In this dissertation we describe a coordinate scaling technique for the numerical approximation of solutions to certain problems posed on unbounded domains in two and three dimensions. This technique amounts to introducing variable coefficients into the problem, which results in defining a solution coinciding with the solution to the original problem inside a bounded domain of interest and rapidly decaying outside of it. The decay of the solution to the modified problem allows us to truncate the problem to a bounded domain and subsequently solve the finite element approximation problem on a finite domain. The particular problems that we consider are exterior problems for the Laplace equation and the time-harmonic acoustic and elastic wave scattering problems. We introduce a real scaling change of variables for the Laplace equation and experimentally compare its performance to the performance of the existing alternative approaches for the numerical approximation of this problem. Proceeding from the real scaling transformation, we introduce a version of the perfectly matched layer (PML) absorbing boundary as a complex coordinate shift and apply it to the exterior Helmholtz (acoustic scattering) equation. We outline the analysis of the continuous PML problem, discuss the implementation of a numerical method for its approximation and present computational results illustrating its efficiency. We then discuss in detail the analysis of the elastic wave PML problem and its numerical discretiazation. We show that the continuous problem is well-posed for sufficiently large truncation domain, and the discrete problem is well-posed on the truncated domain for a sufficiently small PML damping parameter. We discuss ways of avoiding the latter restriction. Finally, we consider a new non-spherical scaling for the Laplace and Helmholtz equation. We present computational results with such scalings and conduct numerical experiments coupling real scaling with PML as means to increase the efficiency of the PML techniques, even if the damping parameters are small.

In response to viral infection, host cells activate various antiviral defence mechanisms to inhibit virus replication. Therefore in order for a virus to replicate efficiently, it must counteract cellular antiviral defence. Promyelocytic leukemia protein (PML) is a cellular protein involved in intrinsic immunity. It inherently forms nuclear bodies (PML-NBs) that assemble at the site of viral genomes. Proteins related to epigenetic regulation are recruited to PML-NBs, and silence viral gene transcription. This study focuses on the role of two herpes simplex virus type 2 (HSV-2) proteins, ICP0 and Us3, in disrupting PML-NBs and counteracting cellular antiviral defence. En passant mutagenesis was used to create recombinant HSV-2 viruses lacking ICP0, Us3, or both ICP0 and Us3. Growth analysis of these recombinants indicates no growth defects for the ICP0Δ virus, while the Us3Δ virus grows to one log lower titres than wild type virus (WT). By contrast, the ICP0Δ virus displays a delay in PML-NB disruption, but the Us3Δ virus is as efficient as WT. However, Us3 is still important for PML-NB disruption, since the ICP0Δ/Us3Δ double mutant exhibits a greater delay than the ICP0Δ single mutant. Although PML is a mediator of the interferon (IFN) response and it was predicted that ICP0 and Us3 interfere with the IFN response through disruption of PML-NBs, my results show that only some HSV-2 Us3Δ clones are hypersensitive to the effects IFN, and others are resistant. Us3 affects more than one cellular pathway, and those cellular pathways are affected by more than one viral protein. I conclude that the activities of multiple viral proteins create a fine balance between activating cellular pathways to promote virus replication, and inhibiting cellular antiviral defence. / Thesis (Master, Microbiology & Immunology) -- Queen's University, 2014-01-23 10:55:16.715

PML is involved in many cellular processes. It organizes nuclear structures PML nuclear bodies (PML NBs) and it associates with nucleolus in response to ribosomal stress to form PML nucleolar associations (PNAs). The function of PNAs is unclear. To elucidate this question, one can attempt to identify proteins interacting with PML at nucleolus. The common method is co- immunoprecipitation, however, this approach cannot be used for PML due to its low solubility. To defeat this, an alternative way of proximity-dependent biotin labelling could be used. The goal of this work was to explore a suitability of biotin labelling for identification of PML nucleolar partners. For this purpose I prepared constructs of wild type or mutated PML with GFP and biotin ligase for transient and stable expression and analysed their propensity to form PML NBs and doxorubicin-induced PNAs, and biotinylate their vicinity. In transient expression, both fusion proteins formed PML NBs and only wild type but not mutated PML IV formed PNAs after doxorubicin treatment with preserved biotinylation capability. In stable expression of fusion proteins in cells with PML knockout the number and composition of PML NBs was aberrant and no PNAs were observed. However, this system was utilized for optimization of solubilisation of biotinylated...

TRF1, telomeric-repeat binding factor 1, is a component of the six-subunit protein complex, referred to as shelterin, which is essential for not only regulating telomere length maintenance but also protecting mammalian telomeres from being recognized as damaged DNA. TRF1 acts as a negative mediator of telomerase-dependent telomere elongation in telomerase-expressing cells, whereas it promotes alternative lengthening of telomeres (ALT) activity by regulating ALT features including the production of extrachromosomal telomere-repeat (ECTR) DNA such as C-circles, and ALT-associated promyelocytic leukemia bodies, or APBs. The activity of TRF1 is tightly regulated by post-translational modification such as phosphorylation. This thesis sets out to investigate the function of TRF1 phosphorylation on threonine-271 (T271) and threonine-371 in telomere maintenance. The results presented in this thesis demonstrate that TRF1 phosphorylation on T271 positively regulates the association of TRF1 to telomeric DNA in telomerase expressing cells. In ALT cells, TRF1 phosphorylation on both T271 and T371 is shown to be important for the formation of APBs. Furthermore, the work presented here suggests that transcription-associated DNA damage mediates the association of phosphorylated (pT371)TRF1 with APBs. / Thesis / Master of Science (MSc) / TRF1, telomeric-repeat binding factor 1, is a component of the shelterin complex, which is essential for regulating telomere length maintenance and protecting mammalian telomeres from being recognized as damaged DNA. TRF1 acts as a negative mediator of telomerase-dependent telomere elongation in telomerase-expressing cells, whereas it promotes alternative lengthening of telomeres. The activity of TRF1 is tightly regulated by phosphorylation. This thesis sets out to investigate the function of TRF1 phosphorylation on threonine-271 and threonine-371 in telomere maintenance. Understanding how post-translational modifications on TRF1 may be linked to telomere homeostasis will be crucial for our understanding in cancer cell biology.

No description available.

<p>Optical waveguide is a very important component in numerous optical structures, devices and photonic circuits. With the rapid development of fabrication technologies, increasing integrated complexity and different materials characteristics, there is higher demand on high-index contrast waveguide with arbitrary cross section and anisotropic material, which indicates the need to develop an efficient, high-performance mode solver to analyze optical waveguides to reduce the fabrication cycle and total cost. Modeling and simulation methods, including Finite Difference Time-Domain (FDTD) method, Finite Element Method (FEM), Beam Propagating Method (BPM), Mode Matching Method (MMM) and Couple Mode Theory (CMT), etc, have been popular for years. Among those methods, FEM is a good and efficient method, especially for its superiority on arbitrary meshes.</p> <p>In this thesis, both scalar and vectorial FEM mode solvers are implemented with an emphasis on dealing with the radiation and evanescent modes by enclosing the whole region with the Perfect Matched Layer (PML) and Perfect Reflecting Boundary (PRB). Thus, the unbounded and continuous radiation modes together with evanescent modes are replaced by what we called "complex modes", but still keeping the completeness and orthogonality properties.</p> / Master of Applied Science (MASc)

PML et les corps nucléaires (CN) sont impliqués dans la défense antivirale. En effet, notre équipe a montré que la surexpression de PMLIII confère la résistance au virus de la stomatite vésiculaire, au virus de l'influenza, au virus foamy mais pas au virus de l’encéphalomyocardite (EMCV). J’ai montré dans mon travail de thèse que l’EMCV contrecarre le pouvoir antiviral de PMLIII en induisant sa dégradation par un processus dépendant du protéasome et de SUMO. Cependant, les cellules de souris invalidées pour PML sont plus sensibles à l’infection par l’EMCV que les cellules issues de souris parentales. Pour déterminer l’isoforme de PML responsable de cet effet antiviral, j’ai analysé l’effet des sept isoformes de PML (PMLI-VII) et j’ai montré que seule l’expression en stable de PMLIV confère la résistance à l’EMCV en séquestrant la polymérase virale 3Dpol au sein des CN PML. De plus la déplétion de PMLIV augmente la production de l’EMCV dans les cellules traitées par l’interféron. Ces données indiquent le mécanisme par lequel PML confère la résistance à l’EMCV et révèlent que PML est l’une des protéines médiatrices des effets anti-EMCV de l’interféron. / PML and nuclear bodies (NBs) are implicated in antiviral defense. Indeed, our team showed that overexpression of PMLIII confers resistance to vesicular stomatitis virus, influenza virus, foamy virus but not to encephalomyocarditis virus (EMCV). I have shown during my thesis that EMCV counteracts the antiviral effect of PMLIII by inducing its degradation in SUMO and proteasome-dependent way. However, cells derived from PML knockout mice are more susceptible to EMCV infection than wild-type cells. To determine the isoforme of PML implicated in this antiviral effect, I analysed the effect of the seven PML isoforms (PMLI-PMLVII) and I showed that only stable expression of PMLIV confers resistance to EMCV by sequestring the viral polymérase 3Dpol in PML Nbs. In addition, depletion of PMLIV boosted EMCV production in interferon-treated cells. These finding sindicate the mechanism by which PML confers resistance to EMCV and reveal a new pathway mediating the antiviral activity of interferon against EMCV.

Submitted by MARCIA ROVADOSCHI (marciar@unifra.br) on 2018-08-17T19:27:03Z No. of bitstreams: 2 license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Dissertacao_ShayenneSchefferHomrich.pdf: 1706469 bytes, checksum: 48ab5f162c893018778d1ac573ca031d (MD5) / Made available in DSpace on 2018-08-17T19:27:03Z (GMT). No. of bitstreams: 2 license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Dissertacao_ShayenneSchefferHomrich.pdf: 1706469 bytes, checksum: 48ab5f162c893018778d1ac573ca031d (MD5) Previous issue date: 2017-03-28 / The Acute Promyelocytic Leukemia (APL), firstly described in 1957, is the most malignant type of acute leukemia. Currently, the knowledge of its pathophysiological mechanism at molecular levels became possible the development of efficient therapies making APL the most curable leukemia type. In this sense, APL is also used as a model on cancer advances, being the molecular treatment performed with all trans-retinoic acid (ATRA) that presents high efficiency at its control. However, several patients develop differentiation syndrome, as a side effect of this drug. In these terms, compared to another drugs, the cytotoxic antineoplastic agents present particular problems, as poor specificity, high toxicity and resistance susceptibility. An alternative strategy to decrease the ATRA cytotoxicity is the incorporation of this drug in polymer nanocapsules with oily core. In this work nanocapsules with lipid core containing ATRA (NA) were evaluated as their potential to inhibit cellular grow, to induce apoptosis, to interfere the cell cycle, and at APL cellular differentiation using NB4 cell line. Results showed that NA was able to overcome the cellular resistance to AL treatment, decreasing cell viability, inducing apoptosis, through BAX/BCL-2 gene expression, cell cycle arresting at G1 phase and cellular differentiation under 1.5 and 2.0 μM. Additionally, theses systems can contribute to increase the efficacy and reduce the toxicity due to the potential accumulation of nanoparticles at the tumor region due to increased vascular permeability of tumor vases. The ATRA incorporation in lipid nanocarriers is a interesting alternative to make possible its intravenous administration. Moreover, these systems present potential to drug accumulation at tumor tissue through a passive targeting called effect of permeability and increased retention. / A Leucemia Promielocítica Aguda (LPA), primeiramente descrita em 1957 é a forma mais maligna de leucemia aguda. Atualmente, o conhecimento dos seus mecanismos fisiopatológicos em nível molecular possibilitou o desenvolvimento de terapias eficazes fazendo com que a LPA seja a forma mais curável de leucemia. Por este motivo a LPA é também utilizada como modelo para os avanços no tratamento do câncer, sendo o tratamento molecular com ácido all-trans-retinoico (ATRA) o que apresenta alta eficiência no seu controle. Entretanto, inúmeros pacientes adquirem a Síndrome de Diferenciação, como efeito adverso a este medicamento. Diante disto, em comparação com outros fármacos, os antineoplásicos citotóxicos apresentam problemas únicos, como pobre especificidade, elevada toxicidade e susceptibilidade para induzir resistência. Uma estratégia para diminuir a citotoxicidade do ATRA é a incorporação do mesmo em nanocápsulas poliméricas com núcleo oleoso. Neste trabalho nanocápsulas de núcleo lipídico contendo ATRA (NA) foram avaliadas quanto ao seu potencial de inibir o crescimento, induzir a apoptose e interferir com o ciclo celular e na diferenciação de células de LPA, linhagem NB4. Os resultados demonstraram que a NA foi capaz de superar a resistência celular ao tratamento com AL, reduzindo a viabilidade celular, induzindo apoptose, pela expressão dos genes BAX/BCL-2, parada do ciclo celular em G1 e diferenciação celular nas concentrações de 1,5 e 2,0 μM. Adicionalmente, estes sistemas podem contribuir para o aumento da eficácia e redução da toxicidade devido ao potencial para acúmulo das nanopartículas na região tumoral graças à permeabilidade vascular aumentada dos vasos tumorais. A incorporação de ATRA em nanocarreadores lipídicos constitui uma alternativa interessante para viabilizar sua administração intravenosa. Além disso, estes sistemas apresentam potencial para acúmulo do fármaco na região tumoral, por meio de um direcionamento passivo chamado de efeito de permeabilidade e retenção aumentada.

The promyelocytic leukemia protein (PML) is a tumour suppressor. It has been reported that PML interaction with the p53 protein is involved in the activation of cell cycle checkpoints and, when persistent, may lead to the premature onset of cellular senescence. Cellular senescence is a state of permanent cell growth arrest that is associated with characteristic morphological and metabolic changes and persistent DNA damage signalling. Importantly, PML nuclear bodies coassociate with persistent DNA damage foci in senescent cells; however, the role of this interaction is still obscure. My goal was to characterize the role of PML in DNA damage response (DDR) and the induction of premature cellular senescence after genotoxic stress, namely X-radiation, using both siRNA-mediated PML knock down (PML KD) and complete PML knock out (PML KO) in human cells. The dynamics of DNA damage foci, levels of various proteins involved in DDR, and proliferation rate were measured in both PML KD and KO cells. No significant changes in the formation of DNA damage foci, activated DDR (p53 and Chk2), activated p21CIP1/WAF1 cyclin-dependent kinase inhibitor, senescent morphology, and SA-β-galactosidase activity in PML KO cells were observed. However, PML KO cells displayed higher levels of retinoblastoma protein (Rb) and...

Promyelocytic leukemia protein (PML) is a tumour suppressor which is frequently downregulated in human tumours. PML plays a role in many cellular processes including DNA damage response, senescence and apoptosis and is mainly localized in special structures called PML nuclear bodies (PML NBs). The nucleolus is a key nuclear compartment, where transcription of ribosomal DNA and biogenesis of ribosomes take place. The nucleolus is also called a stress sensor because of its role, for instance, in stabilization of tumour suppressor p53. Localization of PML to the nucleolar periphery appears to be prominent after disturbance of nucleolar functions - for example inhibition of rRNA transcription or processing. Thus the relationship between the nucleolus and PML nuclear bodies may be important for cellular response to stress. However, the role of PML nucleolar associations in nucleolar function including mechanism of formation of these structures remain unclear. Here we characterised PML nucleolar structures and mechanism of their formation. We showed that formation of PML nucleolar structures is not caused by replication stress, is not dependent on any specific phase of cell cycle and is not caused by DNA damage response but is induced by topological stress due to inhibition of toposiomerase function....