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Game Theory in Waste Management
Osička, Ondřej ; Vašík, Petr (referee) ; Hrdina, Jaroslav (advisor)
V této práci je vytvořen model rozhodovací situace v odpadovém hospodářství využívající metody teorie her. Model tvoří nekooperativní hra pro reprezentaci konfliktu zpracovatelů odpadu a kooperativní hra pro reprezentaci konfliktu producentů odpadu. Pro konflikt zpracovatelů odpadu je k nalezení strategií při volbě cen na bráně využit koncept Nashovy rovnováhy, takto nalezené stabilní strategie mohou sloužit jako předpověď budoucí situace. Pro zpřesnění množin strategií jsou určeny dolní a horní meze. Pro konflikt producentů odpadu se uvažuje spolupráce všech producentů a určuje se pro ni přerozdělení nákladů pomocí Shapleyho hodnoty a nucleolu. Pro konflikt více producentů jsou vyvinuty aproximační algoritmy pro Shapleyho hodnotu i nucleolus. Tyto algoritmy jsou založeny na předpokladu, že se vzdálení hráči vzájemně neovlivňují. Model je aplikován na situaci v České republice. Pro konflikt zpracovatelů odpadu je nalezen jeden bod Nashovy rovnováhy. Pro konflikt producentů odpadu jsou určeni někteří producenti s vysokým kooperativním potenciálem.
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Role of the WIP1 phosphatase in the nucleolus
Palková, Natálie ; Macůrek, Libor (advisor) ; Sztacho, Martin (referee)
Protein phosphatase 2C delta (known as WIP1) is an important negative regulator of the DNA damage response (DDR) signalling. As a chromatin-bound protein, it dephosphorylates and thus inactivates ATM kinase and the transcription factor p53. Increased expression of WIP1 suppresses the function of the tumour suppressor p53 and contributes to the development of several cancer types, including breast and brain tumours. In recent years, it has been shown that WIP1 can also regulate cellular processes that are not directly linked to DDR, such as ensuring telomere stability. However, alternative functions of the WIP1 protein have not yet been fully understood. In this work, we described a novel role of the WIP1 phosphatase in the nucleolus, the organelle responsible for ribosome biogenesis. We found that WIP1 associates with many nuclear proteins, and using deletion mutants, we identified a nucleolar localisation sequence (NoLS) at the C-terminus of the protein. Using super-resolution microscopy, we detected the localisation of WIP1 phosphatase in the fibrillar centres of the nucleolus. We employed an inducible Cas9 system for generating double-strand breaks in ribosomal DNA and found that WIP1 has an impact on recruitment of DNA repair factors to the nucleolar caps. Analysis based on quantitative...
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Cell response to genotoxic stress-based anti-cancer therapies
Imrichová, Terezie ; Hodný, Zdeněk (advisor) ; Rossmeislová, Lenka (referee) ; Rotrekl, Vladimír (referee)
The dissertation deals with a cell response to genotoxic stress, specifically to anti-cancer treatments with a genotoxic mechanism of action. In principle, cells can respond to these perturbing stimuli in several ways: in case of severe DNA damage, they usually undergo apoptosis or enter senescence. In case of minor DNA damage, or upon defective checkpoint mechanisms, they may continue the cell cycle, either with successfully repaired DNA or with mutations of various kind. Thanks to selection pressure, the mutations that provide cells with a certain growth advantage under conditions of continuing genotoxic stress, gradually accumulate and render the tumor treatment-resistant. In my thesis, I focus on several aspects of this whole process. First, I participated in a characterization of a radioresistant and anoikis-resistant population of prostate cancer cells. This population was generated by irradiating cells 35 times by 2 Gy, a regime used in clinics. After this treatment, a population of low-adherent cells emerged that demonstrated increased expression of EMT- and stem cell markers. The low-adherent state of these cells was maintained by Snail signaling and their anoikis resistance by ERK1/2 signaling. Interestingly, after a protracted period of time, these cells were able to re-adhere and...
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Replication and transcription of nucleolar DNA
Flusser, Michal ; Smirnov, Evgeny (advisor) ; Staněk, David (referee)
The nucleolus is the most prominent compartment of the cell nucleus and is the place where ribosomal RNAs (rRNAs) are synthesized, processed and assembled with ribosomal proteins. Although the nucleolus has been studied for decades its structural and functional organization is still unclear. In particular, the role of various types of DNA participating in the formation of nucleoli along with ribosomal genes is not understood. The present thesis summarizes the current knowledge and views on the nucleolus, focusing on the two synthetic processes, replication and transcription, in mammalian cells. Specific features of these processes in the context of nucleolar ultrastructure remains an unsolved problem of the modern molecular biology.
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Role of tumour suppressor PML in nucleolar functions
Kučerová, Alena ; Hodný, Zdeněk (advisor) ; Stejskalová, Eva (referee)
The cell nucleus is a complex structure composed of different parts, the nucleolus and PML nuclear bodies are important compartments of the nucleus. In the nucleolus, transcription of ribosomal DNA and biogenesis of ribosomes take place. The nucleolus may regulate the expression of proteins and thus the subsequent cell growth through regulating the amount of ribosomes. The nucleolus is also a sensor of stress. PML nuclear bodies play an important role in many cellular process - response to stress, virus infection or DNA damage. PML nuclear bodies consist of many proteins, the major protein is PML protein (Promyelotic leukemia protein). PML protein is coded by PML gene, it is spliced postrancriptionally and it has several isoforms. PML protein is an important cellular regulator and also a tumor suppressor. The nucleolus and PML protein cooperate together and have a functional relationship, which is not entirely clear. It was shown that PML protein changes its localization after exposure to stress and it goes near the nucleolus or into the nucleolus and this happens mainly in primary cells (the reason can be that the level of PML protein downregulates in tumour cells). The relationship between the nucleolus and PML nuclear bodies is important for cell response to stress. Keywords: nucleolus,...
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Study of the organization and dynamics of the membraneless cell compartments
Blažíková, Michaela
of Doctoral Thesis Title: Study of the organization and dynamics of the membraneless cell compartments Author: Michaela Blažíková Institute: Charles University in Prague, Faculty of Mathematics and Physics, Institute of Physics of Charles University Supervisor: Doc. RNDr. Petr Heřman, CSc., Charles University in Prague, Faculty of Mathematics and Physics, Institute of Physics of Charles University Abstract Eukaryotic cells contain many organelles and specific bodies. Beside the membrane delimited organelles such as nucleus, mitochondria or Golgi apparatus there are other structurally and functionally distinct membraneless structures in the cells. In this work we studied the self-organization processes, i.e. the processes that do not require specific interactions, of membraneless structures in nuclei, cytoplasm and plasma membrane of mammalian cells and yeast. The research was focused on the formation of nucleoli and Cajal bodies in mammalian cell nulei and processing bodies (P- bodies) in the cytoplasm of mammalian cells. The organization of MCC domains in the yeast plasma membrane (Membrane compartment of Can1) was studied as well. It was shown that nonspecific interactions as the result of macromolecular crowding could be one of the main driving forces in formation and stabilization of these...
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Cell response to genotoxic stress-based anti-cancer therapies
Imrichová, Terezie ; Hodný, Zdeněk (advisor) ; Rossmeislová, Lenka (referee) ; Rotrekl, Vladimír (referee)
The dissertation deals with a cell response to genotoxic stress, specifically to anti-cancer treatments with a genotoxic mechanism of action. In principle, cells can respond to these perturbing stimuli in several ways: in case of severe DNA damage, they usually undergo apoptosis or enter senescence. In case of minor DNA damage, or upon defective checkpoint mechanisms, they may continue the cell cycle, either with successfully repaired DNA or with mutations of various kind. Thanks to selection pressure, the mutations that provide cells with a certain growth advantage under conditions of continuing genotoxic stress, gradually accumulate and render the tumor treatment-resistant. In my thesis, I focus on several aspects of this whole process. First, I participated in a characterization of a radioresistant and anoikis-resistant population of prostate cancer cells. This population was generated by irradiating cells 35 times by 2 Gy, a regime used in clinics. After this treatment, a population of low-adherent cells emerged that demonstrated increased expression of EMT- and stem cell markers. The low-adherent state of these cells was maintained by Snail signaling and their anoikis resistance by ERK1/2 signaling. Interestingly, after a protracted period of time, these cells were able to re-adhere and...
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Study of the mechanism of gene expression regulation at the level of functional organization of chromatin domains.
Hornáček, Matúš ; Cmarko, Dušan (advisor) ; Kučera, Tomáš (referee) ; Stixová, Lenka (referee)
- 1 - ABSTRACT Nucleoli are formed on the basis of genes of ribosomal DNA (rDNA) clusters called Nucleolus Organizer Regions (NORs). The essential structural components of the nucleoli, Fibrillar Centers (FC) and Dense Fibrillar Components (DFC), together compose FC/DFC units. These units are centers of rDNA transcription by RNA polymerase I (pol I), as well as the early processing events, in which an essential role belongs to fibrillarin. Each FC/DFC unit probably corresponds to a single transcriptionally active gene. In our work we study changes of FC/DFC units in the course of cell cycle. Correlative light and electron microscopy analysis showed that the pol I and fibrillarin positive nucleolar beads correspond to individual FC/DFC units. In vivo observations showed that at early S phase, when transcriptionally active ribosomal genes were replicated, the number of the units in each cell increased by 60 to 80 %. During that period the units transiently lost pol I, but not fibrillarin. Then, until the end of interphase, number of the units did not change, and their duplication was completed only after the cell division, by mid G1 phase. This peculiar mode of reproduction suggests that a considerable subset of ribosomal genes remain transcriptionally silent from mid S phase to mitosis but become again active...
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Analysis of the intracellular localization of nucleophosmin: effect of C-terminal mutations
Kráčmarová, Markéta ; Brodská, Barbora (advisor) ; Čáp, Michal (referee)
C-terminal mutations of the phosphoprotein nucleophosmin (NPM) are the most frequent genetic aberration detected in adult acute myeloid leukemia (AML). I focused on characterization of type A, B and E of AML-related C-terminal mutations. The plasmids bearing fluorescently labeled wild type or mutated NPM have been constructed to characterize mutation-induced changes in the localization of NPM. Mammalian cell lines HEK293T, HeLa and NIH 3T3 were used for production of the chimeric proteins. The intracellular localization of the mutated forms of NPM was analyzed by immunofluorescence staining and fluorescence microscopy of the living cells. The localization of the mutNPM type A and B was almost identical and predominantly cytoplasmic, while mutNPM type E was detected in nucleolus and cytoplasm simultaneously. However localization of the mutated forms was greatly influenced by the used cell line. It has been demonstrated that the exogenous NPM interacts with the endogenous NPM and that they mutually affect their intracellular localization due to heterooligomer formation. Detailed analysis of the relationship between the C-terminal mutations and the localization of the mutated NPM improves understanding of specific mutation effect on the formation and progression of AML and also specifies its prognostic...
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Role of tumour suppressor PML in nucleolar functions
Kučerová, Alena ; Hodný, Zdeněk (advisor) ; Stejskalová, Eva (referee)
The cell nucleus is a complex structure composed of different parts, the nucleolus and PML nuclear bodies are important compartments of the nucleus. In the nucleolus, transcription of ribosomal DNA and biogenesis of ribosomes take place. The nucleolus may regulate the expression of proteins and thus the subsequent cell growth through regulating the amount of ribosomes. The nucleolus is also a sensor of stress. PML nuclear bodies play an important role in many cellular process - response to stress, virus infection or DNA damage. PML nuclear bodies consist of many proteins, the major protein is PML protein (Promyelotic leukemia protein). PML protein is coded by PML gene, it is spliced postrancriptionally and it has several isoforms. PML protein is an important cellular regulator and also a tumor suppressor. The nucleolus and PML protein cooperate together and have a functional relationship, which is not entirely clear. It was shown that PML protein changes its localization after exposure to stress and it goes near the nucleolus or into the nucleolus and this happens mainly in primary cells (the reason can be that the level of PML protein downregulates in tumour cells). The relationship between the nucleolus and PML nuclear bodies is important for cell response to stress. Keywords: nucleolus,...
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