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SMV-2023-57: EM analysis of microorganisms II
Hrubanová, Kamila
The aim of the contract research was the expert analysis of microbiological samples with biotechnological significance with the intention of describing the ultrastructure of the cells, which depends on the cultivation conditions of the industrial process. The collaboration included cryogenic preparation of samples, followed by microbial microscopy using low-temperature electron microscopy (cryo-SEM), and selected samples were processed for transmission electron microscopy (TEM). Furthermore, spectroscopic measurements were performed using Raman spectroscopy.
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SMV-2023-56: EM analysis of microorganisms
Hrubanová, Kamila
The aim of the contract research was the expert analysis of microbiological samples with the intention of describing morphological changes dependent on culture conditions. The collaboration included cryogenic preparation of samples, followed by microbial microscopy using low-temperature electron microscopy (cryo-SEM), and selected samples were processed for transmission electron microscopy (TEM). Furthermore, spectroscopic measurements were performed using Raman spectroscopy.
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SMV-2023-54: EM Nematodes II 2023
Hrubanová, Kamila
The aim of the contract research was the expert analysis of biological samples with the intention of describing morphological features for species classification. As part of the collaboration, chemical preparation of the samples was carried out, followed by observation of the bodies of the nematodes themselves in different positions so that individual morphological characters could be distinguished using an electron microscope.
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SMV-2023-55: EM Nematodes I 2023
Hrubanová, Kamila
The aim of the contract research was the expert analysis of biological samples with the intention of describing morphological features for species classification. As part of the collaboration, chemical preparation of the samples was carried out, followed by observation of the bodies of the nematodes themselves in different positions so that individual morphological characters could be distinguished using an electron microscope.
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Complementary analysis of procaryotic cells by electron microscopy and Raman spectroscopy
Ikrényiová, Terézia ; Sedláček, Petr (referee) ; Hrubanová, Kamila (advisor)
This master thesis deals with conventional methods of bacterial cell analysis, polyhydroxyalkanoates, Raman spectroscopy and electron microscopy in the theoretical part. The production of polyhydroxybutyrate by selected thermophilic bacteria and their analysis by gas chromatography, cryogenic scanning electron microscopy and Raman spectroscopy is described in the experimental part. The chosen sample was analyzed by a transmission electron microscope. Comparing the results from previous mentioned methods it was found that the bacteria Schlegelella thermodepolymerans accumulated the highest amount of PHB. The lowest amount of PHB was obtained by bacteria Rubrobacter xylanophilus. The assumption that the PHB granules formed so-called needle-like plastic deformations during freeze-fracturing was affirmed by cryo-SEM photos analysis. Moreover, it was found that the bacterial cell characterization deduced from microscopic observation of samples corresponded to the description in the literature. TEM provided better resolution photos and in consequence the cells and PHB are more visible. The thesis is also focused on chemical fingerprint analysis of cells by Raman spectroscopy. Several biomolecules were identified by measured Raman spectra for the particular samples.
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Scanning Electron Microscopy and its Applications for Sensitive Samples
Hrubanová, Kamila ; Nováček, Jiří (referee) ; Schröfel,, Adam (referee) ; Krzyžánek, Vladislav (advisor)
Předložená dizertační práce s názvem “Rastrovací elektronová mikroskopie a její aplikace pro senzitivní vzorky” pojednává o problematice rastrovací elektronové mikroskopie v kontextu instrumentálního a metodologického vývoje vedoucího k inovativnímu řešení, které je dobře aplikovatelné zejména v mikrobiologickém výzkumu. Součástí práce je rozprava o historii a současném stavu elektronové mikroskopie (EM) jakožto vědecké zobrazovací a analytické techniky, tato část se nachází v úvodních kapitolách. Nepopiratelný přínos EM v biologických a lékařských oborech je dokazován mnoha citovanými vědeckými publikacemi. Předložená dizertační práce přináší novinky z oblasti přípravy preparátů a kryogenní rastrovací elektronové mikroskopie (cryo-SEM) vyvinuté na pracovišti Ústavu přístrojové techniky AV ČR, v.v.i. v Brně. Jedná se především o návrhy a výrobu speciálních držáků vzorků a vývoj nových metodik v oblasti přípravy mikrobiologických preparátů vedoucích k nalezení optimálních parametrů jednotlivých procesů. V experimentální části se nachází ověření metodologických postupů při studiu hydratovaných a na elektronový svazek senzitivních preparátů. Následné srovnání různých přístupů na definovaném biologickém systému z oblasti mikrobiologie přispívá k rozšíření interpretace doposud známých výsledků. Mezi zkoumanými mikrobiologickými kmeny byly biofilm-pozitivní bakterie Staphylococcus epidermidis a kvasinky jako Candida albicans a Candida parapsilosis, jež jsou považovány za klinicky významné, protože se podílejí na vzniku závažných infekcí zejména u imunokompromitovaných pacientů. Dále byl studován vliv růstu biofilmu bakterie Bacillus subtilis na biodeteriorizaci a biodegradaci poly--kaprolaktonových fólií. Vývoj v oblasti cryo-SEM byl aplikován ve výzkumu mikrobů s biotechnologickým potenciálem, jako jsou např. Cupriavidus necator a Sporobolomyces shibatanus.
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Monte Carlo simulations of electron scattering in scanning transmission electron microscopy
Záchej, Samuel ; Hrubanová, Kamila (referee) ; Krzyžánek, Vladislav (advisor)
This thesis deals with an electron scattering in STEM microscopy on objects with dif-ferent shapes, such as cuboid, sphere and hollow capsule. Monte Carlo simulations are used for description of multiple electron scattering. Except the theoretical analysis of the electron scattering and simulation methods, the thesis contains design and realiza-tion of an algorithm simulating electron scattering in given objects. In addition, there is a design for robustness evaluation of the simulation, based on comparison between results and known signals for a given object. Reliability of the algorithm was verified by experimental measurements of the electron scattering on a carbon layer.
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Complementary analysis of procaryotic cells by electron microscopy and Raman spectroscopy
Ikrényiová, Terézia ; Sedláček, Petr (referee) ; Hrubanová, Kamila (advisor)
This master thesis deals with conventional methods of bacterial cell analysis, polyhydroxyalkanoates, Raman spectroscopy and electron microscopy in the theoretical part. The production of polyhydroxybutyrate by selected thermophilic bacteria and their analysis by gas chromatography, cryogenic scanning electron microscopy and Raman spectroscopy is described in the experimental part. The chosen sample was analyzed by a transmission electron microscope. Comparing the results from previous mentioned methods it was found that the bacteria Schlegelella thermodepolymerans accumulated the highest amount of PHB. The lowest amount of PHB was obtained by bacteria Rubrobacter xylanophilus. The assumption that the PHB granules formed so-called needle-like plastic deformations during freeze-fracturing was affirmed by cryo-SEM photos analysis. Moreover, it was found that the bacterial cell characterization deduced from microscopic observation of samples corresponded to the description in the literature. TEM provided better resolution photos and in consequence the cells and PHB are more visible. The thesis is also focused on chemical fingerprint analysis of cells by Raman spectroscopy. Several biomolecules were identified by measured Raman spectra for the particular samples.
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