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The methods of analysis with a focused ion beam, commonly termed as nuclear microscopy, include quantitative physical processes like PIXE and RBS. The element concentrations in a sample can be quantitatively mapped with a sub-micron spatial resolution and a sub-ppm sensitivity. Its fully quantitative and non-destructive nature makes it particularly suitable for analysing biological samples. The applications in biomedical research are manifold. The iron overload hypothesis in Parkinson\\\'s disease is investigated by a differential analysis of human substantia nigra. The trace element content is quantified in neuromelanin, in microglia cells, and in extraneuronal environment. A comparison of six Parkinsonian cases with six control cases revealed no significant elevation in iron level bound to neuromelanin. In fact, a decrease in the Fe/S ratio of Parkinsonian neuromelanin was measured, suggesting a modification in its iron binding properties. Drosophila melanogaster, or the fruit fly, is a widely used model organism in neurobiological experiments. The electrolyte elements are quantified in various organs associated with the olfactory signalling, namely the brain, the antenna and its sensilla hairs, the mouth parts, and the compound eye. The determination of spatially resolved element concentrations is useful in preparing the organ specific Ringer\\\'s solution, an artificial lymph that is used in disruptive neurobiological experiments. The role of trace elements in the progression of atherosclerosis is examined in a pilot study. A differential quantification of the element content in an induced murine atherosclerotic lesion reveals elevated S and Ca levels in the artery wall adjacent to the lesion and an increase in iron in the lesion. The 3D quantitative distribution of elements is reconstructed by means of stacking the 2D quantitative maps of consecutive sections of an artery. The feasibility of generating a quantitative elemental rodent brain atlas by Large Area Mapping is investigated by measuring at high beam currents. A whole coronal section of the rat brain was measured in segments in 14 h. Individual quantitative maps of the segments are pieced together to reconstruct a high-definition element distribution map of the whole section with a subcellular spatial resolution. The use of immunohistochemical staining enhanced with single elements helps in determining the cell specific element content. Its concurrent use with Large Area Mapping can give cellular element distribution maps.

Sphaerodoridae is a group of benthic marine worms (Annelida) characterized by the presence of spherical tubercles covering their whole surface. They are commonly considered as belonging to Phyllodocida although sistergroup relationships are still far from being understood. Primary homology assessments of their morphological features are lacking, hindering the appraisal of evolutionary relationships between taxa. Therefore, our detailed morphological investigation focuses on different Sphaerodoridae as well as on other members of Phyllodocida using an integrative approach combining scanning electron microscopy (SEM) as well as immunohistochemistry with standard neuronal (anti-5-HT) and muscular (phalloidin-rhodamine) markers and subsequent CLSM analysis of whole mounts and sections. Furthermore, we provide histological (HES) and light microscopical data to shed light on the structures and hypothetical function of sphaerodorid key morphological features. We provide fundamental details into the sphaerodorid morphology supporting a Phyllodocida ancestry of these enigmatic worms. However, the muscular arrangement and the presence of an axial muscular pharynx is similar to conditions observed in other members of the Errantia too. Furthermore, nervous system and muscle staining as well as SEM and histological observations of different types of tubercles indicate a homology of the so called microtubercles, present in the long-bodied sphaerodorids, to the dorsal cirri of other Errantia. The macrotubercles seem to represent a sphaerodorid autapomorphy based on our investigations. Therefore, our results allow comparisons concerning morphological patterns between Sphaerodoridae and other Phyllodocida and constitute a starting point for further comparative investigations to reveal the evolution of the remarkable Sphaerodoridae.

For the past decades, Kelvin probe force microscopy (KPFM) developed from a sidebranch of atomic force microscopy to a widely used standard technique. It allows to measure electrostatic potentials on any type of sample material with an unprecedented spatial resolution. While the technical aspects of the method are well understood, the interpretation of measured data remains object of intense research. This thesis intends to prove an advanced view on how sample systems which are typical for ultrahigh resolution imaging, such as organic molecular submonolayers on metals, can be quantitavily analysed with the differential charge density model. In the first part a brief introduction into the Kelvin probe experiment and atomic force microscopy is given. A short review of the theoretical background of the technique is presented. Following, the differential charge density model is introduced, which is used to further explain the origin of contrast in Kelvin probe force microscopy. Physical effects, which cause the occurence of local differential charge densities, are reviewed for several sample systems that are of interest in high resolution atomic force microscopy. Experimental evidence for these effects is presented in the second part. Atomic force microscopy was used for in situ studies of a variety of sample systems ranging from pristine metal surfaces over monolayer organic adsorbates on metals to ferroelectric substrates both, with and without organic thin film coverage. As the result from these studies, it is shown that the differential charge density model accurately describes the experimentally observed potential contrasts. This implies an inherent disparity of the measurement results between the different Kelvin probe force microscopy techniques; a point which had been overseen so far in the discussion of experimental data. Especially for the case of laterally strong confined differential charge densities, the results show the opportunity as well as the necessity to explain experimental data with a combination of ab initio calculations of the differential charge density and an electrostatic model of the tip-sample interaction.

In the past decades, numerous single-molecule techniques have been developed to investigate individual bio-molecules and cellular machines. While a lot is known about the structure, localization, and interaction partners of such molecules, much less is known about their mechanical properties. To investigate the weak, non-covalent interactions that give rise to the mechanics of and between proteins, an instrument capable of resolving sub-nanometer displacements and piconewton forces is necessary. One of the most prominent biophysical tool with such capabilities is an optical tweezers. Optical tweezers is a non-invasive all-optical technique in which typically a dielectric microsphere is held by a tightly focused laser beam. This microsphere acts like a microscopic, three-dimensional spring and is used as a handle to study the biological molecule of interest. By interferometric detection methods, the resolution of optical tweezers can be in the picometer range on millisecond time scales. However, on a time scale of seconds—at which many biological reactions take place—instrumental noise such as thermal drift often limits the resolution to a few nanometers. Such a resolution is insufficient to resolve, for example, the ångstrom-level, stepwise translocation of DNA-binding enzymes corresponding to distances between single basepairs of their substrate. To reduce drift and noise, differential measurements, feedback-based drift stabilization techniques, and ‘levitated’ experiments have been developed. Such methods have the drawback of complicated and expensive experimental equipment often coupled to a reduced throughput of experiments due to a complex and serial assembly of the molecular components of the experiments. We developed a high-resolution optical tweezers apparatus capable of resolving distances on the ångstrom-level over a time range of milliseconds to 10s of seconds in surface-coupled assays. Surface-coupled assays allow for a higher throughput because the molecular components are assembled in a parallel fashion on many probes. The high resolution was a collective result of a number of simple, easy-to-implement, and cost-efficient noise reduction solutions. In particular, we reduced thermal drift by implementing a temperature feedback system with millikelvin precision—a convenient solution for biological experiments since it minimizes drift in addition to enabling the control and stabilization of the experiment’s temperature. Furthermore, we found that expanding the laser beam to a size smaller than the objective’s exit pupil optimized the amount of laser power utilized in generating the trapping forces. With lower powers, biological samples are less susceptible to photo-damage or, vice versa, with the same laser power, higher trapping forces can be achieved. With motorized and automated procedures, our instrument is optimized for high-resolution, high-throughput surface-coupled experiments probing the mechanics of individual biomolecules. In the future, the combination of this setup with single-molecule fluorescence, super-resolution microscopy or torque detection will open up new possibilities for investigating the nanomechanics of biomolecules.

Title: The preparation and study of catalytic system Cu(O)-CeO2 using surface analytical methods Author: Břetislav Šmíd Department: Department of Surface and Plasma Science Supervisor of the doctoral thesis: Doc. Mgr. Iva Matolínová, Dr. Abstract: This work is concerned with a study of copper/copper oxide - cerium dioxide systems and their interaction with CO and H2O molecules. Investigated samples were prepared in the form of powder catalysts and also as very well defined model inverse systems. The low temperature CO oxidation powder catalysts were studied by means of XPS, XRD, SEM, TEM and in micro-reactor system allowing the CO oxidation examination. The study of H2O adsorption and co-adsorption of H2O with CO were carried out on model inverse systems CeOx(111)/Cu(111) in ultra-high vacuum conditions using X-ray, synchrotron radiation (SRPES), resonant (RPES) photoelectron spectroscopies and LEED. It was observed on the stoichiometric surface water adsorbs molecularly at 120 K while on the reduced surface and surface of CeO2 islands on Cu(111) the H2O adsorption is partially dissociative with formation of OH groups. The increase of Ce3+ species (i.e. surface reduction) observed after H2O adsorption was explained as an electronic effect of the Ce 4f charge accumulation and Ce 5d charge depletion....

CD47 is a so-called "don't eat me" signal, which protects cells from phagocytosis. Its high expresion on tumor cells brings new perspective to the tumor therapy. Monoclonal antibodies, which are these days undergoing clinical trials, prevent CD47 binding to the SIRPA inhibitory receptor on macrophages, and so they enhance their phagocytic functional capacity. In this way they enable phagocytic removal of tumor cells. Overall expression, structural conformation and stoichiometry of CD47 on a particular cell predestine whether it will be phagocytised. The aim of the thesis is to develop and test methods to characterise expression parameters of CD47 via flow cytometry (FCM), quantitative PCR (qPCR) and microscopy. To achieve this goal I performed competition tests of commercially available antibodies in order to characterise their binding epitopes on cell lines. After performing tSNE analysis of primary BCa patient samples I correlated CD47 expression with other cell surface markers. I focused on CD47 expression in various differentiation stages of the tumor. To better understand the relationship between CD47 expression and differentiation status of cells I performed qPCR analysis of particular transcription factors. Using cell lines I examined method for phagocytosis quantification, which will be...

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Pavel Jůda - Abstract The cell nucleus is a complex cellular organelle. The nucleus and nuclear processes are organized into functionally and morphologically separated nuclear subcompartments. This thesis is particularly concerned with the three following nuclear subcompartments: sites of DNA replication, Polycomb bodies and nuclear inclusions constituted of inosine monophosphate dehydrogenase 2 (IMPDH2). First, we examined the relationship between MCM proteins and DNA replication. Using immunofluorescent labeling of cells extracted prior fixation and applying cross-correlation function analysis, we showed that MCM proteins are present at the sites of active DNA synthesis. Our results contributed to the solving of the first part of so-called MCM paradox. Second, we studied the structural basis of the Polycomb bodies. Based on fluorescence microscopy studies, Polycomb bodies have been considered to be the nuclear subcompartments formed by the accumulation of Polycomb proteins in the interchromatin compartment. In our work, using correlative light electron microscopy and experimental changes in macromolecular crowding, we clearly showed that a Polycomb body is a chromosomal domain formed by an accumulation of heterochromatin structures, rather than a typical nucleoplasmic body. Third, we were interested in...

Electrically tunable lenses exhibit strong potential for fast motion-free axial scanning in a variety of microscopes. However, they also lead to a degradation of the achievable resolution because of aberrations and misalignment between illumination and detection optics that are induced by the scan itself. Additionally, the typically nonlinear relation between actuation voltage and axial displacement leads to over- or under-sampled frame acquisition in most microscopic techniques because of their static depth-of-field. To overcome these limitations, we present an Adaptive-Lens-High-and-Low-frequency (AL-HiLo) microscope that enables volumetric measurements employing an electrically tunable lens. By using speckle-patterned illumination, we ensure stability against aberrations of the electrically tunable lens. Its depth-of-field can be adjusted a-posteriori and hence enables to create flexible scans, which compensates for irregular axial measurement positions. The adaptive HiLo microscope provides an axial scanning range of 1 mm with an axial resolution of about 4 μm and sub-micron lateral resolution over the full scanning range. Proof of concept measurements at home-built specimens as well as zebrafish embryos with reporter gene-driven fluorescence in the thyroid gland are shown.