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Integer programming and its applications
Eliáš, Marek ; Pergel, Martin (advisor) ; Hladík, Milan (referee)
In this thesis we present and implement several graph algorithms. In the rst part, we discus algorithm for the minimum weighted perfect matching in bipartite and general graphs based on the primal-dual method and their modi cations. In the second part, there are algorithms for the max-cut in planar graphs and Christo des' heuristic for TSP. We present full descriptions of these algorithms providing either proof of correctness or reference to the literature. The last part deals with two approaches which we use to visualise these algorithms with di erent degree of interactivity both allowing custom graph on input.
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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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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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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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DC to DC inverter for backup power supplies
Eliáš, Marek ; Zemánek, Miroslav (referee) ; Boušek, Jaroslav (advisor)
This thesis deals with the design of a DC/DC converter designed for charging supercapacitors from the 36 V voltage source and consequent back transformation of supercapacitors voltage to the required output voltage. In the thesis the designs of decreasing and increasing DC/DC converters including schematics and calculations of individual components are presented and described. The calculations necessary for the supercapacitors to meet the 10Wh energy condition and the voltage balancer on the capacitors are given below. Completely designed equipment will be assembled and tested on supercapacitors with lower energy.
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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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