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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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Applications of CRISPR-Cas9 for genetic engineering in parasitic protists
Ročeň, Milan ; Tachezy, Jan (advisor) ; Rada, Petr (referee)
The CRISPR / Cas system serves as a cellular defense mechanism that protects bacteria and archaea from foreign DNA, especially bacteriophages. Its product forms a ribonucleoprotein complex, whose components are sgRNA and Cas endonucleases. Using sgRNAs, which are complementary to foreign DNA, this complex recognizes the DNA and Cas endonucleases induce double-strand breaks. This method is applied both in primary research, where it is applicable for functional analysis of proteins and the study of gene expression, as well as in applied research, where it can apply, for example, in the production of genetically modified organisms or genetically attenuated vaccines. This work summarizes the current knowledge of the CRISPR / Cas system and its application for gene manipulation in parasitic protists.
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Influence of competition to structure of protist communities
Škvorová, Marie ; Bestová, Helena (advisor) ; Svoboda, Pavel (referee)
This work deals with competition as well as mechanisms of coexistence of species. The introduction presents comtemporary coexistence theory. There are two types of differences - niche and relative fitness differences. Fitness differences increase inter-species competition. This is a novell result, current theory expected differences decrease competition in any case. This work summarized results of experimental works that have investigated various aspects of co- existence theory, with special focus on protists. Competition was found to be an important mechanism in creating patterns of community assembly, unfortunately drawing common results is complicated. According to competition-relatedness hypotheses, within some competition lines competition decreased with relatedness. This relation however does not hold always. There are two conditions: functional traits must bear a phylogenetic signal and must be evolutionally conserved. Studies on protists imply that higher number of species should be included instead of pairwise combination tests in order to get valid information on relation of species. This could be similar for traits. Plants experiments have shown that competition may be affected by traits only in complex systems with a number of traits included. Such experiment involving protists have...
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Practical Exercises in Biology of Unicellular Organisms (Protista) for Elementary Schools with Emphasis on the Use of Staining Techniques
Šalounová, Jana ; Mourek, Jan (advisor) ; Říhová, Dagmar (referee)
4 Abstract The main goal of my thesis was to create our own proposals for laboratory work in biology of unicellular organisms (Protista). I designed the laboratory tasks, so that they can be mastered by the pupils of sixth year of primary school. Creating the proposals for laboratory exercises was preceded by the work in the laboratory at Charles University in Prague, Faculty of Education, the Department of Biology and Environmental Studies. In the laboratory, I verified the methods of cultivation of selected representatives of ciliates (Paramecium caudatum), amoebae (Amoeba proteus) and euglenids (Euglena gracilis) and selected methods of dyeing their different organels. Key words: protists, Paramecium caudatum, Amoeba proteus, Euglena gracilis, cultivation, dying
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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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Protein import into mitochondria and peroxisomes of parasitic protists
Žárský, Vojtěch ; Tachezy, Jan (advisor) ; Hampl, Vladimír (referee)
The presented thesis includes three related projects, that are linked by a common interest in the evolution of eukaryotic organelles and machineries that import proteins into these compartments. The first project considers the possibility of peroxisomes (eukaryotic organelles known in aerobic organisms) being conserved in two related anaerobic protists: a free-living amoeba Mastigamoeba balamuthi and a parasite Entamoeba histolytica. The most important hint for the presence of peroxisomes was the discovery of proteins that are homologous to known components of the peroxisomal protein import machinery. The second project aims to characterize the unknown protein translocase of the inner membrane (TIM) in the mitosomes (extremely reduced mitochondria) of an anaerobic protozoan Giardia intestinalis. We have discovered an important subunit of the mitosomal translocase (Tim44), which usually tethers the Hsp70/PAM (presequence translocase-associated motor) complex to the TIM translocon. The last project shows that the protein translocase of the outer mitochondrial membrane in trypanosomatids is related to a typical eukaryotic channel Tom40. This finding is important because the absence of Tom40 was previously considered an ancestral feature of trypanosomatids.
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Seasonal dynamics and diversity of protist organisms in peat bog microhabitats.
Mutinová, Petra ; Kulichová, Jana (advisor) ; Šťastný, Jan (referee)
This bachelor thesis summarizes the literature dealing with diversity of protist organisms in peatlands. First part presents brief general characteristics of peatlands for the acquisition of basic knowledge about this ecosystem. Further, this work concerns closely with spatial dynamics of protists in peatlands, with emphasis on microbiotops. The final part reviews available information on seasonal dynamics of protist organisms in peatlands and also on the factors that have an influence on seasonality. This work concludes that the community of protist organisms in peatlands is different from those observed in other ecosystems. The composition of the community of protists in peatlands is very heterogeneous, because it depends on the type of microbiotop and prevailing physicochemical conditions. The communities of protist organisms are subject to seasonal dynamics as well. Nonetheless, this issue is largely unexplored so far, because there are substantially less recent studies concerning peatlands than for example other aquatic ecosystems that are frequently used for water quality monitoring.
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Communities of protists and invertebrate animals in freshwater aquaria and possibilities of their use in teaching
Hásková, Barbora ; Mourek, Jan (advisor) ; Hanel, Lubomír (referee)
This bachelor thesis focuses on the hidden but very diverse community of protists and microscopic invertebrates in freshwater aquaria. Samples of these micro-organisms were obtained from microscopic slides submerged in aquaria for several weeks. The main output of this thesis is a multimedia didactical atlas of characteristic protists and invertebrates inhabiting freshwater aquaria. In total, eleven members from two phyla of protists and six phyla of invertebrate animals are presented using own original micrographs and short videosequences. The atlas was prepared in two forms - a text document and a web page. Potential of the atlas for use in biology teaching and extracurricular education is discussed. Key words: zoology, protists, invertebrates, teaching, didactics, communities
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Diversity and biogeography of protists
Ryšánek, David ; Kulichová, Jana (referee) ; Škaloud, Pavel (advisor)
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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