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Regulation of cell cycle in Bacillus subtilis.
Zelenka, Tomáš ; Lichá, Irena (advisor) ; Harant, Karel (referee)
2 Abstract Relations between several events running in bacterial cell during cell cycle were the subject of many studies during last years. More advanced techniques showed, that bacterial cell life has much more variable factors, than we supposed before. Relatively recent researches managed to reveal function and in few events molecular principle of several mechanisms coordinating those events such as progression of replication and its initiation, segregation of newly replicated chromosomes and after all synchronization of complex cell division machinery. Furthermore it showed variability of those events during changing living conditions of the cell. Keywords: Cell cycle, regulation, initiation, replication, segregation of chromosome, cytokinesis, Bacillus subtilis
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Pyrosequencing analysis of fungal assemblages and the effect of ITS rDNA intragenomic variation on diversity estimates
Zelenka, Tomáš ; Kolařík, Miroslav (advisor) ; Větrovský, Tomáš (referee)
The ITS region of nuclear ribosomal DNA has recently become a frequently studied region for its use as a barcode marker. It is employed in environmental metagenomic analyses, the determination of fungi and in studies of fungal phylogenetics. In genomes, rDNA occurs in the form of large multicopy tandem arrays. Thus common Sanger sequencing leads to a consensus of many copies which in fact conceals most of the potential intragenomic variation. However 454 pyrosequencing reveals the sequence of single copies. Although it is believed that most of the variation among copies is reduced during a process called concerted evolution, some variation might still be conserved, including variation of non-functional pseudogenes. As a consequence, when using 454 pyrosequencing, we are not able to discriminate between this variation and real diversity. This could have a huge impact on the estimation of real diversity as well as on the correct assessment of pyrosequence studies. This thesis reviews current knowledge of intragenomic variation among fungi and summarizes some papers applying pyrosequencing in the research of fungal diversity. At the same time it indicates intragenomic variation as a potential cause of untrue diversity in diversity studies. Up until now there hasn't existed any experimental survey covering...
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Energy passive kindergarten
Zelenka, Tomáš ; Kalánek, Jiří (referee) ; Ostrý, Milan (advisor)
The subject of the diploma thesis is a design of a kindergarten in a passive standard standing on a plot situated in the center of Fulnek. The building has two floors and the first floor is embedded in the terrain. The vertical load-bearing structures consist of sand-lime masonry with a contact thermal insulation system. The building is based on foundation strips due to the type of subsoil. The roofing is then solved by a single-layer flat roof with a vegetation layer.
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Dwelling house Kociánka
Zelenka, Tomáš ; Kalánek, Jiří (referee) ; Ostrý, Milan (advisor)
The subject of the bachelor thesis is the design of an apartment house with eight flats standing alone on the plot, which is situated in the brno-sadová district. The building is five-storey, with one underground floor with garages and four above-ground floors. The vertical load-bearing structures are sand-lime masonry fitted with a contact heating system. The object is based on CFA piled and base plate relative to the subsoil type. Roofing is then solved by a double-skinned flat roof with a ventilated air gap
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Identification and activation of a cryptic biosynthetic gene cluster for manumycin-type metabolites in Saccharothrix espanaensis DSM44229
Zelenka, Tomáš ; Petříčková, Kateřina (advisor) ; Beranová, Jana (referee)
1 Abstract: Secondary metabolism of Gram-positive soil bacteria from the genus Streptomyces is a inestimable source of natural products including manumycins, which belong to a polyketide group. These products possess weak antimicrobial, but important antiinflammatory, and antitumor activities. Streptomyces sp. offers broad amounts of yet undiscovered antibiotics, potentially utilizable in clinical medicine. This fact makes out of these organisms a promising solution to our present problem with rising antibiotic resistance among microorganisms. Two main ways are applied in this research: There are efforts of prepairing new derivates based on known products and creating various modifications in their structure. Next, new producers are discovered by "genome mining" methods, activation of silent gene clusters, followed by improvements of antibiotic production. One of those silent clusters was found in the Saccharothrix espanaensis DSM44229 strain. The genetic information has been transferred to a heterologous host in order to characterize its product. Cluster activation and production of novel manumycin-type metabolites occurred in the host after the transfer.
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Pyrosequencing analysis of fungal assemblages and the effect of ITS rDNA intragenomic variation on diversity estimates
Zelenka, Tomáš ; Kolařík, Miroslav (advisor) ; Větrovský, Tomáš (referee)
The ITS region of nuclear ribosomal DNA has recently become a frequently studied region for its use as a barcode marker. It is employed in environmental metagenomic analyses, the determination of fungi and in studies of fungal phylogenetics. In genomes, rDNA occurs in the form of large multicopy tandem arrays. Thus common Sanger sequencing leads to a consensus of many copies which in fact conceals most of the potential intragenomic variation. However 454 pyrosequencing reveals the sequence of single copies. Although it is believed that most of the variation among copies is reduced during a process called concerted evolution, some variation might still be conserved, including variation of non-functional pseudogenes. As a consequence, when using 454 pyrosequencing, we are not able to discriminate between this variation and real diversity. This could have a huge impact on the estimation of real diversity as well as on the correct assessment of pyrosequence studies. This thesis reviews current knowledge of intragenomic variation among fungi and summarizes some papers applying pyrosequencing in the research of fungal diversity. At the same time it indicates intragenomic variation as a potential cause of untrue diversity in diversity studies. Up until now there hasn't existed any experimental survey covering...
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Regulation of cell cycle in Bacillus subtilis.
Zelenka, Tomáš ; Lichá, Irena (advisor) ; Harant, Karel (referee)
2 Abstract Relations between several events running in bacterial cell during cell cycle were the subject of many studies during last years. More advanced techniques showed, that bacterial cell life has much more variable factors, than we supposed before. Relatively recent researches managed to reveal function and in few events molecular principle of several mechanisms coordinating those events such as progression of replication and its initiation, segregation of newly replicated chromosomes and after all synchronization of complex cell division machinery. Furthermore it showed variability of those events during changing living conditions of the cell. Keywords: Cell cycle, regulation, initiation, replication, segregation of chromosome, cytokinesis, Bacillus subtilis
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Comparison of ITS nrDNA and alternative markers for fungal metabarcoding in environmental samples
Zelenka, Tomáš ; Kolařík, Miroslav (advisor) ; Mašek, Tomáš (referee)
The study of fungal diversity may lead to many fundamental discoveries and conclusions. Molecular genetics, and particularly high throughput sequencing methods using short DNA fragments as barcodes, has recently experienced a boom. The most frequently used marker for fungal research is the partial region of nuclear ribosomal DNA called ITS (Internal Transcribed Spacer). It occurs in the form of tandem repetitions of up to 200 copies. This fact greatly simplifies its amplification from the environment but also introduces some negatives. One of them can be an existence of intragenomic and intraspecific variability which confounds diversity estimates by exaggerating the real number of species. Using alternative low-copy markers can easily prevent these problems. In this study EF-1α and RPB2 protein- coding genes were compared with traditionally used ITS1 and ITS2 markers. An artificial mock community was created by blending genomic DNA of different fungal lineages. The community was sequenced for all markers and the data were processed according to guidelines commonly used in environmental studies. The results show that ITS2 is unequivocally a more suitable marker for environmental studies than other compared markers. The average coefficient of overestimation was deemed to be approximately two for ITS1, ITS2,...
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