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Utilization of pulse labelling techniques for studying the dynamics of proteins and protein complexes
Polák, Marek ; Novák, Petr (advisor) ; Obšil, Tomáš (referee) ; Vrbacký, Marek (referee)
(In English) Mass spectrometry (MS) techniques are routinely used to probe the structure and dynamics of proteins and protein complexes. Although MS techniques lack the high resolution of data provided by X-ray crystallography, NMR, or cryo-EM, they excel in providing insights into analyte dynamics, structure, and interactions with other components, such as ligands. This doctoral thesis presents a contribution to the field of structural biology employing and extending covalent labelling approaches, namely Fast Photochemical oxidation of Proteins (FPOP) and oxidation by singlet oxygen (1 O2). These approaches were followed to study the structure, dynamics, and interaction of proteins, nucleic acids, and protein-DNA complexes in solution. Initially, FPOP was used to investigate the interaction interface of FOXO4 and DAF16-DNA response element and to show the possibilities of analyzing such a complex using both 'bottom- up' and 'top-down' approaches. Furthermore, an isotope depletion strategy combined with multiCASI-ECD proved effective in delivering structural information with the highest possible resolution for mapping protein-DNA interfaces. This research showcases how information derived from structural proteomic methods can guide the construction of in-silico models for protein-DNA complexes with...
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The laser beam use in a production of parts for manipulating technique
Polák, Marek ; Kalivoda, Milan (referee) ; Osička, Karel (advisor)
This Diploma thesis trests of laser and his localisation in production sphere. It briefly describes principle, function and possibilities of laser, mainly laser technology by machining. It tafgets the possibilities of laser by cutting. The diploma thesis was elaborated in conjunction with the company Manex & Co, a. s., producer of handling systems. It disposes of CNC cutting machinery, which is fully engaged. A chain gear from ČSN 41 1363 was produced in terms of this diploma thesis.
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Legislature of European Union for the waste disposal.
Polák, Marek ; Beňo, Zdeněk (referee) ; Jícha, Jaroslav (advisor)
This bachelor thesis acquaints with legislation on enviroment protection in Czech Republic. The main part of this thesis is waste management oriented, especially to the waste law in Czech Republic, then is maked the mention of the waste legislation in Austria and Germany. The next point of this thesis is refering to waste conditioning by combustion, disposal and recycling and then comparing the states in theese ways of waste conditioning is mentioned .
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Multi-storey precast structure
Polák, Marek ; Šimůnek, Petr (referee) ; Perla, Jan (advisor)
The final thesis is focused on reworking hospital pavilion from cast-in-place structure to precast concrete frame. Calculation of internal forces is made by software system SCIA Engineer. Main load-bearing elements are inner beam, outside beam and all columns in axis 2-C. This thesis contains assembly report, structural design, calculations and drawings of the designed parts, joint details, assembly material drawing and hand calculation.
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Reinforced concrete structure of a family house
Polák, Marek ; Matušíková, Anna (referee) ; Šulák, Pavel (advisor)
The bachelor's thesis deals with the static design of two variant ceiling construction of family house and their economic comparison. Firs variant is reinforced concrete slab, and the other is half prefabricated ceiling HELUZ MIAKO. The thesis also deal with design and assessment foundation lane. Calculation of internal forces is made by software system SCIA Engineer and this results are compared with results of simplified method. Design, assessment and drawing documentation were made by the valid standards on these calculations.
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Evolution and Adaptability of Complex Applications
Polák, Marek ; Holubová, Irena (advisor) ; Rahayu, Wenny (referee) ; Krátký, Michal (referee)
Evolution and Adaptability of Complex Applica- tions Abstract In these days the applications become more complex that causes maintenance problems while evolving these applications. A change in one part of the appli- cation can significantly affect other parts of the application. The next aspect can be related systems which communicate with this application. They must be updated to satisfy their functionality. These problems can concern multiple do- mains, e.g., UML diagrams, XML schema diagrams, relational schemas, etc. We focus on this problem from the perspective of the MDA, which uses the platform independent model (PIM) for a general view of the problem and the platform specific model (PSM) for particular domains. Moreover, these models can be in- terconnected. We propose novel PSM models from various widely used domains, operations over these models and algorithms for model transformations. Thanks to the MDA principle, it is possible to combine presented models and model a complex application. All models and related algorithms we present were experi- mentally implemented and tested in the DaemonX framework on real-word data for their verification. 1
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Extension of the XML Check system
Hudeček, Petr ; Holubová, Irena (advisor) ; Polák, Marek (referee)
In this thesis, we improve the 2011 homework manager called XML Check. It is a web application used in the course XML Technologies at MFF UK and FEL ČVUT. Students and teachers have identified a number of deficiencies in the system that we are fixing. They have also suggested new functionality that we are implementing. Checking submissions for plagiarism is the most important new feature. This check is now applied to each new submission. We tried several different algorithms for this (Levenshtein distance, Greedy-String-Tiling algorithm and Zhang-Shasha tree edit distance) and we compare these algorithms. We determine their performance based on experiments on student submissions from the past four years. The improved system is now in active use.
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Utilization of protein radical foootprinting for stuctural biology
Polák, Marek ; Novák, Petr (advisor) ; Junková, Petra (referee)
(In English) The reaction of highly reactive oxygen radicals with protein solvent-accessible residues can be utilized to map protein landscape. Fast photochemical oxidation of proteins (FPOP) is an MS- based technique, which utilizes highly reactive radical species to oxidize proteins and map protein surface or its interactions with their interaction partners. In this work, FPOP was employed to study protein-DNA interactions. First, a full-length of FOXO4-DBD was successfully expressed and purified. The ability of the protein to bind its DNA-response element was verified by electrophoretic and MS-based techniques, respectively. Optimal experimental conditions were achieved to oxidize the protein itself and in the presence of DNA, respectively. Oxidized samples were analyzed by bottom-up and top-down approach. In the bottom-up experiment, modification of individual residues was precisely located and quantified. Different extend of modification was observed for protein alone and in complex with DNA. To avoid experimental artifacts analyzing multiply oxidized protein, standard bottom up approach was replaced by a progressive top-down technology. Only a singly oxidized protein ion was isolated, and further fragmented by collision-induced dissociation (CID) and electron-capture dissociation (ECD),...
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Evolution of the use of memory
Polák, Marek ; Holan, Tomáš (advisor) ; Kadlec, Rudolf (referee)
The task of the bachelor work is to give a proposal and its implementation of application for simulating evolution of population. The outcome is a study of dependency of memory usage on energy of organishms in their environment. From ndings of simulation batches it could be said what parameters are useful for given environment from view of count of conditions to spent of energy, which organishm leeds to its life.
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Discharge of a debtor - one of modes of insolvency solution
Polák, Marek ; Smolík, Petr (advisor) ; Zoulík, František (referee)
The legal enactment No. 182/2006 Sb., Insolvency Act that came into force on January 1st 2008 introduced the new concept of Discharge of Debts in the Czech Law system. This mode of solution is intended solely for non-entrepreneurs (this institute cannot be used for companies or individual entrepreneurs). Personal bankruptcies account for the majority of insolvency proceedings in the territory of the Czech Republic and it can be assumed that this long-lasting trend will continue to grow. The institute of Discharge of Debts gives consumers an effective opportunity to legally get rid of their debts through one of two ways, namely repayment schedule and sale of the debtor's assets, and start again with a clean slate as an active member of the Economic Society. The aim of this thesis is to give a comprehensive analysis of the institute of Discharge of Debts, from defining the causes that lead to bankruptcy, interpretation of basic concepts, to the description of the necessary proceedings leading to the declaration of bankruptcy, process of Discharge of Debts itself and differences of its two basic ways. This theoretical basis is supplemented by my knowledge that I have gained during my internship in a law office, which also performs the function of insolvency trustee. The thesis is composed of eight...
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