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Hydrophilic polymers-based delivery systems for the transport and controlled release of siRNA
Blažková, Jana ; Laga, Richard (advisor) ; Vopálenský, Václav (referee)
Therapeutics based on siRNA represent a promising hope for the treatment of many congenital and acquired disorders. This method is based on posttranscriptional silencing of pathological gene or set of genes (RNAi process), which are responsible for the actual cause of the disease. Access is therefore based on the assumption of treatment options for the disease at the point of origin of the defect intervention at the molecular level, which is different from the conventional, so-called symptomatic therapy, which focuses only on the treatment or suppression of symptoms. Despite rapidly increasing understanding of gene function and cause a number of genetic diseases, the expansion of siRNA therapeutics limited the development of efficient and safe transport systems (vectors). In order to ensure efficient transport of siRNA in vivo conditions, the vectors must sufficiently reduce the size of the siRNA, protect it against degradation during transport, and release in the cytoplasm of the target cell. For this purpose they were developed sophisticated transport systems based on viral and non-viral origin. This diploma thesis is focused on the preparation of new transport systems, siRNA-based synthetic hydrophilic polymers, such as non-viral vectors. For in vitro testing the effectiveness during transport of siRNA...
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Gene expression study of oxysterol signal pathway in breast cancer patients
Kloudová, Alžběta ; Souček, Pavel (advisor) ; Vopálenský, Václav (referee)
Hormonal therapy is a common part of breast carcinoma treatment in patients whose tumors express estrogen and progesterone receptors. The aim of hormonal therapy is to prevent proliferative effect of hormones througt their receptor proteins in order to inhibit tumor growth. However, certain number of tumors is resistant to hormonal therapy despite expression of hormonal receptors. Presently, the reasons of this resistance are not fully understood. Oxysterols are hydroxylated cholesterol derivates, which may play some role in development of the resistance. They may interfere with hormonal therapy effect and influence some signal pathways leading to cancer progression. This study comes with results of gene expression of proteins influenced by oxysterol action, metabolic and transport proteins, transcription factors and members of signaling pathways that may be related to oxysterol effect. This thesis identifies some candidate genes for future analysis on the basis of comparison of gene expression between estrogen receptor positive and negative tumors and correlation with clinopathological data. The final goal should lead to discovery of new diagnostic markers for breast cancer therapy. Powered by TCPDF (www.tcpdf.org)
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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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Factors affecting gene expression in Bacillus subtilis
Sudzinová, Petra ; Krásný, Libor (advisor) ; Vopálenský, Václav (referee) ; Vohradský, Jiří (referee)
Bacterial DNA-dependent RNA polymerase (RNAP) is a key enzyme of bacterial transcription. Its activity must be tightly regulated. This could be done on the level of promoter DNA topology recognition, by changing the intracellular levels of metabolites, or by binding proteins, known as transcription factors. Even though the RNAP regulatory network has been intensively studied for decades, new regulators are still being described. The main focus of this Thesis is to characterize some of them: i) HelD, a novel RNAP interacting factor, with so far unknown protein 3D structure; ii) RNase J1, an enzyme with a unique mechanism of functioning; iii) Spx, a major regulator of gene expression in Bacillus subtilis, with still new roles to be defined and iv) the effect of the topological state of promoters on transcription. We identified HelD as an interacting protein of RNAP in Bacillus subtilis and described its biochemical properties. It stimulates transcription in an ATP-dependent manner, by enhancing recycling of RNAP molecules (Publication I). We published the first insight into the HelD structure by SAXS (small angle X-ray scattering) and deepened the understanding of HelD domain composition (Publication III). And finally, we were able to solve the cryo-EM structure of HelD:RNAP complexes from...
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Synthesis of proteins containing non-canonical amino acids
Knetl, Adam ; Vopálenský, Václav (advisor) ; Plocek, Vítězslav (referee)
0 Abstract: Non-canonical amino acids allow the introduction of new chemical properties into proteins, which is useful both for studying proteins, and designing proteins. However, the synthesis of proteins containing non-canonical amino acids faces problems with decreased effectivity of translation. This thesis examines the role of genetic code for coding non-canonical amino acids, proteosynthesis and aminoacilation of tRNA and finally the non-canonical amino acids and their application in proteins while including examples.
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Preparation and validation of a system for the study of regulation of gene expression of yeast linear cytoplasmic plasmids
Horáčková, Kamila ; Vopálenský, Václav (advisor) ; Čáp, Michal (referee)
There is currently very few information about the transaltion of linear cytoplasmatic plasmids occured in yeast cells Kluyveromyces lactis. However, there is a relatively well developer information about their transcription apparatus. A study of transkript linear plasmids revealed an atypical organization at the 5ʼ end. Those ends contain nontemplate polyadenylation and they are missing the N7 methylguanosine hat. Because of the presence of this structure, which is localized at 5ʼend of plasmids specific mRNA, raised a question regarding the iniciation of the translation. The present thesis is focused on the preparation of reporter systém suitable for studying the influence of a number of the nontemplate adenosins, which were added at the 5ʼ ends of mRNA linear plasmids. The frist step was making a construction of dual yeast cell plasmids carring two reporters genes, which are under the controle of two different promoters. After a successfull construction, the aktivity of promoters TEF1 and PGK1 was measured, whereby the promoter TEF1 proved twice stronger. The transcription start site of both promotor was determined. The second step was the construction of a reporter system directly in yeast cell plasmid pGKL. Reporter genes were under the controle of two promoters originating from the pGKL...
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Factors affecting gene expression in Bacillus subtilis
Sudzinová, Petra ; Krásný, Libor (advisor) ; Vopálenský, Václav (referee) ; Vohradský, Jiří (referee)
Bacterial DNA-dependent RNA polymerase (RNAP) is a key enzyme of bacterial transcription. Its activity must be tightly regulated. This could be done on the level of promoter DNA topology recognition, by changing the intracellular levels of metabolites, or by binding proteins, known as transcription factors. Even though the RNAP regulatory network has been intensively studied for decades, new regulators are still being described. The main focus of this Thesis is to characterize some of them: i) HelD, a novel RNAP interacting factor, with so far unknown protein 3D structure; ii) RNase J1, an enzyme with a unique mechanism of functioning; iii) Spx, a major regulator of gene expression in Bacillus subtilis, with still new roles to be defined and iv) the effect of the topological state of promoters on transcription. We identified HelD as an interacting protein of RNAP in Bacillus subtilis and described its biochemical properties. It stimulates transcription in an ATP-dependent manner, by enhancing recycling of RNAP molecules (Publication I). We published the first insight into the HelD structure by SAXS (small angle X-ray scattering) and deepened the understanding of HelD domain composition (Publication III). And finally, we were able to solve the cryo-EM structure of HelD:RNAP complexes from...
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The role of elF3 a Rps3 in stop codon readthrough
Poncová, Kristýna ; Valášek, Leoš (advisor) ; Vopálenský, Václav (referee) ; Krásný, Libor (referee)
Translation represents a highly regulated, interconnected process of protein synthesis in the cell. It could be divided into 4 phases: initiation, elongation, termination, and ribosomal recycling. Our laboratory is involved in in-depth studies of a complex eukaryotic initiation factor 3 protein (eIF3). We are interested not only in revealing its molecular roles in the translational cycle in general but also in specific mechanisms that allow translational regulation according to specific cellular needs. In the budding yeast, the eIF3 is composed of five essential subunits (a/Tif32, b/Prt1, c/Nip1, g/Tif35 and i/Tif34). In mammals, the protein is even more complex, comprising of 12 subunits (a-i, k-m). eIF3 is a key player not only in translation initiation but also in ribosomal recycling and, surprisingly, in translation termination and stop codon readthrough as well. The latter process harbors important clinical potential, as approximately 1/3 of genetically inherited diseases is caused by the presence of a premature termination codon in the protein-coding region. Therefore, understanding the molecular mechanism underlying this phenomenon provides important tools for the targeted and less toxic drug development approaches needed for patient therapy. In this Ph.D. Thesis, I uncovered the role of...
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Development of a technique for gene transfer into T-lymphocytes using polyomavirus structures and the LAH4 peptide
Schreiberová, Lucie ; Španielová, Hana (advisor) ; Vopálenský, Václav (referee)
Efficient delivery of genetic material to T-lymphocytes is key in gene therapy using T-lymphocytes with chimeric antigen receptors. Current procedures require the use of potentially dangerous viral vectors or large amount of input material. The diploma thesis therefore focuses on exploring new approaches for gene transfer into T-lymphocytes: use of safe virus-like particles (VLPs) derived from mouse polyomavirus in combination with the amphipathic cationic peptide LAH4. LAH4 has the potential to increase the efficiency of DNA and viral vector transport into cells. The system which combines VLPs and the LAH4 peptide was optimized for the delivery of reporter gene (encoding GFP and luciferase) to the model T-cell line Jurkat. It has been found that Jurkat cells cannot be efficiently transduced by DNA packed into VLPs. When cells were transfected only with DNA and LAH4, consistent results were not obtained, and the transfection efficiency ranged from 0.5 to 19%. The diploma thesis also analysed the effect of phosphorylation of viral structures on gene transfer. The impact of treatment of virus particles by alkaline phosphatase on the infectivity of the virus was studied and it was necessary to analyse the effect of the reaction components. Sublytic concentration of Triton-X100 in the reaction buffer...
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