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Phonotactic framework of the Czech word and stress-group
Churaňová, Eliška ; Volín, Jan (advisor) ; Palková, Zdena (referee)
This master thesis provides a relatively detailed description of the consonant-vowel structure of standard spoken Czech. The first part covers approaches to and findings on the combinatorial system and distribution of sound units in speech; aspects of continuous speech segmentation into intonation phrases and stress groups, phonotactics of languages in general and Czech in particular, and speech rhythm are also addressed. Recordings of 12 professional speakers of Czech - comprising 6639 words and 5368 stress groups in total - have been used to create data sets that have enabled the author to describe CVCV structures of Czech words and stress groups. The results of this research present frequencies of words and stress groups and their relations to word-class dimension, frequencies of phones in words and stress groups; in this respect, both syllabic liquids and glottal stops have been taken into account. Further, the thesis includes an overview of the most frequent CVCV patterns in words and stress groups and their variability with regard to word classes. The final part focuses on how frequently consonants, vowels and their pairs and trios occur at different places within a unit. The results are continuously compared both between themselves and with the research that used the larger SYN2005 written...
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Antagonistic regulation by global transcription factors Tup1p, and Cyc8p of Flo11 and Flo11 -dependent phenotypes in wild yeast
Nguyen Van, Phu ; Palková, Zdena (advisor) ; Heidingsfeld, Olga (referee) ; Malcová, Ivana (referee) ; Demnerová, Kateřina (referee)
Biofilms are a common mode of yeast growth in which cells adhere to each other and adhere to biotic and abiotic surfaces to form complex multicellular structures. Living together in biofilms provides cells with several benefits, compared to planktonic cells such as protection and resistance to antimicrobials, environmental stresses and host immune attacks. Biofilms may play many important roles in commercial industries. But they are considered to be extremely dangerous in clinical settings. There is thus great interest in studying biofilms and how to eliminate them. In this study, we used wild yeast Saccharomyces cerevisiae colony biofilm as an ideal system to investigate potential functions of the yeast Cyc8p-Tup1p transcriptional corepressor complex in the regulation of yeast adhesion and biofilm formation on agar and at solid-liquid interfaces. Unexpectedly, we found that Cyc8p and Tup1p antagonistically control FLO11 expression and the formation of structured biofilm colonies on agar. Cyc8p itself acts as a key repressor of FLO11 and biofilm colony formation, whereas Tup1p promotes the formation of biofilm colonies and induces FLO11 expression by inhibiting the repressive function of Cyc8p and preventing Flo11p degradation possibly by inhibiting an extracellular protease. Other typical features...
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Dynamics of yeast colony differentiation: New approaches
Jurečková, Gabriela ; Palková, Zdena (advisor) ; Zimmermannová, Olga (referee)
The yeast Saccharomyces cerevisiae when growing on solid medium forms structured colonies. During its development, two subpopulations of cells are formed, termed as U cells ("upper cells") and L cells ("lower cells"). This nomenclature derives from their position within the colony. These cells differ from each other considering their morphology, metabolism, physiology and are characterized by varying degrees of resistance to stress. This diploma thesis deals with new methodological approaches that can be used in further research of yeast differentiation. The first part deals with yeast differentiation and de-differentiation. In the experimental part, the development of mechanically mixed yeast colonies was monitored. The development was monitored in situ in the colony section using fluorescence and "wide-field" microscopy. The ability to de-differentiate of already specialized cells was evaluated mainly according to the nature of the expression of the fluorescently labeled protein Ato1p, which serves as a protein marker of U cells. The second part deals with the optogenetic system EL222 and its possible use in yeast. Many optogenetic tools have been described to control various cellular processes using light. One of these optogenetic tools is the EL222 system, which allows the induction of...
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Differentiation of yeast colonies: The role of selected transcription factors and metabolic proteins
Plocek, Vítězslav ; Palková, Zdena (advisor) ; Heidingsfeld, Olga (referee) ; Sychrová, Hana (referee)
5 Abstract Although yeasts are unicellular microorganisms, they form complex multicellular formations such as biofilms and colonies under natural conditions. Within these structures, processes such as cell differentiation, specialization by particular cell populations and cell signalling, which are typical of multicellular organisms, take place. The literature introduction to this thesis summarizes current knowledge regarding the development of biofilms and colonies, in particular those of the model organism, Saccharomyces cerevisiae, and some selected regulations that are important for the formation of multicellular structures. In the results section, I focus on two lines of research. The first is directed towards mechanisms, involved in the formation of multicellular structures. In studying the formation of SLI biofilms (biofilms at the solid/liquid interface), we have documented the antagonistic role of the regulators CYC8 and TUP1 in their formation and have also described the effect of the presence of glucose on the development and stability of SLI biofilms of strain BR-F. During this study we[D1] have developed an imaging method that allows us to prepare and observe the internal structure (vertical cross-section) of SLI biofilms, as well as the growth of unattached cells, under physiological...
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Autophagy in yeast
Nejedlý, Adam ; Palková, Zdena (advisor) ; Libus, Jiří (referee)
Autophagy is a process of degradation of the cell cytoplasm, proteins, and organelles. It appears mainly as a response to a lack of nutrients or damage of cell structures and components. Yeast Saccharomyces cerevisiae and also Komagataella phapphi are the main model organisms for the research of autophagy. Autophagy is classified by two main criteria. Firstly, we divide autophagy into macroautophagy and microautophagy. During macroautophagy, the phagophore vesicle, called the autophagosome, is created around sequestrated cargo and then fuses with the vacuole. Microautophagy is a process in which a vacuolar membrane directly surrounds and sequester degraded cargo. During non-selective (bulk) autophagy, a random non- specific portion of cytoplasm is degraded. On the other hand, selective autophagy serves as a pathway for the degradation of specific proteins and organelles. Autophagy research has nowadays a great medical significance thanks to the role of autophagy defects in a wide area of human diseases.
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Ammmonium transport in yeast
Faltýnková, Kateřina ; Palková, Zdena (advisor) ; Princová, Jarmila (referee)
Bachelor thesis - Kateřina Faltýnková - Ammmonium transport in yeast Ammonium and ammonia are an essential nutrient for every yeast cells, not only in metabolism, for example in amino acid synthesis, but also as signalling molecules that serve for communication between colonies or for the regulation of pseudohyphal growth. Transport of ammonia and ammonium ions requires active transport, which is provided by MEP permeases inside the cell likely by exporters ATO proteins out of the cell. In this work there are described families of genes MEP and ATO with main focus on their importance for uptake and export of ammonium ions by yeast and also the regulation of these two gene families in the yeast Saccharomyces cerevisiae, Candida albicans, Cryptococcus neoformans a Yarrowia lipolytica.
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Formation of protein granules in differentiated cells of yeast colonies
Kočířová, Eliška ; Palková, Zdena (advisor) ; Heidingsfeld, Olga (referee)
Saccharomyces cerevisiae is a unicellular eukaryotic organism capable of forming organized multicellular communities - colonies and biofilms. During development, colonies of laboratory strains differentiate into specifically localized cell subpopulations - U and L cells, located in the upper and lower part of the colony, respectively. The U and L subpopulations of cells vary in morphology, metabolic processes and stress resistance. Protein granules are membrane-less "organelles" found in both unicellular and multicellular eukaryotic organisms. The formation of protein granules is related to the physiological state of the cell (e.g. chronological and replicative aging), but also to changing environmental conditions and to cellular responses to stress factors. A relatively large fraction of proteins relocalizes to some type of protein granule during the lifespan of the cell. Granule formation can increase fitness of cells, help them to cope with limiting energy resources, and plays a crucial role in the adaptation of cells to stress conditions. Localization of many proteins in the cell varies depending on its physiology. Therefore the specific localization of such proteins may be considered as a "marker" of a specific physiological condition. There are proteins in each type of granule that can be...
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Antagonistic regulation by global transcription factors Tup1p, and Cyc8p of Flo11 and Flo11 -dependent phenotypes in wild yeast
Nguyen Van, Phu ; Palková, Zdena (advisor) ; Heidingsfeld, Olga (referee) ; Malcová, Ivana (referee)
Biofilms are a common mode of yeast growth in which cells adhere to each other and adhere to abiotic surfaces to form complex multicellular structures. Living together in biofilms provides cells with several beneficial features compared to planktonic cells. Undoubtedly, protection and resistance are advantages of life inside colony biofilms. Biofilms are found in many environments and play many important roles in commercial industries. However, biofilms can also be extremely dangerous in clinical settings. There is thus great interest in studying biofilms and how to eliminate them. In this study, we used wild yeast Saccharomyces cerevisiae colony biofilm as an ideal system to investigate potential functions of the yeast Cyc8-Tup1 transcriptional corepressor complex in the regulation of yeast adhesion, and biofilm formation on agar and at solid-liquid interfaces. Unexpectedly, we have found that Cyc8p and Tup1p antagonistically control the formation of structured biofilm colonies on agar and FLO11 expression. Cyc8p itself acts as a key repressor of FLO11, whereas Tup1p promotes the formation of biofilm colonies and induces FLO11 expression by inhibiting the repressive function of Cyc8p and preventing Flo11p degradation possibly by inhibiting an extracellular protease. In addition, other features...
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Chemical signaling among microorganisms
Karásek, Filip ; Palková, Zdena (advisor) ; Převorovský, Martin (referee)
The work summarizes the knowledge about chemical communication among microorganisms, focusing mainly on the quorum sensing phenomenon, but briefly discussing also other molecules with signaling function. The work presents fundamental information on quorum sensing and some other signaling molecules in selected grampositive and gramnegative bacteria and in yeast. It also describes an universal system of communication among different bacteria and briefly mentions communication between bacteria and yeast. Key words: Quorum sesnig, signal molecule, signal pathway, bacteria, yeast, communication
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Regulation of yeast chronological ageing
Fedorová, Viktória ; Palková, Zdena (advisor) ; Malcová, Ivana (referee)
After exhausting the nutrients from medium, yeast cells enter the stacionary phase, in which they adapt their metabolism and physiological functions and undergo chronological ageing characterized by a non-dividing, or only slowly-dividing cell state. This type of ageing is comparable with post-mitotic ageing of cells in higher eukaryotes. Chronologically aged yeast populations form two subpopulations of interdependent cells in liquid cultures as well as in colonies grown on solid media. Chronological ageing is understood as a period of time during which yeast population is able to survive in the stacionary phase, and is regulated by caloric restriction and evolutionary conserved pathways, which respond to various substances, such as carbon or amino acids. Metabolites produced by cellular processes or various chemicals found in the natural environment of these single-celled organisms also have regulatory effects on yeast chronological ageing. Key words: yeast, Saccharomyces cerevisiae, stationary phase, chronological ageing of yeast, cell differentiation, regulatory pathways, metabolites
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