Dissertations / Theses on the topic '2D gel'

This thesis is composed of three separate projects: 1. Proteomics is the study of complex protein mixtures found in a cell, organ, or entire organism. The vast concentration range of these samples, estimated at approximately 150,000-fold for simple unicellular eukaryotes is beyond current detection methods. We present a technology called Structured Illumination (SI) Gel Imager that employs an LCD projector to selectively illuminate fluorescently labeled proteins separated into individual protein spots on 2-dimensional electrophoresis (2DE) gels. SI Gel Imager images have a dynamic range of approximately 1,000,000-fold, making it a valuable tool for proteomic detection. 2. 2DE gels possess the ability to separate proteins with extremely high resolution of molecular-weight and isoelectric-point. However, they suffer from variable sample loss incurred during protein reduction and alkylation steps required for subsequent sequencing by mass-spectrometry, up to about 30% of the starting sample. We present a protein equilibration method utilizing agarose stacking gels to reduce experiment variability and sample loss. 3. 2DE-based proteomics is a time-consuming process, requiring up to 3 days, and suffers from low reproducibility. To provide undergraduates to the experience of conducting proteomics research, we developed the Proteomics Platoon approach, where a group of undergraduate students work in two-person teams to perform proteomic experiments using a wide variety of biological samples. The close-knit nature of the Platoon further fosters collaboration, communication and mentorship while completing complex scientific projects. The Platoon approach serves as a model for involving undergraduates in complex research projects.

2',3'-Cyclic nucleotide 3 '-phosphodiesterase (CNP) is an early marker for oligodendrocytes, and it is suspected to be implicated in the expansion of membranes during myelination. We have previously generated transgenic mice that overexpress CNP. These mice showed altered oligodendroyte development, produced aberrant myelination, and had less MBP accumulated in myelin. More interestingly, ODCs isolated from those mice had a tremendous increase in the process extension formation. The purpose of the present study is to compare the protein expression pattern in the myelin isolated from control and CNP overexpressing mice (L191), using two-dimensional gel electrophoresis. We found that CNP overexpression increases HSC70, and HSP70, and decreases MAG expression in myelin. We also found that the mRNA for MAG, in L191 brain was identical to control brain during all stages of development. These findings suggest that CNP may be implicated with HSC70 in vesicular transport, and this may explain the mechanism of process extension mediated by CNP.

Post-genomic biomedical science requires quantitative proteomics. In most cases this involves differential protein expression analysis using matched pairs of simultaneously detectable labelling reagents for specific protein amino acids. In this thesis the development and optimisation of a novel cysteine labelling strategy, that is based on the use of iodoacetyl derivatives of Cy3 and Cy5 (ICy3/5) and 2D-difference gel electrophoresis (2D-DIGE) is described. The differentially labelled samples are separated on a single 2D gel and detected by multi-wavelength fluorescence scanning. The method is used to analyse standard proteins and then cell lysates to define the stoichiometry, sensitivity and specificity of this labelling technique. A comparative study of this new proteomic ICy dye protocol with the current NHS-Cy dye labelling system and methods that employ commonly used protein staining methods is described. The method is then used for cysteine labelling of proteins in non-reduced, denatured biological samples allowing accurate monitoring and sensitive detection of redox-dependent thiol modifications and expression level changes. The method is shown to be compatible with the use of MALDI mass spectrometry to identify proteins by analysis of trypsinised ICy labelled peptide digests. Using parallel sample analysis within single gels, the ICy-dye reagents were used to detect redox-, ErbB-2- and growth factor-dependent changes in a human mammary luminal epithelial cell system which was exposed to hydrogen peroxide or to growth factor stimulation. The conventional lysine labelling 2D-DIGE technique was also used in parallel to assess the new ICy labelling strategy for determination of the effects of oxidative stress on protein isoform levels. This study has revealed the identity of proteins involved in the response to oxidative stress and growth factor stimulation in the context of ErbB-2 growth factor receptor over-expression. In addition, this labelling strategy was also used to detect changes in thiol reactivity that follow the UV irradiation of plasma proteins as part of a study designed to evaluate the effect of UV disinfection on plasma product safety for clinical use.

La compréhension des mécanismes cellulaires et moléculaires qui sont mis en jeu au moment de la croissance et la maturation pré-ovulatoire induite par la LH, permettra de définir des marqueurs de qualité et de maturité du follicule destiné à ovuler, et ainsi de mieux anticiper le moment de l’ovulation. L’objectif majeur de cette thèse était d’identifier certain des facteurs régulateur impliqués dans la maturation folliculaire par deux approches globales d’analyse protéomique et transcriptomique. La première étude a permis d’établir pour la première fois les cartes protéiques du liquide folliculaire équin et canin. Les analyses comparatives des liquides folliculaires provenant de différents stades physiologiques n’ont montré, dans nos conditions expérimentales, que peu de différences. Nos résultats obtenus dans la deuxième étude indiquent que les différentes méthodes enrichissement du liquide folliculaire peuvent améliorer, pour certaines de manière conséquente, la résolution des gels 2D-PAGE. Notre étude transcriptomique globale a révélé un groupe de gènes différentiellement exprimés dans les cellules folliculaires aux différents stades étudiés. Ces gènes sont potentiellement impliqués pendant le développement folliculaire dans l’espèce équine. Les deux approches (protéomique et transcriptomique) que nous avons utilisées au cours de ce travail sont complémentaires car la connaissance des gènes exprimés par les cellules folliculaires peuvent permettre d’identifier certains gènes codant pour des protéines sécrétoires retrouvées dans le liquide folliculaire
An understanding of the cellular and molecular mechanisms involved in the growth and maturation of the preovulatory follicle induced by LH, will help us to understand and identify the markers of quality and maturity of the follicle destined to ovulate, and better anticipate the time of ovulation. The main objective of this thesis was to identify some regulatory factors involved in follicle maturation using two global approaches: proteomic and transcriptomic analysis. The first study established for the first time the protein map of equine and canine follicular fluids. The comparative analyses of follicular fluid from different physiological stages were shown little or no difference in our experimental conditions. Results obtained with the second study suggested that between depletion and enrichement methods, the enriched follicular fluid can improve for some consistent manner, the resolution of 2D-PAGE gels. Our global transcriptomic study revealed a group of genes differentially expressed in follicular cells at different physiological stages. These genes are potentially involved during follicle development in the equine species. The two approaches (proteomic and transcriptomic) that we used in this work are complementary, as the knowledge of genes expressed by follicle cells can help to identify some genes coding for secretory proteins secreted in follicular fluid

La formation d'émulsions eau-dans-huile stables est un problème majeur rencontré par les pétroliers au niveau de la production mais aussi du raffinage. Afin d'essayer de prévoir ce phénomène, Total a développé une méthode de classement des huiles qui permet, à partir de leurs propriétés physico-chimiques, de déterminer a priori leur capacité à former ou non des émulsions stables. Cependant, les mécanismes interfaciaux sous-jacents ainsi que l’influence des molécules tensioactives du brut sur la stabilité des émulsions n’est pas très clair. Notre travail a consisté à étudier la contribution des acides naphténiques et des asphaltènes dans les phénomènes observés. L’étude d’huiles réelles a permis d’établir un lien entre la stabilité des émulsions et la formation à l'interface d'un gel 2D. Les études menées sur les huiles réelles dont les acides naphténiques ont été extraits ont permis de montrer que ces derniers, en compagnie de leurs formes ionisées, les naphténates, ont la capacité de réduire la stabilité des émulsions en diminuant la résistance du gel interfacial, ou même en empêchant sa formation. Les expériences réalisées sur les huiles réelles dépourvues d’asphaltènes ont permis de confirmer le rôle stabilisant des asphaltènes. Les résultats obtenus suggèrent que les asphaltènes s’adsorbent sur le gel 2D déjà formé par des tensioactifs passés de l’huile vers l’eau et le rapprochent ainsi de sa transition vitreuse. La résistance du gel interfacial s'en trouve alors augmentée, ce qui conduit à la formation d'émulsions plus stables. En croisant le classement industriel des bruts opéré par Total et les résultats de l’étude, un mécanisme global, régi par la compétition entre les acides naphténiques, les naphténates et les asphaltènes à l’interface E/H est proposé pour expliquer les différences de stabilité observées avec les différentes huiles. Lorsque les acides et les naphténates sont suffisamment concentrés, ils empêchent la formation du gel interfacial et les émulsions sont peu stables. Lorsqu’ils sont moins concentrés le rôle des asphaltènes peut alors devenir prépondérant en donnant une cohésion plus importante au gel qui se rapproche de sa transition vitreuse, ce qui conduit en général au renforcement de la stabilité des émulsions formées
Water-in-crude oil emulsions are a major issue for oil companies in both production and refining facilities. Thanks to physical and chemical characterizations, Total set a classification which allows the decision of a crude oil ability to create stable emulsions. However the interfacial mechanisms implied and the influence of the indigenous surfactants of crude oil remain unclear. Our work consists in studying the naphthenic acids and asphaltenes contribution to the w/o emulsion stability. The study of realistic crude oils enabled the discovery of a link between the emulsion stability with the formation of a very particular interfacial behavior: a two-imensional gel. Experiments with desacidified oils have proven the destabilizing ability of naphthenic acids and their ionized form, naphthenates. They actually decrease the interfacial gel strength and can even prevent the gel formation. Asphaltenes-free crude oils have permitted to confirm the stabilizing role of asphaltenes. Rather than adsorbing directly on the interface, asphaltenes seem to adsorb on the interfacial gel already formed. The gel strength is thus increased and lead to higher emulsion stability. Thanks to these results and the industrial classification of crude oil developed by Total, a global mechanism explaining the emulsion stability process has been proposed. This mechanism is governed by the competition between asphaltenes, naphthenates and naphthenic acids at the water/oil interface. If the concentration of naphthenic acids and naphthenates is high enough, the interfacial gel cannot be formed and the emulsions are unstable. If the crude oil is not acidic enough, the asphaltenes influence increases dramatically and implies the strengthening of the gel which becomes closer to his glass transition. This generally leads to the formation of more stable emulsions

Depuis ces dernières années, la chimie du titane et plus particulièrement celle du dioxyde (TiO2) fait l'objet d'une grande activité de recherche tant sur le plan fondamental qu'appliqué. Les principales applications concernent, en effet, des thématiques associées aux problèmes de protection de l'environnement qui ont pour objectifs la purification de l'air et la dépollution de l'eau à travers la photocatalyse. Dans de telles applications, les performances de TiO2 pourraient être optimisées par un contrôle spécifique, à l'échelle micro- ou mésostructurale, de la morphologie du matériau. La nano-structuration de TiO2 peut s'avérer également très intéressante dans la réalisation de membranes pour la séparation des gaz, de matériaux d'électrode nanoporeux pour le développement de nouveaux types de cellules solaires, et comme couches actives dans la conception de systèmes électrochromes. . .

This diploma thesis is focused on studies of changing of protein profile during barley malting. Substantial part of this work is devoted to the proteomics identification of barley proteins which change during malting and so become more stationary and they influence quality of beer (haze and foam in beer). For this experiment was used barley variety Jersey. In the theoretical part of this thesis there is information about beer, manufacturing of beer with description of important commodities for manufacturing of beer and information about barley malting and information about malting process. Next there is description of methods for separation of proteins (1D gel electrophoresis and 2D gel electrophoresis), MALDI TOF/TOF mass spectrometry and this use for the analysis and identification of proteins, the use of matrices and ways of the sample preparation. In the experimental part of this thesis there was carried out the optimisation of the dosage of sample for 1D gel electrophoresis and the optimisation of staining. The 15 % TRIS-HCl gel was the best, this gel was stained by Commassie Brilliant Blue G-250. For illustration of changes was made 2D gel electrophoresis. With help of method peptide mass fingerprinting and MS/MS protein of barley – protein Z, -amylase subtilisin inhibitor, -amylase a peroxidase were identificated. The analysis of barley extract intact proteins was carried out, this analysis was focused on changes of important barley protein LTP 1.

A esquizofrenia é uma doença crônica, grave e incapacitante que afeta cerca 24 milhões de pessoas em âmbito mundial. É caracterizada por uma desorganização no pensamento que prejudica a funcionalidade do indivíduo. Existem intervenções que são efetivas e contribuem para a diminuição da prevalência do transtorno, pois ajudam o portador a levar uma vida produtiva e integrada à sociedade, porém devem ser ministradas nos estágios iniciais da doença. No entanto, existe uma grande dificuldade em se diagnosticar a esquizofrenia precocemente devido a sua complexidade e às sutilezas dos seus sintomas apresentados antes do surgimento da psicose. O cérebro não é acessível a exames invasivos in vivo e por esse motivo a exploração de fluidos periféricos é de grande importância. As plaquetas e neurônios serotonérgicos possuem características bioquímicas e morfológicas em comum que possibilitam a comparação entre a estrutura e a função de ambos e, por causa dessa similaridade, muitos trabalhos utilizam plaquetas como modelo para o estudo de doenças neuropsiquiátricas, inclusive a esquizofrenia. A detecção precoce da esquizofrenia é um objeto de investigação atual e relevante não somente para revolucionar os meios atuais de diagnóstico, mas também para desenvolver novos tratamentos aplicados aos estágios iniciais da doença, diferenciar os subgrupos de doentes e monitorar as intervenções preventivas. A proposta do presente trabalho é fazer o estudo da expressão de proteínas em plaquetas de pacientes esquizofrênicos e controles com o objetivo de identificar proteínas candidatas a biomarcadores utilizando técnicas proteômicas quantitativas e confiáveis, como 2D-DIGE e a espectrometria de massas.
Schizophrenia is a disabling, serious, and chronic illness, which affects about 24 million people worldwide. It is characterized by a severe disorganization of the thoughts that harms the social life of patients becoming them dependent of the family and/or government. There are effective treatments that contribute to decrease the prevalence of the disorder because they improve the life and social conditions of the patients, but they are only advantageous if the intervention is made in the early stages of the disease. It is difficult to obtain early diagnosis due to the complexity of the disease and its insidious symptoms before the beginning of the psychosis. The brain is not easily accessed in vivo and, because of this, it is very important to study the peripheral tissues like blood, which makes the use of the platelets very interesting. Furthermore, platelets and serotonergic neurons share biochemical and morphological characteristics that allows the comparison between structure and function of both. From these similarities many authors has used platelets as a neuron model to study many neurodegenerative diseases including schizophrenia. The early detection of schizophrenia is a current and suitable goal, not only to improve the early diagnosis but also to develop new treatments, differentiate the subtypes, and monitor the preventive interventions. The purpose of this project is to do a comparative screening of expressed proteins in platelets from schizophrenics and controls with the objective of finding differently expressed proteins that could be candidates to biomarkers using 2D-DIGE and mass spectrometry.

Cellulosic biomass is the major organic matter produced in the biosphere. The biodegradation of this cellulosic material is achieved by enzymatic activities of the cellulose degrading microorganisms. These organisms usually express a complex extracellular or a membrane bound cellulolytic system comprising combination of several cellulase enzymes. Cellulases are the group of hydrolytic enzymes capable of hydrolysing insoluble cellulose to glucose. Phlebia gigantea is an aggressive white rot basidiomycete with ability to tolerate resinous extracts on freshly cut wood and higher growth rate. This helps the fungus to colonise the sapwood preventing other fungi from becoming established. Early research on the cellulase system of this organism reported the presence of a cellulase system composed of P-glucosidase, endoglucanase and a cellobiohydrolase. Based on these unpublished studies, our aim was to obtain a complete sequence of putative cellobiohydrolase I (CbhI) from this organism. Attempts to identify and isolate the cellulase gene resulted in an incomplete cDNA sequence of I 154 bp. To understand the cellulase system, expression and regulation of the cellulase enzymatic activity was examined for incubation of P. gigantea on substrates glucose, xylose, Avicel, carboxymethyl cellulose and cellobiose. The pH, total protein and biomass production results indicated that the capacity of P. gigantea to degrade cellulose is dependent upon the nature of the carbon source and the regulation of the cellulase synthesis is repressed in the presence of simple sugars like glucose and xylose. The study employed the highly effective method of purification by affinity adsorption and purified cellulase complex in large quantity. Characterisation of the kinetic properties of this cellulase complex revealed that the rate of cellulase catalysis were optimum at pH 5.0 and temperature 50GC. The purified complex was comprised of multiple proteins and demonstrated significant CMCase and CBHase activity on zymogram analysis. The purified cellulase complex was characterised by 2D gel electrophoresis and by peptide mass finger printing using MALDI-TOF massspectrometry analysis. The 2D gel analysis of the purified cellulase complex showed 15 spots within the range of pI 3.5 to pI 7 and the molecular weight between 20KDa to 100KDa. Three protein spots were selected based on the IEF and SDS zymogram and identified using MALDI-TOF MS analysis. These proteins were identified based on the peptide mass data belonging to the 6-phospho-a-glucosidase, p-glucosidase and glycosyl hydrolase family 13 a-amylase or pullulanases, suggesting the divergent evolution of specific cellulase proteins. This study showed P. gigantea as a potential cellulase source and the cellulase complex secreted by the induction of substrate, comprises a variety of enzymes related to hydrolysis of cellulose biomass. It is evident from this and previous studies that P. gigantea cellulase complex comprises of a specific set of enzymes that possess the ability to degrade crystalline cellulose and is one of the first organisms to colonise freshly cut wood. Further studies on the cellulase system of this primary colonist may open up the prospects to utilise this organism as the potential onsite bioreactor agent, pre-treating the biomass and increasing the economic feasibility of the industrial bioenergy processes.

Doutoramento em Ciência e Engenharia de Materiais
Alkali tantalates and niobates, including K(Ta / Nb)O3, Li(Ta / Nb)O3 and Na(Ta / Nb)O3, are a very promising ferroic family of lead-free compounds with perovskite-like structures. Their versatile properties make them potentially interesting for current and future application in microelectronics, photocatalysis, energy and biomedics. Among them potassium tantalate, KTaO3 (KTO), has been raising interest as an alternative for the well-known strontium titanate, SrTiO3 (STO). KTO is a perovskite oxide with a quantum paraelectric behaviour when electrically stimulated and a highly polarizable lattice, giving opportunity to tailor its properties via external or internal stimuli. However problems related with the fabrication of either bulk or 2D nanostructures makes KTO not yet a viable alternative to STO. Within this context and to contribute scientifically to the leverage tantalate based compounds applications, the main goals of this thesis are: i) to produce and characterise thin films of alkali tantalates by chemical solution deposition on rigid Si based substrates, at reduced temperatures to be compatible with Si technology, ii) to fulfil scientific knowledge gaps in these relevant functional materials related to their energetics and ii) to exploit alternative applications for alkali tantalates, as photocatalysis. In what concerns the synthesis attention was given to the understanding of the phase formation in potassium tantalate synthesized via distinct routes, to control the crystallization of desired perovskite structure and to avoid low temperature pyrochlore or K-deficient phases. The phase formation process in alkali tantalates is far from being deeply analysed, as in the case of Pb-containing perovskites, therefore the work was initially focused on the process-phase relationship to identify the driving forces responsible to regulate the synthesis. Comparison of phase formation paths in conventional solid-state reaction and sol-gel method was conducted. The structural analyses revealed that intermediate pyrochlore K2Ta2O6 structure is not formed at any stage of the reaction using conventional solid-state reaction. On the other hand in the solution based processes, as alkoxide-based route, the crystallization of the perovskite occurs through the intermediate pyrochlore phase; at low temperatures pyrochlore is dominant and it is transformed to perovskite at >800 °C. The kinetic analysis carried out by using Johnson-MehlAvrami-Kolmogorow model and quantitative X-ray diffraction (XRD) demonstrated that in sol-gel derived powders the crystallization occurs in two stages: i) at early stage of the reaction dominated by primary nucleation, the mechanism is phase-boundary controlled, and ii) at the second stage the low value of Avrami exponent, n ~ 0.3, does not follow any reported category, thus not permitting an easy identification of the mechanism. Then, in collaboration with Prof. Alexandra Navrotsky group from the University of California at Davis (USA), thermodynamic studies were conducted, using high temperature oxide melt solution calorimetry. The enthalpies of formation of three structures: pyrochlore, perovskite and tetragonal tungsten bronze K6Ta10.8O30 (TTB) were calculated. The enthalpies of formation from corresponding oxides, ∆Hfox, for KTaO3, KTa2.2O6 and K6Ta10.8O30 are -203.63 ± 2.84 kJ/mol, - 358.02 ± 3.74 kJ/mol, and -1252.34 ± 10.10 kJ/mol, respectively, whereas from elements, ∆Hfel, for KTaO3, KTa2.2O6 and K6Ta10.8O30 are -1408.96 ± 3.73 kJ/mol, -2790.82 ± 6.06 kJ/mol, and -13393.04 ± 31.15 kJ/mol, respectively. The possible decomposition reactions of K-deficient KTa2.2O6 pyrochlore to KTaO3 perovskite and Ta2O5 (reaction 1) or to TTB K6Ta10.8O30 and Ta2O5 (reaction 2) were proposed, and the enthalpies were calculated to be 308.79 ± 4.41 kJ/mol and 895.79 ± 8.64 kJ/mol for reaction 1 and reaction 2, respectively. The reactions are strongly endothermic, indicating that these decompositions are energetically unfavourable, since it is unlikely that any entropy term could override such a large positive enthalpy. The energetic studies prove that pyrochlore is energetically more stable phase than perovskite at low temperature. Thus, the local order of the amorphous precipitates drives the crystallization into the most favourable structure that is the pyrochlore one with similar local organization; the distance between nearest neighbours in the amorphous or short-range ordered phase is very close to that in pyrochlore. Taking into account the stoichiometric deviation in KTO system, the selection of the most appropriate fabrication / deposition technique in thin films technology is a key issue, especially concerning complex ferroelectric oxides. Chemical solution deposition has been widely reported as a processing method to growth KTO thin films, but classical alkoxide route allows to crystallize perovskite phase at temperatures >800 °C, while the temperature endurance of platinized Si wafers is ~700 °C. Therefore, alternative diol-based routes, with distinct potassium carboxylate precursors, was developed aiming to stabilize the precursor solution, to avoid using toxic solvents and to decrease the crystallization temperature of the perovskite phase. Studies on powders revealed that in the case of KTOac (solution based on potassium acetate), a mixture of perovskite and pyrochlore phases is detected at temperature as low as 450 °C, and gradual transformation into monophasic perovskite structure occurs as temperature increases up to 750 °C, however the desired monophasic KTaO3 perovskite phase is not achieved. In the case of KTOacac (solution with potassium acetylacetonate), a broad peak is detected at temperatures <650 °C, characteristic of amorphous structures, while at higher temperatures diffraction lines from pyrochlore and perovskite phases are visible and a monophasic perovskite KTaO3 is formed at >700 °C. Infrared analysis indicated that the differences are due to a strong deformation of the carbonate-based structures upon heating. A series of thin films of alkali tantalates were spin-coated onto Si-based substrates using diol-based routes. Interestingly, monophasic perovskite KTaO3 films deposited using KTOacac solution were obtained at temperature as low as 650 °C; films were annealed in rapid thermal furnace in oxygen atmosphere for 5 min with heating rate 30 °C/sec. Other compositions of the tantalum based system as LiTaO3 (LTO) and NaTaO3 (NTO), were successfully derived as well, onto Si substrates at 650 °C as well. The ferroelectric character of LTO at room temperature was proved. Some of dielectric properties of KTO could not be measured in parallel capacitor configuration due to either substrate-film or filmelectrode interfaces. Thus, further studies have to be conducted to overcome this issue. Application-oriented studies have also been conducted; two case studies: i) photocatalytic activity of alkali tantalates and niobates for decomposition of pollutant, and ii) bioactivity of alkali tantalate ferroelectric films as functional coatings for bone regeneration. Much attention has been recently paid to develop new type of photocatalytic materials, and tantalum and niobium oxide based compositions have demonstrated to be active photocatalysts for water splitting due to high potential of the conduction bands. Thus, various powders of alkali tantalates and niobates families were tested as catalysts for methylene blue degradation. Results showed promising activities for some of the tested compounds, and KNbO3 is the most active among them, reaching over 50 % degradation of the dye after 7 h under UVA exposure. However further modifications of powders can improve the performance. In the context of bone regeneration, it is important to have platforms that with appropriate stimuli can support the attachment and direct the growth, proliferation and differentiation of the cells. In lieu of this here we exploited an alternative strategy for bone implants or repairs, based on charged mediating signals for bone regeneration. This strategy includes coating metallic 316L-type stainless steel (316L-SST) substrates with charged, functionalized via electrical charging or UV-light irradiation, ferroelectric LiTaO3 layers. It was demonstrated that the formation of surface calcium phosphates and protein adsorption is considerably enhanced for 316L-SST functionalized ferroelectric coatings. Our approach can be viewed as a set of guidelines for the development of platforms electrically functionalized that can stimulate tissue regeneration promoting direct integration of the implant in the host tissue by bone ingrowth and, hence contributing ultimately to reduce implant failure.
Tantalatos e niobatos alcalinos, como K(Ta / Nb)O3, Li(Ta / Nb)O3 and Na(Ta / Nb)O3, são uma família atrativa de compostos ferroeléctricos livres de chumbo com estrutura perosvquítica. As suas propriedades versáteis fazem destes potencialmente interessantes para aplicações em microelectrónica, foto catálise, energia e biomédica. Entre os compostos acima citados, os compostos de tantalato de potássio, KTaO3 (KTO), tem atraído bastante atenção como substitutos para o amplamente conhecido titanato de estrôncio, SrTiO3 (STO). KTO é um óxido perovsquítico com comportamento paraelétrico quântico, quando eletricamente estimulado, e elevada polaribilidade tornando viável engenhar as suas propriedades através de estímulos internos e externos. No entanto os problemas na sua produção, quer em macroescala quer em nanoestruturas 2D, tornam estes compostos numa alternativa pouco viável para a substituir o STO. Consequentemente, e de forma a contribuir cientificamente para aumentar o conhecimento sobre as aplicações dos tantalatos, os principais objectivos desta tese são: i) produzir e caracterizar filmes finos de tantalatos alcalinos através de deposição de solução química em substratos rígidos, à base de silício, e a baixas temperaturas de forma a serem compatíveis com a tecnologia de silício; ii) complementar o conhecimento científico sobre estes materiais funcionais relativamente às suas características termodinâmicas; iii) explorar aplicações alternativas para os tantalatos alcalinos, como a foto catálise. No que diz respeito à síntese, foi focalizada no entendimento da formação de fase no tantalato de potássio sintetizado por diferentes métodos, de modo a controlar a cristalização da estrutura perovsquítica desejada e evitar a formação da fase pirocloro a baixas temperaturas e fases deficientes em potássio. Em tantalatos alcalinos o processo de formação da fase desejada está longe de estar plenamente analisado, como é o caso das perovsquites que contêm chumbo, consequentemente o trabalho foi inicialmente focado na compreensão da relação processo-fase para identificar as forças motrizes responsáveis por regular o processo de síntese. Foi realizada um estudo comparativo da formação de fase via método convencional de reação do estado sólido e via método de sol-gel. A análise estrutural revelou que a estrutura piroclórica intermédia K2Ta2O6 não foi formada em nenhuma etapa da reação via método do estado sólido. Por outro lado em processos baseados em solução, como os baseados em alcóxidos, a cristalização perovsquítica ocorre através da indesejada fase pirocloro intermédia; a baixas temperaturas a fase pirocloro é dominante e sofre a transformação para perovsquite a >800 °C. A análise cinética efectuada usando o modelo Johnson-Mehl-Avrami-Kolmogorow e a difração de raio-X quantitativa (DRX), demonstraram que nos pós obtidos pelo método sol-gel, a cristalização ocorre em duas etapas: i) no estágio inicial a reação é denominada por nucleação primária, o mecanismo é controlado por fronteira de fase, e ii) no segundo estágio, o baixo valor do expoente de Avrami, n ~ 0.3, não segue nenhuma categoria reportada impossibilitando assim uma clara identificação do mecanismo. Posteriormente, e em colaboração com o grupo da Professora Alexandra Navrostky da Universidade da Califórnia, Davis, foram realizados estudos de termodinâmica, usando calorimetria de solução de óxidos fundidos a alta temperatura. Foram calculadas as entalpias de formação das três estruturas: pirocloro, perovsquite e tetragonal tungsténio bronze K6Ta10.8O30 (TTB). As entalpias de formação relativas aos óxidos correspondentes, ∆Hfox, para KTaO3, KTa2.2O6 e K6Ta10.8O30, são -203.63 ± 2.84 kJ/mol, 358.02 ± 3.74 kJ/mol e -1252.34 ± 10.10 kJ/mol, respectivamente; enquanto que as relativas aos elementos, ∆Hfel, para KTaO3, KTa2.2O6 e K6Ta10.8O30 são 1408.96 ± 3.73 kJ/mol, -2790.82 ± 6.06 kJ/mol e -13393.04 ± 31.15 kJ/mol, respectivamente. As possíveis reações de decomposição, de KTa2.2O6 para KTaO3 e Ta2O5 (reação 1) ou para K6Ta10.8O30 e Ta2O5 (reação 2), foram propostas e o cálculo das entalpias resultou em 308.79 ± 4.41 kJ/mol e 895.79 ± 8.64 kJ/mol, respectivamente. As reações são fortemente endotérmicas, indicando que estas decomposições são energeticamente desfavoráveis, uma vez que é improvável que qualquer termo de entropia possa sobrepor-se a uma entalpia tão positiva. Os estudos termodinâmicos provaram que o pirocloro é energeticamente mais estável que a perovsquite para temperaturas baixas. Assim, a organização local dos precipitados amorfos canaliza a cristalização para a estrutura mais favorável, que é a pirocloro com uma organização local similar; a distância entre os vizinhos mais próximos na fase amorfa, ou na fase ordenada a baixo alcance, é similar à do pirocloro. Tendo em conta a derivação estequiométrica no sistema KTO, selecionar a técnica de fabricação / deposição de filmes finos mais apropriada é uma questão-chave, especialmente no que concerne aos óxidos ferroeléctricos complexos. A deposição por solução química tem sido o método de processamento mais reportado, para crescimento de filmes finos de KTO, mas o método clássico de alcóxidos permite cristalizar a fase perovsquite a temperaturas >800 °C enquanto que a temperatura máxima de estabilidade para os substratos de silício platinizado é ~700 °C. Portanto, foi usado um processo alternativo baseado em dióis, com precursores carboxilados de potássio, com o objectivo de estabilizar os precursores em solução, evitando assim o uso de solventes tóxicos e diminuindo a temperatura de cristalização da fase perovsquite. A análise dos pós revelou que no caso de KTOac (solução baseada em acetato de potássio), uma mistura de fase perovsquite e pirocloro foi detectada a uma temperatura de apenas 450 °C, e a transformação gradual em estrutura perovsquítica monofásica ocorre quando as temperaturas sobem acima de 750 °C, no entanto a fase KTaO3 monofásica não é obtida. No caso do KTOacac (solução com acetil-acetona de potássio, cadeia alquílica longa carboxilato de metal), um amplo pico é detectado a temperaturas <650 °C, característico de estruturas amorfas, enquanto que a elevadas temperaturas, os planos de difração das fases pirocloro e perovsquite são visíveis e a perovsquite KTaO3 monofásica é conseguida a temperaturas >700 °C. A análise de infravermelhos mostrou que estas diferenças acontecem devido à deformação da estrutura base dos carbonatos sob aquecimento. Uma série de filmes finos de tantalatos alcalinos foram depositados por spincoating em substratos de silício, usando a metodologia baseada em dióis. Filmes monofásicos de perovsquite KTaO3 depositados usando solução de KTOacac foram obtidos a uma temperatura de apenas 550 °C; os filmes foram recristralizados em fornos de aquecimento rápido em atmosfera de oxigénio durante 5 minutos com taxa de aquecimento de 30 °C/seg. Outras composições, LiTaO3 (LTO) e NaTaO3 (NTO), foram depositados com sucesso em substratos de silício a 650 °C. O carácter ferroeléctrico do LTO à temperatura ambiente foi provado. Infelizmente, não foi possível medir as propriedades eléctricas do KTO no condensador paralelo devido às interfaces filme-substrato ou filme-eléctrodo. Assim sendo, estudos futuros são necessários para compreender esta questão. Foram também conduzidos estudos com vista às possíveis aplicações; dois casos de estudo: i) estudo da atividade fotocatalítica de tantalatos e niobatos alcalinos para decomposição de poluentes, e ii) estudo de bioatividade de filmes ferroelétricos de tantalatos alcalinos como revestimento funcional para regeneração óssea. Recentemente, tem sido dedicada muita atenção ao desenvolvimento de novos materiais fotocatalíticos, e as composições à base de óxido de tântalo e nióbio tem demonstrado capacidade de fotocatálise na reação de separação da água devido ao elevado potencial das bandas de condução. Assim, várias composições das famílias dos tantalatos e niobatos alcalinos foram testadas como catalisadores para degradação do azul de metileno. Os resultados mostram valores de atividade promissores para alguns dos compostos, sendo o KNbO3 o mais ativo de entre os testados, alcançando valores acima de 50 % na degradação do pigmento após 7 h sob exposição a UVA. No entanto algumas modificações nas composições dos pós podem melhorar a sua performance. No que concerne à regeneração óssea, é importante obter plataformas que através de estímulos apropriados consigam assegurar a adesão e direcionar o crescimento, a proliferação e a diferenciação celular. Neste contexto, foi aqui explorada uma estratégia alternativa para revestimento de implantes ósseos, baseada na regeneração óssea mediada por sinais elétricos. Esta estratégia implica revestir substratos metálicos de aço inoxidável tipo 316L (316L-SST), com camadas de LiTaO3 ferroeléctrico, funcionalizadas através de polarização elétrica ou de irradiação com luz UV. Foi demonstrado que a formação de fosfato de cálcio na superfície e a adsorção de proteínas é consideravelmente melhorada quando o 316L-SST é revestido com filmes ferroelétricos funcionalizados. Esta estratégia pode ser encarada como um conjunto de orientações para o desenvolvimento de plataformas eletricamente funcionalizadas, capazes de estimular a regeneração de tecidos, promovendo a associação direta do implante com os tecidos hospedeiros, contribuindo assim para a redução de falhas na reabilitação com implantes ósseos.

Ph.D.
Molecular Microbiology and Immunology
Both poxviruses and γ2-herpesviruses share the K3-family of viral immune evasion proteins. These proteins are characterized by an amino-terminal RING-CH domain followed by two transmembrane domains. We analyzed several human homologues of the K3-family termed membrane-associated RING-CH (MARCH) proteins. All MARCH proteins localized to subcellular membranes while several reduced surface levels of known K3-family substrates. Thus, MARCH proteins appear to be structurally and functionally homologous to viral K3 proteins. One of the major challenges in determining the function of this family is the identification of their physiological substrates. To overcome this we created a quantitative proteomics approach which can be used to identify novel substrates for both the K3- and MARCH-families. Using stable isotope labeling by amino acids in cell culture, we compared the proteome of plasma membrane, golgi, and endoplasmic reticulum membranes in the presence and absence of K5 and MARCH-VIII. Quantitative mass spectrometric protein identification from these fractions revealed that CD316 (bone marrow stromal antigen 2), CD166 (activated leukocyte cell adhesion molecule) and syntaxin-4 were consistently underrepresented in the plasma membrane of K5 expressing cells, while CD44, CD81 (TAPA-1) and B-cell receptor-associated protein 31kDa (Bap31) were consistently underrepresented in the plasma membrane of MARCH-VIII expressing cells. Furthermore, downregulation of each of these proteins was independently confirmed. Our results both identify and characterize a novel family of human ubiquitin ligase enzymes and elucidate a novel technique which can analyze this family and be easily adapted to the analysis of other cellular enzymes viral immune modulators.

Doctor of Philosophy (PhD)
Proteomics is rapidly achieving recognition as a complimentary and perhaps superior approach to examine global changes in protein abundance in complex biological systems and the value of these techniques in neuropsychiatry is beginning to be acknowledged. Characterizing the brain’s regional proteomes provides a foundation for the detection of proteins that may be involved in disease-related processes. Firstly, optimal conditions were achieved for the application of two dimensional-gel electrophoresis (2D-GE)-based proteomics with postmortem human brain tissue. These optimized techniques were then applied to soluble fractions of adjacent grey and white matter of a single cytoarchitecturally defined area (Brodmann area 9; BA9) and of two adjacent regions of frontal white matter (BA9 and CC body) from healthy individuals. These normative proteomic comparisons highlighted the importance of correct tissue sampling, i.e. proper separation of regional white matter, as heterogeneity in the respective proteomes was demonstrated. Furthermore, they stressed the necessity for future molecular brain mapping studies. The main focus of this thesis however, was to examine the proteomes of brain regions specifically vulnerable to alcohol-induced damage underlying cognitive dysfunction. Alcoholic patients commonly experience mild to severe cognitive decline. It is postulated that cognitive dysfunction is caused by an alcohol-induced region selective brain damage, particularly to the prefrontal cortex. The cerebellum is increasingly recognized for its role in various aspects of cognition and alcohol–induced damage to the cerebellar vermis could indirectly affect neurocognitive functions attributed to the frontal lobe. We used a 2D-GE-based proteomics approach to compare protein abundance profiles of BA9 grey and white matter and the cerebellar vermis from human alcoholics (neurologically uncomplicated and alcoholics complicated with liver cirrhosis) and healthy control brains. Among the protein level changes observed are disturbances in the levels of a number of thiamine-dependent enzymes. A derangement in energy metabolism perhaps related to thiamine deficiency seems to be important in all regions analysed, even where there are no clinical or pathological findings of Wernicke-Korsakoff Syndrome. Evidence of oxidative changes was also seen in all regions and effects of liver dysfunction in the vermis found. However, overall, these results highlight the complexity of this disease process in that a number of different proteins from different cellular pathways appear to be affected. By identifying changes in protein abundance levels in the prefrontal grey and white matter and the cerebellar vermis, hypotheses may draw upon more mechanistic explanations as to how chronic ethanol consumption causes the structural and functional alterations associated with alcohol-related brain damage. Furthermore, by comparing these results, we may be able to isolate disturbances in molecular pathways specific to the brain damage caused by alcohol, severe liver dysfunction and thiamine deficiency.

In this work, mixed alkoxides of general formula [V(O)Nbx(OR)(3+5x)] (R = n-C3H7 and C2H5, x = 1, 4.5 and 9) are obtained. They are used to prepare complex (V/Nb)-pentoxides. Different spectroscopic methods, for example UV/VIS, resonance raman, infrared, temperature dependant 51V NMR and two dimensional 1H or 13C NMR, are used to elucidate structural details. It can be shown that the alkoxide precursor is a mixture of monomers and dimers which exchange very quickly. 2 % [V(O)Nb(OPr)8] (Pr = propyl) exists in a 0.1 molar solution. This complex is in equilibrium with V(O)(OPr)3 and Nb(OPr)5. Nb(OPr)5 itself exchanges with [Nb(OPr)5]2. For nuclear magnetic resonance experiments the exchange has to be slowed down using low temperatures.Controlled hydrolysis at 5 °C of a mixture of V(O)(OPr)3 and [Nb(OEt)5]2 in propanol leads to a clear transparent gel. The ratio of V : Nb is 1 : 1, 1 : 4.5 or 1 : 9, and oxalic acid is used as a chelating agent. Moreover, a dried product of a frozen solution of ammonium vanadate and ammonium oxyoxalatoniobate in water is found to be an appropriate precursor for the fore-mentioned oxides. Thermal decomposition of the gels and of the freeze dried products is monitored thermoanalytically and mass spectrometrically.The compositions of the resulting phases are examined and compared with the composition obtained via conventional synthesis (sintering of powder mixtures). Phases VNbxO(2.5+2.5x) (x = 1, 4.5 and 9) are obtained through the sol-gel technique and freeze drying at distinctly lower temperatures. VNbO5 crystallizes between 400 and 650 °C and V4Nb18O55 between 550 and 750 °C. A clean, non-reduced phase, VNb9O25, crystallizes above 1100 °C in oxygen. Below this temperature, solid solutions of V2O5 in TT- or M-Nb2O5 exist. Conventionally, pure VNbO5 is not obtainable. Some sol-gel synthesized products have the advantage of a more complete phase formation. In this way, a new phase of composition VNb9O25 can be found. The phase is homöotypic to M-Nb2O5.An additional advantage of the sol-gel synthesis lies in relatively high surface areas. Adversely, carbon remaining from the alcohol groups favours the thermodynamically stable phase VNb9O25 over the phase V4Nb18O55. Consequently, the freeze drying method seems to be the best way to get metastable phases in the system V2O5/x·Nb2O5.The formation of the complex oxides is controlled through the thermodynamics at phase boundaries. Therefore, to get mixed phases, structurally similar starting materials are preferred. In other words, using V2O5 and TT-Nb2O5 as starting materials the mixed phase similar to TT-Nb2O5 can be obtained. B-Nb2O5 as precursor yields another mixed phase similar to B-Nb2O5. In this work, this effect is called the &quot;structure directing effect&quot;. It is explained through the consumption of free enthalpy at the phase boundaries.As an additional point, catalytic activities of the complex oxides are examined. Because of a synergism of the known good activity of V2O5 and the good selectivity of Nb2O5, a strongly enhanced activity of the mixed oxides is found. Large surface areas further improve the activity. Connections between oxygen partial pressure, band gap and catalytic activity are found. A dilution of V2O5 in Nb2O5 down to 10 mol-% also causes an enhancement of catalytic activity
In der Arbeit werden durch die Synthese gemischter Alkoxide der Gesamtzusammensetzung [V(O)Nbx(OR)(3+5x)] (R = n-C3H7 und C2H5, x = 1, 4,5 und 9) sowie gefriergetrockneter Pulver Ausgangssubstanzen für gemischte, komplexe Vanadium- und Nioboxide erhalten. Untersuchungen mittels UV/VIS-, Resonanz-Raman- und IR-Spektroskopie sowie temperaturabhängiger 51V- und zweidimensionaler 1H-/13C NMR-Spektroskopie zeigen, dass es sich bei der Alkoxid-Vorstufe um ein Gemisch aus monomeren und dimeren Einheiten handelt, die in schnellem Gleichgewicht miteinander stehen. So liegt [V(O)Nb(OPr)8] als Donorkomplex vor, der im Gleichgewicht mit VO(OPr)3 und Nb(OPr)5 steht. Nb(OPr)5 steht wiederum im Gleichgewicht mit [Nb(OPr)5]2. Die Bildung und der Zerfall des Donorkomplexes erfolgen bei Raumtemperatur so schnell, dass er nur durch UV/VIS- und Resonanz-Raman-Spektroskopie sichtbar wird; bei der Kernresonanzspektroskopie muss der Austausch durch tiefe Temperaturen verlangsamt werden.Mittels kontrollierter Hydrolyse einer Mischung aus VO(OPr)3 und [Nb(OEt)5]2 in Propanol mit Oxalsäure als Chelatbildner und der Verlangsamung der Kondensation über die Erniedrigung der Temperatur wird ein homogenes, transparentes Gel aus V2O5 und Nb2O5 hergestellt. Daneben wird durch eine Lösung aus Ammoniumvanadat und Ammoniumoxyoxalatoniobat ein für die Gefriertrocknung geeigneter Precursor zur Synthese der Oxidphasen gefunden. Die Zersetzung des Gels und der gefriergetrockneten Pulver werden mittels DTA, TG und Massenspektrometrie untersucht und die Phasenausbildung mit der Reaktion von konventionellen Festkörpergemengen verglichen.Die dabei entstehenden metastabilen und thermodynamisch stabilen Phasen VNbxO(2,5+2,5x) (x = 1, 4,5 und 9) sind durch das Sol-Gel-Verfahren sowie durch die Gefriertrocknung bei deutlich niedrigeren Temperaturen und mit geringerem Fremdphasenanteil als bei der konventionellen Synthese erhältlich. VNbO5 existiert bis 650 °C, V4Nb18O55 bis 750 °C, darüber wandelt sich jede Zusammensetzung in VNb9O25 bzw. in verschiedene Nb2O5-Modifikationen und V2O5 um. Die Sol-Gel-Methode liefert im Vergleich zur Gefriertrocknung bei 900-1100 °C den Vorteil der schnelleren Phasenausbildung durch die größere Homogenität der Vorstufe. So erhält man Zwischenstufen, die sonst nur mit Beimengungen zu synthetisieren sind. In diesem Zusammenhang kann erstmalig eine zu M-Nb2O5 homöotype Verbindung der Zusammensetzung VNb9O25 erhalten werden. Ein weiterer Vorteil der Sol-Gel-Synthese ist der Erhalt größerer Oberflächen nach der Zersetzung. Nachteilig erscheinen jedoch bei einer Synthese bei tiefen Temperaturen (500-800 °C) die Alkoholatreste. So entstehen wesentlich eher die thermodynamisch begünstigten Phasen, z. B. VNb9O25 vor V4Nb18O55 und V4Nb18O55 vor VNbO5. Weiterhin macht sich die komplizierte Präparation der Gele bemerkbar; daher stellt im Allgemeinen die Gefriertrockung die Methode der Wahl dar.Die Ausbildung der komplexen Oxide erfolgt stark geprägt durch die Thermodynamik an den Phasengrenzen. Daher erfolgt eine bevorzugte Ausbildung strukturähnlicher Mischphasen. Diese erstmalig in diesem Ausmaß festgestellte Tatsache wird in der Arbeit der Strukturdirigierende Effekt genannt. Eine Erklärung dieses Effektes erfolgt anhand des Verbrauchs der Freien Enthalpie an den Phasengrenzen.Aufgrund eines Synergismus der Eigenschaften von V2O5 und Nb2O5 bei der oxidativen Dehydrierung von Propan zu Propen (relativ hohe katalytische Aktivität von V2O5 und hohe Selektivität von Nb2O5) wird eine überproportional hohe katalytische Aktivität bei den Mischoxiden erhalten. Die durch die unkonventionellen Methoden erhaltenen großen Oberflächen verbessern die Aktivität weiter. Es können Zusammenhänge festgestellt werden zwischen der Sauerstoffabgabetendenz, der Redoxkraft, der Bandlücke der Mischoxide und der katalytischen Aktivität. Die Einzigartigkeit des Nb2O5-Wirtsgitters bewirkt bei der Verdünnung von V2O5 darin eine hohe katalytische Leistungssteigerung

Alopecia areata (AA) is a putative autoimmune hair loss disorder. It mainly affects the scalp hair but can also involve body hair, and can also affect the nail and the eye. While there are may be several lines of evidence to support the autoimmune basis of AA, there is still very little information on the hair follicle autoantigen(s) involved in its pathogenesis. In this project, serum antibodies (AA=10, control=10) were used to immunoprecipitate AA-relevant target antigens from normal human scalp hair follicle extracts. These immunoprecipitates were analysed by LC-MALDI-TOF/TOF mass spectrometry for target protein identification. This part of the project involved substantial methods development. Trichohyalin was immunoprecipitated by all AA sera, but by only 5 normal sera. Importantly, the mean Mascot scores of the AA group was significantly higher than the normal group (p=0.005). Keratin 16 was also identified from immunoprecipitates as another potential AA-relevant target antigen. Functional studies by ex vivo whole hair follicle organ culture using commercial antibodies to trichohyalin and keratin 16 significantly inhibited hair fibre elongation compared to controls. Indirect immunofluorescence studies revealed that AA sera contained higher immunoreactivity against normal human scalp anagen hair follicles compared to normal sera. Immunoreactivities were mainly in the outer root sheath and inner root sheath, and less so to the medulla and hair bulb matrix. Double immunofluorescence studies of AA and normal serum with anti-trichohyalin antibody (AE15) revealed co-localisation of 9 of the AA sera antibodies with trichohyalin in the inner root sheath (mostly in Henle's, less in Huxley's/inner root sheath cuticle), but only weakly in 3 normal sera. This study supports the involvement of an antibody response to anagen-specific hair follicles antigens in AA. Moreover, there may be some evidence that these antibodies may have a pathogenic role.

Adaptation to environmental changes is important for the survival of living organisms. Under extreme abiotic conditions, organic molecules (such as lipids, proteins and nucleic acids) are prone to damage. Under these conditions stress response mechanisms are activated, either to prevent the source of damage or to promote the rapid turnover of damaged molecules. Like all photoautotrophic organisms, cyanobacteria are sensitive to high light intensity and oxidative stress, which induces damage to the photosynthetic apparatus. My thesis is divided in two subjects related to particular stress responses in the cyanobacterium Synechocystis sp. PCC 6803: 1) the role of Deg/HtrA proteases and 2) investigations on the small CAB-like proteins. Deg/HtrA proteases are ATP-independent serine endopeptidases with a characteristic C-terminal PDZ domain. These proteases are largely dispersed among living organisms, with many different functions, mostly involved in protein quality control. The genome of Synechocystis sp. PCC 6803 contains three genes coding for Deg/HtrA proteases: HtrA, HhoA and HhoB. These proteases are essential for survival under high light and heat stress, and may overlap in their functions. During my Ph.D. studies I focused on the identification of the precise localization of the Deg/HtrA proteases in the cyanobacterial cell, analyzed the biochemical properties of recombinant Synechocystis Deg/HtrA proteases in vitro and adopted proteomic and metabolomic approaches to study the physiological importance of these proteases. My data show that Deg/HtrA proteases are not only important in stress response mechanisms under adverse conditions, but are also involved in the stabilization of important physiological processes, such as polysaccharides biosynthesis and peptidoglycan turnover. The small CAB-like proteins (SCPs) belong to the light harvesting-like family of stress induced proteins and are thought to be involved in the photoprotection of the photosynthetic apparatus. Five small CAB-like proteins where identified in Synechocystis sp. PCC 6803 (ScpA-E). In my studies I identified another relative to the SCPs, LilA, which I found to be co-transcribed with ScpD. I also focused on the subcellular localization and identification of potential interaction partners of the SCPs.

Die Erkrankung Huntington s Chorea ist eine autosomal dominant vererbte Erkrankung, die gewöhnlich im mittleren Lebensabschnitt beginnt und unausweichlich zum Tode führt. In unserem Bestreben, Proteine zu identifizieren, welche an Prozessen "Upstream" oder "Downstream" des krankheitsverursachenden Proteins Huntingtin beteiligt sind, wurde das Proteom eines sehr gut etablierten Mausmodells mit Hilfe der Großgel 2D-Elektrophorese untersucht. Es konnte zum ersten Mal auf Proteinebene nachweisen werden, dass die Expression von zwei Serinproteasehemmern, alpha1-Antitrypsin und Contraspin und darüber hinaus eines Chaperons, alphaB-Kristallin, im Verlauf der Erkrankung abnimmt. Reduzierte Expression von alpha1-Antitrypsin und Contraspin konnte in Gehirn, Leber, Herz und Testes nahe dem Endstadium der Erkrankung nachgewiesen werden. Hier ist es wichtig festzustellen, dass die Expressionsabnahme von alpha1-Antitrypsin im Gehirn der Abnahme in der Leber im Herzen und in den Testes vorangeht. Eine verminderte Expression des Chaperons alphaB-Kristallin wurde nur im Gehirn gefunden. Für ein weiteres Protein, das Major Urinary Protein, wurde eine verminderte Expression in der Leber und im Urin von betroffenen Mäusen festgestellt. Damit konnte demonstriert werden, dass die Erkrankung auf Proteinebene auch ein Protein, das im Gehirn von transgenen Mäusen nicht vorkommt, beeinflusst. Bei Untersuchungen am Menschen wurde in drei Gehirnregionen von Postmortem-Gehirnen von Huntington s Chorea Patienten eine veränderte Expression von alpha1-Antitrypsin festgestellt. Wenn gewährleistet werden kann, dass die Konzentration von alpha1-Antitrypsin und alphaB-Kristallin während Huntington s Chorea im Gewebe nicht absinkt, könnte dies vielleicht neuronalen Zelltod verhindern und somit bei der Verzögerung des Krankheitsverlaufs nutzbringend eingesetzt werden.
Huntington disease is an autosomal dominantly inherited disease that usually starts in midlife and inevitably leads to death. In an effort to identify proteins involved in processes upstream or downstream of the disease causing huntingtin, the proteome of a well-established mouse model was studied by large-gel 2D electrophoresis. It could be demonstrated for the first time at the protein level that two serin protease inhibitors, alpha1-antitrypsin and contraspin and the chaperone alphaB-crystallin decrease in expression over the course of disease. Importantly, the alpha1-antitrypsin decrease in the brain precedes that in liver, heart and testes in mice. Reduced expression of alpha1-antitrypsin and contraspin could be detected in the brain, liver heart and testes close to terminal disease. Decreased expression of the chaperone alphaB-crystallin was found exclusively in the brain. Reduced expression of the liver specific major urinary proteins not found in the brain, was seen in affected mice, demonstrating that the disease exerts its influence on a protein not present in the brain of transgenic mice at the protein level. When investigating three human brain regions obtained post-mortem from Huntington s disease patients, alpha1-antitrypsin expression was also altered. Maintaining alpha1-antitrypsin and alphaB-crystallin availability during the course of Huntington s disease might prevent neuronal cell death and therefore could be useful in delaying the disease progression.

Bacillus amyloliquefaciens FZB42 ist ein frei lebendes Bakterium, das Pflanzenwurzeln besiedelt und das Pflanzenwachstum durch viele verschiedene Wirkmechanismen anregt. In dieser Arbeit wurden die molekularen Grundlagen dieser positiven Wirkungen, die dieses „Pflanzenwachstum fördernde Rhizobakterium“ (PGPR) auf seine Wirte ausübt, untersucht. Um den gegenseitigen Austausch von B. amyloliquefaciens und seinen Wirtspflanzen zu entschlüsseln, wurden umfangreiche Proteomstudien durchgeführt. Es wurden Referenzkarten der extrazellulären und zytosolischen Proteinfraktionen erstellt. Die größte Anzahl an ausgeschiedenen Proteinen konnte während der stationären Phase beobachtet werden. Die identifizierten extrazellulären Proteine gehören verschiedenen Funktionsklassen an, wobei die prominentesten Klassen am Kohlenhydrat-Abbau und den Transport von Molekülen durch die Zellwand beteiligt sind. Die zytosolischen Extrakte von Kulturen, die in 1C-Medium bzw. Mineralmedium angezogen wurden, und in der zweidimensionalen Gelelektrophorese (2 DE) aufgetrennt wurden, ergaben 461 und 245 verschiedene Protein-Einträge. Die erstellten Referenz-Karten wurden anschließend verwendet, um Proteine und Prozesse, in an der Interaktion mit Pflanzen beteiligt sind, zu identifizieren. Dafür wurden die Bakterien Wurzelexudaten von Mais (Zea mays L.) ausgesetzt. Die Proteine aus zwei Stämmen, denen die globalen Transkriptionsregulatoren (Degu, AbrB) und vier Sigma-Faktoren (SigB, SigM, SigV, und SigX) fehlen, wurden ebenfalls untersucht, um ihre Beteiligung an den bakteriellen Reaktionen auf die Wurzelausscheidungen zu analysieren. Zusammenfassend ist dies die erste Studie, die umfangreiche Proteomdaten von Gram-positiven PGPR präsentiert, wobei gleichzeitig die Veränderung der Expression von extrazellulären und zytoplasmatischen Proteinen, nach Zugabe von Wurzelexudaten, ausgewertet wurde.
Bacillus amyloliquefaciens strain FZB42 is a free-living bacterium that competitively colonizes plant roots and stimulates plant growth by many different modes of action. The molecular basis of singular beneficial effects that this Plant Growth-Promoting Rhizobacteria (PGPR) exert on their hosts have been studied. To decipher the molecular cross-talk of B. amyloliquefaciens and its’ host plants as a whole system, an extensive proteomic approach was performed. Reference maps of the extracellular and cytosolic protein fractions were established. The highest number of secreted proteins was observed during stationary growth phase. Identified extracellular proteins belong to different functional classes, with the most prominent classes involved in carbohydrate degradation and transportation of molecules across the cell wall. Cytosolic extracts obtained from cultures grown in 1C and minimal media subjected to the 2 Dimensional Electrophoresis (2 DE), revealed 461 and 245 different protein entries, respectively. Created reference maps were subsequently used to identify proteins and processes involved in the interaction with plants, prior to exposure of bacteria to maize (Zea mays L.) root exudates. The proteomics of two strains lacking expression of genes coding for global transcriptional regulators (degU, abrB) and four sigma factors (sigB, sigM, sigV, and sigX) were also inves-tigated, in order to analyse their involvement in bacterial responses to root exudates. In summary, this is the first study presenting comprehensive proteomics of Gram-positive PGPR, evaluating at the same time changes in protein expression caused by addition of root exudates at the extracellular and cytosolic level.

Polyaniline nanocomposites doped with poly(vinylsulphonate) (PV-SO3 &minus
) and nanostructured polystyrene (PSNP) latex beads functionalized with amine (PSNP-NH2) and sulphate (PSNP-OSO3 &minus
) were prepared and characterised for use as nitrite electro-catalytic chemosensors and ochratoxin A immunosensors. The resultant polyaniline electrocatalytic chemosensors (PANI, PANI|PSNP-NH2 or PANI|PSNP-OSO3 &minus
) were characterized by cyclic voltammetry (CV), ultraviolet-visible (UV-Vis) spectroscopy and scanning electron microscopy (SEM). Brown-Anson analysis of the multi-scan rate CV responses of the various PANI films gave surface concentrations in the order of 10&minus
8 mol/cm. UV-vis spectra of the PANI films dissolved in dimethyl sulphoxide showed typical strong absorbance maxima at 480 and 740 nm associated with benzenoid p-p* transition and quinoid excitons of polyaniline, respectively. The SEM images of the PANI nanocomposite films showed cauliflower-like structures that were <
100 nm in diameter. When applied as electrochemical nitrite sensors, sensitivity values of 60, 40 and 30 &mu
A/mM with corresponding limits of detection of 7.4, 9.2 and 38.2 &mu
M NO2 &minus
, were obtained for electrodes, PANI|PSNP-NH2, PANI and PANI|PSNP-SO3 &minus
, respectively. Immobilisation of ochratoxin A antibody onto PANI|PSNP-NH2, PANI and PANI|PSNPSO3 - resulted in the fabrication of immunosensors.

Casamento de padrões de pontos é um problema fundamental em reconhecimento de padrões. O objetivo é encontrar uma correspondência entre dois conjuntos de pontos, associados a características relevantes de objetos ou entidades, mapeando os pontos de um conjunto no outro. Este problema está associado a muitas aplicações, como por exemplo, reconhecimento de objetos baseado em modelos, imagens estéreo, registro de imagens, biometria, entre outros. Para encontrar um mapeamento, os objetos são codificados por representações abstratas, codificando as características relevantes consideradas na comparação entre pares de objetos. Neste trabalho, objetos são representados por grafos, codificando tanto as características `locais\' quanto as relações espaciais entre estas características. A comparação entre objetos é guiada por uma formulação de atribuição quadrática, que é um problema NP-difícil. Para estimar uma solução, duas técnicas de casamento entre grafos são propostas: uma baseada em grafos auxiliares, chamados de grafos deformados; e outra baseada em representações `esparsas\', campos aleatórios de Markov e propagação de crenças. Devido as suas respectivas limitações, as abordagens são adequadas para situações específicas, conforme mostrado neste documento. Resultados envolvendo as duas abordagens são ilustrados em quatro importantes aplicações: casamento de imagens de gel eletroforese 2D, segmentação interativa de imagens naturais, casamento de formas, e colorização assistida por computador.
Point set matching is a fundamental problem in pattern recognition. The goal is to match two sets of points, associated to relevant features of objects or entities, by finding a mapping, or a correspondence, from one set to another set of points. This issue arises in many applications, e.g. model-based object recognition, stereo matching, image registration, biometrics, among others. In order to find a mapping, the objects can be encoded by abstract representations, carrying relevant features which are taken into account to compare pairs of objects. In this work, graphs are adopted to represent the objects, encoding their `local\' features and the spatial relations between these features. The comparison of two given objects is guided by a quadratic assignment formulation, which is NP-hard. In order to estimate the optimal solution, two approximations techniques, via graph matching, are proposed: one is based on auxiliary graphs, called deformed graphs; the other is based on `sparse\' representations, Markov random fields and belief propagation. Due to their respective limitations, each approach is more suitable to each specific situation, as shown in this document. The quality of the two approaches is illustrated on four important applications: 2D electrophoresis gel matching, interactive natural image segmentation, shape matching, and computer-assisted colorization.

L'objectif de cette thèse a consisté à étudier des procédés de fabrication de couches de diffusion de gaz (GDL) en silicium poreux appliqués à l'intégration de micropiles à combustible de type PEMFC sur plaquette de silicium. Deux types de couches ont été étudiés : sur surface plane (2D) et sur surface texturée (3D). Les couches de diffusion de gaz ont été réalisées par l'anodisation de silicium de type N fortement résistif. Une localisation des motifs poreux a été obtenue par ouverture d'un masque en polysilicium sur oxyde thermique de silicium. Seules les GDL 2D entièrement macroporeuses assuraient un débit d'hydrogène compatible avec les objectifs de fabrication d'une micropile prototype. Le prototype a permis de valider la compabilité de la couche de diffusion de gaz avec les étapes d'empilement des couches actives constitutive de la micropile. Son fonctionnement nous a permis d'atteindre une densité de puissance de 250 mW/cm²
This thesis work deals with porous silicon gas diffusion layer (GDL) fabrication process. The aim was to integrate this GDL into proton exchange membrane micro fuel cells (PEMFC). Consequently, the GDL must be localized in specific wafer areas. We have also developed 2D and 3D structures. To produce a GDL, we have anodized low doped N type silicon subrates. thus, we have fabricated macroporous GDL and double layer structures made up of a mesaporous layer on a macroporous one. Patterning of the GDL has been obtained through a hard mask (polysilicon on top of a silicon oxide layer) or using a localized doping. We have concluded this work by achieving micro fuel cell prototypes with macroporous silicon gas diffusion layers. After validation of micro PEMFC active layer mechanical stacking, we have measured a maximum power density of about 250 mW/cm²

Dans le cadre d'une thématique générale du Laboratoire Thermique Energétique et Procédés de Pau consacrée à l'étude et l'optimisation d'opérations de séparation solide/liquide tels que le séchage, la déshydratation imprégnation par immersion ou la filtration-compression, le travail porte sur la modélisation des phénomènes de transports de masse, d'énergie et de quantité de mouvement en milieu déformable diphasique solide/liquide, la phase liquide étant binaire. Tout en tenant compte de la diffusion et du comportement rhéologique, la thèse se focalise particulièrement sur la description du transport convectif de la phase liquide sans compromettre la physique par la traditionnelle introduction d'un coefficient de transport équivalent sans fondements. La première étape de la modélisation consiste à décrire classiquement le mouvement de chacune des deux phases continues. Bien qu'à cette échelle les mécanismes soient parfaitement décrits, le passage à la simulation impose une étape d'homogénéisation par prise de moyenne. Ce changement d'échelle, décrit dans une deuxième partie, conduit à un système d'équations à l'échelle locale dans lequel apparaît la loi de Darcy. Le gradient de pression de la phase liquide, moteur naturel du transport, est conservé au détriment de l'habituel gradient de teneur en liquide trouvé dans la littérature suite à l'introduction d'une loi liant pression et fraction volumique liquide. Sans fondements physiques, cette relation se traduit par le coefficient de transport équivalent qui doit être estimé par identification sur des résultats expérimentaux, liant injustement le modèle au procédé. On montre comment l'utilisation d'une telle loi peut être évitée en exploitant simultanément la conservation du volume solide (incompressibilité) et la conservation de la masse solide. Dans la littérature, la première se substitue à la seconde pour en éviter la résolution. Le modèle est ensuite appliqué au séchage convectif 2D d'un milieu élastique linéaire. L'examen des simulations ne révèle aucun lien entre le gradient de pression, moteur du mouvement convectif, et le gradient de teneur en eau, contrairement aux affirmations de la littérature
One of the themes of the " Laboratoire Thermique Energétique et Procédés de Pau " is the study and the optimisation of separation processes as drying, dehydration Impregnation soaking or filtration for example. In this context, this work deals with modelling of energy, mass and momentum transport phenomena in a deformable solid/binary liquid medium. The thesis deals with diffusion and rheological behaviour and focuses on the description of the liquid phase convective transport without introducing an usual non physical equivalent transport coefficient. Conservation equations are first written for each phase. The macroscopic partial differential equations are derived by integrating over a representative volume these microscopic conservation laws. By introducing at phase scale the rheological behavior of a classic fluid for the liquid phase and by integrating the obtained equation, Darcy's law is established. This law links the average liquid velocity to the natural driving force : the pressure gradient. The difficulty is then to express the average pressure of the liquid phase which cannot be deduced from the capillary pressure like in three-phase media. In the literature, authors get round this difficulty by introducing arbitrarily a phenomenological law which supposes that the pressure depends on the liquid volume fraction. This law constitutes an important limitation to the analysis of transport mechanisms. From a physical point of view, the driving force is undoubtedly without any foundations. From a practical point of view, an equivalent transport coefficient must be identified numerically by matching experimental and predicted data in such a way that model and process become dependant. The main novelty of the model proposed is that such a law is not introduced by keeping solid mass conservation and solid volume conservation together. Modelling is then applied to the convective drying of an elastic medium. Two dimensional simulations show notably that pressure gradient and moisture gradient are not linked contrary to the literature hypothesis

The work presented in the thesis is focused on the synthesis of diverse colloidal semiconductor NCs in organic media, their surface design with tiny inorganic and hybrid capping species in solution phase, and subsequent assembling of these NC building units into two-dimensional close-packed thin-films and three-dimensional non-ordered porous superstructures.

Mestrado em Bioquímica
Staphylococcus pseudintermedius is an opportunistic pathogenic bacterium responsible for most skin and post-surgical infections in dogs. The number of bacterial strains resistant to β-lactam antibiotics is increasing and are the major challenges now faced by veterinary medicine. Bacteria that produce biofilm are more resistant to treatment and thus, the production of this structure is already considered a virulence factor. In a biofilm, bacteria are embedded in a matrix of extracellular polymeric substances (EPS) some of which are proteins. With the objective to know more of this array element, the characterization of the biofilm matrix proteome (BMP) from a highly virulent S. pseudintermedius strain isolated from a dog with severe pyoderma was performed. Biofilm was developed by culturing the S. pseudintermedius strain 5819/10 in specific media. The biofilm matrix was then be separated from bacterial cells and evaluated for their protein content and complexity. Finally, the proteome was separated by 1D electrophoresis and characterized by nanoLC-ESI-Q-TOF and analysed using bioinformatics tools. The BMP of strain S. pseudintermedius 5819/10 consisted in a diverse group of proteins, where 63% of the proteins could be related to either the extracellular region or the plasma membrane, as protein complexes, and most of them had functions essential to cell survival. However, it was not possible to establish a clear relation between them and biofilm formation. Proteins known to be involved in biofilm formation consisted mostly of regulator factors of biofilm formation as well as virulence factors of-mainly-bacterial cell adhesion and host colonization. The prevalence of adhesins and the almost total absence of proteins involved in EPS synthesis pointed to a biofilm matrix where cells are directly or indirectly closely glued together to each other.
Staphylococcus pseudintermedius (S.pseudintermedius) é uma bactéria patogénica oportunista, responsável pela maioria das infeções cutâneas e pós-cirúrgicas em cães. O número de estirpes resistentes a antibióticos β-lactâmicos está a aumentar constituindo actualmente um dos grandes desafios enfrentados pela medicina veterinária. As bactérias mais resistentes ao tratamento são aquelas que produzem biofilme sendo esta capacidade considerada um fator de virulência. Num biofilme, as bactérias estão envoltas numa matriz de substâncias poliméricas extracelulares (SPE), algumas das quais são proteínas. Tendo por objectivo obter mais informação acerca do biofilme, foi caracterizado o proteoma da matriz do biofilme de uma estirpe bastante virulenta de S. pseudintermedius isolada de um cão com piodermite profunda. Para tal cultivaram-se biofilmes da estirpe de S. pseudintermedius 5819/10 em meio apropriado, separou-se a matriz das suas células bacterianas e avaliou-se as proteínas presentes quanto ao seu conteúdo e complexidade. Posteriormente o proteoma foi separado por electroforese 1D, caracterizado por nanoLC-ESI-Q-TOF e analisado usando ferramentas bioinformáticas Constatou-se que o proteoma da matriz do biofilme da estirpe 5819/10 de S. pseudintermedius é muito diverso e que 63% das proteinas podem estar relacionadas com a região extracelular do biofilme ou da membrana plasmática na forma de complexos proteicos. Verificou-se também que a maioria das proteínas identificadas possui funções essenciais para a sobrevivência da bactéria mas não foi possível estabelecer uma relação clara entre elas e a formação de biofilmes. Algumas proteínas que se sabe estarem envolvidas na formação de biofilmes foram identificadas, tratam-se principalmente de factores reguladores da formação de biofilme e outros factores de virulência relacionados com a colonização de um hospedeiro a adesão bacteriana a uma superfície. A prevalência de adesinas e a ausência quase total de proteínas envolvidas na síntese de SPEs, forneceu dados que apoiam a hipótese que a matriz do biofilme do S. pseudintermedius 5819/10 seja constituída por células directamente ou indirectamente unidas entre si.

碩士
淡江大學
資訊工程學系碩士班
95
In proteomics, 2D gel electrophoresis plays a very important role. We need some processes on these 2D gel electrophoresis images to get information we want. These processes include detection and registration of protein spots. Traditionally, researchers can pick protein spots in the gel images manually. As a result, they spent much time but still made mistakes. For this reason, we proposed a system to assist researchers in dealing with this problem and analyzing protein characteristics. For instance, we got two 2D gel images. One is protein with germs infective, the other is protein with germs anti-infective. In two images, protein spots are different from each other. We take results of detection of protein spots to determine if protein spots change in two images. These changes like getting bigger or smaller, darker or lighter, even disappearing. And, these protein spots are what we are interested. Therefore, we design a system in accordance with demands of researchers. In this system, we mainly take results of detection of protein spots in 2D gel images and develop follow-up capability of matching protein spots. We use methods on mathematics, that is, to select several pairs of spots in two images as landmarks, and then we can find an equation that could transform the source image into the target image. Thus, all spots in images will satisfy this equation and our aim to match these protein spots will be achieved. We show our results of matching depending on demands of users to let them get results efficiently.

碩士
淡江大學
資訊工程學系碩士班
94
2D gel electrophoresis plays an important role in proteomics. It can not only separate protein spots effectively but also identify and quantify the function of proteins. Traditionally, researchers can merely pick protein spots in the gel images with manpower. As a result, the efficiency of the research is critically reduced, and lots of mistakes take place at that time. Therefore, we proposed a system to deal with 2d gel images and to solve this problem. In this system, we mainly use some methods in morphlolgy, for example, we hope to retrieve protein spots from complicated gel images within watershed images segmentation algorithm. When it comes to images segmentation, watershed is the commonest approach, for its ability to segment boundary of spot objects. On the contrary, problems of over segmentation usually occur due to the production of too many local minimums, and this will cause fracture division. As a result, a few pre-processing procedures which can be easily achieved with existing filters should be utilized to improve the effect. By the way, we can also modify local minimums on gradient images before doing images segmentation with images reconstruction technique, that is, local minimums on the protein spots are kept while others are repaired. Therefore, problems of over segmentation can be avoided, and boundary of spots produced are quite complete, too.Using these method, we can detect all of the protein spots in 2D gel images. The system is also able to assign ID numbers to the protein spots and retrieve some annotated information of the spots such as area or location, which can be further analyzed for more researches. Finally, the comparison between the proposed system and another commercial software called Image Master is proceeded, which stands for the reliability of our system.

碩士
國立雲林科技大學
材料科技研究所
99
In this study, several polyol were used to prepare zinc oxide nanoparticles. The relationship between the morphology and the characteristics was researched. Zinc alkoxide were prepared by hydrolyzing zinc acetate dehydrate in the solvents ethyleneglycol (EG), glycerol (G), or diethylene glycol (DEG) at 160?aC, and then were self-assembly into zinc oxide nanostructures with the shape fibers, flakes, or spheres. Effects of various concentrations on the morphology and the change before and after calcinations at 500?aC were studied. X-ray diffraction (XRD) method was used to identify the crystal structures of the zinc oxides. The results were compared with the ones made by a field emission transmission electron microscope (FE-TEM). The results show that the nanostructures are polycrystals. Observations of the surface morphology were made by a field emission scanning electron microscope (FE-SEM). Heat loss and phase change of the nanostructures were studied by a thermogravimetric analyzer/differential scanning calorimeter (TGA/DSC). In this study, optical property and optical catalysis were studied also for different morphology of the zinc oxide. A photoluminescence (PL) was used to study the light emission for different morphology of the zinc oxide. Specific surfaces of the nanoparticles were measured by a specific surface meter. The surface data are useful in the prediction of applications in the catalysis. Catalytical efficiencies were measured by the degradation of methylene blue. ZnO fiber was found to have the best catalytical efficiency. In summary, we have prepared successfully fibers, flakes, and sphere zinc oxide nanostructures by the use of polyol.

碩士
國立清華大學
化學工程學系
95
Two dimensional (2D) chromophore, 9-Hexyl-3,6-di (2’-(6-hydroxy hexyl)sulfonylphenyl)-1’-ethenyl)-9H-carbazole(Cz2PhSO2OH), and one dimensional (1D) chromophore 4-N,N-Bis(2- hydroxy ethylene) amine-4’- nitroazobenzene (DR19) with two reactive site proceeded sol-gel process were studied to compare the effects between dimension of chromophore and nonlinear optical (NLO)stability. Hybrid NLO film with another 2D chromophore,9-Hexyl-3,6-di(2’-(6-hexyl)sulfonylphenyl)-1’-ethenyl) -9H– carbazole (Cz2PhSO26C) ,was studied to compare the influence between physical and chemical bonding. The results show that due to the reinforcement of SiO2 polymeric structure , hybrid NLO films with covalent-bonded 2D chromophore were highly improved in temporal and thermal dynamic stability. There is no decay in second harmonic coefficient (d33) at 100℃ for 200 hr. Effective transition temperature (T0) was raised with the enhancement of temperature and time by means of increasing degree of cross-linking , though d33 owns an optimal value. Moreover, by controlling the poling condition, the degree of cross-linking of SiO2 matrix with 2D and 1D chromophore is identical. As for thermal dynamic stability, NLO films with 2D chromophore (T0 = 110℃) are obviously better than with 1D chromophore (T0 = 80℃). As for temporal stability, effective second order harmonic coefficient (deff) of NLO film with 2D chromophore (65%) is better than with 1D chromophore (30%) under individual effective transition Temperature. For hybrid NLO film, the 2D chromophore would be sublimed during poling process since no chemical bondings between chromophore and matrix.

碩士
臺中技術學院
資訊科技與應用研究所
98
Proteomics, the study on proteins, was first introduced in 1995 by V. Wasinger. Techniques developed, thereafter, for the study of proteins can effectively analyze and identify the various types of protein in very short time. These resulted in increase protein researches using these techniques to study normal and diseased tissue organization; pathogenic and non-pathogenic bacteria; before and after treatment; and protein changes within cells. Proteomics is gradually becoming widely applied in bioinformatics, disease diagnosis and drug therapy design. Currently, the 2DGE image is a popularly used method in the medical community for studying proteins via the electrophoresis separation of proteins. After electrophoresis the protein spots are distributed on a gel. The amount of proteins on the gel is different and their color gradient dependent on the staining. The photographed proteins of the 2DGE images are also dependent on image resolution and brightness contrast settings (controlled by shutter exposures). An inaccurate image could sometimes cause wrong disease diagnostic and also wrong administration of drugs to a patient. viii The High Dynamic Range (HDR) is a technique that renders images photographed in different exposures. This technique ensures the detailed information of an image by rendering images taken at different exposures so that details from different contrastive can preserved in the resulting image. In the proposed research, this concept is applied to the 2DGE images photographed in different brightness at different exposures so that all details on the protein information are retained. Therefore the need to store the different resolution images is important and essential. Currently, the two classes of commonly used lossless compression methods can be distinguished as compression software tools and image compression methods. Compression software tools include WINRAR, WINZIP, 7-ZIP and more. On the other hand, image compression methods include JPEG2000, JPEG-LS, GIF and more. In the paper, we proposed using the Jpeg-LS compression method with its low complexity and high compression efficiency and integrated it with HDR; the improved propose method is called the HDR JPEG-LS compression method. With HDR JPEG-LS, we can effectively increased compression rate and to retain more protein information that is essential for accurate medical diagnostics. Furthermore, the technique can be used to project images for a different exposure based on existent images to study for possible missing protein details to ensure accurate diagnostics.

On retrouve dans le complexe Chrosomus eos-neogaeus une forme cybride ayant le génome nucléaire de C. eos et le génome mitochondrial de C. neogaeus. Ce modèle particulier fournit une occasion unique d’étudier l’influence d’une mitochondrie exogène sur le métabolisme et la physiologie d'organismes vivant en milieu naturel, et s'étant donc adaptés à cette situation cellulaire atypique. La mitochondrie jouant un rôle fondamental vital, nous nous attendons à ce que la présence d’une mitochondrie exogène chez la forme cybride ait un impact sur l’expression de son génome et du protéome qui en découle. L’objectif de ce projet est d’étudier les différences au niveau protéomique entre des individus C. eos purs (forme sauvage) et des cybrides provenant d'habitats similaires afin de faire ressortir au maximum les différences dues à la présence de mitochondries C. neogaeus chez la forme cybride. Pour ce faire, nous avons comparé les protéomes des formes cybride et sauvage en utilisant l'électrophorèse en deux dimensions. Un sous-groupe de protéines produisant un signal spécifique révélé par l’analyse comparative a été identifié et analysé par spectrométrie de masse (LC/MS). Les résultats indiquent que la présence de mitochondries C. neogaeus chez le cybride influence fortement la régulation génique chez ce dernier. De plus, les protéines identifiées apportent des pistes intéressantes supportant l'hypothèse que la présence de mitochondries C. neogaeus chez le cybride rendrait ce biotype plus résistant au froid que la forme sauvage.
The Chrosomus eos-neogaeus genetic complex regroups different forms of hybrids of these two species, among which a cybrid form, that harbours the nuclear genome of C. eos and the mitochondria of C. neogaeus. This peculiar model is thus a unique opportunity to study the influence of an exogenous mitochondria on the metabolism and cellular physiology in a living animal in the wild, and thus perfectly adapted to this atypical cellular environment. Mitochondria being at the core of fundamental biological processes, we expect that the presence of foreign mitochondria will modify gene expression and the resulting proteome of these fishes. The overall goal of this master thesis is thus to compare the proteome of pure (wild type) C. eos with the cybrid form sampled in similar lakes from the same geographical area so that most differences could be attributed to the different mitochondrial genomes. To achieve this goal, we used two dimensional electrophoresis. We selected a sub-group of proteins that showed the most extreme expression differences and identified these spots by mass spectrometric analyses (LC/MS). Results demonstrate that C. neogaeus mitochondria has a strong influence on gene expression in cybrid. Proteins identified bring new clues supporting the hypothesis that cybrid are more cold tolerant than the wild type biotype.

Philosophiae Doctor - PhD
Obesity is a medical condition in which an energy imbalance leads to excessive accumulation of body fat. Obesity leads to a reduction in life expectancy through its association with chronic diseases of lifestyle. The prevalence of obesity is rapidly increasing throughout the world. It is now accepted that most cases of obesity result from an interaction between genetic and environmental factors. This rapid increase in obesity generally leads to an increase in morbidity and mortality from chronic diseases such as cardiovascular disease, type 2 diabetes, osteoarthritis and cancer of which obesity is a risk factor. There is a lack of information in molecular research to explain how obesity predisposes individuals to these diseases. Proteomics is a molecular tool and a set of techniques used to identify changes at protein level from a diseased state. This study aims to identify differentially expressed proteins in serum of obese rats fed different isocaloric diets using proteomics.

Die Demenz mit Lewy-Körperchen (DLB) ist eine progrediente neurodegenerative Erkrankung und stellt nach der Alzheimer-Erkrankung eine der häufigsten Ursachen einer Demenz dar. Betroffene leiden neben dem zentralen Merkmal Demenz an Fluktuationen der Kognition, Parkinsonismus und visuellen Halluzinationen. Charakteristische neuropatholgische Kennzeichen der DLB sind α-Synuklein-enthaltende Lewy-Körperchen und -Neuriten, die sich in kortikalen und subkortikalen Hirnregionen finden. Bei der klinischen Diagnostik dieser Erkrankung sind neben der Beurteilung klinischer Befunde laborchemische, psychometrische, apparative und bildgebende Verfahren von Bedeutung, jedoch ist eine sichere Diagnose nur bioptisch zu stellen. Gegenstand dieser Arbeit war die Untersuchung des Liquorproteomprofils von DLB-Patienten im Vergleich zu neurologisch gesunden Kontrollen und die Identifikation von regulierten Proteinen im Liquor bei der DLB durch Verwendung klassischer Methoden der Proteomik. Nach initialer Depletion von zwölf häufigen Proteinen wurden die Liquorproben mittels zweidimensionaler Gelektrophorese aufgetrennt, die Proteinexpressionsmuster quantitativ verglichen und anschließend insgesamt 23 verschiedene Proteine aus 44 regulierten Gelspots massenspektrometrisch identifiziert. Es fanden sich Proteine involviert in die Immunantwort, den Lipidstoffwechsel, den Glukosestoffwechsel, die Signaltransduktion und die Zellstruktur sowie einige, die sich keiner dieser funktionellen Gruppen zuordnen ließen. Von vier ausgewählten Proteinen - Complement C4a, Transthyretin, Contactin-1 und Chromogranin A - wurden Western Blots angefertigt, wofür Liquor sowohl von DLB-Patienten und gesunden Kontrollen als auch zum weiterführenden Vergleich von Parkinson- und Alzheimer-Patienten verwendet wurde. Die Ergebnisse dieser Arbeit zeigen auf Proteinebene die Vielfalt der biologischen Prozesse, die bei der DLB gestört ist. Zum Teil lassen sich Parallelen zu anderen neurogenerativen Erkrankungen erkennen, einige Proteine konnten jedoch erstmalig und einzig als bei der DLB reguliert nachgewiesen werden.

Indiana University-Purdue University Indianapolis (IUPUI)
Winter survival is variable among commercially grown strawberry (Fragaria x ananassa) cultivars. The main objectives of this study were to evaluate the molecular basis that contribute to this difference in strawberry cultivars and to identify potential biomarkers that can be used to facilitate the development of new strawberry cultivars with improved overwintering hardiness. With these goals in mind, the freezing tolerance was examined for four cultivars, ‘Jonsok’, ‘Senga Sengana’, ‘Elsanta’, and ‘Frida’ (listed from most to least freezing tolerant based on survival from physiological freezing experiments) and the protein expression was investigated in the overwintering relevant crown structure of strawberry. Biomarker selection was based on comparing the protein profiles from the most cold-tolerant cultivar, ‘Jonsok’ with the least cold-tolerant cultivar ‘Frida’ in a comprehensive investigation using two label-free global proteomic methods, shotgun and two dimensional electrophoresis, with support from univariate and multivariate analysis. A total of 143 proteins from shotgun and 64 proteins from 2DE analysis were identified as significantly differentially expressed between ‘Jonsok’ and ‘Frida’ at one or more time points during the cold treatment (0, 2, and 42 days at 2 ºC). These proteins included molecular chaperones, antioxidants/detoxifying enzymes, metabolic enzymes, pathogenesis related proteins and flavonoid pathway proteins. The proteins that contributed to the greatest differences between ‘Jonsok’ and ‘Frida’ are candidates for biomarker development. The novel and significant aspects of this work include the first crown proteome 2DE map with general characteristics of the strawberry crown proteome, a list of potential biomarkers to facilitate the development of new strawberry cultivars with improved cold stress tolerance.

Here we report the identification and approximate quantification of cytochrome P450 (CYP) proteins in human liver microsomes as determined by nano-LC-MS/MS with application of the exponentially modified protein abundance index (emPAI) algorithm during database searching. Protocols based on 1D-gel protein separation and 2D-LC peptide separation gave comparable results. In total, 18 CYP isoforms were unambiguously identified based on unique peptide matches. Further, we have determined the absolute quantity of two CYP enzymes (2E1 and 1A2) in human liver microsomes using stable-isotope dilution mass spectrometry, where microsomal proteins were separated by 1D-gel electrophoresis, digested with trypsin in the presence of either a CYP2E1- or 1A2-specific stable-isotope labeled tryptic peptide and analyzed by LC-MS/MS. Using multiple reaction monitoring (MRM) for the isotope-labeled tryptic peptides and their natural unlabeled analogues quantification could be performed over the range of 0.1-1.5 pmol on column. Liver microsomes from four individuals were analyzed for CYP2E1 giving values of 88-200 pmol/mg microsomal protein. The CYP1A2 content of microsomes from a further three individuals ranged from 165 to 263 pmol/mg microsomal protein. Although, in this proof-of-concept study for CYP quantification, the two CYP isoforms were quantified from different samples, there are no practical reasons to prevent multiplexing the method to allow the quantification of multiple CYP isoforms in a single sample.