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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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Monitoring of mitochondria in living cells using fluorescence methods
Taliánová, Eliška ; Čejková, Darina (referee) ; Čmiel, Vratislav (advisor)
This bachelor thesis deals with the topic of monitoring mitochondria and evaluating their activity. The structure and function of cellular mitochondria are briefly discussed. Contains a list of commonly available fluorescent dyes. It investigates the possibilities of influencing mitochondria in vitro. It deals with the influence of mitochondrial membrane potential by means of various concentrations of glucose and subsequently evaluates mitochondrial activity using the dye JC-10.
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Pozitive and negative selection of mitochondrial genome
Svoboda, Matěj ; Kupková, Kristýna (referee) ; Maděránková, Denisa (advisor)
The bachelor thesis engages with problematics of positive and negative selection of mitochondrial genome. Thesis is divided into two parts. First part grapples with theory and explanation of fundamental definitions, in particular understates mitochondrial genome, nucleotide mutation, positive and negative selection and furthermore evolution models. Second part focuses on processing mitochondrial DNA practically and on establishing functions in programming environment R. The emphasis is foremost on gene sequencing alignment and exploring substitutions. Consequently, obtained outcomes are contrasted with PAML and KaKs Calculator programme outcomes.
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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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Monitoring of mitochondria in living cells using fluorescence methods
Taliánová, Eliška ; Čejková, Darina (referee) ; Čmiel, Vratislav (advisor)
This bachelor thesis deals with the topic of monitoring mitochondria and evaluating their activity. The structure and function of cellular mitochondria are briefly discussed. Contains a list of commonly available fluorescent dyes. It investigates the possibilities of influencing mitochondria in vitro. It deals with the influence of mitochondrial membrane potential by means of various concentrations of glucose and subsequently evaluates mitochondrial activity using the dye JC-10.
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Evaluation of antibiotic-induced mitochondrial superoxide production in adherent cells
Ingrová, Kateřina ; Chmelíková, Larisa (referee) ; Zumberg, Inna (advisor)
The theoretical part of this bachelor´s thesis contains a description of the effect of reactive oxygen species on oxidative stress by mitochondria and the consequences of antibiotics use in cell line culturing. The cell line studied in this bachelor´s thesis is the mesenchymal stem cells (MSCs). The practical part describes the procedure of the experiment including cell culturing, passaging and cell labeling. The proposed experiment was repeated with sufficient number of repetitions. Finally, confocal microscopy images were processed in the MATLAB programming environment.
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The role of mitochondrial DNA in reproduction
Svobodová, Mariana ; Daňková, Pavlína (advisor) ; Jelínková, Ladislava (referee)
The bachelor's thesis focuses on the role of mitochondrial DNA (mtDNA) in human reproduction, especially describing the differences in mtDNA dynamics in oogenesis, spermatogenesis and early embryo development. The physiological function of mtDNA is complemented by its pathologies and their effect on fertility and the ability of the embryo to implant successfully. Furthermore, mtDNA is discussed as a possible diagnostic marker in the evaluation of the quality of sperm, eggs and embryos. These findings of these studies are especially significant for assisted reproduction, where the goal is to select the highest quality embryo with the greatest implantation potential. The work also briefly mentions the presence of cell free mtDNA in the mother's blood and its connection with the development of preeclampsia. Key words: mtDNA, mitochondria, reproduction, (in)fertility
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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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The study of mitochondrial energy-metabolism maturation
Křížová, Jana ; Hansíková, Hana (advisor) ; Pecina, Petr (referee) ; Rauchová, Hana (referee)
During intrauterine development in mammals, the fetus is exposed to a hypoxic environment. To allow proper postnatal adaptation to external conditions, a rapid transition from glycolytic to oxidative metabolism by mitochondria is required in fetal tissues after birth. Mitochondrial maturation is a complex process that is not only transcriptionally regulated. Using techniques such as microarray analysis, quantitative PCR, measurement of enzyme activities or coenzyme Q (CoQ) levels, we have described the acceleration of mitochondrial metabolism in rat liver tissue and skeletal muscle during the perinatal period and correlated the results with those in humans. Of the 1546 rat mitochondrial genes tested, we found statistically significant differences in the expression of 1119 in liver and 827 in muscle. The most significant shift in expression occurred in the rat liver between 20th and 22nd day of gestation, suggesting that the rat fetus is ready for the transition to external conditions at least 2 days before birth. Changes in CoQ levels in both rats and humans show that the amount of CoQ is low inthe prenatal period and increases after birth in both tissues. We have described the atypical kinase Coq8ap as an enzyme whose expression increases significantly after birth. It was previously predicted to...
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Mitochondrial structure and energetic metabolism changes in patients with Huntington's disease and in transgenic minipig model
Vanišová, Marie ; Hansíková, Hana (advisor) ; Kalous, Martin (referee) ; Mühlbäck, Alžbeta (referee)
Huntington's disease (HD) is a severe neurodegenerative disease with autosomal dominant inheritance. HD is caused by the expansion of the CAG triplet in the gene for the huntingtin protein (Htt), which leads to damage and loss of its functions. Htt is essential in the development of the nervous system, it is involved in axonal transport, regulation of mitochondrial metabolism gene expression or spermiogenesis. In HD, the nerve tissue is most significantly damaged, but pathological changes associated with the disease are detected throughout the organism. There is currently no satisfactory treatment. Mitochondrial damage has been shown to significantly affect the progression of HD in patients with HD, but the mechanisms of mitopathy and its development with all the effects on tissue physiology in HD are still not fully understood. The aim of the dissertation theses was to study mitochondrial energy metabolism impairment, mitochondrial network organization and mitochondrial ultrastructure in HD in selected tissues of patients with HD and in a minipig model transgenic for HD (TgHD). Furthermore, the effort was to find and characterize a mitochondrial biomarker of HD, which would well reflect the patient's current clinical phenotype state and it would be possible to monitor changes in its parameters...
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