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Fixation and Mutation
Maloušková, Drahomíra ; Nikitová, Alice (referee) ; Artamonov, Vasil (advisor)
My ending Bachelor work related with all my work in school across my stadies here in FFA of BUT in Brno. Obssesive collectibles of different things and materials are my starting point. My father have this behavioral disorder, and it is really inspirated for me. In fact, I will present cca 13 oil paintings about some objects from his collection and relationships between these in space and time.
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Implementation of an evolutionary expert system
Bukáček, Jan ; Müller, Jakub (referee) ; Karásek, Jan (advisor)
This thesis is focused on working up evolutionals and genetics algorithms issues Especially for multiobjective algorithms VEGA, SPEA and NSGA – II. Thereinafter one of FrameWork working with genetics algorithms namely WWW NIMBUS. From this mentioned algorithms was selected VEGA algorithm for implementation in JAVA to preselected problem. Thereby problem is choice thick columns of profile according to predetermined criteria. Selected algorithm works on division of population into several groups and each group evaluates the resulting fitness function. Here is a sample implementation of this algorithm. Furthermore there is a example of working with FrameWork. In the next section are compared the results of generated progam with results that were obtained by FrameWork WWW NIMBUS. As for VEGA, and the Nimbus there are shown different results. The VEGA is presented also the development of individual fitness functions. Also, there are shown graphs, that can be obtained from NIMBUS. At the end of work is introduced the comparation of the results ane propose possible improvements.
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Prediction of the Effect of Mutation on Protein Solubility
Marko, Július ; Smatana, Stanislav (referee) ; Hon, Jiří (advisor)
Protein solubility is a key problem in production of functional proteins. Prediction of the effect of mutation on protein solubility could save a lot of time and money, as it would provide in silico prediction of solubility enhancing mutations before performing deep mutational scanning in laboratory. In this work, new predictor of the effect of mutation on protein solubility SoluProtMut is introduced that is based on machine learning methods. Most of the existing predictors predict the effect from the amino acid sequence. In addition to the sequence, the tool presented in this work also uses the spatial structure of the protein, which can significantly increase it's accuracy.
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Attributes Calculation for Prediction of Mutation Effect on Protein Function
Šinkora, Jan ; Filák, Jakub (referee) ; Jaša, Petr (advisor)
This thesis deals with issues of bioinformatics, machine learning, algorithms and data structures. The thesis is based on existing applications, Caver and Deleterious, developed by students from the Faculty of Informatics, Masaryk University and the Faculty of Information Technology, Brno University of Technology. The Deleterious framework calculates protein attributes that are important for the prediction of the effect of protein mutations on its function. Caver is a tool that finds tunnels in the 3-dimensional model of a protein. The goal of the thesis is to extend these applications by adding more attributes to the prediction process that could lead to improved prediction. The added attributes are related to detection and measurement of protein pockets.
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Analysis of yeast DNA using pulsed field gel electrophoresis
Kubáčková, Martina ; Drábková, Michaela (referee) ; Márová, Ivana (advisor)
Technique of pulsed field gel electrophoresis (PFGE) has found widespread use in the analysis of the genome of all life organisms. It is applied to the separation of the large DNA molecules above thousands base pairs up to millions of base pairs in size, where using conventional gel electrophoresis techniques are not possible (for instance large bacterial, yeast, fungal or mammalian chromosome). Presented work was realized as a comparative analysis of genome of several carotenogenic yeasts. The conditions of isolation and analysis of chromosomal yeast DNA were optimized. A lysis of yeast cells and deproteination of DNA within agarose chops was shown as the most appropriate method for DNA isolation. Cultivation to late exponential phase (50 hours) is the most suitable to obtaining intact DNA in sufficient amount and quality. Carotenogenic yeasts undergo the random mutagenesis using alkylation reagent ethyl methanesulfonate (EMS). Genome of pigment overproducing mutants was analyzed by pulsed field gel electrophoresis and amount of carotenoids by high pressure liquid chromatography (HPLC). However, overproduction of beta-carotene was analyzed in mutant strains Rhodotorula glutinis (10.6 g/l of biomass enriched 0,34 mg/g of beta-carotene) and Cystofilobasidium capitatum (8.5 g/l of biomass enriched 0,23 mg/g of beta-carotene). Selection of mutant strains overproducing carotenoid pigments was in presented experiment series successful in almost all analyzed strains except in the case of the strain Rhodotorula aurantiaca.
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Molecular genetic analysis of thyroid carcinomas in pediatric and adolescent patients
Bulanová, Barbora ; Kuklíková, Vlasta (advisor) ; Ludvíková, Marie (referee) ; Vícha, Aleš (referee)
Thyroid nodules are rare in pediatric and adolescent patients, but they are at greater risk of malignancy than adult patients. Thyroid carcinomas are the most common endocrine malignancy and their incidence is increasing. Although there are several types of thyroid carcinoma, 90% of cases in pediatric and adolescent patients are papillary thyroid carcinomas (PTCs). The aim of this study was to analyze a large cohort of PTCs from pediatric and adolescent patients, determine their genetic cause, and correlate the findings with clinical pathological data. Another aim was to characterize the most frequent findings and compare them with a cohort of adult patients with thyroid carcinoma positive for the same mutation. The final objective was to optimize a suitable methodology for detecting the most common findings in pediatric and adolescent patients for routine use. Thyroid tumor tissue samples were examined using molecular genetic methods, mostly using next-generation sequencing and real-time PCR analysis. We found that fusion genes were the most common cause of PTC in pediatric and adolescent patients, detected in 56% of patients. In total, 20 different types of fusion genes were identified, some of which have not been previously described in the literature. The fusion genes included the oncogenes...
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Detekce variability rDNA u rostlin
Menšíková, Simona
The ITS1-5,8S-ITS2 sequence region of ribosomal DNA represents one of the most popular molecular marker in phylogenetics. However, detailed analyses of 5,8S rDNA are scarce and most of them deal with the complete region including the internal transcribed spacers ITS. In this thesis, 5,8S rDNA sequences were subjected to bioinformatic analysis to compare the variability of ribosomal genes in monocot and eudicot plants. The analyzed sequence data of the regions ITS1-5,8S rDNA-ITS2 were obtained by an experimental approach from isolated DNA and by searching in nucleic acid databases. The variability was assessed in total 114 sequences for each group. Multiple sequence alignments were used to identify conserved regions and to quantify gene mutations. Higher heterogeneity was detected in the 5,8S rDNA sequences of the eudicot group, but no statistically significant difference in the representation of variable sites (15,2 % and 19,3 %) or in the total number of mutations was confirmed. Manual pseudogene detection, based on plant conserved 5,8S rDNA motifs search, sequence length, content of GC and in silico secondary structure prediction, revealed a total of 12 potentially non-functional copies of the 5,8S rDNA gene.
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Development of a new DNA mutation detection technology for application in cancer diagnostics
Janoušková, Kristýna ; Minárik, Marek (advisor) ; Klepárník, Karel (referee)
The aim of this diploma thesis was to test a new technology for DNA mutation detection and to optimize the parameters related to the introduction of a new method, that uses this technology, into oncological diagnostic practice. The new method consists of an experimental modification of an already used method for the detection of somatic mutations in tumor DNA, which is based on heteroduplex analysis and denaturing capillary electrophoresis. The new aspect of the technology is the use of short oligonucleotide probe, which significantly simplifies the interpretation of data and also enables the simultaneous examination of multiple mutations in one reaction (multiplexes). Key words: DNA, denaturating capillary electrophoresis, heteroduplex, mutation, PCR, probe
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Sequence variants in metastatic colorectal cancer and their evolution during the disease course and treatment
Jandová, Eliška ; Boublíková, Ludmila (advisor) ; Vymetálková, Veronika (referee)
A deeper understanding of the molecular background of colorectal cancer (CRC) can help explain the development of the disease and its resistance to treatment, predict disease progression, and improve treatment prognosis. Some minimal molecular testing has been incorporated into standard clinical management to determine if a particular patient will benefit from a particular therapy, but more and more new genetic alterations are being discovered that appear to be associated with the development of resistance. Tissue biopsy of the tumor is the gold standard in terms of molecular testing, but there is an increasing demand for more non- invasive methods such as liquid biopsy. Using targeted next-generation sequencing, we analyzed sequence variants present in primary tumor, metastases, and cell-free tumor DNA - ctDNA of patients with metastatic CRC. The objectives were to analyze sequence variants of the primary tumor and identify possible pathogenic variants, to analyze differences between DNA of the primary tumor and metastases, to evaluate the use of ctDNA as a diagnostic tool, and to identify potential tumor-specific markers in ctDNA that can be used to monitor disease progression. Our results suggest the feasibility of using ctDNA for diagnostic purposes or even to monitor disease progression, but...
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Circulating tumor DNA in urine and its use as a potential biomarker of colorectal cancer
Surkovová, Veronika ; Ptáčková, Renata (advisor) ; Dračínská, Helena (referee)
Colorectal cancer (CRC) is a serious disease whose incidence has been steadily increasing. There is a high chance of cure and a good quality of life, if the treatment is started in the early stages of this disease. The so-called liquid biopsy, in which biomarkers from various body fluids are obtained and analyzed, could help with early detection of the disease, monitoring of the patient's condition and appropriate determination of the diagnosis. The aim of this study is to isolate and analyse circulating tumor DNA (ctDNA) from the urine of patients with advanced CRC. In these patients the ctDNA was detected in plasma. The method used for analysis is based on the principle of PCR with the formation of heteroduplexes, followed by the separation of "wild type" and mutated DNA fragments by denaturing capillary electrophoresis. Unlike plasma samples, the presence of KRAS mutations was not confirmed in urine samples. Neither the established procedure for plasma analysis, the attempt to enrich ctDNA by so-called purification, nor other tested isolation kits using the selected detection method allowed detection of the KRAS mutation in urine via ctDNA. Although urine ctDNA testing in general appears to be a promising method for improving the treatment level of (colorectal) cancer, and although its use could...
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