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Inhibition of TET-1 protein by iron chelators
Antonyová, Veronika ; Jakubek, Milan (advisor) ; Mikula, Ivan (referee) ; Gumulec, Jaromír (referee)
EN The objective of this work was to study novel synthetic iron chelators and to study their potential use in inhibition of TET1 (ten-eleven translocation methylcytosine dioxygenase 1) protein. Epigenetic mechanisms, such as hydroxymethylation of DNA, are promising target in many serious pathologies, including oncological disorders. In the presented study, we intended to discover novel inhibitors by screening small libraries of heterocyclic molecules, such as pyrrolo[3,2-b]pyrrole derivatives with hydrazide (compound 1) or hydrazone (compound 2-6) iron-binding group and hydrazone-based iron chelators (compound 7-10). Within the scope of this study, we used various analytical and biochemical techniques for the purpose of characterization of novel cancer therapies based on TET1 protein inhibition. The absorbance and the complexation of tested compounds with Fe(II) ions was studied by UV-Vis spectroscopy. Inhibition of TET1 protein was studied by fluorometric assay based on ELISA and further supported by microscale thermoporesis and in silico docking. The cytotoxicity of compounds on cancer cell lines was measured by MTT assay and intracellular distribution was determined by live-cell imaging. This study presents a biochemical analysis of potential TET1 protein inhibitors and brings significant...
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Polyphenols in nutritions and their effect on DNA
Osorio, Juan ; Černayová, Diana (referee) ; Brázda, Václav (advisor)
Epidemiologické studie prokázaly vliv konzumace rostlinných potravin v prevenci široké škály nemocí. Přírodní antioxidanty přítomné v těchto potravinách, mezi nimiž jsou velmi důležité polyfenoly, mohou být zodpovědné za tuto činnost podporující zdraví. Cílem bakalářské práce je ukázat interakci určitých polyfenolů s genetickým materiálem prostřednictvím různých signálních mechanismů, zejména pokud jde o stabilizaci nekanonické struktury DNA G-kvadruplex a poukázat tak na nejselektivnější látku pro inhibici biochemických procesy. Dále práce obsahuje podrobné informace, které mohou pomoci pochopit, jak mohou polyfenolové sloučeniny interagovat s DNA prostřednictvím epigenetických mechanismů a G4 struktur, a které faktory mohou ovlivnit jejich účinnost. Různé experimenty, biologickým a experimentálním opakováním, byly použity k potvrzení interakce mezi sloučeninami a DNA.
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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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Epigenetic inheritance influencing the behavior of future generations and its reversibility during ontogenesis
Freisingerová, Kateřina ; Landová, Eva (advisor) ; Švorcová, Jana (referee)
The aim of this work is to focus on possible mechanisms of transmission of changes that are conditioned by epigenetic modifications that could affect specific behaviour and phenotype in offspring. The inheritance can be channeled through both maternal and paternal lineages. It can be divided into two distinct groups of transmission, namely intragenerational and transgenerational. This work mainly focuses on the possible mechanisms of transgenerational inheritance. Epigenetic mechanisms leading to changes in the phenotype of an organism rely on influencing the regulation of DNA reading. This occurs at several levels such as DNA methylation, chemical modifications such as acetylation and other post-translational modifications, and most importantly non-coding RNA molecules. Today, countless studies are trying to explain these molecular processes mediated by environmental influences. Well known are maternal care, chemicals, or traumatic experiences. There are examples of traumatic environmental influences in which physiological changes in HPA axis regulation can be observed with consequent changes in the expression of genes for depressive and anxiety phenotypes. Most of the experiments focusing on epigenetic transmission are predominantly conducted in mouse or rat models. However, there are also...
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Regulation of histone post-translational modifications and its use in the diagnosis and treatment of lung cancer
Marada, Kryštof ; Janoštiak, Radoslav (advisor) ; Červená, Klára (referee)
The aim of this bachelor's thesis is to summarize the epigenetic mechanisms, namely DNA methylation, non-coding RNA and post-translational modification of histones, within the scope of which the five currently most researched types are described, i.e. acetylation, methylation, phosphorylation, ubiquitinylation and sumoylation. Furthermore, a summary of the modifying enzymes whose function is to add and remove these epigenetic components. And also the description of the proteins that recognize these components. The following is a description of how epigenetic processes are involved in the course of cancer. The remaining part of the work is devoted to lung cancer, its most common causes, what methods are currently used to treat it, and how post-translational modifications of histones could be used in its treatment. Most of this chapter is devoted to histone deacetylase inhibitors, as these inhibitors represent potential as a new component of lung cancer treatment, which also makes them the target of much research.
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Effect of chromatin on the repair of double-strand DNA breaks after cleavage by CRISPR/Cas and other programmable nucleases in plants
Trojan, Jakub ; Přibylová, Adéla (advisor) ; Procházková, Klára (referee)
Plants are highly resistant to ionizing radiation, also thanks to a high-quality repair system for repairing double-stranded breaks. Double-strand breaks in plants are repaired by four repair pathways. Most often, double-strand breaks are repaired by non-homologous end joining (NHEJ), which joins the broken ends without further processing. More accurate but slower and more complex is repair through homologous recombination (HR), which repairs the break using a homologous sequence. HR repair takes place preferentially in a region with active transcription and during the S and G2 phases of the cell cycle. Alternatively, repair further proceeds through single-strand annealing (SSA) or Theta mediated end joining (TMEJ). Both pathways are based on short homology between the overlapping ends of the double-strand break. An often neglected part of repairs is the overcoming of repressive chromatin, which protects the genome from DNA damage and prevents access of nucleases but also acts as a barrier for repair proteins. This work summarizes the current knowledge about DNA repair in plants. Furthermore, describe the influence of chromatin not only on the repair but also on the activity of programmable nucleases used in genetic engineering, such as zinc finger nucleases (ZFNs), transcription activator-like...
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Evolutionary hypotheses of obesity origin
Dundr, Matěj ; Hora, Martin (advisor) ; Vážná, Anna (referee)
Obesity is a major social, ecological, economic and health problem of today's civilization. Humans evolved to adapt to a different environment than the one they live in today, had more exercise and consumed natural food sources. The imbalance in energy intake and expenditure that we observe in today's human populations is the most likely cause of obesity. However, this work will deal with a less discussed view of the origin of obesity, namely the possible explanation of the origin of obesity with evolutionary hypotheses. The work will also try to evaluate and discuss, based on a comparison of the available literature, whether these hypotheses could really clarify the origin of obesity at the global level. In the beginning of the thesis, we present the problem of obesity, its prevalence in the population and comorbidities associated with obesity. The next section describes the diagnosis of obesity, followed by a section on the history of obesity. The main part is devoted to the evolutionary hypotheses of obesity, namely the adaptation to frugality hypothesis, the genetic drift hypothesis and then other ecological- behavioral hypotheses and their evaluation. In conclusion, the work summarizes that the described hypotheses could be useful for clarifying the difference in obesity prevalence between...
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Roles of histone H3 lysine methylation in the gene expression regulation
Čizmazia, Viliam ; Veverka, Václav (advisor) ; Ormsby, Tereza (referee)
Viliam Čizmazia Roles of histone H3 lysine methylation in the gene expression regulation Abstract Histone post-translational modifications play a key role in epigenetic regulation of chromatin land- scape and various cellular functions. They can directly mediate interactions between DNA and histones, but also represent recognition signals for specific reader proteins. A particular type of these modifications, lysine methylation, marks a number of specific sites within the terminal as well or globular regions of histone proteins and encodes for various instructions for DNA-related processes such as gene transcription. The profiles of individual lysine methylations are regulated by specific methyltransferases (writers) and antagonizing demethylases (erasers). Their deregula- tion is often associated with diseases such as developmental abnormalities or cancer. For this rea- son, a number of histone-modifying enzymes are considered attractive therapeutic targets. This review is focused on key players and mechanisms underlying the deposition of the most important histone H3 lysine methylations, their genomic distribution and contextual roles in transcriptional events. In addition, it highlights the importance of structure-based approaches in exploring the molecular details behind the activity of histone...
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Natural epigenetic variation: a driver for adaptation of wild plant populations?
Sammarco, Iris ; Latzel, Vít (advisor) ; Johannes, Frank (referee) ; Pečinka, Aleš (referee)
A growing body of literature suggests that epigenetic variation might contribute to local adaptation of natural plant populations. Epigenetic mechanisms, such as DNA methylation, can in fact quickly alter phenotypes in response to environmental changes. Furthermore, these changes can be inherited across several generations (especially clonal), suggesting that DNA methylation may enable heritable phenotypic variation and eventually contribute to adaptation. However, it is still unclear whether epigenetic mechanisms can have an adaptive potential in plants, or in other words, whether they present variation among natural populations, are inherited across generations and have fitness effects. During my PhD project, together with my co-authors, I tested these conditions on several natural populations of two non-model clonal plant species, the wild strawberry (Fragaria vesca) and the black poplar (Populus nigra). To do so, I used the current gold standard for DNA methylation analysis (Whole Genome Bisulfite Sequencing), which allowed me to characterize the genome-wide DNA methylation level of individual plants at the single base-resolution. For both species, I found extensive DNA methylation diversity among populations, which was partially affected by the natural climatic conditions of the populations...
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Stárnutí rybích oocytů a modifikace histonů
WAGHMARE, Swapnil Gorakh
Cellular ageing is characterized by a loss of functional abilities over time. Epigenetic changes are one of the factors that contribute to ageing. Epigenetic regulators control the cellular gene activity without any alteration of the underlying DNA sequence. Epigenetic regulators like DNA methylation, histone modifications, and non-coding RNAs have been related to the ageing process. Histone modifications are among the most crucial and common epigenetic configurations that play a critical role in the post-fertilization success and early embryo development. Oocyte carries essential information to orchestrate embryogenesis and to remodel the parental genomes. The underlying molecular pathways driving oocyte ageing remain unknown. Investigations and understanding of the molecular mechanisms behind oocyte ageing are needed. Therefore, the investigation of the oocyte ageing, focusing on histone modifications were done. Egg phenotype and functional changes during fish oocyte ageing were examined. Despite being widely used as a model organism, the impact of oocyte ageing on ploidy abnormalities was not yet studied in zebrafish (Danio rerio). Therefore, the investigation on ploidy anomalies in embryos originating from different aged oocytes in zebrafish was performed. In the molecular analysis, histone modifications with a special focus on acetylation were performed. Histone acetyltransferase activity was assessed to get more information on the dynamics of histone acetylation during fish oocyte ageing. The current study reports that maintenance and manipulation of zebrafish oocytes at 26 °C for 2 hours post-stripping (HPS) was possible without significantly reducing fertilization potential. Almost complete loss of egg viability was observed at 6 HPS in zebrafish. In addition, physical abnormalities were observed in all larvae derived from 4 and 6 HPS-old oocytes. Compared to 0 and 2 HPS, the proportion of ploidy abnormal embryos was significantly greater at 4 HPS in zebrafish. The egg eyeing and hatching rates were significantly decreased by the elapsing time of oocyte ageing in common carp (Cyprinus Carpio). A significant decrease in embryo survival rate at 1 HPS was observed in grass carp (Ctenopharyngodon idella). The specific histone acetylation on H3K9, H4K5 and H4K8 didn't exhibit significant differences in different aged oocytes of common carp and grass carp. However, the histone H3K14ac and H4K16ac didn't show a signal either in fresh or aged oocytes in common carp and grass carp. The H4K12ac increased significantly at 28 HPS in common carp while decreased significantly at 1 and 4 HPS in grass carp. The histone acetyltransferase (HAT) activity showed an increasing trend during in vivo and in vitro oocyte ageing in common carp. The HAT activity increased significantly at 30 HPS in grass carp. The observed histone acetylation marks are reported to be species-specific and oocyte stage dependant. Therefore, the obtained results are the first to report the presence of H3K9ac, H4K5ac, H4K8ac, and H4K12ac, as well as the absence of H3K14ac and H4K16ac in common carp and grass carp metaphase II oocytes. Additionally, our findings suggest the possibility of developing an epigenetic marker for egg quality associated with fish oocyte ageing.
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