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Molecular dynamics simulations of complexes consisting of proteins and nucleic acids
Hammer, Jiří ; Barvík, Ivan (advisor) ; Obšil, Tomáš (referee)
The goal of this diploma thesis was to study interactions of Argonaute (Ago) protein in a complex with nucleic acids. Based on the available crystal structures of full length Argonaute (from A. aeolicus, Aa-Ago) and/or its domains (human PAZ domain, Hs-PAZ), twelve different simulations were computed. Two initial simulations used model of Aa-Ago with either a duplex of DNA/RNA or RNA/RNA. Major difference was in behavior of the PAZ domain (especially its arginine residues), which tolerated the guide DNA in one simulation, but was disturbing the RNA guide strand in the second. Such an interaction could serve as a mechanism of the substrate recognition. In additional simulations (3-9) employing the Hs-PAZ domain, where no disturbance was found in the DNA/RNA hetero-duplex. Different arrangements of the active site geometry as well as empirical parameterizations of Mg2+ ion were probed and analyzed. The DD-catalytic motif plus D683 in Aa-Ago (equivalent to H807 in human Argonaute2) was observed to coordinate the Mg2+ ion in one and two metal ion dependent catalysis models. Highly conserved R570 and E578 created mutual hydrogen bonds and hence stabilized the active site. To make the cleavage irreversible, a role for the first (unpaired) nucleotide from 5'-end of the guide strand was suggested. It lies in a...
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Molecular dynamics simulations of complexes consisting of proteins and nucleic acids
Hammer, Jiří ; Barvík, Ivan (advisor) ; Obšil, Tomáš (referee)
The goal of this diploma thesis was to study interactions of Argonaute (Ago) protein in a complex with nucleic acids. Based on the available crystal structures of full length Argonaute (from A. aeolicus, Aa-Ago) and/or its domains (human PAZ domain, Hs-PAZ), twelve different simulations were computed. Two initial simulations used model of Aa-Ago with either a duplex of DNA/RNA or RNA/RNA. Major difference was in behavior of the PAZ domain (especially its arginine residues), which tolerated the guide DNA in one simulation, but was disturbing the RNA guide strand in the second. Such an interaction could serve as a mechanism of the substrate recognition. In additional simulations (3-9) employing the Hs-PAZ domain, where no disturbance was found in the DNA/RNA hetero-duplex. Different arrangements of the active site geometry as well as empirical parameterizations of Mg2+ ion were probed and analyzed. The DD-catalytic motif plus D683 in Aa-Ago (equivalent to H807 in human Argonaute2) was observed to coordinate the Mg2+ ion in one and two metal ion dependent catalysis models. Highly conserved R570 and E578 created mutual hydrogen bonds and hence stabilized the active site. To make the cleavage irreversible, a role for the first (unpaired) nucleotide from 5'-end of the guide strand was suggested. It lies in a...
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Cost Management and Budgeting in the Government Sector
Hammer, Jiří ; Vítek, Leoš (advisor) ; Ochrana, František (referee) ; Nemec, Juraj (referee)
Dissertation deals with the issue of cost management and budgeting through the methodology ABC / ABM. Using the ABC model allows for higher transparency in the costs in state organisational units. At the same time more effective cost management, including budget, through causal relationship between processes in organizations and their costs. Dissertation redefines the process of creating a model for state organisational units and analyzes the influence of various factors on the level of individual cost categories. In summarizing the outcome of the ratios based on the number of employees used to calculate the costs they are not very useful. The results of the regression analysis will confirm that a significant impact is mainly used asset value and technological developments.
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Technique of playing the French Horn with a focus on embouchure Problems
Hammer, Jiří ; DIVOKÝ, Zdeněk (advisor) ; BABORÁK, Radek (referee)
The theme of this thesis is aimed at helping a player to handle embouchure issues. The embouchure of this work is a comprehensive outline form proofing techniques that even without audiovisual examples helped the players to understand and acquire all the right ways to play. The result is a comprehensive list of methods of work with the embouchure. In practice, this work is recommended for use all of hornists, who want to master technique of playing the French horn.
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Management system of excise taxes by the Customs Administration of the Czech Republic
Lambora, Martin ; Hammer, Jiří (advisor) ; Vítek, Leoš (referee)
The Bachelor's Thesis deals with excise taxes system in the Czech Republic administrated by the Customs Administration of the Czech Republic since 2004. The main goal of this work is to analyze a profitability of excise taxes using a method of comparison of tax revenues and administrative expenditures during a period from 2004 to 2011. Due to selected allocation parametres there is possible to assign administrative expenses to excise taxes species and evaluate administrative burdens and final expensiveness. The thesis also discusses two basic tax functions and defines the primary one. On the grounds of obtained results there is also assessed (to a certain degree) the efficient behavior of Customs Administration of the Czech Republic as a tax administrator.
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New approaches to tax administration
Postránecký, Tomáš ; Vítek, Leoš (advisor) ; Hammer, Jiří (referee)
The thesis deals with different ways of managing the tax administration in member and non-OECD countries. The first part is devoted to tax administration management systems and methods to measure their performance. In the next part, I tried to summarize how the tax administration in Czech republic and selected OECD countries is managed. Finally, I described the evolution of the organization of tax administration and created indicators for measuring performance of Czech republic tax administration over the last 8 years.
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Customs and tax evasions
Badíková, Pavla ; Hammer, Jiří (advisor) ; Vítek, Leoš (referee)
The batchelor thesis is focused on customs and tax evasion. It is divided into two thematic parts. The first part describes the general customs regulations, their development and compares the view of violation of customs regulations in selected countries. The second part focuses on the excise tax, contains a general description of the mechanism and than focuses on evasion of excise duty. End of this part analyses the impact of tax evasion on public finances. In conclusion is description of environmental tax.
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Management of Universities
Medunová, Lucie ; Vítek, Leoš (advisor) ; Hammer, Jiří (referee)
This thesis analyses higher education systems in the Czech Republic and abroad, specifically in Slovakia, Germany and Austria. The first part deals with the economical view of higher education and social and economical importance of the education. The second part deals with higher education system in the Czech Republic, specially with its legislation, funding, structure and evolution. Marginally, the work deals with the ongoing reform of higher education. Next section focuses on higher education abroad, with an emphasis in its funding. The aim of this chapter is to detect differences between higher education systems in the Czech Republic and abroad, and compared the effectiveness of these systems. The content of the last chapter is a comparison of six specific universities, particularly their organizational structures.
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Measurement of competitiveness of the Czech Republic and options for its improvement
Dryzgalovich, Anton ; Vítek, Leoš (advisor) ; Hammer, Jiří (referee)
This thesis deals with price and non-price competitiveness of the Czech Republic and analytical analysis of the basic factors that are affecting it. Among others, evaluate the position of the CR in international capital, goods and service markets, states strengths and weaknesses of the Czech economy, outlines the complex interdependencies among the different factors of competitiveness and provides a comprehensive picture of the current situation in various spheres of economic activities. The first chapter explains the specifics of measuring competitiveness and represents foreign and domestic organizations that are regularly engaged in such research, including the format of their final reports. Furthermore, it compares the approach of studies themselves and presents its unique contribution to the overall understanding of the issue. The second chapter contains the results of the competitiveness of the Czech Republic and recommendations on options for improvement.
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Tax reforms in modern history of the Czech Republic
Nováková, Aneta ; Svátková, Slavomíra (advisor) ; Hammer, Jiří (referee)
My Bachelor thesis is focused on tax reforms from view of the theory. The study is trying to accurately define the concept of reform and describe the most important tax changes in the period, which are called reforms. The main aim is to analyze and evaluate whether these "tax reforms" between 1993 - 2009 in the Czech Republic constitute a theoretical concept indeed. Regarding the theme extent, the focus of my thesis is mainly on four periods. We can say that clear and precise definition of reform does not exist. To a considerable extent is up to us, as we interpret the definition. Reforms are always made in response to certain changes in the systems.
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