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Development of Meta-Server for Prediction of Mutations Effects on Protein Function
Lisák, Peter ; Burgetová, Ivana (referee) ; Jaša, Petr (advisor)
This bachelor thesis deals with analysis of genomic data, more specifically prediction of effects of mutations on protein function using a protein sequence or tertiary structure. The theoretical introduction describes the basics of genetics and bioinformatics and is followed by description of selected prediction tools such as SIFT, MAPP and AUTO-MUTE. A unified interface for work with different tools is proposed in the thesis. The meta-server interface allows running a computation and collecting results from one site. meta-server combines results of implemented tools and provides a consensual prediction, which is expected to be more accurate than the results from individual tools. Finally, testing of meta-server on the real data and comparisons of predictions with the experimentally obtained results are presented.
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Functional Annotation of Nucleotide Polymorphism Using Evolution Strategy
Šalanda, Ondřej ; Martínek, Tomáš (referee) ; Bendl, Jaroslav (advisor)
This thesis brings a new approach to the prediction of the the effect of amino acid substitution. The main goal is to create a new meta-tool, which combines evaluations of eight already implemented prediction tools. The use of weighted consensus over those tools should lead to better accuracy and versatility of prediction. The novelty of developed tool lies in involving evolution strategy with experimentally defined parameters as a way to determine the best weight distribution. At the end, a complex comparison and evaluation of results is given.
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Analysis of TP53 gene transcriptional varians in human leucemic cells
Vlahová, Veronika ; Mgr.Diana Grochová, Ph.D. (referee) ; Malčíková,, Jitka (advisor)
The theoretical part of the thesis summarizes general information about the human TP53 gene and p53 protein, which is encoded by this gene. There is also dealt with the transcriptional variants - p53 isoforms. The experimental part is focused on the detection of isoform p53 and its shorter, yet undescribed form. The starting material is peripheral blood of patients from University Hospital Brno, from which RNA was isolated. Subsequently, RNA was transcribed by reverse transcription into cDNA which was amplified by polymerase chain reaction (PCR). Experimental measurements demonstrate that p53 occurs in all the B-lymphocytes of patients with chronic lymphocytic leukemia. It also demonstrats the existence of a shorter form of p53.
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Attributes Calculating for Prediction of Effects of Mutation on Protein Function
Matějíček, Jiří ; Burgetová, Ivana (referee) ; Jaša, Petr (advisor)
This bachelor thesis deals with the bioinformatics techniques for the acquisition of attributes useful for prediction of mutation effects on the protein function. The work primarily aims to develop a user-friendly application for calculation of attributes of mutations from the protein sequence and structure. The developed application serves for integration of specialized tools such as FoldX. The standardized interface enables to implement additional computational tools and collect a diverse set of attributes from different sources. These attribute sets can then serve as an input for different prediction methods and help to improve predictions of mutation effects.
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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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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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