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The importance of predisposition examination of late Alzheimer´s disease using methods of molecular biology
KOPAČKOVÁ, Michaela
Alzheimer's disease is the most common type of dementia. It affects up to 70% of cases from approximately 38 million people worldwide suffering from some type of dementia. Alzheimer's disease usually affects patients over 65 years of age, however, there are exceptions. It is presumed that the number of people with Alzheimer's disease will grow constantly in the future too. Its etiopathogenesis is not yet fully understood, that is why it is important to investigate dementia further, whether in terms of specific environmental and genetic risk factors, or in view of the economic burden for the society. The presented bachelor's thesis summarises findings about Alzheimer's disease, its neurobiology, etiology, diagnostics and genetic predispositions, in particular the ApoE, APP, PSEN1 and PSEN2 genes. The presence of epsilon 4 gene allele for apolipoprotein E provably contributes to the increased risk of the late form of Alzheimer's disease. On the contrary, mutation in APP, PSEN1 and PSEN2 genes are connected with Alzheimer's disease with the early onset of the disease, before 65 years of age. The objective in the experimental part was to manage the practical isolation of DNA from peripheral blood and buccal swab, preparation and execution of PCR reaction, detection of PCR products by gel electrophoresis and independent examination of ApoE gene by a certified CVD StripAssay Kit from ViennaLab company (PentaGen). The work also includes the optimisation of another molecular genetic method for the detection of variant alleles of ApoE gene. This method was carried out by a certified DiaPlexQTM ApoE Kit from SolGent Co., Ltd. The principle of detection in this case is based on real-time PCR.
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Genetická analýza vybrané dědičné choroby u psů
VOLNÁ, Jitka
In my thesis I concentrated on an analysis of biological samples of 60 dogs, which manifested epilepsy. The aim was to find out the relation between genotype of the selected locus and the occurrence of epilepsy. Based on the results of the analysis, I assessed, whether there is a demonstrable relation between the occurrence of epilepsy and genotype in a particular locus. According to the results, no influence of genotype on the age of first epileptic seizure was proved.
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DNA čipy a jejich využití pro molekulární diagnostiku a predikci u onkologických onemocnění
VORÁČKOVÁ, Lucie
Many visible factors produced during carcinogenesis refer to oncological disease, e.g. modified gene's expression or increased number of miRNA. These factors can be diagnosed by analyzing of gene's expression. For this diagnostics, there are used many methods, of whom DNA microarray analysis is the most significant progress in genetic research. A large number of DNA sequences can be detected DNA with microarrays on a single microarray in a relatively short time. This analysis means a positive turnover for the diagnosis and prediction of disease.
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Comparison of genomes by synteny block analysis
Pavel, Tomáš ; Škutková, Helena (referee) ; Maděránková, Denisa (advisor)
The theoretical part of this bachelor thesis is aimed at basics of genetics. Term of gene and mutation are introduced in this section. There are gene and chromosome mutations mentioned and described. Following section is devoted to comparative genomics and especially to synteny. There is described what the synteny actually is and how the synteny arises. The end of the theoretical part of this thesis is about the evolution and there are described ways of sorting permutation vectors. The practical part of this bachelor thesis includes description of developed software. Output of this software is a dot-plot which shows detected synteny blocks. Indexes of these blocks are listed in GUI. The second important output is number of permutation steps. This number determines evolutionary distance between two analysed DNA sequences. The very last section is aimed at analyse of synthetic and real DNA sequences.
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Identifying CpG islands in genomes of eukaryotes
Urbánková, Kateřina ; Provazník, Ivo (referee) ; Maděránková, Denisa (advisor)
Bachelor thesis deals with searching CpG islands in DNA. The theoretical part describes the structure and composition of deoxyribonucleic acid, chromosomes and genes. There is basic information about human and chimpanzees genome and specification of CpG islands. Practical part consists of a program that searches for CpG islands in sequences, it displayes and saves it. This work includes analysis of genes which are common for Homo sapiens, Pan troglodytes, Mus musculus and Bos taurus.
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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 Detection in DNA Sequences
Roubalík, Zbyněk ; Burgetová, Ivana (referee) ; Martínek, Tomáš (advisor)
Gene detection in DNA sequences is one of the most difficult problems, which have been currently solved in bioinformatics. This thesis deals with gene detection in DNA sequences with methods using Hidden Markov Models. It contains a brief description of the fundamental principles of molecular biology, explains how genetic information is stored in DNA sequences, as well as the theoretical basis of the Hidden Markov Models. Further is described subsequent approach in the design of specific Hidden Markov Models for solving the problem of gene detection in DNA sequences. Is designed and implemented application, which uses previously designed Hidden Markov model for gene detection. This application is tested on the real data, results of these tests are discussed in the end of the thesis, as well as the possible extension and continuation of the project.
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Molecular Signature as Optima of Multi-Objective Function with Applications to Prediction in Oncogenomics
Aligerová, Zuzana ; Maděránková, Denisa (referee) ; Provazník, Ivo (advisor)
Náplní této práce je teoretický úvod a následné praktické zpracování tématu Molekulární signatura jako optimální multi-objektivní funkce s aplikací v predikci v onkogenomice. Úvodní kapitoly jsou zaměřeny na téma rakovina, zejména pak rakovina prsu a její podtyp triple negativní rakovinu prsu. Následuje literární přehled z oblasti optimalizačních metod, zejména se zaměřením na metaheuristické metody a problematiku strojového učení. Část se odkazuje na onkogenomiku a principy microarray a také na statistiku a s důrazem na výpočet p-hodnoty a bimodálního indexu. Praktická část je pak zaměřena na konkrétní průběh výzkumu a nalezené závěry, vedoucí k dalším krokům výzkumu. Implementace vybraných metod byla provedena v programech Matlab a R, s využitím dalších programovacích jazyků a to konkrétně programů Java a Python.
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Evolutionary algorithms
Bortel, Martin ; Karásek, Jan (referee) ; Burget, Radim (advisor)
Thesis describes main attributes and principles of Evolutionary and Genetic algorithms. Crossover, mutation and selection are described as well as termination options. There are examples of practical use of evolutionary and genetic algorithms. Optimization of distribution routes using PHP&MySQL and Google Maps API technologies.
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