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Application of the Nambu mechanics formalism in atmospheric dynamics
Procházková, Zuzana ; Šácha, Petr (advisor) ; Badin, Gualtiero (referee)
Nambu mechanics is a generalization of Hamiltonian mechanics that uses multiple conserved quantities as Hamiltonians. In this thesis, we review Nambu mechanics and its application on the equations of incompressible flow and shallow water equations. The Nambu form of the equations of incompressible flow is guessed based on its Hamiltonian form and derived conserved quantities. With the example of the shallow water equations a more general method of Nambu form derivation is illustrated. Based only on the knowledge of the Hamiltonian and the potential enstrophy moments conservation, the shallow water equations are written as a sum of the Nambu brackets and a Poisson bracket. For the classical potential enstrophy, the derived equations are up to constant factors equivalent to the known form of the shallow water equations. The notation by antisymmetric Nambu brackets is convenient for finding conservative schemes and the theory can be also used for example for the study of deviations of flow from stationary flow.
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Optimization of recombinant protein expression in HEK293 cell line
Bláha, Jan ; Bezouška, Karel (advisor) ; Šácha, Pavel (referee)
Mammalian cells have become the dominant system for recombinant expression of pharmaceutical proteins. This system is becoming suitable also for structural biology, with the advances in methodology of transient transfection of mammalian cells. This work dealt with optimization of recombinant expression in HEK293T and HEK293-6E cell lines in various media using easily quantifiable markers - secreted alkaline phosphatase (SEAP) and green fluorescent protein (GFP). Emphasis was placed on optimizing key factors behind the creation of transfection complex - the ratio of DNA to polyethyleneimine and the amount of DNA used. The positive influence of histone deacetylases inhibitor valproic acid and also of casein hydrolysate Tryptone N1 was also studied. (The thesis is written in Czech.)
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On the internal gravity wave - atmospheric circulation interaction
Procházková, Zuzana ; Šácha, Petr (advisor) ; Podglajen, Aurélien (referee)
Internal gravity waves (GWs) are an important component of the atmospheric dynamics, significantly affecting the middle atmosphere by momentum and energy transport and deposition. In order to be able to improve global circulation models, in which the majority of the GW spectrum is not resolved, it is necessary to quantify their effects as precise as possible. We study GWs in a high-resolution simulation of the WRF model around Southern Andes, Antarctic Peninsula and South Georgia Island. We analyse a Gaussian high-pass filter method for separation of GWs from the basic flow. To overcome an observed problem of dependence of the method on a cutoff parameter, we propose an improved method that determines the parameter at each time step from the horizontal kinetic energy spectrum. The differences between the methods are further examined using the horizontal kinetic energy spectrum, vertical potential energy spectrum and forcing to the divergence equation evaluated by the active wind method, which is a recent theory-based method that divides the flow into a balanced flow and a perturbation field. The results suggest that the high-pass filter method does not produce correct results for time periods with strong wave activity.
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Usage possibilities of the cloud products of satellite datasets
Šácha, Petr
Title Usage possibilities of the cloud products of satellite datasets Author: Bc. Petr Šácha Department: Department of Meteorology and Environment Protection Supervisor: RNDr. Petr Pišoft Ph.D. Supervisor's e-mail address: Petr.Pisoft@mff.cuni.cz Abstract: Cloudiness plays an important role in the global energy and water cycle. In particular, the presence of clouds dominates the planetary albedo and takes part in many climate feedback processes. In this thesis a short informational overview of remote sensing, a description of EUMETSAT, satellites, which it used, its part CM- SAF and a search retrieval of current research is given at first. Then the study is focused on the cloud satellite products, especially on CFC (cloud fractional cover) and CTY (cloud type) products. Data sets of daily averages of these products are compared with the daily averages created from the surface SYNOP observations of the total cloud cover and cloud type in the area of the Czech Republic. In the case of big variances between the two examined datasets of daily averaged cloud coverage, possible causes like the sampling error, dependence on season, localization of the station and the elevation and type of cloudiness, are searched. Several statistic analyses and validation scores are computed. Finally, possibilities of the examined...
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Application of the Nambu mechanics formalism in atmospheric dynamics
Procházková, Zuzana ; Šácha, Petr (advisor) ; Badin, Gualtiero (referee)
Nambu mechanics is a generalization of Hamiltonian mechanics that uses multiple conserved quantities as Hamiltonians. In this thesis, we review Nambu mechanics and its application on the equations of incompressible flow and shallow water equations. The Nambu form of the equations of incompressible flow is guessed based on its Hamiltonian form and derived conserved quantities. With the example of the shallow water equations a more general method of Nambu form derivation is illustrated. Based only on the knowledge of the Hamiltonian and the potential enstrophy moments conservation, the shallow water equations are written as a sum of the Nambu brackets and a Poisson bracket. For the classical potential enstrophy, the derived equations are up to constant factors equivalent to the known form of the shallow water equations. The notation by antisymmetric Nambu brackets is convenient for finding conservative schemes and the theory can be also used for example for the study of deviations of flow from stationary flow.
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Generation and Characterization of Glutamate Carboxypeptidase II (GCPII)-Deficient Mice
Vorlová, Barbora ; Šácha, Pavel (advisor) ; Eckschlager, Tomáš (referee) ; Bařinka, Cyril (referee)
Glutamate carboxypeptidase II (GCPII) is a transmembrane glycoprotein, which consists of short intracellular and transmembrane domains, and a large extracellular domain possessing carboxypeptidase activity. In the human body, GCPII fulfils a neuromodulatory function in the brain and facilitates folate absorption in the small intestine. In addition to the brain and small intestine, high level of GCPII is also present in the prostate and kidney. However, GCPII function in these tissues has not been determined yet. To study the role of GCPII in detail, several research groups attempted to inactivate GCPII encoding gene Folh1 in mice. Surprisingly, the experiments led to rather conflicting results ranging from embryonic lethality to generation of viable GCPII-deficient mice without any obvious phenotype. This dissertation project aimed to dissect the discrepancy using alternative strategy for gene modification. For this purpose, we designed TALENs that specifically targeted exon 11 of Folh1 gene and manipulated mouse zygotes of C57BL/6NCrl genetic background. We analysed all genetically modified mice of F0 generation for presence of TALEN-mediated mutations and established 5 different GCPII-mutant mouse colonies from founder mice that altogether carried 2 frame-shift mutations and 3 small in-frame...
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Epigenetically based chemoresistance of cancer cells
Feriančiková, Barbara ; Eckschlager, Tomáš (advisor) ; Šácha, Pavel (referee)
Cancer, despite significant advances in diagnosis and treatment, is the second most common cause of death in economically advanced countries. The main reason for the failure of anticancer therapy is the development of chemoresistance, which can be either internal or acquired, and is primarily mediated by the activation of various key regulators (eg MDR, PI3K/Akt, etc.). Genetic and epigenetic mechanisms are involved in activating these pathwa- ys. Significant epigenetic mechanisms that can participate in chemoresistance include regula- tion of gene expression by microRNA (miRNA) and long noncoding RNA (lncRNA). Dere- gulated expression of these non-coding RNAs has been observed in many diseases and their involvement in the initiation and progression of malignant tumors has been demonstrated. In this study, we investigated the expression of long non-coding RNA MIAT in hypoxia (1% O2) in chemosensitive and chemoresistant neuroblastoma cell lines (NBL), as hypoxia is a significant negative prognostic factor of many tumors and is involved in chemoresistance. Relative expression of MIAT was influenced by the number of cultured cells, where expression was increased by culturing more cells. MIAT expression was also significantly increased after 6 hours of NBL culture UKF-NB-4 in hypoxic conditions, and...
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Structure and Function of Glutamate Carboxypeptidase II
Šácha, Pavel ; Konvalinka, Jan (advisor) ; Šedo, Aleksi (referee) ; Blahoš, Jaroslav (referee)
4 Závěr GCPII je důležitý protein, který hraje roli v mnoha fyziologických i patologických procesech. Proto bylo třeba získat větší množství enzymaticky aktivního proteinu pro jeho další biochemický výzkum. Heterologní expresí v hmyzích buňkách S2 bylo exprimováno a následně purifikováno dostatečné množství velmi čistého a aktivního enzymu. To umožnilo jeho biochemickou charakterizaci, krystalizaci a později vedlo i k vyřešení krystalové struktury. GCPII je aktivní v širokém rozmezí pH 6 - 8, s maximem kolem pH 7,5. Zjistili jsme, že kromě přirozeného substrátu Ac-Asp-Glu GCPII štěpí také acetylované dipeptidy Ac-Asp-Met, Ac-Glu-Met, Ac-Glu-Glu, Ac-Ala-Glu a Ac-Ala-Met. U těchto substrátů byly změřeny kinetické parametry štěpení. Nalezení dalších substrátů může vést k objevení dosud nepopsaných fyziologických rolí GCPII. Také byly porovnány hodnoty IC50 inhibitorů známých z literatury u námi připravené GCPII a GCPII izolované z potkaních mozků. IC50 bylo u všech méně specifických inhibitorů nižší u rekombinantní GCPII než u GCPII izolované z mozků. Rozdíly ve výsledcích vysvětlujeme vazbou méně specifických inhibitorů na jiné proteiny preparátů z mozku. Vůbec nepochybujeme o tom, že data získaná za použití čistého rekombinantního proteinu jsou přesnější než ta, ktará byla získána ze špatně definovaných...
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Mitochondrial beta-lactamase and its role in humans
Baudyšová, Alžběta ; Šácha, Pavel (advisor) ; Pecina, Petr (referee)
Cancer is one of the most frequent causes of death. Fortunately, human body has a number of various mechanisms that protect cells from tumorigenic transformation. One of those mechanisms are tumor suppressor genes. The latest described tumor suppressor gene encodes LACTB protein. LACTB is the mammalian homolog of bacterial beta-lactamases and penicillin binding proteins (PBPs). PBPs are involved in construction of bacterial cell walls (specifically in the synthesis of peptidoglycan) and they could be inhibited by penicillin antibiotics. Beta-lactamases are able to break the beta-lactam ring of penicillin and provide resistance to the antibiotics. The main topic of this work will be the LACTB protein. LACTB is localizated in the intermembrane space of mammalian mitochondria. Here it forms filaments whose physiological function still remains unknown. LACTB, apart from its connection with cancer, was also associated with obesity and penicillin allergy. Main focus of this work will be to gather all known information about the LACTB protein and put them into a wider context.
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