The study of cellular migration dynamics and strategies plays a relevant role in the understanding of both physiological and pathological processes. An important example could be the link between cancer cell motility and tumor evolution into metastatic stage. These strategies can be strongly influenced by the extracellular environment and the consequent mechanical constrains. In this framework, the possibility to study the behavior of single cells when subject to specific topological constraints could be an important tool in the hands of biologists. Two-photon polymerization is a sub-micrometric additive manufacturing technique that allows the fabrication of 3D structures in biocompatible resins, enabling the realization of ad hoc biochips for cell motility analyses, providing different types of mechanical stimuli. In our work, we present a new strategy for the realization of multilayer microfluidic lab-on-a-chip constructs for the study of cell motility which guarantees complete optical accessibility and the possibility to freely shape the migration area, to tailor it to the requirements of the specific cell type or experiment. The device includes a series of micro-constrictions that induce different types of mechanical stress on the cells during their migration. We show the realization of different possible geometries, in order to prove the versatility of the technique. As a proof of concept, we present the use of one of these devices for the study of the motility of murine neuronal cancer cells under high physical confinement, highlighting their peculiar migration mechanisms.

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Caged compounds are a class of photosensitive reagents used to stimulate cells with spatial control down to a sub-cellular level, and millisecond temporal control. They comprise of biologically important molecule which is modified with a photolabile protecting group. In the absence of light, caged compounds are physiologically silent but irradiation with light induces the release of biologically active species. Illumination under two-photon conditions is particularly advantageous as it enables restriction of the photolysis volume to ~1 fL and it provides deeper penetration into scattering samples. This thesis reports the development of new protecting groups for two-photon uncaging in neuroscience. Mechanistically, the deprotection in these novel groups is designed to operate via an intramolecular photoinduced electron transfer (PeT) between the absorbing unit (electron-donor) and the release module (electron-acceptor). The modular design of these cages ensures separation of absorption and release steps, and allows each process to be tuned and optimized independently. Chapter 1 provides an introduction to the two-photon absorption phenomenon and a historic overview of the uncaging technique. It also discusses recent advances in the development of two-photon sensitive probes used in neuroscience. Chapter 2 describes the exploration of molecular designs for novel protecting groups. A two-photon absorbing dye (electron-donor; fluorene dye) and three different release units (electron-acceptors; nitrobenzyl, pyridinium and phenacyl) were identified as suitable building blocks for the current project. Efficiency of the intramolecular electron transfer between chosen units was evaluated using model dyads which constitute covalently linked electron-donor and acceptor species. Chapter 3 is devoted to the synthesis and photophysical evaluation of nitrobenzyl-based protecting group. Chapter 4 describes the preparation of pyridinium-derived protecting group and demonstrates PeT-mediated release of tryptophan and GABA under one- and two-photon excitation. Hydrolytic instability of pyridinium esters is highlighted. Chapter 5 reports the synthesis, hydrolytic stability and one-photon uncaging efficiency of phenacyl-based derivatives. Chapter 6 discusses properties of developed caged compounds and compares them with other compounds reported in literature. It contains overall conclusions and outlook for the current project. Chapter 7 details the experimental procedures and the characterization of compounds synthesized during this work.

The work of this dissertation has been to prove that the coherence of multiphoton excitation can be studied by an appropriately phased and time delayed sequence of pulses. An application of this fundamental study of coherence has been made for the enhancement of third harmonic generation. The coherent recovery of the energy lost to the two photon absorption process enalled a larger propagation distance for the fundamental than in an interaction which is incoherent or coherent, but not using a 90 degree phase shifted pulse pair. Phase matching over this longer propagation distance gave an enhancement of third harmonic generation.

L’avènement des lasers impulsionnels nanosecondes à femtosecondes a permis un développement rapide de techniques permettant de sonder et/ou de transformer les matériaux à l’échelle locale par des processus d’absorption non linéaire. Ce saut technologique a vu l’émergence de nombreuses applications associées au phénomène de confinement spatial. La stéréolithographie 3D par photopolymérisation biphotonique constitue un exemple typique d’application à forte valeur ajoutée qui offre de prometteuses perspectives en terme d’écriture à l’échelle nanométrique. Un enjeu fondamental constitue alors l’élaboration de nouveaux photoamorceurs très réactifs et activables à deux photons. Dans ce contexte, ce manuscrit présente une étude photophysique et photochimique de deux séries de photoamorceurs biphotoniques ‘Donneur/Accepteur’ intégrants des stilbènes comme relais électroniques avec pré-organisation dans des structures bichromophores. Les processus primaires photoinduits, les mécanismes de photoamorçage, la photoréactivité à l’echelle locale sont décrits et étudiés méthodiquement. Enfin, le potentiel appliqué de cette nouvelle génération de photoamorceurs est mis en évidence en microfabrication multiphotonique à travers l’élaboration de structure 3D à l’échelle µm. / The advent of pulsed laser technologies has promoted the rapid growth of new emerging research domains which aim at probing and/or transforming materials at local scale using non linear absorption processes. A large range of applications takes benefit of the inherent spatial containment observed in non linear absorption processes so as to control photoreactions at nm-scale. The field of multiphoton fabrication (or stereolithography) addresses this fundamental issue and has developed rapidly so that it is no longer a rapid prototyping technology but a real manufacturing technique that is commercially available. The development of multiphoton stereolitography also requires highly reactive two-photon activable (2PA) initiators whose design and elaboration are the subject of considerable molecular engineering research. In this context, the present manuscript describes the photophysical and photochemical properties of two series of 2PA initiators. Such novel D--A structures have be designed by associating distinctive Donor and Acceptor groups into stilbene arms used as ‘electron relay’ and organized into a (multi)branched architecture. The photoinduced primary processes, the global photoinitiating mechanisms as well as the photoreactivity are described methodically. We finally demonstrate the applied potential of this new type of two-photon initiators in multiphoton stereolitography.

La "cryopolymérisation" permet d'obtenir des gels de polymère macroporeux ou "cryogels". Cette méthode a été utilisée pour la synthèse d'hydrogels thermosensibles à base de pNIPA. La température critique TC correspondant à la transition de volume a été déterminée par des mesures de taux de gonflement et par DSC. La macroporosité (distribution de la taille des pores et épaisseur des parois) et son évolution en fonction de T ont été étudiées par la microscopie biphotonique donnant des informations à l'échelle du µm à plusieurs dizaines de µm. La diffusion de rayons X (SAXS et WAXS) a été utilisée pour caractériser la structure multi-échelle (de quelques dixièmes à quelques dizaines de nm) du gel constituant les parois des macropores. Les courbes de diffusion ont été décrites analytiquement. L'évolution des dix paramètres contenus dans l'équation a été étudiée en fonction de T et discutée. Enfin, des expériences utilisant les phonons hyperfréquences générés par la technique des réseaux transitoires avec détection hétérodyne (HD-TG) ont été réalisées. Ces mesures ont permis de déterminer la vitesse de propagation de l'onde ultra-sonore (à 340 MHz), son atténuation, et la constante de diffusion thermique à différentes températures. / "Cryopolymerisation" yields macroporous gels named "cryogels". The method was used to synthesise thermosensitive pNIPA based hydrogels. The critical temperature TC corresponding to the volume phase transition was determined by swelling ratio measurements and DSC. The macroporosity (pore size distribution and wall thickness) and its change with temperature, was investigated by two-photon microscopy yielding information at the micrometer scale (a few tenths to tens of micrometers). X-ray scattering (SAXS and WAXS) was used to characterise the multi-scale structure of the gel forming the pore walls. The scattering curves were described analytically. The variation with temperature of the 10 parameters contained in the equation was investigated and discussed. Finally, heterodyne detected transient grating experiments were performed on a bulk pNIPA gel. These measurements allowed the determination of the speed of the ultrasonic wave (at 340 MHz), its attenuation and the thermal diffusion constant in the gel at different temperatures.

4 Abstract The present thesis focuses on testate amoebae (TA) and their relationship to their natural environment, as well as on relevant microscopic imaging methods. The bulk of the data has been published in original scientific papers and is compiled into three separate chapters (Pt I, Pt II and Pt III), each annotated by a brief introduction. (Pt I) The methods section is devoted to specialized microscopic techniques employed to broaden the scope of the ecological analyses. In particular, precise discrimination between live and dead individuals, biomass determination inside individual tests and a multi-modal visualization of the cytoplasm and organelles enhance the data. Laser scanning confocal microscopy and two-photon microscopy are the main imaging modalities employed to study TA morphology in detail. The data have implications for taxonomy and ecophysiology, including the use of TA as bioindicators of pollution. (Pt II) An actuoecological analysis focuses on the seasonal variability of TA species composition in a freshwater ecosystem, namely the Komo any ponds in Prague, during the course of the year. The species composition variation is correlated to simultaneously recorded limnological parameters such as temperature, pH, contamination by (heavy) metals (As, Cd, Mn, Ni, Fe, Pb), polycyclic aromatic...

Univerzita Karlova v Praze Přírodovědecká fakulta Studijní program: Vývojová biologie (P1520) Studijní obor: Vývojová biologie (1501V000) Oleksandr Chernyavskiy Zdokonalené metody pro snímání obrazových dat a analýzu tkání a buněk pomocí konfokální a multifotonové mikroskopie Improved Methods of Image Acquisition and Analysis of Tissues and Cells by Confocal and Multi-Photon Microscopy Abstrakt disertační práce Školitel: RNDr. Lucie Kubínová CSc Praha, 2015 Abstract The aim of this study was to develop methods and approaches for image acquisition with subsequent image analysis of data, obtained by confocal and two- photon excitation microscopy as well as their combination, enabling new possibilities of visualization and assessment of information on biological tissues and cell structures in 3D and their measurement. We focused on methods that exploited advantages of confocal and multi-photon excitation microscopy. Our further aim was to demonstrate the applicability of non-invasive approach for in vivo applications, usefulness and the relevance of these methods in several special biological applications with emphasis on improved image acquisition, analysis and evaluation of real biological specimens. The present work was not oriented on just one specific biological problem, but rather to methodological...

L’objectif de cette thèse a été de synthétiser, caractériser et évaluer l’efficacité de photosensibilisateurs (PS) activables par excitation mono- et bi-photonique pour la thérapie photodynamique (PDT). Les PSs sont des dérivés de porphyrines qui ont été associés à différents composés incluants des sondes d’imagerie, des vecteurs, ou des nanoparticules, dans le but d’améliorer l’efficacité du traitement. Un PS a ainsi été relié à deux complexes de Gd(III) pour former un agent moléculaire théranostique afin de pouvoir suivre l’évolution de la PDT par imagerie par résonance magnétique (IRM). Cet agent théranostique conserve les bonnes propriétés photophysiques du PS et sa relaxivité remarquable permet l’imagerie à des concentrations plus faibles que les agents de contraste commerciaux. L’association d’un PS avec un vecteur, l’acide folique ou la biotine, a permis d’augmenter la sélectivité envers les cellules cancéreuses. L’augmentation de la phototoxicité envers des cellules HeLa pour ces deux PSs par rapport au PS non vectorisé montre le potentiel de ces deux PSs vectorisés pour la PDT par excitation mono et bi-photonique. Enfin, plusieurs PS ont été liés ou incorporés dans des cubosomes pour améliorer leur biodistribution et leurs phototoxicités ont été étudiées. Ces études montrent pour la première fois la possibilité d’utiliser des cubosomes comme formulation pour les PSs. / The aim of this thesis was to synthesize, characterize and evaluate the efficiency of new photosensitizers (PS) for Photodynamic Therapy (PDT) activated by a one- or two-photon absorption. Theses PSs are composed of π-extended porphyrins linked to imaging probes, targeting moieties or nanoparticles to improve the treatment efficiency. A PS was linked to two Gd(III) complexes to form a molecular theranostic agent allowing the monitoring of the PDT outcome by Magnetic Resonance Imaging (MRI). This molecular theranostic agent retains the good photophysical properties of the PS and its high relaxivity allows the imaging at a lower concentration than the commercial contrast agents. In order to increase the selectivity towards cancer cells a PS was linked to folic acid or biotin, two targeting compounds. The increase of the phototoxicity towards HeLa cells of these two targeted PSs compared to a non-targeted PS reveals the potential for one- and two-photon PDT. Finally, several PSs have been linked to cubosomes to increase the biodistribution and their phototoxicity has been investigated. This study shows for the first time that cubosomes can be used as a formulation for PSs.