O cancro cítrico é uma das doenças mais temidas da citricultura devido ao seu poder de proli-feração nas fazendas, aos danos causados às plantas e aos frutos e à forma de combate adota-da pelos órgãos responsáveis através da erradicação das plantas contaminadas e de outras em sua vizinhança. No Brasil, um dos principais motivos que minimiza a eficiência da erradicação do cancro cítrico é a confirmação do diagnóstico, que necessita ser realizada em alguns laboratórios credenciados. A análise de muitas amostras em conjunto com o tempo gasto com o transporte aumenta a chance de proliferação da doença no campo. Neste trabalho aplicamos técnicas de espectroscopia da fluorescência em folhas de culturas cítricas na intenção de pro-por um método de diagnóstico do cancro cítrico a ser realizado na fazenda e com resposta em tempo real. As amostras experimentais são folhas de variedades cítricas sadias e contaminadas com cancro ou outras doenças. Iniciamos o trabalho aplicando espectroscopia da fluorescência no laboratório. Os resultados provaram a viabilidade do método, mas revelou uma enorme sobreposição de dados ao tentar discriminar o cancro de outra doença. Análises com-plementares nos revelaram que os experimentos deveriam ser feitos no campo, identificando plantas contaminadas e tomando a fluorescência de folhas sadias como referência. A espec-troscopia da fluorescência no campo foi feita com um espectrômetro portátil. O resultado nos possibilitou propor critérios de discriminação do cancro baseado em figuras de mérito. O melhor critério apresentou 79% de acertos, com 88% de sensibilidade e 68% de especificidade. Concluímos que os valores poderiam ser melhores se a espectroscopia fosse realizada com imagens, pois as variações do espectro ocorrem devido ao posicionamento da fibra na lesão do cancro. Passamos a estudar a espectroscopia das imagens da fluorescência com um sistema baseado em um espectrógrafo. Os resultados provaram a viabilidade do estudo e revelaram particularidades espaciais e espectrais das doenças. Infelizmente essa instrumentação só pode ser usada no laboratório, por isso optamos por desenvolver outro sistema mais simples e robusto, a base de uma roda de filtros com filtros passa-banda. Os re-sultados revelaram novas particularidades espaciais e espectrais das amostras, porém nos revelou a necessidade de um processamento de imagem para obter análises quantitativas. O sistema de imagens com filtro ainda foi usado em outro experimento complementar onde as imagens forneceram resultados quantitativos, provando a funcionalidade da técnica. / Citrus canker is one of the most feared diseases of citrus due to its dissemination in the farms, the damage caused to plants and fruits and how to combat adopted by national government through the eradication of infected plants and others in your neighborhood. In Brazil, one of the main reasons that minimizes the effectiveness of citrus canker`s eradication is the confir-mation of the diagnosis by specialized laboratories. The time spent to transport and to analyses many samples increases the chance of canker spreading in the field. In our work we apply spectroscopic techniques of fluorescence in leaves of citrus crops with the aim to propose a method for diagnosis of citrus canker to be held on the farm and real-time response. The expe-rimental samples are leaves of healthy citrus varieties and contaminated with canker or other diseases. We began the work by applying fluorescence spectroscopy in the laboratory. The results proved the feasibility of the method, but showed a huge overlap of data to try to dis-criminate cancer from other diseases. Further analysis revealed that those experiments should be done in the field, focusing to identify infected plants and taking the fluorescence of healthy leaves as a reference. Fluorescence spectroscopy in the field was made with a portable spectrometer. The result allowed us to propose some criteria for canker discrimination based on figures of merit. The best criteria presents 79% correct tests, with 88% sensitivity and 68% specificity. We conclude that these values could be better if the spectroscopy was performed with images, because the variations of the spectrum are due to the positioning of the fiber over the canker lesion. We study the spectroscopy of fluorescence images with a system based on a spectrograph. The results proved its feasibility and revealed spatial and spectral particular features of the diseases. Unfortunately, this instrumentation can only be used in the laborato-ry, so we decided to develop another system more simple and robust. The new system is based on a filter wheel with band-pass filters. The results revealed new spatial and spectral characteristics of the samples, but revealed the need for an image processing for quantitative analysis. This imaging system was still used in another supplementary experiment where the images have provided quantitative results, proving the functionality of the technique.

Le stratum corneum (SC), couche supérieure de l’épiderme, est composé principalement de cornéocytes entourés d’une matrice lipidique. Cette structure particulière confère au SC son rôle de barrière et protège l’organisme de la perte en eau, de la pénétration de substances exogènes et de l’irradiation ultra-violette (UV). La matrice lipidique du SC est constituée de trois lipides majeurs : les céramides, les acides gras et le cholestérol organisés en phase cristalline. Cette matrice est la principale voie de pénétration des molécules exogènes à travers la peau. L’estimation de l’absorption cutanée pour l’analyse du risque des produits cosmétiques est basée sur les recommandations de l’Organisation de Coopération et de Développement Économiques (OCDE) qui prend en compte les propriétés physicochimiques des molécules i.e. Log Pow (lipophilie) et MW (masse moléculaire). En effet, l’OCDE considère une absorption de 100% pour une molécule ayant une MW inférieure à 500g/mol et un Log Pow compris en -1 et +4. En dehors de ces valeurs, l’OCDE applique une estimation de 10%. Hors, cette estimation est bien souvent loin de la réalité et a besoin d’être affinée. Notre travail s’est focalisé sur le développement d’un critère d’évaluation de la pénétration cutanée afin de moduler les données de l’OCDE par trois approches différentes : chromatographie d’affinité, spectroscopie de fluorescence et microspectroscopie infra-rouge à transformée de Fourier (FTIR) avec une source synchrotron. Etant donné que les propriétés barrières de la peau sont étroitement liées à la composition en céramides du SC, les méthodes développées en chromatographie d’affinité et spectroscopie de fluorescence se sont focalisées sur l’interaction céramide-molécules. Un critère prédictif de la pénétration percutanée a été défini avec chacune de ces méthodes :  et I. La troisième méthodologie a consisté à développer un autre critère (Sindex) par microspectroscopie FTIR avec une source synchrotron. La distribution cutanée des molécules a été suivie sur coupes microtomées de biopsies humaines. A partir de Sindex, une cartographie prédictive de la pénétration percutanée des molécules a été établie. Notre design expérimental comprenait des molécules (filtres UV, conservateurs, actifs cosmétiques) avec des Log Pow et MW variés (cf annexe 1). La pénétration cutanée de ces molécules a été étudiée avec une méthode de référence : cellules de Franz couplées à la chromatographie. Ces données de référence ont servi à valider les modèles et critères prédictifs développés. Ce travail a permis d’explorer de nouvelles pistes pour l’étude prédictive de la pénétration percutanée et de développer ainsi de nouveaux critères. Utilisés en complément des propriétés physicochimiques des molécules, ces nouveaux critères permettent d’affiner l’estimation de la pénétration cutanée de molécules exogènes pour l’analyse du risque. / The stratum corneum (SC) is the upper skin layer and due to its particular composition, corneocytes embedded in a lipidic matrix, it owns a role of barrier function and protects our body against water loss, penetration of exogenous molecules and UV irradiation. Its lipidic matrix is composed of three major lipids: fatty acids, cholesterol and ceramides, organised in liquid crystalline phase. This high cohesion creates cement between corneocytes. This cement is the principal pathway taken by the exogenous molecules to penetrate the skin. Percutaneous penetration estimation of cosmetic products is today based on the Organisation for Economic Co-operation and Development (OECD) recommendations, regarding molecules structural characteristics i.e. Log Pow (polarity) and MW (molecular weight). The OECD claims that 100% dermal absorption may be assumed if the exogenous molecule molecular mass is lower than 500 g/mol and Log Pow ranged between -1 and +4. Besides these values, a 10% coefficient is applied. This approach is sometimes far from reality. Our work focused on developing new evaluation criteria of percutaneous penetration from three different approaches: affinity chromatography, fluorescence spectroscopy and FTIR microspectroscopy with a synchrotron source in order to modulate OECD predictions. Considering that skin barrier properties are closely linked to ceramide composition and conformation within the SC, two methods were developed to study the interaction between ceramides and exogenous molecules by affinity chromatography and fluorescence spectroscopy. A predictive criterion of percutaneous penetration was developed from each of these methods:  and I. The third methodology consisted of developing a predictive criterion, Sindex, by FTIR microspectroscopy with a synchrotron source, on microtomized cuts of human skin biopsies. A predictive cartography was build from Sindex. Our experimental design included exogenous molecules (e.g. UV filters, preservatives, cosmetic actives) with various Log Pow and MW (cf annexe 1). Molecules skin penetration was studied with a Franz cell device coupled to HPLC analysis. These results served as reference data to validate our predictive models and criteria.This work permitted to set up new methods for predicting skin penetration of exogenous molecules and to develop complementary predictive criterion to Log Pow and MW. These new criterion will serve to modulate OECD predictions.

A bactéria Xylella fastidiosa (X. fastidiosa) é um patógeno de planta que causa a clorose variegada dos citros, também conhecida como amarelinho. Xylella fastidiosa é uma bactéria limitada ao xilema, sendo transmitida de planta a planta através de insetos vetores. Através da determinação experimental da seqüência primária de algumas proteínas marcadamente expressas pela X. fastidiosa e a comparação destas com seqüências de ácidos nucléicos do genoma identificou entre elas três ORFs codificadoras de proteínas que podem estar relacionadas à patogenicidade desta bactéria no seu hospedeiro. No entanto, a função biológica destas proteínas ainda não foi funcionalmente caracterizada. Para investigar o papel biológico e realizar estudos de estrutura e função, as ORFs correspondentes as proteínas hidroxinitrila liase, corismato sintase e proteína D do sistema de transporte e secreção Tat foram clonadas, seqüenciadas e expressas em Escherichia coli. As proteínas recombinantes expressas foram purificadas por cromatografia de afinidade e suas identidades verificadas por seqüenciamento. As proteínas purificadas foram encontradas como uma única banda em SDS-PAGE. As proteínas recombinantes, pela primeira vez isoladas, foram caracterizadas em termos de estabilidade conformacional e comportamento estrutural frente a mudanças de pH e temperatura utilizando-se as espectroscopias de dicroísmo circular e fluorescência. O sucesso na construção do gene sintético e na clonagem em vetores de expressão de E. coli resultou em quantidade satisfatória de expressão das proteínas recombinantes. Duas delas apresentaram-se na formas solúveis, facilmente purificadas e ativas e permitindo suas caracterizações. / Xylella fastidiosa is the causal agent of citrus variegated chlorosis, also known as \"amarelinho\". Xylella fastidiosa inhabits exclusively the xylem vessels, and is transmitted by sharpshooter vectors. The experimental determination of the primary sequence of some markedly expressed proteins for X. fastidiosa and the comparison with the nucleic acids sequence of its genome aided the identification of three of them as being proteins involved in host pathogenicity. However, the biological role of these proteins should be assigned experimentally. In order to investigate the biological role, function and structure, ORFs corresponding to hydroxynitrile liase, chorismate synthase and type V secretory pathway proteins were cloned, sequenced and expressed in Escherichia coli. The expressed recombinant proteins were purified by immobilized metal affinity chromatography (Ni-NTA resin) and their identities were verified by protein sequencing. The purified proteins were found as a single band on SDS-PAGE. The successful cloning and heterologous expression of recombinant HNL in E. coli resulted in a satisfactory amount of expressed protein. Two of the expressed recombinant proteins were soluble, easily purified, and isolated in an active form. X. fastidiosa recombinant proteins, for the first time isolated, were characterized according to enzyme conformational stability and structural behavior as a function of pH and temperature using circular dichroism and fluorescence spectroscopy.

Absolute K-shell x-ray cross sections and Auger-electron cross sections are measured for carbon for 0.6 to 2.0 MeV proton incident on CH₄, n-C₄H₁₀ (n-Butane), i-C₄H₁₀ (isobutane), C₆H₆ (Benzene), C₂H₂ (Acetylene), CO and CO₂. Carbon K-shell fluorescence yields are calculated from the measurements of x-ray and Auger-electron cross sections. X-ray cross sections are measured using a variable geometry end window proportional counter. An alternate method is described for the measurement of the transmission of the proportional counter window. Auger electrons are detected by using a constant transmission energy Π/4 parallel pi ate electrostatic analyzer. Absolute carbon K-shell x-ray cross sections for CH₄ are compared to the known results of Khan et al. (1965). Auger-electron cross sections for proton impact on CH₄ are compared to the known experimental values of RΦdbro et al. (1979), and to the theoretical predictions of the first Born and ECPSSR. The data is in good agreement with both the first Born and ECPSSR, and within our experimental uncertainties with the measurements of RΦdbro et al. The x-ray cross sections, Auger-electron cross sections and fluorescence yields are plotted as a function of the Pauling charge, and show significant variations. These changes in the x-ray cross sections are compared to a model based on the number of electrons present in the 2s and 2p sub shells of these carbon based molecules. The changes in the Auger-electron cross sections are compared to the calculations of Matthews and Hopkins. The variation in the fluorescence yield is explained on the basis of the multiconfiguration Dirac-Fock model.

Alzheimer’s disease (AD) is currently considered the most prevalent neurodegenerative disease and places a large financial burden on society as healthcare resources are limited and the disease does not have a cure. Alzheimer’s disease is characterized by the presence of amyloid beta (Aβ) plaques and neurofibrillary tangles; however current literature suggests Aβ oligomers are the main aggregating species leading to AD symptoms. Therefore, the underlying cause of Alzheimer’s, accumulation of amyloid beta, is currently being studied in hopes of developing treatment options. Our research aims at determining the mechanism and kinetics of Aβ oligomer dissociation into non-toxic monomers in the presence of denaturants or small molecule dissociators. These highly active small molecule dissociators, selected from the Apex Screen 5040 library, were previously identified by ELISA studies by the laboratory of Dr. Harry LeVine. We have used fluorescence correlation spectroscopy (FCS) to characterize the size distribution and mole fraction of synthetically prepared fluorescein labeled Aβ (1-42) oligomers. Our FCS results show that in the presence of denaturants or small molecule dissociators, oligomer dissociation may proceed by at least two different mechanisms; high order cooperative dissociation and linear dissociation. A cooperative mechanism is more desirable for therapeutics as oligomer directly dissociates into monomer rather than through various oligomer intermediates. Our FCS studies show the most efficient dissociators proceed through the cooperative dissociation mechanism. We also observed a large retardation of the oligomer dissociation in the presence of gallic acid. We also started preliminary work to develop a total internal reflection fluorescence (TIRF) spectroscopy method to image Aβ (1-42) oligomers. This technique if successful will help to verify the two distinct mechanisms seen by FCS or determine if there is one mechanism that occurs at different rates as TIRF allows for faster analysis.

This Thesis is a characterization study on substances having potency as drugs as well as on a lipid based drug-delivery matrix. The optical properties of newly synthesized molecules with proven pilicide properties have been characterized with several spectroscopic methods. These methods include optical absorption and fluorescence as well as time-resolved fluorescence. Upon covalently linking compounds with high quantum yields of fluorescence to specific parts of the pilicide, the biological impact was found to increase for some of the derivatives. Furthermore, by expanding the aromatic part of the pilicide molecule, a significant increase in the inherent fluorescence was obtained. The S0-S1 absorption band for these molecules was found to originate from an impure electronic transition, vibronically promoted by intensity borrowing from higher electronic states. Included in this Thesis is the measurement of how deeply some in this class of newly synthesized molecules become situated when placed inside ganglioside GM1 micelles, and how the molecules’ reorientation is affected. By means of radiation-less energy transfer, it was shown that the molecules place themselves close to the hydrophobic-hydrophilic interface inside the GM1 micelles. As a consequence they are exposed to a densely packed environment, which inhibits the free tumbling of the molecule. This restricted tumbling could be measured by means of time-resolved depolarization experiments. The release of drug-like fluorescent molecules is investigated from a lipid mixture, which upon equilibrium with water forms a mixture of inverted hexagonal and cubic phases. The lipid matrix displayed an extended release over the course of weeks, in vitro, for molecules having a large variation in hydrophobicity.

ABSTRACT Protein-protein interactions play a central role in most biological processes. One such biological process is the maintenance of a reducing environment inside the cell. To maintain an internal reducing environment, living cells have evolved two enzymatic systems (glutathione and thioredoxin (Trx) systems). The Trx system is composed of the enzyme TrxR and its substrate Trx. The two proteins constitute an important thiol-dependent redox system that catalyzes the reduction of many proteins that are responsible for a variety of cellular functions. The system relies on transient protein-protein interactions between Trx and TrxR for its function. Cross-reactivity of components of the Trx system between species has been shown to be medically relevant. For example, Helicobacter pylori Trx (HP Trx) is thought to mediate catalytic reduction of human immunoglobulins and thus facilitate immune evasion. It has also been proposed that Helicobacter pylori gains access to the impenetrable gastric mucous layer by using secreted HP Trx to reduce the disulfide bonds present in the cysteine-rich mucin regions that are responsible for cross-linking mucin monomers. Therefore, disruption of secreted HP Trx-host protein interaction may result in restoration of the viscoelastic and hydrophobic protective properties of mucus. Previous studies aimed at understanding the nature of cross-reactivity of Trx system components among various species have shown that Trxs have higher affinity for cognate TrxRs (same species), than for TrxRs from different species. However, the basis for this specificity is not known. A growing body of evidence suggests that most protein-protein interactions are mediated by a small number of protein-protein interface residues, referred to as hot spot residues or binding epitopes. Therefore, understanding the biochemical basis of the affinity of proteins for their partners usually begins by identifying the hot spot residues responsible for the protein complex interactions. In this study, the crystal structures of Deinococcus radiodurans thioredoxin reductase (DR TrxR) and Helicobacter pylori TrxR (HP TrxR) were determined at 1.9 Å and 2.4 Å respectively. Analysis of the Trx-binding sites of both structures suggests that the basis of affinity and specificity of Trx for TrxR is primarily due to the shape rather than the charge of the surface. In addition, the complex between Escherichia coli thioredoxin reductase (EC TrxR) and its substrate thioredoxin (EC Trx) was used to identify residues that are responsible for TrxR-Trx interface stability. Using computational alanine scanning mutagenesis and visual inspection of the EC TrxR-Trx interface, 22 EC TrxR side chains were shown to make contact across the TrxR-Trx interface. Although more than 20 EC TrxR side chains make contact across the TrxR-Trx interface, our results suggest that only 4 residues (F81, R130, F141, and F142) account for the majority of the EC TrxR-Trx interface stability. Individual replacement of equivalent DR TrxR residues (M84, K137, F148, F149) with alanine resulted in drastic changes in binding affinity, confirming that the four residues account for most of TrxR-Trx interface stability. These hot spot residues are surrounded by less important residues (hydrophobic and hydrophilic) that are also predicted to contribute to interface stability. F148 and F149 are invariant across bacterial TrxRs, however other residues that contact Trx are less conserved including M84 and K137. When M84 and K137 were changed to match equivalent E. coli TrxR residues (K137R, M84F); D. radiodurans TrxR substrate specificity was altered from its own Trx to that of E. coli Trx. The results suggest that a small subset of the TrxR-Trx interface residues are responsible for the majority of Trx binding affinity and specificity, a property that has been shown to general to protein-protein interfaces.

Biodegradable, edible wheat gluten films offer a renewable alternative to plastic food packaging or can be incorporated directly in the food product. Wheat gluten is a good option because it forms a fibrous network, lending strength and elasticity to films. The goal of this research project was to produce, with a water-based film formulation and methodology, smooth, homogeneous wheat gluten films with low water vapour permeability (WVP). The water-based film formulation also served to compare the FT Wonder wheat cultivar, grown in Ontario, to commercially produced wheat gluten and determine the effect of wheat source on the film properties, surface morphology, surface hydrophobicity, WVP, and film swelling in water for different pH, temperature and casting surface conditions. Fluorescence, SPR, and casting formulation viscosity provided preliminary information on the mechanism of film formation and on gluten protein structure induced by modifying the film formulation. This research provides an alternate use for some Ontario wheat cultivars based on their properties in films compared to commercial sources of gluten. As a result, using Ontario cultivars to prepare gluten film packaging material has potential as an alternate source of income for Ontario farmers. This research also defines the film properties for gluten films produced from aqueous solutions, helping to identify processing parameters that could bring gluten films on par with plastic packaging and make gluten films a viable alternative food packaging material. Finally, it was determined that the water vapour permeability of wheat gluten films was not correlated to film surface contact angle.

ABSTRACT Protein-protein interactions play a central role in most biological processes. One such biological process is the maintenance of a reducing environment inside the cell. To maintain an internal reducing environment, living cells have evolved two enzymatic systems (glutathione and thioredoxin (Trx) systems). The Trx system is composed of the enzyme TrxR and its substrate Trx. The two proteins constitute an important thiol-dependent redox system that catalyzes the reduction of many proteins that are responsible for a variety of cellular functions. The system relies on transient protein-protein interactions between Trx and TrxR for its function. Cross-reactivity of components of the Trx system between species has been shown to be medically relevant. For example, Helicobacter pylori Trx (HP Trx) is thought to mediate catalytic reduction of human immunoglobulins and thus facilitate immune evasion. It has also been proposed that Helicobacter pylori gains access to the impenetrable gastric mucous layer by using secreted HP Trx to reduce the disulfide bonds present in the cysteine-rich mucin regions that are responsible for cross-linking mucin monomers. Therefore, disruption of secreted HP Trx-host protein interaction may result in restoration of the viscoelastic and hydrophobic protective properties of mucus. Previous studies aimed at understanding the nature of cross-reactivity of Trx system components among various species have shown that Trxs have higher affinity for cognate TrxRs (same species), than for TrxRs from different species. However, the basis for this specificity is not known. A growing body of evidence suggests that most protein-protein interactions are mediated by a small number of protein-protein interface residues, referred to as hot spot residues or binding epitopes. Therefore, understanding the biochemical basis of the affinity of proteins for their partners usually begins by identifying the hot spot residues responsible for the protein complex interactions. In this study, the crystal structures of Deinococcus radiodurans thioredoxin reductase (DR TrxR) and Helicobacter pylori TrxR (HP TrxR) were determined at 1.9 Å and 2.4 Å respectively. Analysis of the Trx-binding sites of both structures suggests that the basis of affinity and specificity of Trx for TrxR is primarily due to the shape rather than the charge of the surface. In addition, the complex between Escherichia coli thioredoxin reductase (EC TrxR) and its substrate thioredoxin (EC Trx) was used to identify residues that are responsible for TrxR-Trx interface stability. Using computational alanine scanning mutagenesis and visual inspection of the EC TrxR-Trx interface, 22 EC TrxR side chains were shown to make contact across the TrxR-Trx interface. Although more than 20 EC TrxR side chains make contact across the TrxR-Trx interface, our results suggest that only 4 residues (F81, R130, F141, and F142) account for the majority of the EC TrxR-Trx interface stability. Individual replacement of equivalent DR TrxR residues (M84, K137, F148, F149) with alanine resulted in drastic changes in binding affinity, confirming that the four residues account for most of TrxR-Trx interface stability. These hot spot residues are surrounded by less important residues (hydrophobic and hydrophilic) that are also predicted to contribute to interface stability. F148 and F149 are invariant across bacterial TrxRs, however other residues that contact Trx are less conserved including M84 and K137. When M84 and K137 were changed to match equivalent E. coli TrxR residues (K137R, M84F); D. radiodurans TrxR substrate specificity was altered from its own Trx to that of E. coli Trx. The results suggest that a small subset of the TrxR-Trx interface residues are responsible for the majority of Trx binding affinity and specificity, a property that has been shown to general to protein-protein interfaces.

Fluorescence correlation spectroscopy has become a standard technique for modern biophysics and single molecule spectroscopy research. Here is presented a novel widefield extension of the established single-point technique. Flow in microfluidic devices was used as a model system for microscopic motion and through widefield fluorescence correlation spectroscopy flow profiles were mapped in three dimensions. The technique presented is shown to be more tolerant to low signal strength, allowing image data with signal-to-noise values as low as 1.4 to produce accurate flow maps as well as utilizing dye-labeled single antibodies as flow tracers. With proper instrumentation flows along the axial direction can also be measured. Widefield fluorescence correlation spectroscopy has also been utilized to produce super-resolution confocal microscopic images relying on the single-molecule microsecond blinking dynamics of fluorescent silver clusters. A method for fluorescence modulation signal extraction as well as synthesis of several novel noble metal fluorophores is also presented.