The efficacy Biological wastewater treatment process is largely dependent on the formation of microbial flocs and settleability before the water is released into the environment. Settleability and flocculation are reliant upon stable physicochemical parameters. Extracellular polymeric substance constituents dictate physicochemical parameters of flocs. The fluctuation of these constituents within mixed microbial flocs is poorly studied. A novel aspect of this research was the use of CLSM data to get a semi- quantitative assessment of the constituents within mixed microbial flocs. Wastewater treatment flocs were characterized for eubacterial ecology, physicochemical properties, and they were visualized through correlative microscopy. It was observed that the microbial communities from the three sampling sites exhibited significant variability in numerous physicochemical properties. Overall, these results provide a first step to examine micro-localization of physicochemical properties, architecture and processes within flocs that may help better understand the causes of floc- related inefficiencies in biological wastewater treatment. / Canadian Hemophilia Society

Les protéines eucaryotes Elmo (Engulfment and Cell Motility) forment une famille de régulateurs conservés qui jouent un rôle central dans les processus biologiques reposant sur le remodelage du cytosquelette d'actine comme la phagocytose et la migration cellulaire et régulé par les GTPases de la famille Rho. Les protéines Elmo régulent la fonction des protéines Dock (Downstream of Crk), qui sont des Facteurs d'Echange de Guanine (GEF) atypiques pour les GTPases Rac1 et Cdc42. Le mécanisme de régulation connu à ce jour, repose sur l'interaction entre les 200 résidus C-terminaux d'Elmo et les 180 premiers résidus N-terminaux de Dock. Cependant, le rôle précis des différents domaines et motifs identifiés dans ces régions n'est pas encore défini. En effet, les données fonctionnelles, biochimiques et structurales rapportées à ce jour semblent contradictoires quant à la contribution de l'extrémité C-terminale d'Elmo qui comprend un motif polyproline et le domaine SH3 N-terminal de Dock. Nous avons donc étudié la contribution de l'extrémité C-terminale de Elmo1 à l'interaction entre Elmo1 et le domaine SH3 de Dock1 en utilisant notamment la résonance plasmonique de surface. Nos données démontrent la capacité du domaine SH3 de Dock1 à interagir avec Elmo1, indépendamment de l'extrémité C-terminale contenant le motif polyproline. Toutefois, la présence de cette région conduit à une augmentation significative du temps de demi-vie du complexe Elmo1/Dock1. En parallèle, des expériences de diffusion des rayons X aux petits angles nous ont permis de déterminer des enveloppes tridimensionnelles de la protéine Elmo1. Ces données nous permettent ainsi de proposer un premier modèle à basse résolution dans lequel nous localisons les parties N et C-terminales de Elmo1. De façon surprenante cette étude semble indiquer un changement de conformation de la région N-terminale de Elmo1 ainsi qu'une interaction possible de cette même région avec le domaine SH3 de Dock1.

La Beta-2-microglobuline est une protéine de 12kDa, impliquée dans une maladie dûe à un mauvais repliement: l'amylose liée à la dialyse. Elle constitue donc un modèle pour la formation de fibrilles amyloides et pour le repliement des protéines. La B2M est un objet à la fois difficile et fructueux à étudier. La production de B2M est complexe et demande une optimisation important pour obtenir une protéine correctement repliée et atteindre des rendements approprié pour des études de RMN et SAXS. Le repliement de la B2M est sensible au solvent, à la température, à la concentration et souvent aux conditions de préparation. Pourtant notre étude, à l'aide de plusieurs méthodes biophysiques, a pu révéler plusieurs faits essentiels de son mécanisme de repliement et de la structure et propriétés des intermédiaires. Un premier résultat est que le repliement et l'oligomérisation sont deux processus concourants. Une découverte majeure est l'existence d'un équilibre monomère oligomère entre deux états I1 et I2 intermédiaires du repliement. Détecté indirectement à l'aide de RMN temps réel comme SOFAST, I2 a été directement charactérisé en SAXS: Il s'agit probablement d'un dimère. Les états intermédiaires de repliement de B2M avaient été pointés comme favorisant la formation de fibrilles: cela s'explique facilement avec l'existence d'un intermédiaire dimérique. Une combinaison de méthodes biophysiques permet la caractérisation de cet équilibre monomère-oligomère. En SAXS, puis confirmé en RMN, la stoichiométrie de l'équilibre est celle d'un monomère-dimère. Des travaux complémentaires utilisant les techniques développées pour cette étude pourront servir à caractériser plus finement cet équilibre. L'étude approfondie du repliement de B2M pousse les techniques biophysiques dans leurs retranchements: la sensibilité et le temps d'acquisition pour la RMN, la polydispersité pour le SAXS. Pourtant dans les deux cas un grand oligomère I3, qui disparait en quelques minutes, a pu être détecté, ce qui fut confirmé par UV-Fluo. La caractérisation d'I3 demandera des dévelopements méthodologiques supplémentaires, ainsi qu'un nouveau plan d'expérience. D'autres méthodes comme la spectrométrie de masse nano-ESI pourraient représenter des sources d'information utiles. S'attaquer aux limites des méthodes biophysiques pousse au développement méthodologique. Ainsi pour étudier la structure et dynamique d'I1, la méthode d'acquisition continue des données a permis l'attribution des résonnances de cette espèce qui a une demi vie de quelques dizaines de minutes. Un échange conformationnel a été découvert pour l'état I1 du mutant W60G, en développant une méthode de relaxation RMN: R2-BEST-TROSY. Les méthodes développées pour cette étude pourront servir des études sur le repliement d'autres protéines, mais aussi dans d'autres contextes où la demi-vie des objets étudiés est courte, comme dans les expérience RMN intracellulaires. Cette étude est évidemment éloignée d'une application directe dans le combat contre les maladies du mauvais repliement des protéines. Pour autant, la découverte d'états intermédiaires oligomériques souligne que l'oligomérisation et le repliement ne devraient pas être étudiés séparément, mais sont des processus liés. Les développements méthodologiques de cette étude pourront aussi être appliqués à d'autres protéines comme à d'autres contexte. Il est donc permis d'espérer que ces questionnements et développements permettront d'avancer vers une meilleure compréhension de ces maladies.

The chloride/proton antiporter ClC-5 is primarily expressed in the kidney where it aids in re-absorption of proteins from the glomerular filtrate. Functional disruption of ClC-5 causes Dent’s Disease – a renal condition characterized by proteinuria and kidney failure in a third of all cases. The majority of disease-causing mutations translate into premature truncations of the carboxy-terminal (Ct) region of ClC-5 and are predicted to disrupt the protein-protein interactions mediated by this domain. In this thesis, direct ATP binding to the two cystathionine β-synthase (CBS) domains of ClC-5 was demonstrated. ATP binding enhanced the global compactness of the ClC-5 Ct region likely through a clamping motion of the CBS domains around the nucleotide. Along with ATP, the sodium proton exchange regulatory factor 2 (NHERF2) also binds ClC-5; however, the molecular mechanism behind this interaction was unknown as ClC-5 lacked the PDZ binding motif traditionally localized at the Ct end of bait proteins. Here, we also identified a class I PDZ binding motif (657-660; TSII) within the internal sequence of ClC-5. Despite the buried position of this motif in the Ct peptide’s X-ray crystal structure (PDB: 2J9L), the high propensity of this region for dynamic flexibility prompted us to test whether it could mediate NHERF2 interactions. In support of this hypothesis, we demonstrated that the motif is transiently available to interact directly with NHERF2 in vivo and to enable an enhancement in receptor-mediated endocytosis in mammalian cells. Collectively, these results gave further evidence that the intracellular Ct region of ClC-5 serves as a hub to mediate interactions essential for its maturation, stability, and trafficking in renal epithelium, as well as providing further insights into the molecular basis of Dent’s Disease.

No presente trabalho, o peptídeo inseticida recombinante Jaburetox-2Ec, derivado da urease de Canavalia ensiformis (Jack bean) foi estudado, principalmente através de técnicas de espectroscopia de espalhamento de luz e raios-X. Foi analisada a tendência do peptídeo a se agregar em diferentes condições físico-químicas quando em solução aquosa, e a sua interação com membranas de lipossomas miméticos de plaquetas humanas. A partir dos dados de raio hidrodinâmico, raio de giro, e massa molar ponderal média obtidos do peptídeo em solução, foi possível observar uma tendência para maior agregação numa faixa em torno de pH 5,5, bem como ausência de agregação em pH inferior a 4,0 e superior a 7,0. Não se verificou nenhum efeito visível no nível de agregação com a adição de agente redutor ou íons, sendo que a exposição ao oxigênio do ar levou a um aumento da mesma. Os estudos de interação do Jaburetox-2Ec com lipossomas revelaram uma significante mudança estrutural na membrana, que se mostrou mais intensa com uma maior concentração do peptídeo. Foram, através de software, feitos ajustes teóricos das curvas de espalhamento de raios-X à baixos ângulos dos lipossomas, a fim de quantificar as mudanças nos parâmetros físicos das membranas causados pela ação do peptídeo. A formação de poros na membrana pelo peptídeo foi proposta como explicação para os resultados encontrados. / In the present work, the insecticide recombinant peptide Jaburetox-2Ec, derived from Canavalia ensiformis (Jack bean) urease, was studied, primarily by light and X-ray scattering techniques. Its tendency to aggregate in aqueous solution under different physical-chemical conditions, and its interaction with human platelet mimetic liposome membranes were analyzed. From the data relative to hydrodynamic radii, radii of gyration and mean molecular weight obtained from the peptide in aqueous solution, it was possible to observe a tendency for greater aggregation around pH 5.5, as well as an absence of aggregation at values of pH below 4.0 and above 7.0. No visible effect on the level of aggregation was verified with the addition of reducing agent or ions, whereas the exposure to oxygen in the air resulted in an increase in this level. The studies of Jaburetox-2Ec interaction with liposomes revealed a significant structural change in the membrane, which was shown to be more intense in higher peptide concentrations. Software-assisted theoretical fits were made for the experimental small-angle X-ray scattering curves aiming to quantify the changes in the physical parameters of the membranes caused by peptide action. The formation of pores in the membrane was proposed as an explanation to the results found.

No presente trabalho, o peptídeo inseticida recombinante Jaburetox-2Ec, derivado da urease de Canavalia ensiformis (Jack bean) foi estudado, principalmente através de técnicas de espectroscopia de espalhamento de luz e raios-X. Foi analisada a tendência do peptídeo a se agregar em diferentes condições físico-químicas quando em solução aquosa, e a sua interação com membranas de lipossomas miméticos de plaquetas humanas. A partir dos dados de raio hidrodinâmico, raio de giro, e massa molar ponderal média obtidos do peptídeo em solução, foi possível observar uma tendência para maior agregação numa faixa em torno de pH 5,5, bem como ausência de agregação em pH inferior a 4,0 e superior a 7,0. Não se verificou nenhum efeito visível no nível de agregação com a adição de agente redutor ou íons, sendo que a exposição ao oxigênio do ar levou a um aumento da mesma. Os estudos de interação do Jaburetox-2Ec com lipossomas revelaram uma significante mudança estrutural na membrana, que se mostrou mais intensa com uma maior concentração do peptídeo. Foram, através de software, feitos ajustes teóricos das curvas de espalhamento de raios-X à baixos ângulos dos lipossomas, a fim de quantificar as mudanças nos parâmetros físicos das membranas causados pela ação do peptídeo. A formação de poros na membrana pelo peptídeo foi proposta como explicação para os resultados encontrados. / In the present work, the insecticide recombinant peptide Jaburetox-2Ec, derived from Canavalia ensiformis (Jack bean) urease, was studied, primarily by light and X-ray scattering techniques. Its tendency to aggregate in aqueous solution under different physical-chemical conditions, and its interaction with human platelet mimetic liposome membranes were analyzed. From the data relative to hydrodynamic radii, radii of gyration and mean molecular weight obtained from the peptide in aqueous solution, it was possible to observe a tendency for greater aggregation around pH 5.5, as well as an absence of aggregation at values of pH below 4.0 and above 7.0. No visible effect on the level of aggregation was verified with the addition of reducing agent or ions, whereas the exposure to oxygen in the air resulted in an increase in this level. The studies of Jaburetox-2Ec interaction with liposomes revealed a significant structural change in the membrane, which was shown to be more intense in higher peptide concentrations. Software-assisted theoretical fits were made for the experimental small-angle X-ray scattering curves aiming to quantify the changes in the physical parameters of the membranes caused by peptide action. The formation of pores in the membrane was proposed as an explanation to the results found.

Submitted by Carolina Tatiani Alves Ferreira null (carolinatatiani@hotmail.com) on 2016-10-11T17:47:48Z No. of bitstreams: 1 dissertacao_final.pdf: 2971956 bytes, checksum: ff2c42bfe3830597c9ccad5a4c364c97 (MD5) / Approved for entry into archive by Juliano Benedito Ferreira (julianoferreira@reitoria.unesp.br) on 2016-10-18T17:04:39Z (GMT) No. of bitstreams: 1 ferreira_cta_me_sjrp.pdf: 2971956 bytes, checksum: ff2c42bfe3830597c9ccad5a4c364c97 (MD5) / Made available in DSpace on 2016-10-18T17:04:39Z (GMT). No. of bitstreams: 1 ferreira_cta_me_sjrp.pdf: 2971956 bytes, checksum: ff2c42bfe3830597c9ccad5a4c364c97 (MD5) Previous issue date: 2016-08-31 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / Estudos recentes têm explorado o comportamento de macromoléculas em solução e a implicação das mudanças conformacionais. Apesar da importância deste assunto, há um número limitado de técnicas para observar as alterações nestes sistemas. Isto se deve a complexidade e aos altos custos envolvidos. Uma técnica que apresenta vantagens com relação aos tamanhos das proteínas estudadas e baixos custos em comparação à outras similares é o espalhamento de raios-X à baixo ângulo , ou SAXS - do inglês small angle X-ray scattering. Entretanto, os resultados possuem uma baixa resolução, pois consiste apenas no "envelope" da partícula e não possui nenhuma informação sobre as estruturas secundárias, terciárias ou quaternárias. O objetivo deste trabalho é o desenvolvimento de uma ferramenta capaz de descrever teoricamente estruturas terciárias em solução, baseado no conhecimento das estruturas secundárias e do perfil de espalhamento de SAXS. As simulações geram novas conformações por um algoritmo de pivot. O critério de Metropolis minimiza a energia potencial formada pela energia de Lennard-Jones e um termo associado à similaridade entre os perfis de espalhamento teórico e experimental. Esta ferramenta obteve resultados iniciais satisfatórios e, após uma fase de calibração, estará disponível online à comunidade científica, no site: http://oliveira.df.ibilce.unesp.br/. / Recent studies have been exploring the dynamical behavior of macromolecules in solution and the implication of conformational changes. Despite all the importance revolving this subject, there are a limited number of techniques to observe these system variations. This is due to the complexity and costs involved. One interesting technique that presents no protein size limitations and has relatively low costs is the Small Angle X-ray Scattering (SAXS). However, it provides low-resolution results, consisting only of the particle’s “envelope” that does not provide any accuracy on secondary, tertiary or quaternary structures. This work aims the development of a tool to provide theoretical structural description of representative conformations in solution based only on the secondary structure informations and the experimental scattering profile. The simulations generates new conformations by a pivot algorithm. The Metropolis criteria minimizes the potential energy composed by a Lennard-Jones term and an energetic term related to the similarity of the experimental and theoretical scattering profiles. The software achieved some satisfactory initial results and it will be available online to the scientific community, after a calibration phase, at http://oliveira.df.ibilce.unesp.br/.

No presente trabalho, o peptídeo inseticida recombinante Jaburetox-2Ec, derivado da urease de Canavalia ensiformis (Jack bean) foi estudado, principalmente através de técnicas de espectroscopia de espalhamento de luz e raios-X. Foi analisada a tendência do peptídeo a se agregar em diferentes condições físico-químicas quando em solução aquosa, e a sua interação com membranas de lipossomas miméticos de plaquetas humanas. A partir dos dados de raio hidrodinâmico, raio de giro, e massa molar ponderal média obtidos do peptídeo em solução, foi possível observar uma tendência para maior agregação numa faixa em torno de pH 5,5, bem como ausência de agregação em pH inferior a 4,0 e superior a 7,0. Não se verificou nenhum efeito visível no nível de agregação com a adição de agente redutor ou íons, sendo que a exposição ao oxigênio do ar levou a um aumento da mesma. Os estudos de interação do Jaburetox-2Ec com lipossomas revelaram uma significante mudança estrutural na membrana, que se mostrou mais intensa com uma maior concentração do peptídeo. Foram, através de software, feitos ajustes teóricos das curvas de espalhamento de raios-X à baixos ângulos dos lipossomas, a fim de quantificar as mudanças nos parâmetros físicos das membranas causados pela ação do peptídeo. A formação de poros na membrana pelo peptídeo foi proposta como explicação para os resultados encontrados. / In the present work, the insecticide recombinant peptide Jaburetox-2Ec, derived from Canavalia ensiformis (Jack bean) urease, was studied, primarily by light and X-ray scattering techniques. Its tendency to aggregate in aqueous solution under different physical-chemical conditions, and its interaction with human platelet mimetic liposome membranes were analyzed. From the data relative to hydrodynamic radii, radii of gyration and mean molecular weight obtained from the peptide in aqueous solution, it was possible to observe a tendency for greater aggregation around pH 5.5, as well as an absence of aggregation at values of pH below 4.0 and above 7.0. No visible effect on the level of aggregation was verified with the addition of reducing agent or ions, whereas the exposure to oxygen in the air resulted in an increase in this level. The studies of Jaburetox-2Ec interaction with liposomes revealed a significant structural change in the membrane, which was shown to be more intense in higher peptide concentrations. Software-assisted theoretical fits were made for the experimental small-angle X-ray scattering curves aiming to quantify the changes in the physical parameters of the membranes caused by peptide action. The formation of pores in the membrane was proposed as an explanation to the results found.

L'ivoire d'éléphant est un matériau biologique composé de fibres de collagène (CF) à 30 % massique et de particules d'hydroxyapatite carbonatées et enrichies en Mg à 70 % massique (Mg-carb-HAP). Il présente une structure hiérarchique complexe de la macro à la nano-échelle. La relation entre le motif macroscopique de Schreger observé à la surface des sections transverses des défenses et la micro-morphologie de l'ivoire en 3D (réseau tubulaire et orientations secondaires des CF) a été établie. Les marqueurs chimiques (Ca, P, Mg, Sr) et structuraux (épaisseurs et organisation des particules de Mg-carb-HAP) témoins des processus de formation de l'ivoire ont été déterminés. La diagenèse précoce en milieu marin a ensuite été étudiée par une approche physico-chimique combinant les analyses MEB, PIXE/RBS-EBS et SAXS. Les mécanismes d'altération identifiés sont les adsorptions des ions du milieu extérieur (Cl, Sr, Fe, Cu) à la surface des défenses, les échanges entre les ions exogènes et endogènes de l'ivoire et l'augmentation de la cristallinité des Mg-carb-HAP. Bien qu'immergées dans le même environnement diagénétique, les trois défenses du site des Poulins présentent différents états d'altération. Un bon état de préservation macroscopique ne reflète pas forcément un bon état de conservation de la dentine à l'échelle moléculaire. Finalement, l'ancienne polychromie et la dorure d'origine des ivoires d'Arslan Tash (Syrie, 800 av. J.C.) ont été restituées par des analyses non-invasives par FX en plein champ et PIXE/RBS-EBS. Les couleurs identifiées sont: le bleu et le vert égyptiens (Cu), avec des teintes plus ou moins claires (Pb), le rouge et l'orange (Fe). / Elephant ivory is a biological material composed of collagen fibers (CF) at 30 wt. % and Mg-enriched carbonated hydroxyapatite particles at 70 wt. % (Mg-carb-HAP). It has a complex hierarchical structure from macro- down to nano-scale. The relationship between the macroscopic Schreger patterns observed on the surface of transverse sections of tuks and the 3D micro-morphology of ivory (tubular network and CF secondary orientations) has been established. Chemical (Ca, P, Mg, Sr) and structural markers (thickness and organization of particles Mg-carb-HAP) which control the formation of ivory have been determined. Early diagenesis in the marine environment was then studied by means of SEM, PIXE/RBS-EBS and SAXS analyses. Diagenetic mechanisms were identified, as ionic adsorptions from marine environment to the tusk surfaces, ionic substitutions between exogenous and endogenous ivory ions and increased crystallinity of Mg-carb-HAP. Different states of preservation were observed among three tusks coming from the same submarine archaeological site. Good macroscopic preservation states of the surface does not necessarily reflect good preservation states of the dentin at the molecular level. Finally, the former polychromy and gilding of ivories from Arslan Tash (Syria, 800 BC.) have been reconstructed by non-invasive FF-FX and PIXE/RBS-EBS analyses. Egyptian blue and green (Cu) with different shades (Pb), as well as red and orange (Fe) have been identified. The gilding technique consisted of applying a 2 µm thick gold leaf. Over time, these decorations altered ivory surfaces inducing, among others, the formation of Au nanoparticles derived from the weathering of the gold leafs.

Les nanocolloïdes magnétiques sont des dispersions de nanostructures magnétiques dans un liquide porteur. Par la combinaison des propriétés du liquide et des particules magnétiques, ces dispersions peuvent être confinées, déplacées, déformées et contrôlées par l'application d'un champ magnétique externe et ont ainsi de nombreuses applications en nanosciences et les nanotechnologies. Nous avons étudié la dispersion de nanoparticules magnétiques (NPM) dans les solvants eutectiques profonds (DES). Ces solvants, constitués d'un mélange entre un sel d'ammonium (ici le chlorure de choline (Ch) et un donneur de liaison H (ici, l'ethyleneglycol (EG) ou l'urée (U)) ont des propriétés proches des liquides ioniques tout en étant biodégradables. L'un des verrous concernant ces dispersions est la nature des forces impliquées dans la stabilité colloïdale. En effet, on ne peut plus expliquer la stabilité des dispersions dans ces milieux par le modèle DLVO, classiquement utilisé dans l'eau, du fait de leur force ionique élevée. Nous avons dans en premier temps caractérisé soigneusement deux DES (ChEH (1:3) et ChU (1:2) en mol) du point de vue de la densité et viscosité pour des températures entre 20 et 45°C. Ceci nous a permis de montrer la forte association de ces liquides. Un protocole de dispersion de nanoparticules de maghémite (Fe2O3) ou de ferrite mixte (CoxZn1-xFe2O4) est ensuite proposé, et les dispersions sont étudiées par diffusion de rayonnement (lumière et SAXS). Il s'est avéré que les particules les plus petites étaient les mieux dispersées. Enfin, un test de synthèse de NPM dans des solutions d'argile a permis d'obtenir une polydispersité plus faible en sortie de synthèse. / Magnetic nanocolloids are dispersions of magnetic nanostructures in a carrier fluid. Thanks to the original properties of both the liquid and the magnetic particles, these dispersions can be confined, moved, deformed and controlled by applying an external magnetic field. Such dispersions thus have many applications in nanoscience and nanotechnologies.We studied the dispersion of magnetic nanoparticles in deep eutectic solvents (DES). These solvents (DES), obtained by mixing a quaternary ammonium salt (e.g., choline chloride Ch) and a hydrogen bond donor (e.g., ethyleneglycol EG or Urea U) have properties similar to ionic liquids, and are also biodegradable. One of the questions about these dispersions is the nature of the forces implied in colloidal stability, since the DLVO model classically used in water cannot be invoked here due to the very high ionic strength of the solvent.In a first step, we have carefully characterized two DES ((ChEG (1:3) and ChU (1:2) in mol), measuring the density and viscosity for temperatures between 20 and 45°C. We could thus show the high association in these liquids.A protocol to disperse nanoparticles of maghemite (Fe2O3) or mixed ferrite (CoxZn1-xFe2O4) is then proposed, and the obtained dispersions are studied by dynamic light scattering and SAXS. The size polydispersity was reduced by size sorting, and it reveals that the smallest particles are the most easy to disperse in the DES.Last, a synthesis of NMP in clay dispersion was tested and showed promising results with a reduced size polydispersity.