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Similarity/dissimilarity analysis of genomic data on the basis of graphical representation
Těthal, Jiří ; Provazník, Ivo (referee) ; Maděránková, Denisa (advisor)
The work deals with the identification of species of animal through the density of nucleotids of mitochondrial gene CO1. In the first part the theory summarized information about DNA barcoding and the mitochondria, cellular organel that with this method is closely related. The second part deals with virtually comparing different sequences using the density of nucleotides. For this it was created program, which uses two functions, the first of the specified nucleotide sequence calculates the density and one can compare the density by distance methods.
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Comparison of mitochondrial DNA for species identification
Labounek, René ; Provazník, Ivo (referee) ; Maděránková, Denisa (advisor)
The work deals with the method of recognizing species on the analysis of mitochondrial DNA segment. This analysis and classification using segment gene called CO1 in literatures such as barcode of life. In the beginning of work is analyzed the mitochondrial theory of heredity and conditions of formation of barcode. Practical use is based on this theory in creating database of barcodes generated to different animal species. Data used for creating the library are drawn from public databases NCBI and BOLD Systems. The next part of this work concerns about methods of comparison of the individual barcodes to the others and especially to the barcode of human. Three main computing methods were used tore these analyses: Needleman-Wunsch algorithm, Smith- Waterman algorithm and comparison of similarities using distance matrix. This work also concerns about transformation of DNA molecule sequences from symbols to numeric formats, which is required for the distance matrix comparison method. Algorithms for searching for a barcode of a species and vice versa were created to ease the work with data.
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Computational modelling of mechanical tests of animal cell
Orlová, Lucie ; Fuis, Vladimír (referee) ; Burša, Jiří (advisor)
Předkládaná diplomová práce se zabývá stavbou živých živočišných buněk a jejich odezvou na mechanické zatěžování. Zobecněným zaměřením práce je popis mechanického chování buňky nejenom ve fyziologickém, ale i v patologickém stavu. Výchozím předpokladem pro úspěšné řešení zadané úlohy je vysoce interdisciplinární přístup kombinující výpočtové přístupy mechaniky těles (v~tomto případě metodu konečných prvků) s lékařským výzkumem. Nejdůležitějším bodem při tvorbě výpočtového modelu, pomocí něhož je možné aproximovat chování živé buňky při zatížení, je zejména identifikace mechanicky významných komponent a~jejich materiálových parametrů. V tomto případě jsou jako mechanicky význačné identifikovány spojité součásti jádro, membrána a cytoplazma, které jsou nově propojeny s prvky diskrétními (mitochondriální sítí) v hybridním modelu, jehož platnost je ověřena pomocí experimentálních dat. Tento model slouží jako podklad k vyhodnocení míry vlivu mitochondrií na celkovou tuhost buňky.
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Ferrous nanoparts localization in inner organelles
Solař, Jan ; Janoušek, Oto (referee) ; Čmiel, Vratislav (advisor)
This bachelor‘s thesis describes a behavior of iron nanoparticles in human mesenchymal stem cells. First section deals with methods of fluorescent labelling of organelles and nanoparticles and settings of confocal microscope for their detection. Next section describes the iron nanoparticles metabolism and accumulation in cells. Finally, there is a section about the developement of the software utility for the localization and for the quantitative analysis of the fluorescence organelles and nanoparticles inside the living cells.
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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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