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Factors interacting with bacterial RNA polymerase
Sudzinová, Petra ; Krásný, Libor (advisor) ; Fišer, Radovan (referee)
The bacterial cell must be able to rapidly change its gene expression to survive unstable external conditions. Transcription is the key level that affects gene expression. The pivotal enzyme of transcription is RNA polymerase (RNAP). Activity of RNAP is tightly regulated by transcription factors (TFs). These factors affect RNAP in different ways. This work presents an overview of various proteins and others factors, description of their effects on transcription and also mechanisms of their actions. TFs could be divided according to various criteria. In this work, TFs are divided according to how they interact with RNAP: TFs interacting only with RNAP; TFs binding simultaneously DNA and RNAP; TFs interacting with RNA and RNAP. This work presents a comprehensive overview of various TFs that are involved in the bacterial cell's reprogramming of gene expression that is required to withstand the changes in the environment.
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Catalytic function of DNA-dependent RNA polymerases
Sýkora, Michal ; Vopálenský, Václav (advisor) ; Lichá, Irena (referee)
DNA-dependent RNA polymerase is a highly organised protein complex that is responsible for gene expression and its regulation. Multisubunit RNA polymerase with its several catalytic activities is responsible for transcription of genes to RNA copies in all cellular organisms. During transcription RNA polymerase undergoes substantial conformational changes depending on the conditions in a particular cell. RNA polymerase in a state designated as an elongation complex passes through repetitive cycles of adding a nucleotide to the growing RNA chain. The active center contains two magnesium ions which coordinate the reactive groups of substrates. Furthermore, the active center contains structural elements that participate in binding of substrate, propper orientation of substrate towards the template strand and translocation of the RNA polymerase. The most important of these mobile structural elements are the bridge helix and the trigger loop whose conformational changes accompanies nucleotide addition cycle. Advances in the structural and biochemical characterization of RNA polymerase open new possibilities in the understanding of the transcription mechanism, its fidelity and control.
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delta subunit of bacterial RNA pol and its role in regulation of gene expression in B. subtilis
Dvořáček, Lukáš ; Krásný, Libor (advisor) ; Vopálenský, Václav (referee)
Delta subunit of bacterial RNA pol and its role in regulation of gene expression in B. subtilis. In this work I focus on regulation of eubacterial gene expression. First, I describe recent knowledge about a key stage of gene expression - transcription, focusing on regulation of trancription iniciation via small effector molecules (guanosine tetraphosphate, initiating nucleoside triphosphate) that are important for the regulation of ribosomal RNA. Second, in the experimental part of my work, I focus on the role of the _ protein, a subunit of RNA polymarase in gram positive bacteria, in transcription iniciation and its effects on regulation of RNA polymerase by the concentration of initiating nucleoside triphosphates.
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Role of Smarca5 (Snf2h) during transcription of transfected DNA template.
Zikmund, Tomáš ; Stopka, Tomáš (advisor) ; Smetana, Karel (referee)
Cellular and tissue characteristics are results of dynamic regulation of gene expression. DNA wrapped into proteins, referred to as chromatin, requires involvement of mechanisms guiding accessibility of specific sequences. In higher organisms, chromatin remodeling proteins are indispensable in regulating chromatin structure including ISWI ATPase SMARCA5. SMARCA5 is involved in almost any transaction on DNA including transcription, however precise in vivo role of SMARCA5 in these processes remains unknown. To advance understanding of specific role of SMARCA5 in the development of chromatin structure during transcription we devised cellular model in which SMARAC5 level is manipulated while chromatin structure development and transcriptional response are monitored. Our data indicate that the transfected DNA template that is transcribed is enriched with histone H3 and its specific methylation of Histone H3 lysine (K) 4, a mark of active chromatin structure. Overexpression of SMARCA5 results within the reporter gene coding sequence in ~2,5-3 fold increase of both H3 occupancy an its modification H3K4Me3. Increased DNA template commitment into chromatinization is associated with repression of reporter gene expression. These results are supported by studies indicating dynamic development of nucleosomal...
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The delta subunit of RNA polymerase from gram positive bacteria
Matějčková, Jitka ; Beranová, Jana (referee) ; Krásný, Libor (advisor)
1 Abstrakt Aby bakteriální buňka přežila neustále se měnící podmínky, musí se na ně adaptovat. Tato adaptace je podmíněna změnou genové exprese. Klíčovým krokem genové exprese je transkripce. Hlavním enzymem bakteriální transkripce je RNA polymerasa (RNAP), což je esenciální vícepodjednotkový enzym. RNAP je nejvíce prostudována u Escherichia coli, modelového organismu gram negativních bakterií. Porovnala jsem E. coli a Bacillus subtilis (zástupce gram pozitivních bakterií) a shrnula jsem rozdíly v RNAP a transkripci. Jejich RNA polymerasy se liší přítomností podjednotky δ u gram pozitivních bakterií. Tato podjednotka zvyšuje promotorovou selektivitu, recykluje jádro RNAP a celkově stimuluje syntézu RNA. Podjednotka δ ovlivňuje sporulaci a virulenci některých bakterií. V této práci jsem shromáždila současné poznatky o jednotlivých částech genové exprese, zejména o regulaci iniciace transkripce a o podjednotce δ RNAP.
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A Comprehensive Study of The Dzikowian Manuscript Focusing on a Graphic, Language and Textual Analysis of the Czech Postil
Svobodová, Andrea ; Dittmann, Robert (advisor) ; Kosek, Pavel (referee) ; Komárek, Karel (referee)
Mgr. Andrea Svobodová Komplexní studium Rukopisu dzikovského se zam ením na grafickou, jazykovou a textovou analýzu eské sbírky kázání A Comprehensive Study of The Dzikowian Manuscript Focusing on a Graphic, Language and Textual Analysis of the Czech Postil Abstract The thesis submits a comprehensive philological analysis of the Dzikowian Manuscript, an insufficiently explored late medieval manuscript containing two postils, de tempore in Latin and de sanctis in Old Czech. The thesis aims to specify the place of this work in the context of medieval preaching, to critically review the previous research and to find new paths of research in evaluating this work. It is divided into three chapters, their common topic being attribution of both the postils on the grounds of codicological, content, and especially language features. Special emphasis is put on description of non-standard language phenomena, their interpretation being a key factor for transcription rules (one of the main results achieved apart from precising probable dating and localisation is a complete transcription of the Old Czech postil). The phenomena described enrich the existing inventory of deviations from the standard language and call for relating to other sources traditionally categorised as dialectal and thus for elaborating diachronic...
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Transcription motif finding algorithms
Peřinová, Barbora ; Škutková, Helena (referee) ; Maděránková, Denisa (advisor)
This bachelor thesis deals with finding transcription motifs in DNA sequences. The first part describes the DNA transcription process, the significance of transcription motifs and provides an overview of transcription motif databases. The second part contains the classification of transcription motif finding algorithms, and details seven existing algorithms. In the practical part, functions for the analysis according to the Oligo-Analysis algorithm were created. Created functions were validated on the artificially created sequences with introduced motifs. The analysis of two families of coregulated genes was realized and the results were compared with the values achieved by the authors of the Oligo-Analysis algorithm.
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Nucleotide density for finding CpG islands
Sikorová, Eva ; Provazník, Ivo (referee) ; Maděránková, Denisa (advisor)
This bachelor thesis deals with searching for CpG islands in the DNA sequences using the nucleotide density vectors. The first part includes view of the DNA structure, the genetic information expression, more detailed analysis of CpG islands and primarily their detection methods. In the practical part the algorithm for graphical representation of nucleotides on the basis of their densities and detections of CpG islands of artificially created and real DNA sequences was realized in the MATLAB program. The thesis includes the analysis of twenty sequences with the expected content of CpGIs and the comparison of results between the created program and two search engines.
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Fourier transformation for exon prediction
Rusina, Michal ; Škutková, Helena (referee) ; Maděránková, Denisa (advisor)
In this bachelor thesis there are described the methods of the prediction of exon. The first part is aimed at the difference between the prokaryotic and eukaryotic organisms, the description of the DNA structure and the explanation of the terms exon and intron. The second section of the theoretic part includes four methods of the prediction of exons namely dynamic programming, neural networks, hidden Markov models and discrete Fourier transform. In the practical part there was created the program called Predikce_exonu that searches exons in nucleotide sequences and works on the principle of the Fourier transform. This algorithm together with 3 freely available programs was tested on 25 sequences and the success of their prediction was described by sensitivity and specificity.
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