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Taxonomic overview of the genus Arthroderma with focus on species associated with reptiles and bats
Kolarczyková, Daniela ; Hubka, Vít (advisor) ; Dobiáš, Radim (referee)
The genus Arthroderma belongs to a group of geophilic dermatophytes that primarily degrade keratin in soil and occasionally cause infections in humans and animals. This species-rich genus has received particular attention in recent years in terms of species occurring in human clinical material or clinical samples isolated from rodents and other mammals, which has been associated with a significant increase in the number of its species. In this thesis, the species diversity of the genus Arthroderma was investigated in material isolated from snakes, bats and cave sediment, a substrate that has been almost unexplored in terms of the occurrence of this genus. The strains studied were isolated during research on bats diseased by "white nose syndrome" and snakes by "snake fungal disease". In the past, the genus Arthroderma has been studied either on the basis of morphology or, after the advent of molecular methods, in terms of multigene phylogeny. However, no monographs have simultaneously combined phenotypic and molecular genetic criteria to assess species boundaries across the genus or a significant part of it. This is one of the reasons why species boundaries are often unclearly defined. Thus, another aim of this work was to improve the multigene phylogeny of the genus by incorporating new strains,...
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Metagenomic analysis of child gut microbioma
Zourková, Tereza ; Škutková, Helena (referee) ; Bartoň, Vojtěch (advisor)
The thesis is focused on the influence of the metagenome on child growth and the reasons for the usefulness of investigating the consequences of changes in the human intestinal microbiome. It also describes the general problematics of the microbiome and the history of its studies. The composition of the human intestinal microbiome and the connection with the immune system or, for example, hormone production, are also described here. The thesis also contains information on some methods of metagenome analysis, namely microscopic methods using previous cultivation, mass spectrometry and sequencing methods. The data analysis procedure using various bioinformatics software, with which the data were appropriately pre-processed, is also described here. Filtered data in this way are ready for the following metagenome profiling, which is also described here. At the end of the thesis, the profiling results are evaluated, based on which the course of changes in the microbiome during the aging of the child are estimated, which is the main goal of this bachelor's thesis.
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Role of the serotonin receptor type 7 (5-HT7) in autoimmune disease
NUßBAUMER, Mia
Serotonin receptor type 7 (5-HT7) displays immunomodulatory functions and is overexpressed in individuals with Crohn's disease. Here, we set out to determine 5-HT7 mode of interaction with its cognate proteins Gs and G12. A unique type of coupling, termed 'inverse coupling' is known to occur between the 5-HT7 receptor and the Gs protein. The aim of our research was to determine whether G12 can also undergo this kind of coupling. We found that the G12 protein has a surprisingly lower mobility than Gs implying a specific interaction with a membrane domain or another membrane-localized protein. For both G proteins, we were unable to detect their inverse coupling with the 5-HT7 receptor at room temperature. Our findings indicate peculiar differences in G protein mobility and emphasize the importance of temperature for studies of interactions between G proteins and G protein-coupled receptors.
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Software for DSLR control for use in microscopy
Mokrejš, Jakub ; Janoušek, Oto (referee) ; Čmiel, Vratislav (advisor)
This master's thesis initially deals with a review of cameras used in microscopy, describing their properties and the difference between microscopic and DSLR cameras. Furthermore, it describes the programs used by microscopic cameras for control via a computer. The thesis then defines the technologies used for software development and presents a design of the software's program equipment. The practical part of the thesis first describes the technologies used for software development along with a development diagram. The next section describes the functions that the software uses to communicate with the DSLR camera and introduces the software's graphical user interface. The conclusion of the practical part is devoted to testing the software itself, where it also presents various ways of its control. The test results are then evaluated in the discussion.
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Integration of laser ablation into the workflows of FIB-SEM systems
Valenta, Jakub ; Adámek, Martin (referee) ; Búran, Martin (advisor)
Cílem této diplomové práce je ověření vlivu různých nastavení parametrů systému laserové ablace na různé typy mikroelektronických materiálů. Práce má za úkol popsat účel analýzy skrytých defektů v těchto strukturách a způsob jejich řešení. V rámci práce jsou řešeny principy funkce obráběcích a zobrazovacích zařízení na úrovni mikro- či nanometrových velikostí struktur. Předmětem zkoumání je především operační rozdíl mezi procesy obrábění pomocí iontového svazku a pomocí laserového paprsku a jeho integrace do oblasti zajištění kvality. Jde o propojení laserových zařízení se systémy iontových a~elektronových svazků. V práci jsou také popsány výsledky experimentů, během kterých byla provedena analýza defektů vybraných struktur.
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Molekulárně-biologická diagnostika lidských polyomavirů
Ryšavá, Markéta
Most of the human population encounters human polyomaviruses during childhood, when the first infection is asymptomatic or with mild symptoms. However, these viruses persist in the human body and most often, they reactivate during immunosuppression. Together with JC virus reactivation, the progressive multifocal encephalopathy is associated. Hemorrhagic cystitis is associated with BK virus, resulting in the loss of allograft during kidney transplantation. Accurate diagnostics can detect viruses in a timely manner and mitigate tissue damage. This diploma thesis deals with biotechnologies, which can be used in virus detection with a focus on real time PCR, which is the gold standard in virus diagnostics. The literary research summarizes basic information about polyomaviruses with a focus on human BKV and JCV polyomaviruses. It summarizes the biotechnological methods used for detection of polyomaviruses, both in routine diagnosis and in alternative approaches involving biosensors and CRISPR. The experimental part of the work includes the design of a detection system for polyomaviruses from in silico genome analysis, through the design of potential primers, to theoretical specificity analysis. The practical part of the work compares the efficiency and sensitivity of amplification of two reaction mixtures, where one is intended for simple systems and the other for multiplexes. It also includes testing of selected additives of PCR and determining the sensitivity and validity parameters of the reaction mixture test selected for PCR system development. The results showed that detection using a multiplex reaction mixture is sufficiently sensitive, as it meets the conditions and requi-rements of clinical recommendations and at the same time shows very good values of sensitivity and specificity of the test comparable to published technologies. This reaction mixture appears to be relevant to the use of the development and optimization of a PCR system for the detection of polyomaviruses.
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Analysis of gonosomal mosaic using FISH method
ŠUTKOVÁ, Jana
In my bachelor thesis I dealt with the analysis of gonosomal mosaics. Mosaicism can be described as a condition in which two or more distinct cell lines originating from a single zygote are found in one organism. In women, the most common mosaic forms are Turner syndrome and triple X syndrome or superfemale. In the male population, Klinefelter syndrome and XYY syndrome (supermale) are most commonly detected. Mosaicism can be investigated by fluorescence in situ hybridization. In the theoretical part of my bachelor's thesis I focused on congenital chromosomal mosaicism, especially on its variants such as Klinefelter syndrome, Turner syndrome, triple X and XYY syndrome. Furthermore, in this part I dealt with fluorescence in situ hybridization. I described fluorescence per se and then its application in clinical practice, where several types of fluorescence in situ hybridization are used. In the practical part I examined the number of gonosomal chromosomes using fluorescence in situ hybridization. I prepared this part in the laboratory of the Faculty of Health and Social Sciences of the University of South Bohemia in České Budějovice. I examined 40 anonymized samples from 20 probands. Capillary blood samples and buccal swabs were taken from each of them. After hybridization of samples with centromeric probe for X and Y chromosomes microscopy was performed. In the last part of this bachelor thesis I dealt with the processing of the results obtained by fluorescence microscopy. Thus, a total of 6 cases of mosaicism were detected in women (the percentage of mosaic cells was above the admissible limit). In males there were a total of 2 cases of increased percentage of mosaic cells.
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