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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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Hardware Acceleration of Algorithms for Approximate String Matching
Nosek, Ondřej ; Kořenek, Jan (referee) ; Martínek, Tomáš (advisor)
Methods for aproximate string matching of various sequences used in bioinformatics are crucial part of development in this branch. Tasks are of very large time complexity and therefore we want create a hardware platform for acceleration of these computations. Goal of this work is to design a generalized architecture based on FPGA technology, which can work with various types of sequences. Designed acceleration card will use especially dynamic algorithms like Needleman-Wunsch and Smith-Waterman.
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Alcoholism in the family
PODGORSKÁ, Kateřina
The purpose of the thesis is to look into the lives of adult children of alcoholics. The aim of the thesis is to compare the links among the educational environment, genetic predisposition of children of alcoholics and their own choice and attitude towards alcohol. I will find out if the children of alcoholics live a different life than the one handed down to tohem in their childhood. The thesis is divided into a theoretical part, I focus on information about alcohol, addictions and family. This information is fundamental for the practical part. The practical part is devoted to research about adult children of alcoholics. Using the method of semi-structured interviews, I try to achieve the main goal of the work. In the end, I will eveluate whether I have fulfilled the objective of the bachelor's thesis.
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Detection of mutation causing plycystic kidney disease
SLÁDKOVÁ, Nikola
In my bachelor's thesis, I dealt with the detection of the mutation in the PKD2 gene, which causes polycystic kidney disease. The disease is interesting because it is not only caused by a single specific mutation that affects a particular gene, but the disease is highly variable and can be caused by several mutations located on different chromosomes and even at different sites in a given exon. The subject of my research was a family of four. Based on the results of using clinical diagnostics, one member of the family was confirmed to have polycystic kidney disease. The aim of this thesis was to detect the possible PKD2 mutation in the family members, and thus to confirm the presence of polycystic kidney disease. The next aim was the optimization of the designed primers for the PCR reaction. In the theoretical section of this thesis, I focused on the issue of polycystic kidney disease, classification of polycystic kidney disease based on the inheritance type, and the protein products of the PKD2 and PKD1 genes. I also mentioned the anatomy of the kidneys, their function, and also the structure of a nephron. I also dealt with the health problems that accompany the disease, as well as its diagnostics and subsequent treatment. In the practical section of this thesis, I described the process of the laboratory diagnostics used to search for a mutation in the PKD2 gene, specifically in its first five exons. The diagnostics consisted of the DNA isolation, PCR reaction, gel electrophoresis, and subsequent Sanger sequencing. However, due to limited laboratory capacity, I did not personally perform the Sanger sequencing. The samples prepared for sequencing were sent to the SEQme company. In the end, I examined the electrophoreograms and the results from the obtained sequences. I had a total of 20 sequenced samples for the evaluation, always 4 samples for each exon. I was not able to prove the possible mutation in any of them. The remaining exons would also need to be examined for a complete diagnostics of the disease.
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Multilevel selection theory
Mihulka, Tomáš ; Švorcová, Jana (advisor) ; Toman, Jan (referee)
Multilevel selection is an attempt to unify different approaches to the Level of selection problem. This paper examines the principles, starting points, variants and problems of this concept. Particular emphasis is placed on the relationship of this theory to Gene's-eye view and the presentation of evidence of the usefulness of Multilevel selection in analyzing evolutionary changes.
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Endometriosis, its aetiopathogenesis and influence on female's fertility
Selková, Katarína ; Daňková, Pavlína (advisor) ; Crha, Igor (referee)
Endometriosis is an estrogen-dependent disease of women of reproductive age. It is often considered as one of the main causes of female infertility. Its development and progression are influenced by several exogenous and endogenous factors. It is a heterogeneous disease and one of the most important tasks is to identify the candidate genes. That will allow us to better understand why and under what circumstances endometriosis develops. Because not all women with endometriosis are infertile, I focused in this thesis at selected candidate genes, their alleles and epigenetic dysregulation that could link endometriosis to infertility. From the available literature WNT4, HOXA gene cluster, ESR1, PGR, FN1, VETZ, GREB1 appear to play a major role in the pathogenesis of endometriosis. These genes also play an important role in various biological pathways and their dysregulation leads to low implantation / complete implantation failure, insufficient oogenesis, embryogenesis, and infertility in patients with endometriosis. Identification of genes whose dysregulation induces the development of endometriosis in the population is important, given the increasing incidence of endometriosis and infertility rates in recent years. With further research on pathogenesis of endometriosis it would be possible to make...
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Ukládání tuku u modelových zvířat a obezita
Petrlák, František
This bachelor thesis focuses on fat accumulation in animal models and obesity, which is very serious global problem and is associated with lots of other diseases. The first part is about lipid metabolism and the energy balance, which is essential in association with obesity. This occurs when the energy balance in imbalance in the interest of energy intake. Next part is about adipose tissue, its dividing into white and brown adipose tissue and differences between them. A considerable part of the thesis is about genetic and non-genetic causes of obesity and impact of epigenetic modifications. Furthermore, the literature on selected genes (PPARy, FABP4, FTO, LEP, LEPR and MC4R) is processed for metabolism and the mechanism of fat storage in animals and humans. The bachelor thesis ends with the treatment of obesity.
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Clinicopathological and molecular biologic characteristics of selected cutaneous epithelial and nonepithelial tumors
Kastnerova, Liubov ; Kazakov, Dmitry (advisor) ; Šíma, Radek (referee) ; Feit, Josef (referee)
The doctoral thesis MD. Liubov Kastnerova (previous name Kyrpychova) is focused on the histomorphological and molecular biologic features of selected cutaneous epithelial and nonepithelial tumors and is structured as a commentary to the 20 articles published during four years, representing the completed scientific projects in the Ph.D. course. In eight papers, the author of the thesis is the first author, whereas she coauthored in the remaining 12 papers. The thesis is composed of the commented files of authors own publications and it is divided into cutaneous epithelial and nonepithelial tumors. The first section, «Cutaneous epithelial tumors», includes 14 articles that are subdivided into two parts: adnexal tumors (9 articles) and lesions of anogenital mammary-like glands (5 articles). Of the nine articles on adnexal tumors, there are 5 articles focused on various benign and malignant adnexal lesions with apocrine or eccrine differentiation. Novel findings in this part include the identification of hitherto unreported alterations of the MYBL1 gene in adenoid cystic carcinoma of the skin and lack of deletion of the 1p36 locus in this neoplasm; the lack of a correlation between cellular composition and the presence CRTC1-MAML2 fusions in hidradenoma, the absence of CRTC3-MAML2 fusions in this tumor,...
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Multilevel selection theory
Mihulka, Tomáš ; Švorcová, Jana (advisor) ; Toman, Jan (referee)
Multilevel selection is an attempt to unify different approaches to the Level of selection problem. This paper examines the principles, starting points, variants and problems of this concept. Particular emphasis is placed on the relationship of this theory to Gene's-eye view and the presentation of evidence of the usefulness of Multilevel selection in analyzing evolutionary changes.
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