Cell-semiconductor hybrid systems are a potential centerpiece in the scenery of biotechnological applications. The selection and study of promising crystalline semiconductor materials for bio-sensing applications is at the basis of the development of such hybrid systems. In this work we introduce crystalline SiC as an extremely appealing material for bio-applications. For the first time we report biocompatibility studies of different SiC polytypes whose results document the biocompatibility of this material and its capability of directly interfacing cells without the need of surface functionalization. Since the successful implementation of biosensors requires a good understanding and versatile control of the semiconductor surface properties, the chemistry, crystallography and electronic status of different SiC surfaces are extensively studied while their surface morphologies are thoroughly controlled via hydrogen etching. Also, investigations of the effect of cell surface charge on the electronic status of SiC surfaces are attempted adopting a contactless surface potential monitoring technique. The results obtained from these contactless measurements lead to the development of theoretical models well-suited for the description of cell-semiconductor hybrid systems electronic interactions.

Title: Computer Modeling of Tissue Development Author: Vojtěch Bednář Department: Department of applied mathematics Supervisor: Doc. RNDr. Zdeněk Hedrlín, CSc. Abstract: This thesis describes hybrid individual cell-based approach to modeling of systems of biological cells. In the first part reaction-diffusion model of environment is introduced together with vax equilibrium and model of a cell based on zygotic graph and cummulative states. Further, simulations modeling three biologically motivated situations are introduced: Lumen formation, tumor growth, and cellular migration in chronic inflammation. The first model shows a scenario of hollow structure formation based on directional division and cellular migration. The second model is concerned with the growth of a progeny of a slightly damaged cell. The resulting tumor exhibits three stages of malign transformation. Further, emergence of an aggressive tumor without detectable precursor is observed on one hand and a continual transformation of a benign neoplasm into a malign one is seen on the other hand. Each of these cases is a consequence of different parametrization of the model situation. The last model analyses the role of membrane enzymatic activity in migrating cells of the immune system in chronic inflammation. In this model it is observed that...

Imaging Time-of-Flight secondary ion mass spectrometry (ToF-SIMS) has been developed to perform 2D imaging and depth profiling of biological systems with micron or submicron scale lateral resolution, which can be attributed to the advent of polyatomic ion beam particularly C60+ and new concept of ToF-SIMS instrument, the J105 3D Chemical Imager (J105). These recent advances in ToF-SIMS have opened a new dimension for biological analysis. In this study, 2D and 3D imaging have been performed on two biological systems, Xenopus laevis (X. laevis) zygote/embryo and murine embryonic fibroblasts NIH 3T3 BXB-ER cells to explore the capability of ToF-SIMS to handle the biological samples with extreme topography and high resolution depth profiling of microdomains, which still represent major challenges for the ToF-SIMS. The study on X. laevis embryo explored the capability of ToF-SIMS to handle spherical samples (approx. 1-1.2 mm in diameter), identify lipid species in mixtures of lipid extraction from the zygotes and image of an intact embryo in 2D/3D during dynamic biological events, e.g., fertilisation and early embryo development. For the first time the J105 and conventional BioToF-SIMS instrument were employed for the study of developmental biology. The major classes of lipid were identified through multiple lipid assay in a single analytical run using ToF-SIMS. Topography effects of the embryo were assessed through imaging a single intact zygote/embryo that revealed secondary ions loss at the edge of the single cell. However, the topography effects on the mass resolution could be minimised using the J105. Moreover, in situ lipid profiling of the zygote revealed different lipid compositions and intensities on the membrane of the animal and vegetal hemispheres. Furthermore, high resolution imaging and depth profiling that performed on a single intact cell in a time course study visualised the egg-sperm fusion sites on the membrane of the zygote 10 min post-insemination and lipids arrangement on the membrane of the embryo through the early development stages. Subcellular signalling upon the fertilisation was also spatially located on the serial cryosections of a single zygote. With the NIH 3T3 BXB-ER cells, the study firstly adopted a finely focused C60+ beam to track morphological changes and rearrangement of subcellular organelle mitochondria (0.5-2 µm) in response to the activation of Raf/ERK (extracellular signal regulated kinase) pathway using the J105. The SIMS images of the unlabelled cells showed the shifting of membrane distribution and nuclei shrinking following Raf/ERK activation. The mitochondria fluorescence probe within the cells were located 3-dimensionally using confocal microscopy and ToF-SIMS, which revealed the distribution pattern of condensing in the two sides of the nuclei following the Raf/ERK activation. Coupled with scanning electron microscopy (SEM), the three imaging modes showed good agreement in cellular morphological changes and subcellular mitochondrial rearrangement without or following Raf/ERK activation, demonstrating an integrated approaching to study the biological processes at subcellular dimension.

Made available in DSpace on 2016-12-12T20:27:39Z (GMT). No. of bitstreams: 1 Heric Denis Farias.pdf: 2196819 bytes, checksum: ebe776ba26727b6ab81d9c4b1fb49e5d (MD5) Previous issue date: 2016-09-25 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / The application of high electric fields on biological cells causes the formationof pores in the cell membrane, thereby causing an increase in their permeability. This phenomenon, called electropermeabilization have attracted increasing attention due to its wide application in biotechnology. Even being known for decades, the pore opening process in biological cell membranes is still not fully understood, nor was it even properly modeled. In this paper, two types of modeling are presented, which allow characterizing the electropermeabilization in biological cell suspensions. One of the methods is based on the analysis of the electrical impedance spectra of suspensions using genetic algorithm to determine parameters of a generic model dielectric dispersion. The other method uses instantaneous voltage and current values applied to a cell suspension during the electroporation experiment to determine the variation of the medium conductivity and thus, through the analytical model proposed by Ramos and colleagues (RAMOS et al., 2012), determine the cell conductivities. By modeling the impedance spectrum, it was observed the change in the dielectric dispersion of the sample due to the electropermeabilization process, in addition to obtaining the electrical conductivity and permittivity of the involved media. Using the electroporated cell model proposed by Ramos and colleagues (RAMOS et al., 2012), it was possible to determine the change of membrane conductance during the electropermeabilization. The validity of this model is assessed using finite element simulations, which showed good agreement with the analytical model used. Genetic algorithms are used in obtaining the parameters of the various models presented, showing great robustness in obtaining parameters based on the git between experimental and theoreticalcurves. / A aplicação de campos elétricos intensos em células biológicas provoca a formação de poros na membrana celular, causando assim o aumento de sua permeabilidade. Este fenômeno, denominado de eletropermeabiliza ção têm atraído cada vez mais atenção devido a sua ampla aplicação em biotecnologia. Mesmo sendo conhecido há várias décadas, o processo de abertura de poros em membranas de células biológicas ainda não é plenamente entendido e nem foi ainda corretamente modelado. Neste trabalho, apresenta-se dois tipos de modelagem que permitem a caracterização da eletropermeabilização em suspensões de células biológicas. Um dos métodos baseia-se na análise do espectro de impedância elétrica de suspensões com o uso de algoritmo genético para determinar parâmetros de um modelo genérico de dispersão dielétrica. O outro método utiliza valores instantâneos de tensão e corrente aplicados em uma suspensão de células durante um experimento de eletropermeabiliza ção para determinar a variação da condutividade do meio e com isso, através do modelo analítico proposto por Ramos e colaboradores (RAMOS et al., 2012), determinar a condutividade das células. Através da modelagem do espectro de impedância, foi possível verificar a alteração da dispersão dielétrica da amostra devido ao processo de eletropermeabiliza ção, além da obtenção das condutividades e permissividades elétricas dos meios envolvidos. Utilizando o modelo de célula eletropermeabilizada proposto por Ramos e colegas (RAMOS et al., 2012), foi possível obter a variação da condutância de membrana durante a eletropermeabilização. A validade deste modelo é avaliada utilizando simulações em elementos infinitos, as quais apresentaram grande concordância com o modelo analítico utilizado. Algoritmos genéticos são utilizados na obtenção dos parâmetros dos diversos modelos apresentados, mostrando grande robustez na obtenção de parâmetros baseada no ajuste entre curvas experimentais e teóricas.

Parmi les nanoparticules aptes à accompagner la radiothérapie en clinique, les nanoparticules à base d’oxyde de gadolinium paraissent pertinentes, de part leur multimodalité en imagerie et leur effet radiosensibilisant prouvé in vitro et in vivo. Cet effet de radiosensibilisation est exceptionnel notamment sur des cellules cancéreuses radiorésistantes de la lignée SQ20B (carcinome squameux tête et cou) et uniquement pour des doses modérées de nanoparticules (aux alentours de 0.6 mM en Gd). Les clichés de microscopie électronique ont montré que ce maximum de radiosensibilisation est dû à une internalisation maximale des particules dans le cytoplasme, notamment par macropinocytose. Ce mécanisme d’internalisation est caractérisé par la formation de vésicules de grandes tailles, ou macropinosomes. Il se produit suivant deux étapes : la formation d’agglomérats de nanoparticules à proximité de la membrane cellulaire puis la récupération de ceux-ci par les lamellipodes de la cellule. La première étape est fortement dépendante des caractéristiques physicochimiques des particules, plus particulièrement leur potentiel zêta qui détermine la taille de l’agglomérat, et de la distance les séparant de la cellule. Dans des gammes de taille et de distance à la membrane optimales aux concentrations modérées, l’agglomérat peut être récupéré par les lamellipodes de la cellule. Il s’en suit une protubérance sur la membrane plasmique formant un macropinosome contenant les agglomérats de nanoparticules. Cet endosome précoce suivra ensuite le schéma d’endocytose classique dans le cytoplasme en fusionnant avec des corps multivésiculaires, uniquement visible en microscopie électronique à transmission, pouvant contenir des enzymes de dégradation détruisant leur contenu. Ces enzymes rendent le pH acide à l’intérieur de la vésicule. Plus les nanoparticules sont proches du noyau cellulaire plus leur effet radiosensibilisant sera efficace. Les espèces oxygénées réactives (ROS) et les électrons Auger et secondaires peuvent atteindre l’ADN du noyau plus facilement. A faibles doses (<0.4 mM) très peu de nanoparticules sont internalisées et un effet linéaire de la radiosensibilisation est observé jusqu'à 0.6 mM. A fortes doses (> 0.7 mM) les nanoparticules forment une couronne autour de la membrane cellulaire agissant comme écran, empêchant ainsi les ROS et les électrons générés de pouvoir atteindre l’ADN et induire des cassures, le noyau étant situé à quelques micromètres de la membrane cellulaire. Les résultats obtenus ouvrent la voie sur la nécessité de contrôler l'internalisation cellulaire des nanoparticules en contrôlant leur chimie, laissant envisager ainsi des opportunités prometteuses dans le domaine de la radiothérapie assistée par nanoparticules délivrant de faibles doses de radiation aux patients. / Over the last few decades, nanoparticles have been studied in theranostic field with the objective of exhibiting a long circulation time through the body coupled to major accumulation in tumor tissues, rapid elimination, therapeutic potential and contrast properties. In this context, we developed sub-5 nm gadolinium-based nanoparticles that possess in vitro efficient radiosensitizing effects at moderate concentration when incubated with head and neck squamous cell carcinoma cells (SQ20B). Two main cellular internalization mechanisms were evidenced and quantified: passive diffusion and macro- pinocytosis. Whereas the amount of particles internalized by passive diffusion is not sufficient to induce in vitro a significant radiosensitizing effect, the cellular uptake by macropinocytosis leads to a successful radiotherapy in a limited range of particles incubation concentration. Macropinocytosis processes in two steps: formation of agglomerates at vicinity of the cell followed by their collect via the lamellipodia (i.e. the “arms”) of the cell. The first step is strongly dependent on the physicochemical characteristics of the particles, especially their zeta potential that determines the size of the agglomerates and their distance from the cell. These results should permit to control the quantity of particles internalized in the cell cytoplasm, promising ambitious opportunities towards a particle-assisted radiotherapy using lower radiation doses.

L’acoustique picoseconde est une technique qui permet de générer et de détecter des ondes acoustiques de longueur d’onde submicrométrique par l’utilisation d’impulsions lumineuses ultrarapides (100 fs). Si la technique commence à être appliquée industriellement pour le contrôle non-destructif de films solides micrométriques, comme les microprocesseurs, très peu d’études concernent son application aux milieux liquides ou mous, malgré son potentiel unique pour les mesures acoustiques très hautes fréquences (supérieur à la dizaine de GHz). Ce travail de thèse dresse un premier panorama d’applications possibles de la technique d’acoustique picoseconde pour l’étude d’une cellule biologique unique, dont l’épaisseur peut être d’une centaine de nanomètres à quelques micromètres. Les résolutions atteintes permettent des applications pour l’imagerie et la tomographie acoustique d’une cellule unique par la détermination locale de ses propriétés physiques. Un modèle de simulation analytique est développé pour aider à la compréhension des signaux détectés et pour la résolution du problème inverse. La génération acoustique est simulée en résolvant les équations couplées de diffusion de la chaleur et de la propagation acoustique. La détection optique est ensuite étudiée en résolvant l’équation de Maxwell où les phénomènes thermiques et acoustiques perturbent l’indice optique du matériau. Pour les besoins expérimentaux, une enceinte biologique, étanche et thermostatée, est conçue. De même, le montage laser est adapté pour permettre une détection bicolore de l’onde acoustique se propageant dans la cellule. Enfin, un microscope combinant la visualisation des cellules par épifluorescence au dispositif laser expérimental est développé. Ce dernier permet de localiser précisément les éléments subcellulaires de la cellule, pour ensuite les étudier par acoustique picoseconde. La démonstration du potentiel de la méthode pour l’imagerie cellulaire et l’évaluation de sa sensibilité est faite sur cellule végétale. Ensuite, une mesure quantitative des propriétés viscoélastiques de cellules ostéoblastes (MC3T3-E1), adhérentes sur un matériau mimant une prothèse de titane, est réalisée. Puis, l’effet du peptide RGD et de la protéine BMP-2 sur les propriétés viscoélastiques de la cellule ostéoblaste est quantifié. Ce travail est réalisé en partenariat avec une équipe de recherche en bio-ingénierie et reconstruction tissulaire, l’U577. / The picosecond ultrasonics technique is well suited to generate and to probe acoustic waves of submicromic wavelength using ultrafast light pulses (100 fs). If the technique starts to be used for non-destructive testing in industry, for micrometric solid films (microprocessor) for example, very few applications concern liquids or soft media, despite its unique potential for acoustic measurements at very high acoustic frequencies (up to ten GHz). This PhD study gives a first comprehensive overview of the applications of the picosecond ultrasonics technique for the study of a single biological cell, the thickness of which can be from around 100 nm to a few µm. Measurement accuracy is high enough for imaging a single cell and for evaluating its local physical properties. To understand the detected data, an analytical model is developed. This model is used too for the inverse model resolution. The acoustic generation is simulated solving the coupled equations of heat diffusion and of acoustic wave propagation. Optical detection is then studied solving the Maxwell equations where both thermal and acoustic phenomena perturb optical index of the media. For experiments, a biocompatible sample holder, leakproof and thermocontrolled, is built. In the same way, the optical experimental setup is adapted to allow a two color probing of the ultrafast photo-acoustic response in a single cell. Finally, a microscope combining cell fluorescence visualisation and the picosecond ultrasonic laser setup is developed. It allows to localize precisely the cell sub-components and to probe them by the picosecond ultrasonics technique. The demonstration of the technique for the single cell imaging and the evaluation of its accuracy is performed on vegetal cells. Then, a quantitative measurement of the viscoelastic properties of single osteoblast cells (MC3T3-E1), adhering on a bone substitute material (Ti6Al4V), is performed. RGD peptide and BMP-2 proteins effects on the cell osteoblast viscoelastic properties are quantified. This work is performed with a tissue or bone substitute engineering research team.