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Algebra of dual quaternions in image analysis
Hrubý, Jan ; Návrat, Aleš (referee) ; Hrdina, Jaroslav (advisor)
This work has two goals. Firstly it is to acquaint the reader with the classical use of quaternions and dual quaternions in geometry. Secondly the generalization of the Fourier transform into the set of dual quaternions. At first it goes into algebraic properties and structure of quaternions and ways of their inscriptions. Later dual numbers are introduced and consecutively with their help dual quaternions. Then the work deals with description of rotations and translations using quaternions and dual quaternions, that enable their easy description. Finally the discreet dual quaternion Fourier transform is defined, and for its effective calculation the algorithm is derived, which is then brought into effect as a code in program environment MATLAB.
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Web Application for Bioinformatics Education - Genetic Code
Kilián, Martin ; Martínek, Tomáš (referee) ; Burgetová, Ivana (advisor)
This thesis briefly describes basic informations in moleculary biology. Thesis deals with a transfer of information from DNA into RNA through uprotein, are also briefly described the methods and algorithms dealing with the detection of genome. The larger part deals with the recognition cue coded signals and determination of sequences and their subsequent transcription and translation, which demonstration program was needed to create. The final result is s web application as the education system.
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Gene Searching - Web Application
Stiborová, Lucie ; Koutný, Jiří (referee) ; Burgetová, Ivana (advisor)
The aim of my Bachelor's Thesis is to create a user interface and to implement the web application with the genes' searching. This is the educational application when each user has a possibility of entering own nucleotide sequences or selecting a redefined chain. This application has to be able to read, process and decide on the existence of a potential gene. On the base of this simple statistic method the result is given back to the user.
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3D scene reconstruction using Clifford algebras
Hrubý, Jan ; Návrat, Aleš (referee) ; Hrdina, Jaroslav (advisor)
Tato diplomová práce má za cíl seznámit čtenáře se stále ještě relativně novou a neznámou oblastí matematiky, s geometrickou algebrou. Nejdříve jsou uvedeny základní definice a poté jsou studovány vlastnosti obecné geometrické algebry. Další velká část textu se věnuje Konformní geometrické algebře, která je v současnosti jedna z nejvíce zkoumaných a aplikovaných geometrických algeber. Jsou popsány její algebraické a geometrické vlastnosti, konkrétně schopnost reprezentovat určité geometrické objekty jako vektory. Taktéž umožňuje počítat jejich průniky a konformní transformace. Další část textu je zaměřena na aplikace Konformní geometrické algebry, nejdříve k popisu kinematiky robotické ruky a poté v binokulárním viděni.
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Origins of the European approach to environmental justice
Valachová, Emilie ; Tesař, Jakub (advisor) ; Dostál, Jan (referee)
This thesis deals with the process of diffusion of the idea of environmental justice to Europe. Using the examples of Great Britain and Slovakia, it traces how environmental justice reached these countries and how it changed in the process. The thesis focuses on the academic discussion as one of the segments of the discourse on environmental justice. Based on the theory of translation, it examines the spaces where experts have encountered the idea of environmental justice. Furthermore, it is interested in the theoretical foundations and the content of environmental justice in the local discourse, especially concerning the transformations of the concept in order to bring it closer to the local context. Employing the interpretative qualitative analysis of academic publications written by authors affiliated with British or Slovak institutions, it has been established that the process of translation to Europe remains incomplete and does not occur uniformly. American publications have played a greater role in the UK and linking of environmental justice with sustainable development has become an important mechanism of translation here. In contrast, Slovak academic debate has been influenced by personal contacts with the international sphere. However the translation to Slovakia is currently taking place...
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Where transcription meets translation
Hegrová, Karolína ; Krásný, Libor (advisor) ; Mašek, Tomáš (referee)
Transcription and translation are key steps in gene expression. The RNA polymerase (RNAP) plays a major role in the transcription process, while the ribosome is involved in translation. In bacteria, these two processes are not separated. RNAP and the ribosome interact, and its called transcription- translation coupling. In this thesis, I discuss the mechanism of transcription and translation, with the main focus on transcription-translation interactions. I divide these interactions into indirect, which are caused by regulátory molecules, and direct, where the ribosome directly binds with RNAP. When physical binding occurs, either a tight junction between these molecules occurs or a bridge is formed by transcription factors. Then I describe regulatory function of this connection and explain the exceptions where transcription and translation don't link. In the last part of the thesis, I focus on elongation factor Tu (EF-Tu), its important role in metabolism, its interactions with MreB protein, and how this factor is used by some bacteriophages. Finally, I mention its possible role in transcription-translation interactions. Key words: transcription, translation, transcription-translation coupling, RNA polymerase, ribosome, transcription factors, EF-Tu
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Cellular factors influencing the antibiotic resistance by ABC-F proteins
Kýr, Jan ; Balíková Novotná, Gabriela (advisor) ; Dolejšová, Tereza (referee)
Antibiotic resistance is one of the main problems modern medicine has to face. In order to control it, it is important first to understand the mechanisms by which resistant pathogens bypass antibiotic treatment. One of the important protein families conferring resistance to 50S binding antibiotics is the ARE ABC-F protein family. A member of this protein family is the MsrA protein, which confers resistance to 14- and 15-membered macrolides. Loss-of-function mutations in the non-essential chaperone ClpX were found to a significant ly enhance the action of the MsrA protein. This leads to the significant increase in the resistance conferred by this protein. The exact mechanism by which ClpX affects MsrA function is still unknown. In this the diploma thesis was demonstrated that chaperone protein ClpX affects the resistance to erythromycin conferred by MsrA protein, due to the interaction with an unknown essential protein, which is mediated by a functional N-terminal zinc-binding domain of the chaperone. Furthermore, it was demonstrated in this work that loss of GluTR function influence the MsrA ability to confer resistance. The results of this work will bet he basis for further reasearch, which will lead to a more detailed understanding of the mechanism of resistance conferred by these proteins and...
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The role of ribosomal proteins in the plant development
Jirásková, Veronika ; Raabe, Karel (advisor) ; Smýkal, Petr (referee)
The translation is one of the fundamental cell processes, in which the protein is synthesized according to the sequence of the mRNA molecule. The foremost recognized element of the translation machinery is the ribosome, a molecule complex composed by rRNAs and ribosomal proteins. In plants, ribosomal proteins are encoded by more than one gene, which may lead to sub- functionalization and neo-functionalization of ribosomal protein paralogs in plant development or in the reaction to the contemporary environment. Assembly of ribosomal subunits from different ribosomal protein paralogs could lead to functionally distinct pools of ribosomes with specialized role in the translation and its regulation in plants. The aim of this work is to review current data regarding the individual ribosomal proteins function within the plant growth and development. Keywords translation, translation regulation, ribosome, ribosomal proteins
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Molecular dynamics simulations of biomolecular complexes consisting of proteins and nucleic acids
Melcr, Josef ; Barvík, Ivan (advisor) ; Bok, Jiří (referee)
Literature search on the Elongation factor Tu (EF-Tu), which is involved in the process of translation of genetic information, was performed. Further, computational methods as molecular dynamics (MD) and Monte Carlo (MC) were studied. Then, computer programs for MD and MC simulations of a Lennard-Jones gas were developed. MD simulations were further applied to EF-Tu using the NAMD and ACEMD software packages. Multiprocessor PC clusters and programmable NVIDIA GPUs were used. MD simulations of EF-Tu uncovered binding of monovalent ions in nearby of the EF-Tu active site. The impact of Na$^+$ binding on evolutionarily conserved residues (His85, Val20, Ile61, Asp21, Tyr47, Asp87, etc.) was studied in detail.
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