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Diversity and function of pattern structures in the microworld
Hirnerová, Anna ; Škaloud, Pavel (advisor) ; Němcová, Yvonne (referee)
This thesis summarizes current knowledge of patterns and structures at various scales, with an emphasis on the use of these patterns in the microworld and also on the materials that are most often used. Patterns are applied in all areas of natural processes and human activity. There are many analogous models at different scales, but we do not know if they have the same self-organizing mechanisms. Many patterns formed by microorganisms can be prepared without their presence, on the basis of physical and chemical methods, so they are probably created under certain parameters that can be influenced by a given protist. These patterns are evolutionarily advantageous for microorganisms, because they provide them with a number of functional adaptations, mainly in connection with defense against predators and movement in the water column, which is based on the organism's life strategy. The mathematical description of the pattern is extremely important for its further research and for determining the laws that have allowed the organism to benefit from its parameters. Keywords: pattern, structure, convection, reaction - diffusion model, geometry, protist, microorganism, skeletons, shells, scales
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Sexual reproduction of ochrophyte algae
Procházková, Kateřina ; Eliáš, Marek (advisor) ; Kulichová, Jana (referee)
Sexual reproduction is one of the specific features of eukaryotes. Almost all the knowledge that we have about the sexual process is based on studies conducted on animals and plants. In fact, we know only a tiny fraction of what protist organisms could reveal about distribution and other aspects of the sexual process. For the vast majority of them we miss any evidence that the sexual process actually occurs. However, it is conceivable that the putative protist asexuality is only a human artifact. Likewise, for most ochrophyte algae, which are the main subject of this thesis, the sexual process is unknown. It has been observed only in individuals belonging to six of the sixteen hitherto described classes of Ochrophyta. In some cases, an enviromnental factor that stimulates the formation of gametes was also found. The gradual clarification of the phylogeny that we can expect in the years coming, along with knowledge of biology of ochrophyte algae, can provide more information about sexuality in this group.
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Sexual incompatibility of protist cryptic species
Jelínková, Lucie ; Škaloud, Pavel (advisor) ; Urbánková, Pavla (referee)
The systematic and the evolutionary biology attempt to define a species category or a species taxon from the beginning of their existence. Specific taxons are considered species on the base of different criteria, so on the base of different species concepts. Most of these concepts emerged previous century. The biological species concept has been assumed to be most important species concept for dozens of times. It was based on a presence of the reproduction isolation of two species. However, its applicability was questioned by the existence of many asexual lineages and also the lineages with a large degree of hybridization between an approved species. This thesis is trying to give a description of the biological species concept and its changes during the time. And it is also trying to answer the question of its simultaneous usability for protist.
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The method of DNA barcoding and its use in protists
Rotterová, Johana ; Čepička, Ivan (advisor) ; Fiala, Ivan (referee)
DNA barcoding is a molecular method of species identification based on short regions of DNA sequences. These DNA barcodes should be unique for each species. The sequences within species should be identical or very much alike, while between species they should display a significant amount of differences. The sequences of an undetermined specimen can be compared with sequences vouchered to a particular species in a global DNA barcode database. The database was developed with the aim to simplify traditional taxonomy, eliminate its problems and accelerate its approaches. However, DNA barcoding has its own limitations that may hinder achieving its original goals and a compliance with the concept. The aim of this bachelor thesis consists of explaning the evolution of DNA barcoding through time and assessing the importance of this method at present, particularly in protists. Species identification may be very difficult in many protist groups, which can be explained by several reasons. To appraise this method completely is a hard task, because creation of the database has not yet been finished and official DNA barcodes have not been chosed for many groups. We can only find out in the future, therefore i will only focus on factors that influence the success of DNA barcoding at present.
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Diversity and biogeography of protists
Ryšánek, David ; Škaloud, Pavel (advisor) ; Kulichová, Jana (referee)
My bachelor thesis consists of two parts. The first part is a literature review, the second part is a practical one, which contains the results of my own research. The first part of my thesis is devoted to the literature review, dealing with two current views on biodiversity and biogeography of protists. The first theory, model of protist ubiquity is described in a few points and illustrated by several examples. Likewise is presented the second hypothesis of moderate endemicity model. In conclusion, both models are compared and advantages and disadvantages of each theory are pointed out. In the second part of this thesis I briefly describe the genus Klebsormidium, which is followed by an optimization of molecular methods to study biodiversity and biogeography of this genus.
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Evolution of silica structures in SAR protists
Čížková, Natálie ; Čertnerová, Dora (advisor) ; Kulichová, Jana (referee)
Silicon is an important element in the earth's crust. In nature it mainly occurs in the form of silicic acid. This element is used by marine and freshwater organisms to form their siliceous structures. The organisms that make up these structures are located throughout the phylogenetic tree and are not limited just to protist groups. The SAR line includes Stramenopila, Alveolata and Rhizaria. The main protist taxa forming the mentioned siliceous structures are in these groups. These are mainly diatoms, silicoflagellates, radiolarians and the group chrysophyceae. The formation of siliceous structures usually provides evolutionary benefits to organisms, such as protection of the cell from actions of biotic and abiotic factors. The availability of dissolved silicon changed during evolution, thus affecting the appearance and functionality of the structures of individual species. Structural changes were manifested by thinning of the shells, change of cell size, enlargement or decrease of pores, increase of the number of thorns or, conversely, their loss. The individual lines thus had to choose the best possible strategies in response to the decreasing availability of silicic acid. Therefore, there was frequent competition between the groups for the remaining dissolved silicon. The current diversity of...
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Genome size estimation in protists
Lukeš, Jiří ; Čertnerová, Dora (advisor) ; Veselská, Tereza (referee)
This bachelor's thesis presents the current knowledge of the size of the genome in protists with a focus on the description and comparison of individual methods that were used to solve this issue. Genome size is a characteristic trait of all living organisms and other physiological features related to genome size are also mentioned. Of the selected methods, the greatest emphasis is placed on the flow cytometry, which is considered reliable and currently provides the most data on the size of protist genomes. In addition to flow cytometry, the contribution of whole genome sequencing to understanding the size of protist genomes is mentioned. Problems with estimating the size of protist genomes results from the heterogeneity of protists as a study group and from the non-uniform procedures within individual methods, which make possible comparisons difficult. Protists are evaluated in the work as an insufficiently studied group, within which the size of the genome varies by approximately 200,000×. The conclusion of the thesis summarizes the current knowledge about the genome size of relatively studied groups of protists. Key Words: Genome size, C-value, Protists, Flow cytometry, whole-genome sequencing, pulsed field gel electrophoresis, Feulgen densitometry, microspectrophotometry
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A comparison of metabarcoding and morphology-based identification of protist communities
Tučková, Kateřina ; Škaloud, Pavel (advisor) ; Steinová, Jana (referee)
This thesis is focusing on metabarcoding; its history, principles and current use in science. Metabarcoding brings us a new way to observe a diversity of protists. Although the protists are ubiquitous on the Earth and play a key role in the majority of biological processes, our knowledge of their diversity is still very poor. Traditional microscopy techniques are mostly based on morphology-based identification of taxa. However, they are not so suitable for investigating protist diversity due to their small size, low concentration in the environment, and the convergent morphological evolution of many groups. Similarly, the metabarcoding has its pros and cons, as well. This thesis summarizes pros and cons of both techniques, trying to emphasize the need to both of them to gain a more complete insight into the diversity of protists on the Earth.
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Protein composition of the cytoskeleton of protists
Švagr, Eva ; Hampl, Vladimír (advisor) ; Pánek, Tomáš (referee)
While we have a good understanding of the roles of actin and tubulin filaments in the cell cytoskeleton, intermediate filaments (IFs) are often overlooked. However, the importance of IFs becomes quite apparent, as proteins similar to IF proteins have been identified in many protist cells. This holds particularly for the cells of protists, where even the functions of some members of the of actin and tubulin superfamilies remain unclear. Intermediate filaments are still not well established as components of protist cytoskeletons, in contrast to their more thoroughly studied counterparts in Metazoa. Protist and metazoan IF proteins are dissimilar in their sequence; however, they share similarities in structure, and they assemble autonomously into analogous filaments. IF-like proteins have been localized to striated fibers or unique cytoskeletal components in several organisms, even though not much is known about the protein composition of these striated fibers to date. This suggests that IF-like proteins might be a universally present component of these striated fibers often seen in protist cells. Keywords: Protists, cytoskeleton, microtubules, microfilaments, intermediate filaments, fibrils, protein composition
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