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Surface-plasmon-resonance (SPR) sensors are widely used in biological, chemical, medical, and environmental sensing. This dissertation describes the design and development of dual-mode, self-referencing SPR sensors supporting two surface-plasmon modes (long- and short-range) which can differentiate surface binding interactions from bulk index changes at a single sensing location. Dual-mode SPR sensors have been optimized for surface limit of detection (LOD). In a wavelength interrogated optical setup, both surface plasmons are simultaneously excited at the same location and incident angle but at different wavelengths. To improve the sensor performance, a new approach to dual-mode SPR sensing is presented that offers improved differentiation between surface and bulk effects. By using an angular interrogation, both surface plasmons are simultaneously excited at the same location and wavelength but at different angles. Angular interrogation offers at least a factor of 3.6 improvement in surface and bulk cross-sensitivity compared to wavelength-interrogated dual-mode SPR sensors. Multi-mode SPR sensors supporting at least three surface-plasmon modes can differentiate a target surface effect from interfering surface effects and bulk index changes. This dissertation describes a tri-mode SPR sensor which supports three surface plasmon resonance modes at one single sensing position, where each mode is excited at a different wavelength. The tri-mode SPR sensor can successfully differentiate specific binding from the non-specific binding and bulk index changes.

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.

Widefield surface plasmon resonance (WSPR) microscopy provides high resolution imaging of interfacial interactions. We report the application of the WSPR imaging system in the study of the interaction between keratinocytes and liquid crystals (LC). Imaging of fixed keratinocytes cultured on gold coated surface plasmon substrates functionalized with a thin film of liquid crystals was performed in air using a 1.45NA objective based system. Focal adhesion of the cells adhered to glass and LC were further studied using immunofluorescence staining of the vinculin. The imaging system was also simulated with 2x2 scattering matrix to investigate the optical reflection of the resonant plasmonic wave via the glass/gold/cell and glass/gold/LC/cell layers. WSPR imaging indicated that keratinocytes are less spread and formed distinct topography of cell-liquid crystal couplings when cultured on liquid crystal coated substrates. The simulation indicates that glass/LC shifted the surface plasmon excitation angle to 75.39 degrees as compared to glass/air interface at 44 degrees . The WSPR microcopy reveals that the cells remodelled their topography of adhesion at different interfaces.

Plasmonics techniques, such as surface plasmon resonance (SPR) and surface-enhanced Raman scattering (SERS), have been widely used for chemical and biochemical sensing applications. One approach to excite surface plasmons is through the coupling of light into metallic grating nanostructures. Those grating nanostructures can be fabricated using state-of-the-art nanofabrication methods. Laser interference lithography (LIL) is one of those methods that allow the rapid fabrication of nanostructures with a high-throughput. In this thesis, LIL was combined with other microfabrication techniques, such as photolithography and template stripping, to fabricate different types of plasmonic sensors. Firstly, template stripping was applied to transfer LIL-fabricated patterns of one-dimensional nanogratings onto planar supports (e.g., glass slides and plane-cut optical fiber tips). A thin adhesive layer of epoxy resin was used to facilitate the transfer. The UV-Vis spectroscopic response of the nanogratings supported on glass slides demonstrated a strong dependency on the polarization of the incident light. The bulk refractive index sensitivities of the glass-supported nanogratings were dependent on the type of metal (Ag or Au) and the thickness of the metal film. The described methodology provided an efficient low-cost fabrication alternative to produce metallic nanostructures for plasmonic chemical sensing applications. Secondly, we demonstrated a versatile procedure (LIL either alone or combined with traditional laser photolithography) to prepare both large area (i.e. one inch2) and microarrays (μarrays) of metallic gratings structures capable of supporting SPR excitation (and SERS). The fabrication procedure was simple, high-throughput, and reproducible, with less than 5 % array-to-array variations in geometrical properties. The nanostructured gold μarrays were integrated on a chip for SERS detection of ppm-level of 8-quinolinol, an emerging water-borne pharmaceutical contaminant. Lastly, the LIL-fabricated large area nanogratings have been applied for SERS detection of the mixtures of quinolone antibiotics, enrofloxacin, an approved veterinary antibiotic, and one of its active metabolite, ciprofloxacin. The quantification of these analytes (enrofloxacin and ciprofloxacin) in aqueous mixtures were achieved by employing chemometric analysis. The limit of quantification of the method described in this work is in the ppm-level, with <10 % SERS spatial variation. Isotope-edited internal calibration method was attempted to improve the accuracy and reproducibility of the SERS methodology. / Graduate / 2018-02-17

La leishmaniose est causée par un parasite protozoaire du genre Leishmania. Cette maladie infecte environ 12 millions de personnes dans le monde et en menace 350 millions dans 98 pays. Il existe trois formes majeures de leishmaniose : cutanée, mucocutanée et viscérale. L'infection se produit par le dépôt des parasites sous forme de promastigotes dans la peau de l'hôte mammifère via la piqûre d’un phlébotome. Les parasites peuvent migrer au sein de la matrice extracellulaire avant d’infecter les macrophages. Bien que la plupart des études réalisées jusqu’ici aient été consacrées aux interactions des parasites Leishmania avec leurs cellules cibles, quelques interactants extracellulaires ont déjà été identifiés. Dans cette étude, nous avons étudié pour la première fois le répertoire d’interactions de 24 souches de promastigotes intacts, vivants (6 espèces aux différents tropismes) avec environ ~70 biomolécules de la matrice extracellulaire de l’hôte à l’échelle moléculaire en utilisant des puces à protéines et à glycosaminoglycanes et la résonance plasmonique de surface en mode imagerie. Nous avons identifié 27 nouveaux partenaires (23 protéines et 4 glycosaminoglycanes) des promastigotes de Leishmania. Les souches partagent des partenaires communs tels que le plasminogène, TEM-8 et la tropoélastine, qui est dégradée in vitro par la majorité des souches. Les Leishmania se lient à plusieurs régulateurs de l’angiogenèse et à des glycosaminoglycanes. Dans une seconde partie, nous avons cloné deux protéines de L. major, l’énolase et la superoxyde dismutase, toutes deux identifiées dans le sécrétome de Leishmania, afin d’étudier leur répertoire d’interactions. L’énolase possède un répertoire d’interactions (13 partenaires) supérieur à celui de la superoxyde dismutase (6 partenaires) mais toutes deux interagissent également avec le plasminogène, l’ectodomaine de TEM-8, l’endostatine et l’héparine. Enfin, dans une troisième partie, nous avons créé une base de données, LeishMatrixDB, qui recense toutes les interactions des parasites Leishmania, ou leurs molécules, avec les composants de la matrice extracellulaire de l’hôte décrites dans la littérature / Leishmaniasis is a vector-borne disease caused by parasitic protozoa of the genus Leishmania. 12 million people are presently infected worldwide and the disease threatens 350 million people in 98 countries around the world. There are three main types of the disease: cutaneous, mucocutaneous and visceral. Infection occurs by the deposition of promastigote form into the mammalian skin via the bite of phlebotomine sandflies within the extracellular matrix proteins prior infecting macrophages. Most studies have focused on the interaction of Leishmania promastigotes with their cellular targets, some extracellular partners have been identified. In this study, we investigated for the first time the interplay between 24 strains of intact, live, parasites (6 species of different tropisms) and ~70 biomolecules of the host extracellular matrix at the molecular level using protein and glycosaminoglycan arrays probed by surface plasmon resonance imaging. We have identified 27 new partners (23 proteins and 4 glycosaminoglycans) of Leishmania promastigotes. All strains tested shared 3 common partners such as plasminogen, TEM-8 and tropoelastin, which is degraded in vitro by most Leishmania tested. Leishmania bound to several regulators of angiogenesis and to glycosaminoglycans. In a second part, we cloned two L. major proteins, enolase and superoxyde dismutase, both identified in Leishmania secretome in order to study their interaction repertoire. Enolase had a larger interaction repertoire (13 partners) than superoxide dismutase (6 partners) but both bound to plasminogen, ectodomain of TEM-8, endostatin and heparin. In a third part, we have created a database, LeishMatrixDB, which lists all the interactions of Leishmania, or their molecules, with host extracellular components from the literature

Dépistage du VIH, test de grossesse, mais également surveillance des eaux, détection de contaminants agro-alimentaires : la biodétection est au coeur des problématiques de santé actuelles. Dans ce contexte, les biocapteurs plasmoniques connaissent depuis quelques années un essor particulièrement important : de plus en plus de sociétés, telles que HORIBA Scientific, proposent des prototypes commerciaux, destinés tant à des utilisateurs du domaine de la recherche que de l'industrie. Basée sur le phénomène de résonance des plasmons de surface (communément appelé SPR) la biodétection plasmonique repose sur l'extrême sensibilité d’une onde évanescente se propageant à l’interface entre un film d’or, la biopuce, et le milieu diélectrique couvrant, siège des interactions biomoléculaires étudiées. De manière plus concrète, toute adsorption de matériel biologique se produisant à cette interface entraîne une modification importante des propriétés optiques d’un faisceau de lumière réfléchi par la biopuce : le principe de transduction par SPR consiste alors à mesurer directement ces variations. A l'heure actuelle, différents modes d'interrogation, offrant des performances intéressantes, mais également des limitations propres à chaque configuration. Pour répondre aux exigences de précision et de dynamique de mesure posées par de nombreuses applications, un développement théorique et instrumental, présenté dans ce document, a été initié dans le but de proposer un nouveau un nouveau mode d'interrogation des biopuces plasmoniques : l'interrogation multi-spectrale. Les résultats obtenus par cette technique ont été exploités pour concevoir et réaliser une source multi-spectrale à base de LEDs, particulièrement avantageuse vis-à-vis des configurations existant à l'heure actuelle. La caractérisation du système développé dans le cadre du diagnostic génétique (mucoviscidose) et celui du cancer, ouvre la voie à une nouvelle génération de biocapteurs performants, compacts et de coût relativement raisonnable, présentant un potentiel industriel certain. / Biodetection is at the core of the current health concerns, as shown through the variety of applications to HIV screening, food contaminant analysis or water quality monitoring. In this field, plasmonic biosensing is a well-established label-free technique on the market: commercial systems from HORIBA Scientific are currently available for both research and industrial users.Based on the surface plasmon resonance (SPR) phenomenon, plasmonic biodetection uses the high sensitivity of an evanescent wave propagating along a metallic film (forming the biochip) and the surrounding dielectric medium interface. More specifically, the adsorption of biomolecules onto the metal surface induces a strong change in the optical properties of a light beam reflected by the biochip: the main principle of plasmonic transduction consists in measuring these physical changes. Several interrogation techniques have therefore been developed to access such optical information, but they fail in meeting the most demanding user requirements for precise, real-time, high-throughput measurement.Initiated by these issues, the instrumentation work presented in this document has led to the development of a novel SPR interrogation technique, referred to as multi-spectral interrogation. Moreover, the promising results obtained have been pushed forward to propose a multi-spectral illumination system based on LEDs, providing attractive performances compared to existing configurations. The biosensing potential of the developed system, demonstrated through applications to genetic diagnosis and cancer detection, opens the door to a new generation of compact, high-performance, low-cost SPR sensors.

Breeding for abiotic stress tolerance is one of main topics in plant breeding. Oilseed rape breeding programs were for a long time focused on morphological and physiological parameters. In this thesis few experiments focused on identification of genes involved in abiotic stress reaction were performed using RT-qPCR (quantitative reverse transcription PCR). Simultaneously SPR (surface plasmon resonance) method were used as modern optical method facilitating very low native protein concentration even in presence of other substances. This method facilitates quantification of concrete proteins by binding them to specific antigen and in oilseed rape research it was not used by now. ERD10 protein was identified by SPR as protein involved in cold stress reaction (or acclimation). The results show ERD10 accumulation in standard conditions affects dynamics of its accumulation change during cold stress. In case we are searching for genotypes great in acclimation ability even during short and warm autumn SPR method should be suitable method for fast, easy and relatively cheap screening of large number of genotypes in breeding collections. Also genes LTI78, RCI2A, NRP1 and two genes for hypothetical proteins were analysed. Their relative expression during cold stress was markedly increased too. Very little is known about these genes and proteins nowadays therefor it will be interesting topic of our oncoming experiment. Relative expression of genes picked according to MALDI-TOF/TOF analysis results was also tested in microspore embryo regenerants stressed by simulated drought. Genes for lactoylglutathione lyase I, phospholipase D 1 and peroxiredoxin antioxidase were tested. In tolerant cultivar was markedly decreased gene expression of peroxiredoxin antioxidase in standard conditions and early stress. These gene will be subject for next research as potential marker for more tolerant genotypes selection.

[pt] Neste trabalho é apresentado um estudo sobre nanopartículas metálicas, passando brevemente pela Teoria de Maxwell-Garnett do meio efetivo além de ter sido feita uma pequena pesquisa acerca dos trabalhos já existentes nessa área. É apresentada ainda uma proposta de um sensor à fibra óptica baseado no fenômeno da Ressonância Plasmonica de Superfície Localizada, que utiliza essas nanopartículas cujas propriedades ópticas são sensíveis às mudanças das características do meio onde estão imersas. Esse tipo de sensor é uma ferramenta simples e muito eficiente, além de ser de baixo custo financeiro. A descrição deste sensor mostra ainda três processos distintos de fabricação dessas nanopartículas, as configurações utilizadas para a aquisição dos dados experimentais, e a análise dos mesmos, incluindo a simulação computacional feita para o melhor entendimento dos resultados obtidos. / [en] In this work a study about metallic nanoparticles is presented. A brief revision of the Maxwell-Garnett Theory for the effective medium is made, in addition to a bibliographical research concerning the existing works on the topic. A proposal of a fiber optic sensor based in the Localized Surface Plasmon Resonance phenomena using these metallic nanoparticles, whose optic properties are sensible to changes in the medium in which they are immersed, is also made. This kind of sensor is a simple and efficient tool, in addition to also having low financial cost. Three distinct processes for fabrication of these nanoparticles are discussed. The setups used for the acquisition of the experimental data and the analysis of this data, including the computational simulation made to improve the understanding of the obtained results, are also discussed.

Diese Arbeit leistet einen Beitrag zum Verständnis optischer Anregungen in metallischen Nanostrukturen. Am Beispiel ausgewählter Strukturen werden experimentell die Dynamik dieser Anregungen mit Femtosekunden-Zeitauflösung und ihre elektromagnetischen Moden auf der Nanometer-Längenskala untersucht. Anhand winkel- und zeitaufgelöster Transmissionsexperimente an metallischen Dünnfilmgittern wird gezeigt, dass resonante Oberflächenplasmon-Polaritonen (OPPen) wesentlich die optischen Eigenschaften dieser Strukturen beeinflussen. Die Lebensdauer solcher Anregungen wird ermittelt und damit nachgewiesen, dass Kopplungen zwischen OPP-Resonanzen drastische Lebensdauer-Modifikationen zur Folge haben. In einem eigens konstruierten, spektral auflösenden optischen Nahfeldmikroskop werden die elektromagnetischen Feldverteilungen der OPPen direkt abgebildet. Derartige Experimente erlauben erstmals eine Zuordnung der räumlichen Moden zur zeitlichen Dynamik verschiedener OPP-Resonanzen. Diese Erkenntnisse ermöglichen zudem eine Interpretation des nahfeldmikroskopischen Bildkontrasts bezüglich der Beiträge verschiedener vektorieller Komponenten des optischen Nahfeldes. Die selektive Abbildung unterschiedlicher elektrischer und magnetischer Feldkomponenten in Abhängigkeit vom Sondentyp wird demonstriert. Darüberhinaus wird die OPP-Erzeugung in einem Gitter auf dem Schaft einer Nahfeldspitze ausgenutzt, um propagierende OPPen im Apex zu konzentrieren. Ein weiterer Teil der Arbeit nutzt elektrische Feldüberhöhungen an scharfen Metallspitzen für die lokalisierte Erzeugung nichtlinearer optischer Signale. Die Beobachtung intensiver Multiphoton-Elektronenemission nach Femtosekundenanregung stellt ein zentrales Ergebnis dar. Dieser Prozess wird umfangreich charakterisiert und findet seine erste Anwendung in einer neuartigen Rastersondentechnik, in der die örtlich variierende Elektronenemission der Bildgebung dient. / This thesis contributes to the understanding of optical excitations in metallic nanostructures. In experiments on selected model structures, the dynamics of these excitations and their electromagnetic spatial modes are investigated with femtosecond temporal and nanometer spatial resolution, respectively. Angle- and time-resolved transmission experiments on metallic thin film gratings demonstrate the dominant role resonant surface plasmon polaritons (SPPs) play in the optical properties of such structures. The lifetimes of these excitations are determined, and it is shown that coherent couplings among SPP-resonances result in drastic lifetime modifications. The spatial SPP mode profiles are imaged using a custom-built near-field optical microscope. The experiments reveal a direct correlation between the spatial mode structure and the dynamics of different SPP resonances. These findings allow for an interpretation of the near-field optical image contrast in terms of the contributions of different vectorial components of the electromagnetic near-field. A selective imaging of different electric and magnetic field components is demonstrated for various types of near-field probes. Furthermore, the excitation of SPPs in periodic structures is employed in a novel type of near-field tip. The resonant excitation of SPPs in a nanofabricated grating on the shaft of a sharp metallic tip results in their concentration at the tip apex. The final part of the thesis highlights the importance of optical field enhancements for the local generation of nonlinear optical signals at the apex of sharp metallic tips. Specifically, the observation of intense multiphoton electron emission after femtosecond excitation is a major result. This process is thoroughly characterized, and a novel scanning microscopy application based on this effect is presented. In this technique, an image contrast with nanometer resolution arises from spatially varying electron emission rates.