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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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Biochemistry and pathobiochemistry of phylloquinone and menaquinones
Dunovská, Kateřina ; Klapková, Eva (advisor) ; Uřinovská, Romana (referee) ; Skoumalová, Alice (referee)
Vitamin K belongs to the family of fat-soluble vitamins, which is not determinated in clinical laboratories. It is a cofactor necessary for posttranslational γ-carboxylation of glutamyl residues in selected proteins such as the osteocalcin, and procoagulation factors II, VII, IX, X. Vitamin K deficient individuals appear to have more undercarboxylated proteins, which are functionally defective. Lack of this vitamin has been associated with risk of developing osteoporosis and cardiovascular diseases. The aim of this work was to develop and validate the HPLC method and the LC-MS/MS method for determination of three vitamin K's forms - vitamin K1, MK-4 and MK-7 in serum. After successful validation of both methods, patient samples and healthy population samples were measured. There were measured 350 patient samples by HPLC method. These samples were divided into two groups - patients with diagnostic of osteoporosis and patients without osteoporosis. We measured 946 samples by LC-MS/MS method. Samples were divided into groups: patients with osteoporosis, patients without osteoporosis, healthy population, patients with osteopenia and patients with cystic fibrosis. The reference range of vitamin K in healthy population was obtained by LC-MS/MS method. The next aim was to compare the effectiveness of...
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Charakterizace jaderného proteomu rostlin
Svetláková, Anna
Nuclear proteome contains important regulatory proteins that are directly involved in gene regulation mechanisms. It is estimated that about 30% of genes encode for proteins that are destined into the nucleus, but a large dynamic range in protein concentration results in some nuclear proteins being present at concentrations orders of magnitude lower than others and these are thus hidden in standard total protein extracts. This thesis The characterization of the plant nuclear proteome briefly reviews present-day knowledge of nuclear proteomics and summarises extraction protocols. In the experimental part, two different fractionation protocols were evaluated. Analyses of nuclear protein extracts increased the number of identified proteins, but the quantitative comparison with the results of total protein extractions indicate that at least some nuclear proteins were lost or depleted in the process. Finally, the effect of plant hormone cytokinin on barley nuclear proteins was analysed. In total, 65 known nuclear proteins (10% of identified proteins in the nuclear fraction) were found and 15 of them were differentially abundant in response to the cytokinin treatment, including e.g. RNA helicase SUB2 and a salt-stress response protein.
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Kvantifikácia proteínov pomocou hmotnostnej spektrometrie a jej využitie pri sledovaní degeneračných zmien proteínu
Blaženiaková, Karina
Protein posttranslational modifications may play an important role in regulatory pathways but some of them are also the result of stress and protein ageing. This thesis Protein quantitation and its application in the monitoring of degenerative protein modifications briefly reviews major protein posttranslational modifications involved in degenerative processes. The experimental part utilises SRM-based targeted mass spectrometry to identify sites of stress-induced posttranslational modifications. Based on the available spectral libraries, a highly abundant barley seed protein was selected (Serpin-Z4) and the method for a targeted analysis of its tryptic peptides was optimised. Altogether, relative abundances of 14 peptides representing more than 50% of the protein sequence coverage were followed. The damage was induced by incubating barley seed powder at 99°C for 0.5-24 h or with hydrogen peroxide (0-30%). Abundances of seven and four peptides were significantly dicreased by heat and oxidative damage, respectively. The mapping of these peptides to the protein's 3D structure revealed that most of the altered peptides are exposed on the surface and thus present a likely target of stress-induced modifications. Finally, the SRM-based method was tested on food extracts.
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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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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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Antioxidant and antiinflammatory effects of bilirubin.
Valášková, Petra ; Muchová, Lucie (advisor) ; Martínková, Markéta (referee) ; Dvořák, Karel (referee)
For a long time, bilirubin (BR) has been considered a waste molecule with potential toxic effects especially on the central nervous system. Later, it was found that BR exhibited cytoprotective effects and mildly elevated BR levels showed antioxidant, anti-inflammatory and immunomodulatory properties, however, exact mechanisms of the anti-inflammatory actions of BR have not been fully understood yet. The main aim of this study was to assess the protective effects of BR using experimental in vivo and in vitro models in relation to inflammation and oxidative stress. Partial goal was to establish validated analytical method for determination of BR and lumirubin. Gunn and heterozygous rats were treated with lipopolysaccharide (LPS, 6 mg/kg, IP) or vehicle (saline). After 12 hours, blood and organs were collected for analyses of inflammatory and hepatic injury markers. Primary rat hepatocytes were treated with BR and TNF-α, HepG2 and SH-SY5Y cell lines were treated with BR and chenodeoxycholic acid. LPS-treated Gunn rats had a significantly decreased inflammatory response and hepatic injury compared to LPS- treated normobilirubinemic controls. We found different profile of leukocytes subsets and decreased systemic mRNA expressions and concentrations of IL-6, TNF-α, IL-1β and IL-10 in Gunn rats. Hepatic mRNA...
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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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Detection of Sap2 in the secretome of Candida albicans cell wall and secretory mutants
Kollárová, Nikola ; Janďourek, Ondřej (advisor) ; Konečná, Klára (referee)
Candidate: Nikola Kollárová Title of diploma thesis: Detection of Sap2 in the secretome of Candida albicans cell wall and secretory mutants Charles University, Faculty of Pharmacy in Hradec Králové, Department of Biological and Medicinal Sciences Complutense University of Madrid, Faculty of Pharmacy, Department of Microbiology II Study program: Pharmacy Backgound: The aim of this diploma thesis was to search for C. albicans proteins involved in the secretion of the secreted aspartyl proteinase 2 enzyme (Sap2) evaluating the ability to degrade BSA (bovine serum albumin) as a source of nitrogen in several cell wall and secretory mutants of C. albicans. The work was carried out at the Department of Microbiology II, Faculty of Pharmacy, Complutense University of Madrid. Methods: The supernatant samples of several Candida albicans mutants were tested by SDS-PAGE electrophoresis and stained. Bands corresponding to BSA were observed and compared to controls. The other method was counted with 96-well plate. Results: The correlation between optical density and degradation of BSA was observed. Some mutants with disability to degrade BSA were found in a pilot screening of the ability to degrade BSA using 96-well plate method. That fact was confirmed by SDS-PAGE electrophoresis. C. albicans mutants showing...
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Narušení metabolismu proteinů a jeho efekt na signalizaci cytokininů
Dufek, Martin
Cytokinins are N6 substituted adenine derivatives that affect many aspects of plant growth and development. A multistep phosphorelay systém, including hybrid sensor kinases, histidinecontaining phosphotransfer proteins and two sets of response regulators, is the key part of cytokinin signaling. However, a recent evidence indicates a crucial role for the proteasomeubiquitin systém (UPS) in the cytokinin response. Here, in this thesis entitled 'Protein metabolism disruption and its effect on cytokinin signaling' the major protein degradation mechanisms are outlined and the present-day model of cytokinin metabolism and signaling is discussed. In the experimental part, the UPS-cytokinin interaction is probed in a growth response experiment, an LC-MS proteome analysis and by the datamining of previously published proteomics data. The results indicate an interesting dosage-dependent balance between cytokinin- and proteasome-mediated signaling, and a huge impact of proteasome inhibition on cytokinin response proteins. Key words: proteasome, ubiquitin, growth response, protein degradation, LC-MS, proteome
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