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Digital processing of plant genomes
Jugas, Robin ; Škutková, Helena (referee) ; Sedlář, Karel (advisor)
This work continues in development of DNA numerical representation’s field in the recent years. The aim of this bachelor thesis is to work out an overview of numerical representations of DNA sequences and to describe the differences and properties of nuclear and mitochondrial genetic code focused on plants. Final objective is analysis of usability these signal’s representations for classification of organisms. The theoretical part is focused on description of biological facts, overview of conversion methods of DNA sequences into signals, the methods of organisms classification and the DTW algorithm. The practical part contain the created GUI application for organism classification based on numerical sequences and the analysis of usability these numerical representations for classification. The outputs of cluster analysis of numerical sequences are compared with the phylogenetic tree.
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Digital signal processing of mitochondrial genomes
Sonnenschein, Jiří ; Vítek, Martin (referee) ; Škutková, Helena (advisor)
The aim of this thesis is to test new less hardware demanding method of mitochondrial genom classification, for which numerical representation of biological sequences is used. Introductory part is focused on description of nucleic acids and mitochondrion. In following part of thesis, types of numerical representation of biological sequences without losing the original biological information are described. There are introduced possibilities of phase and frequency-domain analysis and principles of cluster analysis and dendrogram construction methods. Practical part of this work deals with analysis of mitochondrial genome for which cumulated and unwrapped phases are calculated. Mitochondrial sequences are compared by cluster analysis and dendrogram is constructed.
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Developmental, pathobiochemical and molecular aspects of selected inborn errors of metabolism
Kolářová, Hana ; Honzík, Tomáš (advisor) ; Drahota, Zdeněk (referee) ; Morava Kozicz, Eva (referee)
Inborn errors of metabolism represent a heterogenous group of rare conditions, most having an incidence of less than 1 in 100,000 births. Because of their low prevalence, they are on the margin of attention of general research and even more so of large pharmaceutical companies. Study of rare diseases is the only way to design therapeutic options in order to improve quality of life of affected patients. Present Thesis particularly focuses on disturbances in mitochondrial energy metabolism. The main goals were the characterization of mitochondrial biogenesis within foetal development, as well as in childhood and adulthood. Another aim was to define clinical, biochemical and molecular aspects of mitochondrial optic neuropathies in childhood and adulthood. This work supported the earlier observations that gestational week 22 is the edge of viability, which has to be taken into account in upcoming discussions about guidelines on resuscitation of preterm neonates. Secondly, over last four years, we managed to examine and describe large cohort of patients with optic neuropathies based on a mitochondrial dysfunction. We have managed to characterize the biochemical and molecular-genetic background in more than 200 patients, and both selected cases (LHON/MELAS overlap syndrome) and cohort studies (MELAS,...
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Effect of lipophilic cation on the toxicity of phosphonium salts in parasitic protists
Čadková, Aneta ; Mach, Jan (advisor) ; Trnka, Jan (referee)
The mitochondrion is an essential organelle responsible for energy metabolism and maintaining cellular homeostasis. Disruption of their function can have serious consequences for the entire cell and organism. Given their key role in the organism, they become an attractive target for drugs. In this thesis, we examine the impact and significance of phosphonium salts as potential mitochondrial-targeted therapeutics. The investigated compounds have modified anchors based on the commonly used triphenylphosphonium cation (TPP+ ). These substances have the ability to permeate the phospholipid bilayer and accumulate on the inner mitochondrial membrane. Our research focuses on selected model organisms of the class Kinetoplastida and opportunistic pathogenic fungi. These pathogenic organisms are responsible for severe infectious diseases in humans. Our aim is to compare the effectiveness of phosphonium salts with different anchor modifications against these organisms and attempt to elucidate their mechanism of action. We have found that the modified salts are capable of inhibiting the growth of parasitic protists at nM concentrations, affecting mitochondrial respiration, membrane potential, and mitochondrial integrity. However, there is no increase in the level of oxygen radicals. We are assuming that the...
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Characterisation of novel mitochondrial proteins in \kur{Trypanosoma brucei}
RAŠKOVÁ, Vendula
This study analyses and characterises novel mitochondrial proteins in the parasitic protist Trypanosoma brucei. Applying phylogenetic analysis was described the evolutionary origin of ZapE protein in eukaryotes, using a newly developed proximity-dependent biotinylation approach (BioID2) we identified ZapE interaction partners like Oxa1. We also discovered a relationship when distribution of mitochondrial ZapE is restricted only to organisms with Oxa1, respiratory complexes, and a mitochondrial genome. TbPams were detected by phylogenetic analyses as orthologs of corresponding proteins in Opistokonts. We analyse the function of TbPam18 and TbPam16 in the replication of the mitochondrial DNA and determine, how the TMDs of TbPam18 and TbPam16 are essential for their functions. Finally, we evaluated a set of putative mitochondrial proteins of the heterolobosean N. gruberi defined by Localisation of Organelle Proteins by Isotope Tagging (LOPIT) and analyse the origin of mtFfh and mtFtsY.
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Mitochondrion of Trimastix pyriformis
Novák, Lukáš ; Hampl, Vladimír (advisor) ; Kolísko, Martin (referee)
2013 DIPLOMOVÁ PRÁCE Lukáš Novák Abstract Free-living microaerophilic protist Trimastix pyriformis is closely related to oxymonads which are the largest eukaryotic group without any known mitochondrion. In contrast to oxymonads, an enigmatic reduced mitochondrion has been found in the cell of T. pyriformis. In EST data of T. pyriformis, a number of genes has been identified whose products are putatively localized in the mitochondrion. Among these are genes for all the components of the glycine cleavage system, [FeFe]hydrogenases and the mitochondrial marker Cpn60. We performed experiments in order to determine the cellular localization of these proteins. Our results show that the glycine cleavage system is localized in the mitochondrion. Results of the experiments carried out in order to localize two hydrogenases suggest also the mitochondrial localization but are not fully convincing. The attempt to localize Cpn60 has failed. We have also identified a set of new genes in transcripts of T. pyriformis and Monocercomonoides sp. (Oxymonadida). These genes code for some components of the SUF system of FeS cluster synthesis and a peroxidase rubrerythrin. Key words: Trimastix, Monocercomonoides, mitochondrion, hydrogenosome, mitosome, hydrogenase, glycine cleavage system, SUF system.
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Iron-Sulfur cluster assembly in Monocercomonoides exilis
Vacek, Vojtěch ; Hampl, Vladimír (advisor) ; Balk, Janneke (referee) ; Tsaousis, Anastasios (referee)
In the search for the mitochondrion of oxymonads, DNA of Monocercomonoides exilis - an oxymonad isolated from the gut of Chinchilla, was isolated and its genome was sequenced. Sequencing resulted in a fairly complete genome which was extensively searched or genes for mitochondrion related proteins, but no reliable candidate for such gene was identified. Even genes for the ISC pathway, which is responsible for Fe-S cluster assembly and considered to be the only essential function of reduced mitochondrion-like organelles (MROs), were absent. Instead, we were able to detect the presence of a SUF pathway which functionally replaced the ISC pathway. Closer examination of the SUF pathway based on heterologous localisation revealed that this pathway localised in the cytosol. In silico analysis showed that SUF genes are highly conserved at the level of secondary and tertiary structure and most catalytic residues and motifs are present in their sequences. The functionality of these proteins was further indirectly confirmed by complementation experiments in Escherichia coli where SUF proteins of M. exilis were able to restore at least partially Fe-S cluster assembly of strains deficient in the SUF and ISC pathways. We also proved by bacterial adenylate cyclase two-hybrid system that SufB and SufC can form...
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The role of mitochondria in cardioprotective effect induced by hypoxia in rat
Lomnický, Matouš ; Žurmanová, Jitka (advisor) ; Hlaváčková, Markéta (referee)
Aerobic organisms need sufficient oxygen supply to maintain homeostasis. These organisms are frequently exposed in hypoxic environments naturally, and also occur in hypoxic states in various pathological conditions. Cardioprotective effect of hypoxia had been recognised more than 30 years ago; and later on, cardioprotective effects of ischemic preconditioning were discovered. Long term exposure to hypobaric hypoxia activates cardioprotective mechanisms, which lower the aftermathes of short term ischemia of myocardia and the effects of further health complications. The core of protective mechanisms has not yet been fully clarified. This work deals with the significance of mitochondria on cardioprotection during hypobaric hypoxia adaptation. This work describes physiological adaptive processes on selected animals on natural hypoxic conditions and also molecular mechanisms, examined on experimental models. Molecular mechanisms of the origins of cardioprotective effects discovered so far, mainly indicate PKC signal pathways through thyrosine kinase and mitogenes of activated kinase and also indicate an activation of sarcKATP-channels and mitoKATP-channels. Opening of these channels can protect mitochondria against a Ca2+ overload, or can lead to an increase in mitochondrial capacity which is possibly connected...
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Impact of the glycine-rich loop on the function of processing peptidases of the mitochondrial type
Kučera, Tomáš
A B S T R A C T The majority of the mitochondrial proteins is synthetized on the cytosolic ribosomes in the form of the protein precursors bearing mitochondrion-targeting signal presequences. Once the protein precursor has reached the mitochondrial matrix the signal presequence is no longer necessary and is cleaved off by heterodimeric mitochondrial processing peptidase (MPP; α/β). Although the crystal structure of MPP is available, the MPP mechanism of function is still matter of discussion. An all atomic, non-restrained molecular dynamics (MD) simulation in explicit water was used to study in detail the structural features of the highly conserved glycine-rich loop (GRL) of the regulatory α-subunit of the yeast MPP. Wild-type and GRL-deleted MPP structures were studied both in the presence and absence of a substrate in the peptidase active site. Targeted MD simulations were employed to study the mechanism of substrate translocation from the GRL to the peptidase active site. We demonstrate that the natural conformational flexibility of the GRL is crucial for the substrate translocation process from outside the enzyme towards the MPP active site. We show that the α-helical conformation of the substrate is important not only during its initial interaction with MPP (i.e. substrate recognition), but also later,...
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