5 Abstract Cytochrome P450 1A1 (CYP1A1) is one of the major isoforms of the cytochrome P450 superfamily. It is primarily an extrahepatic enzyme which is responsible for oxidation of many polycyclic aromatic hydrocarbons and other xenobiotics. Besides of the role in detoxification metabolism CYP1A1 is the one most important isoform involved in activation of procarcinogens. The main aim of this project was preparation of two modifications of the rat CYP1A1 gene with codon optimization for expression in E. coli by gene synthesis. One was wild type (wt1A1) and the other was with modified N-terminal anchor (mod1A1) - for both modifications with or without His Tag at the C-end of CYP1A1. Furthermore, an aim was to compare their level of expression in different strains of E. coli and try to purify and assess enzymatic activity of the gene's products. From pre-prepared oligonucleotides 2 "syntons" (parts of gene) were synthetized and separately inserted into pUC19. After verified sequence of the "syntons" they were cleaved from pUC19 and inserted together into pET-22b. These vectors were prepared for transformation of 3 strains of E. coli (BL-21 (DE3) GOLD, RIL a RIPL). For production of proteins many conditions were tested: temperature (18, 22, 24, 27 a 37 řC), time of production (untill 48 hours), concentration...

Poorly water-soluble drugs (PWSDs), to date, require advanced formulation techniques to improve solubility and achieve the required plasma concentration to show a therapeutic effect when orally administered. Lipid-based formulations (LBFs) are an enabling strategy that is being used to improve the oral delivery of PWSDs. The aim of this study was to investigate the effect of lipid-based formulation, Type IIIA-LC, on the solubilization patterns of PWSDs, namely, carvedilol and felodipine. Solubility studies, for both drugs, were performed with LBF dispersed in -1) dog intestinal fluid (DIF), and 2) water, to identify and compare the extent of solubility in different matrices, and in silico to identify interesting patterns with any correlations in experimental and computational data. Solubility studies showed that carvedilol had better solubility in LBF when compared to felodipine. Computational studies showed that both drugs solubilized in the colloid in both digested and undigested states. Effect of drug loading had no significant difference on the solubilization patterns of both drugs. The maximum drug loading done was for 100 molecules though there is the possibility of the colloid having a higher capacity. Digestion did not seem to have a significant effect on the distribution of both drugs. In vitro and in silico data were in qualitative agreement and therefore, this computational model can be further used to study the specific processes causing solubilization, improvement, and development of new LBFs.

Diazotrophic microbes reside in soybean nodules; however, other non-nitrogen fixing bacteria are a part of the interior nodule microbiome. Results from a previous greenhouse study show that a novel species of Pseudomonas associates with soybean nodules as a plant-growth promoting rhizobacteria (PGPR). This study observes the soybean growth promoting potential of Pseudomonas spp. in a field setting. Additionally, this study observed differences in soybean growth promotion based on amending the plant with isolated strains or a mixed culture of the species' strains. Two cultivars of soybean (Asgrow AG46X6 and Pioneer P48A60X) were either amended with isolated strains of the novel Pseudomonas spp. (referred to as PAMW1 and BUMW2 in this study), a mix of the two strains, or an uninoculated control. The study recorded measurements to observe growth, yield, and nitrogen fixation differences. The study uses two-way factorial ANOVAs and non-parametric, multivariate analyses to determine differences in growth promotion among samples. Soybean amended with PAMW1 has greater shoot mass, biomass, and height than other treatments. Through nonmetric multidimensional scaling (NMS), samples amended with a mixed culture or PAMW1 may be different regarding growth promotion relative to the non-amended samples. Univariate results support the hypothesis that the novel Pseudomonas spp. benefit soybean in a field setting. However, it is inconclusive whether a mixed culture amendment of multiple strains alters the overall growth promotion of soybean compared to samples amended with isolated strains. / Master of Science / Soil hosts a relatively abundant and diverse community of microorganisms. Moreover, the area of soil that interacts closely with plant roots and their associated exudates, called the rhizosphere, has a significantly greater microbial abundance than surrounding bulk soil. Interactions between microbes and the plant often promote plant growth because of secondary metabolites produced by these beneficial microbes. One particular bacterial species, belonging to the Pseudomonas genus, was discovered and extracted from the soybean nodule interior. Nitrogen-fixing bacteria predominantly reside in the soybean nodule, yet this microorganism cannot fix nitrogen. Although trace amounts of non-nitrogen-fixing bacteria reside in the soybean nodule, this novel species has a relatively high abundance. This study determines the benefits of this species in the soybean nodule. Following positive results in a greenhouse study, this field experiment observes variance in soybean growth and productivity based on their received bacterial amendment. For this study, two soybean cultivars were either amended with an isolated strain of this species, a mix of the two strains, or left uninoculated to serve as a control. Numerous recorded measurements serve as indices of soybean growth and productivity. The results suggest that this novel Pseudomonas species benefits the plant by significantly improving biomass. With further research, this species can potentially serve as an environmentally sensitive and sustainable alternative to fertilizers through its ability to promote soybean growth.

During the last decade, ultrasonic manipulation has matured into an important tool with a wide range of applications, from fundamental cell biological research to clinical and industrial implementations. The contactless nature of ultrasound makes it possible to manipulate living cells in a gentle way, e.g., for positioning, sorting, and aggregation. However, when manipulating cells using ultrasound, especially using high acoustic amplitudes, a great deal of heat can be generated. This constitutes a challenge, since the viability of cells is dependent on a stable physiological temperature around 37°C.      In this Thesis we present applications of ultrasonic manipulation of fluids, particles, and cells in temperature-controlled micrometer-sized devices fabricated using well established etching techniques, directly compatible with high-resolution fluorescence microscopy. Furthermore, we present ultrasonic manipulation in larger up to centimeter-sized devices optimized for fluid mixing and cell lysis. In the present work, two new ultrasonic manipulation platforms have been developed implementing temperature control. These platforms are much improved with increased performance and usability compared to previous platforms. Also, two new ultrasonic platforms utilizing low-frequency ultrasound for solubilization and cell lysis of microliter-volumed and milliliter-volumed samples have been designed and implemented.      We have applied ultrasound to synchronize the interaction between large numbers of immune, natural killer cells, and cancer cells to study the cytotoxic response, on a single cell level. A heterogeneity was found among the natural killer cell population, i.e., some cells displayed high cytotoxic response while others were dormant. Furthermore, we have used temperature-controlled ultrasound to form up to 100, in parallel, solid cancer HepG2 tumors in a glass-silicon multi-well microplate. Next, we investigated the immune cells cytotoxic response against the solid tumors. We found a correlation between the number of immune cells compared to the size of the tumor and the cytotoxic outcome, i.e., if the tumor could be defeated.             Finally, the effect of high acoustic pressure amplitudes in the MPa-range on cell viability has been studied in a newly developed platform optimized for long-term stable temperature control, independent on the applied ultrasound power. Lastly, we present two applications of ultrasonic fluid mixing and lysis of cells. One platform is optimized for small microliter-sized volumes in plastic disposable chips and another is optimized for large milliliter-sized volumes in plastic test tubes. The latter platform has been implemented for clinical sputum sample solubilization and cell lysis for genomic DNA extraction for subsequent pathogen detection / Ultraljudsmanipulering har under de senaste tio åren mognat och utvecklats till ett verktyg med ett brett användningsområde. Idag kan man finna applikationer inom allt från cellbiologisk grundforskning till industri samt sjukvård. Ultraljudsmanipuleringens kontaktlösa natur gör det till en varsam metod för att manipulera celler, till exempel inom positionering, sortering och aggregering. När ultraljud med hög amplitud används kan värmeutvecklingen, som är oundviklig, bli ett problem. För att kunna säkerställa hög cellviabilitet krävs temperaturkontroll som kan hålla en fysiologisk, stabil temperatur på 37°C.      I denna avhandling presenterar vi tillämpningar av temperaturkontrollerad ultraljudsmanipulering i mikrometerstora anordningar fabricerade med väletablerade etsningstekniker.  Dessa anordningar är optimerade för att vara fullt kompatibla med högupplöst fluorescensmikroskopi.  Vi demonstrerar även ultraljudsmanipulering i centimeterstora anordningar optimerade för omrörning och blandning av vätskor samt lysering av celler. Två nya plattformar för ultraljudsmanipulering med inbyggd temperaturkontroll har utvecklats. Dessa två plattformar erbjuder ökad prestanda, flexibilitet samt även användarvänlighet. Utöver dessa plattformar har ytterligare två anordningar för lågfrekvent ultraljudssolubilisering och cellysering av mikroliter- och milliliterstora prover konstruerats.      I denna avhandling har vi tillämpat ultraljud för att synkronisera interaktionen mellan populationer utav immunceller (natural killer-celler) och cancerceller för att på cellnivå studera det cytotoxiska gensvaret. Vi fann en heterogenitet hos immuncellspopulationen. Det manifesterade sig i en fördelning av immuncellerna, från celler med stort cytotoxiskt gensvar till inaktiva immunceller. Vi har dessutom använt temperaturkontrollerad ultrasljudsmanipulering för att skapa solida cancertumörer utav HepG2-cancerceller, upp till 100 stycken parallellt, i en multihåls-mikrotiterplatta bestående av glas och kisel. Med hjälp av dessa tumörer har vi studerat det cytotoxiska gensvaret från immuncellerna. Vi fann att förhållandet mellan antalet immunceller och storleken på tumören bestämde utfallet, det vill säga om tumören kunde bekämpas.      Vi presenterar dessutom effekten utav högamplitudsultraljudsexponering av cancerceller i en plattform speciellt designad för höga tryckamplituder med implementerad ultraljudseffektsoberoende temperaturkontroll. Slutligen presenterar vi två tillämpningar av ultraljud för vätskeblandning och cellysering. Den första tillämpningen är anpassad för små volymer i plastchip för engångsbruk och den andra är optimerad för större volymer i plastprovrör. Den senare tillämpningen är speciellt framtagen för ultraljudssolubilisering och cellysering utav kliniska sputumprover för att möjliggöra DNA-extrahering för detektion av smittämnen. / <p>QC 20150522</p>

Neuf maladies neurodégénératives sont le produit de l’expression de gènes mutés, dans lesquels le codon CAG est répété au-delà d’un seuil pathologique. Ceci produit des protéines mutantes dans lesquelles sont insérés des segments de polyglutamines (polyGln), qui perdent leur activité et acquièrent une nouvelle fonction, ce qui est toxique pour le neurone. Ces altérations sont attribuables aux propriétés particulières de la polyGln. En effet, ces dernières possèdent la capacité de s’assembler pour former des corps d’inclusion intracellulaires. Cette propension à l’agrégation de la polyGln rend difficile l’étude de ces pathologies. C’est ainsi que l’utilisation de peptides peut s’avérer une approche avantageuse. Toutefois, la synthèse de polyGln est associée à de nombreuses délétions et nécessite l’ajout de groupements chargés afin de permettre leur purification. Cependant, ce prérequis donne lieu à des interactions électrostatiques qui biaisent la structure et la cinétique d’agrégation de ces peptides, en plus d’interférer avec l’évaluation d’éventuels agents thérapeutiques. L’objectif du projet est de développer un système permettant l’étude de la polyGln en s’affranchissant des effets de charges. Pour ce faire, deux approches ont été explorées, la première utilise la polyGln non chargée et la seconde utilise une structure polyGln-morpholine ayant des charges labiles en fonction du pH. Ces peptides ont été produits en utilisant une approche linéaire de synthèse peptidique sur support solide avec protection maximale des chaînes latérales. La purification a été effectuée par chromatographie de haute performance en phase inverse en milieu acide. Ces stratégies ont permis de produire des peptides de polyGln de grande pureté avec des rendements acceptables. Une procédure de solubilisation des peptides alliant sonication et lyophilisation a été développée afin d’étudier chacun de ces peptides à l’aide de diverses techniques physicochimiques, telles que la diffusion de la lumière, la spectroscopie de résonance magnétique nucléaire, Raman et UV-visible, le dichroïsme circulaire et la microscopie optique polarisée. La polyGln non chargée solubilisée dans le trifluoroéthanol-eau a montré que la taille des particules et la vitesse d’agrégation sont proportionnelles à la fraction volumique en eau. De plus, la structure secondaire en solution est à prédominance alpha et semble être peu sensible à la fraction d’eau jusqu’à un certain seuil (25%) après lequel la structure aléatoire prédomine. L’analyse des agrégats à l’état solide montre des structures hélicoïdales > aléatoires et ont les caractéristiques des fibrilles amyloïdes. Le peptide de polyGln-morpholines a un pKa de 7,3 en milieu aqueux. Il demeure en solution lorsque le pH < pKa et à faible force ionique, alors qu’il s’autoassemble lorsque ces conditions ne sont pas respectées. Ceci suggère que la répulsion électrostatique est responsable de la stabilisation du peptide en solution. La dimension fractale nous indique que le peptide forme des agrégats compacts dont les constituants ont une taille de 2,5 nm, compatibles avec une conformation aléatoire compacte, en coude bêta ou hélicoïdale. Ceci est en accord avec l’étude structurale des peptides en solution qui a montré des espèces aléatoires > bêta > alpha. De plus, en RMN, l’élargissement des signaux du 1Hγ en cours d’agrégation suggère une interaction via les chaînes latérales. Les analyses en phase solide ont plutôt montré une prédominance de structures bêta et alpha. L’inhibition de l’agrégation à pH 8 varie selon rouge de Congo > tréhalose, alors que le peptide liant la polyGln 1 et la thioflavine T ne semble pas avoir d’effet. Ces approches ont donc permis pour la première fois de s’affranchir des effets de charges auparavant inhérents à l’étude de la polyGln en solution et par conséquent d’obtenir des informations inédites quant à la solubilité, la structure et la cinétique d’agrégation. Enfin, le dispositif à charges labiles permet d’évaluer l’efficacité d’éventuels agents thérapeutiques à pH quasi physiologique. / Nine neurodegenerative diseases come from mutated genes expression in which the CAG codon is repeated above a pathological threshold. This is producing mutant proteins, in which are inserted polyglutamine (polyGln) segments, which lose their activity and acquire a new function that is toxic for the neuron. These alterations are related to the peculiar properties of the polyGln. Indeed, these polypeptides have the capacity of autoassemble to form intracellular inclusion bodies. This aggregation tendency of polyGln makes difficult the study of these pathologies. Thus, the use of peptides could constitute an advantageous approach. However, the synthesis of polyGln is associated with numerous deletions and necessitates the addition of charged moieties to achieve purification. Unfortunately, this requirement creates electrostatic interactions that modify the structure and aggregation kinetics of these peptides, in addition to interfering with the evaluation of potential therapeutical agents. The aim of this project is to develop a system to study polyGln without the charge effects. To do so, two approaches were explored, the first used uncharged polyGln and the second used a polyGln-morpholine structure bearing pH-dependent labile charges. These peptides were produced by solid-support synthesis using a linear and maximal protection approach. Purification was performed by reverse phase high-performance liquid chromatography. These strategies allowed the production of peptides of high purity in good yields. A solubilization procedure combining sonication and lyophilization was developed to study each of these peptides by physicochemical techniques such as light scattering, magnetic resonance, Raman and UV-visible spectroscopies, circular dichroism and polarized optical microscopy. The uncharged polyGln solubilized in trifluoroethanol-water showed that particle size and aggregation kinetics are proportional to volumetric water fraction. Furthermore, the secondary structure in solution is alpha-predominant and seems rather insensitive to water fraction up to a threshold (25%) above which random coil structure predominates. The analysis of solid-state aggregates showed that helicoidal structures are more abundant than random structures and have the characteristics of amyloid fibrils. The polyGln-morpholines peptide has a pKa of 7.3 in aqueous media. It is soluble when pH < pKa and at low ionic strength, but it autoassociates when these conditions are not respected. This suggests that electrostatic repulsion is responsible for the stabilization of the peptide in solution. The fractal dimension indicates that the peptide forms compact aggregates whose constituents are 2.5 nm in size, in agreement with compact random coil, beta-hairpin or helicoidal structures. This is in agreement with the results of solution peptide structure studies showing that random coil > beta > alpha. Furthermore, the broadening of 1Hγ NMR signals while the peptide is aggregating suggests an interaction between side-chains. Solid-phase studies showed predominant beta and alpha structures. The aggregation inhibition at pH 8.0 was higher for Congo red than for trehalose, while polyglutamine binding peptide 1 and thioflavine T did not seem to be effective. These approaches permitted for the first time to overcome the charge effects that were previously inherent to polyGln solution studies and to obtain new information about solubility, structure and aggregation kinetics. Finally, the labile charge groups allow the evaluation of the efficiency of potential therapeutic agents at near physiological pH.

Nombre de principes actifs rencontrent des problèmes liés à leur faible hydrosolubilité : mauvaise biodisponibilité, métabolisation désactivante, effets secondaires. Pour contourner ce problème, des polyélectrolytes amphiphiles aléatoires ont déjà été étudiés. S'ils ont amélioré la solubilité apparente de composés hydrophobes, ils étaient parallèlement toxiques ou non dégradables, donc non éliminables par l'organisme. Dans ce mémoire, nous présentons la synthèse de différentes malolactones substituées. La copolymérisation anionique par ouverture de cycle de ces lactones a permis d'obtenir une famille de polyanions amphiphiles aléatoires avec un taux d'hydrophobisation variable et contrôlé, et des chaînes latérales, aliphatiques ou aromatique, de différentes longueurs. Ces polymères augmentent la solubilité aqueuse apparente de composés hydrophobes. Lorsque le composé est cationique, une synergie entre interactions hydrophobes et électrostatiques a été mise en évidence. La solubilité apparente de molécules anti-infectieuses a ainsi pu être améliorée de plusieurs ordres de grandeur. Dans les conditions d'une administration intraveineuse (NaCl 9 g.L-1 et pH = 7,5), ces polymères forment préférentiellement des micelles intramoléculaires qui ne sont pas sensibles aux effets de dilution. Un tel système de transport de principes actifs ne produirait donc aucune libération prématurée. Ces polymères étant de plus dégradables, ils pourraient libérer le principe actif et seraient éliminables par l'organisme. Les polymères présentés dans ce manuscrit remplissent les principaux critères physico-chimiques pour former un système de transport de molécules actives. / Lots of drugs meet some problems because of their poor water-solubility : poor bioavailability, desactivating metabolization, side effects. To overcome these problems, some amphiphilic polyelectrolytes have already been studied. They increased the apparent water-solubility of hydrophobic compounds, but were toxic or not degradable, thus could not be eliminated from the body. In this work, we describe the synthesis of various substituted malolactones. Anionic ring opening copolymerization of these lactones yielded random amphiphilic polyanions with varying and controlled hydrophobization ratio and aliphatic and aromatic side chains with different lengths. These polymers increase the apparent water-solubility of hydrophobic compounds. A synergy between hydrophobic and electrostatic interactions has been demonstrated when the compound is cationic. The apparent solubility of anti-infectious drugs could thus be increased by several orders of magnitude. Under intravenous injection conditions (NaCl 9 g.L-1 and pH = 7,5), these polymers form preferentially intramolecular micelles, which are not sensitive to dilution effects. As a consequence, such a drug transport system would yield no premature release. Being also degradable, these polymers could release the drug and be eliminated from the body. They meet all main physico-chemical criteria to become a drug transport system.

L’élaboration de récepteurs artificiels pouvant reconnaître soit des ions métalliques soit des molécules chargées ou neutres avec une haute affinité et une grande sélectivité est l’un des objectifs majeurs de la chimie supramoléculaire. En effet, de tels récepteurs ont de potentielles applications dans de nombreux domaines comme en imagerie médicale ou en analyse environnementale. Afin de pouvoir obtenir des récepteurs sophistiqués, il faut cependant généralement passer par une étape d’ingénierie de la molécule dont la conception concrète nécessite une fonctionnalisation ad hoc. Cela requiert souvent la mise au point de méthodes originales de synthèse accompagnée d’un travail méthodologique important. Par ailleurs, alors que l’eau, de par ses propriétés physico-chimiques, joue un rôle tout à fait particulier dans la reconnaissance moléculaire (effet hydrophobe) et dans les réactions enzymatiques (transfert d’électrons et de protons), la majorité des études décrites dans la littérature ont été faites en solvant organique. Si quelques récepteurs, principalement basés sur des molécules intrinsèquement hydrosolubles (telles que la cyclodextrine ou le cucurbiturile) ont permis d’enrichir la chimie supramoléculaire dans l’eau, l’étude comparée de récepteurs en milieux organique et aqueux, qui apporterait de nombreuses informations est, elle, en revanche peu explorée par la communauté supramoléculaire. Ce travail de thèse s’insère dans ces deux cadres et cherche à répondre en partie à ces problématiques. Il est axé sur : (i) le développement d’une méthodologie unique pour la fonctionnalisation sélective de calix[6]arènes; et (ii) la synthèse et l’étude de nouveaux récepteurs hydrosolubles dérivés du calix[6]tren. La première partie de ce travail décrit le développement d’une stratégie supramoléculaire, qui consiste en l’utilisation des propriétés réceptrices du macrocycle calix[6]arène comme un outil pour sa monofonctionnalisation sélective. Le champ d’application d’une telle approche est notamment étudié à partir de différents récepteurs calix[6]arèniques dont la reconnaissance est basée sur divers types d’interactions (interactions ioniques ou chimie de coordination). Ces travaux s’insèrent dans un cadre plus général de fonctionnalisation sélective de macrocycles via assistance supramoléculaire, qui fait l’objet du chapitre introductif de cette partie. Les propriétés émergentes de ces nouveaux ligands monofonctionnalisés sont également présentées dans ce document. La deuxième partie du travail concerne l’hydrosolubilisation de ligands calixaréniques et l’étude de leurs propriétés de reconnaissance ainsi que celles de leurs complexes (Zn(II), Cu(II)) correspondants dans l’eau. L’étude est pour cela dirigée vers l’hydrosolubilisation d’un récepteur qui s’est révélé particulièrement prometteur en solvant organique, mais qui n’était pas soluble en milieu aqueux : le calix[6]tren. / The elaboration of artificial receptors that can bind either metal ions or charged/neutral species with a high affinity and a high selectivity is one of the major goals of supramolecular chemistry. Indeed, such receptors have potential applications in many fields such as in medical imaging or in environmental analysis. In order to obtain sophisticated receptors however, one has generally to go through a step of molecular engineering. This often requires the development of original synthetic methods, accompanied by an important methodologic work. Furthermore, although water, by its special physico-chemical properties, plays a particular role in molecular recognition (hydrophobic effect) and in enzymatic reactions (transfer of electrons and protons), the majority of the studies reported in the literature have been conducted in organic solvent. If a few receptors, mainly based on intrinsically water-soluble molecules (such as cyclodextrin and cucurbituril) have permitted to enrich the field of supramolecular chemistry in water, the comparative study of given receptors in both organic and aqueous environment, which could be very informative, has been less explored by the supramolecular community. The present work fits into these two frameworks and seeks to answer, in part, to these problematics. The work is centered around: (i) the development of an unique methodology for the selective functionalization of calix[6]arenes; and (ii) the synthesis and study of new water-soluble derivatives of calix[6]tren. The first part of this work describe the development of a supramolecular strategy that relies on the use of the host-guest properties of the calix[6]arene macrocycle as a tool for its selective monofunctionalization. The scope of such approach is studied using several different calix[6]arene-based receptors which recognition process is based on different type of interactions (ionic interaction or coordination chemistry). The emerging properties of these newly monofunctionalized ligands are also presented in this document. The second part of this work deals with the water-solubilization of calix[6]arene ligands and the study of their coordination properties towards Zn(II) and Cu(II). The work is for this directed towards the water-solubilization of a receptor which revealed to be particularly promising in organic solvent, but that was not soluble in water: the calix[6]tren.

Neuf maladies neurodégénératives sont le produit de l’expression de gènes mutés, dans lesquels le codon CAG est répété au-delà d’un seuil pathologique. Ceci produit des protéines mutantes dans lesquelles sont insérés des segments de polyglutamines (polyGln), qui perdent leur activité et acquièrent une nouvelle fonction, ce qui est toxique pour le neurone. Ces altérations sont attribuables aux propriétés particulières de la polyGln. En effet, ces dernières possèdent la capacité de s’assembler pour former des corps d’inclusion intracellulaires. Cette propension à l’agrégation de la polyGln rend difficile l’étude de ces pathologies. C’est ainsi que l’utilisation de peptides peut s’avérer une approche avantageuse. Toutefois, la synthèse de polyGln est associée à de nombreuses délétions et nécessite l’ajout de groupements chargés afin de permettre leur purification. Cependant, ce prérequis donne lieu à des interactions électrostatiques qui biaisent la structure et la cinétique d’agrégation de ces peptides, en plus d’interférer avec l’évaluation d’éventuels agents thérapeutiques. L’objectif du projet est de développer un système permettant l’étude de la polyGln en s’affranchissant des effets de charges. Pour ce faire, deux approches ont été explorées, la première utilise la polyGln non chargée et la seconde utilise une structure polyGln-morpholine ayant des charges labiles en fonction du pH. Ces peptides ont été produits en utilisant une approche linéaire de synthèse peptidique sur support solide avec protection maximale des chaînes latérales. La purification a été effectuée par chromatographie de haute performance en phase inverse en milieu acide. Ces stratégies ont permis de produire des peptides de polyGln de grande pureté avec des rendements acceptables. Une procédure de solubilisation des peptides alliant sonication et lyophilisation a été développée afin d’étudier chacun de ces peptides à l’aide de diverses techniques physicochimiques, telles que la diffusion de la lumière, la spectroscopie de résonance magnétique nucléaire, Raman et UV-visible, le dichroïsme circulaire et la microscopie optique polarisée. La polyGln non chargée solubilisée dans le trifluoroéthanol-eau a montré que la taille des particules et la vitesse d’agrégation sont proportionnelles à la fraction volumique en eau. De plus, la structure secondaire en solution est à prédominance alpha et semble être peu sensible à la fraction d’eau jusqu’à un certain seuil (25%) après lequel la structure aléatoire prédomine. L’analyse des agrégats à l’état solide montre des structures hélicoïdales > aléatoires et ont les caractéristiques des fibrilles amyloïdes. Le peptide de polyGln-morpholines a un pKa de 7,3 en milieu aqueux. Il demeure en solution lorsque le pH < pKa et à faible force ionique, alors qu’il s’autoassemble lorsque ces conditions ne sont pas respectées. Ceci suggère que la répulsion électrostatique est responsable de la stabilisation du peptide en solution. La dimension fractale nous indique que le peptide forme des agrégats compacts dont les constituants ont une taille de 2,5 nm, compatibles avec une conformation aléatoire compacte, en coude bêta ou hélicoïdale. Ceci est en accord avec l’étude structurale des peptides en solution qui a montré des espèces aléatoires > bêta > alpha. De plus, en RMN, l’élargissement des signaux du 1Hγ en cours d’agrégation suggère une interaction via les chaînes latérales. Les analyses en phase solide ont plutôt montré une prédominance de structures bêta et alpha. L’inhibition de l’agrégation à pH 8 varie selon rouge de Congo > tréhalose, alors que le peptide liant la polyGln 1 et la thioflavine T ne semble pas avoir d’effet. Ces approches ont donc permis pour la première fois de s’affranchir des effets de charges auparavant inhérents à l’étude de la polyGln en solution et par conséquent d’obtenir des informations inédites quant à la solubilité, la structure et la cinétique d’agrégation. Enfin, le dispositif à charges labiles permet d’évaluer l’efficacité d’éventuels agents thérapeutiques à pH quasi physiologique. / Nine neurodegenerative diseases come from mutated genes expression in which the CAG codon is repeated above a pathological threshold. This is producing mutant proteins, in which are inserted polyglutamine (polyGln) segments, which lose their activity and acquire a new function that is toxic for the neuron. These alterations are related to the peculiar properties of the polyGln. Indeed, these polypeptides have the capacity of autoassemble to form intracellular inclusion bodies. This aggregation tendency of polyGln makes difficult the study of these pathologies. Thus, the use of peptides could constitute an advantageous approach. However, the synthesis of polyGln is associated with numerous deletions and necessitates the addition of charged moieties to achieve purification. Unfortunately, this requirement creates electrostatic interactions that modify the structure and aggregation kinetics of these peptides, in addition to interfering with the evaluation of potential therapeutical agents. The aim of this project is to develop a system to study polyGln without the charge effects. To do so, two approaches were explored, the first used uncharged polyGln and the second used a polyGln-morpholine structure bearing pH-dependent labile charges. These peptides were produced by solid-support synthesis using a linear and maximal protection approach. Purification was performed by reverse phase high-performance liquid chromatography. These strategies allowed the production of peptides of high purity in good yields. A solubilization procedure combining sonication and lyophilization was developed to study each of these peptides by physicochemical techniques such as light scattering, magnetic resonance, Raman and UV-visible spectroscopies, circular dichroism and polarized optical microscopy. The uncharged polyGln solubilized in trifluoroethanol-water showed that particle size and aggregation kinetics are proportional to volumetric water fraction. Furthermore, the secondary structure in solution is alpha-predominant and seems rather insensitive to water fraction up to a threshold (25%) above which random coil structure predominates. The analysis of solid-state aggregates showed that helicoidal structures are more abundant than random structures and have the characteristics of amyloid fibrils. The polyGln-morpholines peptide has a pKa of 7.3 in aqueous media. It is soluble when pH < pKa and at low ionic strength, but it autoassociates when these conditions are not respected. This suggests that electrostatic repulsion is responsible for the stabilization of the peptide in solution. The fractal dimension indicates that the peptide forms compact aggregates whose constituents are 2.5 nm in size, in agreement with compact random coil, beta-hairpin or helicoidal structures. This is in agreement with the results of solution peptide structure studies showing that random coil > beta > alpha. Furthermore, the broadening of 1Hγ NMR signals while the peptide is aggregating suggests an interaction between side-chains. Solid-phase studies showed predominant beta and alpha structures. The aggregation inhibition at pH 8.0 was higher for Congo red than for trehalose, while polyglutamine binding peptide 1 and thioflavine T did not seem to be effective. These approaches permitted for the first time to overcome the charge effects that were previously inherent to polyGln solution studies and to obtain new information about solubility, structure and aggregation kinetics. Finally, the labile charge groups allow the evaluation of the efficiency of potential therapeutic agents at near physiological pH.

Bluetongue virus belongs to the Orbivirus genus from the Reoviridae family. It infects predominantly domestic and wild ruminants and is economically significant worldwide. Bluetongue virus VP7 forms the intercepting layer between the outer capsid (VP2 and VP5) and VP3 which surrounds the genomic material. BL21(DE3), NiCo21(DE3), C43(DE3) pLysS and KRX Escherichia coli cells were transformed with a pET28a plasmid with the cDNA sequence encoding Bluetongue virus VP7. Expression of Bluetongue virus VP7 was tested at post induction temperatures between 16˚C and 37 ˚C, at inducer concentrations between 0.1 mM and 1.0 mM isopropyl-β-D-thiogalactopyranoside in BL21(DE3), NiCo21(DE3) and C43(DE3) pLysS cells and 0.05 % and 0.15 % rhamnose for KRX cells, in two types of growth media (LB and 2xYT) and post-induction growth times between two and 16 hours. Under all conditions tested; Bluetongue virus VP7 expression was found to be predominantly in the insoluble fraction (pellet). BL21(DE3) and NiCo21(DE3) cells were chosen and grown for five hours post induction, induced with 0.1 mM isopropyl-β-D-thiogalactopyranoside and grown at a post-induction temperature of 37 ˚C. Bluetongue virus VP7 in bacterial cell inclusion bodies was solubilised using urea and a freeze-thaw step. Solubilisation was tested with urea concentrations between 2 M and 8 M, with solubilisation efficiency not increasing past 5 M urea. Solubilized Bluetongue virus VP7 was purified using nickel-affinity chromatography. Purified Bluetongue virus VP7 was then probed with far-UV circular dichroism and intrinsic fluorescence in several buffer conditions including different urea and guanidinium chloride concentrations as well as in the presence of glycerol and sodium chloride. Guanidinium chloride was able to cause Bluetongue virus VP7 unfolding, and the unfolding transition had 94 % and 89 % reversibility at 218 nm and 222 nm respectively. Bluetongue virus VP7 was shown to contain a native-like structure in 20 % glycerol and in up to 8 M urea and was found to be stable till at least 55 ˚C, even in the presence of 5 M urea. Glycerol and sodium chloride influenced the conformation of the protein resulting in different unfolding transitions. Thermal unfolding of Bluetongue virus VP7 was found to be irreversible. / Life and Consumer Sciences / M. Sc. (Life Sciences)

Made available in DSpace on 2015-04-20T12:31:32Z (GMT). No. of bitstreams: 1 Aloisio Freitas Chagas Junior.pdf: 1425510 bytes, checksum: 861fcee7c2ea43864c650307852db610 (MD5) Previous issue date: 2007-04-13 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / To increase the rhizobia contribution to plants nutrition and development is necessary to develop researches for selecting more efficient nitrogen fixation strains. This research work had as objectives, to accomplish morphologic characterization of rhizobia isolated from Amazonian soils; laboratory evaluations about the tolerance to acidity and toxic Al, the capacity to solubilize calcium (P-Ca) and aluminum (P-Al) phosphates, the indole-acetic acid production (AIA); the ability of the isolates to induce nodulation and to fix nitrogen under the acidity and low fertility conditions of the regional soils in greenhouse experiment; to genetically characterize the isolated ones selected using the PCR-RFLP technique. The infectivity test showed that there was significant increase in the cowpea biomass. With relationship to the phenotypic characterization, the 200 isolates showed a great diversity. Among these, 165 and 127 presented high tolerance within the media with pH 4,5 and pH 4,5 + Al, respectively. From the 200 isolates, 68 solubilized P-Ca and 47 P-Al, and 32 isolates solubilized both P-Ca and P-Al. The AIA production significantly increased (p <0,01) with tryptophan quantities added in the medium for 19 of the 92 isolates tested in the experiment. It was observed production of dry matter and nodule number and mass superior simbiotic to the control treatment and similar to the fertilized treatment for various rhizobia isolates. The 20 selected isolates evaluated presented high genotypic diversity, with the derived dendrogram PCR-RFLP profiles showing that they can be divided inside two main genders, Rhizobium and Bradyrhizobium. Associating the results of simbiotic efficiency and nodulation, it was observed that the isolates of rhizobia from Amazonian soils presented good results, and they can be recommended for tests of agronomic efficiency for cowpea bean. / Para aumentar a contribuição de rizóbia na nutrição e desenvolvimento de plantas é necessário desenvolver pesquisas de seleção de estirpes mais eficientes quanto à fixação do N2. Este trabalho teve como objetivos, realizar a caracterização morfológica de isolados de rizóbio oriundos de solos amazônicos; avaliar em laboratório, a tolerância à acidez e Al tóxico, a capacidade de solubilização de fosfato de cálcio (P-Ca) e alumínio (P-Al), a produção de acido indol-acético (AIA); a capacidade de isolados em induzirem nodulação e fixarem nitrogênio sob as condições de acidez e baixa fertilidade dos solos regionais em casa-de-vegetação; caracterizar geneticamente os isolados selecionados usando a técnica de PCR-RFLP. Os testes de infectividade mostraram que houve aumento significativo na biomassa de caupi. Quanto à caracterização fenotípica, os 200 isolados mostraram uma grande diversidade. Dentre estes, 165 e 127 isolados apresentaram elevada tolerância nos meios de cultura com pH 4,5 e pH 4,5 + Al, respectivamente. Dos 200 isolados testados, 68 solubilizaram P-Ca e 47 P-Al, sendo que 32 solubilizaram tanto o P Ca quanto o P Al. A produção de AIA aumentou significativamente com as doses de triptofano adicionadas ao meio (p<0,01) para 19 dos 92 isolados testados no experimento. Observou-se produção de matéria seca, número e massa seca dos nódulos e acúmulo de nitrogênio superiores ao tratamento testemunha e similares ao tratamento adubado para vários isolados de rizóbia. Os 20 isolados selecionados e avaliados apresentaram alta diversidade genotípica, onde o dendrograma derivado de perfis de PCR-RFLP mostrou que podem ser divididos dentro de dois gêneros principais, Rhizobium e Bradyrhizobium. Associando-se os resultados de eficiência simbiótica e nodulação, observou-se que os isolados de rizóbio de solos da Amazônia apresentaram bom desempenho e podem ser recomendados para testes de eficiência agronômica em feijão caupi.