Human immunodeficiency virus (HIV) Rev and Hepatitis B virus (HBV) e-antigen are both viral proteins that have key functions in their respective viral replication cycles. Both have evaded crystallization for decades due to their tendency to aggregate and/or form higher-order species. In this thesis the structure determination of HIV Rev and HBV e-antigen is presented—achieved via complexing with monoclonal antibody Fab fragments—and their structures are analysed. HIV Rev is a small regulatory protein that mediates the nuclear export of viral mRNAs, an essential step in the HIV replication cycle. In this process, Rev cooperatively oligomerises onto a highly structured RNA motif, the Rev response element. The structure of Rev (complexed with Fab), determined to 2.3 Å resolution, reveals a molecular dimer where the ordered portion of each subunit (N-terminal domain; NTD; residues 9-65) contains two coplanar a-helices arranged in hairpin fashion. Rev subunits dimerise via interaction of identical hydrophobic patches that overlap to form a V-shaped assembly. Mating of hydrophobic patches on the outer surface of the dimer promotes higher order interactions. Cryo-electron microscopy and helical image reconstruction of in vitro assembled Rev filaments were performed to better understand higher-order Rev oligomerisation. Reconstructions of Rev filaments were determined to ~13 Å resolution, permitting docking of the Rev NTD structure. Conformational variability of the Rev dimer subunits and use of a third ligomerisation interface engender filaments that can expand and contract. Both characteristics were also observed in the crystal structures of Rev. Surface features of the Rev filaments are altered in different expansion states, which may have implications for the assembled forms that Rev adopts during nuclear export of RNA and subsequent re-import into the nucleus. Various models for Rev oligomerisation onto the viral RNA are proposed. Chronic Hepatitis B virus (HBV) infection afflicts millions worldwide with cirrhosis and liver cancer. HBV e-antigen (HBeAg), a clinical marker for disease severity, is a soluble variant of the protein (core antigen, HBcAg) that forms the building-blocks of capsids. HBeAg is not required for virion production, but is implicated in establishing immune tolerance and chronic infection. The crystal structure of HBeAg clarifies how the short N-terminal propeptide of HBeAg induces a radically altered mode of dimerisation relative to HBcAg (~140 rotation), which is locked into place through formation of intramolecular disulfide bridges. This structural switch precludes capsid assembly and engenders a distinct antigenic repertoire, explaining why the two antigens are cross-reactive at the T-cell level (through sequence identity) but not at the B-cell level (through conformation). The structure offers insight into how HBeAg may establish immune tolerance for HBcAg while evading its robust immunogenicity.

Solid state chemical storage of hydrogen in metals offers promising advantages over compressed hydrogen gas and condensed liquid hydrogen, especially for mobile applications with respect to safety and energy efficiency. However, no single metal hydride simultaneously satisfies the essential performance criteria for onboard hydrogen storage namely, high gravimetric and/or volumetric energy density, fast kinetics and favorable thermodynamics. Recently, a breakthrough achievement was made by the development of reactive hydride composites in which two metal hydride systems (e.g. NaBH₄ and MgH₂) are mixed together resulting in better sorption properties than the individual pure systems. In this approach, the formation of MgB₂ by exothermic reaction destabilizes the composite and consequently reduces the overall enthalpy and sorption temperature of the endothermic desorption reaction. In this work the thermodynamic and kinetic properties of reactions in 2NaH + MgB₂ + 4H₂ ↔ 2NaBH₄ + MgH₂ and 3NaH + MgB₂ + 4H₂ ↔ 2NaBH₄ + NaMgH₃ were established using multiple experimental techniques like volumetric measurements, ex-situ and in-situ X-ray diffraction, calorimetry, and especially electron microscopy. Under the applied experimental conditions of 50 bar hydrogen and 400 °C during the hydrogenation of 2NaH + MgB2 and 0.1 bar hydrogen and 450 °C during the dehydrogenation of 2NaBH₄ + MgH₂, both reactions were kinetically limited and proceeded in multisteps. The absorption reaction was partial, being restricted by the unexpected formation of NaMgH₃ which limits the formation of NaBH₄ while the desorption reaction was complete and limited by the growth of MgB₂ through some intermediate complexes at the Mg/NaBH₄ interface where the intermediate phase forms a barrier to diffusion. Conversely, in the 3NaH + MgB₂ system, absorption in 100 bar hydrogen and 300 °C was complete but slow, while in the 2NaBH₄ + NaMgH₃ system, complete desorption was achieved in multisteps under 0.1 bar hydrogen and 450 °C. The formation of intermediate and stable complexes during these reactions poses a significant restraint to hydrogen sorption reactions. However, lower onset sorption temperatures have been established in these systems than in the pure compounds due to their simultaneous destabilization in the composite state. This study have demonstrated the complexity of desorption and absorption mechanisms in these composite systems and the difficulty of obtaining such reactions at low temperatures required for mobile applications. This understanding of the rate limiting reaction steps in reactive hydride composites provides the basis for further optimization of these materials for efficient hydrogen storage applications.

A large number of proteins interact with biological membranes, either integrated in the membrane (PepTSo2), embedded on a membrane surface (5-lipoxygenase) or encircling a cutout of lipid bilayer (apolipoprotein1 (apoA-I). They function as transporters, receptors or biocatalysts in cellular processes like inflammation or cholesterol transport which are touched upon here. Malfunction of specific membrane proteins are the cause for several diseases or disorders. Knowledge of protein structure supports understanding of its mechanism of function. Here, transmission electron microscopy (TEM) was used for structure determination. To obtain structure information to high resolution for membrane proteins, normally surrounded by lipids, demands specific methods and materials for stabilization. Stabilized in detergent the structure of the bacterial transporter PepTSo2 was shown to form a tetramer even bound to substrate. However, with a protein based stabilizer, Salipro, the structure of PepTSo2 could be determined to high resolution. High density lipoprotein (HDL) in blood plasma, involved in the removal of cholesterol from peripheral tissues, have a central role in cardiovascular function, metabolic syndrome and diabetes. The HDL-particle is composed of two copies of ApoA1 and around hundred lipid molecules. From TEM data, for the first time the clearly discoidal shape could be shown by 3-dimendional reconstructions. These were used for modelling the ApoA1 protein dimer by a "biased fitting" procedure. The results indicate how ApoA1 folds around a lipid bilayer in a disc-shaped structure. Modified HDL called nanodiscs were here used to show the Ca2+ dependent binding of 5-lipoxygenase on the nanodisc bilayer and thereby increased production of the inflammatory mediator leukotrieneA4. Dimerization of 5-lipoxygenase inactivates these functions. / <p>QC 20170323</p>

The objective of this research project was to evaluate the mechanical, morphological, and permeability properties of electrospun blends of polydioxanone and poly(lactic acid) for application as vascular grafts. Mechanical analysis was performed by uniaxial tensile testing to examine the peak load, peak stress, elastic modulus, and strain at break of the fibrous materials. The morphological characteristics of the polymer blends were analyzed using phase contrast microscopy, scanning electron microscopy, and image analysis software. Scanning electron microscopy and image analysis software were used to assess fiber diameter and pore size of electrospun scaffolds. Scaffold permeability measurements were also used to calculate fiber diameter and pore size, and the values were compared to those obtained using image analysis. The material property results acquired from the research suggest that the electrospun polymer blends have potential for use in vascular graft applications.

L'infection par le virus de l'hépatite C (HCV) reste aujourd'hui une cause majeure d'hépatite chronique, de cirrhose du foie et de carcinome hépatocellulaire. L'attachement cellulaire et l'entrée de HCV sont médiés par les protéines d'enveloppe E1 et E2. De nouveaux récepteurs ont été récemment identifiés mais l'entrée du virus dans les hépatocytes reste énigmatique et n'a jamais été visualisée. Nous avons tout d'abord caractérisé le modèle des pseudo-particules HCV (HCVpp) encryomicroscopie électronique en transmission (cryo-MET). Ce sont des particules sphériques de 100 nm de diamètre portant à leur surface E1 et E2. Nous avons ensuite visualisé l'entrée des HCVpp dans les hépatocytes en MET conventionnelle en utilisant des lignées d'hépatome et des hépatocytes primaires humains(PHH). Ces derniers maintiennent leur polarité en culture comme en témoigne la persistance de canalicules biliaires, tels que dans les hépatocytes natifs. Après synchronisation à 4°C avec les cellules, les HCVpp sont retrouvées liées aux prolongements cellulaires via des 'piliers', et sont ensuite internalisées à 37°C par endocytose dépendante de la clathrine. Ces 'piliers', actuellement en cours d'identification par immunomarquages, sont internalisés avec les HCVpp dans les hépatocytes au sein de vésicules de clathrine ; ce suivi est effectué par des approches de congélation haute pression et de tomographie électronique. Enfin, les évènements d'endocytose des HCVpp dans les PHH se sont avérés rares, avec une cinétique ralentie comparée aux lignées cellulaires. Ces études en MET soulignent l'importance d'utiliser un modèle cellulaire physiologique polarisé pour l'étude du mécanisme d'entrée de HCV. / Hepatitis C virus (HCV) infection is a major cause of chronic hepatitis, liver cirrhosis and hepatocellular carcinoma. Receptor recognition, cell binding and membrane fusion rely on HCV envelope proteins E1 and E2. New receptors were recently discovered; however HCV entry into hepatocytes remains largely unknown and has not yet been visualized. At first, we characterized HCV pseudoparticles (HCVpp) by cryo-transmission electron microscopy (cryo-TEM). They appeared as regular spherical structures of ca. 100-nm, with E1 and E2 at their surface. By conventional TEM, we then visualized HCVpp entry into hepatocytes, using hepatoma cells and primary human hepatocytes (PHH) as a more physiological cell model.PHH maintain their polarity in culture as attested by TEM observation of persistent bile canaliculi. At 4°C, viral particles were primarily found attached to microvilli at the cell surface via molecular bridges and, after warming to 37°C, they were internalized by endocytosis in clathrin-coated pits and vesicles. Using freeze substitution and electron tomographyapproaches, these bridges were found intimately surrounding HCVpp inside the clathrincoated vesicles, suggesting a concomitant internalization. The nature of these bridges is currently under investigation by immunogoldlabeling approaches. Finally, we reproducibly observed less HCVpp internalization events in PHH compared to hepatoma cells, and the kinetics of these events seemed delayed, probably due to PHH polarity. To conclude, ourTEM approach proved powerful to visualize HCV entry, and highlights the importance of studying a physiological cell model to understand HCV entry mechanism.

Ce travail présente les résultats d'un modèle théorique de précipitation de particules Al$_2$Cu dans un alliage d'aluminium de fonderie de type 319 traité thermiquement T7, prenant en compte les équations de la théorie de la coalescence. L'utilisation d'une distribution de taille de particules expérimentale discrétisée comme point de départ du modèle rend possible l'utilisation d'une équation de flux afin de modéliser l'évolution du rayon moyen des particules dans un élément de volume représentatif de l'alliage. L'utilisation d'un schéma numérique implicite permet de ramener la résolution du problème physique à l'inversion d'une matrice tridiagonale. Ainsi, l'évolution du rayon critique de coalescence, du nombre total et de la fraction volumique de précipités sont obtenus pour plusieurs vieillissements. Les résultats du modèle a été confrontés aux résultats des mesures expérimentales qui ont été réalisées à l'aide d'observations en microscopie électronique à transmission et qui ont permis une mesure de la taille des précipités. Ces derniers ont été assimilés à des sphères de volume équivalent aux plaquettes réelles et ont été analysés numériquement. Les résultats fournis par le modèle théorique sont en bon accord avec les mesures expérimentales et ont permis le couplage du modèle de coalescence avec un modèle micromécanique fondé sur la théorie des dislocations et calibré à l'aide d'essais de traction en température. Il permet de déterminer la limite d'élasticité de l'alliage pour un vieillissement jusqu'à 1000h compris entre 23°C et 300°C. La limite d'élasticité est alors assimilée à une somme de trois contraintes~: une contrainte liée à la friction de réseau (contrainte de Peierls), une contrainte liée au contournement des précipités par les dislocations (contrainte d'Orowan) et une contrainte liée à la présence de solution solide. Enfin, des essais de fatigue oligocyclique à différentes températures ont permis de déterminer les variables internes de la loi de comportement macroscopique. Il s'agit d'une loi élasto-viscoplastique de type Lemaitre et Chaboche, à laquelle la limite d'élasticité calculée par le modèle micromécanique est couplée. Ainsi, le comportement physique macroscopique de l'alliage est fonction de la coalescence des précipités. Des calculs 1D ou 3D, par éléments finis, permettent alors de déterminer le comportement général d'une culasse soumise à de la fatigue thermomécanique / This work highlights the results of a theoretical Al$_2$Cu particles coarsening model in a T7 thermal treated 319 aluminum alloy. As an input of the model, the experimental and discretised size distribution of the precipitates, in a 1$mu$m$^3$ representative volume element of the alloy, is used and coupled to a flux equation. The use of a numerical implicit scheme allows us to solve the problem by the inversion of a tridiagonal matrix. Thus, the evolution of the critical radius of coarsening, of the total number and of the volumical fraction of particles are modeled in a range of temperature going from 23°C to 300°C up to 1000h ageing time. Results were then compared to transmission electron microscope observations and are in good agreement with experimental measurements. Hence, the model was then coupled to a micro-mechanical model which is based on the theory of dislocations. It determines the real yield stress of the alloy generated by the interaction of the dislocations with the lattice (Peierls stress), with the precipitates (Orowan stress) and with the atoms in solid solution. Both models were then combined into a mechanical macro-scale model in order to represent the LCF behavior of the material. An elasto-viscoplastic law has been used and all the internal variables were experimentally determined using LCF stress/strain loops for the mechanical steady state. The simulation results are in good agreement with the experiments. Finally, 1D and 3D finite element computations could be run, taking into account the evolution of the microstructure during ageing and its impact on the evolution of the mechanical properties, to determine the head cylinder behavior under thermomechanical fatigue

No description available.

Master of Science / Department of Biological and Agricultural Engineering / Donghai Wang / Currently, the majority of adhesives used for wood veneer, plywood, and composite applications are formaldehyde-based. Formaldehyde is derived from petroleum and natural gas, making it non-renewable and toxic. Therefore, extensive research has been conducted to develop bio-based adhesives to replace formaldehyde-based adhesives. Soy protein has shown great potential to partially replace formaldehyde adhesives, and canola protein has similar properties to soy protein. However, little research has been conducted on the feasibility of using canola protein for wood adhesive applications. The objective of this research was to study the adhesion performance of canola protein. Canola protein was modified with different chemical modifiers including sodium dodecyl sulfate (SDS), calcium carbonate (CaCO[subscript]3), zinc sulfate (ZnSO[subscript]4), calcium chloride (CaCl[subscript]2), and 2-octen-1-ylsuccinic anhydride (OSA) as well as combined chemical modifications. The wet, dry, and soak shear strengths of the adhesive formulations were determined. Viscosity testing, differential scanning calorimetry, and TEM and SEM imaging were used to characterize protein properties. Chemical modification with SDS (1%, 3%, and 5%), CaCO[subscript]3 (1%, 3%, and 5%), ZnSO[subscript]4 (1%), and OSA (2%, 3.5%, and 5%) improved the dry and soak shear strengths compared to unmodified canola protein. Canola protein modified with 3.5% OSA had improved wet, dry, and soak shear strengths. Combined chemical modification of canola protein did not show significant improvement on shear strength. Thermal modification of canola protein adhesives showed a trend of increasing shear strength with increasing press temperature. The data suggests that with further research, canola protein has potential to be used as a commercial adhesive or as an additive to formaldehyde-based adhesives to make them more environmentally-friendly.

L'optimisation du couplage lumière-matière requiert la connaissance de l'orientation du dipôle émetteur associé à une source de photons, ainsi que de la distribution de champ électrique du mode excité. Afin de maximiser le couplage entre des émetteurs fluorescents et des nanostructures, nous avons établi une méthode qui permet de déterminer l'orientation d'un dipôle d'émission. Les calculs en champ électrique, associés à une analyse en polarisation, constituent une modélisation complète, pouvant être généralisée à diverses situations expérimentales. Nous appliquons ensuite la méthode proposée à des nanocristaux colloïdaux de CdSe/CdS et CdSe/ZnS sphériques, ainsi qu'à des nanobâtonnets de CdSe/CdS. Nous avons déterminé, par une analyse en polarisation, l'orientation complète d'un dipôle émetteur individuel. Nous avons ensuite étudié le couplage de la lumière à des plasmons grâce à des réseaux périodiques métalliques. Des mesures de réflectivité spéculaire ont mis en évidence un couplage efficace de la lumière incidente à des plasmons de surface sur une large gamme de longueurs d'onde. Des mesures de microscopie électronique par photoémission (PEEM), basées sur la collection d'électrons photoémis à la surface du métal, ont permis d'étudier le couplage de la lumière aux modes plasmons de surface, avec une haute résolution spatiale (25 nm). L'excitation de l'échantillon par un laser, dont on varie la longueur d'onde et la polarisation, fournit une cartographie de la distribution du champ à la surface. Les échantillons étudiés ont mis en évidence différentes signatures de couplage du faisceau incident aux modes plasmoniques (franges d'interférences, points chauds). / The emission features of a single emitter embedded in a nanostructure are closely related to the local environment parameters, as well as to the orientation of the dipole itself. In order to maximize the coupling of fluorescent emitters to nanostructures, we established a model to determine the 3D-orientation of an emitting dipole. I developed an analytic description of a method which allows a measurement of a single dipole orientation to be performed, in various experimental configurations. I then applied this method to colloidal semiconductor nanocrystals (spherical CdSe/CdS and CdSe/ZnS nanocrystals and CdSe/CdS dot-in-rods). By using a polarization analysis, I determined the 3D-orientation of a single emitting dipole. This study led us to the particular conclusion that the emitting dipole associated to a dot-in-rod is not aligned with the elongated axis of the dot-in-rod. In a second part, I studied the coupling between light to surface plasmons modes using periodic metallic gratings. Specular reflectivity measurements highlighted an efficient coupling between the incident visible light and surface plasmons polaritons for a large range of wavelengths. Photoemission electron microscopy (PEEM) measurements, based on the collection of photo-emitted electrons on the surface of the sample, allowed the coupling of light to plasmonic modes to be investigated with a high spatial resolution (25 nm). The sample is excited by a laser tunable in polarization and wavelength, providing a map of the electric field on the surface. The samples showed two different signatures of a coupling to plasmonic modes (interference fringes and hot spots).

Considerando que o licor pirolenhoso obtido de diferentes tipos de biomassa possui atividades antivirais, o principal objetivo da presente pesquisa foi avaliar a ação antimicrobiana do licor pirolenhoso obtido na pirólise do bambu (Dendrocalamus asper), e de suas frações metanólica e hexânica, em relação às bactérias Escherichia coli e Staphylococcus aureus. O licor pirolenhoso foi recuperado da pirólise em mufla laboratorial, nas temperaturas de 250°C, 350°C e 550°C, os quais foram submetidos a separação líquido-líquido com metanol e hexano gerando as frações metanólica e hexânica. Os licores pirolenhosos integrais (na dose de 5,0 mg por disco) e suas respectivas frações metanólica e hexânica (na dose de 0,125mg por disco), foram aplicadas no ensaio de difusão em disco com as bactérias E. coli e S. aureus; sendo que nesse ensaio a fração metanólica do licor obtido a 350°C (FMeOH350) apresentou melhor eficiência e consistência nos resultados e foi selecionada para continuidade da pesquisa. Através da análise por cromatografia gasosa acoplada a espectrometria de massa foi possível identificar qualitativamente 92 compostos químicos na fração FMeOH350. Essa fração foi aplicada no ensaio de difusão com as bactérias E. coli e S. aureus nas doses de 0,125 mg, 0,500 mg, 0,750 mg e 1,000 mg. O tratamento com a fração metanólica obtida a 350°C inibiu o crescimento celular das bactérias, na região ao redor da aplicação das amostras (halo de inibição), e causou uma variedade de deformações morfológicas em tamanho e deformidades nas paredes celulares das bactérias, comprovadas por aplicação da microscopia eletrônica de varredura, estabelecendo um perfil de atividade antimicrobiana. Esses resultados estão em acordo com a Política Nacional de Incentivos ao Cultivo e Manejo Sustentável do Bambu, bem como traz benefícios para a sociedade e o ambiente como um todo, demonstrando a possibilidade de agregar valor a um subproduto da pirólise. / Considering that the pyroligneous liquor obtained from various types of biomass has antiviral activity, the main objective of the present study was to evaluate the antimicrobial action of the pyroligneous liquor obtained in the pyrolysis of bamboo (Dendrocalamus asper) and its methanolic and hexanic fractions, in relation to Escherichia coli and Staphylococcus aureus bacteria. The pyroligneous liquor was recovered by laboratorial bamboo pyrolysis at temperatures of 250°C, 350°C and 550°C, which were then fractioned by liquid-liquid separation with methanol and hexane. The three integral pyroligneous liquor (dosage of 5,0 mg per disc) and its respective methanolic and hexanic fractions (dosage of 0,125 mg per disc) were used in the diffusion disc assay of E. coli and S. aureus; and the result was the methanolic fraction obtained at 350°C (MeOHF350) showing the better efficiency and results consistence, being selected for the research continuity. Through gas chromatography coupled to mass spectrometry it was possible to qualitatively identify 92 chemical compounds in this methanolic fraction. The MeOHF350 fraction was used in the diffusion disc assay of E. coli and S. aureus at dosages of 0.125, 0.500, 0.750 and 1.000 mg. Treatment with the methanolic fraction obtained at 350°C inhibited cellular growth, in the region around of samples application (inhibition halo), caused a variety of morphological variations in size as well as deformities in the bacterial cell walls, proved through scanning electron microscopy, establishing an antimicrobial activity profile. This finding supports the National Policy for Incentives for Sustainable Management and Cultivation of Bamboo (PNMCB) and has benefits to the society and environment as a whole, demonstrating the possibility of adding value to a byproduct of pyrolysis.