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Unix Tools for Application and System Profiling
Dressler, David ; Chalupníček, Kamil (referee) ; Kašpárek, Tomáš (advisor)
The main goal of this thesis was to demonstrate usage of tools for application and system profiling. Initially, these tools was found and studied. They was also divided into categories according to their purpose. After that, these tools was compared according to their complexity of use and invasiveness. As the result of this comparison, these tools was divided into three groups, that express measure of complexity and invasiveness. As technology, used for creating models, was chosen Apache server and NFS server. Virtualization by hyper-v technology was used for putting these models into operation. There was created four virtual machines. Fist one for Apache server, another one for NFS server. Third was for mirroring content of Apache server and the last one for load generation. The last part of this thesis was to demonstrate usage of found tools on the created models.
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Invasiveness and hybridisation in evolution of closely related species
Gruntová, Martina ; Hojka, Jakub (advisor) ; Urfus, Tomáš (referee)
Plant invasiveness, or the extensive spreading of a plant species into new and non-native areas, is an important and frequently discussed process in botany, influenced by many internal and external factors that determine how a plant will spread and how successful will the spreading be. One of the important factors affecting the level of invasiveness is the ability to hybridise and also ability to become polyploids, because via those processes plants acquire genetic variation that can provide advantageous predispositions for their dispersal. Plants and their spreads are also influenced by external ecological factors, i.e. the environment in which they grow, other species sharing the same habitat, and e.g. climate change or human activity, which change the environmental characteristics and therefore also the areas of distribution. The aim of this thesis is to find links between hybridisation and the success of plant dispersal, and subsequent invasiveness (i.e. the spread of a plant in a non-native range), by using the genus Rorippa as a model. The Central European lineage of lowland species of the genus Rorippa represents a suitable group to study these processes due to the frequency of hybridisation, the variability of ploidy levels and the previously detected invasiveness of one of the species (R....
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Effect of polyploidization on species invasive success
Líblová, Zuzana ; Münzbergová, Zuzana (advisor) ; Rooks, Frederick (referee)
Polyploid variants of many species of plants are strikingly frequently found among alien plants on all continents. They also very often have a much larger distribution range of its occurrence, compared to diploid plants in the place of their origin. In many cases, the polyploid cytotype also has increased tolerance to various stress factors or a physiological and morphological characteristics that allow them to survive the conditions in which the diploid plants would have little chance to survive. All this suggests that polyploidy is likely to bring plants an evolutionary advantage over their diploid ancestors, and polyploids therefore can successfully colonize new territories. This thesis summarizes the findings about the possible consequences of polyploidy at different levels in relation to their effects on the properties supporting plant invasive ability. It presents also known hypotheses dealing with possibilities of why plants become invasive after introduction. This is followed by sections devoted to flow cytometry, an important modern method for determining genome size and ploidy level. In conclusion it briefly describes the model species bird vetch (Vicia cracca) and the results of measurements of the degree of ploidy of seeds of this plant from Alaska and Japan.
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The role of cell polarity signaling in the plasticity of cancer cell invasiveness
Gandalovičová, Aneta ; Brábek, Jan (advisor) ; Cvrčková, Fatima (referee)
Throughout the last few years cancer research has focused on studying the origin of secondary tumors, i.e. metastases, which are a direct outcome of the ability of cancer cells to disseminate from the primary tumor and invade the adjacent tissue. Generally, cancer cells migrate by two distinct mechanisms- amoeboid or mesenchymal. Whereas the mesenchymal migration mode can be described as "path generating", the amoeboid mode resembles a "path finding" way of migration. Both types of invasion are regulated by divergent signaling pathways that are closely related to cell polarity and cytoskeleton reorganization. Responsible for cell polarization are not only the polarity complexes Par, Scribble and Crumbs, but also phosphoinositides and Rho GTPases Rac, Rho and Cdc42, which, additionally, regulate the dynamics of the cytoskeleton. By a mutual interplay they regulate cell motility. It cannot come as a surprise that their deregulation commonly results in tumorigenesis. A more thorough comprehension of the signaling pathways leading to cancer cell invasiveness is a necessary step towards understanding the complex problem of metastasis. Key words: invasiveness, amoeboid, mesenchymal, cell polarity, motility, Rho GTPases, polarity complexes
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The biological importance of CAS SH3 domain tyrosine phosphorylation
Janoštiak, Radoslav ; Brábek, Jan (advisor) ; Dvořák, Michal (referee)
Protein CAS is a major tyrosine-phosphorylated protein in cells transformed by v-crk and v-src oncogenes. It is a multidomain adaptor protein, which serves as a scaffold for assembly of signalling complexes which are important for migration and invasiveness of Src-transformed cells. A novel phosphorylation site in N-terminal SH3 domain was identified - tyrosine 12 located on binding surface of CAS SH3 domain. To study biological importance of tyrosine 12 phosphorylation, non-phosphorylable (Y12F) and phosphomimicking ( Y12E) mutant of CAS were prepared. We found that phosphomimicking mutation Y12E leads to decreased interaction of CAS SH domain with kinase FAK a phosphatase PTP-PEST and also reduce tyrosine phosphorylation of FAK. Using GFP-tagged CAS protein, we show that Y12E mutation caused delocalization of CAS from focal adhesion but has no effect on localization of CAS to podosome-type adhesion. Non-phosphorylable mutation Y12F cause hyperphosphorylation of CAS substrate domain and decrease turnover of focal adhesion and associated cell migration of mouse embryonal fibroblasts (MEFs) independent to integrin singalling. Analogically to migration, CAS Y12F decrease invasiveness of Src-transformed MEF. The results of this diploma thesis show that phosphorylation of Tyr12 in CAS SH3 domain is...
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The use of CAM assay for characterization and study of cancer cell invasive properties
Vágnerová, Lenka ; Dvořák, Michal (advisor) ; Geryk, Josef (referee)
The chorioallantoic membrane (CAM) of chicken embryos belongs to the in vivo model systems frequently used for the study of angiogenesis and cell invasiveness. Using CAM assay we have tested selected chicken sarcoma cell lines characterized by different angiogenic properties and different ability to form metastasis. In addition to CAM assay, several other methods have been used to characterize the phenotype of these cell lines. We have selected a few proteins which could significantly influence the angiogenic and metastatic properties of investigated cell lines. We have established cell lines stably overexpressing these genes and compared their phenotypes with parental cell lines. We have shown that genes encoding ISL1, ARNT2, PROM1, HOXA11 proteins participate, in our experimental model, in activation of programes controlling angiogenesis and cell invasion.
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Structural and regulatory aspects of Src kinase activation
Koudelková, Lenka ; Brábek, Jan (advisor) ; Brdička, Tomáš (referee) ; Hejnar, Jiří (referee)
Src kinase plays a crucial role in a multitude of fundamental cellular processes. Src is an essential component of signalling pathways controlling cellular proliferation, motility or differentiation, and is often found deregulated in tumours. Src activity is therefore maintained under stringent and complex regulation mediated by SH3 and SH2 domains and the phosphorylation state of tyrosines 416 and 527. Active Src adopts an open conformation whereas inactive state of the kinase is characterised by a compact structure stabilised by inhibitory intramolecular interactions. We identified phosphorylation of tyrosine 90 within binding surface of SH3 domain as a new regulatory switch controlling Src kinase activation. Using substitutions mimicking phosphorylation state of the residue we demonstrated that tyrosine 90 phosphorylation controls Src catalytic activity, conformation and interactions mediated by the SH3 domain, representing a positive regulatory mechanism leading to elevated activation of mitogenic pathways and increased invasive potential of cells. Based on correlation between compactness of Src structure and its catalytic activity, we constructed a FRET-based sensor of Src conformation enabling to measure the dynamics of Src activation in cells with spatio-temporal resolution. We found that...
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The role of mitochondrial respiratory chain in invasiveness and metastasis of cancer cells and possible therapeutic interventions
Legátová, Anna ; Brábek, Jan (advisor) ; Truksa, Jaroslav (referee)
The mitochondrial respiratory chain, also called the electron transport chain (ETC), has a pivotal role in key features of cancer cells e.g., proliferation, the metabolic shift from oxidative phosphorylation (OXPHOS) to aerobic glycolysis, or the ability to form metastases. This review summarizes current knowledge about ETC and its relationship to cancer, especially to invasiveness and metastases formation. Firstly, it deals with a process called the Warburg effect and with metabolic complexity in the tumor microenvironment. Then it shows how OXPHOS activity affects invasiveness of cancer cells and metastases formation, and it points out the connection between invasiveness and increased levels of ETC-generated reactive oxygen species. At the end, the review deals with possible use of ETC inhibitors in anticancer therapy.
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Structural and regulatory aspects of Src kinase activation
Koudelková, Lenka
Src kinase plays a crucial role in a multitude of fundamental cellular processes. Src is an essential component of signalling pathways controlling cellular proliferation, motility or differentiation, and is often found deregulated in tumours. Src activity is therefore maintained under stringent and complex regulation mediated by SH3 and SH2 domains and the phosphorylation state of tyrosines 416 and 527. Active Src adopts an open conformation whereas inactive state of the kinase is characterised by a compact structure stabilised by inhibitory intramolecular interactions. We identified phosphorylation of tyrosine 90 within binding surface of SH3 domain as a new regulatory switch controlling Src kinase activation. Using substitutions mimicking phosphorylation state of the residue we demonstrated that tyrosine 90 phosphorylation controls Src catalytic activity, conformation and interactions mediated by the SH3 domain, representing a positive regulatory mechanism leading to elevated activation of mitogenic pathways and increased invasive potential of cells. Based on correlation between compactness of Src structure and its catalytic activity, we constructed a FRET-based sensor of Src conformation enabling to measure the dynamics of Src activation in cells with spatio-temporal resolution. We found that...
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Structural and regulatory aspects of Src kinase activation
Koudelková, Lenka
Src kinase plays a crucial role in a multitude of fundamental cellular processes. Src is an essential component of signalling pathways controlling cellular proliferation, motility or differentiation, and is often found deregulated in tumours. Src activity is therefore maintained under stringent and complex regulation mediated by SH3 and SH2 domains and the phosphorylation state of tyrosines 416 and 527. Active Src adopts an open conformation whereas inactive state of the kinase is characterised by a compact structure stabilised by inhibitory intramolecular interactions. We identified phosphorylation of tyrosine 90 within binding surface of SH3 domain as a new regulatory switch controlling Src kinase activation. Using substitutions mimicking phosphorylation state of the residue we demonstrated that tyrosine 90 phosphorylation controls Src catalytic activity, conformation and interactions mediated by the SH3 domain, representing a positive regulatory mechanism leading to elevated activation of mitogenic pathways and increased invasive potential of cells. Based on correlation between compactness of Src structure and its catalytic activity, we constructed a FRET-based sensor of Src conformation enabling to measure the dynamics of Src activation in cells with spatio-temporal resolution. We found that...
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