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Characterization of selected RAB GTPase activating protein (RAB GAP) of Arabidopsis thaliana
Metlička, Jáchym ; Hála, Michal (advisor) ; Eliáš, Marek (referee)
8 ABSTRACT Rab GTPases (Rabs) are the most populous branch of eukaryotic Ras GTPase superfamily. In active GTP-binding conformation, they serve as key instruments in defining transient membrane identity and through various effectors regulate formation, transport, conversion, and fusion of membrane vesicles. This is important for upkeep of compartmentalized structure of eukaryotic cells and for facilitating both endo- and exocytic processes. Rabs are converted into GDP-binding conformation by interactions with Rab GTPase activating proteins (Rab GAPs) that possess ability to significantly speed up weak intrinsic GTP hydrolytic activity of Rabs. Through this process, Rab GAPs can limit scope of the Rabs' activity and lay out spatiotemporal boundaries for varying Rab populations. In this thesis, I tried to characterize a Rab GAP, GAP2, seemingly necessary for standard development of thale cress plants. Besides TBC catalytic domain, GAP2 (product of At2g39280 gene) possesses a C-terminal coiled-coil motif, which was previously found to interact with Rab GTPases. Experiments aiming to complement T-DNA insertion mutant in GAP2, elucidate GAP2 intracellular localization, novel interacting partners, and character of interaction with the Rabs discovered in the pilot study were undertaken. The results suggest that...
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Mitochondrion of oxymonads
Vacek, Vojtěch ; Hampl, Vladimír (advisor) ; Eliáš, Marek (referee)
Oxymonads are among the last larger eukaryotic groups in which mitochondrion-like organelles were not detected. Among almost one million transcriptome sequences of oxymonad Monocercomonoides we found sequences for only three proteins commonly associated with mitochondrion-like organelles - pyruvate:ferredoxin oxidoreductase (PFO), [FeFe]hydrogenase and pyridine:nucleotide transhydrogenase (PNT). Out of these tree proteins PNT is most closely associated with mitochondrion-like organelles. Although the transcriptome data set is quite large we did not detect any other mitochondrial proteins including proteins for synthesis of FeS clusters and proteins associated with mitochondrial protein import. In the phylogenetic tree, PNT from Monocercomonoides formed a clade with sequences of other eukaryotes. This suggests that PNT of Monocercomonoides is likely of mitochondrial origin; however, the possibility that Monocercomonoides acquired PNT by lateral gene transfer cannot be excluded. We tried to localize PNT in the cell of Monocercomonoides by immunofluorescent microscopy but the results were difficult to interpret. We could not prove the presence of mitochondrion-like organelle in Monocercomonoides. If there is any such organelle, it is highly probable that this organelle is very reduced because we did not find...
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Reductive Evolution of Mitochondria - Related Organelles in Anaerobic Protist
Rada, Petr ; Tachezy, Jan (advisor) ; Embley, Martin (referee) ; Eliáš, Marek (referee)
Charles University in Prague, Faculty of Science Department of Parasitology Ph.D. study program: Parasitology Abstract of the Ph.D. Thesis Reductive Evolution of Mitochondria - Related Organelles in Anaerobic Protist Petr Rada Supervisor: Prof. RNDr. Jan Tachezy,Ph.D. Advisor: Doc. RNDr. Ivan Hrdý, Ph.D. Praha, 2011 1 ABSTRACT Trichomonas vaginalis and Giardia intestinalis are parasitic protists of the Excavata group. Both contain anaerobic forms of mitochondria called hydrogenosomes (Trichomonas) and mitosomes (Giardia). Hydrogenosomes produce hydrogen and ATP by substarte level phosphorylation and mitosomes represent the highly-reduced form of mitochondria that do not participate in cellular energy metabolism and ATP generation. Both types of organelles lost the majority of mitochondrial pathways and their genomes during the mitochondrion to hydrogenosome transition. Consequently, hydrogenosomes and mitosomes facilitate translocation of nuclearly encoded proteins into the matrix of the organelle as well as exchange of metabolites and ions across their membranes. Little is known about the membrane machineries required for the biogenesis of the organelle and metabolite exchange and the limited knowledge of mitosomal proteomes has been mostly gained from genomic analysis and localization studies of a few...
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Diversity and species concept of the Vischeria/Eustigmatos complex (Eustigmatophyceae)
Procházková, Kateřina ; Eliáš, Marek (advisor) ; Oborník, Miroslav (referee)
Vischeria and Eustigmatos are closely related genera occurring in terrestrial habitats. These genera were distinguished by the differences in the features of the cell wall (projections and ridges of different form, smooth surface respectively). Up to date three species of the genus Eustigmatos and twelve species of the genus Vischeria have been described, but nine of the Vischeria species have been rarely, if ever, observed since the original description. This work is focused on evaluating molecular variability, diversity, and taxonomy of the Vischeria/Eustigmatos complex. Ninety seven strains, obtained from public algal collections or newly isolated from localities from all over the world, were studied, including the type strains of two Eustigmatos species and three Vischeria species. Phylogenetic analyses of the ITS2 rDNA and rbcL sequences showed that these genera are not genetically separated. The five types strains each represented a separate evolutionary lineage. Some of the additional lineages included strains morphologically corresponding to the species Eustigmatos magnus. Some of the newly isolated strains are according to the markers examined genetically indistinguishable from known strains from public algal collections. However, some of them are new lineages. Only one of the phylogenetic...
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Erdos-Szekeres type theorems
Eliáš, Marek ; Matoušek, Jiří (advisor) ; Cibulka, Josef (referee)
Let P = (p1, p2, . . . , pN ) be a sequence of points in the plane, where pi = (xi, yi) and x1 < x2 < · · · < xN . A famous 1935 Erdős-Szekeres theorem asserts that every such P contains a monotone subsequence S of √ N points. Another, equally famous theorem from the same paper implies that every such P contains a convex or concave subsequence of Ω(log N) points. First we define a (k + 1)-tuple K ⊆ P to be positive if it lies on the graph of a function whose kth derivative is everywhere nonnegative, and similarly for a negative (k + 1)-tuple. Then we say that S ⊆ P is kth-order monotone if its (k + 1)- tuples are all positive or all negative. In this thesis we investigate quantitative bound for the corresponding Ramsey-type result. We obtain an Ω(log(k−1) N) lower bound ((k − 1)-times iterated logarithm). We also improve bounds for related problems: Order types and One-sided sets of hyperplanes. 1
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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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Cyanobacteria associated with biofilms of tufa stromatolites in the German creek Westerhöfer
Hodačová, Alena ; Eliáš, Marek (advisor) ; Řeháková, Klára (referee)
This diploma thesis is focused on cyanobacteria which occur in the biofilm of the tufa stromatolite covering the ground of Westerhöfer creek in Lower Saxony in Germany. A study of this creek has already been written (ARP ET AL., 2010) but only for one sampling site (WB 5), with six unidentified phylotypes of nine obtained as the result of that study. One of the aims of my diploma thesis is to identify at least some of them, and to show other groups occurring there. The results of my diploma thesis are divided into two parts. Part One - the morphology of isolates obtained from raw cultures of all sampling sites in the creek. Part Two - a phylogenetical study of 16S rDNA of the isolates and the sequences obtained by cloning of environmental 16S rDNA. The clones were obtained from Kathrin I. Mohr (who worked on the same project in the EPSAG laboratory and who did the cloning immediately after sampling). I also did cloning, but after 2.5 months of cultivation. In the morphological part, I identified 11 morphotypes, corresponding to established genera Aphanothece, Synechococcus, Cyanothece/Gloeothece, Leptolyngbya, Pseudanabaena, Limnothrix, Plectonema, Phormidium, Tolypothrix, and Nostoc. Two of isolates could not be assigned to any morphotype. It is isolate AH 5 and isolate AH 35. In the phylogenetical part I...
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