initial steps that ultimately lead to blindness. To achieve the goal of better understanding ARS, my research project had two parts. In the first part, I performed a retrospective clinical study in which I analyzed the glaucoma-related clinical presentation of ARS patients with FOXC1 and PITX2 defects. This study showed a good genotype-phenotype correlation which may be important for the physician in dealing with ARS patients. Patients with FOXC1 mutations had the mildest prognosis in glaucoma development, while patients with PITX2 defects and patients with FOXC1 duplication had a more severe prognosis in glaucoma development than patients with FOXC1 mutations. I tried to determine the best treatment for glaucoma in these patients. Unfortunately, in this study, current medical therapies did not successfully lower intraocular pressure or prevent progression of glaucoma in ARS patients with FOXC1 or PITX2 alterations. This clinical study also provided useful diagnostic criteria to identify the gene responsible for ARS. The second part of the project was to study the gene regulatory pathways of the PITX2 gene, mutations of which cause ARS. PITX2 is a transcription factor that regulates the expression of genes in the eye. The discovery of direct downstream targets of PITX2 is necessary for understanding the genetic mechanisms underlying complex, highly regulated processes such as development and underlying heritable human disorders. To find direct target genes of PITX2, I have used a recently developed method: the hormone receptor (HR)-inducible expression system for transcription factors coupled microarray analysis. The results obtained using this method have involved PITX2 in control of cellular stress. Recent investigations have suggested significant roles for cellular stress in glaucoma pathology. Understanding the control of these key aspects of cell function will have profound implications for understanding and treating the glaucoma that is the most clinically serious consequence of mutations of PITX2.

Mitochondrial function is critical for the survival of eukaryotes. Hence, mitochondrial dysfunctions are involved in numerous human diseases. An essential process for a normal mitochondrial function is mitochondrial gene expression which is tightly regulated in response to various physiological changes. The accurate control of mitochondrial gene expression is essential in order to provide the appropriate oxidative phosphorylation capacity for diverse metabolic demands. Recent findings in the basic mitochondrial replication and transcription regulation helped advance our understanding of organelle function and basic pathogenetic mechanisms of mitochondrial DNA mutations associated with oxidative phosphorylation defects. Mitochondrial transcription is regulated by the mitochondrial transcription termination factor (mTERF) both at the initiation and termination levels. A protein family containing highly conserved mTERF motifs has been identified recently and its members named generically as "terfins." In this work, one of these factors, mTERFD3, has been characterized in vitro and in vivo. The mTERFD3 protein is highly conserved throughout evolution. It is a mitochondrial protein localized to the matrix and is abundantly expressed in high energy demand tissues. We found that it contains 4 putative leucine zippers and is able to form dimers in vitro. We showed that mTERFD3 binds mtDNA at the transcription initiation site in the mtDNA regulatory region. These findings suggest that mTERFD3 may be involved in regulating mitochondrial gene expression at the transcriptional initiation level. In order to study the functional significance of mTERFD3 in vivo we developed a mouse deficient in mTERFD3 using a gene trapping strategy. The KO mice had a normal lifespan but showed decreased weight gain and decreased fat content in females. Fibroblasts isolated from KO mice displayed decreased growth rate when compared with WT in respiratory media, and had decreased complex IV activity. Consistent with the above findings, we found that muscle, one of the tissues with high energy demands, showed abnormal mitochondrial function, displaying features characteristic of mitochondrial myopathy such as decreased muscle strength and endurance. Muscle mitochondria of the KO mice showed a significant decrease in the complex II +III and complex IV activity. The decrease in OXPHOS complexes activity was associated with increased citrate synthase activity, suggesting mitochondrial proliferation, a feature typical for mitochondrial disorders. Another important finding was a decrease in the muscle mitochondrial transcripts in the KO animals associated with decreased steady state levels of OXPHOS subunits. Together these data suggest that mTERFD3 is a mitochondrial protein involved in the regulation of mtDNA transcription. mTERFD3 KO is not embryonic lethal suggesting that it is involved in the fine tuning of mitochondrial transcription. We conclude that mTERFD3 is a mitochondrial protein that modulates oxidative phosphorylation function, probably by directed interactions with the mtDNA regulatory region. This work shows the importance of mTERFD3, an mTERF family member, in the mitochondrial gene expression regulation.

The Estrogen Receptor alpha (ER alpha) is a multi-domain transcription factor that has been extensively studied due to its known involvement in breast cancer treatment and progression. Subsequent studies have shown coregulators are extensively involved in modulating the transcriptional activation of ER alpha and many of these proteins possess enzymatic functions. Coregulators are divided into two categories, coactivators which enhance transcriptional output and corepressors which decrease transcriptional output. One protein responsible for Angelman syndrome, E6-associated protein (E6-AP) was found to be a coactivator of ER alpha and possessed ubiquitin ligase activity; however, the ubiquitin ligase activity has been shown not to be essential to E6-AP coactivation ability. The current work was undertaken to explore the role of E6-AP in the regulation of ER alpha. E6-AP was found to play a role in a unique ligand-independent degradation pathway. Because the degradation effect was ligand-independent, it was proposed that the degradation signal mediating the event occurred through phosphorylation of E6-AP. In silico analysis of E6-AP indicated several potential phosphorylation sites on the E6-AP protein. Numerous phosphorylation sites of E6-AP were confirmed by western blot and mass spec indicating a possible phosphorylation signal mediating E6-AP/ER alpha interaction. Because it has been shown that the ligase function of E6-AP is not required for its coactivation, we then examined E6-AP coactivation of ERα in the presence of ligand. One well studied gene TFF-1 (pS2) was examined as a model ERα target gene. Estrogen-mediated transcription from TFF-1 was decreased with knockdown of E6-AP in both MCF-7 and T47D cell lines. Furthermore, under E6-AP knockdown conditions, ChIP of p300, a known histone acetyl transferase (HAT), indicated a reduced recruitment to the TFF-1 promoter in both cell lines. Interestingly, the reduced recruitment of p300 had a cell specific effect on phosphorylated RNA polymerase II (pRNA pol II) recruitment indicating cell specific functions of E6-AP. Further investigation also found a gene specific effect for E6-AP on pRNA pol II recruitment. The current work provides a new role for E6-AP as a coactivator of ER alpha in the form of a scaffold allowing creation of fully functional transcription complexes in a gene and cell specific manner.