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Syndromes associated with numerical aberrations of gonosomes
Sluková, Kristýna ; Mrňáková, Hana (advisor) ; Trková, Marie (referee)
Before the offspring is born, multiple flaws in the DNA, that strongly influence its future life, can occur. These may include differences in the structure of the Chromosomes or their overall quantity. Deviations from the standard genetic attributes of those Chromosomes will cause anatomic and physiological changes on the specimen. These changes act in a repetitive manner if certain conditions are met and because of multiple combinations of symptoms, genetic syndroms with similar manifestations have been categorized and named. As these abnormalities occur in early pre-natal stages od the offspring's development, there is no way of preventing them, avoiding them or completely curing them.
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Learning Progression-Based Assessment of Modern Genetics
Procházka, Marek ; Janštová, Vanda (advisor) ; Jáč, Martin (referee)
Molecular biology and genetics represent some of the most challenging biological topics for students, a correct understanding is also essential for the other chapters of biology and chemistry. The learning progression test is a tool that allows to determine the level of understanding of the given fields, which can serve as feedback that can be followed up in a targeted manner in further teaching. The aim of this work was to translate and subsequently validate the test of learning progression in molecular biology and genetics from the English original "Learning Progression-Based Assessment of Modern Genetics". Another goal of the thesis was to explain the possible influence of variables (e.g. participation in a biology seminar, science competitions or future study focus) on the overall score. Validation took place in several phases (checking the translation by experts and didactics, testing at schools and subsequent evaluation and analysis). Grammar school students completed the test online during biology class. They achieved a low level of understanding of heredity at the molecular level, further in the area of the influence of the environment on genetic information, the transfer of genetic information to offspring, and in general it is difficult for them to apply theoretical knowledge to specific...
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Molecular genetic analysis of thyroid carcinomas in pediatric and adolescent patients
Bulanová, Barbora
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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GUI for Handling Genetic Programming Chromozome
Staurovská, Jana ; Žaloudek, Luděk (referee) ; Jaroš, Jiří (advisor)
The main goal of this thesis is to create a program for manipulation with genetic programming chromosomes, which should allow export to a vector graphics format, moving of gates, their colouring and other graphical operations, and will work on different operating systems (mainly Microsoft Windows and Linux). For better understanding, the basic principles of cartesian genetic programming are described in theoretical part.
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Analysis of Genomic Data with the Assistance of Algorithm BLAST
Křížová, Martina ; Burgetová, Ivana (referee) ; Jaša, Petr (advisor)
This Bachelor Thesis describes analysis of genomic data with assistance of algorithm BLAST. In theoretic part, it describes genomes, their importance and structure. In this thesis, you can find a description of algorithm BLAST, Smith-Waterman and Needleman-Wunsch and with algorithm BLAST connected Karlin-Altschul statistics. This thesis is discussing types of databases such as spatial, deductive and relational which store genomic data. Second part is concerned with design and implementation of application which use mentioned algorithm and database Oracle 10g R2. Testing and confrontation output of algorithm is also a part of this work.
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Computational Methods for Annotation Analysis of Genetic Variations
Fülöp, Tibor ; Bendl, Jaroslav (referee) ; Martínek, Tomáš (advisor)
Analýza a interpretace variací DNA je důležité pro zkoumání genetického pozadí dědičnosti, nemocí a jiných fenotypových rysů. Tato práce stručně úvadí oblasti molekulární biologie a základních principů genetiky, popisuje metody pro anotační analýzy genetických variací, genomové asociační studie a metody pro analýzy obohacení s jejich implementací. V rámci této práce jsme představili nový webový nástroj Varanto, který může být použit k anotaci, vizualizaci a analýze genetických variací. Může být použit k analýze obohacení anotací pomocí hypergeometrického testu pro danou množinu variací. Varanto obsahuje uživatelské webové rozhraní vyvinuté pomocí frameworku Shiny jazyka R. Výkon a funkcionalita nástroje jsou testovány a demonstrovány podle výkonových benchmarků a na základě analýzy a interpretace dat z dříve publikovaných genomových asociačních studií.
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A Tool for Visual Analysis of Circuit Evolution
Staurovská, Jana ; Minařík, Miloš (referee) ; Sekanina, Lukáš (advisor)
The main goal of the master's thesis is to compose a study on cartesian genetic programming with focus on evolution of circuits and to design a concept for visualisation of this evolution. Another goal is to create a program to visualise the circuit evolution in cartesian genetic programming, its generations and chromosomes. The program is capable of visualising the changes between generations and chromosomes and comparing more chromosomes at once. Several user cases had been prepared for the resulting program.
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Application for Alignment of DNA Parts
Kašpárek, Tomáš ; Žák, Jakub (referee) ; Rozman, Jaroslav (advisor)
This thesis deals with DNA sequences alignment methods with focus on execution speed of given task and its optimality. The outcome of this thesis results in multiple programs, which presents DNA alignment algorithms and their versions programmed with OpenCL libraries, which are optimized on calculation rate. Text of this thesis apprises reader with DNA alignment problematic and its importance in biology. Further, algorithms for DNA alignment and options of their speed-up using libraries like CUDA or OpenCL are presented.
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Alignment of DNA Parts
Pejř, Václav ; Burgetová, Ivana (referee) ; Rozman, Jaroslav (advisor)
This thesis deals with finding the possibilities within the sphere of alignment of DNA sequences. Based on these findings, the best solution should be found with regard to the quickness of computation and quality of alignment. Following this I intend to implement and thus create a functioning program that will do the alignment. The thesis starts with introducing issues dealing with biology, DNA and genetics. The introduction is followed by a survey of algorithms that are used for alignment, their evaluation and selection of the most appropriate algorithm for the implementation. The thesis also focuses on the usage of parallel programming by means of OpenCL libraries. The alignment is being done above many sequences at the same time, so that the methods how this process can be done and how to reach the best results are being examined.
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