Microchimerism arises from the exchange of cells between genetically distinct individuals. The coexistence of genetically distinct cell populations within a single organism has possible effects on health and functioning of individuals immune systems, but the exact mechanisms of action are often not yet known. With the development of microscopic technologies and software for data analysis, the possibilities of detection and phenotyping of these rare cell populations are expanding. My intention in this work is to find maternal microchimerism in embryonic tissues (E13) and intestines of breastfed pups using MHCII/EGFP knock-in mouse model. Several different technologies potentially suitable for the detection of maternal microchimeric cells in offspring tissues (light sheet fluorescent microscopy - LSFM, virtual slide microscopy and flow cytometry) were selected. Advanced analysis of the obtained samples from the light sheet microscopy using the creation of a neural network was used here. The presence of maternal microchimerism was not demonstrated by flow cytometry. Using LSFM, image data were obtained from intestinal samples of suckling pups, which were processed by the neural network method. Data analysis of embryos (E13) obtained by the same method did not allow data analysis due to high...

This thesis presents the recent progress of diffusion measurements in nanoporous host systems by micro-imaging. Interference microscopy is applied as a powerful tool to record transient, intracrystalline concentration profiles of different sorbate species in the porous framework of two different zeolites, viz. ZSM-5 (MFI) and ZSM-58 (DDR). These profiles, yielding high temporal and spatial resolutions of about 10 s and 0.45 μm, follow the change of the refractive index of the host-guest system during uptake and release of certain guest molecules. With the thus accessible changes of concentration and particle fluxes, mass transport parameters, such as intracrystalline diffusivity and surface permeability, can be obtained by the use of the very fundamental equations on diffusion. Additionally, in two examples of never before performed types of experiments, further insights into challenging fields of host-guest interactions are provided: The well known phase transition in MFI type zeolites covering high benzene loadings is investigated in a single crystal study, allowing to follow the change of the sorbate phase in great detail. Furthermore, in DDR zeolites, a new way of data analysis facilitates to study the uptake and release of binary mixtures. Here, from the two-dimension profiles obtained by interference microscopy, the local concentrations of the sorbate species could be retrieved by using the so-called ideal adsorbed solution theory.

Streptomyceten sind in der Lage verschiedene, schwer zugängliche Naturstoffe abzubauen. Darunter stellt das Chitin, aufgrund der chemischen Zusammensetzung, nicht nur eine Kohlen-, sondern auch eine wichtige Stickstoff-Quelle dar. Neben den vielfältigen Chitinasen wird dem chitinolytischen System von Streptomyceten eine neue Klasse von Proteinen zugewiesen, die spezifisch verschiedene Formen des kristallinen Chitins sowie Chitosan erkennen und mit unterschiedlichen Affinitäten an sie binden. Das CHB1-Protein (18,7 kDa) zeigt eine starke Tendenz zu Aggregatbildung. Die biochemischen Untersuchungen lassen schließen, dass intermolekulare Disulfidbrücken dabei eine eher unwesentliche Rolle spielen und deuten auf hydrophobe Wechselwirkungen als Ursache der CHB1-Aggregierung hin. Vergleichsstudien mit CHB1-Deletionsmutanten demonstrierten, dass die Aggregation durch N- und C-terminale Domänen nicht beeinflusst wird. Die Bindestudien zeigten die Wichtigkeit der beiden Domänen für die Chitinerkennung. Eine Computervorhersage zeigte in CHB1 ein hohes Potential für die N- bzw. O-Glykosylierung von mehreren N- und T-Resten, darunter auch eines NXS/T-Glykosylierungs-Motivs. Vorläufige weitere Studien lassen eine Verknüpfung des Proteins mit kurzen Oligosacchariden vermuten. Fluoreszenzmikroskopische in situ Untersuchungen der Co-Kulturen von Streptomyceten und Mucor rouxii ermittelten eine enge Interaktion von CHB1 und chitinhaltigen Pilz-Hyphen, die als neues Subprinzip der Biofilm-Entwicklung definiert werden kann. Durch Anwendung von CHB1 wurde auch ein neuer, spezifisch für hoch assoziierte Chitin-Assemblierungen Test für Chitinsynthase-Aktivität entwickelt, welcher eine schnelle Identifizierung von Chitinsynthase-Proben ermöglicht. CHB1 wurde als Hilfsmittel in Studien zur Chitin-Biogenese in Saccharomyces cerevisiae eingesetzt.

Unicellular algae (microalgae) are able to produce a number of substances such as starches, oils, proteins, carotenoids, polyphosphates, or crystalline purines directly from inorganic sources by photosynthesis. Different species of microalgae can be used for the economic production of various biomolecules. Due to their autotrophic nature, microalgae are also unique as they can synthesize complex isotopically labeled biomolecules from simple isotopically labeled inorganic substances. Analysis of the chemical composition of microalgae by means of chemical-analytical methods is relatively complex, time-consuming, and laborious. Confocal Raman microscopy represents one of the optical methods by which the chemical composition of microalgae can be determined in situ, i.e. directly within intact cells. This technique combining confocal optical microscopy with Raman spectroscopy enables fast and non- destructive analysis of the chemical composition of substances in the investigated objects, including the effect of isotopic labeling. The chemical composition of the investigated objects is reflected by their Raman spectra, in the case of Raman mapping of microscopic objects by their chemical maps. In this work, a specific case of isotopic labeling was studied, namely the effect of heavy water (D2O) on the deuteration...

The master´s thesis deals with the study of optical properties of thin transparent layers on the organic materials (PPV, P3HT, TiO2, DPP) and especially with the determination of dispersion dependences of refractive index of prepared thin layers. In the theoretical part there are described principles of deposition thin layers of the analyzed materials and their properties. In addition, there are also described methods of optical properties measurements (optical and interference microscopy and ellipsometry). The combination of interference microscope with digital camera was used for determination of refractive index. The image analysis was used for the determination of parameters (with help of the software HarFA). The images of thin layers surfaces were analyzed from the side of the metal contact as well as from the side of glass. In conclusion, there are presented results of the refractive index of the thin layers obtained from the measured values.

During operational conditions of internal combustion turbines of turbojet engines, the impeller are stressed by load cycles which vary in time, temperature and stress. In the course of operation, the blades are exposed to a considerable number of degradation effects, particularly high-temperature corrosion, fatigue processes and creep. The presented work is aimed at the study of the structure cast nickel-base superalloy INCONEL 713 LC, creep tests exposured. The structural changes (degradation) was clasification by the help of image analyses. Operational conditions of heat parts, used in gas turbines and turbo-compressors, were simulated by creep tests of Inconel 713 LC nickel superalloy during a constant load of temperatures ranging from 750 up to 950°C. Changes in the structure dependent upon time, temperature and stress applied were analysed by means of light and electron microscopy methods and image analyses after the fracture of test bars.

The thesis is aimed at the characterization of carbon nanotubes and silver nanowires by Scanning Probe Microscopy, namely Scanning Tunneling Microscopy (STM), Atomic Force Microscopy (AFM), Conductive AFM (CAFM) and Scanning Near-Field Optical Microscopy (SNOM). Carbon nanotubes were analyzed by STM, AFM and CAFM microscopy. In a designed apparatus the silver nanowires were fabricated by template assisted deposition and were analyzed with respect to their geometry (AFM), local conductivity (CAFM) and optical properties (SNOM, microreflex spectroscopy). It was found that preferential type of carbon nanowires depends on the fabrication process. The measurements of local conductivity of the nanotubes revealed the similarity with the STM measurements. The AFM measurements of silver nanowires confirmed their growth inside the pores of polycarbonate template. Single nanowires exhibits the semiconducting behavior according to I--V measurement and localized plasmon resonances.

Cryogenic electron microscopy (cryo-EM) is an evolving field allowing molecular visu- alizations with picometer resolutions. Images are acquired by shooting electrons through molecular samples and detecting the scattered electrons. From such data, 3D shapes of the molecules can be inversely reconstructed. Currently, describing and simulating the cryo-EM image formation is based either on naive transmittance models or complicated wave-function formalisms. In this thesis, we explore the possibility of simulating cryo-EM image formation via Monte Carlo electron tracing. We combine a delta-tracking algorithm with an elec- tron elastic differential cross-section function and Rutherford formulae to derive two Monte Carlo estimators. The derived models are implemented in a high-performance C++/CUDA environment and compared with other common models. Our particle-based simulated images show considerable similarity to the wave-based state-of-the-art multi- slice model. We also evaluate our models on class averages of real measurements. Both of our proposed models have significantly higher normalized cross-correlation scores with the measured class averages when compared to the most commonly used transmittance model. The thesis proves the viability of a particle-based Monte Carlo simulation of elec- tron microscope...

Fluorescence microscopy is an invaluable technique for studying the intricate process of organism development. The acquisition process, however, is associated with the fundamental trade-off between the quality and reliability of the acquired data. On one hand, the goal of capturing the development in its entirety, often times across multiple spatial and temporal scales, requires extended acquisition periods. On the other hand, high doses of light required for such experiments are harmful for living samples and can introduce non-physiological artifacts in the normal course of development. Conventionally, a single set of acquisition parameters is chosen in the beginning of the acquisition and constitutes the experimenter’s best guess of the overall optimal configuration within the aforementioned trade-off. In the paradigm of adaptive microscopy, in turn, one aims at achieving more efficient photon budget distribution by dynamically adjusting the acquisition parameters to the changing properties of the sample. In this thesis, I explore the principles of adaptive microscopy and propose a range of improvements for two real imaging scenarios. Chapter 2 summarizes the design and implementation of an adaptive pipeline for efficient observation of the asymmetrically dividing neurogenic progenitors in Zebrafish retina. In the described approach the fast and expensive acquisition mode is automatically activated only when the mitotic cells are present in the field of view. The method illustrates the benefits of the adaptive acquisition in the common scenario of the individual events of interest being sparsely distributed throughout the duration of the acquisition. Chapter 3 focuses on computational aspects of segmentation-based adaptive schemes for efficient acquisition of the developing Drosophila pupal wing. Fast sample segmentation is shown to provide a valuable output for the accurate evaluation of the sample morphology and dynamics in real time. This knowledge proves instrumental for adjusting the acquisition parameters to the current properties of the sample and reducing the required photon budget with minimal effects to the quality of the acquired data. Chapter 4 addresses the generation of synthetic training data for learning-based methods in bioimage analysis, making them more practical and accessible for smart microscopy pipelines. State-of-the-art deep learning models trained exclusively on the generated synthetic data are shown to yield powerful predictions when applied to the real microscopy images. In the end, in-depth evaluation of the segmentation quality of both real and synthetic data-based models illustrates the important practical aspects of the approach and outlines the directions for further research.

Die Keimstreifverlängerung der Malacostraca wird durch ein festgelegtes Zellteilungsmuster der posterioren Teilungszone erreicht. Dort geben anfangs in einem Halbkreis angeordnete Ektoteloblasten ihre Tochterzellen nach anterior ab, welche das für malakostrake Krebse typische Gittermuster ausbilden. Dabei spielen die Ektoteloblasten eine besondere Rolle, da sie das Zellmaterial für die anschließende Segmentierung produzieren. Im Gegensatz zu Vertretern basal abzweigender Taxa der Malacostraca, bei denen sich der Halbkreis der Ektoteloblasten aus zwei Halbreihen oder aus einem Zellring bildet, sind bei den Isopoden, zu denen auch die Kellerassel Porcellio scaber zählt, die Ektoteloblasten von Beginn an in einem Halbkreis angeordnet. Das Teilungsmuster bei der Verlängerung des Keimstreifens wurde bereits bei vielen Vertretern der Malacostraca, einschließlich P. scaber, ausführlich untersucht. Daten über die Bildung der Ektoteloblasten und den Beginn ihrer Teilungsaktivität fehlen dagegen weitestgehend. Im Rahmen der vorliegenden Arbeit wurde daher mit Hilfe von Zellmarkierungsversuchen mit Vitalfarbstoffen (wie z.B. Alexa Fluor 488 und Tetramethylrhodamin) und der 4D-Mikroskopie die Bildung der Keimscheibe, die Gastrulation und der Beginn der Keimstreifverlängerung bei P. scaber untersucht. Ein besonderer Fokus lag dabei auf den Ektoteloblasten und den umliegenden Zellen, deren Zelllinien untersucht wurden. Wie in der vorliegenden Arbeit gezeigt werden konnte, sind (i) die Ektoteloblasten bereits vor Beginn der Gastrulation in einem äußeren Halbkreis formiert, (ii) zwei Zellen, die Teile der späteren Mittellinie bilden, bis kurz vor Beginn der Teilungstätigkeit der Ektoteloblasten in deren Reihe eingereiht, (iii) die Ektoteloblasten erst mit der Fertigstellung der ersten e-Reihe als große, verlängerte Zellen erkennbar und es ist (iv) ein zweiter Halbkreis vorhanden, der sich ausschließlich in posteriore Richtung teilt und dadurch den Gastrulationsporus schließt. / In malacostracan crustaceans, the elongation of the germ band is realized by an invariant cell division pattern of the posterior growth zone. The ectoteloblasts are arranged in a semicircle and divide in anterior direction in a fixed pattern. Their progeny are arranged in the typical grid pattern of malacostracan crustaceans and provide the cell material for later segmentation processes. In contrast to other malacostracans, where the ectoteloblast appear in two half rows or a cell ring, the ectoteloblasts are arranged in a semicircle in isopods from the outset. The cell division pattern during elongation of the germ band is well studied in many malacostracan species including the isopod Porcellio scaber. However, details about formation of the ectoteloblasts and beginning of their cell division activity are missing. Therefore, the aggregation of the germ disc, the gastrulation, and the beginning of the elongation of the germ band in Porcellio scaber were examined using vital dyes (e.g. Alexa Fluor 488 and Tetramethylrhodamine) in cell labeling experiments combined with 4Dmicroscopy. The formation and cell-lineages of the ectoteloblasts and their surrounding cells were analyzed. The results suggest that (i) the ectoteloblasts are arranged in a semicircle before gastrulation starts, (ii) two cells forming part of the arising midline are lined up with the ectoteloblasts until they start their cell division activity in a predetermined pattern, (iii) the differentiation of ectoteloblasts is discernable after formation of the first e-row when they appear as big and elongated cells and (iv) a second semicircle exists whose cells divide in posterior direction and, consequently, enclose the gastrulation pore.