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Prediction of the replication origin in prokaryotic genomes
Lebó, Marko ; Maděránková, Denisa (referee) ; Sedlář, Karel (advisor)
This bachelor’s thesis deals with the problem of origin of replication (oriC) detection in genomes of prokaryotic organisms. It describes the differences in the processes of initiation of replication in organism of the both procaryotic domains – Bacteria and Archea. It describes the possibilities of conversion of DNA sequences into their numeric representaions and evaluates their application for oriC detection. Also, it describes different approaches in oriC detection and describes te functioning of already present programmes for oriC detection. Finally, it suggests a new tool for oriC detection in bacterial genomes – FindOri and discusses results, achieved during the testing of this tool.
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Prokaryotic symbionts of protists living in the intestine of wood eating cockroaches and termites
Kubánková, Aneta ; Hampl, Vladimír (advisor) ; Rotterová, Johana (referee)
Termites and wood-eating cockroaches are worldwide successful especially because of their ability to digest lignocellulose efficiently. After a long period of coevolution a complex ecosystem of diverse microorganisms was established in their hindgut. A lot of lineages of flagellates live solely within this unique environment and it is impossible to cultivate them in vitro. As termites are unable to survive without their eukaryotic endosymbionts, also protists are strongly linked to prokaryotes colonizing their cytoplasm and cytoplasmic membrane. Numerous phyla of bacteria participate in nitrogen fixation and efficient nitrogen utilization, synthesis of amino acids, cofactors and vitamines. Some of them take part in the degradation of lignocellulose. Representatives of another domain of prokaryotes, Archea, are important in the final stages of lignocellulose fermentation, because they utilize the produced hydrogen gas in a process of methanogenesis. Large part of our knowledge about the composition and function of the termite gut biota was acquired thanks to metagenomic studies.
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Prediction of the replication origin in prokaryotic genomes
Lebó, Marko ; Maděránková, Denisa (referee) ; Sedlář, Karel (advisor)
This bachelor’s thesis deals with the problem of origin of replication (oriC) detection in genomes of prokaryotic organisms. It describes the differences in the processes of initiation of replication in organism of the both procaryotic domains – Bacteria and Archea. It describes the possibilities of conversion of DNA sequences into their numeric representaions and evaluates their application for oriC detection. Also, it describes different approaches in oriC detection and describes te functioning of already present programmes for oriC detection. Finally, it suggests a new tool for oriC detection in bacterial genomes – FindOri and discusses results, achieved during the testing of this tool.
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