Détecter un ensemble de marqueurs biologiques dans un sérum de patient ou bien des molécules spécifiques d'un herbicide dans un échantillon prélevé dans l'eau d'une rivière ? Etre capable de transformer une interaction biologique en un signal électrique ou encore déposer des volumes infiniment faibles de molécules biologiques sur une surface solide à des fins de diagnostique ? Passer de la fabrication de microcapteurs inertiels pour la navigation à la conception et au développement de biocapteurs micromécaniques ? Nous démontrons que le fil conducteur permettant de faire le lien entre ces domaines en apparence disjoints est matérialisé par des micro- et nanosystèmes électromécaniques développés au sein du LAAS à partir de la feuille blanche jusqu'à l'intégration du système avec son électronique associée. Quel lendemain pour les bio- microsystèmes électromécaniques ? Faut-il encore miniaturiser ? Est-il pertinent d'entreprendre le contraire ? Comment poursuivre l'aventure transdisciplinaire en étant sûr du fait que la réussite est au bout de la route ? Nous tentons de répondre à l'ensemble de ces questions tout au long de ce manuscrit retraçant l'ensemble de nos travaux de recherche effectués au LAAS et ailleurs depuis l'an 2000.

The objective of this thesis is to introduce and demonstrate a novel magnetic bead detector based on inductive detection at the ferromagnetic resonance (FMR) frequency for use in bio-sensing applications. Detection ability is demonstrated through theoretical arguments, numerical computer simulations, and experimental characterization of micro-fabricated detectors. The detector is composed of two uniplanar rf waveguides (coplanar waveguide and slotline) terminated together at a short-circuit junction, which serves as the sensitive area. Experimental characterization of a micro-fabricated junction gives a signal ranging between 1 microvolt/volt and 12 microvolts/volt, depending on the number of beads at the junction as well spatial distribution of the beads. The locations around the tips of the CPW were shown to be the most sensitive. A more complex rf circuit design was created employing the detection junction, and detection of magnetic beads was successfully shown at rf frequencies around 6 GHz in this configuration. Due to lack of FMR characterization data for magnetic beads in the literature, several varieties of magnetic beads were characterized using a CPW transmission line and custom apparatus to determine FMR properties. Finally, successful detection of magnetic beads was demonstrated in a system-level integration experiment employing the detector junction in combination with microfluidics and bio-chemical surface modifications. / Graduation date: 2010

A terrestrial robotic electrophysiology platform has been developed that can hold a moth (<italic>Manduca sexta</italic>), record signals from its brain or muscles, and use these signals to control the rotation of the robot. All signal processing (electrophysiology, spike detection, and robotic control) was performed onboard the robot with custom designed electronic circuits. Wireless telemetry allowed remote communication with the robot. In this study, we interfaced directionally-sensitive visual neurons and pleurodorsal steering muscles of the mesothorax with the robot and used the spike rate of these signals to control its rotation, thereby emulating the classical optomotor response known from studies of the fly visual system. The interfacing of insect and machine can contribute to our understanding of the neurobiological processes underlying behavior and also suggest promising advancements in biosensors and human brain-machine interfaces.

Nanomaterials are the heart of nanoscience and nanotechnology. Research into nanostructures has been vastly expanding worldwide and their application spreading into numerous branches of science and technology. The incorporation of these materials in commercial products is revolutionising the current technological market. Nanomaterials have gained such enormous universal attention due to their unusual properties, arising from their size in comparison to their bulk counterparts. These nanosized structures have found applications in major devices currently under development including fuel cells, computer chips, memory devices, solar cells and sensors. Due to their aforementioned importance nanostructures of various materials and structures are being actively produced and investigated by numerous research groups around the world. In order to meet the market needs the commercialisation of nanomaterials requires nanomaterial fabrication mechanisms that will employ cheap, easy and low temperature fabrication methods combined with environmentally friendly technologies. This thesis investigates low temperature growth of various one-dimensional nanostructures for their potential application in chemical sensors. It proposes and demonstrates novel materials that can be applied as catalysts for nanomaterial growth. In the present work, zinc oxide (ZnO) and silicon (Si) based nanostructures have been fabricated using low temperature growth methods including hydrothermal growth for ZnO nanowires and plasma-enhanced chemical vapour deposition (PECVD) technique for Si nanostructures. The structural, optical and electrical properties of these materials have been investigated using various characterisation techniques. After optimising the growth of these nanostructures, gas and biosensors have been fabricated based on Si and ZnO nanostructures respectively in order to demonstrate their potential in chemical sensors. For the first time, in this thesis, a new group of materials have been investigated for the catalytic growth of Si nanostructures. Interesting growth observations have been made and theory of the growth mechanism proposed. The lowest growth temperature in the published literature is also demonstrated for the fabrication of Si nanowires via the PECVD technique. Systematic studies were carried out in order to optimise the growth conditions of ZnO and Si nanostructures for the production of uniformly shaped nanostructures with consistent distribution across the substrate. v The surface structure and distribution of the variously shaped nanostructures has been analysed via scanning electron microscopy. In addition, the crystallinity of these materials has been investigating using Raman and X-ray diffraction spectroscopies and transmission electron microscopy. In addition to the fabrication of these one-dimensional nanomaterials, their potential application in the chemical sensors has been tested via production of a glucose biosensor and an isopropyl alcohol vapour gas sensor based on ZnO and Si nanostructures respectively. The operation of the devices as sensors has been demonstrated and the mechanisms explored.

Cette thèse s’inscrit dans le cadre d’une cotutelle internationale entre l’institut FEMTO-ST à Besançon en France et l’université de Sherbrooke au Canada. Elle porte sur l’élaboration d’un biocapteur, potentiellement à bas coût, pour la détection de pathogènes dans les secteurs de l’agroalimentaire, de l’environnement et de la biosécurité. Le modèle biologique visé est la bactérie Escherichia coli, dont les souches pathogènes sont responsables, chaque année et partout dans le monde, de plusieurs crises sanitaires liées à une mauvaise gestion des produits de consommation ou des installations de conditionnement ou de traitements de ces produits. L’utilisation de biocapteurs pour une détection rapide, sensible et sélective d’organismes pathogènes répond ainsi aux inquiétudes quant aux risques d’infection pour la population. La structure du capteur consiste en une fine membrane en arséniure de gallium (GaAs) vibrant sur des modes de cisaillement d’épaisseur générés par champ électrique latéral via les propriétés piézoélectriques du matériau. Nous montrons dans ce travail que le biocapteur offre également des possibilités de microfabrication, de biofonctionnalisation et de régénération intéressantes pour la conception d’un dispositif à bas coût. Le transducteur a été réalisé via des technologies de microfabrication utilisées en salle blanche avec une mise en parallèle des méthodes d’usinage par voie chimique et par plasma, l’objectif étant d’obtenir des membranes minces, planes et avec un état de surface de haute qualité. Une interface fluidique a été mise au point de façon à approvisionner de manière homogène le capteur en fluide. Par ailleurs, nos études se sont portées sur la fonctionnalisation biochimique de l’interface de bioreconnaissance sur l’arséniure de gallium et sa caractérisation fine par les techniques de spectroscopie infrarouge à transformée de Fourier (FTIR). Les résultats de cette étude ont permis de progresser sur la compréhension fondamentale du phénomène d’auto-assemblage de molécules sur GaAs. Un effort particulier a été mis en œuvre pour développer des biointerfaces de haute densité offrant une immobilisation optimale des immunorécepteurs biologiques. Parmi les différentes méthodes de régénération de la biointerface, le procédé de photo-oxydation UV en milieu liquide a démontré un fort potentiel pour des applications de capteurs réutilisables. Enfin, le transducteur a été caractérisé électriquement sous différents environnements. L’impact sur la réponse du résonateur des paramètres électriques, mécaniques et thermiques de ces milieux a été évalué afin de simuler le comportement du dispositif en condition réelle. / Abstract : This PhD thesis was realized in the context of a cotutelle program between FEMTO-ST institute in France and the University of Sherbrooke in Canada. The thesis addresses the development of a potentially low cost sensor dedicated for detection of pathogens in food industry processing, environment and biosafety sectors. Such a sensor could serve detection of Escherichia coli bacteria whose pathogenic strains are the source of foodborne illnesses encountered worldwide every year. Hence, biosensor devices are needed for a rapid, sensitive and selective detection of pathogens to avert, as soon as possible, any sources of contamination and prevent outbreak risks. The design of the sensor consists of a resonant membrane fabricated in gallium arsenide (GaAs) crystal that operates at shear modes of bulk acoustic waves generated by lateral field excitation. In addition to the attractive piezoelectric properties, as shown in this work, fabrication of a GaAs-based biosensor benefits from a well-developed technology of microfabrication of GaAs, as well as biofunctionalization and the possibility of regeneration that should result in cost savings of used devices. The transducer element was fabricated by using typical clean room microfabrication techniques. Plasma and wet etching were investigated and compared for achieving thin membranes with high quality surface morphology. At the same time, we designed and fabricated fluidic elements that allowed the construction of a flow cell chamber integrated in the sensor. Extensive research was carried out with a Fourier transform infrared spectroscopy (FTIR) diagnostic tool to determine optimum conditions for biofunctionalization of the GaAs surface. This activity allowed to advance the fundamental knowledge of self-assembly formation and, consequently, fabrication of high density biointerfaces for efficient immobilization of selected bioreceptors. Among different biochip regeneration methods, it has been demonstrated that liquid UV photooxidation (liquid-UVPO) has a great potential to deliver attractive surfaces for re-usable biochips. Finally, operation of the transducer device was evaluated in air environment and in various liquid media, simulating real conditions for detection.

Luminescent semiconductor quantum dots (QDs) are extensively researched for use in biological applications. They have unique optical and physical properties that make them excellent candidates to replace conventional organic dyes for cellular labeling, multiplexing, nucleic acid detection, and as generalized probes. The primary focus of this dissertation was to utilize quantum dots for improvement in immunoassays. Specifically, atherosclerosis biomarkers were detected simultaneously in an effort to demonstrate advances in early detection diagnostics. Quantum dot-antibody bioconjugates were prepared by encapsulation into mesoporous silica and functionalized with thiol and amine groups to enable bioconjugation. Functionalization of the mesoporous silica quantum dot composites facilitated biocompatibility for use with biological buffers in immunoassays. These bioconjugates were used in a sandwich immunoassay to detect atherosclerosis biomarkers IL-15 and MCP-1. Sandwich assays employ capture antibodies immobilized onto a well plate to bind as much of the antigen as possible. The capture antibodies increased binding by at least 4 times the amount of antigen bound to the surface of a direct detection assay. The sandwich immunoassay was able to detect 1 pg/mL of IL-15 and 50 pg/mL of MCP-1 biomarkers. Human serum albumin nanoparticles (HSAPs) were synthesized via a desolvation and crosslinking method. Human serum albumin is a versatile protein being used in a variety of applications. Quantum dots were loaded into HSAPs as potential detection probes for immunoassays. Efficient loading was not achieved, and the assay was unable to improve current detection limits. Controlled release studies were explored using HSAPs loaded with superparamagnetic iron oxide nanoparticles and a fluorescent drug analog. Exposure to a magnetic field resulted in degradation of the HSAPs. The fluorophore was released and measured to examine how cancer drugs might be controlled through a magnetic field. Gold nanorods and an anticancer drug, Sorafenib, were also encapsulated into HSAPs for treatment of renal cell carcinoma in vivo. Laser irradiation treatment combined with Sorafenib resulted in 100% tumor necrosis and total elimination of any viable tumor present. HSAPs have demonstrated remarkable potential as drug delivery nanocarriers.

Viral proteases are important targets for anti-viral drugs. Discovery of protease inhibitors as anti-viral drugs is aided by an understanding of the interactions between viral protease and inhibitors. This thesis addresses the characterization of protease-inhibitor interactions for application to drug discovery and model system development. The choice of a relevant target is essential to molecular interaction studies. Therefore, full-length NS3 protein of hepatitis C virus (HCV) was obtained, providing a more relevant target and a better model for the development of HCV protease inhibitors. In addition, resistance to anti-viral drugs, a serious problem in the treatment of AIDS, prompted the investigation of resistant variants of human immunodeficiency virus (HIV) protease. Drug resistance was initially explored by characterization of the interactions between a series of closely related inhibitors and resistant variants of HIV protease, using an inhibition assay to determine the inhibition dissociation constants (Ki). The relationship between structure, activity and resistance profiles was not clarified, indicating that the effect of structural changes in the inhibitors and the protease are not predictable and must be analyzed case wise. It was proposed that additional kinetic characterization of the interactions was required and a biosensor-based method allowing for determination of affinity, KD, and interaction rate constants, kon and koff, was adopted. The increased physiological relevance of this method was confirmed, and the affinity data have better correlation with cell culture data. In addition, interactions between clinical inhibitors of HIV protease and enzyme variants indicate that increased dissociation rates (koff) are associated with the development of resistance. Thermodynamic characterization of the interactions between HIV-1 protease and clinically relevant inhibitors revealed distinct energetic characteristics for inhibitors. The resolution of the energetics of association and dissociation identified an inhibitor with unique interaction characteristics and confirmed the validity of using this method for further characterization of molecular interactions. This work resulted in the development of model systems for the analysis of kinetics, resistance and thermodynamic characteristics of protein-inhibitor interactions. The results give increased understanding of the biomolecular interactions and can be applied to drug discovery.

A variety of HIV-1 protease inhibitors and their interactions with the enzyme have been characterized in order to identify novel and improved drugs against AIDS. The investigated inhibitors were represented by clinical and non-clinical inhibitors, active site and allosteric inhibitors, transition-state analogues and metal-ions. In addition, different enzyme variants were used to investigate the contribution of different amino acid residues to the interaction with different ligands. The problem of resistance has been addressed by exploring novel types of inhibitors, and resistant mutants of HIV-1 protease. A study resolving the inhibition of HIV-1 protease by Cu2+ showed that the enzyme can be allosterically inhibited and that copper inhibition is a result of an interaction with His-69 and a subsequent conformational change. Several types of transition-state analogues were analyzed with respect to their inhibition of wild-type and resistant mutants of HIV-1 protease. Unfortunately cyclic compounds were not found to be better than linear compounds. Moreover, it was not possible to identify structure-activity relationships that clearly correlated with efficacy towards mutants and a biosensor based method for more detailed kinetic studies was therefore adopted. By cross-linking the immobilized enzyme on the biosensor matrix, a stable surface was obtained and kinetic rate constants could be determined for the interaction between the enzyme and inhibitors. Additional improvements in the methodology involved identification of a more representative interaction model, allowing more detailed studies of interactions with resistant mutants and varying conditions. Finally, absorption to lipid membranes and interaction with human serum albumin and α1-glycoprotein by clinical drugs were studied in a simplified ADME model system for improvement of the earlier stages of drug development. These studies have revealed important characteristics of these drugs that can potentially be modeled into new compounds that have improved efficacy of both wild-type and resistant mutants of HIV-1 protease.

The present study has focused on characterising protease-ligand interactions in the context of drug discovery. The proteases that have been studied are human matrix metallopeptidase 12 (MMP-12), HIV-protease and Hepatitis C virus (HCV) NS3/NS4A protease. These studies have involved kinetic characterisation of protease-inhibitor interactions using biosensor technology, as well as determination of inhibition and activity regulation by using activity assays. The regulation of MMP-12 activity by calcium was proposed, based on the study of the calcium dependence of MMP-12 activity. Furthermore, it was shown that the high affinity of hydroxamate-based inhibitors of MMP-12 were due to slow dissociation of the enzyme-inhibitor complex by using a new biosensor assay for the study of interactions between MMP-12 and ligands. A study of the pH-dependency of protease-inhibitor interactions revealed that the interaction kinetics of HIV-protease inhibitors differed with pH in a way that could be related to the inhibitor structures. This suggested that the forces of interaction are different in the association and dissociation phases of an interaction. Furthermore, it demonstrated the usefulness of pH as a variable in characterising protein-ligand interactions. Results applicable in the discovery of drugs against Hepatitis C were obtained, with the analysis of structure-activity relationships of novel inhibitors. Furthermore, the mode of binding imposed by key functional groups of the inhibitors was explored by investigating the effect of pH on the interactions with NS3. The results show the importance of using appropriate model systems for drug discovery by selecting relevant targets and assay conditions. Furthermore, the usefulness of kinetic rate information in drug discovery is demonstrated. Thus, by contributing to the knowledge of protease-ligand interactions, applicable to both protease inhibitor interactions and protease activity regulation, this thesis is expected to have an impact on the field of protease inhibitor development and drug discovery in general.

Gene regulation is vital to the success of all living organisms. Understanding this complex process is crucial to our knowledge of how cells function and how in some cases they can lead to debilitating or even fatal disease. In this thesis I focus on a set of DNA-binding proteins known as transcription factors (TFs), proteins fundamental to the process of gene regulation at the level of transcription. I develop assays and techniques for the detection and quantitation of TFs in vitro and in vivo as well as a method for TF encapsulation and release. The advantages of the TF detection assays in this thesis are made possible through the use of single-molecule (sm) fluorescence. This methodology enables detection of individually labeled molecules allowing discrimination of sample heterogeneities inaccessible with ensemble techniques. Here I present two different TF assays based on two sm observables: relative probe stoichiometry and Förster resonance energy transfer (FRET). The first assay design, based on stoichiometry, detects TFs using TF-dependent coincidence of two distinctly labelled DNA ‘half-sites’. I demonstrate sensitive detection (~ pM) in solution and on surfaces, multiplexed detection of multiple TFs, and detection in cell lysates. A kinetic model of the system is also developed, verified experimentally and used to quantify TF concentrations without the need for a calibration curve. The second assay design, based on FRET, is a novel approach to TF detection using TFmediated DNA bending. TFs are detected by bending the sensor and monitored with FRET at the single-molecule or ensemble level. I demonstrate TF detection in purifed form and expressed in cell lysates. As this sensor was designed for use in vivo, methods to hinder nuclease degradation are explored. For TF detection in vivo, I describe a successful strategy to internalise fluorescently labeled molecules into live E.coli. Viability and internalisation efficiency are characterised and ensemble measurements with FRET standards are demonstrated. Importantly, sm FRET measurements in vivo are achieved opening many exciting possibilities. The FRET based TF sensor is then internalised as a step towards real-time in vivo monitoring of TF concentrations. Finally a system based on DNA nanotechnology is presented for the non-covalent encapsulation and release of TFs. Such a system could be delivered into a cell to alter levels of gene expression using external stimuli as inputs. We believe these tools will generate valuable information in the study of prokaryotic gene expression as well as providing a potential commercial avenue towards diagnostics.