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Comparison of detection of biofilm formation in clinical strains of Staphylococcus aureus from wounds using culture and genetic methods.
VÁLKOVÁ, Tereza
The main topic of this bachelor thesis is the bacterium Staphylococcus aureus, its ability to form a biofilm and the diagnostics of this formed biofilm. The theoretical part of the thesis first focuses on the bacterium itself, its morphology, antigenic structure and virulence factors. Furthermore, its pathogenesis and pathogenicity will be described, including the issue of the methicillin-resistant Staphylococcus aureus. The next part focuses on the biofilm. The composition, structure and formation of biofilm will be described, as well as its role in pathogenicity, treatment options and various methods of detection. The practical part describes methods of biofilm detection. The first method is crystal violet staining according to Christensen. This method came out positive for all 94 tested strains of Staphylococcus aureus. Subsequently, these strains were divided into categories according to the strength of biofilm production. The second method was Real-time PCR and the detection of selected genes responsible for biofilm formation: clfA, fnbA and fnbB. 2-3 genes were found in 93 samples, and only one sample contained none of the selected genes. Thus, it was shown that all strains are capable of biofilm formation to varying degrees, and no correlation was found between the presence of the examined genes and the level of biofilm production.
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Audio effect based on signal spectrum modification
Vejvoda, Zdeněk ; Sysel, Petr (referee) ; Schimmel, Jiří (advisor)
The thesis describes the design and the engineering solution of a hardware electronic sound effect that is a mixture of a frequency shifter and a delay effect. Electronic music intruments, sound effects and particularly modular synthesizer of the Eurorack standard are introduced. The firmware, developed utilizing the Max Gen environment and running on an ARM chip, prompted an examination of the Max platform. Finally, the thesis explores the calculations and processes required to construct a fully functional effect module. The device was assembled, tested and measured.
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Bioinformatics of human genome
Kupková, Karolína ; Provazník, Ivo (referee) ; Maděránková, Denisa (advisor)
Bachelor thesis deals with DNA segments containing only adenine and guanine. The theoretical part describes the structure and composition of deoxyribonucleic acid, chromosomes and genes. There are basic informations about chimpanzees and the human genome and conformations of the chains containing adenine with guanine. The practical part consists of a program that searches for the required sections in sequence, it displays and saves it. The thesis includes analysis of genes which are common for humans and chimpanzees, which were analyzed to determine randomness, functionality a preserving of these sections.
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Evolutionary algorithms
Bortel, Martin ; Karásek, Jan (referee) ; Burget, Radim (advisor)
Thesis describes main attributes and principles of Evolutionary and Genetic algorithms. Crossover, mutation and selection are described as well as termination options. There are examples of practical use of evolutionary and genetic algorithms. Optimization of distribution routes using PHP&MySQL and Google Maps API technologies.
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Genetic Algorithm Design for Distribution Network Outfits Optimalization
Ondruš, Tomáš ; Skala, Petr (referee) ; Paar, Martin (advisor)
The work deals with genetic algorithms and their potential use in application software to optimize high voltage switching elements of distribution network. Theoretical part explains the basic concepts of genetic algorithms such as a gene, population and chromosome and basic principles of the development of genetic algorithms.. The main task of the thesis is to design the algorithm that will simulate the distribution of the sectionalizers by telecontrolled section switches or reclosers and analyze how to set the the parameters affecting the convergence speed of genetic algorithm. The basic parameters affecting the convergence of breeding, mutation probability, population size or using of elitism. The second goal is finding a suitable set of input parameters for the selected population sizes without and with using elitism. The results of the work determine the most appropriate settings for each generation and determining the approximate number of generations needed to find the best solution. The genetic algorithm applocation was tested on a less extensive distribution network with six switching elements
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Gene order conservation in bacterial genomes
Martinková, Tereza ; Sedlář, Karel (referee) ; Maděránková, Denisa (advisor)
Theoretical part of the thesis deals with basic concepts such as bacterial genome, comparative genomics and mainly synteny blocks. Here is explained what synteny is and what is its importance. In the theoretical part, the GenBank format is also mentioned, its content and usage. The practical part is focused on searching similarities in DNA sequences of reference bacteria with selected bacteria, their sorting by means of greedy algorithm and visualization of similarities using phylogenetic tree.
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Evolutionary algorithms
Bortel, Martin ; Karásek, Jan (referee) ; Lambertová, Petra (advisor)
Thesis describes main attributes and principles of Evolutionary and Genetic algorithms. Crossover, mutation and selection are described as well as termination options. There are examples of practical use of evolutionary and genetic algorithms. Optimization of distribution routes using PHP&MySQL and Google Maps API technologies.
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Comparison of genomes by synteny block analysis
Pavel, Tomáš ; Škutková, Helena (referee) ; Maděránková, Denisa (advisor)
The theoretical part of this bachelor thesis is aimed at basics of genetics. Term of gene and mutation are introduced in this section. There are gene and chromosome mutations mentioned and described. Following section is devoted to comparative genomics and especially to synteny. There is described what the synteny actually is and how the synteny arises. The end of the theoretical part of this thesis is about the evolution and there are described ways of sorting permutation vectors. The practical part of this bachelor thesis includes description of developed software. Output of this software is a dot-plot which shows detected synteny blocks. Indexes of these blocks are listed in GUI. The second important output is number of permutation steps. This number determines evolutionary distance between two analysed DNA sequences. The very last section is aimed at analyse of synthetic and real DNA sequences.
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Bioinformatic analysis of single nucleotide polymorphisms in the 1000 Genomes Project database
Parobková, Viktória ; Roy, Sudeep (referee) ; Provazník, Ivo (advisor)
Sekvenovanie celého ľudského genómu a nájdenie jeho variácii bolo výzvou počas mnohých rokov. Znalosť všetkých genetických variácií je pozoruhodne prospešná pri výskume chorôb. Táto práca je zameraná na genetické variácie človeka a ich dva hlavné výskumné projekty, The HapMap Project a The 1000 Genomes Project, ktoré pomohli v analýze chorôb. Prvá časť práce je venovaná teoretickému popisu projektov. V nasledujúcej časti práce sú popísané štruktúry databáz u oboch projektov a taktiež je predstavený online nástroj umožňujúci prehľadávanie a sťahovanie ich dát. Následne je prevedená štatistická, populačná a bioinformatická analýza štrukturálnych variácií produkovaných 3 fázou 1000 Genomes projektu.
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