Le système immunitaire est un ensemble de mécanismes impliquant différents types de cellules qui produisent des facteurs solubles (cytokines, chimiokines ou molécules cytotoxiques) qui contribuent à la régulation et aux réponses immunitaires. La caractérisation à l'échelle cellulaire de la production de ces facteurs solubles présente un grand intérêt d'une part sur le plan fondamental pour comprendre les cascades d'événements des régulations cellulaires, et d'autre part dans le suivi de la réponse immunitaire (infections, cancers, auto-immunités, greffes, vaccins, etc.). Cependant, la plupart des techniques actuellement disponibles (ELISpot, cytométrie en flux, microarrays, etc.) ne permettent pas d'étudier plusieurs cytokines en rapport avec le phénotype des cellules sécrétrices et/ou sans marquage et d'analyser les secrétions de cytokines en temps réel par des cellules individuelles. Dans cette étude, une « biopuce à cellules » a été développée pour analyser les secrétions de cytokines par les cellules individuelles (lymphocytes T) in vitro. La biopuce est fonctionnalisée par greffage électrochimique des motifs d'anticorps spécifiques aux protéines membranaires de cellules et/ou d'anticorps spécifiques aux cytokines, tous couplés au pyrrole. Ensuite, un traitement de surface est effectué avec du poly (éthylène glycol) thiol (Thiol-PEG) pour empêcher la fixation non spécifique de cellules sur la surface de la biopuce. Un dispositif microfluidique en polydimethyllsiloxane (PDMS) et maintenu à 37°C a aussi été développé afin d'intégrer toutes les opérations d'analyse et de détection dans un seul système. La biopuce développée dans cette étude permet la capture spécifique et stable de lymphocytes T individuels viables et la détection ultérieure de cytokines sécrétées par chaque cellule individuelle. Dans ce travail, la détection des cytokines sécrétées (IL-2 et IFN-γ) a été effectuée par fluorescence dans un format en sandwich. Cette «biopuce à cellules» est également compatible avec l'imagerie par résonance plasmonique de surface (SPRi), ce qui pourrait permettre de réaliser des analyses en temps réel et la détection sans marquage de plusieurs cytokines sécrétées par des cellules individuelles. Cette technique fournit un outil très prometteur pour l'analyse de marqueurs biologiques et de l'activité de cellules et l'étude des réponses immunitaires. / The immune system is a set of mechanisms involving many different cell types which communicate through downstream signals mediated principally by soluble factors (i.e. cytokines) to protect the host against invading organisms and to control adequate immune responses. The identification and characterization at the cellular level of cytokine production has a huge interest for both fundamental research and clinical studies. However, the majority of techniques currently available (ELISpot, flow cytometry, microarrays, etc.) have several shortcomings including notably the assessment of multiple cytokines in relation to secreting cell phenotypic classification and/or label-free and real-time analysis of cytokine secretions at individual cell level. Hence, in this study, we developed a « cell biochip » to analyze the secretion of cytokines by individual cells (T lymphocytes) activated and cultured in vitro. The biochip is functionalized by electrochemically grafting patterns of pyrrole-conjugated cell membrane-specific and cytokine-specific antibodies and treated with Poly(ethylene glycol)thiol (Thiol-PEG) self-assembled monolayers (SAMs) to stably avoid non-specific binding of cells on the surface. A polydimethyllsiloxane (PDMS)-based microfluidic device maintained at 37°C was also developed in order to integrate all the detection assay operations in a single system. The biochip developed here allows specific and stable capture of viable and bioactive individual T cells and subsequent detection of secreted cytokines in the close vicinity of each individual cell. In this work, the detection of secreted cytokines (IL-2 and IFN-γ) was performed by fluorescence in an immunosandwich assay format. This « cell biochip » is also compatible with surface plasmon resonance imaging (SPRi), which could therefore allow expanding its functionality to enable real-time and label-free detection of multiple cytokines from individual cells. Such technique provides a very promising tool for the analysis of biomarkers and cell activity and the monitoring of immune responses.

L'objectif des travaux est de démontrer que la lithographie douce, quelquefois baptisée " Micro-Contcat Printing (µCP)", constitue une méthode de dépôt de biomolécules présentant de nombreux avantages pour des applications de type Biopuces. Pour la fabrication de puces à ADN, nous démontrons que le µCP est une technique compétitive par rapport au dépôt robotisé de gouttes traditionnellement utilisé. Le coût est inférieur, la densité des puces est augmentée et la qualité et la définition des motifs biomoléculaires sont supérieures. Une étude complète des mécanismes d'encrage des timbres élastomères d'impression ainsi que des mécanismes de transfert par contact des molécules vers le substrat est présentée. Le rôle prépondérant des fragments de polymère non réticulés présents à la surface des timbres est mis en évidence. Dans un second volet nous étudions la possibilité de générer par la même méthode des puces à biomolécules uniques. Nous montrons comment le µCP peut être poussé jusqu'à une résolution sub-micrométrique proche de 50 nm. Deux voies technologiques originales impliquant la lithographie douce sont proposées : l'une pour peigner individuellement en des sites organisés précisément sur la surface des longs brins d'ADN pour des études de génétique, l'autre pour fixer des molécules individuelles d'ADN par une extrémité rendant possible l'étude dynamique de molécules uniques (ADN) sur de larges populations.

<p>Flow-based microfluidic biochips constitute an emerging technology for the automation of biochemical procedures. Recent advances in fabrication techniques have enabled the development of these devices. Increasing integration levels provide biochips with tremendous potential; a large number of bioassays, i.e., protocols for biochemistry, can be processed independently, simultaneously, and automatically on a coin-sized microfluidic platform. However, the increases in integration level introduce new challenges in the design optimization and the testing of these devices, which impede their further adoption and deployment.</p><p>This thesis is focused on enhancing the automated design and use of flow-based microfluidic biochips and on developing a set of solutions to facilitate the full exploitation of design complexities that are possible with current fabrication techniques. Four key research challenges are addressed in the thesis; these include design automation, wash optimization, testing, and defect diagnosis.</p><p>Despite the increase in the number of on-chip valves, designers are still using full-custom methodologies involving many manual steps to implement these chips. Since these chips can easily have thousands of valves, manual design procedure can be time-consuming and error-prone, and it can result in inefficient designs. This thesis presents the first problem formulation for automated control-layer design in flow-based microfluidic biochips and describes a systematic approach for solving this problem. Our goal is to find an efficient routing solution for control-layer design with a minimum number of control pins.</p><p>The problem of contamination removal in flow-based microfluidic biochips must also be addressed. Applications in biochemistry require high precision to avoid erroneous assay outcomes, and they are vulnerable to contamination between two fluidic flows with different biochemistries. This thesis proposes the first approach for automated wash optimization for contamination removal in flow-based microfluidic biochips. The proposed approach ensures effective cleaning and targets the generation of wash pathways to clean all contaminated microchannels with minimum execution time under physical constraints.</p><p>Another practical problem addressed in this thesis is the lack of test techniques for screening defective biochips before they are used for biochemical analysis. This thesis presents an efficient approach for automated testing of flow-based microfluidic biochips. The test technique is based on a behavioral abstraction of physical defects in microchannels and valves. The flow paths and flow control in the microfluidic device are modeled as a logic circuit composed of Boolean gates, which allows test generation to be carried out using standard automatic test-pattern generation tools. Based on the analysis of untestable faults in the logic-circuit model, we present a design-for-testability technique that can achieve 100\% fault coverage.</p><p>Finally, this thesis presents a technique for the automated diagnosis of leakage and blockage defects. The proposed method targets the identification of defect types and their locations based on test outcomes. It reduces the number of possible defect sites significantly while identifying their exact locations.</p><p>In summary, this thesis has led to a set of optimization and testing methods for flow-based microfluidic biochips. The results of this research are expected to not only shorten the product development cycle, but also accelerate the adoption and further development of this emerging technology by facilitating the full exploitation of design complexities that are possible with current fabrication techniques.</p> / Dissertation

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Integration and miniaturisation in electronics has undoubtedly revolutionised the modern world. In biotechnology, emerging lab-on-a-chip (LOC) methodologies promise all-integrated laboratory processes, to perform complete biochemical or medical synthesis and analysis encapsulated on small microchips. The integration of electrical, optical and physical sensors, and control devices, with fluid handling, is creating a new class of functional chip-based systems. Scaled down onto a chip, reagent and sample consumption is reduced, point-of-care or in-the-field usage is enabled through portability, costs are reduced, automation increases the ease of use, and favourable scaling laws can be exploited, such as improved fluid control. The capacity to manipulate single cells on-chip has applications across the life sciences, in biotechnology, pharmacology, medical diagnostics and drug discovery. This thesis explores multiple applications of optical manipulation within microfluidic chips. Used in combination with microfluidic systems, optics adds powerful functionalities to emerging LOC technologies. These include particle management such as immobilising, sorting, concentrating, and transportation of cell-sized objects, along with sensing, spectroscopic interrogation, and cell treatment. The work in this thesis brings several key applications of optical techniques for manipulating and porating cell-sized microscopic particles to within microfluidic chips. The fields of optical trapping, optical tweezers and optical sorting are reviewed in the context of lab-on-a-chip application, and the physics of the laminar fluid flow exhibited at this size scale is detailed. Microfluidic chip fabrication methods are presented, including a robust method for the introduction of optical fibres for laser beam delivery, which is demonstrated in a dual-beam optical trap chip and in optical chromatography using photonic crystal fibre. The use of a total internal reflection microscope objective lens is utilised in a novel demonstration of propelling particles within fluid flow. The size and refractive index dependency is modelled and experimentally characterised, before presenting continuous passive optical sorting of microparticles based on these intrinsic optical properties, in a microfluidic chip. Finally, a microfluidic system is utilised in the delivery of mammalian cells to a focused femtosecond laser beam for continuous, high throughput photoporation. The optical injection efficiency of inserting a fluorescent dye is determined and the cell viability is evaluated. This could form the basis for ultra-high throughput, efficient transfection of cells, with the advantages of single cell treatment and unrivalled viability using this optical technique.