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Nuclear Transport Signals in the proteins of the ARP2/3 complex
Němcová, Barbora ; Bellinvia, Erica (advisor) ; Cvrčková, Fatima (referee)
The intracellular movement of macromolecules such as proteins and RNA is essential for maintaining cellular homeostasis and coordinating various cellular processes. In eukaryotic cells, the transport of these molecules between the cytoplasm and the nucleus is carefully regulated. Nuclear transport signals (NTS) play a key role in facilitating the import and export of proteins across the nuclear envelope. The ARP2/3 complex, which is an important regulator of activity dynamics, has been studied mainly for its functions in the cytoplasm, such as cell movement and cell division. However, new findings suggest that the ARP2/3 complex might also have nuclear functions in plants. Plants are unique multicellular organisms that rely on precisely coordinated cellular activities for growth, development, and response to stimuli. Understanding the molecular mechanisms behind nuclear processes in plants has recently become a focus of research. The ARP2/3 complex, which consists of seven subunits, is known for its ability to branch actin filaments and thereby control cellular processes requiring actin remodeling. However, recent studies have revealed a potential link between the ARP2/3 complex and nuclear functions in plants. Proteins associated with the ARP2/3 complex have been found to localize within the plant...
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Identification and characterization of proteins interacting with plant formins
Houšková, Anežka ; Cvrčková, Fatima (advisor) ; Abrhámová, Kateřina (referee)
Formins are evolutionarily conserved proteins participating in actin and microtubule organisation, affecting thus also intracellular transport, cell growth, morphogenesis and cell polarity. All formins contain FH2 domain, known to dimerize and act as a nucleator of actin. Angiosperms have two formin clades, Class I and Class II, which are distinguished by domain organisation. Based on knowledge from animal models and protein sequence homology, two groups of candidate membrane-associated formin interactors have been proposed in Arabidopsis (Cvrčková, 2013). First group of candidates consists of FYVE domain-containing proteins FAB1A (At4g33240) and FAB1B (At3g14270), the other contains proteins with BAR and SH3 domains AtSH3P1 (At1g31440), AtSH3P2 (At4g346600) and AtSH3P3 (At4g18060). Yeast two hybrid assay was used to examine protein interactions of selected proteins from both candidate groups (FAB1A, SH3P2 and SH3P3) with FH2 domains representing both plant formin clades. The same experimental setup was also used to test dimerization among FH2 domains of plant formins. Translational fusions of FH2 domains from Class I formins AtFH1 (At3g25500), AtFH5 (At5g54650) and Class II representatives AtFH13 (At5g58160) and AtFH14 (At1g31810) with the GAL4 activation domain have been co-expressed in yeast with GAL4...
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Genetically modified plants in practical applications
Říhová, Barbora ; Fischer, Lukáš (advisor) ; Cvrčková, Fatima (referee)
Genetic engineering (GI) of plants is a very current topic, and more and more controversial, since it is becoming an inseparable part of our lives. GI has, among other things, a great potential to help solve the current problem of hunger and malnutrition in certain parts of the world. The goal of this project is to clarify what genetically modified (GM) plants are, to present the possibilities of their practical use, to explain methods of preparation and to consider their advantages and eventual risks. By GM plant we understand a plant whose genetic information has been changed by introducing or removing part of the genetic information (a section of DNA, generally a gene). The most frequently used methods of transformation are the transformation by Agrobacterium tumefaciens and the balistic method. GM plants can be used for production of food or feed in better quality and greater quantity, thanks to an introduction of higher resistance, whether it is to biotic stress (pest, virus or bacterial resistance) or to abiotic stress (drought, salinity, toxic substance in the ground..). In particular, the resistance to abiotic stress is an important issue these days, since through the climate changes some regions suffer more and more from insufficient precipitation and consequent drought. Some of the GM plants grown...
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Non-traditional roles of formins besides actin nucleation
Metlička, Jáchym ; Cvrčková, Fatima (advisor) ; Opatrný, Zdeněk (referee)
Formin homology 2 (FH2) domaincontaining proteins (formins) have, since their discovery in 1990, been observed in all analyzed species of eukaryotic kingdoms. Our knowledge of structure and function of the defining FH2 domain has greatly increased over the last couple of years. Its function in nucleation, polymerization and processive capping of actin filaments designates formin protein family an important cytoskeletonremodelling factor. But FH2 domain is just one part of the puzzle additional optional conserved peptide structures surrounding it, as well as concrete variation of the FH2 domain itself, greatly influence the functional properties and cellular localization of the resultant formin protein. Formins have been implicated in variety of cellular processes, which often (but not always) involve the cytoskeleton e.g. Factin network management, crosstalk of Factin filaments and microtubules or plasma membrane. They also partake in processes integral to cell division, function in conserved signalling pathways and much more. This thesis explains the structure and function of FH2 and FH1 domains, outlines the main formin phylogenetic clades in multicellular eukaryotes and reviews various roles that formins fulfill or are thought to fulfill. Such goal, however, is very bold and (considering the...
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Transgenic crops and third world
Andrová, Julie ; Opatrný, Zdeněk (advisor) ; Cvrčková, Fatima (referee)
The issue of transgenic crops and the third world is mostly neglected in secondary education. In view of the fact that it is an interesting topic that gains greater importance worldwide, it would deserve the place in secondary education. It is not necessary to submit information about this topic only in the text form to students but teaching methods that force the students to gain information actively, can be used. Text for teachers was created in diploma thesis. The text could serve as a source of information for teachers in preparing for the lesson about this topic. Then test for students was created. The test consists of tasks that are inspired by the PISA. Students have to gain information actively from the texts in the tasks to solve the tasks correctly. The test consists of three thematic areas (transgenic crops, golden rice, vaccination and edible vaccines) and 16 questions (31 including the sub-questions). The test was verified on a sample of 82 grammar school students at the age of 16 to 19 years. The students were of the four classes in four grammar schools. The students recorded their answers in a data sheet. The data sheet included additional questions that sought the views and attitudes of students towards texts and questions in the test. The teachers completed the questionnaire. The...
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The role of cell polarity signaling in the plasticity of cancer cell invasiveness
Gandalovičová, Aneta ; Brábek, Jan (advisor) ; Cvrčková, Fatima (referee)
Throughout the last few years cancer research has focused on studying the origin of secondary tumors, i.e. metastases, which are a direct outcome of the ability of cancer cells to disseminate from the primary tumor and invade the adjacent tissue. Generally, cancer cells migrate by two distinct mechanisms- amoeboid or mesenchymal. Whereas the mesenchymal migration mode can be described as "path generating", the amoeboid mode resembles a "path finding" way of migration. Both types of invasion are regulated by divergent signaling pathways that are closely related to cell polarity and cytoskeleton reorganization. Responsible for cell polarization are not only the polarity complexes Par, Scribble and Crumbs, but also phosphoinositides and Rho GTPases Rac, Rho and Cdc42, which, additionally, regulate the dynamics of the cytoskeleton. By a mutual interplay they regulate cell motility. It cannot come as a surprise that their deregulation commonly results in tumorigenesis. A more thorough comprehension of the signaling pathways leading to cancer cell invasiveness is a necessary step towards understanding the complex problem of metastasis. Key words: invasiveness, amoeboid, mesenchymal, cell polarity, motility, Rho GTPases, polarity complexes
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Actin nucleation in plant cell
Schiebertová, Petra ; Schwarzerová, Kateřina (advisor) ; Cvrčková, Fatima (referee)
The ability of plant cells to nucleate actin is important especially for dynamic of intracellular movements of organelles and vesicles, cell structure and growth organization and coordination of endo- and exocytosis . Actin nucleation means the development of new actin filaments from G-actin. Actin associated proteins - Arp2/3 complex and formins serve for this purpose. Arp2/3 complex polymerizes new "daughter " filament from the side of the "parent" filament at an angle of 70 degrees and after the nucleation remains at minus end of filaments, thus inducing branching of filaments. Nucleation by Arp2/3 complex further requires nucleation promoting factors - NPFs. Deletion of subunits of Arp2/3 complex is often lethal in animal cells. On the other hand, deletion results in rather mild phenotype in plants. Formins catalyze the formation of direct actin fibers and remain on the plus end of the fiber after nucleation. There are multiple isoforms of formins in plants than in animals, which suggest an important role of formins in plants. New actin nucleators Cobl, Lmod, Spire, JMY and APC containing WH2 (WASP homology 2) domain were identified in non-plant cells. This type of actin nucleation was not described in plants. Kew words: Actin, Arp2/3 complex, formins, Scar/WAVE, Cobl, Lmod, Spire
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The architecture of regulatory network of metabolism
Geryk, Jan ; Flegr, Jaroslav (advisor) ; Cvrčková, Fatima (referee) ; Šafránek, David (referee)
The thesis focus on the modularity of metabolic network and foremost on the architecture of regulatory network representing direct regulatory interactions between metabolites and enzymes. I focus on the "modularity measure" in my first work. Modularity measure is quantitative measure of network modularity commonly used for module identification. It was showed that algorithms using this measure can produce modules that are composed of two clearly pronounced sub-modules. Maximum size of module for which there is a risk that is is composed of two sub-modules is called resolution limit of modularity measure. In my first work I generalize resolution limit of modularity measure. The generalized version provide insight to the origin of resolution limit in the null-model used by modularity measure. Moreover it is showed that the risk of omitting of sub-modular structures applies for bigger modules than mentioned in the original publication. The second work is focused on the question how does the modular structure of E. coli metabolic network change if we add regulatory interactions. I find that the modularity of modular core of network slightly increase after regulatory edges addition. The modularity increase is significant with respect to randomized ensemble of regulatory networks. Identified modules...
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