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Local structures in retrovirus genomes
Sádlová, Adéla ; Kollerová, Silvia (referee) ; Brázda, Václav (advisor)
This bachelor thesis focuses on the study of local structures in the genomes of retroviruses. Retroviruses are a group of viruses with an RNA genome that have the ability to integrate their genome into the host DNA. Local structures in the retroviral genome play an important role in the processes of replication, gene expression regulation, and interactions with host proteins. The aim of this work was to analyze the local structures in selected retroviruses using bioinformatics methods, with G4 Hunter being the key tool for identifying G quadruplexes in the genome. G-quadruplexes are DNA or RNA structures composed of guanine bases arranged into quartets and are connected by stacking guanine tetrads. G quadruplexes are often located in telomeres, gene promoter regions, and can play an important role in regulating gene expression, DNA replication, and other cellular processes. The analysis focused primarily on the presence of potential G-quadruplex-forming sequences (PQS). The results of this work provide important information on the distribution and frequency of PQS in the genomes of selected retroviruses and contribute to a better understanding of their role in viral biology. The results show that G-quadruplexes are significant local structures and are often found in regulatory areas of the genome, indicating their key role in the viral infection process.
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Prediction of Transposons in DNA
Černohub, Jan ; Vogel, Ivan (referee) ; Martínek, Tomáš (advisor)
Cílem práce je seznámení se s problematikou uchovávání informace v DNA, provést rešerši na téma transpozony, bioinformatické nástroje a algoritmy, které jsou používány k jejich detekci v nasekvenovaných genomech a vytvořit tak stručný úvod do obsáhle problematiky, včetně jejího zasazení do kontextu současně probíhajícího výzkumu v dané oblasti. Na základě přehledu stávajících algoritmů a nástrojů pro detekci transpozonů je navržen a implementován nástroj pro hledání tzv. LTR transpozonů.
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Viruses and cytosketelon of the cell nucleus
Cibulka, Jakub ; Forstová, Jitka (advisor) ; Šťovíček, Vratislav (referee)
The nuclear cytoskeleton (the nucleoskeleton) provides a structural integrity to the nucleus and is involved in number of key processes including transcription, chromatin remodelling and mRNA transport. The nucleoskeleton consists of nuclear lamins, nuclear actin and other proteins. Some viruses, which replicate themselves in the nucleus, use nuclear cytoskeleton in their life-cycle. On the other hand the nucleosketon may also represent a barrier for viral infection. Herpesviruses need nuclear actin for capsid assembly and transport, but they have to desintegrate the nuclear lamina in order to escape the nucleus. Nuclear actin also participates in the morphogenesis and probably nuclear export of baculovirus capsids. Some retroviruses transport their unspliced RNAs from the nucleus using nuclear actin and there is also some evidence of retrovirus-induced nuclear lamina disruption. In this work, I focus on the interactions of above-mentioned viruses with the nuclear cytoskeleton (namely nuclear actin and lamins).
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Significantion of sumoylation for infection by selected viruses replicated in the cell nucleus
Sejpková, Marie ; Forstová, Jitka (advisor) ; Frydrýšková, Klára (referee)
This work introduces association between viruses and host cell with respect to sumoylation process. The main aim is referring to influence of this modification both on virus replication strategy and cell cycle. Sumoylation is essential process for cell regulation interfering with general regulation pathways including those performed by e.g. p53 or PML bodies and also epigenetic changes of chromatin. For viruses, sumoylation means stabilization of viral proteins and better timing each phase of viral cycle through viral protein. One point of view is competition of cell and virus for SUMO machinery. Viruses take advantage of sumoylation for inhibition antiviral defense of cells, regulation cell cycle mainly in apoptosis induction and in general for more successful infection. There are cumulating evidence of new proteins and phenomena connected with sumoylation mechanisms as well as viruses exploiting sumoylation for their benefit. Utilization and abuse of sumoylation by viruses point to future possibilities of cell manipulation and virus ability to intervene to this still relatively poorly understood type of cell regulation.
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POSITIVE AND NEGATIVE HOST FACTORS OF AVIAN SARCOMA AND LEUKOSIS VIRUSES
Krchlíková, Veronika ; Elleder, Daniel (advisor) ; Růžek, Daniel (referee) ; Španielová, Hana (referee)
Identification and characterization of the host cell factors that either support or inhibit virus replication constitutes a major direction in virological research. In this work we focus on several such host factors in the context of avian cell. Chicken Tva, cell entry receptor for subgroups A and K of Avian sarcoma and leukosis virus (ASLV), was identified to be orthologous to human receptor for cellular uptake of cobalamin (Cbl). Here, we describe Cbl uptake in chicken cells and its dependency on Tva. Additionally, we characterize in vivo Tva knockout in chicken. Chicken Tvb receptor conferring susceptibility to subgroups B, D and E of ASLV was previously shown to participate in virus-induced cytopathic effects. In this work, we identify a natural ligand of Tvb and investigate its participation in apoptosis. RIG-I-like receptors (RLR) are a key family of cytosolic viral RNA sensors. The activation of these receptors leads to establishment of an antiviral state in the cell. In this study, we describe repeated evolutionary losses of RLR genes in birds: the loss of MDA5 in two avian orders and the loss of RIG-I in multiple species. Tetherin is an antiviral restriction factor blocking the release of newly formed viral particles. We identify tetherin orthologs in avian species and investigate...
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Reporter expression system for study of silencing of provirus integrated inside transcriptionally active gene
Slavková, Martina ; Hejnar, Jiří (advisor) ; Španielová, Hana (referee)
Retroviral vectors are used as mighty tools for an introduction of recombinant genes into the recipient genome in gene therapy trials. In the vector design, great emphasis is put on safety and efficiency. In spite of a great progress in retroviral vector design with the purpose to stabilize its expression, e.g. introduction of protective elements into the viral regulatory sequences, the current approaches are still not sufficiently effective and the majority of proviruses is transcriptionally silenced. The understanding of the silencing mechanism is of special importance to the optimization of the vector design and handling. In this master thesis, I have designed and constructed an expression system for study of the mechanism involved in the silencing of retroviruses integrated inside gene bodies. This artificial system will be utilized for testing of hypothesis that retroviruses integrated into gene bodies are silenced by DNMT-dependent mechanism and this process is triggered by transcriptional read-through of the provirus from nearby host promoter. I have obtained preliminary results suggesting the validity of the suggested hypothesis; however the verification of general validity of this hypothesis for various retroviruses and elements will be a matter of further studies in our laboratory. Powered by...
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Significantion of sumoylation for infection by selected viruses replicated in the cell nucleus
Sejpková, Marie ; Forstová, Jitka (advisor) ; Frydrýšková, Klára (referee)
This work introduces association between viruses and host cell with respect to sumoylation process. The main aim is referring to influence of this modification both on virus replication strategy and cell cycle. Sumoylation is essential process for cell regulation interfering with general regulation pathways including those performed by e.g. p53 or PML bodies and also epigenetic changes of chromatin. For viruses, sumoylation means stabilization of viral proteins and better timing each phase of viral cycle through viral protein. One point of view is competition of cell and virus for SUMO machinery. Viruses take advantage of sumoylation for inhibition antiviral defense of cells, regulation cell cycle mainly in apoptosis induction and in general for more successful infection. There are cumulating evidence of new proteins and phenomena connected with sumoylation mechanisms as well as viruses exploiting sumoylation for their benefit. Utilization and abuse of sumoylation by viruses point to future possibilities of cell manipulation and virus ability to intervene to this still relatively poorly understood type of cell regulation.
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Epigenetic regulation of retroviruses.
Dobšová, Martina ; Trejbalová, Kateřina (advisor) ; Drda Morávková, Alena (referee)
The human genome is the site of integration of the retrovirus HIV-1, ERVWE1 (syncytin-1) is its stable part. Thus as an integral part of the genome, they are under influence of important genome based epigenetics regulations, such as DNA methylation, histone methylation and acetylation. Promoter DNA hypermethylation and histone deacetylation leads to establishment and maintenance of latent state of the HIV-1 virus and formation of the latent reservoir in the CD4+ memory T-cells. This process leads to severe problems during HIV-1 infection treatment by antiretroviral therapy (HAART), as the HIV-1 latent reservoir remains unaffected. Moreover DNA hypermethylation in the promoter of syncytin-1 directs its transcriptional silencing, which is important in tissue specific regulation of this fusogenic protein. In physiological conditions syncytin-1 expression is observed only in placental cells, where the DNA methylation of promoter is decreased. Higher expression level of syncytin-1 was also observed in several other tissues, such as testes, where it is tightly coupled with germ-cells tumors and syncytin-1 promoter hypomethylation. In conclusion, epigenetic regulation of retroviruses by DNA methylation and chromatin modifications highly influence regulation of their expression. Presented bachelor thesis...
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Viruses and cytosketelon of the cell nucleus
Cibulka, Jakub ; Forstová, Jitka (advisor) ; Šťovíček, Vratislav (referee)
The nuclear cytoskeleton (the nucleoskeleton) provides a structural integrity to the nucleus and is involved in number of key processes including transcription, chromatin remodelling and mRNA transport. The nucleoskeleton consists of nuclear lamins, nuclear actin and other proteins. Some viruses, which replicate themselves in the nucleus, use nuclear cytoskeleton in their life-cycle. On the other hand the nucleosketon may also represent a barrier for viral infection. Herpesviruses need nuclear actin for capsid assembly and transport, but they have to desintegrate the nuclear lamina in order to escape the nucleus. Nuclear actin also participates in the morphogenesis and probably nuclear export of baculovirus capsids. Some retroviruses transport their unspliced RNAs from the nucleus using nuclear actin and there is also some evidence of retrovirus-induced nuclear lamina disruption. In this work, I focus on the interactions of above-mentioned viruses with the nuclear cytoskeleton (namely nuclear actin and lamins).
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Prediction of Transposons in DNA
Černohub, Jan ; Vogel, Ivan (referee) ; Martínek, Tomáš (advisor)
Cílem práce je seznámení se s problematikou uchovávání informace v DNA, provést rešerši na téma transpozony, bioinformatické nástroje a algoritmy, které jsou používány k jejich detekci v nasekvenovaných genomech a vytvořit tak stručný úvod do obsáhle problematiky, včetně jejího zasazení do kontextu současně probíhajícího výzkumu v dané oblasti. Na základě přehledu stávajících algoritmů a nástrojů pro detekci transpozonů je navržen a implementován nástroj pro hledání tzv. LTR transpozonů.
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