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Effect of ADAR1 enzyme on hepatitis C virus life cycle
Kubů, Martin ; Vopálenský, Václav (advisor) ; Fraiberk, Martin (referee)
Hepatitis C virus (HCV) is a virus of the family Flaviviridae whose genome consists of ,,+RNA" molecule. It causes the disease hepatitis Cepatitida typu C, which affects tens of millions of people worldwide. Although there is an effective treatment for this type of hepatitis, a preventive vaccine against the HCV virus has not yet been developed. Several ambigious works focused on the relationship between HCV and the enzyme adenosine deaminase acting on double-stranded RNA 1 (ADAR1) were published in the past. This dimeric double-stranded RNA binding enzyme is a part of innate immunity and causes catalytic conversion of adenosine to inosine, which is recognized by cellular mechanisms as guanine, which ultimately leads to mutations in the affected dsRNA molecule. The works published so far attribute an antiviral function to the ADAR1 enzyme in the context of HCV infection. However, vectors containing the entire HCV genome were not used in these works, and a cell line with deletion od the ADAR1 gene has never been used so far. The actual relationship between the ADAR1 enzyme and the HCV virus has not yet been reliably verified. The aim of this thesis was to gain a deeper understanding of the relationship between the HCV virus and the ADAR1 enzyme. For this task, HCV permissive Huh7.5 cell lines with...
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Effect of adenosine deaminase acting on RNA on viral infection of eukaryotic cells
Kubů, Martin ; Vopálenský, Václav (advisor) ; Fraiberk, Martin (referee)
Double-stranded RNA is a molecule rarely found in a cell, but it is specific for viral infection. It is also a substrate of ADAR enzymes. These enzymes convert adenosin to inosine, which is recognized as guanosine by cellular machinery. Apart from editing activity, ADAR enzymes interact with cellular proteins, such as Dicer and protein kinase R, which together with editing affects viral replication. In this work, the information about antiviral activity of ADAR enzymes and their impact on infection of selected primarily human viruses is reviewed.
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The role of RNA-binding proteins in post-transcriptional gene regulation of Trypanosoma brucei
DIXIT, Sameer
This thesis characterizes RNA footprints of several RNA-binding proteins (RBPs) thatare involved in U-insertion/deletion, A-to-I, and C-to-U RNA editing in Trypanosoma brucei. Relying on iCLIP data and biochemical methods it shows that two paralogs proteins from the MRB1 complex regulate distinct editing fates of the mitochondrial transcripts. Further, this thesis provides evidence where the combinatorial interplay of RBPs might fine-tune the levels of edited mRNA. Finally, the presented thesis adds to the growing evidence of the importance of RBPs in post-transcriptional gene regulation.
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High-throughput analysis of uridine insertion and deletion RNA editing in \kur{Perkinsela}
DAVID, Vojtěch
This thesis is a follow-up of my Bachelor thesis about the mitochondrial genome of kinetoplastid protist Perkinsela sp. This work introduces a novel approach in high-throughput analysis method of uridine insertion and deletion RNA editing, describes its background and proposes its further development. Its effect on the interpretation of U-indel editing, both in Perkinsela and in general, is demonstrated via attached manuscript which also introduces other biologically relevant aspects of Perkinsela mitochondrion.
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Assembly and annotation of a mitochondrial genome of kinetoplastid protist \kur{Perkinsela}.
DAVID, Vojtěch
This thesis is based on a collaborative project between Laboratory of Molecular Biology of Protists led by Prof. Julius Lukeš and the laboratory of John Archibald (Department of Biochemistry & Molecular Biology, Dalhousie University, Canada). My contribution to the project, as the name of the thesis suggests is to process DNA and RNA sequencing data from Neoparamoeba pemaquidensis isolate that correspond to the mitochondrion of Perkinsela, also called Ichthyobodo-related organism (IRO). The main aim is to characterize mitochondrial gene content and to attempt to understand the mechanism of U-insertion/deletion RNA editing in Perkinsela and its evolution.
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