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Study of genome of Metschnikowia yeasts by molecular methods
Schneiderwindová, Nicole ; Skoumalová, Petra (referee) ; Němcová, Andrea (advisor)
Yeasts of the genus Metschnikowia belonging to the family Metschnikowiacea are yeasts characterized by vegetative propagation through multilateral budding. These are yeasts widely distributed in nature. More than 35 species occurring have been defined in the wild. They most often occur on flowers, fruits, but also on insects or human skin. They have a wide range of uses due to their antifungal effects in agriculture and the cosmetics industry. This bachelor thesis deals with the study of usage of molecular methods to characterize selected species of yeasts of the genus Metschnikowia. It focuses on a detailed description of the yeast cell structure, karyotype and methods of reproduction in the theoretical part of the work. In the practical part on optimization and description of molecular methods including pulse gel electrophoresis methods used to separate the yeast genome and their subsequent observation of changes in individual parts of genome. First, the yeast was cultured under special conditions that are characteristic of Metschnikowia yeasts, then yeast DNA was isolated using methods suitable for DNA isolation, which was further examined by the PFGE molecular method. The DNA isolation procedure was first optimized for individual yeast strains, as it was necessary to verify the required ratio of low melting agarose to isolated DNA. That was because of it was important for the resulting gel blocks to be suitable for measurement by PFGE analysis. By optimizing the method was possible to create ideal blocks of isolated yeast DNA, which were subsequently subjected to PFGE analysis. Several measurements of PFGE analysis were performed at different time intervals in order to separate small and large yeast chromosomes. The CHEF standard of the yeast Hansenula wingei and the standard of the yeast Schizosaccharomyces pombe were used for the measurements. According to the measurement results, it can be determined that the yeast DNA isolation procedure and subsequent analysis by pulsed gel electrophoresis were successful, as the number of chromosomes of all used yeast species of the genus Metschnikowia was determined.
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Detection of Genome Variations
Beluský, Tomáš ; Vogel, Ivan (referee) ; Martínek, Tomáš (advisor)
An influence of variations in human genome is perceptible at a first glance on human itself to see differences between the individuals and entire populations. Also, behavior or probability of certain diseases are influenced in large way by differences at genome's level. This work presents methods for detecting variations in the human genome that were developed after an arose of the second-generation sequencing technologies. A new tool that combines read pair and split read methods, with information about a depth of coverage was also designed and implemented. The tool was tested on simulated and real data and compared with a reference outputs.
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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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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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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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Comparative and phylogenetic analysis of viruses in the University Hospital Brno
Švestková, Tereza ; Sedlář, Karel (referee) ; Nykrýnová, Markéta (advisor)
This thesis is focused on the SARs-CoV-2 coronavirus associated with severe acute respiratory syndrome, which was first identified in 2019. This coronavirus caused a pandemic that affected almost the entire world. Knowledge of the genetic information is needed for vaccine development, to determine infectivity and to predict the evolution of SARs-CoV-2 variants. To obtain genetic information, RNA must be sequenced and these genomic sequences must be assembled. By comparing the assembled genomes, it is possible to find out which part of the organism has mutated. Phylogenetic analysis is performed on the basis of the concordance or divergence in the assembled genomes, which indicates the evolution of the organism and shows the evolutionary relationship with other organisms. The practical part is focused on the assembly of genomes from samples from patients in the University Hospital Brno and evaluation of the quality of the assembly. After the genomes are assembled, the next goal is to evaluate the variability and subsequent phylogenetic analysis.
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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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Prediction of the replication origin in prokaryotic genomes
Lebó, Marko ; Maděránková, Denisa (referee) ; Sedlář, Karel (advisor)
This bachelor’s thesis deals with the problem of origin of replication (oriC) detection in genomes of prokaryotic organisms. It describes the differences in the processes of initiation of replication in organism of the both procaryotic domains – Bacteria and Archea. It describes the possibilities of conversion of DNA sequences into their numeric representaions and evaluates their application for oriC detection. Also, it describes different approaches in oriC detection and describes te functioning of already present programmes for oriC detection. Finally, it suggests a new tool for oriC detection in bacterial genomes – FindOri and discusses results, achieved during the testing of this tool.
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Bacterial species delineation based on parameters derived from numerical representations of genome
Oweis, Kamil ; Jugas, Robin (referee) ; Maděránková, Denisa (advisor)
Modern methods of processing genomic data yield good results, however they are often redeemed by time consummation. This is mainly the reason why this thesis deals with numerical methods of bacterial genome processing which could be a suitable alternative for current methods, both in terms of quality and computational demands. This thesis presents the current methods used for processing of genomes in silico and proposes suitable numerical presentations for the whole genome analysis. Some of these methods are programmed and used for processing further in this diploma thesis. In it, various mathematical and statistical methods are being tested, ones that could lead to successful species delineation of bacteria by numerical presentations of their genomes.
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Fuzzy classification of DNA sequences
Těthal, Jiří ; Maděránková, Denisa (referee) ; Škutková, Helena (advisor)
The work deals with the fuzzy classification of DNA sequences. In the first part the theory summarized information about Fuzzy logic and methods of its use in the classification of biological sequence data. The second part is practically deal with the classification algorithm for assessing the similarity of sequences. Specifically, the dividing of coding and non-coding parts of the sequence and the use of fuzzy classification in DNA barcoding.
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