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State Space Symmetry Reduction for TBP Analysis
Černý, Ondřej ; Šerý, Ondřej (advisor) ; Poch, Tomáš (referee)
Threaded Behavioral Protocols (TBP) is a specification language for modelling the behavior of software components. This thesis aims at an analysis of TBP specifications within environments which involve an unbounded replication of threads. Such a TBP specification - together with a model of the possible environments - induces infinite state space which contains a vast amount of symmetries caused by thread replication. A model checking technique addressing such a state space and reducing the symmetries by using symbolic counter abstraction is proposed. In order to utilize the symbolic counter abstraction, the properties of the TBP specifications (called provisions) are converted into thread state reachability properties. The proposed analysis is safe in the sense that it discovers all errors in the model. On the other hand, it may yield spurious errors, i.e., errors that do not correspond to any real error in the model. The spurious errors are well identified and further possibilities to reduce them are outlined. Beyond the scope of the specific specifications, this work may also present a small step towards supporting dynamic thread creation in TBP.
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Barack Obama and Middle East
Černý, Ondřej ; Anděl, Petr (advisor) ; Raška, Francis (referee)
The thesis named Barack Obama and Middle East analyzes American foreign policy to-wards the countries of the Middle East region - Iraq, Iran and Israel. After two con-secutive terms of George W. Bush, new policies of the Obama administration are de-fined with the Middle East still in its centre. This paper answers three basic questions: What is Obama's desirable Middle East policy? In what aspects it is different from the steps of his predecessor? To what extent are the pre-election promises fulfilled? The commitments are defined from Obama's speeches and articles made during the peri-od of his candidacy and also from the recommendations of his advisors. The differen-ces between this planned foreign policy and the steps of George Bush are recapitula-ted in the next part. The third part explores the fulfilment of Obama's promises.
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Signalization of adenylate cyclase toxin of Bordetella pertussis in macrophages.
Černý, Ondřej ; Kamanová, Jana (advisor) ; Kuthan, Martin (referee)
Adenylate cyclase toxin (CyaA) is a key virulence factor of Bordetella pertussis, the causative agent of whooping cough. The toxin targets primarily myeloid phagocytes expressing CD11b/CD18 (αMβ2, CR3, Mac-1) and by elevation of cytosolic cAMP levels it paralyses their macropinocytic and opsono-phagocytic functions. Here, we dissected the cAMP-regulated pathway responsible for the block of macrophage macropinocytosis and characterized the capacity of CyaA-treated macrophages to shut- down Akt (protein kinase B, PKB) signaling; that controls nitric oxide (NO) production by macrophages. By using specific activators of protein kinase A (PKA) and for the exchange protein activated by cAMP (Epac), we show that activation of the cAMP effector Epac inhibits macropinocytosis in macrophages. Moreover, upon transfection of macrophages by the constitutively active and dominant negative variants of a downstream effector of Epac, the small GTPase Rap1, inhibition or upregulation of macrophage macropinocytosis was observed, respectively. It was reported previously that the Epac/Rap1 pathway regulates activity of tyrosin phosphatase SHP-1 as well as of protein phosphatase 2 A (PP2A). We show that inhibition of both tyrosin phosphatases and PP2A interferes with CyaA-mediated block of macropinocytosis. These...
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Physiology of Carotenoids Metabolism and Ornamental Signalisation in Animals
Gabrielová, Barbora ; Albrecht, Tomáš (advisor) ; Černý, Ondřej (referee)
This theses deal with the use and utilization of carotenoids in secondary ornamentation, particularly in birds. Carotenoids have an important role in animal organisms, and the honesty of carotenoid-based signalization has traditionally been ascribed to anti-oxidant functioning of carotenoids. However, this view has been changed recently showing the potentially harmful effect of carotenoids. The deposition of carotenoids in ornamentation is driven not only by carotenoid intake, but also by physiological processes within the organism. Importantly, when the conditions are suboptimal (and the oxidative stress increases) unstable long aliphatic chains of carotenoids derive into highly reactive non-colorful apo- carotenals. Hence carotenoids may act as classical handicaps, potentially harmful to organism, and this view changes our understanding of honesty of carotenoid-based signalization. The theses focus on summarizing the current knowledge on physiological functions of carotenoids and how they affect secondary coloration, and consist of three chapters. In the first one the basic description of carotenoids is provided, along with an overview of carotenoid classification. The second chapter deals with physiological aspects which affect the carotenoid intake, metabolisation, transport to ornaments, and hypotheses...
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Stability indicating HPLC method for evaluation of fluoxetine
Černý, Ondřej ; Kastner, Petr (advisor) ; Pilařová, Pavla (referee)
Charles University in Prague Faculty of Pharmacy in Hradec Králové Department of Pharmaceutical Chemistry and Drug Control Candidate: Ondřej Černý Supervisor: PharmDr. Petr Kastner, Ph.D. Title of thesis: Stability inducing HPLC method for evaluation of fluoxetine The purpose of this thesis was to develop and validate the stability - indicating HPLC method for evaluating Fluoxetine-hydrochloride. Fluoxetine-hydrochloride is a drug from the SSRI group used to treat depression of various etiologies. The basic method was adopted from the Czech Pharmacopoeia 2009. The given Pharmacopoeia method is not sufficient, as the peak of the degradation product Fluoxetine-hydrochloride interfered in the so - called dead retention time of the used column. Its quantitative determination was impossible for this reason. Development of the method consisted in adjustment of the mobile phase using gradient elution. The mobile phase was composed of a mixture of methanol, tetrahydrofuran and triethylamine solution, and it was divided into two containers. The container A consisted of the mixture (MeOH : THF) : TEA solution - 70: 30 (v/v) and the container B consisted of the mixture (MeOH : THF) : TEA solution - 5: 95 (v/v). The mixture (MeOH : THF) was prepared in the ratio of 8 : 30 (v/v). The chromatographic conditions...
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Medical cannabis at the pharmacy
Černý, Ondřej ; Kostřiba, Jan (advisor) ; Smejkalová, Lenka (referee)
Charles University Faculty of Pharmacy in Hradec Králové Department of Social and Clinical Pharmacy Candidate: Mgr. Ondřej Černý Supervisor: PharmDr. Jan Kostřiba, Ph.D. Title of thesis: Medical cannabis at the pharmacy Key words: cannabinoids, individual preparation, medical cannabis in the Czech Republic This rigorous thesis is focused on the medical cannabis (MC). The aim of the thesis was first to familiarise the reader with the description of the substances contained in the herbal cannabis and its effects on the human body. Furthermore, state the current position of MC in the Czech Republic. The aim of the experimental part was to present aspects of the implementation of MC treatment at the pharmacy based on the interpretation of legislation. Furthermore, to statistically evaluate the development of this treatment within the hospital pharmacy in České Budějovice. Records of MC dispensed from the register book of addictive substances from 2019 to 2020 were used as a basis for this statistical analysis. The aim was also to evaluate the development of MC treatment throughout the Czech Republic. The data used in this thesis were published on the websites of the State Agency for Medical Cannabis (SAKL) and the State Institute for Drug Control (SÚKL) from 2015 to 2020. The results of the thesis...
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Development of algorithmic thinking in upper secondary education using programmable robotic systems
Černý, Ondřej ; Jeřábek, Tomáš (advisor) ; Štípek, Jiří (referee)
Obsah Použité zkratky ...................................................................................................................... 9 Úvod .................................................................................................................................... 10 Výzkumný problém a cíle práce...................................................................................... 11 Využité metody práce...................................................................................................... 12 1 Teoretická východiska................................................................................................. 13 1.1 Informatické myšlení ............................................................................................ 14 1.2 Algoritmické myšlení ........................................................................................... 18 1.2.1 Algoritmus..................................................................................................... 19 1.2.2 Vlastnosti algoritmů ...................................................................................... 20 1.2.3 Způsoby zápisu algoritmů ............................................................................. 22 1.2.4 Základní algoritmické konstrukce...
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Heterogeneity of expression of virulence factors of Salmonella.
Mathéová, Paulína ; Černý, Ondřej (advisor) ; Lichá, Irena (referee)
The emergence of phenotypically heterogeneous individuals within an isogenic bacterial population is considered to be an important adaptation to the host environment. It allows survival of some bacterial subpopulations under diverse stress conditions caused by the host immune system, the emergence of a "division of labor" and cooperation between individual bacteria. Bacteria of the genus Salmonella are important pathogens in humans and livestock. Many of the key virulence factors of Salmonella are heterogeneously expressed. The phenotypic diversity of individual bacteria allows certain individuals to escape the host's immune system and ensure that the gene pool is preserved to future generations. In case when change in conditions causes complete extinction of part of the Salmonella population from the environment, the remaining individuals are able to restore the size of the population and phenotypic diversity, after overcoming unfavourable conditions. This work summarises the knowledge about heterogeneity of expression of virulence factors of Salmonella and the characteristics of individual subpopulations in different environmental conditions. Keywords: Salmonella, heterogeneity, virulence factors, bet-hedging, division-of-labor, bacterial subpopulations.
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Regulation of virulence factors of Staphylococcus aureus
Šaňková, Michaela ; Lichá, Irena (advisor) ; Černý, Ondřej (referee)
Staphylococcus aureus is a gram-positive pathogenic bacterium that regulates virulence factors production in response to changing environmental conditions. S. aureus cells evolved a complex regulatory network, including a number of regulatory proteins, transcriptional factors and two- component systems. One of the most important S. aureus regulatory systems is the Agr system (Accessory gene regulator) that perceives its own population density by sensing a "quorum-sensing" signal in a form of autoinducing peptid (AIP). Agr system encodes a global regulatory RNAIII that regulates the expression of target virulence factors, which includes surface proteins as well as extracellular toxins and enzymes. The family of global protein regulators SarA and transcriptional sigma factor B also play a significant role in the regulation of S. aureus virulence. The production of virulence factors is also regulated in response to specific signals from extracellular environment by two- component-systems, which includes the regulator of exoprotein production SaeRS, the regulator of autolysis ArlRS and the regulator of respiratory response SrrAB. Key words: Staphylococcus aureus, virulence factors, Agr, quorum-sensing, RNAIII, SarA, SigB
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Signaling effects of adenylate cyclase toxin action on phagocytes
Černý, Ondřej
The adenylate cyclase toxin (CyaA) plays a key role in the virulence of Bordetella pertussis. CyaA penetrates CR3-expressing phagocytes and catalyzes the uncontrolled conversion of cytosolic ATP to the key second messenger molecule cAMP. This paralyzes the capacity of neutrophils and macrophages to kill bacteria by oxidative burst and opsonophagocytic mechanisms. Here we show that CyaA suppresses the production of bactericidal reactive oxygen and nitrogen species in neutrophils and macrophages, respectively. The inhibition of reactive oxygen species (ROS) production is most-likely achieved by the combined PKA-dependent inhibition of PLC and Epac-dependent dysregulation of NADPH oxidase assembly. Activation of PKA or Epac interfered with fMLP-induced ROS production and the inhibition of PKA partially reversed the CyaA-mediated inhibition of ROS production. CyaA/cAMP signaling then inhibited DAG formation, while the PIP3 formation was not influenced. These results suggest that cAMP produced by CyaA influences the composition of target membranes. We further show here that cAMP signaling through the PKA pathway activates the tyrosine phosphatase SHP-1 and suppresses the production of reactive nitrogen species (RNS) in macrophages. Selective activation of PKA interfered with LPS- induced iNOS expression...
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