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The use of "omics" methods in molecular-epidemiologic study in newborns from different localities of the Czech Republic
Hoňková, Kateřina ; Rössner, Pavel (advisor) ; Gábelová, Alena (referee) ; Bláha, Luděk (referee)
The "omics" is a concept of biological disciplines that globally characterizes and quantifies biomolecules involved in the key functions of an organism. The "omics" methods are used e.g. in molecular epidemiology, where they help to evaluate potential biomarkers that identify the impact of environmental factors for human health. In this thesis, the "omics" methods were applied in samples collected from newborns born in localities of the Czech Republic mostly differing by pollution levels from industrial sources. The principal aim was to determine whether environmental changes during prenatal development can affect gene expression and its regulation in newborns. The thesis further aimed to evaluate the level of air pollution at the time of biological samples collection. Using the whole genome approach, differentially expressed genes (DEGs) in newborns from districts Karvina and Ceske Budejovice (CB) were identified. In a pilot study of a small group of newborns from districts Most and CB, differentially methylated CpG sites in DNA were assessed. These sites attenuate gene activity and could be responsible for long-term changes at the genetic level. Finally, the aim was to find differentially expressed small non-coding RNA (DE miRNA) in newborns from Most and CB. Samples of umbilical cord blood from...
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Fungal metabolism modulation by plant substances
Sedláková, Vendula ; Čmoková, Adéla (advisor) ; Kolařík, Miroslav (referee)
Phytochemicals are bioactive substances by which plants affect organisms in their vicinity. Fungi often respond to their presence by metabolism alternation, which is manifested by the production of secondary metabolites, an increase in biomass or the regulation of virulence. These changes can be caused by phytochemicals (e.g. curcumin, EGCG) with abilities to modulate epigenetic information. The first half of the work is devoted to mechanisms of epigenetic modification (e.g. methylation, histone modification), which were studied in fungi. The second half summarizes studies focused on phytochemicals, in which the ability to modify epigenetic information in eukaryotic organisms was observed. The bachelor's thesis thus brings valuable knowledge about the possibility of modifying fungal metabolism by phytochemicals, which are often waste products of industry. Information summarized in this work can have a significant impact on improving biotechnological processes, where there is an effort to increase biomass yield or induce the production of secondary metabolites in cases where their production is normally suppressed. Key words: secondary metabolites, epigenetics, epigenetic modification, phytochemicals, filamentous fungi
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Age estimation from human biological material based on DNA methylation
Matoušková, Laura ; Kulichová, Iva (advisor) ; Priehodová, Edita (referee)
DNA methylation is one of the epigenetics modifications which performs many functions in human body by silencing genes and maintaining genomic stability. Changes in DNA methylation accumulate during life and current studies indicate that the level of methylation in certain loci (CpG dinucletotides) correlates with chronological age. However, the methylation pattern changes not only with increasing age but it can also be affected by our lifestyle choices and biogeographical origin. Therefore, the key for succesful age estimation is finding such CpG loci that are independent (or as little dependent as possible) on other variables. This bachelor thesis describes the issue of age estimation based on DNA analysis of specific methylated DNA loci with focus on its application in forensic practice.
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Importance of epigenetic variability in evolution of clonal plants
Mareš, Štěpán ; Pinc, Jan (advisor) ; Latzel, Vít (referee)
Because of their low genetic variability and limited ability to respond to the changing environment, clonal plants are often considered an evolutionary dead end. On the other hand, numerous recent studies showed that clonal plants can react to the changing environment through epigenetic mechanisms, especially through DNA methylation. Moreover, epigenetic information in clonal plants can be transferred to future generations (so-called transgenerational memory). As a result, epigenetics can ensure better fitness of the next clonal generation. The aim of this work is to summarize the knowledge about the role of epigenetic variability in the life of clonal plants performing limited genetic variability. Key words: epigenetics, DNA methylation, epigenetics variation, clonal plants, transgeneration memory
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Detailed characterization of the interaction between LEDGF/p75 and MeCP2
Naušová, Karolína ; Veverka, Václav (advisor) ; Hrabal, Richard (referee)
Epigenetics investigates heritable phenotype changes that are not caused by alternations in DNA sequence. Major epigenetic mechanisms include covalent DNA modifications (particularly methylation), histone and chromatin modifications and RNA interference. These mechanisms are involved in number of processes from transcription to translation. Lens epithelium-derived growth factor (LEDGF/p75) is ubiquitously expressed in human body and it is considered to be a transcriptional coactivator upregulated upon stress conditions. LEDGF/p75 consists of several domains. The N-terminal PWWP domain plays very important role from epigenetic point of view as it is able to bind di- and trimethylated lysine 36 of histone 3, which is considered as an epigenetic marker of transcriptionally active chromatin. LEDGF/p75 interaction partners include e.g. HIV integrase, MLL1-MENIN complex or MeCP2. A shorter isoform of LEDGF/p75 called LEDGF/p52 shares with LEDGF/p75 its N- terminal part that is responsible for interaction with DNA and chromatin. Methyl-CpG-binding protein 2 (MeCP2) is present everywhere in human body with the highest abundance in brain. MeCP2 is a transcriptional modulator remodelling chromatin, therefore its function is to activate or repress gene depending on the molecular and cellular context. Among...
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Evolutionary aspects of (epi)genetic determination of laterality with a special focus on upper limb
Holoubková, Tereza ; Daňková, Pavlína (advisor) ; Struška, Michal (referee)
Handedness is one of the most distinct asymmetries of the human body. There is approximately 90 % of right-handers in the population, which is the strongest bias in handedness among all primates. Handedness is connected with lateralization of brain for language and is determined both genetically and by the environment. Genetic determination of the handedness has not been yet figured out, although there are many candidate genes and regions. In addition to candidate genes, the genetic determination is shaped by the epigenetic mechanisms and the role of testosterone. Handedness occurred alongside the beginning of the human population development, approximately in the Middle Pleistocene, with the same percentage of left-handers as today. Handedness polymorphism is maintained in the population based on the frequency-dependent model because of the advantages and disadvantages associated with left-handedness.
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The role of epigenetic mechanisms in opiate dependence
Hronová, Anna ; Novotný, Jiří (advisor) ; Netolický, Jakub (referee)
Addiction and tolerance develop with the chronic use of opioids. Opioid drug abuse has social, economic and health consequences. The most commonly abused opioid drug is heroin, but so is morphine, which is used in medicine as an analgesic. Drug dependence includes potentially long-term behavioural abnormalities that are induced by repeated use of opioid drugs. The persistence of behavioural chan- ges suggests that there are long-term changes in gene expression. Research has shown the crucial role of epigenetic mechanisms in managing long-term changes in gene expression. Studies have revealed increased levels of permissive histone acetylation, decreased levels of repressive histone methylation, and changes in DNA methylation patterns and non-coding RNA expression. Within the action of opioids, these epigenetic modifications are limited to the mesolimbic and limbic systems, which play a role in the processing of emotions, motivation or reward. There is still much work to be done in the field of research into the influence of epigenetic mechanisms in opiate dependence. However, research to date has significantly shifted the understanding of how opioids cause permanent changes in brain function with their results and findings.
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Role of sequence context in DNA methylation
Polák, Jan ; Fischer, Lukáš (advisor) ; Širl, Marek (referee)
Cytosine methylation of DNA is a pivotal epigenetic mark, which contributes to the regulation of the gene expresion, silencing of transposable elements, and co-defines chromatine state. There are three cytosine contexts: CG, CHG and CHH (where H stands for C, A, or T). Arabidopsis thaliana (and plants in general) has an arsenal of molecular mechanisms capable of cytosine methylation in all of its contexts. That said, there are two tasks at hand: maintaining of pre-existing methylation and if need be, creating new methylated spots. The actual process of maintaining of the methylation depends on the cytosine context. Methylation of symmetrical contexts of CG and CHG can utilize the information about the methylation pattern from the second DNA strand. The aymmetrical context of CHH, and also CHG need to look for this information elsewhere: in the methylation of the lysine 9 of H3 histone. This creates a self-reinforcing loop and a crosstalk between two epigenetic mechanisms. Maintaince of methylation of CHH is also navigated by small RNA complementary to the locus in question. This mechanism of enzyme navigating by RNA is also used in establishing a new methylated site for all of the contexts. CG methylation is most prevalent in both heterochromatine and euchromatine. It also has a special functions...
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Integration site distribution of expressed proviruses
Miklík, Dalibor ; Hejnar, Jiří (advisor) ; Kejnovský, Eduard (referee) ; Indik, Stanislav (referee)
To establish efficient expression of their genes, retroviruses integrate proviral copies into the genomes of the cells they have infected. Epigenetic events, however, silence expression of the integrated proviruses. This silencing protects host cells from harmful viral spread, but also creates a reservoir of latent proviruses that subsequently hinders the cure of retroviral (e.g., HIV-1) infections. Furthermore, the silencing of retrovirus-derived integrative vectors complicates their application in transgenesis and gene therapy. The goal of this thesis is to describe the interaction between retroviral expression and host (epi)genomic environment at the site of proviral integration. To pursue the goal, we sought to define the (epi)genomic environment of the proviruses, which expression is not affected by the epigenetic silencing. Diverse retroviral vectors derived from avian sarcoma and leukosis virus (ASLV), murine leukemia virus (MLV), and human immunodeficiency virus type 1 (HIV-1) were used as model retroviral systems, and expression stability of the vectors in human cell lines was examined. In order to identify the features unique to integration sites of the active proviruses, we sorted the cells positive for the proviral expression, identified their proviral integration sites, and compared them to...
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The role of SIRT1 during in vitro maturation of oocytes
Landsmann, Lukáš ; Nevoral, Jan (advisor) ; Šolc, Petr (referee)
SIRT1 histone deacetylase acts towards many epigenetic and non-epigenetic targets. The involvement of SIRT1 in oocyte maturation is assumed and the importance of ooplasmic SIRT1 pool for further destiny of matured oocyte is strongly suggested. We hypothesized that SIRT1 play role of the signal molecule in mature oocyte through selected epigenetic and non- epigenetic regulation. We observed SIRT1 re-localization in mature oocyte and the association with spindle microtubules. In matured oocyte, SIRT1 shows a spindle-like pattern and spindle- specific SIRT1 action is supported decreasing α-tubulin acetylation. Based on the observation of histone code in immature and matured oocytes, we suggest that SIRT1 is mostly predestined for epigenetic mode of action in germinal vesicle (GV) of immature oocyte. Accordingly, SIRT1- driven trimethylation of histone H3 on lysine K9 in matured oocyte is considered to be an inheritance of GV epigenetic transformation. Taken together, our observations point out the dual spatiotemporal SIRT1 action in oocyte capable to be switched from epigenetic to the non- epigenetic mode of action readily depending on meiosis progress. Keywords: oocyte, SIRT1, histone, developmental competence, tubuline, epigenetics
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