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Dynamic metabolomic prediction from genetic variation
Nemčeková, Petra ; Weckwerth, Wolfram (referee) ; Schwarzerová, Jana (advisor)
Hordeum vulgare, tak ako mnoho ďalších plodín, trpí redukovaním genetickej rôznorodosti spôsobeným klimatickými zmenami. Preto je potrebné zlepšiť účinnosť jeho kríženia. Oblasť záujmu sa v poslednej dobe obracia na výskum nepriamych selekčných metód založených na výpočetných predikčných modeloch. Táto práca sa zaoberá dynamickou metabolomickou predikciou založenou na genomických dátach, ktoré pozostávajú z 33,005 jednonukleotidových polymorfizmov. Metabolomické dáta zahŕňajú 128 metabolitov 25 rodín Halle exotického jačmeňa. Hlavným cieľom tejto práce je vytvoriť metabolomické predikcie dynamických dát pomocou rôznych metód, ktoré boli vybrané na základe rôznych publikácií. Vytvorené modely napomôžu predikcii fenotypu alebo odhaleniu dôležitých vlastností rastliny Hordeum vulgare.
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The modification of gut microbiota composition by dietary intervention: the effect of plant-based and western-type diet
Ďásková, Nikola ; Cahová, Monika (advisor) ; Beneš, Jiří (referee) ; Tlaskalová - Hogenová, Helena (referee)
This thesis explores the relationship between diet, gut microbiota, and metabolic health, with a particular focus on their association with non-communicable metabolic diseases (NCDs) such as obesity and type 2 diabetes (T2D). The aim of the first study is to assess compositional and metabolic differences in gut microbiota between healthy lean long-term vegans and omnivores. The study reveals that while the gut microbiota composition is not significantly different between the two groups, there are significant differences in the fecal, serum and urinary metabolome. These differences may be attributed to the different availability of substrates in the diet, as the vegan diet is associated with a shift from a proteolytic to a saccharolytic fermentation program. Our results support the hypothesis of both resilience and metabolic flexibility of the adult gut microbiota. In addition to taxonomic analyses, this dissertation also includes metabolomics to evaluate the functional manifestations of the gut microbiota. We introduce a novel method to assess the ability of the gut microbiota to produce beneficial metabolites with a specific focus on butyrate synthesis using qPCR quantification of bacterial butyryl-CoA:acetate CoA-transferase. In silico, we identified bacteria among the human gut microbiota that...
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Dynamic metabolomic prediction from genetic variation
Nemčeková, Petra ; Weckwerth, Wolfram (referee) ; Schwarzerová, Jana (advisor)
Hordeum vulgare, tak ako mnoho ďalších plodín, trpí redukovaním genetickej rôznorodosti spôsobeným klimatickými zmenami. Preto je potrebné zlepšiť účinnosť jeho kríženia. Oblasť záujmu sa v poslednej dobe obracia na výskum nepriamych selekčných metód založených na výpočetných predikčných modeloch. Táto práca sa zaoberá dynamickou metabolomickou predikciou založenou na genomických dátach, ktoré pozostávajú z 33,005 jednonukleotidových polymorfizmov. Metabolomické dáta zahŕňajú 128 metabolitov 25 rodín Halle exotického jačmeňa. Hlavným cieľom tejto práce je vytvoriť metabolomické predikcie dynamických dát pomocou rôznych metód, ktoré boli vybrané na základe rôznych publikácií. Vytvorené modely napomôžu predikcii fenotypu alebo odhaleniu dôležitých vlastností rastliny Hordeum vulgare.
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The role of gut microbiome in the development of type 2 diabetes
Movsesian, Lilit ; Cahová, Monika (advisor) ; Funda, David (referee)
In recent decades, ample evidence of the impact of intestinal microbiota and metabolome on the development of type 2 diabetes and other metabolic disorders such as obesity has been obtained. This thesis provides an overview of known information about this correlation and aims to highlight the importance of further research to identify prospective treatments. Bacterial taxa and metabolites most associated with the incidence of diabetes, as well as those associated with improved glucose and insulin tolerance, are considered. The thesis also compares similarities, differences and contradictions of the discussed studies. Key words: type 2 diabetes, obesity, microbiome, metabolome
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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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Abiotické a biotické faktory ovlivňující klíčení rostlin
Berka, Miroslav
Seed germination and early plant development is a crucial phase of plants' life. Multiple internal and external stimuli influence germination progress and have a serious impact on a plant's survival and vitality. Biotic and abiotic stimuli trigger a whole range of changes, both on molecular and developmental levels, but the complex molecular mechanisms regulating these responses are far from being resolved. This thesis reviews the seed germination process and outlines the role of external stimuli in its progress. The experimental part describes the development of a method for seed germination monitoring, provides new insight into the role of hydrogen peroxide in germination, and analyzes effects of cadmium ions, temperature, salt and drought on proteome and metabolome of germinating seeds of Hordeum vulgare. In total, 2000 proteins and 800 metabolites were identified. The analyses revealed over 95 putative abiotic stress markers, including 63 and 36 proteins and metabolites, respectively
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Zdroj živin a jeho efekt na metabolismus rostlin a jejich vývoj
Sadcovschi, Olga
Plant metabolome reflects plants' fitness and presents an essential source of information for plant molecular biology. This thesis „Nutrition source and its effect on plant metabolism and development“ reviews the role of abiotic factors on plant growth and development, including nutrients, light, temperature and water availability, and outlines modern metabolomics approaches. The experimental part employs several models and demonstrates an application of LC-MS fatty acid analysis and GC-MS metabolomics in the study of response to abiotic or hormonal stimuli, nutrient availability and temperature stress responses. Further, a novel hormonomics approach for poplar leaf analyses was adapted.
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Proteom a metabolom parazitů rodu Phytophthora
Zelená, Pavla
Genus Phytophthora represents a world-wide spread pathogen with more than hundred recognized species and its devastating effect on plants has a serious economic and ecological impact. This diploma thesis entitled „Proteome and metabolome of genus Phytophthora” briefly summarizes knowledge about this pathogen, including its life cycle and interactions with its host. Twelve species representing six Phytophthora clades that were selected for experimental work are then discussed in details. Phytophthora isolates were characterized on proteome and metabolome level employing an LC-MS untargeted proteome profiling and a GC-MS analysis of volatiles. The results were then processed to identify candidate molecules for a targeted identification of Phytophthora and these results were validated in an independent experiment with P. palmivora and Hordeum vulgare. We found that a proteome profiling can be employed as a tool to differentiate individual Phytophthora species and that the marker peptides can be employed for a targeted monitoring of Phytophthora presence in plants.
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