The expansion of gene-specific trinucleotide repeats is responsible for a growing list of human disorders, including myotonic dystrophy type 1 (DM1). Repeat instability for most of these disorders, including DM1, is characterized by complex patterns of inherited and ongoing tissue-specific instability and pathogenesis. While the mechanistic basis behind the unique locus-specific instability of trinucleotide repeats is currently unknown, DNA metabolic processes are likely to play a role. My thesis involves investigating the contribution of DNA replication to the trinucleotide instability of myotonic dystrophy type 1. Herein I have designed an in vivo primate model system, based on the SV40 replication system, to assess the contribution of DNA replication to DM1 repeat instability. This system allows the assessment, under controlled conditions, and manipulation of variables that may affect replication-associated repeat instability, under a primate cellular system. Using the SV40 model system, I not only confirmed previous observations that repeat length and replication direction affect repeat instability, but also for the first time determined that the location of the replication origin relative to the repeat tract plays an important role in repeat instability. This novel observation allowed for the development of a fork-shift model of repeat instability, in which cis-elements adjacent to the repeat tract affect replication, in turn altering the propensity for repeat instability. To further my study of DNA replication in DM1 repeat instability, I have mapped the origin of replication adjacent to the DM1 locus in human patient cells and the tissues of DM1 transgenic mice actively undergoing repeat instability. The position of the replication origins adjacent to the repeat tract at the DM1 locus places several known cis-elements, including CTCF binding sites, in a position to alter replication as predicted by the fork-shift model. My analysis of the CTCF sites showed them capable of altering replication and repeat instability at the DM1 locus. Taken together these results suggest that the placement of replication origins, repeat tracts and cis-elements, may mark trinucleotide repeat tracts, such as the DM1, for locus-, tissue- and development-specific replication-associated repeat instability.

The tumour suppressor p53-binding protein 1 (53BP1) is phosphorylated following DNA double strand breaks (DSBs); however, little is understood about the upstream signaling pathways that control this phosphorylation. Additionally, it is not known how these processes combine with 53BP1 to control the survival of cells following DNA damage such as that imparted by ionizing radiation (IR), which is the basis of radiotherapy. In this thesis, I have shown that 53BP1 is phosphorylated specifically in S-phase cells, but not relocalized to intranuclear foci, in response to severe oxygen stress. This occurs with only partial dependence on the ATM kinase (Chapter 2). Following IR, I find that both ATM and DNA-PKcs contribute to intranuclear phosphorylated 53BP1 foci, but that this phosphorylation is independent of proximal signaling molecules that control the localization of 53BP1 to initial DSBs (Chapter 3). Furthermore, I show that 53BP1 loss confers sensitivity to IR and this can be further augmented by inhibition of ATM and DNA-PKcs kinases suggesting that there are both 53BP1-dependent and -independent pathways of survival from IR (Chapter 4). These findings may have important implications for molecular pathology and personalized medicine as 53BP1 has recently been found to be activated or lost in subsets of human tumours. I have collaborated to initiate the development of a novel system to interrogate the implications of 53BP1 loss as traditional siRNA approaches in human cancer cells were not feasible (Chapter 5 and Appendix 2). This system can be used in vivo as tumour xenografts to further understand how 53BP1 and the tumour microenvironment interact endogenously and in response to IR. I also present the possibility and proof of concept for the use of 53BP1 as a biomarker in primary human prostate cancer tissue where little is known about 53BP1 biology (Chapter 5).

Ovarian cancer (OCa) remains the leading cause of death due to a gynecologic malignancy in North American women, and the pathogenesis of this disease is a consequence of the interplay between DNA, RNA and proteins. The genomes of these cancers are characterized by numerical and structural aberrations, resulting in copy number changes of the affected regions. The serine protease, Kallikrein 6 (KLK6), is a promising biomarker and is over-expressed in OCa. However, the mechanisms leading to the observed KLK6 overexpression are poorly understood; and to date, no study examining the chromosomal contributions to the overexpression have been conducted. Utilization of multi-colour Fluorescence in situ Hybridization (FISH)-based technologies to untreated primary serous OCa samples and cancer cell lines, showed that the KLK locus, on 19q13.3/4, is involved in both numerical and structural aberrations; was subject to high-level copy-number heterogeneity (p<0.001); and structural rearrangements of 19q were significantly co-related to grade (p<0.001). Patients with a loss of the KLK locus, or no structural rearrangement on 19q, experienced a trend towards longer disease free survival (DFS and better overall survival (OS), over those with a gain or amplification, or with breakage events on 19q. KLK6-specific immunohistochemistry (IHC) showed weak correlation with KLK6 copy-number, suggesting other mechanisms together with copy-number, drives its over-expression. Among these mechanisms are microRNA (miRNAs), also shown to be affected by the copynumber changes in OCas. Therefore, we investigated the role of miRNAs in OCa and their role in KLK6 regulation. Specifically, we examined the copy-number status and miRNA expression in a representative OCa cell line, OVCAR-3. miRNA expression profiling of OCa cell lines and primary tumours showed their differential expression, including the decrease in expression of the let-7 family members, which are predicted to target KLK6. Indeed, when hsa-let-7a was transiently transfected into OVCAR-3, a reduction of secreted KLK6 protein was detected. Thus, the contribution of numerical and structural aberrations of the OCa genome can directly affect the expression KLK6 through copy-number, but is also aided post-transcriptionally by miRNAs.

In this study, vibrational properties and stability of delta-Scuti like pulsating pre-main sequence stars have been investigated. Studies were held in the mass range 2-4 Mo and limited to radial linear adiabatic pulsations. Numerical computations were performed by the oscillation program written by Kirbiyik &amp / Al-Murad (1993). The models were selected to be at the latest phases of the pre-main sequence evolution where the luminosity starts to increase. We have limited our calculations upto the end of the radiative inner regions, since at the surface of the star, our adiabatic perturbation computation does not perfectly fit to the relatively thin non-adiabatic convective envelope of the star. The results of the stability analysis showed that the PMS models undergo an instability whose time period is a function of mass. Instability Strip of pulsating PMS stars was re-drawn with comparison to M. Marconi &amp / F.Palla (1998). The effect of gravitational contraction on stability was also investigated.

In this study, experimental investigation of solid propellant combustion instability using an end burning T-Burner setup is performed. For this purpose, a T-Burner setup is designed, analyzed, constructed and tested with all its sub components. T-Burner setup constructed is mainly composed of a base part, a control panel and the T-Burner itself. Combustion chamber, pressure stabilization mechanism, pressurization system, measurement instruments and data acquisition systems form the T-Burner. Pressure stabilization mechanism is utilized in two different alternatives, first of which is by the use of nitrogen gas and a small surge tank with a cavitating venturi. This is a brand new approach for this kind of system. The second alternative is the use of a choked nozzle for pressure stabilization. Resonance frequencies of the system with the two different pressure stabilization mechanisms are experimentally evaluated. Helmholtz frequency of the T-burner constructed is calculated and no Helmholtz instability is observed in the system. Constructed T-Burner setup is operated for a specific solid propellant. System worked successfully and pressure data are obtained. Pressure data revealed oscillatory behaviour. Decay and growth rates of pressure oscillations are used for the calculation of pressure response of the propellant tested. By the use of this T-Burner comparison of the behavior of different propellants can be performed. It can be used as a test device for measuring quantitatively the response of a burning propellant to unsteady motions.

Chromosomal rearrangements play a major role in the evolution of eukaryotic genomes. Genomic aberrations are also a hallmark of many tumors and are associated with a number of hereditary diseases in humans. The presence of repetitive sequences that can adopt non-canonical DNA structures is one of the factors which can predispose chromosomal regions where they reside to instability. Palindromic sequences (inverted repeats with or without a unique sequence between them) that can adopt hairpin or cruciform structures are frequently found in regions that are prone for gross chromosomal rearrangements (GCRs) in somatic and germ cells in different organisms. Direct physical evidence was obtained that double-strand breaks (DSBs) occur at the location of long inverted repeats, a triggering event for the genomic instability. However, the mechanisms by which palindromic sequences lead to chromosomal fragility are largely unknown. The overall goal of this research is to elucidate the mechanisms of DSB and GCR generation by palindromic sequences in yeast, Saccharomyces cerevisiae.

A new approach was developed to determine the operational stability margin of a laboratory scale combustor. Applying modern and robust techniques and tools from Dynamical System Theory, the approach was based on three basic steps. In the first step, a gray-box thermoacoustical model for the combustor was derived. The second step consisted in applying System Identification techniques to experimental data in order to validate the model and estimate its parameters. The application of these techniques to experimental data under different operating conditions allowed us to determine the functional dependence of the model parameters upon changes in an experimental control parameter. Finally, the third step consisted in using that functional dependence to predict the response of the system at different operating conditions and, ultimately, estimate its operational stability margin. The results indicated that a low-order stochastic non-linear model, including two excited modes, has been identified and the combustor operational stability margin could be estimated by applying a continuation method.

The evolution of column instabilities that lead to break up of a microscale liquid jet is studied experimentally using shadowgraph technique. The jet formation is investigated over a range of Reynolds number, Pressure Ratio, and Ohnesorge number which are varied by the driving pressure, observation chamber pressure, and the jet liquid. Over the range of these parameters, the jet experiences different break up mechanisms as a result of different dominant instabilities. The present investigation discusses both break up mechanisms that are similar to the break up of macroscale jets and some new microscale break up phenomena.

Excessive vibrations continue to be a major hurdle in improving machining efficiency and achieving stable high speed cutting. To overcome detrimental vibrations, an enhanced understanding of the underlying nonlinear dynamics is required. Cutting instability is commonly studied through modeling and analysis which incorporates linearization that obscures the true nonlinear characteristics of the system which are prominent at high speeds. Thus to enhance cutting dynamics knowledge, a comprehensive nonlinear turning model that includes tool-workpiece interaction is experimentally validated using a commercial laser vibrometer to capture tool and workpiece vibrations. A procedure is developed to use instantaneous frequency for experimental time-frequency analysis and is shown to thoroughly characterize the underlying dynamics and identify chatter. For the tests performed, chatter is associated with changing spectral components and bifurcations which provides a view of the underlying dynamics not experimentally observed before. Validation of the turning model revealed that the underlying dynamics observed experimentally are accurately captured, and the coupled tool-workpiece chatter vibrations are simulated. The stability diagram shows an increase in the chatter-free limit as the spindle speed increases until 1500rpm where it begins to level out. At high speeds the workpiece dominates the dynamics, and excessive workpiece vibrations create another stability limit to consider. Thus, workpiece dynamics should not be neglected in analyses for the design of machine tools and robust control laws. The chip formation mechanisms and high speeds make micro-milling highly non-linear and capable of producing broadband frequencies that negatively affect the tool. A nonlinear dynamic micro-milling model is developed to study the effect of parameters on tool performance through spectral analysis using instantaneous frequency. A lumped mass-spring-damper system is assumed for modeling the tool, and a slip-line force mechanism is adopted. The effective rake angle, helical angle, and instantaneous chip thickness are accounted for. The model produced the high frequency force components seen experimentally in literature. It is found that increasing the helical angle decreased the forces, and an increase in system stiffness improved the dynamic response. Also, dynamic instability had the largest effect on tool performance with the spindle speed being the most critical parameter.

[Truncated abstract] Advanced laser interferometer gravitational wave detectors require an extremely high optical power in order to improve the coupling between the gravitational wave signal and the optical field. This high power requirement leads to new physical phenomena arising from nonlinear interactions associated with radiation pressure. In particular, detectors with multi-kilometer-long arm cavities containing high density optical fields suffer the possibility of 3-mode opto-acoustic interactions. This involves the process where ultrasonic vibrations of the test mass cause the steady state optical modes to scatter. These 3-mode interactions induce transverse optical modes in the arm cavities, which then can provide positive feedback to the acoustic vibrations in the test masses. This may result in the exponential growth of many acoustic mode amplitudes, known as Parametric Instability (PI). This thesis describes research on 3-mode opto-acoustic interactions in advanced interferometric gravitational wave detectors through numerical investigations of these interactions for various interferometer configurations. Detailed analysis reveals the properties of opto-acoustic interactions, and their dependence on the interferometer configuration. This thesis is designed to provide a pathway towards a tool for the analysis of the parametric instabilities in the next generation interferometers. Possible techniques which could be helpful in the design of control schemes to mitigate this undesirable phenomenon are also discussed. The first predictions of parametric instability considered only single interactions involving one transverse mode and one acoustic mode in a simple optical cavity. ... In Chapter 6, I was able to make use of a new analytical model due to Strigin et al., which describes parametric instability in dual recycling interferometers. To make the solution tractable, it was necessary to consider two extreme cases. In the worst case, recycling cavities are assumed to be resonant for all transverse modes, whereas in the best cases, both recycling cavities are anti-resonant for the transverse modes. Results show that, for the worst case, parametric gain values as high as ~1000 can be expected, while in the best case the gain can be as low as ~ 3. The gain is shown to be very sensitive to the precise conditions of the interferometer, emphasising the importance of understanding the behaviour of the detectors when the cavity locking deviates from ideal conditions. Chapter 7 of this thesis contains work on the observation of 3-mode interactions in an optical cavity at Gingin, which confirms the analysis presented here, and also a paper which shows how the problem of 3-mode interactions can be harnessed to create new devices called opto-acoustic parametric amplifiers. In the conclusions in Chapter 8, I discuss the next important steps in understanding parametric interactions in real interferometers – including the need for more automated codes relevant to the design requirements for recycling cavities. In particular, it is pointed out how the modal structure of power and signal recycling cavities must be understood in detail, including the Gouy phase for each transverse mode, to be able to obtain precise predictions of parametric gain. This thesis is organised as a series of papers which are published or have been submitted for publication. Such writing style fills the condition for Ph.D. thesis at the University of Western Australia.