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Microarray Data Interpretation
Ludwig, Petr ; Šilhavá, Jana (referee) ; Smrž, Pavel (advisor)
This Bachelor thesis explains the basics of biochip or microarray data interpretation, starting with short introduction to genetics, especially genetic information significance evaluating. The focus was set mainly on the set of scripts transforming and analyzing the sample data. The data used in this thesis are a result of biochip analysis of the Colon Tumor tissues. The secondary result represents disclosing the main marker for this particular type of cancer, the primary result is evaluation of marker significance in the context of signaling pathways. The resulting pathways are sorted by relevance.
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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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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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Birth
Piskova, Olena ; Klímová, Barbora (referee) ; Gabriel, Michal (advisor)
The thesis is a continuation of my subject, "Why?", Also includes the theme of man and the environment. I started to be interested in the controversial topic of genetically modified organisms, genetic engineering. I found a personal story in it. Now it is difficult to comment on the extent to which these researches are important, but we shouldn’t stop there.
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Entity
Jindra, Jakub ; Turek, Filip (referee) ; Hájek, Václav (advisor)
Informace může vytvářet určité entropické krajiny. Entropická krajina je složená ze zdrojů informace. Zdroj může být informačně přínosný nebo úplně zbytečný. Dobrý zdroj vytváří nízkou entropii, vysoký náboj, a špatný zdroj entropii vysokou s nízkým informačním nábojem. Touto optikou pak můžeme vidět fiktivní krajinu, která se kolem nás nalézá. Entita je její vizualizací, vytváří útesy, tam kde byly roviny, hory zkoncentrované informace a měsíční údolí s nulovou hodnotou.
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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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Analysis of selected gene variants in athletes - runners at 400 m
Šplíchalová, Dominika ; Petr, Miroslav (advisor) ; Šteffl, Michal (referee)
Title: Analysis of selected gene variants in athletes - runners at 400 m Objectives: This work aims to find out what the genetic profile of athletes - runners at 400 meters, who are working in lactate mode, looks like. Methods: A cross-sectional investigation involved 203 East European Caucasian males and was conducted collaboratively at the FTVS UK and Józef Piłsudski University of Physical Education in Warsaw (AWF Warsaw). The athletes, after a brief warm- up, participated in a single 30-second Wingate test. DNA samples were collected non-invasively through saliva swabs. Lactate levels were measured using an invasive approach. Results: In the polymorphisms rs4646994 gene ACE was found to have a significant difference in genotypic (p = 0.001, x2 = 14.90) and allelic (p = 0.004, x2 = 8.52) frequencies between the overall athlete group and the controls. A notable difference in the ACE gene showed the comparison of the genotypes (p = 0.001, x2 = 13.66) and between the alleles (p = 0.003, x2 = 8.89) between the control group and elite athletes. The last statistically significant difference was observed among the genotypes (p = 0.03, x2 = 6.79) between the sub-elite athletes and the control group. When assessing the genotypic and allelic frequencies for the polymorphisms rs1815739 in the ACTN3 gene, we...
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Strategies and results in the development of insulin derivatives for the treatment of diabetes
Pokorný, Štěpán ; Jiráček, Jiří (advisor) ; Hlouchová, Klára (referee)
The aim of this bachelor's thesis is to present insulin analogs and to analyse the direction of development of these organic compounds. The text contains basic information on this subject (e.g. the history of Diabetes Mellitus, the first treatment, the discovery of insulin (1921) and the experiments that preceded this discovery...). The thesis also explains the basic differences between type 1 and type 2 Diabetes Mellitus and the resulting differences in treatment. It mainly summarizes, the specific types of analogs, their chemical composition and the nature of their action. The main contribution of this work lies in the analysis of insulin analogs and the overview of the course in which the development of these analogues is proceeding or what innovations we can expect in diabetes therapy in the upcoming years. The thesis draws primarily from peer-reviewed scientific papers, articles and books (older as well as more recent ones) and from the expertise of the IOCB laboratory. All sources are well cited at the end of the work.
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Maternal effect in selected rodent species: positive and negative effect on offspring fitness
Malá, Jana ; Landová, Eva (advisor) ; Stopková, Romana (referee)
This work describes the most studied mechanisms which could be classified as maternal effects. Here I focus on the effects of body weight, health status, intestinal microflora and age of the mother in model rodent organisms. I also present factors such as the position of the young in the uterus, population density, stress and especially maternal care, which accompanies this entire work. Each of these mechanisms can positively or negatively influence offspring fitness, depending on specific environmental conditions. Maternal behaviour is presented here in the form of research, which documents both epigenetic and genetic influences acting on its final form. Maternal care as an element of maternal behaviour shows a different measure between individuals, indicated by the frequency of licking and cleaning offsprings. By evaluation of maternal care, we can find in laboratory populations two stable phenotypes of individuals with different behavioural manifestations in terms of sexual behaviour, stress reaction, aggression or cognitive abilities. The discussion critically evaluates whether maternal care really affects reproductive success and whether it can therefore be considered an adaptive mechanism. According to the available information, low maternal care appears to be a more beneficial strategy in...
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