<p> Many adult stem cells are characterized by prolonged quiescence, promoted by cues from their niche. Upon tissue damage, a coordinated transition to the activated state is necessary for successful repair. Non-physiological breaks in quiescence often lead to stem cell depletion and impaired tissue restoration. Here, I identify cadherin-mediated adhesion and signaling between muscle stem cells (satellite cells; SCs) and their myofiber niche as a mechanism that orchestrates the quiescence-to-activation transition. Conditional removal of N-cadherin and M-cadherin in mice leads to a break in SC quiescence with long-term expansion of a regeneration-proficient SC pool. These SCs have an incomplete disruption of the myofiber-SC adhesive junction, and maintain niche residence and cell polarity, yet show properties of SCs in a state of transition from quiescence towards full activation. Among these properties is nuclear localization of b- catenin, which is necessary for this phenotype. These findings are consistent with the conclusion that injury-induced perturbation of niche adhesive junctions is a first step in the quiescence-to-activation transition. </p><p>

<p> Parkinson&rsquo;s disease (PD) is an adult onset neurodegenerative disease that is characterized by deficiencies in movement, cognition, and Lewy body neuropathology within the brain. Motor and cognitive deficiencies progressively worsen through the course of disease concurrent with increasing neuropathology and neurodegeneration. Approximately 10&ndash;15% of PD patients have a family history of PD with a confirmed genetic cause. Presently PD pathogenesis is incompletely understood and there are no treatments capable of halting or reversing this disease. The extended disease-course and age-dependent nature of PD, especially in genetic cases where a mutation is present from birth, affirm that aging itself is the most important risk factor for disease. We hypothesize that specific cellular changes that occur during the normal process of aging confer susceptibility to disease-causing mutations which, while tolerated at younger ages, contribute to disease with age. Accurate animal models of PD and aging provide the ability to elucidate disease mechanisms and explore novel strategies targeting the aging process. To test the role of aging in PD we utilize the nematode <i>Caenorhabditis elegans</i> because this animal has been used extensively to study animal aging at a cellular level. We confirm that disease phenotypes in genetic <i>C. elegans</i> models of PD such as neurodegeneration, protein aggregation, and mitochondrial deficits are proportional to this organism&rsquo;s brief lifespan. This indicates that PD progresses according to biological age and not merely to chronological time. As a proof-of-principle we also show that delaying aging by mutation of the gene encoding the insulin-IGF receptor, <i>daf-2</i>, can rescue multiple deficits present in nematode models of PD. Overall we demonstrate that biological aging is a crucial for the development of various PD associated phenotypes and that delaying aging is sufficient to delay these phenotypes. Therefore targeting aging itself may be a sound strategy for the halting or the prevention of PD.</p><p>

<p> Many reptiles display temperature-dependent sex determination (TSD), in which the primary sex is determined by incubation temperatures rather than sex chromosomes. However, temperature is not the only factor that play critical roles in sex determination in the species with TSD. Previous studies in the snapping turtle, a species with TSD, showed that dihydrotestosterone (DHT) induces ovary development at temperatures that normally produce males or mixed sex ratios. In addition, the feminizing effect of DHT was found to be associated with increased expression of the ovary-determining gene <i>Foxl2</i>, suggesting a potential androgen-<i>Foxl2</i> regulatory mechanism. This dissertation aims to clarify the molecular mechanisms underlying TSD in several aspects. First, determine the role of androgen in TSD; second, identify novel thermosensitive genes involved in TSD and lastly, reconstruct gene regulatory networks underlying sex determination. </p><p> To test the hypothetical androgen-<i>Foxl2</i> interaction, I cloned the proximal promoter (1.6 kb) and coding sequence for snapping turtle <i> Foxl2</i> (t<i>Foxl2</i>) in frame with mCherry, a red fluorescent protein. The t<i>Foxl2</i>-mCherry fusion plasmid or mCherry plasmid were stably transfected into mouse KK1 granulosa cells. Although expression of t<i>Foxl2</i>-mCherry was not affected by androgen treatment in KK1 cells, androgen inhibited expression of the endogenous mouse Foxl2 gene, suggesting the androgen-Foxl2 interaction does exist but it differs between species. We also found t<i>Foxl2</i>-mCherry potentiated low dose DHT effects on aromatase expression, which has not been reported in any other studies. </p><p> To identify novel sex-determining genes in TSD, I first <i>de novo </i> assembled and annotated the transcriptome of the snapping turtle using next-generation sequencing (NGS) and then performed RNA-seq analyses on the newly assembled reference transcriptome. With the differential gene expression analyses, I identified 293 thermosensitive genes. Among these genes, I find AEBP2, JARID2, and KDM6B of particular interest because these genes could influence expression of many other genes via epigenetic modifications. </p><p> To further investigate the molecular mechanisms underlying sex determination, I reconstructed gene regulatory networks using an entropy based network reconstructing algorithm&mdash;ARACNE with public microarray experiments in mouse gonads. The subsequent hub gene analyses revealed the basic molecular pathways underlying gonadal development and the master regulator analyses identified 110 candidate sex-determining genes including both known sex-determining genes and novel candidate genes. </p><p> My findings demonstrate that androgens can influence expression of key ovarian genes but further studies are needed to understand the androgen signaling in TSD. Furthermore, my study provides a first description of the snapping turtle transcriptome and the effects of temperature on transcriptome-wide patterns of gene expression during the TSP. In addition, hub genes and master regulators identified for mammalian gonad determination will guide the direction of future studies in the field of sex determination. However, additional studies are needed to validate the computational findings.</p><p>

The effect of mechano-chemically bound polypropylene modifiers on the mechanical performance and thermal-oxidative stability of polypropylene composites has been studied. The mechanical performance of unmodified polypropylene containing silane coupled glass and Rockwool (mineral) fibre was poor by comparison with a similar commercially produced glass reinforced composite; this was attributed to poor fibre-matrix adhesion. Mechano-chemical binding with unsaturated additives was obtained in the presence of a free radical initiator (di-cumyl peroxide). This process was inhibited by stabilisers present in commercial grades of polypropylene composites by chemical bond formation between the chemically bound modifier and the silane coupling agent on the fibre surface, resulting in a dramatic improvement in the mechanical properties, dimensional stability and retention of mechanical performance after immersion in fluids typically found in under-bonnet environments.A feature unique to some of these modifiers was their ability not only to enhance the mechanical properties of polypropylene composites to levels substantially in excess of currently available commercial materials, but their ability to act as effective thermal-oxidative polypropylene stabilisers. The mode of action was shown to be a chain-breaking mechanism and as a result of the high binding levels achieved during melt processing, these modifiers were able to efficiently stabilise polypropylene in the most severe volatilising and solvent-extracting environments, thus giving much better protection to the polymer than currently available commercially stabilised grades of polypropylene.

<p> Sanfilippo syndrome type B (Mucopolysaccharidosis type IIIB; MPS IIIB) is a lysosomal storage disorder affecting primarily the brain and is characterized by profound intellectual disability, dementia, and a lifespan of about twenty years. The cause is a mutation in the gene encoding &alpha;&ndash;<i> N</i>-acetylglucosaminidase (<i>NAGLU</i>), a lysosomal enzyme, leading to the deficiency of NAGLU and accumulation of heparan sulfate. I am investigating a stem cell gene therapy approach in a <i>Naglu-/-</i> mouse model. I think that iNSCs overexpressing NAGLU can engraft and reduce neural pathology in the mouse model. Here I report that NAGLU overexpressed in neural stem cells derived from induced pluripotent stem cells (iNSCs) is capable of being taken up by deficient cells. I used flow cytometry and Lysotracker to demonstrate that NAGLU can reduce deficient cells&rsquo; lysosomal volume <i> in vitro</i>, suggesting that NAGLU treatment has a biological effect. iNSCs overexpressing <i>NAGLU</i> were injected into the brains of 1 day old <i>Naglu-/-</i> mice. iNSCs were detected 10 weeks after injection. Brain sections possessed NAGLU activity greater than or equal to heterozygous controls, activity was detected distal to injection sites, and transplanted animals showed reduction in LAMP1, GFAP, and CD68. The results suggest that engineered iNSCs could be used to deliver enzyme and treat MPS IIIB.</p>

<p> Despite being comprised of networks with extensive positive feedback, the brain is able to prevent runaway activity. Neural networks are remarkably good at maintaining an activity setpoint while still permitting learning-related or developmental plasticity. To accomplish the delicate balance between change and stability, neural networks employ a group of homeostatic negative feedback mechanisms. This suite of homeostatic mechanisms sense and adjust neuronal excitability to keep firing rates within some target range. To date, the most well described manner in which neurons homeostatically regulate their excitability is through adjustment of excitatory or inhibitory synaptic weights, or by modulating their intrinsic excitability. It is perplexing why the neuron should have several means to accomplish the same outcome. Experiments demonstrating the collaborative or solo induction of homeostatic mechanisms have provided only limited insight into how homeostatic signaling pathways are organized to generate and maintain firing rate set-points (FRSP).</p><p> In order for neurons to maintain a FRSP, deviations from this value must modulate an internal signal that subsequently triggers homeostatic mechanisms to restore excitability to its set-point. The CaMKIV pathway is a calcium-dependent signaling element that plays a crucial role in regulating excitatory synaptic strength. The CaMKIV cascade is highly sensitive to activity and can modulate transcription, making it an ideal candidate to integrate incoming activity and modulate the excitability of neurons. Therefore, the major aim of this thesis was to characterize the role of CaMKIV in inducing multiple forms of homeostatic plasticity in tandem. Here we leverage our expertise in measuring homeostasis in neocortical neurons <i>in vitro</i> to determine how manipulating the activation state of nuclear CaMKIV affects neuronal excitability. </p><p> We found that excitatory synaptic scaling and intrinsic plasticity were bidirectionally induced by manipulating CaMKIV activity even without any perturbations to network activity. In contrast, CaMKIV had no impact on inhibitory synaptic weights. Additionally, we found that CaMKIV activity bidirectionally regulated spontaneous firing rates. Taken together, our data suggests that CaMKIV activity is used by the neuron to monitor the firing set point and gate homeostatic mechanisms to correct for drift from this target. The data presented in this thesis contribute that excitatory synaptic scaling and intrinsic excitability are tightly coordinated through bidirectional changes in the same signaling pathway, while inhibitory synaptic scaling is sensed and regulated through an independent signaling mechanism. This body of work contributes to a better understanding of neuronal homeostasis and will hopefully help us determine how malfunctions in homeostatic plasticity contributes to neurological and neurodevelopmental disorders.</p><p>

The Notch and TGF13 signaling pathways have been shown to play important roles in regulating endothelial-to-mesenchymal transition (EndMT) during cardiac morphogenesis. EndMT is the process by which endocardial cells of the atrioventricular canal and the outflow tract repress endothelial cell phenotype and upregulate mesenchymal cell phenotype. EndMT is initiated by inductive signals emanating from the overlying myocardium and inter-endothelial signals and generate the cells that form the heart valves and atrioventricular septum. The Notch and TGFf3 pathway are thought to act in parallel to modulate endothelial phenotype and promote EndMT. Vascular endothelial (VE) cadherin is a key regulator of cardiac endothelial cell phenotype and must be downregulated during EndMT. Accordingly, VE-cadherin expression remains stabilized in the atrioventricular canal and outflow tract of Notchl-deficient mouse embryos, while activation of the Notch or TGFP pathways results in decreased VE-cadherin expression in endothelial cells. However, the downstream target gene(s) that are involved in regulating endothelial cell phenotype and VE-cadherin expression remain largely unknown. In this thesis the transcriptional repressor Slug is demonstrated to be expressed by the mesenchymal cells and a subset of endocardial cells of the atrioventricular canal and outflowtract during cardiac morphogenesis. Slug is demonstrated to be required for cardiac development through its role in regulating EndMT in the cardiac cushion. Data presented in Chapter 6 further suggests that Slug-deficiency in the mouse is compensated for by a increase in Snail expression after embryonic day (E) 9.5, which restores EndMT in the cardiac cushions. Additionally, the Notch pathway, via CSL, directly binds and regulates expression of the Slug promoter, while a close Slug family member, Snail is regulated by the TGFB pathway in endothelial cells. While Notch does not directly regulate Snail expression, Notch and TGFB act synergistically to regulate Snail expression in endothelial cells. It is further demonstrated that Slug is required for Notch mediated EndMT, binds to and represses the VE-cadherin promoter, and induces a motile phenotype. Collectively the data demonstrate that Notch signaling directly regulates Slug, but not Snail, expression and that the combined expression of Slug and Snail are required for cardiac cushion morphogenesis. / Medicine, Faculty of / Medicine, Department of / Experimental Medicine, Division of / Graduate

Fusion genes caused by chromosomal rearrangements are a common and important feature in haematological malignancies, but have until recently been seen as unimportant in epithelial cancers. The discovery of recurrent fusion genes in prostate and lung cancer suggests that fusion genes may play an important role in epithelial carcinogenesis, and that they have been previously under-reported due to the difficulties of cytogenetic analysis of solid tumours. In particular, breast cancers often have complex, highly rearranged karyotypes which have proved difficult to analyse using classical cytogenetic techniques. The aim of this project was to search for fusion genes in breast cancer by using high-resolution mapping of chromosome rearrangements in breast cancer cell lines. Mapping the chromosome rearrangements was initially done using high-resolution DNA microarrays and fluorescence in-situ hybridisation, but moved to high-throughput sequencing as it became available. Interesting candidate genes identified from the mapped chromosome rearrangements were investigated on a larger set of cell lines and primary tumours. The complete karyotypes of two breast cancer cell lines were constructed using a combination of microarrays, fluorescence microscopy, and high-throughput sequencing. A number of potential fusion genes were identified in these two cell lines. Although no expressed fusion genes were found, the complete karyotypes gave insight into the number and mechanisms of chromosome rearrangement in breast cancer, and identified interesting candidate genes which may be of importance in tumourigenesis. Two genes which were fused in other breast cancer cell lines, BCAS3 and ODZ4, were disrupted by chromosome rearrangements and identified as interesting candidate genes in tumorigenesis. A bioinformatic pipeline to process high-throughput sequencing data was set up and validated, and shown to more accurately predict fusion genes than other methods, and can be used to investigate further cell lines and tumours for recurrent fusion genes. The pipeline was used to analyse data from 3 other breast cancer cell lines and predict chromosomal rearrangements and fusion genes, several of which were found to be expressed. Of the fusions predicted in the cell line ZR-75-30, 7 expressed fusion genes were identified, and may have functional significance in breast cancer.

Under suitable conditions an unfolded protein molecule refolds spontaneously into a precise three-dimensional shape (known as its conformation), which is fixed by the chemical structure of the molecule. Can the relationship between the shape and chemical sequence of a protein ever be fully understood? I still cannot answer this question, which has troubled me for several years. It may seam surprising that one can work on a problem that could be insoluble. My reasons are as follows: Firstly, the folding problem is the most fundamental problem of theoretical molecular biology. Life is ordered in space and time: a body is an ordered aggregate of cells; a cell is an ordered aggregate of macromolecules; and a macromolecule is an ordered aggregate of atoms. The building blocks of living matter are highly ordered protein molecules, which also use their precise shapes to catalyse the biochemical reactions that make life dynamic. Proteins are to life sciences what the atom is to physics and chemistry. When physical laws determine how the thousands of atoms of a protein fold from a random coil into a precise three dimensional arrangement, dead matter comes to life. The complex order that is found in proteins is unknown in physics or chemistry; it is as if a motor car assembled itself when all the pieces were joined in a line and shaken about. Using electronic computers it may be possible to mimic nature and calculate how the amino acid sequence determines the folded shape of a protein. Apart from many practical uses, a general solution to the folding problem would be fundamentally important.

Proteins of uniform sequence and stereochemistry can be produced in bacterial cells for use in fundamental studies of polymer morphology. In earlier work, a copolypeptide with repetitive sequence 1, designed to adopt a lamellar architecture upon crystallization, was synthesized using genetic engineering techniques. Solid state studies indicated that the material did not adopt the desired architecture, perhaps because the odd number of amino acids in the repeat unit prevented the formation of the appropriate chain trajectory for chain folding, disrupting the normal hydrogen bond pattern associated with $\beta$-sheets (a key component of the desired chain-folded assembly). It was asserted that this energetic liability would be offset by adding hydrogen-bonding pairs to the bulk structure, by insertion of additional alanylglycine dyads in sequence 1.$$\lbrack\rm (AlaGly)\sb3ProGluGly\rbrack\sb{\rm m}\eqno{\bf 1}$$ To test this premise, solid state analysis of a series of repetitive copolypeptides with increasing numbers of alanylglycine dyads (sequences 2) was accomplished.$$\lbrack\rm (AlaGly)\sb{\rm n}ProGluGly\rbrack\sb{\rm m}\quad n = 3, 4, 5, 6\eqno{\bf 2}$$In a preliminary study, a copolypeptide with repetitive sequence ((AlaGly)$\sb4$ProGluGly) $\sb{14}$ was synthesized. X-ray diffraction and infrared analysis of this material indicated an increase in solid state order over that of polypeptides with sequence 1. Mass analysis of this material using matrix-assisted laser-desorption/ionization (MALDI) mass spectrometry prompted the discovery of sequence errors in the DNA code for the protein. This analysis and the analysis of other chain-length variants of sequence 2 (n = 4, m = 10, 12, 16, and 20) highlighted the utility of the MALDI technique for the assessment of protein sequence, molecular weight and purity. Analysis of proteins with sequence 2 (m = 16, n = 3, 4, 5, 6) using differential scanning calorimetry, infrared spectroscopy, electron microscopy and X-ray diffraction was consistent with an increase in solid-state order with an increase in the number of alanyl-glycine dyads in the repetitive sequence. A model is presented featuring folded chains, which is rationalized on the basis of comparison of the X-ray scattering patterns of the materials with those of poly(L-alanylglycine).