Her2-positiver Brustkrebs, der Subtyp des Mammakarzinoms, bei dem eine Überexpression des epidermalen Wachstumsfaktor-Rezeptors-2 (ErbB2/Her2) vorliegt, hat für die betroffenen Frauen eine besonders schlechte Prognose. Eine positive Korrelation zwischen der ErbB2-Expression in Brusttumoren und der Expression des Makrophagen-Migration-inhibierenden Faktors (MIF), einem inzwischen gut bekannten tumorfördernden Protein, konnte bereits gezeigt werden. Ferner konnte gezeigt werden, dass MIF durch das Hitzeschockprotein 90 (Hsp90) in einem Mausmodell des Her2-positiven Brustkrebses stabilisiert wird. Der zugrundeliegende Mechanismus war bisher unverstanden. In dieser Doktorarbeit konnte erstmalig demonstriert werden, dass Hitzeschockfaktor-1 (HSF-1), der Transkriptionsfaktor der stressinduzierten Hitzeschockproteine (HSP), einschließlich Hsp90, in ErbB2-überexprimierenden SK-BR-3-Brustkrebszellen konstitutiv durch ErbB2 aktiviert wird. Durch eine Behandlung mit dem ErbB2-Inhibitor CP724.714 konnte die aktivierende Serin326-Phosphorylierung von HSF-1 verhindert werden. Als Folge wird, wie durch Western-Blot-Analysen gezeigt, die HSP-Maschinerie inhibiert und tumorfördernde Hsp90-Klienten wie MIF, Akt, mutiertes p53, ErbB2 und HSF-1 destabilisiert. Außerdem konnte die unterbleibende HSF-1-Aktivierung durch quantitative PCR-Analysen und Immunfluoreszenzmikroskopie bestätigt werden. Die mechanistischen Untersuchungen konnten die hier erstmalig beschriebene ErbB2-Akt-HSF-1-Achse aufdecken, über die HSF-1 in SK-BR-3-Zellen reguliert wird. Ferner konnte eine ErbB2-Inhibition sogar die HSF-1-Aktivierung durch einen Hitzeschock unterbinden. Unsere Ergebnisse zeigen zum ersten Mal, dass die ErbB-2-Überexpression in SK-BR-3-Zellen eine konstitutive HSF-1-Aktivierung bewirkt, mit der Folge, dass tumorfördernde Hsp90-Klienten wie MIF, HSF-1 selbst, ErbB2 und mutiertes p53 stabilisiert werden. Die neu entdeckte ErbB2-Akt-HSF-1-Hsp90-Klienten-Achse legt möglicherweise neue Angriffspunkte für zusätzliche Pharmaka bei der Therapie Her2-positiven Brustkrebses offen.

The Horizon Simulation Framework (HSF) is an open-source community driven mod- eling and simulation tool developed over 15 years by a lineage of Cal Poly graduate students. The tool excels in its flexibility to model an assortment of complex systems, with prebuilt modeling elements available for the simulation of space missions. A high-level simulation tool like HSF lends itself to an agile development cycle as system constraints can be quickly identified through day in the life simulation of the modeled system. The objective of the work presented in this thesis is to refactor the way in which several modeling elements are loaded in the simulation framework. A focus is placed on improving how relationships between various modeling elements are initialized to allow the flow of information between distant assets that was previously not possible. Further improvements were made to the framework with the objective of standardizing how information is communicated from user input files to locations in the framework that depend on the inputs. After implementing these updates, a demonstration scenario was created to validate the developments implemented.

Este projeto tem dois objetivos. Primeiramente estudou-se a aplicabilidade dos splines tricúbicos para a construção de superfícies de energia potencial globais. Um dos obstáculos que este método tem de superar e a escolha de um sistema de coordenadas apropriado, que minimize a influência de pontos não físicos. Para isto, propôs-se o uso do sistema de coordenadas de Pekeris, nunca usado para este fim. Este procedimento foi realizado para três sistemas químicos bem descritos na literatura, [Cl,H2], [F,H,D] e [H,O,Cl], cujas superfícies de energia potencial e propriedades das reações foram usadas como referência. Com base nestes modelos, aplicamos o método proposto variando-se a quantidade e a disposição dos nós das interpolações, a fim de verificar sua influência na qualidade das superfícies interpoladas. Os resultados mostram que as superfícies construídas por este método reproduzem muito bem os cálculos de dinâmica química, tanto por métodos quânticos quanto por métodos clássicos. Para isto, os nós da interpolação devem cobrir as regiões mais importantes da superfície de energia potencial e os valores mais baixos das coordenadas de Pekeris devem ser priorizados. O segundo objetivo consiste na aplicação deste procedimento na construção da superfície de energia potencial [H,S,F]. Com esta superfície, diversas características deste sistema foram analisadas, tais como geometrias dos pontos estacionários, energias relativas e frequências vibracionais. Os valores obtidos estão de acordo com os dados descritos na literatura. A superfície construída também foi usada para a realização de cálculos de dinâmica para a reação F+HS → S+FH. Observamos a existência de dois tipos de mecanismos, um com a formação de um intermediário de longa duração e outro com a abstração direta do átomo de hidrogênio. / This project has two goals. First, we studied the applicability of the tricubic splines to construct global potential energy surfaces. One of the diculties this approach has to overcome is the choice of an appropriate coordinate system that minimises the in uence of non-physical points. For such, we proposed the use of the Pekeris coordinate system, never employed for this purpose. This procedure was carried out for three well described systems, [Cl,H2], [F,H,D] and [H,O,Cl], whose potential energy surfaces and reaction properties were taken as references. Based on these models, we applied the proposed method varying the amount and arrangement of the interpolation knots, to verify their influence on the quality of the interpolated surfaces. The results showed that surfaces constructed by this approach reproduce very well the chemical dynamics calculations, both for the quantum as well as for the classical methods, provided that the interpolation knots cover the most important regions of the potential energy surfaces, and the lower values of the Pekeris coordinates are prioritised. The second goal was the application of this procedure to the construction of the [H,S,F] potential energy surface. With this surface, several characteristics of this system were analysed, such as the geometry of the stationary points, relative energies and vibrational frequencies. The values obtained are in agreement with the data described in the literature. The constructed surface was also used for quantum dynamics calculations on the reaction F + HS → S + FH. We observed two kinds of mechanisms, one of them with the formation of a long-living intermediate and the other with the direct abstraction of the hydrogen atom.

Este projeto tem dois objetivos. Primeiramente estudou-se a aplicabilidade dos splines tricúbicos para a construção de superfícies de energia potencial globais. Um dos obstáculos que este método tem de superar e a escolha de um sistema de coordenadas apropriado, que minimize a influência de pontos não físicos. Para isto, propôs-se o uso do sistema de coordenadas de Pekeris, nunca usado para este fim. Este procedimento foi realizado para três sistemas químicos bem descritos na literatura, [Cl,H2], [F,H,D] e [H,O,Cl], cujas superfícies de energia potencial e propriedades das reações foram usadas como referência. Com base nestes modelos, aplicamos o método proposto variando-se a quantidade e a disposição dos nós das interpolações, a fim de verificar sua influência na qualidade das superfícies interpoladas. Os resultados mostram que as superfícies construídas por este método reproduzem muito bem os cálculos de dinâmica química, tanto por métodos quânticos quanto por métodos clássicos. Para isto, os nós da interpolação devem cobrir as regiões mais importantes da superfície de energia potencial e os valores mais baixos das coordenadas de Pekeris devem ser priorizados. O segundo objetivo consiste na aplicação deste procedimento na construção da superfície de energia potencial [H,S,F]. Com esta superfície, diversas características deste sistema foram analisadas, tais como geometrias dos pontos estacionários, energias relativas e frequências vibracionais. Os valores obtidos estão de acordo com os dados descritos na literatura. A superfície construída também foi usada para a realização de cálculos de dinâmica para a reação F+HS → S+FH. Observamos a existência de dois tipos de mecanismos, um com a formação de um intermediário de longa duração e outro com a abstração direta do átomo de hidrogênio. / This project has two goals. First, we studied the applicability of the tricubic splines to construct global potential energy surfaces. One of the diculties this approach has to overcome is the choice of an appropriate coordinate system that minimises the in uence of non-physical points. For such, we proposed the use of the Pekeris coordinate system, never employed for this purpose. This procedure was carried out for three well described systems, [Cl,H2], [F,H,D] and [H,O,Cl], whose potential energy surfaces and reaction properties were taken as references. Based on these models, we applied the proposed method varying the amount and arrangement of the interpolation knots, to verify their influence on the quality of the interpolated surfaces. The results showed that surfaces constructed by this approach reproduce very well the chemical dynamics calculations, both for the quantum as well as for the classical methods, provided that the interpolation knots cover the most important regions of the potential energy surfaces, and the lower values of the Pekeris coordinates are prioritised. The second goal was the application of this procedure to the construction of the [H,S,F] potential energy surface. With this surface, several characteristics of this system were analysed, such as the geometry of the stationary points, relative energies and vibrational frequencies. The values obtained are in agreement with the data described in the literature. The constructed surface was also used for quantum dynamics calculations on the reaction F + HS → S + FH. We observed two kinds of mechanisms, one of them with the formation of a long-living intermediate and the other with the direct abstraction of the hydrogen atom.

Various genes have evolved to protect the cell against stressor-induced damage or death including the heat shock proteins (HSPs). Stressor-induced HSP gene expression involves the activation of heat shock factor (HSF), which binds to the heat shock element (HSE) found in the promoter region of <em>hsp</em> genes. Previously, our laboratory has examined the expression and function of <em>hsp</em> genes in the South African clawed frog, <em>Xenopus laevis</em>. Amphibians are particularly susceptible to adverse environmental conditions, including high temperatures and toxicants. In contrast to the many known inducers of HSF activation in poikilothermic vertebrates, few inhibitors have been either discovered or described in the literature. The present study has compared for the first time the effect of two heat shock response (HSR) inhibitors, quercetin and KNK437, on <em>hsp</em> gene expression in <em>Xenopus</em> A6 cells, demonstrating their efficacy in poikilotherms. Northern blot and densitometric analysis showed that cells treated with either quercetin or KNK437 decreased the heat shock-induced accumulation of <em>hsp70</em>, <em>hsp47</em>, and <em>hsp30</em> mRNAs. Additionally, constitutive levels of <em>hsp47</em> and <em>hsc70</em> mRNAs were reduced. In comparison, neither quercetin nor KNK437 affected the levels of constitutively expressed <em>ef1&alpha;</em> mRNAs under control or heat shock conditions. Western blot and densitometric analysis in this study showed that under heat shock conditions, exposure to quercetin or KNK437 significantly decreased the accumulation of HSP30, and that KNK437 was more effective in doing so than quercetin. In comparison, levels of actin were not significantly affected by either heat shock or exposure to DMSO, quercetin, or KNK437. These findings suggest that one mechanism by which quercetin and KNK437 inhibits the HSR in <em>Xenopus</em> is through the inhibition of HSF activity. <br /><br /> Results of this study also suggest that KNK437 inhibits the acquisition of thermotolerance in poikilotherms, similar to observations in mammalian systems. In the presence of KNK437, cells given a 2 h heat pretreatment at 33ºC followed by a thermal challenge for 1 h at 37ºC, showed numerous ruffled membrane edges and some aggregates of disrupted stress fibers. In comparison, cells directly challenged for 1 h at 37ºC, showed a marked decrease in HSP30, which was located predominantly at the cellular periphery in conjunction with actin aggregates. These cells showed virtually no intact stress fibers spanning cells and no coherent cell-cell connections. A 3-D analysis of cells given a 1 h thermal challenge at 37ºC (after a prior 2 h heat shock at 33ºC) in the absence of KNK437, showed numerous linear actin bundles transversing the entire cell, even extending into areas of cell-cell contact, and abundant HSP30 concentrated in the perinuclear region surrounding an intact nucleus. However, in the presence of KNK437, there was a significant emergence of membrane ruffles indicating global instability of cellular adhesion. This study has demonstrated that KNK437, which is the more specific and efficient HSR inhibitor, will be an important inhibitor to compare with the well-documented quercetin for future investigations.

Various genes have evolved to protect the cell against stressor-induced damage or death including the heat shock proteins (HSPs). Stressor-induced HSP gene expression involves the activation of heat shock factor (HSF), which binds to the heat shock element (HSE) found in the promoter region of <em>hsp</em> genes. Previously, our laboratory has examined the expression and function of <em>hsp</em> genes in the South African clawed frog, <em>Xenopus laevis</em>. Amphibians are particularly susceptible to adverse environmental conditions, including high temperatures and toxicants. In contrast to the many known inducers of HSF activation in poikilothermic vertebrates, few inhibitors have been either discovered or described in the literature. The present study has compared for the first time the effect of two heat shock response (HSR) inhibitors, quercetin and KNK437, on <em>hsp</em> gene expression in <em>Xenopus</em> A6 cells, demonstrating their efficacy in poikilotherms. Northern blot and densitometric analysis showed that cells treated with either quercetin or KNK437 decreased the heat shock-induced accumulation of <em>hsp70</em>, <em>hsp47</em>, and <em>hsp30</em> mRNAs. Additionally, constitutive levels of <em>hsp47</em> and <em>hsc70</em> mRNAs were reduced. In comparison, neither quercetin nor KNK437 affected the levels of constitutively expressed <em>ef1&alpha;</em> mRNAs under control or heat shock conditions. Western blot and densitometric analysis in this study showed that under heat shock conditions, exposure to quercetin or KNK437 significantly decreased the accumulation of HSP30, and that KNK437 was more effective in doing so than quercetin. In comparison, levels of actin were not significantly affected by either heat shock or exposure to DMSO, quercetin, or KNK437. These findings suggest that one mechanism by which quercetin and KNK437 inhibits the HSR in <em>Xenopus</em> is through the inhibition of HSF activity. <br /><br /> Results of this study also suggest that KNK437 inhibits the acquisition of thermotolerance in poikilotherms, similar to observations in mammalian systems. In the presence of KNK437, cells given a 2 h heat pretreatment at 33ºC followed by a thermal challenge for 1 h at 37ºC, showed numerous ruffled membrane edges and some aggregates of disrupted stress fibers. In comparison, cells directly challenged for 1 h at 37ºC, showed a marked decrease in HSP30, which was located predominantly at the cellular periphery in conjunction with actin aggregates. These cells showed virtually no intact stress fibers spanning cells and no coherent cell-cell connections. A 3-D analysis of cells given a 1 h thermal challenge at 37ºC (after a prior 2 h heat shock at 33ºC) in the absence of KNK437, showed numerous linear actin bundles transversing the entire cell, even extending into areas of cell-cell contact, and abundant HSP30 concentrated in the perinuclear region surrounding an intact nucleus. However, in the presence of KNK437, there was a significant emergence of membrane ruffles indicating global instability of cellular adhesion. This study has demonstrated that KNK437, which is the more specific and efficient HSR inhibitor, will be an important inhibitor to compare with the well-documented quercetin for future investigations.

Heat shock proteins (hsp) and heat shock transcription factors (HSF) have important roles in the development of the eye lens. Our lab previously demonstrated that knockdown of hsp70 gene expression using morpholino antisense technology (MO) resulted in a small lens phenotype in zebrafish (Danio rerio) embryos. A less severe phenotype was seen with knockdown of hsf1, suggesting other factors that regulate hsp70 are involved during lens formation. Both HSF1 and HSF4 are known to play a role in mammalian lens development. An expressed sequence tag encoding zebrafish HSF4, named hsf4a, has been identified and a second splice variant, hsf4b, has been predicted in the Ensembl database. The objectives of this thesis were to characterize the zebrafish HSF4 and compare its expression to other HSFs as well as investigate its role in lens development. Analysis of zebrafish HSF4 sequence was performed using standard in silico analytical software. The deduced amino acid sequence of HSF4a shares structural similarities with mammalian HSF4 including the lack of an HR-C domain. This domain is absent due to a C-terminal truncation within zebrafish HSF4a relative to the mammalian protein. HSF4b is identical to the HSF4a sequence with the exception of an additional 155 amino acids at the carboxyl end of the protein which contains an HR-C domain, unlike mammalian HSF4. Surprisingly, electrophoretic mobility shift assays (EMSA) demonstrated that the binding affinity of zebrafish HSF4 to discontinuous HSEs is more similar to HSF1 than to other HSF4 proteins. The amino acid sequence of zebrafish HSF4 DNA binding domain was also more similar to HSF1 than other HSF4 proteins. These results, along with a phylogenetic analysis of HSF proteins from eleven species, suggest that HSF1 was an evolutionary precursor of HSF4 and that functions of this protein may differ between zebrafish and mammals. The expression level for each of the three zebrafish HSFs was determined in adult tissues and in developing embryos by quantitative reverse transcription polymerase chain reaction (qPCR) analysis. Expression of both hsf4 transcripts was observed predominantly in the eye but only observed in developing embryonic tissue at 60 hours post fertilization or later. This, together with the lack of an observable phenotype following MO knockdown of hsf4, suggests that HSF4 likely has a role in later stages of lens development. Additionally, hsf1 and hsf2 expression were detected in all tissues and in all stages of development as well as being present as maternal transcripts in zebrafish eggs. The results presented in this thesis demonstrate that while zebrafish HSFs share some similarity with HSF proteins from other species, they also have structural characteristics and expression patterns unique to the zebrafish.

Model-Based Systems Engineering in industry has been constantly increasing its presence within the aerospace industry. SysML is one such MBSE tool that shows complex system organization and relationships. The Horizon Simulation Framework is another MBSE tool, created by Cal Poly students, that gives users the ability to run “day-in-the-life” simulations of systems. Finding a way to link these two tools could allow systems engineers to reap the benefits of both. This thesis investigates the background and design process involved with developing the code that can convert an output file generated in SysML, into a format specifically made for the Horizon Simulation Framework. The goal was to create an interface that can allow users to model a system in SysML, and analyze the model and verify system requirements using HSF. Another goal was to expand the capabilities of the Horizon Simulation Framework by designing and develop a module that would allow users to define and analyze system-level requirements. To evaluate the effectiveness of both codes, the Aeolus example case was used. A SysML model of the system was created as the product of another thesis; SysML based CubeSat Model Design and Integration with the Horizon Simulation Framework. The Aeolus SysML model was converted and used as input in an HSF simulation. The SysML model simulation data was compared against those of the original test case. To test the requirement module, system level requirements were formulated within the Aeolus system and run in simulation, providing an analysis of the results. The results of the analysis confirmed a successful conversion of the SysML model into an equivalent HSF model and a successful analysis of system-level requirements.

This thesis examines the feasibility of substituting the system input script of Cal Poly’s Horizon Simulation Framework (HSF) with a Model Based Systems Engineering (MBSE) model designed with the Systems Modeling Language (SysML). A concurrent student project, SysML Output Interface Creation for the Horizon Simulation Framework, focused on design of the HSF Translator Plugin which converts SysML models to an HSF specific XML format. A SysML model of the HSF test case, Aeolus, was designed. The original Aeolus HSF input script and the translated SysML input script retained the format and dependency structure required by HSF. Both input scripts returned identical results and thus validated the feasibility of linking SysML with HSF through the HSF Translator Plugin. A second SysML model of the Cal Poly CubeSat mission, ExoCube, was also designed and converted into an HSF input script. The ExoCube input script also retained the format and dependency structure required by HSF. This demonstrated that future SysML models can be used in conjunction with the HSF Translator Plugin to create a functional HSF system input script.

No description available.