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Novel hepatitis C virus proteins
Zeman, Jakub ; Vopálenský, Václav (advisor) ; Horníková, Lenka (referee)
The hepatitis C virus (HCV) is a major etiological agent of chronic liver diseases. More than 170 million people worldwide are chronically infected, and more than 100 thousand of them develop hepatocellular carcinoma a year. HCV is an enveloped, positive-sense single-stranded RNA virus (+ssRNA virus) of the family Flaviviridae. Its genome is translated to produce a single polyprotein precursor that is further processed by cellular and viral proteases to form 10 viral proteins. Moreover, there is another protein encoded in an alternative reading frame. Two alternative translation mechanisms have been proposed for expression of this alternative reading frame protein (ARFP): a frameshift mechanism and translation initiating from internal start codons. Despite ten years of research its role in vivo is not yet explained. It appears that secondary structures in the core encoding region of HCV genome but not ARFP expression are required for robust viral translation and replication. The results of recent studies suggest that mutations distorting these structures may result not only in slowing down the viral cycle but also in a brand new and utterly unusual serological profile in patients as well as an increased level of expression of ARFP.
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Analysis of miRNAs in HPV-associated carcinomas
Pagáčová, Lucie ; Tachezy, Ruth (advisor) ; Vopálenský, Václav (referee)
Papillomaviruses are small DNA viruses that are associated with the induction of epithelial tumors. HPV is an important infectious agent causing almost 100 % of cervical tumors but it can also cause tumors in other anogenital and head and neck locations in both men and women. Active HPV infection induces changes in miRNA expression that contribute to the tumor formation and progression. It is already known that papillomaviruses do not encode their own viral miRNAs but they affect the expression of cellular miRNAs. In my thesis I have in selected epithelial tumors (vulva, cervix, anus and tonsils) determined their etiology and analyzed the presence of miRNAs in tissues by next generation sequencing. From these data I determined the expression profiles of deregulated miRNAs in tumors relation to healthy tissues of corresponding location. Even though, sufficient number of samples was analyzed, it was not possible to detect HPV-core miRNA common to all analyzed HPV-induced tumors due to the absence of statistically relevant differentially expressed miRNAs in HPV positive vulvar tumors. Among the tumors of the other sites I found an overlap in three miRNAs. One of these miRNAs (miR-139-5p) and another one (miR-9-5p) which I have selected based on the study of other published data, were used for...
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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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Regulation of the expression of MHC class I molecules and other immunoactive molecules on tumor cells
Moravcová, Simona ; Reiniš, Milan (advisor) ; Vopálenský, Václav (referee)
4 Abstract Regulation of the expression of MHC class I molecules and other immunoactive molecules on tumor cells The aim of this master thesis project was to characterize the effects of IFNγ, TNFα and of the epigenetic agents 5-azacytidine (5AC) and 5-aza-2'-deoxycytidine (5AZAD) on the expression of molecules important for antigen presentation and modulation of the immune responses against tumors (MHC class I molecules and other immunoactive molecules CD54, CD80, B7-H1, B7-H2 and CD1d) on tumor cells. The experimental model used for this purpose were the HPV16-associated murine tumor cell lines, either MHC class I positive or negative. The goal was to determine the changes in surface expression of these molecules after treatment by FACS studies and also the expression at the mRNA level using qPCR. Expression of these proteins was also compared in the experiments in vitro on tumor cell lines and ex vivo on tumor cells explanted from animals. The most interesting result is the observation that 5AZAD increases the expression of B7-H1 which inhibits T cell mediated immune response and that 5AZAD and IFNγ act synergistically in the induction of the expression of MHC class I, CD54 and B7-H1 molecules. Klíčová slova: imunoeditace, protinádorová imunita, HVP16, MHC glykoproteiny I. třídy, B7-H1, IFNγ, TNFα,...
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Construction and characterization of recombinant adenylate cyclase toxoid of bacterium Bordetella pertussis carrying mycobacterial antigen TB7.7
Mikulecký, Pavel ; Staněk, Ondřej (advisor) ; Vopálenský, Václav (referee)
Bacterium Mycobacterium tuberculosis is an etiological agent of a deadly disease called tuberculosis that presents a global problem. According to The World Health Organization there are more than 2 billions people infected with latent tuberculosis all over the world. There is still need of specific, sensitive, quick and economic available method for identification of infected individuals. Currently in vitro blood tests are considered to be the best way of diagnosis. They are based on restimulation of specific T lymphocytes by mycobacterial antigens derived from virulent strains. There are several different approaches for enhancing of direct antigen delivery into antigen presenting cells and promising one is a genetically detoxified adenylate cyclase toxin (CyaA) of bacteria Bordetella pertussis. The main aim of the thesis includes construction and subsequent characterization of biological properties of CyaA protein carrying specific mycobacterial antigen TB7.7 in translocating domain. Here is shown that fusion protein CyaA-TB7.7 can form cation selective pores in target cell membranes and is able to deliver antigens into the cytosol of APC to be presented on surface with molecules MHC class II. Genetically detoxified CyaA- TB7.7 protein will be used to supplement current approaches such as also in vitro...
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Photoperiodic entraiment of circadian clock in suprachiasmatic nucleus
Parkanová, Daniela ; Sumová, Alena (advisor) ; Vopálenský, Václav (referee)
Most of physiological processes run in the organisms persistently, they begin in a definite rhythm again and again. The greatest attention is paid to the rhythms, whose period is equal to one day - they are called circadian rhythms. In case of mammals, these circadian rhythms are under control of the central circadian clock that resides in the suprachiasmatic nucleus, a part of the anterior hypothalamus. The mechanism of rhythm generation is based on interacting transcriptional-translational feedback loops that control expression of the clock genes in every single cell. Clock-controlled genes transmit these rhythms into the whole organism where they drive many physiological processes. Clock genes are expressed also in the peripheral oscillators (for example in liver, lungs, heart) and are under direct control of the central oscillator. Circadian clock needs to be entrained everyday to the external time to function precisely. The main entraining cue is the light part of the day. The length of the light part of the day, i.e. photoperiod, changes during the year rapidly in our latitudes and the central oscillator has to adapt to the changes all the time. The length of the photoperiod is encoded directly in the central oscillator by the transcriptional-translational relations among the clock genes and...
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The use of parallel sequencing methods in microbiology.
Pavlíková, Magdaléna ; Najmanová, Lucie (advisor) ; Vopálenský, Václav (referee)
The thesis describes the history of development of sequencing methods with special focus on the modern effective parallel sequencing methods and their application in microbiology. The development and improvements of sequencing systems lead to the acceleration of the process and considerable decrease of price, which consequently allow wider spectrum of applications. Each of the sequencing systems has its characteristic features including drawbacks stemming from the principle of the respective method. Not every method suitable for all the applications. In the thesis the sequencing methods are compared and examined with respect to their appropriateness for certain application fields in microbiology. The currently available sequencing methods are usually categorized into three "generations", distinguished by sets of typical features. First generation methods include the systems of Sanger and Maxam-Gilbert; "next generation" is represented by methods 454, Illumina, SOLiD and Helicos; and finally SMRT, Ion Torrent and the commercially not yet available nanopore sequencing are usually called "next-next generation". Now the sequencing becomes a standard technology of molecular biology, not only in the basic microbiological research, but it is also widely applied in medicine (quick identification of patogenes,...
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Inducible promoters and their use in yeast cell manipulation
Přibáňová, Gabriela ; Palková, Zdena (advisor) ; Vopálenský, Václav (referee)
Promoters which can be regulated by different chemical or physical factors are often used in cell manipulations. This thesis focuses predominantly on promoter systems which use light as an inductor. There are two main approaches to controlling a promoter by light. The first one uses so-called "caged molecules", chemical inducers whose inducing activity is "masked" by a photolabile protecting group. The second approach includes optogenetic systems, which can regulate transcription in cells. These systems are encoded in the DNA of the organism, and light is the only external regulatory stimulus. Photoreceptors that need a specific cofactor (chromophore) are the main components of optogenetic systems. There are several groups of photoreceptors classified by the type of chromophore and photoactivation mechanism. This thesis gives an overview of optogenetic systems used for transcription regulation and focuses on different photoreceptors and induction mechanism used. The systems using photocaged molecules are described as well. Furthermore, the thesis deals with light- systems in yeast as a model organism as well as organism used for biotechnological purposes. Finally, some limitations of light inducible promoters are discussed, including the chromophore type, the wavelength of the light, and the...
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