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The role of the AGO-hook domain of histone chaperone SPT6L in regulation of gene expression
Kašpar, Tomáš ; Čermák, Vojtěch (advisor) ; Převorovský, Martin (referee)
AGO-hook domains present in some eucaryotic proteins are crucial for a binding family of ARGONAUTE proteins (AGO). These AGO proteins are essential in many biological processes regulating gene expression by small RNA (sRNA), which is complementary to the gene that is supposed to be influenced. This thesis claims to find the function of the putative AGO-hook domain of the protein SPT6L. SPT6L is an elongation factor and histone chaperon of a complex of RNA polymerase II (Pol II) where it is acting in the epigenetic marking of histones. SPT6L of Arabidopsis thaliana is one of two paralogues of SPT6 proteins, that is characteristic of the presence of the AGO-hook domain. This is a plant specificity of this protein. What's more, the function of this domain remains unknown. Despite this, it could be assumed that this domain is necessary for binding of AGO proteins in the complex of Pol II, and by these interactions, it can enable guidance of regulation of chromatin modification, or it can co-transcriptionally influence nascent transcripts of Pol II by the sRNA. This thesis casts light on the function of the AGO-hook domain of SPT6L in A. thaliana in processes of gene regulation and protein interactions. It claims to confirm the interaction of the AGO-hook domain of SPT6L protein with AGO proteins and...
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Annotated translation: Old China (H. Bögeholz: Anders reisen: China, 1989)
Drašnarová, Kateřina ; Žárská, Monika (advisor) ; Drahotová, Markéta (referee)
The subject of this bachelor thesis is the annotated translation of the chapter Das alte China, which is a part of the German travel guide book Anders reisen: China. The translation was carried out on the basis of described translation analysis followed by establishment of the translation strategy. At the conclusion of the thesis the concrete translation difficulties and solutions in the area of grammar, stylistics and semantics are being discussed. A constitutive part is also a consideration of the translator's legitimacy of correcting errors in the source text.
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The delta subunit of RNA polymerase from gram positive bacteria
Matějčková, Jitka ; Krásný, Libor (advisor) ; Beranová, Jana (referee)
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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Factors interacting with bacterial RNA polymerase and their effect on the regulation of transcription initiation
Ramaniuk, Volha ; Krásný, Libor (advisor) ; Lichá, Irena (referee) ; Valášek, Leoš (referee)
(ENGLISH) The bacterial cell needs to regulate its gene expression in response to changing environmental conditions. RNA polymerase (RNAP) is the pivotal enzyme of this process and its activity is controlled by a number of auxiliary factors. Here I focus on RNAP-associating factors involved in regulation of transcription in G+ bacteria: factors, initiating nucleoside triphosphates (iNTPs), HelD, δ and small RNA Ms1. The main emphasis is on σ factors from Bacillus subtilis. σ factors allow RNAP to specifically recognize promoter DNA. In my first project I set up in vitro transcription systems with purified alternative σ factors, σB , σD , σH , σI from B. subtilis. Using these systems, I studied the effect of initiating NTP concentration ([iNTP]) on transcription initiation. I showed that promoters of alternative factors are often regulated by [iNTP]. In the next project I comprehensively characterized one of the least explored alternative factors from B. subtilis, I . I identified ~130 genes affected by I , though only 16 of them were directly affected. Moreover, I discovered that I is involved in iron metabolism. Finally, I showed that I binding requires not only the conserved -35 and -10 hexamers, but also extended -35 and -10 elements located in the spacer region. In collaboration with...
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Comparison of effectiveness of teaching using computers vs. 3D models
Andělová, Denisa ; Janštová, Vanda (advisor) ; Jáč, Martin (referee)
Currently, pupils' interest in science continues to decline, although this area of education is very important in every day life (medicine, environment, etc.) and there is high demand for science professions on the labor market. Molecular biology curriculum concerning DNA and the transfer of genetic information is abstract and difficult topic for pupils to imagine, and for teachers to explain. There are many ways to teach this topic. Very popular are iquiry and laboratory practise. But not all schools have their own laboratories, and can teach molecular practical effectivelly. Inquiry based teaching is time consuming to prepare, and not every topic is appropriate to be taught this way. Another possibilities how to visualize "invisible" molecules and processes are computer software and animations or 3D physical model. In my thesis, I examined the effect of using computers and animations to teach abou DNA compared to using a 3D physical model on students' knowledge. I laso tested the possible influence of gender and pupils' preferences on their achieved score on knowledge tests. The research was performed in five classes at three high schools in Prague. Students in year 12 were on different types of high school and some of them took special biology class, their age was between 15 and 18 years. The...
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Interactions of resveratrol derivatives with PXR receptor
Marešová, Veronika ; Pávek, Petr (advisor) ; Trejtnar, František (referee)
Charles University in Prague Department of Pharmacology & Toxicology Student: Supervisor: Prof Title of diploma thesis: Interactions of resveratrol derivatives with PXR receptor Derivatives of resveratrol belong between natural substances contained mainly in red wine and grapefruit. These compounds with stilbene-like structure show antioxidant activity. Pregnane X receptor (PXR) regulates expression of the most important biotransformation enzymes in human liver and intestine including cytochrome P450 3A4 (CYP3A4). Interaction of resveratrol and PXR have already been studied, but published data are contradictory. In my diploma thesis, I studied interaction of resveratrol and its derivatives with PXR. For this purpose, gene reporter assay with quantitative real-time polymerase chain reaction (qRT-PCR) was introduced. It was not possible to conduct experiments in standard way because both resveratrol and its derivatives inhibit lusiferase activities. I studied also effects of resveratrol and its derivatives on expression of CYP3A4 mRNA on differentiated HepaRG cell line. New method gene reporter method with qRT-PCR detection of luciferase was established on hepatoma cell line HepG2 transfected with CYP3A4 reporter construct. Concertation dependent effects of resveratrol and its derivatives were...
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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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Bacterial RNA polymerase and molecules affecting its function
Jirát Matějčková, Jitka ; Krásný, Libor (advisor) ; Vopálenský, Václav (referee) ; Staněk, David (referee)
RNA polymerase (RNAP) transcribes DNA into RNA and is the only transcriptional enzyme in bacteria. This key enzyme responds to external and internal signals from the cell, resolves the intensity of transcription of individual genes and thus regulates gene expression. RNAP is not only affected by its own subunits, but also protein factors, small molecules or small RNAs (sRNAs). The aim of this Thesis was to contribute to the understanding of the regulation of the RNAP and to add missing fragments to this broad topic. The first part of this Thesis is focused on the influence of selected proteins (δ, YdeB, GreA) on the sensitivity of RNAP to the concentration of the initiating nucleoside triphosphate ([iNTP]) during transcription initiation in Bacillus subtilis. We showed that δ affects the sensitivity of RNAP to [iNTP] at [iNTP]-sensitive promoters, but not at [iNTP]-insensitive promoters neither in vitro nor in vivo. The δ subunit is essential for cell survival during competition with other strains, because it enables the cell to react immediately to changing conditions. Further we showed that YdeB protein does not bind to RNAP in B. subtilis, and has not shown any effect on transcription in vitro. We found that both, GreA and YdeB proteins (unlike δ subunit) were unable to affect RNAP by [iNTP] at...
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