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Interactions between Schistosoma spp. and their hosts at the metabolome level
Kurečka, Martin ; Kameník, Zdeněk (advisor) ; Mikeš, Libor (referee)
The blood flukes of the genus Schistosoma are important parasites that cause serious chronic diseases in mammals, including humans, in tropical and subtropical countries. Treatment of these diseases is challenging; therefore, new molecular targets are still being sought for the development of vaccines and more effective drugs. To achieve this, better understanding of interactions between the parasite and the host at the molecular level is an important prerequisite. These processes can be studied by quantitative and qualitative determination of metabolite differences in healthy and infected individuals using metabolomics. The work represents a review of low molecular weight substances in tissues and body fluids of schistosome hosts, in which a change in concentration of metabolites putatively related to the infection was observed. Only metabolites with a hypothetical or known mechanism of these changes in the context of infection are covered. The thesis also includes a brief overview of basic methods of analytical chemistry, which are used in studies based on metabolomics. Key words: Schistosoma spp.; intermediate host; definitive host; spectrometry; metabolomics; low molecular compounds
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Pancreatic Cancer Diagnosis
Bunganič, Bohuš ; Zavoral, Miroslav (advisor) ; Rejchrt, Stanislav (referee) ; Urban, Ondřej (referee)
Pancreatic cancer is a malignant disease with an unfavorable prognosis. Currently, the diagnosis of pancreatic cancer is based mainly on CT, MR and EUS imaging methods, because a reliable biomarker of pancreatic cancer is not available. It is considered a success in the current clinical practice if patients suitable for surgical resection can be selected, because in this group the overall survival is slightly better than in the group where surgery is not technically possible. In the first part, the presented dissertation focuses on testing of already established imaging diagnostic methods used in common practice, i.e. EUS and EUS FNA, as well as modern examination possibilities, such as contrast endosonography, and the comparison of the accuracy of the methods used. The dominant role of the EUS FNA was confirmed. In the next phase of the work, the methodological procedure of EUS FNA collection and the preprocessing of pancreatic tissue samples was tested with regard to the quantity and quality for epigenetic examination and further testing using the prognostic role of KRAS and miR-21. It has been suggested that cytological smears are the most suitable source of biological material for DNA and miRNA analysis, where non-tumor tissue contamination is low. Although the prognostic role of KRAS is...
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Metabolomics in the study of microbiome
Nazmutdinova, Anastasiia ; Kuzma, Marek (advisor) ; Cahová, Monika (referee)
Inflammatory bowel disease is a serious condition with an incomplete etiology and pathogenesis. In this thesis, a mouse model of sodium dextran sulfate-induced inflammation was used to study different changes in the metabolism of germ-free and conventionally raised mice due to the development of the inflammatory process. NMR metabolomics of fecal, urine and serum samples, combined with uni- and multivariate statistical analysis, were used to characterize the changes. It was shown that the metabolic signature differs between germ-free and conventional mice. In germ-free mice, significant amounts of carbohydrates were found in feces. Their levels decreased during inflammation as they were excreted in urine. In contrast to conventional mice, germ-free mice also excreted large amounts of amino acids in feces during the developing inflammation. Disorders of sugar and protein metabolism found in germ-free mice indicate severe malnutrition caused by inflammation. The results show that the presence of a microbiome represents a protective mechanism against significant disruption in the body. A stability study of fecal extracts of healthy conventionally colonized mice confirmed that none of the identified and quantified metabolites showed significant systemic changes in several consecutively collected...
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Influence of intestinal microbiota on development of neurodegenerative diseases
Hakenová, Kristina ; Valeš, Karel (advisor) ; Vodička, Martin (referee)
Aging is associated with natural biological changes, which result in a decrease in the functional capacity of the body, which is also accompanied by an increased incidence of inflammatory processes that contribute to the development of neurodegeneration. The intestinal microbiota and its interaction with the intestine and the central nervous system play a key role in maintaining the function of biological homeostatic systems at an older age. This opens the possibility of influencing or modifying human microbiota for the development of therapeutic strategies. Based on the analysis of stool samples by HPLC MS / MS, the study confirmed the effect of selected probiotics on the modification of metabolic pathways and the proper functioning of the microbiota per se. The greatest effects were observed on tyrosine metabolism, tryptophan metabolism, arachidonic acid metabolism and bile acid biosynthesis metabolism. A positive effect of selected probiotic bacteria was found in the memory component of cognitive functions. Significant improvements were observed in verbal learning and verbal memory. In subjects with mild cognitive impairment, the progression of cognitive deficit has been slowed. Significant improvement was also observed for executive functions. These findings were not followed by a subjective...
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Dynamic Model for Production of Polyhydroxyalkanoates by Thermophilic Bacterium S. thermodepolymerans
Křápková, Monika ; Šafránek, David (referee) ; Sedlář, Karel (advisor)
Tato diplomová práce se zabývá rekonstrukcí dynamického modelu produkce polyhydroxyalkanoátů (PHA) termofilní bakterií Schlegelella thermodepolymerans. První kapitola poskytuje čtenářům krátký úvod do systémové biologie a matematické teorie grafů. Na ni navazuje druhá kapitola zabývající se různými přístupy v dynamickém modelování, včetně běžně používaných nástrojů pro dynamickou analýzu komplexních systémů. Třetí kapitola pak sleduje další pojmy a možnosti týkající se analýzy modelu. Následující kapitola se zaměřuje na metabolomiku a často používané laboratorní techniky a pátá kapitola je pak věnována polyhydroxyalkanoátům, zejména jejich chemické struktuře a vlastnostem. V kapitole šesté je navržen obecný booleovský model pro produkci PHA termofilními bakteriemi. Kapitola sedmá se poté zaměřuje na zdokonalení modelu se zaměřením na S. thermodepolymerans. Výsledný dynamický model je podroben analýze a výsledky jsou diskutovány.
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Metabolipidomic profiling of white adipose tissue by UPLC-MS/MS
Rombaldová, Martina
Obesity is a serious problem in society today [1,2]. It might seems to have been caused simply by excess consumption of food compared to energy expenditure but obesity is actually a complex metabolic disorder centred on adipose lipid metabolism and cellular signalling systems linked to it [3]. Understanding the biology of adipose tissue (AT) is very important for the identification of novel and potential therapeutic targets in order to prevent and treat obesity-related disorders [4]. We utilized analytical approach liquid chromatography coupled to mass spectrometry (LC-MS) to study adipose tissue metabolism. Also, we were especially interested in the effect of omega-3 polyunsaturated fatty acids (PUFA) on that metabolism. Rodent and cell line experiments were performed and analyses were done of white adipose tissue (WAT), serum/plasma samples or cells as well as milk samples from mothers. At first, we established several ultra performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) methods for analysis of acylcarnitines (AC), amino acids (AmA) and other metabolites. Importantly, these methods were able to distinguish isobaric species of AC which is not usually possible. Using these approaches we uncovered several acylcarnitines, i.e. long chain AC, carnitine, acylcarnitine C4 and...
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Metabolom rostlin a jeho proměny v reakci na stres
Dobešová, Markéta
Adverse environmental effects have a significant impact on plants' life and influ-ence the plants' metabolome. Specific stress-related responses are manifested both on plant development and its metabolites. This thesis entitled "Plant metabolome and its response to stress" outlines the composition of plant metabolome and reviews stress-related metabolites and metabolomics processes. The experimental part summarizes the results of two independent experiments. First, Hordeum vulgare response to stress was followed via targeted LC-MS metabolomics and proteome analysis. Next, a drought response was analyzed in Solanum lycopersicum via GC-MS metabolome profiling. Results highlighted a tissue-specific response to stress and pinpointed several putative abiotic stress markers
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Metabolipidomic profiling of white adipose tissue by UPLC-MS/MS
Rombaldová, Martina
Obesity is a serious problem in society today [1,2]. It might seems to have been caused simply by excess consumption of food compared to energy expenditure but obesity is actually a complex metabolic disorder centred on adipose lipid metabolism and cellular signalling systems linked to it [3]. Understanding the biology of adipose tissue (AT) is very important for the identification of novel and potential therapeutic targets in order to prevent and treat obesity-related disorders [4]. We utilized analytical approach liquid chromatography coupled to mass spectrometry (LC-MS) to study adipose tissue metabolism. Also, we were especially interested in the effect of omega-3 polyunsaturated fatty acids (PUFA) on that metabolism. Rodent and cell line experiments were performed and analyses were done of white adipose tissue (WAT), serum/plasma samples or cells as well as milk samples from mothers. At first, we established several ultra performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) methods for analysis of acylcarnitines (AC), amino acids (AmA) and other metabolites. Importantly, these methods were able to distinguish isobaric species of AC which is not usually possible. Using these approaches we uncovered several acylcarnitines, i.e. long chain AC, carnitine, acylcarnitine C4 and...
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Metabolipidomic profiling of white adipose tissue by UPLC-MS/MS
Rombaldová, Martina ; Kuda, Ondřej (advisor) ; Šiklová, Michaela (referee) ; Čajka, Tomáš (referee)
Obesity is a serious problem in society today [1,2]. It might seems to have been caused simply by excess consumption of food compared to energy expenditure but obesity is actually a complex metabolic disorder centred on adipose lipid metabolism and cellular signalling systems linked to it [3]. Understanding the biology of adipose tissue (AT) is very important for the identification of novel and potential therapeutic targets in order to prevent and treat obesity-related disorders [4]. We utilized analytical approach liquid chromatography coupled to mass spectrometry (LC-MS) to study adipose tissue metabolism. Also, we were especially interested in the effect of omega-3 polyunsaturated fatty acids (PUFA) on that metabolism. Rodent and cell line experiments were performed and analyses were done of white adipose tissue (WAT), serum/plasma samples or cells as well as milk samples from mothers. At first, we established several ultra performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) methods for analysis of acylcarnitines (AC), amino acids (AmA) and other metabolites. Importantly, these methods were able to distinguish isobaric species of AC which is not usually possible. Using these approaches we uncovered several acylcarnitines, i.e. long chain AC, carnitine, acylcarnitine C4 and...
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