Variable pressure electron beam etching and lithography for Teflon AF has been demonstrated. The relation between dose and etching depth is tested under high vacuum and water vapor. High resolution structures as small as 75 nm half-pitch have been resolved. Several simulation tools were tested for surface plasmon excitation. Grating based dual mode surface plasmon excitation has been shown numerically and experimentally.

Noble metal nanoparticles supporting localized surface plasmon resonances (LSPR) have been extensively investigated for label free detection of various biological and chemical interactions. When compared to other optical sensing techniques, LSPR sensors offer label-free detection of biomolecular interactions in localized sensing volume solutions. However, these sensors also suffer from a major disadvantage – LSPR sensors remain highly susceptible to interference because they respond to both solution refractive index change and non-specific binding as well as specific binding of the target analyte. These interactions can severely compromise the measurement of the target analyte in a complex unknown media and hence limit the applicability and impact of the sensor. In spite of the extensive amount of work done in this field, there has been a clear absence of efforts to make LSPR sensors immune to interfering effects. The work presented in this document investigates, both experimentally and numerically, dual- and tri-mode LSPR sensors that utilize the multiple surface plasmon modes of gold nanostructures to distinguish target analyte from interfering bulk and non-specific binding effects. Finally, a series of biosensing experiments are performed to examine various regeneration assays for LSPR sensors built on indium tin oxide coated glass substrate.

La gp120 du VIH-1 se fixe aux héparane sulfate (HS) cellulaires, par le biais de la boucle V3 ce qui favorise l'infectivité virale. Cependant, une polyanion solubles (HS12), conjugués à CD4 (mCD4-HS12) a des propriétés antivirales et a montré in vitro une activité contre le VIH-1 à de concentrations nM. En raison de la complexité structurale des HS, le criblage d'oligosaccharides différenciellement sulfatés pour améliorer l'activité de la molécule serait trop difficile. En vue d'obtenir une molécule plus spécifique, de plus haute affinité et plus facile à produire, des peptides mimant les HS ont été synthétisés par nos collaborateurs. Notre but était de cribler ces peptides pour leur capacité à inhiber l'entrée de VIH-1. Nous avons mis en place une plateforme permettant d'immobiliser CCR5 et CXCR4 solubilisés sur des biocapteurs pour cribler des molécules qui inhibent la liaison de gp120-CD4 aux corécepteurs. Pour contrôler le processus de solubilisation, CXCL12, le ligand naturel de CXCR4, a été injecté sur CXCR4 immobilisé. Les affinités des isoformes CXCL12 (α et γ) pour CXCR4 ont été calculées dans les fourchettes de valeurs précédemment décrites avec des techniques différentes prouvant la fonctionnalité de notre système. Nous montrons pour la première fois que les HS régulent différemment les mécanismes de liaison de ces deux isoformes et nous proposons un nouveau mode d'action pour le domaine C-terminal particulièrement basique de CXCL12 γ vis-à-vis de CXCR4. Le système a ensuite été utilisé pour cribler la capacité d'inhibition des peptides mimétiques du HS. Chaque peptide, [S(XDXS)n] contient des acides aminés qui imitent les groupes hydroxyles, carboxyles et sulfates des HS. Le peptide contenant des résidus sulphotyrosines, une fois conjugué à mCD4 (mCD4-P3YSO3), montre un IC50 de l'ordre du nM, pour l'inhibition simultanée de la liaison de gp120 aux HS, à CD4, aux anticorps, aux corécepteurs ainsi que l'infection par VIH-1 in cellulo. Il constitue le premier inhibiteur bivalent de l'entrée qui cible à la fois les virus R5 et X4 et le concept d'un peptide mimétique des HS se prête à une analyse structurale et fonctionnelle de la liaison des chaînes HS aux protéines, une nouvelle technique dans ce domaine.

This dissertation presents subwavelength optics with focus on the theory and applications of subwavelength apertures in a metal film. Two main issues regarding the optics with subwavelength apertures are investigated. As the first issue, the extraordinary optical transmission (EOT) through a single hole in a metallic waveguide is presented. A total transmission through a single subwavelength aperture is theoretically predicted for a perfect electric conductor regardless of the aperture size, without relying on aperture arrays and surface corrugations as presented in previous works. The waveguide EOT is then applied to boost the optical throughput of an apertured near-field scanning optical microscope (NSOM) probe. Using a new structure for the apertured NSOM probe which allows for waveguide EOT, the optical throughput and the damage threshold are boosted by 100× and 40× as compared to a conventional structure, and the experimental findings are backed-up by comprehensive finite-difference time-domain (FDTD) simulations. Single fluorescent molecules are scanned using the EOT apertured NSOM probe, and a spatial resolution of 62 nm is achieved. As the second issue, subwavelength apertures are found useful for optical trapping. A small dielectric particle can significantly change the optical transmission through an aperture by dielectric loading, and subsequently, a large optical force is induced which favors trapping. A self-induced back-action (SIBA) optical trap is designed using a circular nanohole in a gold film. Trapping of 50 nm polystyrene particle is experimentally achieved, which is not possible using a conventional single beam optical tweezers. The circular nanohole SIBA trap works beyond the perturbative regime, as proven by FDTD simulations and a Maxwell stress tensor analysis. We further improve the nanohole trapping using a double-nanohole, which is more sensitive for small dielectric changes due to the intense local field enhancement between its two sharp tips. A single 12 nm silica sphere is experimentally trapped using the double-nanohole, as the smallest trapped dielectric particle reported. We also achieve the trapping of a single protein – a bovine serum albumin (BSA) protein with a hydrodynamic radius of 3.4 nm in the folded form. The trapped BSA is also unfolded by the large optical force, as confirmed by experiments with changing optical power and changing pH. The high signal-to-noise ratio of 33 in monitoring single protein trapping and unfolding shows a tremendous potential for using the double-nanohole as a sensor for protein binding events at a single molecule level. / Graduate

Many biological processes, pathogens, and pharmaceuticals act upon, cellular membranes. Accordingly, cell membrane mimics are attractive targets for biosensing, with research, pathology, and pharmacology applications. Lipid bilayers represent a versatile sensor functionalization platform providing antifouling properties, and many receptor integration options, uniquely including transmembrane proteins. Bilayer-coated sensors enable the kinetic characterization of membrane/analyte interactions. Addressed theoretically and experimentally is the self-assembly of model membranes on plasmonic sensors. Two categories of plasmonic sensors are studied in two parts. Part I aims to deposit raft-forming bilayers on planar nanoaperture arrays suitable for multiplexing and device integration. By vesicle fusion, planar bilayers are self-assembled on thiol-acid modified flame-annealed gold without the need for specific lipid head-group requirements. Identification of coexisting lipid phases is accomplished by AFM imaging and force spectroscopy mapping. These methods are successfully extended to metallic, plasmon-active nanohole arrays, nanoslit arrays and annular aperture arrays, with coexisting phases observed among the holes. Vis-NIR transmission spectra of the arrays are measured before and after deposition, indicating bilayer detection. Finally, the extraction of membrane proteins from cell cultures and incorporation into model supported bilayers is demonstrated. These natural membrane proteins potentially act as lipid-bound surface receptors. Part II aims to encapsulate in model lipid bilayers, metallic nanoparticles, which are used as probes in surface enhanced Raman spectroscopy. Three strategies of encapsulating particles, and incorporating Raman-active dyes are demonstrated, each using a different dye: malachite green, rhodamine-PE, and Tryptophan. Dye incorporation is verified by SERS and the bilayer is visualized and measured by TEM, with support from DLS and UV-Vis spectroscopy. In both parts, lipid-coated sensors are successfully fabricated and characterized. These results represent important and novel solutions to the functionalization of plasmonic surfaces with biologically relevant cell membrane mimics.

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

Protein aggregation is commonly encountered during the manufacture of protein-based bioproducts in processing such as protein expression, purification, refolding, shipping and storage (Volkin and Middaugh, 1992; Brange, 2000). Aggregation may shorten the shelf-life of pharmaceutical proteins (Frokjaer and Otzen, 2005) and induce severe hypersensitivity (Rosenberg, 2006). In addition, several diseases ranging from Alzheimer’s disease to cystic fibrosis are associated with protein aggregation in the form of amyloid fibrils and plaques (Dobson, 1999; Luheshi et al., 2008). Hence, studies on protein aggregation, especially those dealing with high concentrations of proteins, are highly demanded in both academic and industrial laboratories. To address the aforementioned issues, physicochemical factors affecting protein aggregation were investigated systematically in this project. Strategies were developed to inhibit protein aggregation during renaturation and to enhance protein stability against aggregation during and after production, especially when dealing with high protein concentrations. ∆5-3-Ketosteroid isomerase (KSI) was used as a model for aggregation studies during protein renaturation due to its intrinsic aggregation properties. KSI was overexpressed as inclusion bodies (IBs) in Escherichia coli (E. coli). Cost- and time-efficient combination of chemical extraction and one-step affinity purification ensured the production of denatured KSI with high purity at high yield. Several key factors, including protein concentration and ionic strength, were determined to greatly influence KSI aggregation during renaturation. Polymer addition (PEG 3000 and Eudragit S-100) was found to alter KSI aggregation behaviour in a polymer-specific manner, as quantified using reversed phase-high performance liquid chromatography (RP-HPLC) analysis. Light scattering for second virial coefficient (SVC) measurement, surface plasmon resonance (SPR), and microfluidics were applied to study the fundamental mechanism of protein aggregation. Lysozyme was further introduced as a control protein for comparison with KSI. A rapid lumped method was established to measure specific refractive index (∂n/∂c) and SVC values for KSI and lysozyme, which provided quantitative and qualitative information on thermodynamic interactions of molecules in solution. SPR and microfluidics were also used to explore protein aggregation properties. To our best knowledge, it is the first time SPR and microfluidics have been used to investigate protein aggregation behaviour. Both SPR and microfluidics present significant potential for assessing protein aggregation and diagnosis or drug screening of protein aggregation related diseases. The chemical and physical stability of proteins needs to be maintained after successful refolding to ensure an acceptably long shelf life, especially at high protein concentration (Chang and Hermsdorf, 2002). The pharmaceutical effects of lectins on cell growth provided incentive for studies to improve their stability. Human galectin-2 (hGal-2, a homodimeric lectin) was used as a study model in this project. Mutations were introduced at one of the two Cys residues (C57A, C57M, and C57S). Only the C57M variant was highly expressed in bacteria in soluble form. No aggregate of this mutant was detected during 3 weeks of storage. hGal-2 C57M also facilitated site-directed introduction of poly(ethylene glycol) (PEG) into the remaining sulfhydryl group (Cys75). Product analysis revealed rather complete conjugation with one PEG chain per protein subunit in homodimer. Neither secondary structure alteration nor the absence of binding ability to a glycoprotein (asialofetuin) was observed. The results document the feasibility of tailoring a human galectin for enhanced stability against aggregation as well as monoPEGylation, which enables further testing of biological properties including functionality as a growth regulator and the serum clearance rate of hGal-2.

Orientador: Sidney Jose Lima Ribeiro / Banca: Younes Messaddeq / Banca: Denis Boudreau / Banca: Cid Bartolomeu de Araujo / Banca: Anna Marie Ritcey / Banca: Mauricio da Silva Baptista / Banca: Rogéria Rocha Gonçalves / Resumo: Na área biomédica, existe uma crescente demanda por nanossistemas multifuncionais para realização de imageamento e terapia simultaneamente, visando um diagnóstico precoce e máximo benefício terapêutico. Nanopartículas para conversão ascendente de energia (UCNPs) vêm sendo propostas como a sonda biológica ideal devido às suas vantagens únicas relacionadas ao fenômeno de upconversion apresentado por materiais contendo íons lantanídeos, isto é, emissão no visível obtida sob excitação no infravermelho, tais como penetração profunda nos tecidos, uma baixa taxa de autofluorescência e um fotodano mínimo. Além disso, as propriedades luminescentes dos íons lantanídeos podem ser usadas para termometria por serem fortemente dependentes da temperatura. A termometria luminescente é uma técnica de não-contato e alta resolução que vem ganhando atenção na nanomedicina uma vez que a temperatura é um parâmetro fundamental para o funcionamento das células. Danos térmicos às células podem ser localmente fotoinduzidos pelo uso de nanoestruturas metálicas iluminadas em sua banda de ressonância plasmônica por causa da sua elevada absortividade. A primeira parte deste trabalho consiste no desenvolvimento de um sistema multifuncional baseado em nanocascas de ouro (AuNSs) decoradas com UCNPs podendo ser utilizadas para aumentar e medir a temperatura em escala nanométrica. Este sistema foi desenvolvido com a finalidade de uma eventual utilização como agente em terapia fototérmica (PTT), na qual a capac... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: In the biomedical field, there is an increasing demand for multifunctional nanosystems to perform imaging and therapy simultaneously, aiming at early diagnosis and maximum therapeutic benefit. Upconversion nanoparticles (UCNPs) have been proposed as an ideal bio-probe because of their unique advantages related to the upconversion phenomenon presented by materials containing lanthanide ions, e.g. visible emission obtained under near-infrared (NIR) excitation, such as deep tissue penetration, low autofluorescence background and low photo-damage. Moreover, the luminescent properties of lanthanide ions may be used for thermometry because of a strongly temperature-dependent effect. Luminescence nanothermometry is a noncontact and high-resolution technique that has been gaining attention in nanomedicine since temperature is a fundamental parameter in events that occur in cells. The thermal damage of cells may be locally photoinduced by using metal nanostructures illuminated at their localized surface plasmon resonance (LSPR) band because of the enhancement of light absorption. In this work, a multifunctional system was designed combining gold nanoshells (AuNSs) and UCNPs intended as an optical heater and temperature probe at the nanoscale. This system was studied aiming its application as an agent for photothermal therapy (PTT), guided by the thermometer capacity of UCNPs, which allows to optimize the therapeutic benefits. The synthesis of NaGdF4 UCNPs doped with ions Yb3+:Er3+ was... (Complete abstract click electronic access below) / Résumé: Dans le domaine biomédical, il y a une demande croissante pour les nanosystèmes multifonctionnels pour effectuer simultanément l'imagerie et la thérapie, en visant le diagnostic précoce et apporter du bénéfice thérapeutique maximal. Les nanoparticules à conversion ascendante d'energie (UCNPs) ont été proposés comme une bio-sonde idéale en raison de leurs avantages uniques liés au phénomène d'upconversion présenté par les matériaux contenant des ions lanthanides, c'est-à-dire l'émission visible obtenue sous excitation dans le proche infrarouge (NIR), tels qu'une meilleure pénétration dans les tissus, une bas taux d'autofluorescence et un photo-dommage minimal. De plus, les propriétés luminescentes des ions lanthanides peuvent être utilisées pour la thermométrie en raison de leur forte dépendance sur la température. La thermométrie par luminescence est une technique sans contact et à haute résolution qui a attiré l'attention en nanomédecine puisque la température est un paramètre clé dans le fonctionnement des cellules. Des dommages thermiques aux cellules peuvent être localement photoinduits par l'utilisation de nanostructures métalliques illuminées dans leur bande de résonance plasmon en raison de leur absorptivité élevée. La prémière partie de ce travail implique le développement d'un système multifonctionnel, basé sur des nanocoquilles d'or (AuNSs) décorées avec des UCNPs, pouvant être utilisé pour augmenter et mesurer la température à l'échelle nanométrique. Ce système a é... (Résumé complet accès életronique ci-dessous) / Doutor

Les avancées dans le domaine de l'analyse médicale et environnementale exigent des méthodes sensibles et précises pour la détection de molécules organiques nocives. Les travaux de recherche de cette thèse présentent un nouveau système d'affinité pour l'immobilisation de biorécepteurs, de nouvelles stratégies d'amplification du signal et de nouveaux nanomatériaux à base de modèles bio-inspirés afin d'améliorer les performances des biocapteurs ou des biopiles.Dans une première partie, un nouveau système d'affinité supramoléculaire entre la biotine et la beta-cyclodextrine a été étudié et a permis de déterminer une constante d'association de 3 x 10² L.mol-1. Ce système permet l'immobilisation d'une grande variété de biorécepteurs commerciaux marqués avec une biotine sur des surfaces éléctrogénérées pour l'élaboration de biocapteurs. Au-NPs modifiés par des beta-CD a été utilisé avec succès pour "optical antenna" pour l'amplification additionnelle du signal SPRi utilisant des marqueurs QD. La combinaison de ses nano-objets permettent la construction d'immunocapteurs ou de capteurs à ADN très sensible.Dans une deuxième partie, différentes variétés de nanomatériaux tels que les nanodiamants, les nanoparticules magnétiques, les nanotubes de carbone (CNT) et graphène ont été utilisé pour modifier la surface des transducteurs suivies par leur fonctionnalisation non-covalentes par des dérivés pyrène. Le nouveau dépôt de nanotubes « layer-by-layer » et les différentes tailles de nanoparticules avec des porosité variable présentent une approche flexible pour la construction de capteurs enzymatiques et d'immunocapteurs. Le graphène est un matériel d'épaisseur atomique qui doublent la sensibilité SPR pour la détection d'anticorps et d'antigène. Enfin, une réduction bioélectrocatalytique efficace de l'oxygène est reporté en utilisant des CNT fonctionnalisés par les pyrènes pour une application comme biocathode dans les biopiles. / The advancing field of medicine and environmental analysis demands sensitive and accurate methods for sensing harmful organic molecules The research work in this thesis presents a novel affinity system for immobilization of bioreceptors, a novel signal amplification strategy, and novel nanomaterials based bio-designs (architectures) with the improved biosensor or bio-fuel cell (bio-cathode) performances.Firstly, a new affinity system based on supramolecular host-guest interactions between biotin and & beta-CD with an association constant of 3 x 10² M-1 is studied. This allows immobilization of a variety of commercially available biotin labelled bioreceptors for biosensing application. beta-CD modified Au-NPs were successfully applied as optical antenna for additional SPRi signal amplification using QD labels. The beneficial effect of the combination of these nano-objects enables the construction of highly sensitive DNA or immunosensors.Secondly, various kinds of nanomaterials such as nanodiamonds, carbon nanotubes, magnetic nanoparticles, graphene and are employed to modify transducer surface followed by non-covalent functionalization with pyrene derivatives. The novel 3D layer-by-layer deposition of nanotubes and different sized nanoparticles with varying porosity presents a flexible approach towards construction of enzymatic or immuno-sensors. Graphene, a material with atomic thickness doubles the SPR sensitivity towards detection of antibody, anti-CT. Finally, an efficient bioelectrocatalytic reduction of oxygen is reported using pyrene functionalized CNT forest as a bio-cathode for bio-fuel cell applications.

La détection de l'hydrogène est une priorité environnementale. De nombreux capteurs à hydrogène ont déjà été développés, mais aucun d’eux ne répond aux exigences de l'industrie. Les capteurs à fibres optiques, électriquement isolés, sont d’excellents candidats pour fonctionner dans des environnements explosifs. Notre objectif est de développer un capteur à fibres optiques intrinsèque par Résonance de Plasmon de Surface pour la détection d’hydrogène. Dans cette thèse, nous étudions deux designs de capteurs à hydrogène. Le premier, basé sur la modulation d'amplitude, se compose d'une couche mince de Pd déposé sur le cœur de la fibre multimode, après avoir enlevé la gaine optique. Dans le second, basé sur la modulation de longueur d'onde, nous remplaçons la couche de Pd par un empilement de couches (Au / SiO 2 / Pd). Dans cette thèse, nous démontrons que les capteurs plasmoniques peuvent être une solution pour développer des capteurs à hydrogène fiables et rapides. Enfin, nous étudions des alliages de Mg comme matériaux sensibles à l’hydrogène afin d’optimiser la plage de détection des capteurs à hydrogène. / Hydrogen detection is an environmental priority. Numerous hydrogen sensors have been developed, but none of them meet the industry requirements. Optical fiber sensors, electrically isolated, are excellent candidates for operating in explosive environments. Our goal is to develop an intrinsic optical fiber sensor based on Surface Plasmon Resonance. In this thesis, we study two optical fiber hydrogen sensors. The first sensor, based on amplitude modulation, consists of a thin Pd layer deposited on the multimode fiber core, after removing the optical cladding. The second design, based on wavelength modulation, consists of replacing the single Pd layer by a Au/ SiO2/ Pd multilayer stack. We demonstrate in this thesis that plasmonic sensors may be a solution to develop fast and reliable fiber hydrogen sensors. Finally, we study Mg alloys as hydrogen sensitive material in order to improve the detection range of hydrogen sensors.