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Comparison and Transformations of Pathway Databases
Němeček, Pavel ; Šilhavá, Jana (referee) ; Smrž, Pavel (advisor)
The main topic of this work are comparison and transformations of pathway databases. Large part is dedicated to databases KEGG and BioCarta. In work are described formats of provided data. In process of searching for overlapping pathways between databases are used clustering, edit distance, NCBI gene numbers and equivalent relationships comparison. The system was written in C++ and using XML parser. Results are text outputs, eventually files in DOT language, which can be executed with GraphViz to generate graphs.
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The role of ERK1 and ERK2 protein kinases in the MAPK/ERK signaling
Galvánková, Kristína ; Vomastek, Tomáš (advisor) ; Dráber, Peter (referee)
The MAPK/ERK cascade is highly conserved signalling pathway regulating cellular processes which are necessary for cell life, such as proliferation, differentiation, apoptosis or cell migration. All these cellular responses are the result of the processing of extracellular signals through three-tier ERK cascade consisting of protein kinases Raf, MEK and ERK. The signal is transmitted by sequential phosphorylation where RAF phosphorylates MEK and MEK phosphorylates and activates ERK. Protein kinase ERK then phosphorylates and regulates a wide range of substrates at different locations in the cell. This affects the cellular response to the extracellular signal. Regulation of this pathway on every level is very important and is modulated by interaction partners and adaptor proteins. Deregulation of the pathway as well as mutations of individual protein kinases can lead to severe pathological consequences. At the level of ERK, there are two isoforms, ERK1 and ERK2, which are more than 80 % identical at the amino acid level. Their high sequence similarity has triggered the interest of many authors for more detailed examination of both isoforms in respect of their evolutionary conservation and whether they are functionally redundant or whether they have specific functions. The aim of this work is to...
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Stimulace růstu rostlin změnou teplotních podmínek
Mašlaňová, Anna
Ambient temperature is the key factor that may positively or negatively regulate the growth and development of land plants. For instance, the change in temperature conditions determines the leaf development, flowering period and the fruit ripening. In this thesis, we investigate the role of cytokinin (CK) in the response of plants to higher soil temperature. Using genetic and transcriptomic analysis, we have identified several components of CK signaling pathway that orchestrate the increase growth rate of plants growing in the warm (35 °C) soil. The cellular analysis of epidermal leaf cells showed that this higher growth rate is caused by 2-fold higher cell expansion. This pattern of changing cell morphogenesis correlates with decreased levels of active forms of CK that act as a key factor in the maintenance of cell proliferation phase in the leaf.
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Buněčná apoptóza, její průběh a metody detekce
Drápalová, Denisa
Programmed cell death is a series of cascade reactions maintaining the inner homeostasis of an organism. Its relevance is significant as early as in the prenatal period, when it forms body cavities and other organs such as fingers in the process of morphogenesis. This bachelor thesis analyses a topic that is highly discussed among molecular biologists. Since the process affects all living creatures, it draws the attention of many scientists. The thesis summarizes the findings of previously known facts, emphasis is placed on specific genes affecting the apoptosis, including mutations inclining to diseases. It also contains a brief summary of detection methods. A literary research has been developed using currently available scientific articles, journals, and book publications. The work as such provides an insight into a comprehensive complex of information not only about apoptosis but about cell death in general
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Chemical signaling among microorganisms
Karásek, Filip ; Palková, Zdena (advisor) ; Převorovský, Martin (referee)
The work summarizes the knowledge about chemical communication among microorganisms, focusing mainly on the quorum sensing phenomenon, but briefly discussing also other molecules with signaling function. The work presents fundamental information on quorum sensing and some other signaling molecules in selected grampositive and gramnegative bacteria and in yeast. It also describes an universal system of communication among different bacteria and briefly mentions communication between bacteria and yeast. Key words: Quorum sesnig, signal molecule, signal pathway, bacteria, yeast, communication
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The molecular mechanism of CSL protein participation in oxidative stress response in Schizosaccharomyces pombe
Daněk, Petr ; Převorovský, Martin (advisor) ; Sipiczki, Matthias (referee)
Redox homeostasis maintenance is important for proper organism and cell function, for while relatively low amount of reactive oxygen (and nitrogen) species contributes to the fine tuning of signal transduction, excessive concentration of ROS (oxidative stress) has demonstrably harmful effects and is tightly connected to many pathological states. Cells therefore evolved broad palette of antioxidant mechanisms that express striking level of conservation among different species. Large, intricate stress response signaling networks have been already described; nonetheless, novel molecules employed in stress-related signaling are still being discovered. Several studies recently suggested transcription factors CSL, proteins essential for regulation of metazoan development as effectors of Notch signaling, are also involved in response to oxidative stress. The fission yeast Schizosaccharomyces pombe, well established model of response to various stresses, comprises two paralogs of CSL proteins - Cbf11 and Cbf12. We have found cells depleted of cbf11 are highly resistant to hydrogen peroxide. This resistance appears to be caused by upregulation of important stress responsive genes including ctt1, gst2, pyp2, and atf1. Cbf11 is therefore negative regulator of these genes, which suppresses their expression...
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Comparison and Transformations of Pathway Databases
Němeček, Pavel ; Šilhavá, Jana (referee) ; Smrž, Pavel (advisor)
The main topic of this work are comparison and transformations of pathway databases. Large part is dedicated to databases KEGG and BioCarta. In work are described formats of provided data. In process of searching for overlapping pathways between databases are used clustering, edit distance, NCBI gene numbers and equivalent relationships comparison. The system was written in C++ and using XML parser. Results are text outputs, eventually files in DOT language, which can be executed with GraphViz to generate graphs.
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