Mémoire numérisé par la Division de la gestion de documents et des archives de l'Université de Montréal.

Depuis l'apparition du terme "biosensor" à travers un article de Lyons et Clark en 1962, les biocapteurs ont connu un véritable essor tant au niveau académique qu'industriel. Le principal objectif de ce travail de thèse était de créer une surface permettant l'immobilisation spécifique par liaison covalente de simple ou double brin d'ADN puis d'étudier les interactions pouvant exister entre une protéine donnée et l'ADN. Pour préparer la surface à cette immobilisation, nous avons opéré une réduction électrochimique de sel d'aryldiazoniums. Ce type de modification nous a permis de fixer de manière covalente sur la surface conductrice des fonctions de type Ar-SO2Cl. Par l'utilisation de la QCM et de l'AFM, nous avons pu par la suite détailler les mécanismes de fonctionnement de protéines (HsRad51 et Transposase) en interaction avec l'ADN simple ou double brin fixé, que ce soit d'un point de vue cinétique ou bien structural. / Since the emergence of the term "biosensor" through an article of Clark and Lyons in 1962, such devices have experienced a tremendous activity both in the academic and industries. The main objective of this thesis work was to create a surface allowing the specific immobilization of single or double DNA strand by covalent bonding and then study the interactions that may exist between a given protein and DNA. To functionalize the surface, we firstly investigated the electrochemical reduction of aryldiazoniums salt. This kind of methodology has allowed us to covalently graft Ar-SO2Cl functions over the conductive surface which can further react with DNA to immobilize it. By using the QCM and AFM methodologies, we are able to kinetically or structurally detail the intimate mechanisms of interactions between two proteins (HsRad51 and Transposase) and single or double strand DNAs.

Self-assembly of nanoparticles is a promising route to form complex, nanostructured materials with functional properties. Nanoparticle assemblies characterized by a crystallographic alignment of the nanoparticles on the atomic scale, i.e. mesocrystals, are commonly found in nature with outstanding functional and mechanical properties. This thesis aims to investigate and understand the formation mechanisms of mesocrystals formed by self-assembling iron oxide nanocubes. We have used the thermal decomposition method to synthesize monodisperse, oleate-capped iron oxide nanocubes with average edge lengths between 7 nm and 12 nm and studied the evaporation-induced self-assembly in dilute toluene-based nanocube dispersions. The influence of packing constraints on the alignment of the nanocubes in nanofluidic containers has been investigated with small and wide angle X-ray scattering (SAXS and WAXS, respectively). We found that the nanocubes preferentially orient one of their {100} faces with the confining channel wall and display mesocrystalline alignment irrespective of the channel widths.  We manipulated the solvent evaporation rate of drop-cast dispersions on fluorosilane-functionalized silica substrates in a custom-designed cell. The growth stages of the assembly process were investigated using light microscopy and quartz crystal microbalance with dissipation monitoring (QCM-D). We found that particle transport phenomena, e.g. the coffee ring effect and Marangoni flow, result in complex-shaped arrays near the three-phase contact line of a drying colloidal drop when the nitrogen flow rate is high. Diffusion-driven nanoparticle assembly into large mesocrystals with a well-defined morphology dominates at much lower nitrogen flow rates. Analysis of the time-resolved video microscopy data was used to quantify the mesocrystal growth and establish a particle diffusion-based, three-dimensional growth model. The dissipation obtained from the QCM-D signal reached its maximum value when the microscopy-observed lateral growth of the mesocrystals ceased, which we address to the fluid-like behavior of the mesocrystals and their weak binding to the substrate. Analysis of electron microscopy images and diffraction patterns showed that the formed arrays display significant nanoparticle ordering, regardless of the distinctive formation process.  We followed the two-stage formation mechanism of mesocrystals in levitating colloidal drops with real-time SAXS. Modelling of the SAXS data with the square-well potential together with calculations of van der Waals interactions suggests that the nanocubes initially form disordered clusters, which quickly transform into an ordered phase. / <p>At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 4: Manuscript. Paper 5: Manuscript.</p>

Este trabalho teve como objetivo geral a produção de um equipamento pequeno, multifuncional, de baixo custo e útil para as áreas de engenharia química e de química. Quanto à área de engenharia química, manipulam-se amostras em dispositivos miniaturizados que possuem operações unitárias comuns, como por exemplo, misturadores, formação de spray e remoção de partículas. Em química, efetua-se o pré-tratamento de amostras gasosas e possível detecção de compostos orgânicos voláteis (VOCs). A metodologia utilizada seguiu os protocolos para produção de equipamento. O equipamento projetado e construído apresenta três partes distintas e com as seguintes características. As amostras, que podem ser liquidas ou gasosas, são admitidas ou em fluxo contínuo ou de modo estacionário. A manipulação de dispositivos miniaturizados, como por exemplo, mini-misturadores, ocorre em três eixos distintos, o que permite o uso de dispositivos tridimensionais. Para todas as amostras a detecção é baseada em micro-balança de quartzo, com 5 cristais piezelétricos de quartzo (PQC) medindo simultaneamente e independentemente a aquisição de dados online. Quanto a amostras gasosas, é possível a detecção de VOCs na faixa de ppm e em dispositivo miniaturizado (mini manifold) para distribuição do fluxo uniformemente nos 5 PQCs. Através do uso do spray é possível a detecção de gases, líquidos e particulados. O componente sensor nos PQCs é filme fino depositado por plasma e a base de HMDS, hexametildissilazana. Esses filmes foram modificados por exposição à radiação ultravioleta (UVC) e feixe de íons (Ar+ ou He2+), os filmes após exposição mostraram-se mais eficientes na discriminação de VOCs. O equipamento foi construído com modos convencionais de produção, como por exemplo, usinagem com máquinas operatrizes como torno mecânico e fresadoras, e com partes e peças de fácil aquisição no mercado nacional. / This work aimed the production of a small equipment, multi-functional, lowcost and useful for chemical engineering and chemistry areas. Regarding the chemical engineering area samples are handled in miniaturized devices having common unit operations such as mixing, spray forming and removing particles. In chemistry, the pretreatment of gaseous samples and detection of volatile organic compounds (VOCs) could be made. The methodology followed the protocols for production equipment. The equipment designed and built features three distinct parts with the following characteristics. Samples can be liquid or gaseous, they can be admitted or continuous flow or stationary mode. The manipulation of miniaturized devices, such as minimixers occurs in three distinct axes, which allows the use of three-dimensional devices. For all samples the detection is based on quartz microbalance with 5 piezoelectric quartz crystals (PQC) the online data are acquired by measuring simultaneously and independently. As for gaseous samples, it is possible the VOCs detection in the ppm range and miniaturized device (mini manifold) to flow evenly distribution in 5 PQCs. Through the use of spray it is possible to detect gases, liquids and particulates. The sensing component in PQCs is thin film deposited by plasma and the base of HMDS hexamethyldisilazane. These films were modified by exposure to ultraviolet radiation (UVC) and ion beam (Ar+ or He2+) films after exposure were more efficient in the discrimination of VOCs. The equipment was built with conventional production methods, such as, machining with machine tools such as lathes and milling machines,, and parts and pieces of easy acquisition in the domestic market.

Amostras com pequenos volumes e matrizes complexas, como sistemas biológicos, necessitam de preparação criteriosa. Muitas dessas amostras são melhor analizadas em estruturas miniaturizadas devido à necessidade de detectar células e microorganismos em diferentes matrizes. Por essa razão, equipamentos capazes de detectar e destruir microorganismos e estruturas para prévia retenção desses se faz necessários na vida moderna. Chicanas, constrições usadas para reduzir velocidade de fluxo, que podem ser utilizadas para reter compostos, são estruturas macroscópicas para remover resíduos de lagos, fazendas e etc. e chicanas miniaturizadas foram usadas para a adsorção de compostos orgânicos do ar e da água. Assim, esse trabalho tem dois diferentes objetivos: 1) Produção de um equipamento de baixo custo, para teste de partículas ou eliminação de microorganismos e 2) O desenvolvimento de estruturas miniaturizadas para retenção e/ou seleção de partículas e substâncias viscosas de um fluido líquido. A metodologia utilizada foi: 1) Dois software foram escolhidos para esse trabalho. O LabVIEW® 7.0 foi utilizado como plataforma para o desenvolvimento do software do equipamento e o FemLAB® 3.1 para a simulação de estruturas. O equipamento produzido usou Microbalança de Quartzo como detector e um sistema de admissão baseado em uma bomba e tubos. 2) O desenho da estrutura foi otimizado por simulação do comportamento do fluxo. A estrutura otimizada foi feita desmontável, e usinada em polimetilmetacrilato ? acrílico, com ferramentas convencionais. Acrílico foi usado devido à sua transparência óptica, que permite testes com microsocpia óptica. As simulações consideraram N2 e Água como fluidos gasoso e líquido, respectivamente. Avaliou-se o comportamento das partículas (50?m and 13?m) em fluxo gasoso e polidimetilsiloxano (silicone, com viscosidade de 350 cSt) e partículas em fluxo líquido. As estruturas foram caracterizadas quanto à adsorção e retenção de partículas usando equipamento desenvolvido e por microscopia óptica. As estruturas foram, também, continuamente fotografadas durante a execução do experimento e fotos foram utilizadas para determinar o comportamento do fluxo. Os reagentes foram injetados na estrutura em pequenos pulsos. O equipamento mostrou boa performance para detecção de adsorção em fluxo líquido e reprodutibilidade no monitoramento do aquecimento de estruturas. As chicanas mostraram boa capacidade de reter partículas grandes (50?m), mas não pequenas (13?m), tanto para fluxos gasosos como líquidos. Contudo, a estrutura tem pequena capacidade de carga para fluidos líquidos (? 1mg); além disso, a retenção de amostras de silicone na estrutura, utilizando fluido líquido, ocorreu devido à diferença de velocidade entre os fluidos. A simulação e os resultados experimentais apresentam boa correlação. Assim, a chicana mostrou a possibilidade de, seletivamente, separar partículas em fluxos gasosos e líquidos ou reter substâncias viscosas em fluxo líquido. Esses resultados apontam para diversas aplicações, como por exemplo, pré-tratamento para análises biológicas e retenção ou eliminação de microorganismos. / Samples with small volume and complex matrix, such as biological systems, require careful preparation. Many of these samples are better analyzed in miniaturized structures owing to the need of detect cells and microorganisms in different arrays. Therefore equipment able to detect and destroy microorganisms and structures to previously retain them are require in the modern life. Chicanes, i.e. constrictions used to reduce flow velocity, can be useful to retain compounds, are macroscopic devices to remove waste removal from lakes, farms, etc. and miniaturized chicane was used to adsorption of organic compounds from air and water. Thus, this work has two different targets: 1) Production of a low-cost equipment useful for tests of particle or microorganisms elimination and 2) The development of miniaturized structures useful for retention and/or selection of particles and viscous substances from a liquid flow. The methodology used was: 1) Two software were chosen to this work. The LabVIEW® 7.0 was used for development of equipment software and FemLAB® 3.1 for structures simulation. The equipment production used Quartz Crystal Microbalance as detector and an admission system based on simple pumps and plumbing. 2) The design of the structure design was optimized using flow simulation. The optimized design was manufactured in poly(methyl methacrylate) -acrylic, with conventional tools. Acrylic was used due to the optical transparency that allows photographic tests and the structures can be easily disassembled. The simulations considered nitrogen and water for gaseous and liquid flow, respectively. It was evaluated the behavior of particles (50?m and 13?m) on gaseous flow and polydimethylsiloxane (silicone, viscosity of 350 cSt) and particles on liquid flow. The structures were characterized using equipment produced to measure adsorption and optical microscopy to evaluate particle retention. The structures were also continuously photographed during the experiments and the photos were analyzed to determine flow behavior. The reactants were inserted in the structure in small pulses. The equipment shows good performance for detection of adsorption in liquid flows and reproducibility on monitoring heated structures. Chicanes showed good ability to retain big particles (50 ?m) but not small ones (13 ?m) for both liquid and gaseous flow. However, the structure has small load capacity for liquids (? 1 mg). Moreover, the retention of silicone samples in the structure on liquid flow occurs due to the difference in the fluid velocity. The simulation and experimental results are in good agreement and also chicane structure shows the possibility of selectively separate particles from gaseous and liquid flow or retain viscous substances from a liquid flow. These results point out to several applications, such as sample pretreatment for biological analysis and microorganism retention or elimination.

Este trabalho teve como objetivo geral a produção de um equipamento pequeno, multifuncional, de baixo custo e útil para as áreas de engenharia química e de química. Quanto à área de engenharia química, manipulam-se amostras em dispositivos miniaturizados que possuem operações unitárias comuns, como por exemplo, misturadores, formação de spray e remoção de partículas. Em química, efetua-se o pré-tratamento de amostras gasosas e possível detecção de compostos orgânicos voláteis (VOCs). A metodologia utilizada seguiu os protocolos para produção de equipamento. O equipamento projetado e construído apresenta três partes distintas e com as seguintes características. As amostras, que podem ser liquidas ou gasosas, são admitidas ou em fluxo contínuo ou de modo estacionário. A manipulação de dispositivos miniaturizados, como por exemplo, mini-misturadores, ocorre em três eixos distintos, o que permite o uso de dispositivos tridimensionais. Para todas as amostras a detecção é baseada em micro-balança de quartzo, com 5 cristais piezelétricos de quartzo (PQC) medindo simultaneamente e independentemente a aquisição de dados online. Quanto a amostras gasosas, é possível a detecção de VOCs na faixa de ppm e em dispositivo miniaturizado (mini manifold) para distribuição do fluxo uniformemente nos 5 PQCs. Através do uso do spray é possível a detecção de gases, líquidos e particulados. O componente sensor nos PQCs é filme fino depositado por plasma e a base de HMDS, hexametildissilazana. Esses filmes foram modificados por exposição à radiação ultravioleta (UVC) e feixe de íons (Ar+ ou He2+), os filmes após exposição mostraram-se mais eficientes na discriminação de VOCs. O equipamento foi construído com modos convencionais de produção, como por exemplo, usinagem com máquinas operatrizes como torno mecânico e fresadoras, e com partes e peças de fácil aquisição no mercado nacional. / This work aimed the production of a small equipment, multi-functional, lowcost and useful for chemical engineering and chemistry areas. Regarding the chemical engineering area samples are handled in miniaturized devices having common unit operations such as mixing, spray forming and removing particles. In chemistry, the pretreatment of gaseous samples and detection of volatile organic compounds (VOCs) could be made. The methodology followed the protocols for production equipment. The equipment designed and built features three distinct parts with the following characteristics. Samples can be liquid or gaseous, they can be admitted or continuous flow or stationary mode. The manipulation of miniaturized devices, such as minimixers occurs in three distinct axes, which allows the use of three-dimensional devices. For all samples the detection is based on quartz microbalance with 5 piezoelectric quartz crystals (PQC) the online data are acquired by measuring simultaneously and independently. As for gaseous samples, it is possible the VOCs detection in the ppm range and miniaturized device (mini manifold) to flow evenly distribution in 5 PQCs. Through the use of spray it is possible to detect gases, liquids and particulates. The sensing component in PQCs is thin film deposited by plasma and the base of HMDS hexamethyldisilazane. These films were modified by exposure to ultraviolet radiation (UVC) and ion beam (Ar+ or He2+) films after exposure were more efficient in the discrimination of VOCs. The equipment was built with conventional production methods, such as, machining with machine tools such as lathes and milling machines,, and parts and pieces of easy acquisition in the domestic market.

The goal of this research was to develop a novel biosensor for detecting and eliminating pathogenic E. coli. Traditionally, identifying pathogenic E. coli and distinguishing it from harmless environmental strains includes serotyping and DNA sequencing, which can take days or weeks. Our biosensor platform makes use of a material that is part of the immune system from single- multi- cellular organisms that target viruses, fungi, and bacteria called antimicrobial peptides (AMPs). Using the quartz crystal microbalance with dissipation monitoring (QCM-D), we characterized non-specific binding between CP1 to silicon nitride and gold, and covalent binding of cysteine-terminated CP1 (CP1-cys) to gold. QCM-D monitors frequency and dissipative changes resulting from adsorbed mass, and peptide film thickness and density can be calculated using Voigt Viscoelastic modeling. Viability of the E. coli was monitored using a live/dead kit consisting of nucleic acid stains Syto 9 and Propidium Iodide. Successfully immobilizing peptide to a substrate is particularly important if CP1 would be applied on a food processing surface. By immobilizing CP1 to silicon nitride, we measured the binding forces between bacteria and peptides with the atomic force microscope (AFM), and explored important bacterial features such as LPS composition and length that influence binding affinity with CP1. The structure of the LPS is comprised of 3 sections: lipid A, core group, and O-antigen. We are mostly interested in the initial binding between AMP and LPS since our goal is to develop a novel biosensor that can detect pathogenic bacteria within seconds of exposure. Considering the short exposure period, the AMP would only be exposed to the O-antigen and outer core groups, which are repeating sugar chains that are essential for bacterial pathogenicity and adhesion to substrates. Although geared for use as a novel biosensor, results of this study can also be applied to the use of AMPs for replacing or enhancing the activity of antibiotics. Our work suggests that CP1 may not be serotype-specific, but targets the O-antigen before interfering with phospholipid groups of the bacterial membrane. Other factors that assist in pathogenicity, such as LPS length, may also be important for the consideration of CP1 potency.

The bacterial meningitis caused by Neisseria meningitidis is responsible for considerable morbidity and mortality throughout the world. Given the limitations of existing diagnostic tests and the severity of the illness associated with the disease, there is a clear requirement for a rapid and specific diagnostic assay. This thesis describes the development of nanoparticle based tests for the detection of Neisseria meningitidis specific cell surface markers. As an initial target antigen, a recombinant form of highly conserved outer membrane protein, OMP85 was used. Within the OMP85 protein sequence, a predicted antigenic sequence between residues 720 and 745 was identified and found to be unique to this organism. This amino acid sequence was synthesised as peptide (SR1) with a gly-gly-cysteine spacer sequence at the N-terminus using t-boc chemistry. Also, the major virulence factor, capsular polysaccharide of N. meningitidis serogroup B bacteria was purified. Polyclonal antibodies were raised against purified OMP85 antigen in rabbits and against SR1 peptide and also against formalin inactivated N. meningitidis serogroup B whole cell bacteria in sheep. This panel of different antibodies including the commercial anti-capsular monoclonal antibodies were examined for cross reactivity against a range of closely related Gram negative bacteria. Based on these cross-reactivity studies, a highly specific anti-NM antibody was developed following purification of the anti-SR1 antiserum by immuno-affinity chromatography. Purified OMP85 antigen and anti-OMP85 antibody were successfully conjugated on 13, 30, 40, 50 and 60 nm gold nanoparticles by an electrostatic adsorption method. Coupling of the gold nanoparticles results in a shift of the respective surface plasmon peak toward longer wavelengths (in the range of 600-800 nm) resulting in a change of the colour of the colloidal suspension from red to purple to blue. An attempt was made to develop a rapid diagnostic assay based on gold nanoparticle induced colour shift assay for N. meningitidis by utilising the specific interaction of OMP85 and anti-OMP85 antibody conjugated to gold nanoparticles as a model system. However, this system was not reproducible and is likely to be due to problems with stability of gold nanoparticles during the conjugation process. As an alternative approach, a highly selective quartz crystal microbalance (QCM)-based immunosensor was designed using the same OMP85/anti-OMP85 antibody system. A method was developed using polyvinylidene fluoride (PVDF) coated QCM crystals with protein A for the directional orientation of the antibodies. To further enhance the sensitivity of the test, OMP85-conjugated gold nanoparticles were used as signal amplification probes for the reproducible detection of the target down to 300 ng/mL, corresponding to a five fold increase in sensitivity compared to detection of OMP85 antigen alone. Also, this sensor has successfully been employed to detect whole cell bacteria at a concentration as low as 100 cfu/mL. Thus, in this study using the real-time QCM measurements, a novel strategy has been developed for the sensitive detection of both N. meningitidis bacteria and the protein antigen at very low concentrations, using gold nanoparticles as signal amplification probes.

L'objectif visé dans cette étude consiste à développer une méthodologie de caractérisation des interactions ligands/récepteurs cellulaires à la surface d'un transducteur physique. Le ligand immobilisé est représenté par un cyclopentapeptide c(-RGDfK-) dont les propriétés de reconnaissance spécifique pour l'intégrine alphaV beta3 sont bien connues. Les travaux de thèse présentés dans ce manuscrit concernent la synthèse des ligands peptidiques, la mise au point des différentes techniques d'immobilisation de ces ligands et enfin la caractérisation des interactions biomoléculaires avec des cellules exprimant l'intégrine. Le ligand peptidique est présenté de façon multivalente sur un châssis moléculaire cyclodécapeptidique de séquence c(-Pro-Gly-Lys-Lys-Lys-)2. Le greffage des différents motifs se fait via la formation d'un lien éther d'oxime ou d'un lien amide sur les chaînes latérales des lysines orientées de part et d'autre du plan moyen du cyclopeptide. Trois approches ont été mises en œuvre pour fixer les ligands -RGD- sur une surface : le couplage affin, l'insertion dans une bicouche lipidique et le couplage covalent. Les surfaces fonctionnelles résultantes ont été caractérisées par des méthodes physico-chimiques d'analyse de surface et d'interface. Des tests d'adhésion cellulaire, suivis par QCM-D et par microscopie optique, ont ensuite permis de caractériser les propriétés de reconnaissance des ligands peptidiques. La comparaison des signaux de QCM-D et des images de la surface, obtenus à différents taux de greffage du ligand a permis d'identifier une densité de greffage minimale en ligand nécessaire à l'adhésion et à l'étalement des cellules.

<p>En studie i hur känsligheten avtar från ytan hos biosensorer med höga frekvenser presenteras. Med ny teknologi som avancerade elektroakustiska tunnfilms komponenter, så kallade FBARs, blir tidigare outforskade områden som decay längden möjliga att studera.</p><p>För att undersöka hur frekvenssvaret och känsligheten påverkas av interaktioner långt ut från en sensoryta används proteinkemi. Ett protokoll har optimerats innehållande aktivering med EDC/NHS och fibrinogen för att säkerställa en jämn tjocklek och fördelning av ett adsorberat proteinlager över en yta.</p><p>Dessa ytor kontrollerades först med hjälp av ellipsometri och sedan i ett QCM instrument. Alla experiment med de högfrekventa FBAR sensorerna utfördes vid Ångströmslaboratoriet i Uppsala där pågående forskning inom området finns.</p><p>Resultaten bekräftar teorin om en avtagande känslighet i och med ett ökat avstånd från ytan. En experimentell genomförd och beräknad tjocklek för decay längden uppskattades som inte helt stämde överens med den teoretiskt beräknade.</p><p>En ny term föreslås då frekvenssvaret hos en biosensor planar ut. Detta är en effekt som sker vid dubbla tjockleken av den teoretisk beräknade tjockleken av decay längden och har fått namnet; detection length. Efter denna längd eller gräns observeras en inverterad signal som det än så länge inte finns någon förklaring till.</p> / <p>A study of the sensitivity decrease of biosensors working at high frequencies is presented. With new technology such as film bulk acoustic resonators (FBAR), issues like the decay length is no longer irrelevant theory but may cause limitation in the system as well as it offers new detection possibilities.</p><p>To investigate the frequency response and sensitivity, layer-on-layer construction chemistry was used. A protocol involving activation with EDC/NHS and coupling chemistry with fibrinogen was optimized to ensure accurate thickness and uniformly distribution of each layer over the surface.</p><p>Surfaces were characterized using null ellipsometry and the protocol was tested in a traditional quartz crystal microbalance (QCM). Experiments with the FBAR were preformed at the Ångström laboratory in Uppsala were there is ongoing research and development in FBAR technology.</p><p>The results confirmed the theory of decreasing frequency and sensitivity further out from the surface. An experimental and estimated thickness was calculated which to some extent correlates to the theoretically calculated decay length.</p><p>A new terminology is suggested when the frequency levels off. It occurs approximately at twice the distance and thickness of the theoretically calculated decay length and is given the name; detection length. Beyond the detection length an inverted signal is observed which cannot yet be explained for.</p>