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Ddi1-like proteins: a novel family of retroviral-like aspartyl proteases
Šmilauerová, Kristýna ; Grantz Šašková, Klára (advisor) ; Šmahel, Michal (referee)
Ubiquitin-proteasome system is one of the key pathways which maintain cell homeostasis. Its purpose is to degrade damaged, misfolded or unnecessary proteins. It is also involved in multiple other processes such as DNA damage repair, cell cycle control or signaling. The entire system consists of multiple components, which are mutually strictly regulated. Important part of this system is group of so called proteasome adaptor proteins. Their role is to recognize and bind targeted substrates and transport them to the proteasome for degradation. Ddi1-like (abbrev. from DNA damage-inducible protein 1) protein family, a group of proteins with retroviral aspartyl protease-like domain, belongs to proteasome adaptor proteins. Global biological role of this protein family is only partially understood the most studied member is Ddi1 protein from Saccharomyces cerevisiae, and it is thus a subject of active research. This thesis summarizes published information about this protein family, describes its general characteristics and known functions, situates them in the context of cell processes and thereby might suggest the course of further study.
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The Role of DNA Repair in the Onset and Therapy of Ovarian Cancer
Tomášová, Kristýna ; Vodička, Pavel (advisor) ; Čáp, Michal (referee)
DNA repair and DNA damage response are very important biological systems, inevitable to maintain genomic stability and fidelity of the genetic information, for the onset of ovarian cancer. Further, DNA repair is also substantially involved in the response to the therapy, since many chemotherapeutics act as DNA damaging agents. This literary analysis is intended to survay the relevance of DNA repair to ovarian carcinogenesis. Special emphasis is placed on repair defects, as it is inextricably associated with the onset of cancer and treatment outcome. Apart from well-known alternations in ovarian cancer susceptibility genes, such as BRCA1 and BRCA2 involved in homologous recombination repair, ample space will be dedicated to less common gene mutations across different repair pathways. Research confirms that abnormalities in the proteins responsible for homologous recombination repair are the leading cause of ovarian cancer. The majority of authors also suggested that targeting DNA repair pathways, especially base excision repair, can improve chemotherapy efficiency in a synergic manner. The same applies to nucleotide excision repair, which repairs platinum-DNA adducts and thus contibutes to platinum drugs resistance emerging. By way of contrast, mismatch repair in ovarian cancer is rather poorly...
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Potenciální využití WIP1 fosfatasy v terapii nádorového onemocnění prsu
Pecháčková, Soňa ; Macůrek, Libor (advisor) ; Souček, Pavel (referee) ; Krejčí, Lumír (referee)
Cells in our body respond to genotoxic stress by activation of a conserved DNA damage response pathway (DDR). Depending on the level DNA damage, DDR signaling promotes temporary cell cycle arrest (checkpoint), permanent growth arrest (senescence) or programmed cell death (apoptosis). Checkpoints prevent progression through the cell cycle and facilitate repair of damaged DNA. DDR represents an intrinsic barrier preventing genome instability to protect cells against cancer development. WIP1 (encoded by PPM1D) phosphatase is a major negative regulator of DDR pathway and is essential for checkpoint recovery. This thesis contributed to the understanding of molecular mechanisms of WIP1 function and revealed how WIP1 can be involved in tumorigenesis. Firstly, we described that WIP1 protein levels decline during mitosis by APC-Cdc20 dependent proteasomal degradation. WIP1 is phosphorylated at multiple residues which inhibit its enzymatic activity. We propose that inhibition of WIP1 in mitosis allows sensing of low levels of DNA damage that appear during unperturbed mitosis. Further, we identified novel gain-of-function mutations of PPM1D which result in expression of C-terminally truncated WIP1. These truncated WIP1 variants are enzymatically active and exhibit increased protein stability. As result, cells...
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Mercury Electrodes as Tools for Voltammetric Determination of Biologically Active Organic Compounds and for Detection of Their Interaction with DNA
Horáková, Eva ; Vyskočil, Vlastimil (advisor) ; Ludvík, Jiří (referee) ; Vytřas, Karel (referee)
The main aim of this work was to use traditional mercury electrodes for the development of voltammetric methods of determination of organic xenobiotics and for the electrochemical study of the interaction between double-stranded deoxyribonucleic acid (DNA) and these compounds. In relation to my previous research work (conducted in the framework of my diploma thesis), firstly, 4-nitrobiphenyl (4-NBP), the suspected carcinogen, was studied. Interaction of DNA with 4-NBP was studied using differential pulse voltammetry (DPV), cyclic voltammetry (CV), and chronocoulometry at a hanging mercury drop electrode (HMDE), and using CV and alternating current voltammetry at a DNA modified HMDE. Using CV, the reduction mechanism was investigated. The interaction of DNA with 4-aminobiphenyl (4-ABP), a metabolite of 4-NBP, and 4-NBP reduction intermediates was studied. It was found that the interaction of DNA with 4-NBP or 4-ABP results in a formation of a DNA aggregate with these analytes. The second studied analyte was methyl violet 2B (MV). For determination of MV in a buffered solution were used: direct current tast polarography and differential pulse polarography at a dropping mercury electrode, and direct current voltammetry, DPV, and differential pulse adsorptive stripping voltammetry (DPAdSV) at HMDE. The...
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Novel Approaches in Electrochemical Determination of Xenobiotic Compounds and in Study of Their Interaction with DNA
Hájková, Andrea ; Vyskočil, Vlastimil (advisor) ; Trnková, Libuše (referee) ; Labuda, Ján (referee)
Presented Ph.D. Thesis is focused on the development of analytical methods applicable for determination of selected xenobiotic compounds and for monitoring DNA damage they can induce. The main attention has been paid to the development and testing of non-toxic electrode materials for preparation of miniaturized electrochemical devices and novel electrochemical DNA biosensors. 2-Aminofluoren-9-one (2-AFN) was selected as a model environmental pollutant, which belongs to the group of hazardous genotoxic substances. Its carcinogenic and mutagenic effects may represent a risk to living and working environment. 2-AFN has one oxo group, where the cathodic reduction occurs, and one amino group, where the anodic oxidation occurs. The voltammetric behavior of 2-AFN in the negative potential region was investigated at a mercury meniscus modified silver solid amalgam electrode (m-AgSAE) representing a non-toxic and more mechanically robust alternative to mercury electrodes. This working electrode was subsequently used for the development of a newly designed miniaturized electrode system (MES), which has many benefits as the possibility of simple field measurements, easy portability, and the measurement in sample volume 100 µL. Moreover, a glassy carbon electrode (GCE) was used for further investigation of...
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Structure determination of helical domain of DNA damage-inducible protein 2
Staníček, Jakub ; Grantz Šašková, Klára (advisor) ; Obšil, Tomáš (referee)
Human Ddi2 and his homologues are scarcely explored family of ubiquitin- like/ubiquitin-associated domain proteins (UBL/UBA proteins), containing domain which is structurally related to dimeric aspartyl proteases from retroviruses. The most studied of this family is Ddi1 protein from Saccharomyces cerevisiae, which functions within the ubiquitin- proteasome system. This key cellular system exploits tightly regulated enzymatic apparatus for highly selective posttranslational modifications of proteins with molecules of ubiquitin, which serves as intracellular signal determining the proteins fate, importantly its degradation in many cases. Ddi1 plays a role of proteasome adaptor within this context, helping the recognition of ubiquitylated proteins by the proteasome. Even though the function as a proteasome receptor is possible for human Ddi2 protein as well, its cellular role might have been altered during the evolution. One of the important steps in decoding its purpose in cell is exploration of function of its individual domains. This work focuses on structural study of neighbouring region of this protease domain, where the helix-rich region called HDD domain is located. This region of Ddi2 was cloned, expressed and subjected to the NMR measurements. Structural information based on the NMR data was...
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Molecular mechanisms of G2/M checkpoint regulation
Kořínková, Klára ; Macůrek, Libor (advisor) ; Forman, Martin (referee)
Cell division is necessary for maintaining tissue homoeostasis, but at the same time its defects are closely related to the development of many diseases including cancer and premature ageing. Activation of oncogenes leads to replication stress and directly threatens genome stability. The right control of transition between interphase and mitosis is an important mechanism for the protection of genome integrity. Nuclear division is only possible with those cells in which flawless duplication of genetic information occurred. By contrast, cells with damaged DNA structure remain temporarily or permanently stopped at G2 phase of the cell cycle. The topic of this thesis is a detailed literature overview with the subject of molecular mechanisms of the G2/M transition regulation under unperturbed conditions and in the presence of damaged DNA.
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DNA-protein covalent complexes detection as the means for the assessment of the DNA damage induced by topoisomerase poisons.
Karešová, Aneta ; Jirkovská, Anna (advisor) ; Fikrová, Petra (referee)
Charles University in Prague Faculty of Pharmacy in Hradec Králové Department of Biochemical Sciences Candidate: Aneta Karešová Supervisor: PharmDr. Anna Jirkovská, PhD. Title of diploma thesis: DNA-protein covalent complexes detection as the means for the assessment of the DNA damage induced by topoisomerase poisons. Topoisomerase II is essential cellular enzyme, which modifies the secondary structure of DNA. By introducing a temporary double strand break to DNA it relieves a structural tension raised during transcription and translation. Absolutely indispensable is the role of topoisomerase II in the separation of sister chromatids synthesized in the S-phase of the cell cycle. The mechanism of DNA cleavage involves a covalent bond formed between active site tyrosine and 5' phosphate on both of the DNA strands and through the formed break the other strand or the other DNA molecule can pass. After that, the DNA strands are rejoined and topoisomerase II is detached. The indispensability of topoisomerase II mainly for proliferating cells makes it a great target for the antineoplastic drugs and the molecules belonging to the class of topoisomerase II inhibitors (etoposide, anthracyclines) are amongst the most useful anticancer drugs in the clinical practice. These clinically used "topoisomerase...
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Mercury Electrodes as Tools for Voltammetric Determination of Biologically Active Organic Compounds and for Detection of Their Interaction with DNA
Horáková, Eva
The main aim of this work was to use traditional mercury electrodes for the development of voltammetric methods of determination of organic xenobiotics and for the electrochemical study of the interaction between double-stranded deoxyribonucleic acid (DNA) and these compounds. In relation to my previous research work (conducted in the framework of my diploma thesis), firstly, 4-nitrobiphenyl (4-NBP), the suspected carcinogen, was studied. Interaction of DNA with 4-NBP was studied using differential pulse voltammetry (DPV), cyclic voltammetry (CV), and chronocoulometry at a hanging mercury drop electrode (HMDE), and using CV and alternating current voltammetry at a DNA modified HMDE. Using CV, the reduction mechanism was investigated. The interaction of DNA with 4-aminobiphenyl (4-ABP), a metabolite of 4-NBP, and 4-NBP reduction intermediates was studied. It was found that the interaction of DNA with 4-NBP or 4-ABP results in a formation of a DNA aggregate with these analytes. The second studied analyte was methyl violet 2B (MV). For determination of MV in a buffered solution were used: direct current tast polarography and differential pulse polarography at a dropping mercury electrode, and direct current voltammetry, DPV, and differential pulse adsorptive stripping voltammetry (DPAdSV) at HMDE. The...
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Role of Polo-like kinases in the cell cycle and DNA damage response
Kudláčková, Radmila ; Macůrek, Libor (advisor) ; Šolc, Petr (referee)
Within the process of cell division, genetic material must be equally distributed between the two daughter cells. In the next phase, the missing portion of the genome must be synthesized. The entire cycle is regulated by cyclin-dependent kinases (Cdks) in cooperation with cyclins. If the DNA is damaged during the cell cycle, signaling pathways of checkpoints supress cycle progression and enforce the cell cycle arrest until the damage is repaired. Malfunction of the checkpoints results in tumorigenesis. Polo-like kinases (Plks) are, much like Cdks, important regulators of the cell cycle. Plks play significant role mainly in the mitosis and also in a response to the DNA damage. This thesis is focused on human homologues, nevertheless conservation of homologues among organisms is considerable, thus presented findings are of general relevance. Human cells express five proteins from the family of Polo-like kinases, from which Plk1 corresponds to Polo-like kinases of lower eukaryotes. Knowledge on the remaining four kinases is still on the rise.
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