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Methods for class prediction with high-dimensional gene expression data
Šilhavá, Jana ; Matula, Petr (referee) ; Železný, Filip (referee) ; Smrž, Pavel (advisor)
Dizertační práce se zabývá predikcí vysokodimenzionálních dat genových expresí. Množství dostupných genomických dat významně vzrostlo v průběhu posledního desetiletí. Kombinování dat genových expresí s dalšími daty nachází uplatnění v mnoha oblastech. Například v klinickém řízení rakoviny (clinical cancer management) může přispět k přesnějšímu určení prognózy nemocí. Hlavní část této dizertační práce je zaměřena na kombinování dat genových expresí a klinických dat. Používáme logistické regresní modely vytvořené prostřednictvím různých regularizačních technik. Generalizované lineární modely umožňují kombinování modelů s různou strukturou dat. V dizertační práci je ukázáno, že kombinování modelu dat genových expresí a klinických dat může vést ke zpřesnění výsledku predikce oproti vytvoření modelu pouze z dat genových expresí nebo klinických dat. Navrhované postupy přitom nejsou výpočetně náročné. Testování je provedeno nejprve se simulovanými datovými sadami v různých nastaveních a následně s~reálnými srovnávacími daty. Také se zde zabýváme určením přídavné hodnoty microarray dat. Dizertační práce obsahuje porovnání příznaků vybraných pomocí klasifikátoru genových expresí na pěti různých sadách dat týkajících se rakoviny prsu. Navrhujeme také postup výběru příznaků, který kombinuje data genových expresí a znalosti z genových ontologií.
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Estrogen receptor beta (ERβ) in testicular cells and sperm
Dostálová, Pavla ; Žatecká, Eva ; Děd, Lukáš ; Dorosh, Andriy ; Postlerová, Pavla ; Jonáková, Věra ; Dvořáková-Hortová, Kateřina ; Pěknicová, Jana
Estrogen is a steroid hormone that plays an important role during sperm development in the male and female reproductive tract. Estrogen signalling is a complex process that depends on cell milieu and presence of receptors. Thanks to the steroid nature of estrogens, they can pass through the plasmatic membrane and bind to the intracellular estrogen receptors (ERs). Within the cell, there are several pools of ERs. One of them is localized to the cell nucleus and their activation leads to direct or indirect binding to DNA and ultimately to alternation in gene expression (genomic pathway). Other pools of ERs are associated with plasma membrane or are located in cytosol. Activation of membrane associated ERs leads to rapid non-genomic responses. Nowadays, two classical estrogen receptors are known – ERα and ERβ. Since ERβ is a predominant variant in testes, we focused our study on expression of ERβ variants in murine testes and sperm. We detected two variants of ERβ at mRNA level in both, testes and sperm. These variants differ in 54 nucleotids within the ligand binding domain and this variability results in different affinity to estrogen. We analyzed individual testicular cell types (spermatogonia, spermatocytes, spermatids, Sertoli cells) by RT-qPCR. Our results suggest that both ERβ variants are coexpressed in the same cell type and may therefore interact together. This may have consequences in mediating of estrogen signalling. Moreover, ERβ is expressed more in the later stages of spermatogenesis suggesting the role of ERβ in these stages or alternatively in spermatozoa alone. At the protein level, we detected ERβ in nuclear, membrane and cytosolic fraction prepared from testicular tissue suggesting the involvement of both, genomic and non-genomic, pathways of estrogen signaling in testes. In sperm, anti-ERβ antibodies localized ERβ in acrosome region and tail which is in accordance with the known role of estrogen on capacitation, acrosome reaction and motility.
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Analysis of intron sequence variability
Kukačková, Hana ; Provazník, Ivo (referee) ; Kubicová, Vladimíra (advisor)
This bachelor thesis reviews genetic expression, the main characteristics of introns, their importance, and the methodology of their recognition. Practical part focuses on intron variability analysis and conservative sequences searching. In the beginning, there is a structure of nucleic acids with their chemical and physical characteristics reviewed, follow by gene expression description with all steps – transcription, posttranscriptional splicing and translation. Afterwards, there is an analysis of introns importance, introns evolution theories and similarities among different organisms mentioned, follow by some introns recognition methods. Practical part is focused on the initial and terminal regions of introns and conservative dinucleotide sequences verifying. The thesis studies intron – exon and exon – intron boundaries. The last part tries to suggest new potentially conservative sequences – patterns, search for them and check their conservativeness.
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DNA Microarrays Data Analysis
Hebelka, Tomáš ; Jaša, Petr (referee) ; Burgetová, Ivana (advisor)
This work concerns with data analysis of DNA microarrays by using cluster analysis. It explains biological terms - gene expression and DNA microarray. Next, it contains mathematical and informatical description of clustering methods and describes a way to apply these methods to microarrays data. Next, the work contains implementation's detail of clustering methods k-means, DBSCAN and introduces an original clustering algorithm Strom++. Then, description of implementation and application manual follow. Finally, accomplished results are evaluated.
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Nutrigenomics and diseases of civilisation
Sadel, Peter ; Souralová Popelková, Miriam (referee) ; Vránová, Dana (advisor)
The aim of the first part of this bachelor´s thesis is to explain and describe the basic terms which were used as diseases of civilisation, gen, genome, nutrigenomics, nutrigenetics. The second part of this work focuses on the characterization and description of some of the most often occurring diseases of civilisation in this world as obesity, diabetes mellitus or cardiovascular diseases and it has to point at possible causes of their formation and prevention. In the following chapters knowledge and practises of nutrigenomics were used during searching for the reasons of formation and prevention of civilisation diseases. Nutrigenomics is relatively a young discipline of science and only future research and monitoring will show its possible meaning in the future. The main goal of this work was to summarize and clearly demonstrate information about given theme from various information sources.
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Functional analysis of HSP complex expression in response to cold in \kur{Drosophila melanogaster}
ŠTĚTINA, Tomáš
The constitutively obsereved up-regulation of Hsp70 expression often led to premature conclusions about its critical role as a repair mechanism of cold injury that is, besides, expressed by protein misfolding/denaturation. In this study, we analyze the cold tolerance and the expression of 24 different mRNA transcripts of Hsp complex and other genes, that are associated with the repair of injury caused by cold. We use two strains of D. melanogaster: the wild type and the mutant type Hsp70- null, that lacks all 6 copies of the gene hsp70. We found out, that the larvae of two strains do not differ in their patterns of target genes expression during long term acclimation nor during recovery from chronic cold exposure and acute cold shock, therefore there is no transcriptional compensation of any other Hsp gene for the missing hsp70 in Hsp70- strain. The cold tolerance of Hsp70- strain larvae was impaired only, when they were exposed to strong acute cold shock by temperatures below -8°C. No difference in cold tolerance was observed, when the larvae were exposed to chronic cold exposure in 0°C or to mild acute cold shock by temperatures up to -4°C. Based on our results we assess, that the cold injury caused by strong acute cold schock is of another nature than caused by mild cold conditions and only in the first case Hsp70 expression is critical for the repair of cold injury in Drosophila melanogaster larvae.
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Current options for use of metabolomics in plant production
Maršík, Petr ; Vaněk, Tomáš
Metabolomics like other so-called "omics" approaches is based on the characterization and treatment as far as possible in the given dataset biological system. Meaning of each "omics" techniques lies mainly in their mutual integration which leads to the so-called. Systems biology linking output at the level of gene expression, protein translation and file metabolites with genomic data. These relationships are summarized in Fig. 1. The primary goal of systems biology is to understand the biological processes to such an extent that it is possible to predict the function of biological systems from the level of genes through metabolism, physiological processes to growth and development.
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Changes in the expression of selected testicular genes in mice
Valášková, Eliška ; Margaryan, Hasmik ; Žatecká, Eva ; Pěknicová, Jana
The decrease in population fertility has become a major concern in many developed countries. Recent studies show that infertility is affecting an estimated 15% of all couples (World Health Organization, WHO, 2010). Male infertility is the primary or contributing cause in 60% of cases. Male infertility is caused by a number of factors, such as genetic background, various environmental factors and disease. Diabetes mellitus (DM), a serious health problem on its own, is also suspected to be a contributing factor to male infertility. The aim of this project was to analyze the cellular, molecular and genetic effects of diabetic environment on spermatogenesis and sperm quality and to determine the impact of DM on the in vivo reproduction, using the mouse model (Mus musculus) inbred FVB. Diabetes was induced using streptozotocin. We used our knowledge and tools (unique monoclonal antibodies developed by our group) to determine the status of reproductive organs, anogenital distance, and the quality of sperms. Genetic analysis was performed by a quantitative Reverse Transcription Polymerase Chain Reaction (qPCR). We tested selected genes which are expressed in testicular tissue and thus can influence process of spermatogenesis and consequently the sperm quality. Our preliminary data strongly suggest that DM impairs male fertility. We have found significant changes in the body and reproductive organ weight of mice with DM. We have identified qualitative and quantitative changes in the expression of proteins in epididymal fluid and sperms. We have also detected an increased number of apoptotic cells in sperm of diabetic mice compared to the control group. To our knowledge, there is no study assessing the correlation between DM and “unexplained infertility”. In view of this, it is essential to analyze the effects of DM on male fertility, sperm quality, and reproduction parameters.
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Effect of exposure to bisphenol A on gene expression in the testicular tissue in male mice
Dorosh, Andriy ; Elzeinová, Fatima ; Žatecká, Eva ; Kubátová, Alena ; Pěknicová, Jana
Laboratory of Reproductive Biology, Institute of Biotechnology, Academy of Sciences of the Czech Republic, v.v.i., Prague, Czech Republic Bisphenol A (BPA) is a synthetic, endocrine-disrupting compound able to directly bind estrogen receptors. Free BPA has been detected in human samples indicating that humans are internally exposed to BPA. The purpose of this study was to analyse the effect of BPA on the male reproductive system and testicular gene expression in germ cells. We studied the influence of long-term low concentration BPA exposition on male fertility in vivo in a two-generation study in C57BL/6 mouse strain. In this work, BPA was added with water at two environmentally relevant concentrations: 0, 4 and 4 µg/l. We measured the reproductive organs weight and sperm cells morphology and quality. Expression of genes involved in endocrine regulation and energy metabolism in testis was analysed after BPA exposure. Next, the epigenetic mechanisms of gene expression and regulation during the germ cell differentiation and effect of BPA will be analysed.
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