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Cell death-regulating micro RNAs and their role in the development and pathological processes.
Běhounek, Matěj ; Anděra, Ladislav (advisor) ; Seifertová, Eva (referee)
MicroRNAs are small protein non-coding, ~ 22 nucleotides long dsRNAs. Their main task is suppression of gene expression via removal/destabilization of mRNA or its targeting to degradation. These small molecules play an important role in the regulation of many cellular processes and have been found to affect expression of more than 30% of human genes. Among the processes affected or regulated by miRNAa belongs also programmed cell death. Although this work is mainly focused on the analysis and characterization a role of distinct miRNAs in the regulation of apoptotic cell death, miRNAs can also participate in the regulation of autophagic cell death or programmed necrosis. MiRNA can enhance cellular sensitivity to apoptosis by suppressing the expression of death receptor genes, but can also drive cells to apoptosis by regulating expression of anti-apoptotic protein Bcl-2. In many different organisms were already discovered and described thausends of micro RNAs anddozens of them participate in the regulation of cell death. Poor or impaired function of miRNAs and related disturbance in apoptotic signaling could lead to a number of pathological processes as tumorigenesis or disturbances in tissue development and homeostasis. . Understanding how miRNA functions in cell death and possible practical...
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Protein synthesis in cellular stress
Cienciala, Martin ; Pospíšek, Martin (advisor) ; Holá, Dana (referee)
Environmental stress is a daily bread for organisms across many different branches of life. Very complex response mechanisms have evolved to tackle such insults. Yeast Saccharomyces cerevisiae is adapted especially well for counteracting oxidative and osmotic stress. These unfavorable conditions usually lead to inhibition of protein synthesis. The GCN2 kinase is thought to be responsible for this phenomenon. General inhibition of protein synthesis is accompanied by an increase in expression of proteins engaging in stress response. Production of these proteins is often preceded by specialized regulatory processes, that operate on various stages of expression. This thesis will try to present the diversity and complexity of the individual regulatory layers.
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Characterization of the ABC-F protein Sco0636 in Streptomyces coelicolor
Pinďáková, Nikola ; Balíková Novotná, Gabriela (advisor) ; Mikušová, Gabriela (referee)
The main topic of this diploma thesis is ARE (resistance) proteins from the ABC-F family of the second class of ABC proteins. ARE proteins confer resistance to antibiotics that bind to a large ribosomal subunit and therefore inhibit proteosynthesis. One of the ARE proteins is the Lmr (C) protein, which is part of the linkomycin biosynthesis cluster of Streptomyces lincolnensis, and according to new results, Lmr (C) does not have to be just resistant protein but may have also regulatory function. We decided to study Sco0636, the closest homologue to Lmr (C) in Streptomyces coelicolor, which is a model organism in the study of secondary metabolism. Thanks to the production of color pigments, it is possible to monitor the effect of ARE proteins on secondary metabolism directly on the plates. I prepared the deletion mutant and the strain with constitutive expression of sco0636, and observed the effect on the phenotype. I followed the production of a blue asset and set a minimum inhibitory concentration to selected antibiotics, which bind to the ribosome. I have found that Sco0636 gives high resistance to tiamulin and so it has been named TiaA. The deletion of gene sco0636 accelerated production of actinorodine, and constitutive expression of this gene slowed down production. Keywords: ABC proteins,...
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Regulation of mTOR pathway in the oocyte meiosis
Schmidtová, Barbara ; Šušor, Andrej (advisor) ; Krylov, Vladimír (referee)
Mammalian Target of Rapamycin (mTOR) is serin-threonin kinase, which has become a major topic in many studies in the last decade, leading to new insights into how cell works. This kinase is involved in proteosynthesis, metabolism, cell cycle regulation, proliferation and responses to nutrients and growth factors. There are certain diseases caused by mutations in mTOR gene, which lead to abnormal function of this kinase. These diseases include cancer or fertility disorders. mTOR research is also beneficial due to the search for drugs that could rescue its function and thus provide treatment for these diseases. The best-known drug is inhibitor Rapamycin and its derivates. The aim of this bachelor thesis is to summarize the knowledge about how mTOR can be regulated, the role of its substrates in cell function and to define the role of mTOR in oocyte development, translation and human health. Keywords: Oocyte, mTOR, translation, 4E-BP1, MPF, meiosis, AKT
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The role of elF3 a Rps3 in stop codon readthrough
Poncová, Kristýna ; Valášek, Leoš (advisor) ; Vopálenský, Václav (referee) ; Krásný, Libor (referee)
Translation represents a highly regulated, interconnected process of protein synthesis in the cell. It could be divided into 4 phases: initiation, elongation, termination, and ribosomal recycling. Our laboratory is involved in in-depth studies of a complex eukaryotic initiation factor 3 protein (eIF3). We are interested not only in revealing its molecular roles in the translational cycle in general but also in specific mechanisms that allow translational regulation according to specific cellular needs. In the budding yeast, the eIF3 is composed of five essential subunits (a/Tif32, b/Prt1, c/Nip1, g/Tif35 and i/Tif34). In mammals, the protein is even more complex, comprising of 12 subunits (a-i, k-m). eIF3 is a key player not only in translation initiation but also in ribosomal recycling and, surprisingly, in translation termination and stop codon readthrough as well. The latter process harbors important clinical potential, as approximately 1/3 of genetically inherited diseases is caused by the presence of a premature termination codon in the protein-coding region. Therefore, understanding the molecular mechanism underlying this phenomenon provides important tools for the targeted and less toxic drug development approaches needed for patient therapy. In this Ph.D. Thesis, I uncovered the role of...
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Role of small ribosomal proteins forming the decoding site in translation.
Hovorková, Zuzana ; Valášek, Leoš (advisor) ; Hálová, Martina (referee)
Translation is one of the key mechanisms occurring in the cell during every second of its existence. It is a very complex process ensured by three main actors: tRNAs, mRNAs and ribosomes. Despite of being thoroughly studied over decades, the understanding of some of its functional aspects is still rather poor. This bachelor thesis focuses on four small ribosomal proteins listed below that are reaching to the decoding centre of the small ribosomal subunit. It raises awareness of the structure and function of uS12, uS19, eS25 and eS30, their evolution, role within the ribosome, and the influence they have on various stages of translation. In particular, this thesis specifically reviews the importance of these four proteins for the stop codon readthrough. This phenomenon occurs when a near-cognate aminoacyl-tRNA or a natural suppressor tRNA wins with eRF1 over the corresponding stop codon and thus protein synthesis is continued resulting in the existence of a longer protein. It summarizes our current knowledge of its origin, molecular details of its mechanism, its existence in different species, benefits and disadvantages it brings to the life of a cell or even an organism, and finally it sums up all available knowledge for potential future use of readthrough in therapeutics. Key words: translation,...
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The function of ABCF proteins in bacteria
Mičke, Bianka ; Balíková Novotná, Gabriela (advisor) ; Lišková, Petra (referee)
Translation belongs to the most basic processes which happens in the living cells. It is the last step of proteosynthesis when genetic information encoded by the mRNA is transformed into the protein on a ribosome. Organisms have developed a wide range of mechanisms that can regulate it's needs. I focused on one of them - ABCF proteins. This protein group is a member of the ABC transporters superfamily but they haven't a transmembrane domain and their purpose is protect the ribosomes from antibiotics that bind 50S ribosomal subunit or interact with the ribosomes and influence ribosomal functions. Today, we can divide ABCF proteins into the two functional groups: antibiotic resistence proteins (ARE) and proteins with the regulatory functions. The translational regulatory function has been confirmed There is 45 ABCF protein subfamilies spread through the bacteries and eukaryotes but many essential informations like the structure and exact function of them are still missing. My bachelor thesis is analysis and summary of facts that are known about the bacterial ABCF proteins. Key words: ABCF proteins, antibiotic resistence, ARE, translational regulation, ribosome, translation, translational factors
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Regulation of translation in mammalian oocytes and early embryos
Jindrová, Anna ; Šušor, Andrej (advisor) ; Flemr, Matyáš (referee) ; Fulková, Helena (referee)
Fully grown oocytes undergo their further development in the absence of transcription. Completion of meiosis and early embryo development rely on the maternal mRNAs synthetized and stored during earlier development. Thus, the regulation of gene expression in oocytes during that period is controlled almost exclusively at the level of mRNA stabilization and translation. In the same vein, any mRNA metabolism could play a critical function at this stage of development. RNA localization followed by a local translation is a mechanism responsible for the control of spatial and temporal gene expression in the cell. We focused on visualization of mRNA and in situ translation in the mammalian oogenesis and embryogenesis. We characterized localization of global RNA population in the oocyte and early embryo nucleus together with RNA binding proteins. Additionally we visualized specific ribosomal proteins that contribute to translation in the oocyte and embryo. We have shown that the key player of cap-dependent translation mTOR becomes highly active post nuclear envelope breakdown (NEBD) and in turn its substrate, translational repressor 4E-BP1 becomes inactive. Precise localization of inactivated 4E-BP1 at the newly forming spindle of the oocyte indicates the ongoing translation in this area. Furthermore, from...
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Characterization of the ABC-F protein Sco0636 in Streptomyces coelicolor
Pinďáková, Nikola ; Balíková Novotná, Gabriela (advisor) ; Mikušová, Gabriela (referee)
The main topic of this diploma thesis is ARE (resistance) proteins from the ABC-F family of the second class of ABC proteins. ARE proteins confer resistance to antibiotics that bind to a large ribosomal subunit and therefore inhibit proteosynthesis. One of the ARE proteins is the Lmr (C) protein, which is part of the linkomycin biosynthesis cluster of Streptomyces lincolnensis, and according to new results, Lmr (C) does not have to be just resistant protein but may have also regulatory function. We decided to study Sco0636, the closest homologue to Lmr (C) in Streptomyces coelicolor, which is a model organism in the study of secondary metabolism. Thanks to the production of color pigments, it is possible to monitor the effect of ARE proteins on secondary metabolism directly on the plates. I prepared the deletion mutant and the strain with constitutive expression of sco0636, and observed the effect on the phenotype. I followed the production of a blue asset and set a minimum inhibitory concentration to selected antibiotics, which bind to the ribosome. I have found that Sco0636 gives high resistance to tiamulin and so it has been named TiaA. The deletion of gene sco0636 accelerated production of actinorodine, and constitutive expression of this gene slowed down production. Keywords: ABC proteins,...
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3D scene reconstruction using Clifford algebras
Hrubý, Jan ; Návrat, Aleš (referee) ; Hrdina, Jaroslav (advisor)
Tato diplomová práce má za cíl seznámit čtenáře se stále ještě relativně novou a neznámou oblastí matematiky, s geometrickou algebrou. Nejdříve jsou uvedeny základní definice a poté jsou studovány vlastnosti obecné geometrické algebry. Další velká část textu se věnuje Konformní geometrické algebře, která je v současnosti jedna z nejvíce zkoumaných a aplikovaných geometrických algeber. Jsou popsány její algebraické a geometrické vlastnosti, konkrétně schopnost reprezentovat určité geometrické objekty jako vektory. Taktéž umožňuje počítat jejich průniky a konformní transformace. Další část textu je zaměřena na aplikace Konformní geometrické algebry, nejdříve k popisu kinematiky robotické ruky a poté v binokulárním viděni.
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