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Structural and functional study of viral RNA polymerases
Dubánková, Anna ; Bouřa, Evžen (advisor) ; Bařinka, Cyril (referee) ; Plevka, Pavel (referee)
Viral RNA-dependent RNA polymerases (RdRps) are enzymes essential for viral multiplication. The general function of RdRp is universal for all RNA viruses: to recognise viral RNA, bind it and synthesize the complementary RNA strand. This series of steps is absolutely crucial for viral infection. It is important to mention that the non-infected cell is incapable of replicating any RNA. The host cell thus does not naturally express any RdRps. I chose RdRps for my research because these enzymes are key to viral replication and thus an excellent target for antivirals. This study characterises polymerases from Picornaviridae and Flaviviridae families, in depth. Picornaviral replication takes place in viral-induced membrane structures called Replication Organelles (ROs), where the polymerase is localised to the membrane. In this study, we investigated the recruitment of picornaviral polymerase membrane. Subsequently, we focused on the activation of picornaviral RdRp induced by the insertion of the very first residue into the protein core. Next, we focused on the flaviviral RdRps specifically from yellow fever virus (YFV) and Zika virus (ZIKV). This study reports the first structure of a full length YFV polymerase and a model of ZIKV polymerase in complex with RNA. The model of ZIKV RdRp in complex with...
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Decoy effect and its use in marketing
Regnerová, Eva ; Vranka, Marek (advisor) ; Rosenfeldová, Jana (referee)
This bachelor thesis examines decoy effect, a phenomenon of behavioral economics. Above all, it focuses on the asymmetrically dominated effect. The main objective of the thesis is to review recent research dealing with the decoy effect and analyze the possibilities of its use in marketing practise. The thesis consists of theoretical and empirical part. In the first chapter of the theoretical part the principle of the decoy effect is generally explained and its possible modifications are described. The second chapter characterizes the asymmetrically dominated effect, the primary type of the decoy effect. There are discussed possible explanations and limits of the effect. In the chapter there is also described wide scope of experiments testing the effect. Special attention is drawn to the use of the asymmetrically dominated effect in marketing communication. The empirical part is then formed by replication of an experiment focused on the general validity of the asymmetrically dominated effect. In this section the importance of replication of experiments is briefly explained. The results of the original experiment were not replicated. But the results of the experiment showed the asymmetrically dominated effect significant in some research groups.
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Study of the mechanism of gene expression regulation at the level of functional organization of chromatin domains.
Hornáček, Matúš ; Cmarko, Dušan (advisor) ; Kučera, Tomáš (referee) ; Stixová, Lenka (referee)
- 1 - ABSTRACT Nucleoli are formed on the basis of genes of ribosomal DNA (rDNA) clusters called Nucleolus Organizer Regions (NORs). The essential structural components of the nucleoli, Fibrillar Centers (FC) and Dense Fibrillar Components (DFC), together compose FC/DFC units. These units are centers of rDNA transcription by RNA polymerase I (pol I), as well as the early processing events, in which an essential role belongs to fibrillarin. Each FC/DFC unit probably corresponds to a single transcriptionally active gene. In our work we study changes of FC/DFC units in the course of cell cycle. Correlative light and electron microscopy analysis showed that the pol I and fibrillarin positive nucleolar beads correspond to individual FC/DFC units. In vivo observations showed that at early S phase, when transcriptionally active ribosomal genes were replicated, the number of the units in each cell increased by 60 to 80 %. During that period the units transiently lost pol I, but not fibrillarin. Then, until the end of interphase, number of the units did not change, and their duplication was completed only after the cell division, by mid G1 phase. This peculiar mode of reproduction suggests that a considerable subset of ribosomal genes remain transcriptionally silent from mid S phase to mitosis but become again active...
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Role of molecular chaperones Hsp70 and Hsp90 in the replication cycle of DNA viruses
Žáčková, Sandra ; Horníková, Lenka (advisor) ; Poláková, Ingrid (referee)
Molecular chaperones are proteins which enable other proteins to assemble into native conformation and are essential for viability of the cells. Chaperones of the Hsp70 family bind to newly synthetized and denaturated proteins, prevent their aggregation and facilitate their assembly. They participate in assembly and disassembly of oligomers and also in the transport across the membranes. Chaperones of the Hsp90 family do not participate in the assembly of nascent or denaturated proteins. They bind proteins which are nearly in native conformation and enable them to assemble into conformation suitable for ligand binding or interacting with other proteins. These attributes predestinate chaperones to participate in the replication cycle of DNA viruses. A huge amount of proteins is translated during viral infection. These proteins require the chaperones to facilitate their assembly and are also required for assembly into oligomers and macromolecular structures. In addition to capsid assembly the chaperones also participate in transport of genetic information to the sites of replication, disassembly of incoming viral particles or replication of viral DNA. Therefore, the development of specific chaperone inhibitors is a promising approach. They could be used against broad spectrum of viral infections...
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Analysis of Interface Automata with On-Demand Replication
Daniel, Jakub ; Kofroň, Jan (advisor)
Interface automaton is a model of software component behaviour based on finite state machines. It describes component's provided interface, the supported usage, and required interface, the usage of other components. A considerable number of components can be used in parallel with no bound on the level of parallelism. It is not necessary for the model to attempt to capture such unboundedness. An alternative approach is to allow an increment of the level of parallelism on- demand. This thesis analyses on a theoretical level and proposes a final form of an operation to perform such replication to allow creation of models of an arbitrary level of parallelism of certain parts of its behaviour.
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Methodological innovations in psychological research
Frollová, Nikola ; Vranka, Marek (advisor) ; Fabianová, Ivana (referee)
The year 2012 opened an intense debate about the methodological problems of psychological research that lead to excessive publication of unreliable and nonreplicable results. The proposed improvements consist of conducting more replication studies, sharing data openly, limiting the "degrees of researcher freedom ", and improving the understanding and application of statistical methods for data analysis. This bachelor thesis aims to map the aforementioned problems, proposed solutions, as well as possible criticisms and problems with their implementation in practice. The research proposal consists of measuring the prevalence of questionable scientific practices among psychologists in Czech Republic.
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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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Development of ultrastructural methods and their application in studies on the cell nucleus
Filimonenko, Anatoly ; Hozák, Pavel (advisor) ; Nebesářová, Jana (referee) ; Lanctôt, Christian (referee)
Despite the capabilities of molecular-biological methods in deciphering the interplay of different biological molecules and molecular complexes, the understanding of respective functions in living cells requires application of in situ methods. Obviously, these methods should provide maximal resolution and the best possible preservation of the biological object in a native state, as well as correct statistical evaluation of the spatial characteristics of detected molecular players. Transmission electron microscopy provides the highest possible resolution for analysis of biological samples. The simultaneous detection of biological molecules by means of indirect immunolabeling provides valuable information about their localization in cellular compartments and their possible interactions in macromolecular complexes. To analyze this, we have developed a complex stereological method for statistical evaluation of immunogold clustering and colocalization patterns of antigens on ultrathin sections, including a user-friendly interface. Functional microarchitecture of DNA replication and transcription sites has been successfully characterized using the developed stereological tools. Our data demonstrate that DNA replication is compartmentalized within cell nuclei at the level of DNA foci and support the view...
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Analysis of Interface Automata with On-Demand Replication
Daniel, Jakub ; Kofroň, Jan (advisor) ; Bednárek, David (referee)
Interface automaton is a model of software component behaviour based on finite state machines. It describes component's provided interface, the supported usage, and required interface, the usage of other components. A considerable number of components can be used in parallel with no bound on the level of parallelism. It is not necessary for the model to attempt to capture such unboundedness. An alternative approach is to allow an increment of the level of parallelism on- demand. This thesis analyses on a theoretical level and proposes a final form of an operation to perform such replication to allow creation of models of an arbitrary level of parallelism of certain parts of its behaviour.
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Design and Implementation of SAP CAR with Automatic Disaster Recovery Function
Svitálek, Petr ; Dierzé, Lukáš (referee) ; Luhan, Jan (advisor)
The main purpose of this master's thesis is to propose and implement a SAP CAR (customer activity repository) solution as an application into the current enterprise information system. Following the analysis of the existing system, there will be a solution created, which is fulfilling the customer demands and at the same time it is feasible under given conditions and in the current environment. This project is closely related with addressing the disaster recovery issue for making the system highly available. The final design is implemented, tested and then handed over to the customer.
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