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Unravelling molecular mechanisms of the abasic crosslink DNA repair
Hušková, Andrea ; Šilhán, Jan (advisor) ; Bařinka, Cyril (referee) ; Pavlíček, Jiří (referee)
4 Abstract DNA as the primary carrier of genetic information guarantees organisms to live, grow, develop and reproduce. However, this most vital molecule in the cell is subject to various damages every moment. If it is not repaired, the cell and the organism will eventually succumb to inevitable destruction. One of the most serious damages is abasic site interstrand crosslink (Ap-ICL). Ap-ICL is formed spontaneously when an abasic site covalently pairs with an adenine on the opposite strand. The lack of information on repair mechanisms, the influence of the local sequence and its stability leads to questions about the fate, toxicity and occurrence of these lesions in cells. During evolution, several mechanisms have evolved to repair these and other damages to ensure the organism's survival. A recently discovered pathway known to repair Ap-ICL is named after the DNA glycosylase responsible for removing Ap-ICL. NEIL3 DNA glycosylase is recruited to Ap-ICL by ubiquitylation of DNA helicase, which is part of the DNA replication complex. NEIL3 glycosylase contains several zinc-finger domains, that bind to the damaged DNA and ensure its catalytic function. The molecular mechanism of the NEIL3 glycosylase repair process is currently not known. In order to answer the aforementioned unknowns, the rate of formation,...
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Analysis of x-ray diphractograms of organic crystalline solids
Stejkora, Jakub ; Žídek, Jan (referee) ; Salyk, Ota (advisor)
Derivates of diketopyrrolopyrrole are colored pigments with potential use in field of organic semiconductor structures. Their electrical attributes such as conductivity, photocon¬¬ductivity and electroluminescence relate to their crystal structures that determine charge transport path through the compound. For crystallographic structure determination from RTG diffractometry it is needed to grow a measurable single crystal. Growing crystals of derivates of diketopyrrolopyrrols is very difficult due to their poor solubility in all solvents. Several relatively suitable – perhaps even measurable – samples were obtained throughout the testing of series of methods. One of these samples was measured with RTG diffractometry and on the ground of this measurement it was possible to find and solve the crystallographic structure.
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Metastable iron thin films for magnetic metamaterials
Holobrádek, Jakub ; Man, Ondřej (referee) ; Urbánek, Michal (advisor)
Magnetické nanostruktury mají zajímavé vlastnosti, které umožňují jejich aplikace v základním výzkumu i průmyslu. Jednou z těchto vědeckých disciplín je i magnonika - výzkumný obor, který se zabývá fyzikou spinových vln, které lze použít v nediskrétních výpočtech s nízkými ztrátami energie. Výroba magnetických struktur fokusovaným iontovým svazkem (FIB) je alternativní metoda k běžně používaným litografickým metodám. Materiál použitý v této práci - metastabilní železo - je schopen při ozáření iontovým svazkem podstoupit fázovou transformaci z paramagnetické plošně centrované kubické krystalové struktury na feromagnetickou fázi s prostorově centrovanou kubickou krystalovou strukturou. Jednou z vlastností, která ovlivňuje šíření spinových vlny, je magnetická anizotropie. Tato práce představuje vliv depozičních podmínek v ultra vysokém vakuu během přípravy metastabilní železné vrstvy na magnetickou anizotropii struktur vytvořených pomocí FIB do tohoto filmu. Dále prezentujeme souvislosti mezi parametry FIB, krystalografickými vlastnostmi výsledných struktur a jejich magnetickou anizotropií.
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Regulatory mechanism of the cyclin-dependent kinase 16 through the cyclin Y/14-3-3 complex
Janáčková, Zuzana ; Obšil, Tomáš (advisor) ; Pavlíček, Jiří (referee)
CDK16 is a cell-cycle-related cyclin-dependent kinase that functions primarily in neurite growth processes, axonal transport regulation and sperm development. It also plays a role in the progression of X-linked intellectual disability and, together with its activating partner cyclin Y, in the development and progression of various types of cancer. Consequently, CDK16 and cyclin Y could represent potential new therapeutic targets. Both CDK16 and cyclin Y are structurally atypical among similar proteins, and the mechanism of activation of CDK16 by cyclin Y is unclear. However, it is clear from recent studies that the interaction between CDK16 and cyclin Y requires the prior interaction of cyclin Y with 14-3-3 proteins. In addition, for cyclin Y to interact with 14-3-3 proteins, its phosphorylation on the S100 and S326 binding sites of 14-3- 3 is required. To investigate the mechanism of activation of CDK16 by cyclin Y, we decided to characterize the interaction between CDK16, cyclin Y and 14-3-3 proteins in detail. The interaction between CDK16, cyclin Y and 14-3-3 proteins was characterized using biophysical methods including fluorescence anisotropy measurements, native electrophoresis, size exclusion chromatography and protein crystallography. The for- mation of binary pCCNY-14-3-3 and ternary...
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Stability of dispersoids in aluminium alloys at elevated temperatures.
Králík, Rostislav ; Cieslar, Miroslav (advisor)
The AA8079 aluminum alloy prepared by twin-roll casting is commonly used as foil stock for manufacturing of thin packaging foil. Due to the nature of the casting method and material composition microstructure of the material is not homogenous and contains a fraction of intermetallic particles clustered in eutectic colonies. As such, the material requires heat treatment before further processing. Different temperatures of homogenization annealing affect the microstrucutre of the material in different ways. The homogenized material then undergoes a series of rolling passes which causes work hardening. A recrystallization annealing is required at an intermediate gauge before rolling to final thickness to restore ductility of the material. Recrystallization behavior is affected by the present intermetallic particles, their size and distribution. The influence of different homogenized microstructures on control of the recrystallization process through was studied, recrystallization kinetics were evaluated and two main influencing mechanisms - particle stimulated nucleation and Zener drag were identified.
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Krystalizačně-strukturní studie bakteriofágového lysinu ECD7
REINDLOVÁ, Žaneta
This bachelor thesis is focused on the crystallization of newly acquired bacteriophage lysine ECD7. Bacteriophage lysine ECD7 could be one of a new alternative class of antibacterial agents possibly used against infectious diseases. The main goal of this work was to manage the basic crystallization methods, then apply them for crystallization of ECD7 lysine and produce a suitable crystals for X-ray diffraction analysis. Data from X-ray diffraction analysis will help clarify the structure and function of ECD7 lysine.
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Structural and functional study of viral RNA polymerases
Dubánková, Anna ; Bouřa, Evžen (advisor) ; Bařinka, Cyril (referee) ; Plevka, Pavel (referee)
Viral RNA-dependent RNA polymerases (RdRps) are enzymes essential for viral multiplication. The general function of RdRp is universal for all RNA viruses: to recognise viral RNA, bind it and synthesize the complementary RNA strand. This series of steps is absolutely crucial for viral infection. It is important to mention that the non-infected cell is incapable of replicating any RNA. The host cell thus does not naturally express any RdRps. I chose RdRps for my research because these enzymes are key to viral replication and thus an excellent target for antivirals. This study characterises polymerases from Picornaviridae and Flaviviridae families, in depth. Picornaviral replication takes place in viral-induced membrane structures called Replication Organelles (ROs), where the polymerase is localised to the membrane. In this study, we investigated the recruitment of picornaviral polymerase membrane. Subsequently, we focused on the activation of picornaviral RdRp induced by the insertion of the very first residue into the protein core. Next, we focused on the flaviviral RdRps specifically from yellow fever virus (YFV) and Zika virus (ZIKV). This study reports the first structure of a full length YFV polymerase and a model of ZIKV polymerase in complex with RNA. The model of ZIKV RdRp in complex with...
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Stability of dispersoids in aluminium alloys at elevated temperatures.
Králík, Rostislav ; Cieslar, Miroslav (advisor) ; Michalcová, Alena (referee)
Hliníková slitina AA8079 připravena plynulým odléváním mezi válce je běžně používána pro výrobu tenké potravinářské fólie. Vzhledem k použité metodě odlévání a složení slitiny je struktura litého materiálu značně nehomogenní a obsahuje intermetalické fáze, které se shlukují v eutektických koloniích. Litý materiál tak vyžaduje tepelné zpracování před dalšími kroky výroby. Mikrostruktura materiálu po homogenizačních žíháních na různých teplotách je rozdílná, což ovlivňuje další zpracování. Po homogenizaci je materiál válcován což způsobuje snížení tažnosti. Rekrystalizační žíhání je vyžadováno po zválcování na střední tloušťku před finálním válcování, aby byla tažnost obnovena. Chování materiálu během rekrystalizačního žíhání je ovlivněno přítomnými fázemi, jejich velikostí a rozdělením. Byl studován vliv mikrostruktury po homogenizaci na rozdílných teplotách na rekrystalizaci, byla vyhodnocena kinetika rekrystalizace a byly identifikovány dva hlavní mechanismy ovlivňující rekrystalizaci - částicemi stimulovaná nukleace a Zenerův tlak.
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