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Bioinformatics Tool for Protein Structure Prediction
Plaga, Michal ; Burgetová, Ivana (referee) ; Martínek, Tomáš (advisor)
The goal of this thesis is test and comparation of the offline tools for prediction of protein structure and creation of metaprediktor, which allows the user to select the appropriate tool, according to given parameters. Testing tool is based on a dataset of proteins, which is based on the SCOP database and it is trying to be as balanced as possible to include proteins from different families and thus could best evaluate individual tools. The results of this thesis are requirements of metaprediktor and also which data and settings can be allowed and processed and how it will be implemented.
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The role of adhesion of the plasma membrane to the cell wall in the development and function of the root system
Králíková, Dagmar ; Tylová, Edita (advisor) ; Schwarzerová, Kateřina (referee)
Adhesion between the plasma membrane and the cell wall and the existence of the continuum of these two compartments is needed for signal transmission, e.g. under pathogen attack, during cell expansion and cell wall growth, or in response to environmental conditions. This adhesion is, in addition to the turgor, provided by physical connection of both compartments. One of the best-known examples of physical connection is found in the root system, in the Caspary strip region, where it is required to maintain apoplastic barriers of the root system, even under adverse conditions and consequent plasmolysis. There is little information about the physical interconnection and the participating macromolecules but there are candidates, which could participate in this interaction. The diploma thesis deals with arabinogalactan (AGP) proteins with fasciclin-like domain (namely FLA9 and FLA2). These proteins may play a role in the adhesion of plasma membrane and cell wall and may be involved in the growth regulation and development of the root system. Both genes are are relatively strongly expressed in the roots, especially in the elongation zone and in the cortex, including the endodermis (according to chip data). Also, to a smaller extent, the thesis deals with integrin-like At14A protein. The most interesting...
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Plasma membrane - cell wall interactions - adhesion and signalling
Králíková, Dagmar ; Tylová, Edita (advisor) ; Krtková, Jana (referee)
Interaction of the cell wall and plasma membrane is essential for proper cell functioning as it affects, for example, cell growth, water relations or pathogen penetration, and provides protection against external factors. This interaction may take the form of signal exchange or component transport and its necessary prerequisite is the contact between the two structures. The contact is ensured not only by turgor pressure but also by their direct connection. Experimental evidences have long been known to show that this connection indeed exists - for example, Hechtian strands that are visible in the plasmolyzed cell. Another example is band plasmolysis in cells of the endodermis and exodermis with the Casparian strips, where the plasma membrane is still attached to the cell wall at the site of the strip. This attachment contributes to the protective feature of the apoplastic barrier and allows maintaining it even during plasmolysis. The anatomic aspects of the phenomenon have long been investigated, but specific proteins providing this interaction at the molecular level have not yet been experimentally confirmed. The aim of the bachelor thesis is to summarize recent findings about the mechanisms ensuring the physical connection (adhesion) between the plasma membrane and the cell wall in the plant...
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Bioinformatics Tool for Protein Structure Prediction
Plaga, Michal ; Burgetová, Ivana (referee) ; Martínek, Tomáš (advisor)
The goal of this thesis is test and comparation of the offline tools for prediction of protein structure and creation of metaprediktor, which allows the user to select the appropriate tool, according to given parameters. Testing tool is based on a dataset of proteins, which is based on the SCOP database and it is trying to be as balanced as possible to include proteins from different families and thus could best evaluate individual tools. The results of this thesis are requirements of metaprediktor and also which data and settings can be allowed and processed and how it will be implemented.
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