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’avènement de la microscopie biphotonique et des techniques dites de « super-résolution » ont permis d’améliorer les performances de la microscopie de fluorescence et de l’appliquer à l’imagerie intravitale et à l’analyse des tissus biologiques. Ces techniques requièrent néanmoins l’emploi de sondes aux propriétés optiques et biologiques optimisées.Plusieurs séries de colorants cationiques basés sur le motif vinyl-triphénylamine (TP) ont été développés pour le marquage d’ADN. Ces fluorophores rouges ou jaunes dont l’émission de fluorescence est commutée par l’interaction avec l’ADN sont des ligands de petit sillon de l’hélice B et possèdent des sections efficaces d’absorption à deux photons élevées.Les TP marquent l’ADN du noyau des cellules fixées ou en apoptose avec une intensité et un contraste élevés. Elles sont non-cytotoxiques, photostables et sont perméables à la membrane cellulaire. L’optimisation des propriétés a permis d’obtenir la TP-2Bzim, qui possède une brillance biphotonique parmi les plus élevées rapportées dans la littérature pour des molécules de faible poids moléculaire (383 GM) et permet une détection en microscopie biphotonique à basse concentration et à faible puissance d’excitation. En cellules vivantes, les TP sont localisées dans les mitochondries mais, sous excitation mono- ou bi-photonique constante, elles déclenchent l’apoptose de la cellule et se relocalisent dans le noyau. Le phénomène peut être imagé par fluorescence, et les TP pourraient donc être employées comme photosensibilisateurs théranostiques.Enfin, une stratégie de synthèse pour fonctionnaliser la TP-2Bzim a été développée. Elle a ainsi pu être couplée à des oligonucléotides et à un PNA pour la détection d’hybridation par fluorescence et à l’acide folique et à la spermidine pour le ciblage de cellules cancéreuses. / Significant advances were made in the field of in vivo fluorescence imaging thanks to the recent development of biphotonic microscopy and super-resolution techniques, rendering intravital imaging and biological tissues analysis possible. Those techniques however require the use of new probes with optimized optical and biological properties.Several series of cationic dyes for DNA staining were developed based on the vinyl-triphenylamine (TP) scaffold. Those new switchable yellow or red fluorophores bind in the minor-groove of DNA and display high two-photon absorption cross-sections. Two anionic derivatives were also designed for staining HSA.In fixed or apoptotic cells, the cationic dyes stain nuclear DNA with a high brightness and contrast. They are non-cytotoxic, photostable and cell permeant. The molecule with the most optimized properties, TP-2Bzim, has one of the highest two-photon brightness to date (383 GM in DNA), allowing sensible detection in biphotonic microscopy at low concentration and excitation power. In live cells, the dyes are localized in the mitochondria, but it appears that upon constant mono- or bi-photonic excitation they trigger cell apoptosis within a few minutes and are released in the nucleus. Since the phenomenon can be imaged by fluorescence microscopy, the TP dyes could thus be used as photosensitizers for theranostics.A synthetic pathway was also developed to functionalize the TP-2Bzim. It was then coupled by “click-chemistry” to short oligonucleotides or PNA sequences for fluorescence in situ hybridization, and to folic acid and spermidine for cancer cells targeting.

Photodynamic therapy (PDT) is an alternative treatment of cancer requiring the use of chromophore molecules (photosensitizers), which can induce cell death after light excitation. Gold nanoparticles (AuNP), exhibiting localized Surface Plasmon Resonance, can enhance the photophysical response of chromophores located in their vicinity, and thus improve their therapeutic action. Moreover, the use of highly localized two-photon chromophores (photosensitizers and fluorophores), capable to undergo a localized excitation by light in the Near InfraRed region, should increase the penetration depth into tissues, thus improve the treatment efficiency (by PDT) and the imaging (by fluorescence microscopy) of cancer tissues.In this work, we describe the elaboration of water-soluble hybrid nano-objects for PDT and fluorescence bioimaging applications, composed of two-photon chromophore-polymer conjugates grafted onto gold nanoparticles. In order to obtain these nano-objects we follow a multistep strategy: i) the synthesis of a well-defined water-soluble chromophore-polymer conjugates; ii) the end-group oriented grafting of chromophore-polymer conjugates onto 20 nm AuNP. The coupling of hydrophobic two-photon chromophores on linear water-soluble copolymer chains (poly(N-acryloylmorpholine-co-N-acryloxysuccinimide)), obtained by controlled/living RAFT polymerization, resulted in well-defined water-soluble chromophore-polymer conjugates, with different polymer lengths (2 000 g.mol-1 < Mn < 37 000 g.mol-1) and architectures (random or block), and a controlled number of chromophores per chain (varying between 1 and 21). Their grafting onto 20 nm AuNP gave water-soluble hybrid nano-objects with high grafting densities (~0.5 chains/nm²). The role of the polymer chain being to tune the distance between chromophores and AuNP surface, we have evidenced the increase in the polymer corona thickness of grafted AuNP (estimated by TEM) with the increasing polymer Mn, corroborating with the corresponding distance-dependent fluorescence properties of those. Finally, the in cellulo biological properties of two-photon chromophore-polymer conjugates, before and after grafting onto AuNP, have been investigated, highlighting their potential for two-photon bioimaging and PDT applications.

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Se describe la aplicación de pulsos láser ultracortos (≤10fs) en espectroscopía y microscopía de dos fotones llevada a cabo en nuestro grupo de investigación, subrayando las ventajas y requerimientos de este enfoque. Además se presenta una breve descripción de la manipulación de pulsos, de las distorsiones de fase experimentadas por los pulsos láser de femtosegundo y de cómo corregir tales distorsiones utilizando manipuladores de pulsos. / Femtosecond laser pulses in two-photon spectroscopy and microscopy: The application of shaped ultrashort laser pulses (≤10fs) in two-photon spectroscopy and microscopy carried out in our group is  described, highlighting the advantages and requirements of this approach. In addition, a brief description of pulse shaping, phase distortions experienced by femtosecond laser  pulses and how to correct these distortions using a pulse shaper is also presented.

No description available.

Le glioblastome (GB) est une tumeur hétérogène, agressive devant laquelle les possibilités thérapeutiques disponibles restent limitées. L’étude de la zone péritumorale macroscopiquement normale (ZMN) des GB est essentielle à la compréhension de ses mécanismes de progression et de récidive. Le premier objectif de ce travail de Thèse a été de comparer les données de transcriptomique et de protéomique issues de l’analyse de la zone tumorale des GB dans le cadre du Projet Gliome Grand Ouest. Le taux de concordance entre les 2 modalités est faible, retrouvant toutefois comme point commun une dysrégulation de la protéine légère des neurofilaments qui pourrait servir de biomarqueur potentiel des GB. Le deuxième objectif de ce travail de Thèse a été la caractérisation de la ZMN des GB. Nous avons mis en évidence que cette zone, dont l’aspect est similaire à première vue à celui du tissu cérébral sain, n’est pas une simple zone de transition entre le GB et le tissu cérébral sain. En effet, la ZMN est une entité spécifique possédant des caractéristiques qui lui sont propres, comme la présence d’un phénotype particulier de cellules tumorales infiltrantes et de cellules stromales et une sur’expression des protéines CRYAB et H3F3A. Ce travail de Thèse a aussi été l’occasion de développer de nouvelles techniques d’imagerie per-opératoire de la ZMN, afin d’évaluer la présence d’un contingent tumoral et ainsi optimiser la qualité de la résection chirurgicale. La caractérisation de cette ZMN nous permet de mieux appréhender son implication dans la tumorogenèse et la présence de caractéristiques spécifiques de cette zone ouvre la porte à la détection de biomarqueurs spécifiques, ainsi qu’au développement de thérapies ciblées. Ce travail de Thèse a été valorisé par 2 publications, 2 articles soumis et un brevet est en cours de dépôt et d’évaluation par un cabinet de brevet. / Glioblastoma (GB) is a heterogeneous andaggressive tumor, before which therapeutic options arelimited. The study of the macroscopically normalperitumoral brain zone (PBZ) of GB is essential tounderstand its mechanisms of progression andrecurrence.The first objective of this thesis work was tocompare the transcriptomic and proteomic data from theGB tumor area obtained through the “Grand Ouest”glioma Project. The concordance rate between the 2modalities is low. However, one of the common featureis the dysregulation of neurofilament light polypeptide,which could serve as a biomarker potential of GB.The second objective of this thesis was thecharacterization of the PBZ. We have shown that thisarea, similar at first glance to that of healthy braintissue, is not a simple transition area between the GBand healthy brain tissue but a specific entity withcharacteristics of its own. For example, the ZMNpresents a particular phenotype of infiltrating GB cellsand stromal cells and a surexpression of CRYAB andH3F3A proteins.This thesis work was also an opportunity todevelop new intraoperative imaging techniques of thePBZ, with the aim to assess the presence of a tumoralinfiltration and optimize the quality of the surgicalresection.The characterization of this PBZ allows us tobetter understand its involvement in tumorigenesis andthe presence of specific characteristics of this areaopens the door for the detection of specific biomarkersand the development of targeted therapies.This thesis work was led to 2 publications, 2articles submitted and a patent being evaluated andredacted by a patent office.

Neurogenesis is the process of generation of neurons during embryonic development and adulthood. The focus of this doctoral work is the study of the cell biological aspects of neurogenesis and the mechanisms regulating the switch of neural stem cells from proliferation to differentiation. During embryonic development neurogenic divisions occur at the apical or basal side of the pseudostratified epithelium that forms the wall of the neural tube, the neuroepithelium. Apical asymmetric neurogenic divisions (AP) give rise to a neuron and a progenitor cell, while basal symmetric neurogenic divisions (BP) give rise to two neurons. The first part of this thesis is focused on the study of some cell biological aspects of BPs. We first validated the use of the Tis21-GFP knock in mouse line, previously generated in our laboratory. We found that the totality of neurogenic progenitors is marked by the expression of a nuclear GFP. We calculated the abundance of BPs overtime since the onset of neurogenesis showing that BPs overcome APs over development. We studied the loss of apical contact of the basal dividing cells. We found that both neurogenic and non-neurogenic basally dividing progenitors miss the apical contact; which is lost prior mitosis. We generated and characterized a second mouse line, the Tubb3-GFP line expressing a plasma membrane-localized GFP in neurons. These two lines were crossed to obtain a new line (TisTubb-GFP) allowing detection of neurogenic divisions and tracking daughter cells. Using this model: (i) we imaged symmetric neurogenic divisions of BPs, identifying daughter cells as neurons, during imaging; (ii) we compared the kinetics of betaIII-tubulin-GFP appearance after apical or basal mitosis, showing that daughters of BPs express betaIII-tubulin-GFP faster than daughters coming from apical divisions; (iii) we imaged neuronal migration and localization of the Golgi apparatus. Neurogenesis in the adult is confined to two specific regions in the telencephalon: the sub ependymal zone, lining the ventricle, and dentate gyrus of the hippocampus. The second part of this thesis focuses on the adult neurogenic progenitors lineage. Tis21-GFP expression was found and characterized in the two adult neurogenic regions from early postnatal to adulthood. Using a panel of markers for the adult neurogenic cell lineage and confocal imaging, we characterized Tis21-GFP expression, in the dentate gyrus. Tis21-GFP is first expressed in the neurogenic subpopulation of doublecortin positive cells. Tis21-GFP is inherited by the neurons and eventually degraded. Moreover, our data suggest that mitotic Tis21-GFP cells are an indicator of the levels of neurogenesis more accurate than doublecortin positive cells, in the early postnatal mouse. (Anlage Quick time movies 77,88 MB)

It is emerging that the brain’s vasculature consists of a highly spatially heterogeneous network; however, information on how various vascular characteristics differ between brain regions is still lacking. Furthermore, aging studies rarely acknowledge regional differences in the changes of vascular features. The density of the capillary bed is one vascular feature that is important for the adequate delivery of nutrients to brain tissue. Additionally, capillary density may influence regional cerebral blood flow, a parameter that has been repeatedly correlated to cognitive-behavioural performance. Age-related decline in capillary density has been widely reported in various animal models, yet important questions remain concerning whether there are regional vulnerabilities and what mechanisms could account for these regional differences, if they exist. Here we used confocal microscopy combined with a fluorescent dye-filling approach to label the vasculature, and subsequently quantified vessel length, tortuosity and diameter in 15 brain regions in young adult and aged mice. Our data indicate that vessel loss was most pronounced in white matter followed by cortical, then subcortical gray matter regions, while some regions (visual cortex, amygdala, insular cortex) showed little decline with aging. Changes in capillary density are determined by a balance of pruning and sprouting events. Previous research showed that capillaries are naturally prone to plugging and prolonged obstructions often lead to vessel pruning without subsequent compensatory vessel sprouting. We therefore hypothesized that regional susceptibilities to plugging could help predict vessel loss. By mapping the distribution of microsphere-induced capillary obstructions, we discovered that regions with a higher density of persistent obstructions were more likely to show vessel loss with aging and vice versa. Although the relationship between obstruction density and vessel loss was strong, it was clear obstruction rates were insufficient to explain vessel loss on their own. For that reason, we subsequently used in vivo two-photon microscopy to track microsphere-induced capillary obstructions and vascular network changes over 24 days in two areas of cortex that showed different magnitudes of vessel loss and obstruction densities: visual and retrosplenial cortex. Surprisingly, we did not find evidence for differences in vessel pruning rates between areas, as we would have expected. Instead, we observed brain region-specific differences in recanalization times and rates of angiogenesis. These findings indicate that age-related vessel loss is region specific and that regional susceptibilities to capillary plugging and angiogenesis must be considered to explain these differences. Altogether, this work supports the overarching hypothesis that regional differences in vascular structure and function contribute to a regionally heterogeneous phenotype in the aging brain. / Graduate

Indiana University-Purdue University Indianapolis (IUPUI) / Introduction: Multiphoton fluorescence excitation microscopy (MPM) is an invaluable tool for studying processes in tissue in live animals by enabling biologists to view tissues up to hundreds of microns in depth. Unfortunately, imaging depth in MPM is limited to less than a millimeter in tissue due to spherical aberration, light scattering, and light absorption. Spherical aberration is caused by refractive index mismatch between the objective immersion medium and sample. Refractive index heterogeneities within the sample cause light scattering. We investigate the effects of refractive index mismatch on imaging depth in MPM. Methods: The effects of spherical aberration on signal attenuation and resolution degradation with depth are characterized with minimal light absorption and scattering using sub-resolution microspheres mounted in test sample of agarose with varied refractive index. The effects of light scattering on signal attenuation and resolution degradation with depth are characterized using sub-resolution microspheres in kidney tissue samples mounted in optical clearing media to alter the refractive index heterogeneities within the tissue. Results: The studies demonstrate that signal levels and axial resolution both rapidly decline with depth into refractive index mismatched samples. Interestingly, studies of optical clearing with a water immersion objective show that reducing scattering increases reach even when it increases refractive index mismatch degrading axial resolution. Scattering, in the absence of spherical aberration, does not degrade axial resolution. The largest improvements in imaging depth are obtained when both scattering and refractive index mismatch are reduced. Conclusions: Spherical aberration, caused by refractive index mismatch between the immersion media and sample, and scattering, caused by refractive index heterogeneity within the sample, both cause signal to rapidly attenuate with depth in MPM. Scattering, however, seems to be the predominant cause of signal attenuation with depth in kidney tissue. Kenneth W. Dunn, Ph.D., Chair