Exposure of hepatoma cell lines to the polycyclic aromatic hydrocarbon benzo[a]pyrene (B[a]P) is serving as a model for a systems biological study concerning the response of cells to contaminant molecules. Several aspects of the cellular distribution of the aryl hydrocarbon receptor (AhR) and its ligand B[a]P have been addressed by different live cell imaging techniques: The intracellular distribution of the B[a]P/AhR complex is visualized by means of confocal laser scaning microscopy (cLSM) and the intracellular transport rates of the complex is investigated by fluorescence recovery after photobleaching (FRAP) technique. Furthermore, cLSM image stacks of living cells are generated for the modeling of three dimensional (3-D) cell geometries. In order to prevent photochemical damage of the living cells induced by UV excitation of B[a]P, visualization is done by B[a]P’s auto fluorescence using near infrared two-photon-excitation. Murine Hepatoma 1c1c7 cells are exposed to graded concentrations of B[a]P (50 nM to 20 μM) for different incubation time periods (15 minutes to 48 hours). The highest amounts of B[a]P were found in lipid droplets and lysosomes, where the B[a]P molecules are collected and form large aggregates. We were able to work with concentrations down to 50 nM corresponding to that used for genomic and proteomic investigations. Also, for the first time imaging of B[a]P metabolites inside lipid droplets is presented in this work. The data and the model developed in this study will provide new insights into the systematic regulation of the B[a]P, the AhR as well as the receptor-ligand-complex pathway and the study will also serve as a prototype for elucidating other stress response pathways in the future.

Biomedical imaging requires high resolution to see the fine features of a sample and fast acquisition to observe live cells that move. Optical coherence tomography (OCT) is a powerful technique which uses optical interference for non-invasive high resolution 3D imaging in biological samples. The resolution of OCT is determined by the length over which the light used will in- terfere. Unfortunately, dispersion hurts the imaging resolution by broadening interference features. A technique called quantum-OCT (QOCT)[1] is immune to dispersion but re- quires entangled photon pairs. The need for entanglement drastically reduces the number of photons available for imaging, making QOCT too slow to be practical. Chirped-pulse interferometry (CPI) is also immune to dispersion. A chirped pulse is one where the fre- quency, or colour, of the light changes from red to blue from one end of the pulse to the other. CPI relies on frequency correlations created by applying different chirps to two sep- arate pulses. This method had the disadvantage of being limited to a single predetermined chirp rate, and discarded 50% of the power. However CPI has better resolution than OCT, automatic dispersion cancellation, and 10,000,000 times the signal strength of QOCT [13]. A new, much more flexible and efficient method of CPI will be demonstrated by creating the frequency correlations entirely in a single pulse. This new method is referred to as non- linear chirped pulse interferometry (NL-CPI). The non-linear chirp required in NCPI is very difficult to produce using only conven- tional optics. In this thesis we document the construction and characterization of a new method of creating the desired chirp using a programmable pulse-shaper (PS). We build a PPS and then demonstrated its functionality by compressing a 105nm FWHM bandwidth pulse to under 17f s, near its transform limited time duration. We also show that the values given to the PPS for dispersion are accurate by calculating and then compensating the dispersion caused by various optical elements in the CPI interferometer. Conventional OCT systems are immune to dispersion common to both arms of the interferometer. Non-linear interferometers experience broadening due to this dispersion, making them more difficult to use with fibre based interferometers common in conventional OCT. We show that NL-CPI can compensate for dispersion common to both arms of the interferometer, making NL-CPI more appealing as a replacement for conventional OCT. In this thesis we experimentally implement and demonstrate a prototype setup using non-linear CPI for dispersion-cancelled imaging of a mirror, with a resolution comparable to conventional OCT systems. We then use the system to produce 2-D cross sectional images of a biological sample, an onion. Q-OCT has previously been used to image an onion[16], but required treating the onion with gold nano particles to achieve a useful signal. The onion we used had no special treatment. In addition our axial scanning rate is also 10000 times faster than Q-OCT.

Biomedical imaging requires high resolution to see the fine features of a sample and fast acquisition to observe live cells that move. Optical coherence tomography (OCT) is a powerful technique which uses optical interference for non-invasive high resolution 3D imaging in biological samples. The resolution of OCT is determined by the length over which the light used will in- terfere. Unfortunately, dispersion hurts the imaging resolution by broadening interference features. A technique called quantum-OCT (QOCT)[1] is immune to dispersion but re- quires entangled photon pairs. The need for entanglement drastically reduces the number of photons available for imaging, making QOCT too slow to be practical. Chirped-pulse interferometry (CPI) is also immune to dispersion. A chirped pulse is one where the fre- quency, or colour, of the light changes from red to blue from one end of the pulse to the other. CPI relies on frequency correlations created by applying different chirps to two sep- arate pulses. This method had the disadvantage of being limited to a single predetermined chirp rate, and discarded 50% of the power. However CPI has better resolution than OCT, automatic dispersion cancellation, and 10,000,000 times the signal strength of QOCT [13]. A new, much more flexible and efficient method of CPI will be demonstrated by creating the frequency correlations entirely in a single pulse. This new method is referred to as non- linear chirped pulse interferometry (NL-CPI). The non-linear chirp required in NCPI is very difficult to produce using only conven- tional optics. In this thesis we document the construction and characterization of a new method of creating the desired chirp using a programmable pulse-shaper (PS). We build a PPS and then demonstrated its functionality by compressing a 105nm FWHM bandwidth pulse to under 17f s, near its transform limited time duration. We also show that the values given to the PPS for dispersion are accurate by calculating and then compensating the dispersion caused by various optical elements in the CPI interferometer. Conventional OCT systems are immune to dispersion common to both arms of the interferometer. Non-linear interferometers experience broadening due to this dispersion, making them more difficult to use with fibre based interferometers common in conventional OCT. We show that NL-CPI can compensate for dispersion common to both arms of the interferometer, making NL-CPI more appealing as a replacement for conventional OCT. In this thesis we experimentally implement and demonstrate a prototype setup using non-linear CPI for dispersion-cancelled imaging of a mirror, with a resolution comparable to conventional OCT systems. We then use the system to produce 2-D cross sectional images of a biological sample, an onion. Q-OCT has previously been used to image an onion[16], but required treating the onion with gold nano particles to achieve a useful signal. The onion we used had no special treatment. In addition our axial scanning rate is also 10000 times faster than Q-OCT.

Exposure of hepatoma cell lines to the polycyclic aromatic hydrocarbon benzo[a]pyrene (B[a]P) is serving as a model for a systems biological study concerning the response of cells to contaminant molecules. Several aspects of the cellular distribution of the aryl hydrocarbon receptor (AhR) and its ligand B[a]P have been addressed by different live cell imaging techniques: The intracellular distribution of the B[a]P/AhR complex is visualized by means of confocal laser scaning microscopy (cLSM) and the intracellular transport rates of the complex is investigated by fluorescence recovery after photobleaching (FRAP) technique. Furthermore, cLSM image stacks of living cells are generated for the modeling of three dimensional (3-D) cell geometries. In order to prevent photochemical damage of the living cells induced by UV excitation of B[a]P, visualization is done by B[a]P’s auto fluorescence using near infrared two-photon-excitation. Murine Hepatoma 1c1c7 cells are exposed to graded concentrations of B[a]P (50 nM to 20 μM) for different incubation time periods (15 minutes to 48 hours). The highest amounts of B[a]P were found in lipid droplets and lysosomes, where the B[a]P molecules are collected and form large aggregates. We were able to work with concentrations down to 50 nM corresponding to that used for genomic and proteomic investigations. Also, for the first time imaging of B[a]P metabolites inside lipid droplets is presented in this work. The data and the model developed in this study will provide new insights into the systematic regulation of the B[a]P, the AhR as well as the receptor-ligand-complex pathway and the study will also serve as a prototype for elucidating other stress response pathways in the future.

Fluorescence microscopy offers the opportunity to image biological samples noninvasively in real time and has become an essential analytical tool in the biomedical laboratory. Nonetheless, the phenomenon of diffraction imposes stringent limitations on the resolving power of conventional microscopes, preventing the spatial resolution of fluorescent species co-localized within areas of nanoscaled dimensions. Time, however, can be exploited to distinguish fluorophores within the same subdiffraction area, if their fluorescence can be switched independently, and reconstruct sequentially their spatial distribution. In this context, photolytic reactions and photochromic transformations can be invoked to switch fluorescence under optical control. Fluorescent units, such as inorganic semiconductor nanoparticles and organic dyes, and photoactive components can be operated within a common supramolecular matrix or integrated within the same molecular construct to produce photoswitchable fluorescent assemblies. In the resulting systems, electronic communication between the components can be designed in order to photoactivate or photodeactivate fluorescence respectively. Both mechanisms can be exploited to overcome diffraction, and ultimately permit the reconstruction of images with resolution down to the nanometer level, in combination with appropriate illumination protocols.

No description available.

Ce travail de thèse se situe à l’interface de deux domaines : la culture cellulaire en trois dimensions et l’imagerie sans lentille.Fournissant un protocole de culture cellulaire plus réaliste sur le plan physiologique, le passage des cultures monocouches (2D) à des cultures tridimensionnelles (3D) - via l’utilisation de gels extracellulaires dans lesquels les cellules peuvent se développer dans les trois dimensions - permet de faire de grandes avancées dans de nombreux domaines en biologie tels que l’organogénèse, l’oncologie et la médecine régénérative. Ces nouveaux objets à étudier crée un besoin en matière d’imagerie 3D.De son côté, l’imagerie sans lentille 2D fournit un moyen robuste, peu cher, sans marquage et non toxique, d’étudier les cultures cellulaires en deux dimensions sur de grandes échelles et sur de longues périodes. Ce type de microscopie enregistre l’image des interférences produites par l’échantillon biologique traversé par une lumière cohérente. Connaissant la physique de la propagation de la lumière, ces hologrammes sont rétro-propagés numériquement pour reconstruire l’objet recherché. L’algorithme de reconstruction remplace les lentilles absentes dans le rôle de la formation de l’image.Le but de cette thèse est de montrer la possibilité d’adapter cette technologie sans lentille à l’imagerie des cultures cellulaires en 3D. De nouveaux prototypes de microscopes sans lentille sont conçus en parallèle du développement d’algorithmes de reconstructions tomographiques dédiés.Concernant les prototypes, plusieurs solutions sont testées pour converger vers un schéma alliant deux conditions. La première est le choix de la simplicité d’utilisation avec une culture cellulaire en boîte de Petri standard et ne nécessitant aucune préparation spécifique ou aucun changement de contenant. Cette condition entraînant de fortes contraintes géométriques sur l’architecture, la deuxième est de trouver la meilleure couverture angulaire possible des angles d’éclairage. Enfin, une version adaptée aux conditions en incubateur est développée et testée avec succès.Concernant les algorithmes, quatre types de solutions sont proposés, basées sur le théorème de diffraction de Fourier classiquement utilisé en tomographie diffractive optique. Toutes cherchent à corriger deux problèmes inhérents au microscope sans lentille : l’absence de l’information de phase, le capteur n’étant sensible qu’à l’intensité de l’onde reçue, et la couverture angulaire limitée. Le premier algorithme se limite à remplacer la phase inconnue par celle d’une onde incidente plane. Rapide, cette méthode est néanmoins source de nombreux artefacts. La deuxième solution, en approximant l’objet 3D inconnu par un plan moyen, utilise les outils de la microscopie sans lentille 2D pour retrouver cette phase manquante via une approche inverse. La troisième solution consiste à implémenter une approche inverse régularisée sur l’objet 3D à reconstruire. C’est la méthode la plus efficace pour compenser les deux problèmes mentionnés, mais elle est très lente. La quatrième et dernière solution est basée sur un algorithme de type Gerchberg-Saxton modifié avec une étape de régularisation sur l’objet.Toutes ces méthodes sont comparées et testées avec succès sur des simulations numériques et des données expérimentales. Des comparaisons avec des acquisitions au microscope classique montrent la validité des reconstructions en matière de tailles et de formes des objets reconstruits ainsi que la précision de leur positionnement tridimensionnel. Elles permettent de reconstruire des volumes de plusieurs dizaines de millimètres cubes de cultures cellulaires 3D, inaccessibles en microscopie standard.Par ailleurs, les données spatio-temporelles obtenues avec succès en incubateur montrent aussi la pertinence de ce type d’imagerie en mettant en évidence des interactions dynamiques sur de grandes échelles des cellules entres elles ainsi qu’avec leur environnement tridimensionnel. / This PhD work is at the interface of two fields: 3D cell culture and lens-free imaging.Providing a more realistic cell culture protocol on the physiological level, switching from single-layer (2D) cultures to three-dimensional (3D) cultures - via the use of extracellular gel in which cells can grow in three dimensions - is at the origin of several breakthroughs in several fields such as developmental biology, oncology and regenerative medicine. The study of these new 3D structures creates a need in terms of 3D imaging.On another side, 2D lens-free imaging provides a robust, inexpensive, non-labeling and non-toxic tool to study cell cultures in two dimensions over large scales and over long periods of time. This type of microscopy records the interferences produced by a coherent light scattered by the biological sample. Knowing the physics of the light propagation, these holograms are retro-propagated numerically to reconstruct the unknown object. The reconstruction algorithm replaces the absent lenses in the role of image formation.The aim of this PhD is to show the possibility of adapting this lens-free technology for imaging 3D cell culture. New lens-free microscopes are designed and built along with the development of dedicated tomographic reconstruction algorithms.Concerning the prototypes, several solutions are tested to finally converge to a scheme combining two conditions. The first requirement is the choice of simplicity of use with a cell culture in standard Petri dish and requiring no specific preparation or change of container. The second condition is to find the best possible angular coverage of lighting angles in regards of the geometric constraint imposed by the first requirement. Finally, an incubator-proof version is successfully built and tested.Regarding the algorithms, four major types of solutions are implemented, all based on the Fourier diffraction theorem, conventionally used in optical diffractive tomography. All methods aim to correct two inherent problems of a lens-free microscope: the absence of phase information, the sensor being sensitive only to the intensity of the incident wave, and the limited angular coverage. The first algorithm simply replaces the unknown phase with that of an incident plane wave. However, this method is fast but it is the source of many artifacts. The second solution tries to estimate the missing phase by approximating the unknown object by an average plane and uses the tools of the 2D lens-free microscopy to recover the missing phase in an inverse problem approach. The third solution consists in implementing a regularized inverse problem approach on the 3D object to reconstruct. This is the most effective method to deal with the two problems mentioned above but it is very slow. The fourth and last solution is based on a modified Gerchberg-Saxton algorithm with a regularization step on the object.All these methods are compared and tested successfully on numerical simulations and experimental data. Comparisons with conventional microscope acquisitions show the validity of the reconstructions in terms of shape and positioning of the retrieved objects as well as the accuracy of their three-dimensional positioning. Biological samples are reconstructed with volumes of several tens of cubic millimeters, inaccessible in standard microscopy.Moreover, 3D time-lapse data successfully obtained in incubators show the relevance of this type of imaging by highlighting large-scale interactions between cells or between cells and their three-dimensional environment.

Gold nanoparticules (GNPs) are of great interest for several applications in nanomedicine ; espacially in imaging and sensing, drug delivery or photothermal therapy because of their unique physical and chemical properties. For all theses applications, a better understanding of the interaction of GNPs with biomolecules and their uptake into cells is of great importance. Thus the main objective of this thesis was to study the toxicity of GNPs in biological media based on their sizes, shapes and surface chemistries. Cytotoxicity studies on human cells were done in vitro in presence of six GNP samples having spherical and flower shapes. We compared the cytotoxic effects and showed that it was largely higher for flower-shaped GNPs than spherical ones. Further we built-up the optical assembly and the set-up of the Fluorescence Correlation Spectroscopy (FCS). Followed by the set-up, the sensitivity, the resolution and other parameters were determined during the characterization of the FCS sytem. Then FCS was used to characterize fluorescent molecule-conjugated GNP, wich were fabricated in the interest of biomedical applications. In the next step, we characterized the diffusion behavior of MitoTracker dye labeled mitochondria by FCS in order to be able to compare in future the mitochondrial diffusion after incubating with GNPs, wich is described as the perspectives. / Les nanoparticules d'or (NPO) sont d'un grand intérêt pour de nombreuses applications en nanomédecine (en particulier pour l'imagerie, la détection de pathologies, la délivrance de médicaments ou la thérapie photothermique) en raison de leurs propriétés physiques et chimiques. Pour toutes ces applications, une meilleure compréhension de l'interaction des NPO avec les biomolécules et leur absorption dans les cellules est d'une importance primoridale. Ainsi, l'objectif principal de cette thèse était d'étudier la toxicité des NPO dans les milieux biologiques en fonction de leurs tailles, leurs formes et leurs chimies de surface. Des études de cytotoxicité sur des cellules humaines ont été réalisées in vitro, en présence de six types différents de NPO de forme sphérique et de nano-fleur. Nous avons comparé les effets cytotoxiques et montré qu'ils étaient largement supérieurs pour les NPO en forme de nano-fleur par rapport au NPO sphériques. En outre, nous avons mis en place un système de corrélation de spectroscopie de fluorescence (CSF). La sensibilité, la résolution et les principaux paramètres du système ont été déterminés lors de sa caractérisation. La CSF a ensuite été utilisée pour caractériser des NPO fluorescentes fabriquées pour des applications biomédicales. Nous avons également caractérisé la diffusion de Mitotracker, un marqueur des mitochondries par CSF afin d'être en mesure de comparer la diffusion mitochondriale après incubation de NPO.

Les conjugués QD-sdAbs sont des nano-sondes qui associent un quantum dot (QD) et des anticorps de domaine simple (sdAbs). Ces nano-sondes fluorescentes permettent des immunomarquages sur coupes tissulaires et sur cellules. L’objectif de ce travail est de montrer l’intérêt de l’excitation multi-photonique pour la détection et la localisation très spécifiques de biomarqueurs tumoraux.L’excitation multi-photonique des nano-sondes QD570-sdAb anti-CEA a été étudiée, sur coupes d’appendice et de carcinome du côlon humains pour optimiser le rapport signal/auto-fluorescence. L’utilisation du QD comme capteur d’énergie d’excitation dans un modéle de FRET QD-fluorophore organique a été démontré. Un modéle innovant pour une détéction ultra spécifique du CEA sur cellules MC38 CEA par double immunomarquage spécifique pour un transfert d’énergie résonnant entre QD et Alexa Fluor à été mis en oeuvre.Les résutats montrent l’intérêt de l’excitation multi-photonique par rapport à l’excitation à 458,9 nm pour la discrimination et l’optimisation du rapport signal/auto-fluorescence. Il est 40 fois supérieur en excitation à 800 nm qu’à 458,9 nm sur les coupes étudiées.L’utilisation des conjugués QD556-sdAb anti-CEA et d’un anticorps monoclonal permet un double immunomarquage du CEA membranaire sur cellules MC38 CEA. L’utilisation du QD comme nano-capteur d’énergie d’excitation multi-photonique permet une séléctivité d’excitation et un FRET entre QD et Alexa Fluor. Ce schéma permet une détéction spectrale aisée du FRET et une localisation très spécifique et sensible du CEA membranaire. Ceci est conforté par la diminution du temps de déclin du QD556 donneur d’énergie non radiative. / The QD-sdAbs conjugates are nano-sensors that combine a quantum dot (QD) and single domain antibodies (sdAbs). These fluorescent nanoprobes allow immunostaining on tissue sections and cells. The objective of this work is to show the interest of the multi-photon excitation for the detection and highly specific location of tumor biomarkers.Multi-photon excitation of anti CEA QD570-sdAb nanoprobes was investigated on human appendix and colon carcinoma slides for specifical detection and an optimization of the signal/auto-fluorescence emission ratio. The use of QD as excitation energy sensor for a QD-organic fluorophore FRET model has been shown. An innovative model for ultra-specific detection of CEA on MC38 CEA membrane cells by double immunostaining for a resonant energy transfer between QD and Alexa Fluor has been implemented.Our results shows the great interest of the multi-photon excitation compared to 458.9 nm excitation for discrimination and optimization of the signal / autofluorescence. It is 40 times higher at 800 nm two photon excitation has 458.9 nm one photon excitation on the studied sections.The use of conjugated QD556-sdAb anti-CEA and a conventional monoclonal antibody allows a double immunostaining on CEA on MC38 CEA membrane cells. The QD is use as multi-photon excitation energy nano-sensor enables an excitation selectivity and FRET between QD and Alexa Fluor. This configuration enables easy spectral detection of FRET and a very specific and sensitive location of membrane CEA. This is reinforced by the decrease in decay time of QD556 as donor of non radiative energy.

Les nanoparticules polymériques fluorescentes apparaissent comme des outils importants pour l'imagerie en temps réel des processus biologiques au niveau moléculaire et cellulaire. L’objectif de mon projet de doctorat a été d’optimiser les nanoparticules polymériques fluorescentes pour l’imagerie biologique. Premièrement, nous avons pu, en faisant varier la chimie des polymères, obtenir un très bon contrôle de leur taille. Ceci a permis de mettre en évidence l’importance de la taille des NPs pour des applications intracellulaires avec une taille maximale de 23 nm pour une distribution dans tout le cytosol. Deuxièmement, nous avons pu montrer que la simple adsorption d’un amphiphile PEGylé de type Pluronic permet la stabilisation des nanoparticules dans des milieux biologiques. Le nombre de molécules incorporées et leur stabilité ont été étudiés en combinant des techniques de FRET et de FCS. Les meilleures formulations résultent en une stabilité des nanoparticules in vivo, ce qui a permis leur imagerie en tant que particules individuelles dans les vaisseaux sanguins du cerveau de souris. Troisièmement, le transfert d’énergie entre différents fluorophores encapsulés dans les NPs a été étudié et optimisé. / Fluorescent polymeric nanoparticles appear as important tools for real-time imaging of biological processes at the molecular and cellular level. The objective of my PhD project was to optimize fluorescent polymeric nanoparticles for biological imaging. First, by varying the chemistry of the polymers, we have been able to obtain a very good control of their size. This made it possible to highlight the importance of NPs size for intracellular applications with a maximum size of 23 nm for optimal distribution throughout the cytosol. Secondly, we have shown that simple adsorption of a PEGylated amphiphiles pluronic family allows the stabilization of nanoparticles in biological media. The number of incorporated molecules and their stability has been studied by combining FRET and FCS techniques. The best formulations result in nanoparticle stability in vivo, which allowed their imaging as individual particles in the blood vessels of the mouse brain. Third, energy transfer among different fluorophores encapsulated in NPs has been studied and optimized.