Transition metal oxides (TMO) have proven to exhibit novel properties such as high temperature superconductivity, magnetic ordering, charge and spin density waves, metal to insulator transitions and colossal magnetoresistance. Among these are a spin-orbit coupling (SOC) induced Mott insulator Sr2IrO4. The electric transport properties of this material remain finite even at cryogenic temperatures enabling its complex electronic structure to be investigated by a scanning tunneling microscope. At T = 77 K, we observed two features which represent the Mott gap with a value of 2D ~ 615 meV. Additionally an inelastic loss feature was observed inside this gap due to a single magnon excitation at an energy of ~ 125 meV. These features are consistent with similar measurements with other probes. In addition to these features, at T = 4.2 K lower energy features appear which are believed to be due to additional magnetic ordering. Another material that exhibits a unique physical behavior is the sliding charge density wave (CDW) material TaS3. It is a quasi-one dimensional material that forms long narrow ribbon shaped crystals. It exhibits anomalies including non-ohmic conductivity, a decrease in the Young’s modulus, a decrease in the shear modulus and voltage induced changes in the crystal’s overall length. In addition, we have observed the torsional piezo-like response, voltage induced torsional strain (VITS), in TaS3 which was first discovered by Pokrovskii et. al. in 2007. Our measurements were conducted with a helical resonator. The VITS response has a huge effective piezoelectric coefficient of ~ 104 cm/V. In addition we have concluded that the VITS is a very slow response with time constants of ~ 1 s near the CDW depinning threshold, that these time constants are dependent on the CDW current, and we suggest that the VITS is due to residual twists being initially present in the crystal.

Présentation d'un système d'analyse d'image effectué avec les contraintes suivantes : obtenir un nombre suffisant de niveaux de différenciation permettant de traiter l'information non seulement avec des critères de forme mais également avec des critères lies au comportement du signal ; avoir la possibilité d'analyser des images de grande taille ; ne pas figer le traitement au problème posé.

A relatively new application for the laser is in fluorescence microscopes. The fluo- rescence microscope needs a high power light source input. Using a laser source improves the precision of the microscope. A pulsed laser source enhances the performance of the fluorescence microscope and a laser diode can be overdriven without being damaged. The thesis investigates which properties of the laser pulses are needed regarding pulse width, pulse period and waveform. The thesis also investigates which properties are desired for the electrical pulses driving the laser, and how they can be generated using electrical components. The desired laser pulse should have a pulse width of 100 ps and a pulse period of 50 ns. The laser pulse should also have a well-defined wavelength, stable output power and it should be able to quickly turn on and off. To achieve this laser pulse, the desired input to the laser diode should have an input voltage of 5 V, an input current of 250 mA, a pulse width of 100 ps and a pulse period of 50 ns. For generating this pulse the chosen pulse generator, an SRD, should have low junction capacitance, low package capacitance and low package inductance. The chosen amplifier, a MESFET, desires low drain current and should have high transconductance and a large negative threshold voltage.

This thesis examines the role of microscope technology in informing medical and anatomical knowledge during the Enlightenment. Past historians have claimed that microscopy generally stagnated until the popularisation of achromatic microscopes and cell theory in the middle of the nineteenth century. As evidence for this decline, historians have pointed to the poor quality and slow development of microscope designs until the popularisation of achromatic microscopes in the 1820s. In contrast, this thesis highlights the role of specific Enlightenment-era microscopes in answering medical and anatomical questions. It suggests that medical microscopy was far more advanced than previous scholarship has ascertained. Thus far, instrument historians have focused more attention on competing instrument makers as opposed to rival instrument users. This thesis presents several case studies which explore both makers and users. These concern the histories of Enlightenment-era epidemiology, reproduction theory, anatomy, and physiology as well as the different types of microscopes which influenced these fields. In terms of methodology, this thesis neither follows nor casts doubt on any particular theory of historical development; rather, it attempts to shed further light on available primary sources and their contexts. Presenting key case studies illustrates the difficulties that early microscope users faced in acquiring and publishing new observations. To explore the practice of early microscopy further, this thesis presents re-enactments of these case studies using Enlightenment-era microscopes and modern tissue samples. Thus, this thesis is a call to broaden the scope of primary sources available to historians of science and medicine to include instruments and re-enactments. This thesis finds that technological advances did not correlate to microscopical discovery in medicine or anatomy. Both simple and complex microscope designs aided anatomical and medical research. Broader advances in anatomy, physiology, and medical etiology dictated the utility of medical microscopy. Although various groups, such as the French clinicians, saw little need for microscopy towards the end of the eighteenth century, microscope-based evidence continued to play a diagnostic role among lesser-known practitioners despite its lack of visibility in medical literature.

Résumé : La compréhension des contraintes qui régissent l'assemblage des machineries supramoléculaires – qu'elles soient solubles ou bien ancrées dans les membranes biologiques – est un enjeu scientifique majeur.Le système de de sécrétion type VI (T6SS) est un organelle bactérien récemment mis en évidence qui a pour particularité de posséder une origine évolutive commune avec le bactériophage T4. En raison de cette origine évolutive commune, certaines sous unités du T6SS et du bactériophage T4 présentent des structures comparables. Cependant, un grand nombre des sous unités du T6SS reste à caractériser. Parmi celles-ci, les protéines SciB et SciC sont retrouvées dans tous les systèmes de sécrétion de type VI suggérant que ces deux protéines participent à la formation du "core-complexe": le complexe minimal requis pour le fonctionnement du T6SS. / The recently identified type VI secretion system has been demonstrated to be involved in most of these processes. The T6SS is a highly complex macromolecular machine that allows Gram-negative bacteria to deliver effector proteins to both prokaryotic and eukaryotic cells in a contact-dependent manner. The T6SS promotes therefore antibacterial competition, virulence towards eukaryotes or even both. The T6SS is composed of a minimal set of 13 subunits, which are currently believed to form the core apparatus. They assemble two distinct sub-complexes: one is a cytosolic contractile structure related to the tail of contractile bacteriophages, whereas the other spans the whole cell envelope. Therefore, the T6SS is generally depicted as an inverted phage tail anchored to the cell envelope through its membrane-associated complex. Contractile tails are currently thought to assemble from four structural elements: the baseplate, the internal tube, the contractile sheath and the tail terminator. The aim of my Ph.D. work was to further characterize the assembly and function of the T6SS phage tail-like complex in enteroaggregative E. coli. In this thesis document, I provide evidence that the internal tube assembles from Hcp hexamers stacked in a head-to-tail manner and that this internal cylinder is used as a template during sheath assembly. I also characterized a sub-complex of three proteins (TssEFG) that forms the baseplate of the T6SS and controls the polymerization of the tube and sheath. Finally, I recently showed that the T6SS functions like a nano-crossbow to kill target cells as the contraction of the T6SS results in prey cell death during interbacterial competition.

Ce manuscrit de thèse est composé de trois parties dédiées aux développements technologiques nécessaires à l'étude de la polarité et des contraintes mécaniques dans les cellules épithéliales. La première partie décrit les développements technologiques et méthodologiques qui ont été réalisés en micro-fabrication et traitement de surface, acquisition et analyse d'image, et mesure des forces de traction. La deuxième partie décrit l'étude de l'organisation spatiale du système d'adhérence des cellules épithéliales. De la régulation de leur polarité à celle de leur fonction, l'architecture des cellules épithéliales est profondément liée à leur système d'adhérence. Nous avons utilisé les micropatrons adhésifs pour contrôler la géométrie de la matrice extra-cellulaire pour examiner l'effet de l'adhérence des cellules avec la matrice sur la position des zones d'adhérence intercellulaire. Nos résultats montrent que l'organisation spatiale de l'adhérence cellule-matrice joue un rôle déterminant sur celle de l'adhérence intercellulaire. Ils montrent également que cette organisation dirige ensuite la position du centrosome et l'orientation de l'ensemble de la polarité interne. Lors d'une réorganisation spatiale de l'épithélium, comme c'est le cas au cours de la transition épithélium-mésenchyme, les systèmes d'adhérence et la polarité interne subissent tous les deux de profondes modifications. Néanmoins, les cellules semblent capables de les réguler de façon indépendante selon le type de stimulus qui induit la réorganisation. La dernière partie est une analyse des paramètres physiques impliqués dans l'architecture épithéliale. En parallèle des régulations biochimiques, les contraintes mécaniques jouent également un rôle fondamental dans la régulation des processus morphogenétiques. L'association de l'ensemble de nos développements technologiques (patterning de substrat déformable, logiciel de détection et de mesure de force, contrôle du positionnement des cellules) nous a permis d'analyser précisément les propriétés mécaniques des architectures multicellulaires. Nous avons découvert que l'organisation spatiale du système adhérence était un régulateur majeur de l'intensité et de la répartition des forces intra-cellulaires. Cette observation nous a permis de proposer une modification du modèle actuel de distribution des contraintes dans un épithélium qui prend en compte l'anisotropie des forces inter-cellulaires en réponse à l'hétérogénéité de la matrice extra-cellulaire. Ce nouveau modèle physique permet de rendre compte des positions adoptées par les cellules en réponse aux différentes géométries de la matrice extra-cellulaire. / This thesis dissertation is comprised of three major parts. The first part devotes to all the technological developments that have been realized in my thesis study. These developments in microfabrication, in image acquisition and analysis, and in the traction force analysis had solved various problems we have encountered during our study of epithelial architecture. The second part describes the study of the spatial organization of the adhesion systems in epithelia. From their polarity, their functioning, to their remodeling, the epithelial architecture is deeply linked with the adhesion systems. With the capability to well define the location of cell-matrix interaction, we examined how the intercellular adhesion was organized according to the cell-matrix adhesion. Our results highlighted the instructive role of cell-matrix adhesion in organizing the intercellular adhesion. This organization subsequently governed the internal polarity which was indicated by the centrosome positioning. During epithelial remodeling, both the adhesion system and internal polarity were subjected to modification. Nevertheless they could be regulated differently depending on the context of remodeling. The last part is focused on the physical aspect of the epithelial architecture. Apart from the biochemical signaling network, mechanical force is also a substantial ingredient in morphogenesis. Together with our techniques in micropatterning the soft gel, the development of software for traction force microscope, and our knowledge of cell-cell positioning, we were able to analyze precisely the mechanical property of the multicellular architecture. We found that the cellular contractility was modulated by the spatial organization of the adhesion system. It permitted us to complete the current physical model of epithelial geometry with an anisotropic term for contractility. This new physical model could effectively account for the cell positioning on various matrix geometries.

Les cellules tumorales circulantes (CTC) sont des cellules présentes en très faible proportion (une cellule pour un million de cellules normales) dans la circulation sanguine, et qui jouent un rôle important dans le processus de métastase responsable de la majorité des décès de patients atteints de cancer. La détection du cancer à un stade précoce augmente les chances de survie des patients. Le but de ce travail a été de développer un ensemble de technologies permettant de mieux caractériser et détecter les CTC.Nous avons concentré notre étude sur les cellules ayant un phénotype hybride, entre épithélial et mésenchymal, qui pourraient correspondre à des CTC de plus fort potentiel métastatique compte tenu du rôle joué par la transition épithelio-mésenchymateuse dans ce processus. Nous avons tout d’abord isolé, par immunofluorescence et cytométrie en flux, une lignée cellulaire de cancer (A549, le carcinome de poumon humain) co-exprimant la E- et la N-cadhérine, de sorte qu’elle puisse être utilisée comme modèle de CTC dans le développement de nouvelles techniques de détection. Nous avons en particulier adapté le système de microscopie de fluorescence et d’analyse d'images PathfinderTM à haut-débit de la société Imstar S.A. pour identifier efficacement quelques milliers de cellules A549 mélangées à du sang de patient, après une étape de filtration par la taille. Afin d’améliorer l’identification des cellules hybrides, nous avons évalué la technique de transfert de Förster résolue en temps qui pourrait révéler avec un excellent rapport signal/bruit la présence à la membrane cellulaire d’agrégats compacts de N- et E-cadhérines. Enfin, afin d’augmenter le nombre de biomarqueurs simultanément détectés par immunofluorescence nous avons contribué à la mise au point de nanocristaux semi-conducteurs fluorescents conjugués avec un anticorps dirigé contre une protéine d'intérêt. Au final, nos résultats fournissent un ensemble de technologies qui pourront être utilisées pour améliorer la détection et la caractérisation des CTC. / Circulating tumor cells (CTCs) are rare cells (one in millions of normal cells) in blood circulatory system playing a key role in the process of metastasis, which is responsible for the majority of death of patients with cancer. Detecting cancer at early stage can give patients higher chances of survival. The aim of this work is to develop a set of technologies capable of characterizing and detecting the CTCs. We restricted our study to CTCs with hybrid phenotype, between epithelial and mesenchymal, that could correspond to circulating cells with the highest metastatic potential, considering the relation of the Epithelial to Mesenchymal Transition to cancer. Using immunofluorescence and flow cytometry, we first isolated a cancer cell line (A549, human lung carcinoma) co-expressing E- and N-cadherin, which is further used as a CTC model in the development of new detection techniques. In particular, we showed that the high throughput automated fluorescence microscope and image processing Imstar S.A. PathfinderTM system can recover efficiently a few thousands of A549 cells spiked in a blood sample, after an initial size-filtering step. We also used time-gated Fluorescence Resonant Energy Transfer to investigate the presence of E- and N-cadherin clusters at the cell membrane that could enhance the detection sensitivity of hybrid phenotype. Finally, in view of increasing the number of simultaneous biomarkers detection by immunofluorescence we contributed to the development of fluorescent semiconductor nanocrystals conjugated with antibody directed against the protein of interest. Altogether, our results provide a set of technologies that can be used to improve the detection and characterization of CTCs.

A microscopia de varredura por tunelamento (MVT) é uma nova maneira de se observar experimentalmente o efeito Kondo. Quando uma concentração de átomos é adicionada a um meio metálico (metal hospedeiro), a corrente de tunelamento passa a depender de fatores de origem não geométrica. O rearranjo das cargas dentro do volume metálico (oscilações de Friedel) e o espalhamento de spins eletrônicos (efeito Kondo), devido a introdução de impurezas, mudam o valor da corrente e influenciam o levantamento da topografia do espécime examinado. Esses fatores devem ser considerados para que a topografia gerada seja condizente com a topografia verdadeira. Utilizamos como modelo teórico para descrição desse sistema, o modelo de Anderson de uma impureza para simular o espécime examinado e uma banda de condução livre para representar os elétrons da agulha metálica do microscópio. Nossa abordagem usa a fórmula de Kubo para o cálculo da corrente de tunelamento, supondo Hamiltoniano de tunelamento como perturbação e o potencial elétrico no regime linear. Apresentamos inicialmente um estudo para o Modelo do Nível Ressonante, isto é, o modelo de Anderson sem correlação, com o objetivo de demonstrar a precisão do método do Grupo de Renormalização Numérico. Em seguida, analisamos o Modelo de Anderson correlacionado. Os resultados tanto para a condutância em função da distância entre ponta e impureza a temperatura fixa, como para condutância em função da temperatura e distância fixa, permitem interpretação física transparente desde que levem em conta a ressonância de Kondo na densidade espectral. / The scanning tunneling microscopy (STM) is a new way to observe experimentally the Kondo effect. When a concentration of atoms id added to a sample (host metal), the tunneling current begins to depend on other non-geometric factors. The rearrangement of charges in the metallic bulk (Friedel oscillations) and the electronic spin scattering (Kondo effect), due to the presence of impurities, change the current value and affect the sample´s topography. These factors must be considered in order to make a correspondence between the generated topography with the true one. As a theoretical description of the system, we use the single impurity Anderson model to simulate the examined sample and a free conduction band to represent the electrons of the microscope metallic tip. Our treatment uses the Kubo formula to calculate the tunneling current, assuming the tunneling Hamiltonian as a perturbation and the electric potential in the linear regime. We initially present a study of the Resonant Level Model, i.e, the Anderson model without correlaction, to show the accuary of the Numerical Renormalization Group procedure. In the next step, we analyse the correlated Anderson model. The dependence of the conductance on tip-impurity distance, at constant temperature, and its dependence on temperature for constant tip-impurity distance, allow a clear physical interpretation after taking into account the Kondo resonance in the spectral density.

O mecanismo de formação e origem das alterações nucleares ainda é pouco conhecido, sendo o micronúcleo a mais estudada. As células tumorais geralmente apresentam vários tipos de alterações nucleares que estariam associadas à instabilidade genética. O objetivo deste trabalho foi analisar as possíveis associações entre alterações nucleares e citoesqueleto em células HK2 e A549, derivadas de carcinoma de pulmão humano. Otimizamos a metodologia de uso do MCVL para redefinir as alterações nucleares e caracterizar os principais filamentos do citoesqueleto em preparações coradas por Feulgen ou imunofluorescência. As células da linhagem HK2 apresentaram fibras de actina dispostas concentricamente e em "clusters" e os filamentos de tubulina apareceram de forma radial, enquanto que o padrão de distribuição em A549 foi mais semelhante ao das células normais (BRL3A). Os filamentos de lamina B foram os mais importantes para evidenciar as alterações nucleares, porém essas alterações não puderam ser relacionadas com alterações do citoesqueleto. / The origin and mechanism of formation of the nuclear alterations is largely unknown, with the micronucleus being the most well studied alteration. Tumor cells generally present various types of nuclear alterations witch can be associated with genetic instability. The propose of this study was to analyze the possible association between nuclear alterations and the cytoskeleton in the human lung carcinoma cells HK2 and 549. The method of LSM was optimized to redefine the nuclear alterations and to characterize the principal cytoskeletal filaments in preparations stained with Feulgen’s reagent or submitted to imunofluorescent methods. The HK2 cells presented actin fibres arranged either concentrically or in clusters and tubulin filaments arranged radially, while in the A549 cells the distribution pattern was similar to that of normal cells (BRL3A). The lamin B filaments were the most important to identify nuclear alterations, as these alterations could not be related to cytoskeletal alterations.

La quantification du protéome à très haute sensibilitée n’est actuellement pas réalisable, et est un problème pour l’analyse de cellule isolée, d’échantillon rare ou pour la détection de protéine de faible abondance. Afin d’améliorer la sensibilité, une idée est d’utiliser un microscope capable de détecter des protéines individuellement. Il faut pour cela dans un premier temps mesurer la proportion du protéome actuellement marquée par une sonde fluorescente afin de pouvoir faire des mesures quantitatives. Avec des conditions dénaturantes et la détection des amines, on arrive à marquer jusqu’à 75% du protéome d’un lysat cellulaire, avec un marquage plus efficace quand la protéine est de grande taille. Dans un deuxième temps, il faut séparer par la taille le protéome afin de réaliser un profil protéique. Si la puce microfluidique ne permet pas la réalisation d’un profil avec une résolution, le micro SDS-PAGE en est capable en permettant également l’observation du profil par microscopie, autorisant la détection jusqu’à 10 ng de protéines par bande et ainsi permettant d'obtenir un profil à partir de seulement 100 cellules. Cette sensibilité a permis l’identification de quatre lignées cellulaires de cancer du sein, avec un fort potentiel pour une application pour le diagnostic de cellule cancéreuse provenant de petite biopsie, plus facile pour le patient. / Proteomic quantification at very high sensitivity is not achieved yet, even if they are a need to realize this quantification for the analysis of uncommon samples at a single cell level, or for the detection of low abundance protein. To improve this sensitivity, one way is to use a microscope able to detect single-molecule. In this optic, the first step to enable precise quantification is to measure the proportion of the proteome that is labeled by a fluorescent probe. When using strong denaturant conditions combined with a probe able to detect the amine of the protein, we are able to label up to 75% of the proteome from a cell lysate, with an increase in the labeling efficiency when the protein is bigger. The second step necessitates the protein separation by size in order to realize a proteome profile. Two technics were used for that, the microfluidic chip and the micro SDS-PAGE. The second one enables the possibility to scan the profile by microscopy, allowing the detection of up 10 ng of protein and then permits the analysis of only 100 cells. This sensitivity enables the differentiation of 4 different proteome profiles from cell lines originated from breast cancer, with a potential in the diagnostic of cancer cell from a smaller biopsy, allowing a less painful experience for the patient.