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Demonstration of Selected Graph Algorithms
Galanská, Katarína ; Martiško, Jakub (referee) ; Křivka, Zbyněk (advisor)
This thesis deals with re-architecture of an existing application for the demonstration and visualization of selected graph algorithms. The goal of this thesis is to convert the application into multiple modules and make it easier to extend. OSGi technology helps to achieve the modularity. Its principles are explained and used to design and implementation of modules. With new architecture is also implemented the support for multilingual user interface using Eclipse Plugin internationalization. Graph algorithms represented as modules use OSGi Services. Dynamicity is ensured by installing the module and registering its service during the program's run time. The implementation also includes the creation of new modules for Prim's, Kruskal's, Edmond Karp's and modified Hierholzer's algorithm.
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Návrh implementace MST protokolu do prostředí univerzitní sítě
Zigmund, Martin
Zigmund, M. The proposal for the implementation of the MST protocol in the university network environment. Bachelor thesis. Brno: Mendel University, 2023. This bachelor thesis deals with the proposal of the implementation of the MST protocol into the university network. This implementation is based on the analysis of the MST protocol and the current state of computer network at the Mendel university in Brno. Based on the provided information, a home and university model connections are created and tested in the home and university network. Convergence, STP security and also the protocol migration to a newer version are tested on the model connections. On the basis of the performed tests, several proposals have been drawn up to protocol migration and university network appearance when the MST protocol is implemented and subsequently used. The result of the work is the verification of the fact that the newer type of STP can be successfully used simultaneously with older versions, and the migration of this protocol can be achieved in different ways.
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Modulation of interactions between interleukins and their receptors
Nepokojová, Tereza ; Schneider, Bohdan (advisor) ; Obšilová, Veronika (referee)
Scaffolds are proteins with high conformational stability, allowing us to implement multiple mutations into specific parts of the protein. Even with these mutations, the structural integrity of the protein is maintained as well as its physical-chemical properties. These mutations give the specific scaffold new properties. In most cases it is the binding specificity towards previously chosen target. The biggest advantages of scaffolds are their small size, stability, low-cost manufacturing, and easiness of preparation. Scaffold utilized in this thesis is unique for having two binging surfaces designed on which it can be mutated. Each of those two surfaces can be separately mutated to develop a binging site for two different proteins. In our case these mutations led to binding two nonidentical receptors of a human cytokine. Mutations are made with a use of yeast display, one of the methods of directed evolution. The main focus of this thesis is changing an expression system of the binding proteins from the yeast system to a bacterial one, their production and purification followed by characterization of those binding proteins using biophysical methods. These methods were used to evaluate structural and thermal stability, and binding affinity to both receptors of the beforementioned binding proteins....
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Structural biology of receptor NKp44 and its ligand PCNA
Herynek, Štěpán ; Vaněk, Ondřej (advisor) ; Kubíčková, Božena (referee)
Natural killer cells (NK cells) are part of the immune system in human and other mammals. The task of these cells, which belong to the non-specific immunity, is to induce apoptosis in other cells of the body that may represent a threat for the body (i.e., tumour or virally infected cells). NK cells have a variety of surface receptors to recognize their target cells. A number of receptors are well-known today and they may be divided into groups based, e.g., on their structural similarities or on the type of signal which these receptors present to NK cells. Accordingly, we distinguish activation and inhibitory receptors. Inhibitory receptors inhibit NK cell response, while activation receptors elicit this response. During NK cell contact with another cell, the resulting NK cell behaviour is always the result of a certain balance of activation and inhibitory receptor responses. The NKp44 receptor is an immunoglobulin-like receptor. This receptor is very unique among other receptors in many respects, for example because it is associated with both activation and inhibitory motif. The ligand of this receptor is a proliferating cell nuclear antigen (PCNA). PCNA is a clamp protein important, inter alia, during DNA replication, in which it anchors other replisome proteins. This work is focused on...
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Demonstration of Selected Graph Algorithms
Galanská, Katarína ; Martiško, Jakub (referee) ; Křivka, Zbyněk (advisor)
This thesis deals with re-architecture of an existing application for the demonstration and visualization of selected graph algorithms. The goal of this thesis is to convert the application into multiple modules and make it easier to extend. OSGi technology helps to achieve the modularity. Its principles are explained and used to design and implementation of modules. With new architecture is also implemented the support for multilingual user interface using Eclipse Plugin internationalization. Graph algorithms represented as modules use OSGi Services. Dynamicity is ensured by installing the module and registering its service during the program's run time. The implementation also includes the creation of new modules for Prim's, Kruskal's, Edmond Karp's and modified Hierholzer's algorithm.
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Study of interactions between the FOXO3-DNA binding domain and small-molecular compounds
Dolejš, Vojtěch ; Obšilová, Veronika (advisor) ; Martínková, Markéta (referee)
This diploma thesis is part of a project aiming for the development of low molecular compounds which would be capable to inhibit the interaction between human transcription factor FOXO3 and DNA. Main goal of this thesis is the characterization of the interaction between the low molecular inhibitor S9 and the DNA-binding domain of FOXO3 protein (FOXO3-DBD) by using variety of biophysical methods such as NMR, microscale thermophoresis and native electrophoresis. FOXO transcription factors are important and evolutionary conserved regulatory proteins, which are involved in many crucial cellular processes. The activity of FOXO proteins is regulated by posttranslational modifications, out of which the most important are phosphorylation, acetylation and ubiquitination. Forkhead transcription factors participate in a variety of different cellular functions and are part of several signaling pathways. Its expression might be tissue specific. They contain approximately 100 amino acids long DNA- binding domain composed of several parts. Among its main functions belong the regulation of cell cycle and apoptosis, proliferation and cell differentiation, metabolism control and stress- response regulation. Tumor cells of lymfoblastome have developed resistance against chemotherapy by increasing activity of FOXO3...
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Preparation and characterization of neutral trehalase for structural studies
Šmídová, Aneta ; Obšilová, Veronika (advisor) ; Jiráček, Jiří (referee)
This study is part of a project which aim is solving the structure of the catalytic domain of neutral trehalase Nth1 from Saccharomyces cerevisiae. The main goal of this thesis is the preparation of new constructs of yeast Nth1 and optimization of their purification protocols, the selection of the ideal buffer for crystallization trials using the method of differential scanning fluorimetry (DSF) and at last the protein crystallization. Another part of the thesis is the measurement of the enzymatic activity of pNth1 WT in the presence of Bmh1 protein, verification of trehalose binding to the selected constructs of Nth1 using differential scanning fluorimetry (DSF), thermoforesis (MST) and further crystallization with trehalose. Neutral trehalase is highly conserved trehalase that has been found in a wide variety of organisms. These enzymes belong to the class of hydrolases, subgroup of glycosidases and hydrolytically cleave trehalose into two glucose molecules. Trehalose is a naturally occurring non-reducing disaccharide serving in yeast cells a source of carbon and energy as well as protection against stress conditions such as a thermal shock. Trehalose hydrolysis is essential for flying insects, because it is present as the main sugar component of insect haemolymph, therefore trehalase inhibitors...
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