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Bioinformatic analysis of PHA synthases of thermophilic bacteria
Brondová, Zuzana ; Brázda, Václav (referee) ; Obruča, Stanislav (advisor)
The thesis deals with bioinformatics analysis, the aim of which was to find a suitable producer of PHA for new generation industrial biotechnologies from the collection of found thermophilic bacteria. Part of experiments was the finding of several thermophilic bacteria based on the similarity of the protein sequence of the phaC gene of the bacterium Cupriavidus necator. The next part of thesis was a literature search of the abilities of these thermophilic bacteria focused on culture conditions and the spectrum of usable substrates. Subsequently, five bacteria were selected for use in NGBI based on the information obtained. Freely available databases were used during the experimental work, and evolutionary analysis were performed in MEGA X and Operon-mapper. Rubrobacter xylanophilus with collection number DSM 9941 was selected from the collection of bacterial strains as the most promising PHA producer for NGIB. The high culture temperature of up to 70 ° C and a large amount of utilized carbohydrate substrates were considered decisive. An interesting result of the analysis was to find the gene sequences of two classes of PHA synthase – I. and III. class, as for a single bacterial strain from the entire collection. Additional genes linked to PHA metabolism were found in genome analysis.
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The impact of cannabidiol consumption on oral microbiome composition
Richweissová, Viktória ; Bartoň, Vojtěch (referee) ; Čejková, Darina (advisor)
The composition of oral microbiome plays a significant role in maintaining both oral, and overall systemic health. When in equilibrium, the oral microbiome maintains the oral cavity in health. However, certain ecological shifts in the microbiota allow pathogens to manifest and cause various oral and systemic diseases. The analysis of the oral microbiome makes it possible to define the role of its components in health and disease, and the effect of various therapeutic techniques on its composition. This bachelor's thesis investigates the possible effect of toothpaste with cannabidiol on oral microbiome. The aim of this work is the bioinformatics analysis of oral microbiome communities before and after using CBD toothpaste using pipeline QIIME 2.
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Isolation and detection of DNA from plant species important for food prodution
Orel, Matúš ; Rittich, Bohuslav (referee) ; Kovařík, Aleš (advisor)
In the food industry, it is very important to take care of the quality, safety and organoleptic properties of the products supplied. For this reason, food must be checked. However, not all information can be found using conventional techniques such as immunoassays, chromatographic techniques, etc. DNA-based techniques can be used for these cases where traditional procedures are insufficient. Among them, the best known technique is PCR. The aim of the thesis was to isolate DNA from vegetable samples (broccoli, beetroot, carrot and pepper). DNA was isolated using the magnetic particle method and the traditional CTAB method. Both methods were able to isolate the DNA from the vegetable samples in quality and at a concentration suitable for PCR, where the 35S rDNA gene region was amplified (more precisely about 700 bp of the 18S-ITS1-5,8S region). After amplification, the PCR products were subjected to restriction reactions and the results compared to bioinformatic analysis. These steps have succeeded in finding suitable enzymes for diferentiation of PCR products from the tested vegetable species.
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Analysis of local structures in DNA molecules
Nyczová, Adéla ; Smetana, Jan (referee) ; Brázda, Václav (advisor)
Local DNA structures are alternative DNA conformations which can be formed aside from typical B-DNA conformation. These structures often play pivotal roles in regulation of basic biological processes, such as DNA replication, transcription or binding of specific ligands. This biological significance makes alternative DNA secondary structures a potential drug target. In this diploma thesis, local structures in genomes of viruses from Flaviviridae and Retroviridae families are analysed using bioinformatics tools. Furthermore, these structures are visualised using atomic force microscopy.
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Presence and localization of local DNA structures in papillomavirus genomes
Vyoralová, Andrea ; Kollerová, Silvia (referee) ; Brázda, Václav (advisor)
Papillomaviruses are sexually transmitted pathogens with a genome length of about 8 kbp. The probability that an adult person will suffer from a papillomavirus infection is up to 80–90%. In most cases, the immune system will eliminate the infection. However, in women it can lead to the development of cervical cancer. That is caused by the high-risk human papillomaviruses, against which vaccination is available. Sequences rich in guanine have been found in the genomes of papillomaviruses, in these sequences the formation of G-quadruplexes occur. They are formed by stacked G-tetrads and are stabilized by monovalent cations, most often K+ and Na+. They are found e.g. in telomeres, oncogene promoters, transcription factor binding sites and recombination sites. Inverted repeats (IR) are also found in the genomes of these viruses. They consist of sequences of nucleotides followed by its reverse complement. Inverted repeats are being referred to as hotspots of genomic instability because they fold into hairpin or cruciform structures that disrupt DNA replication. G4Hunter and Palindrome analyzer were used to analyze the genomes. The analysis revealed that the presence of PQS (Potential Quadruplex-forming Sequence) is higher in papillomaviruses infecting vertebrates than in viruses infecting humans due to the higher content of guanine and cytosine which are connected to the formation of PQS. A higher frequency of PQS presence was found in the genomes of papillomaviruses than in Archaea, Bacteria and Homo sapiens. IR analysis showed that the shortest IRs (6 bases) are the mostly present in the genome and also that IRs formed of 25–30 bases are found in only a few genomes.
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Transcriptomic analysis of Mesocestoides corti
Korená, Lucie ; Leontovyč, Roman (advisor) ; Převorovský, Martin (referee)
Some species of parasites, including helminths, can inhibit carcinogenesis in their hosts. The antitumoral effect has been discovered in the tapeworms Taenia crassiceps and Echinococcus granulosus, which genes associated with cancer regression have been identified. The effect of melanoma suppression has also been observed in tapeworm Mesocestoides corti by the Laboratory of Helminthology, Department of Parasitology, Faculty of Science, Charles University, however the mechanism-of-action, remains unknown. For the upcoming research it was essential to have the complex molecular data such as transcriptome of the developmental stage s of M. corti. This work is focused on the transcriptomic profiling of the tapeworm M. corti and the differential gene expression in two different strains of murine hosts (inbred and outbred) using the RNA-Seq. The main goal was to identify upregulated transcripts in the tapeworms from the murine hosts that could have a potential effect on cancer regression. Differential gene expression analysis was performed, and the results showed that tapeworms in murine hosts (regardless of strain) had more upregulated transcripts than tapeworms cultured in vitro. Analysis of highly upregulated transcripts in the tapeworms that were grown in the murine hosts identified several...
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The impact of cannabidiol consumption on oral microbiome composition
Richweissová, Viktória ; Bartoň, Vojtěch (referee) ; Čejková, Darina (advisor)
The composition of oral microbiome plays a significant role in maintaining both oral, and overall systemic health. When in equilibrium, the oral microbiome maintains the oral cavity in health. However, certain ecological shifts in the microbiota allow pathogens to manifest and cause various oral and systemic diseases. The analysis of the oral microbiome makes it possible to define the role of its components in health and disease, and the effect of various therapeutic techniques on its composition. This bachelor's thesis investigates the possible effect of toothpaste with cannabidiol on oral microbiome. The aim of this work is the bioinformatics analysis of oral microbiome communities before and after using CBD toothpaste using pipeline QIIME 2.
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Analysis of quantitative and qualitative genetic features in the pathogenesis of hereditary solid tumors.
Zemánková, Petra ; Kleibl, Zdeněk (advisor) ; Živný, Jan (referee) ; Tichý, Boris (referee)
Cancer the second most common causes of death in the Czech Republic. Carriers of mutations in genes predisposing to hereditary cancers represent a small but clinically significant group of high risk individuals. Today, dozens of predisposing genes for hereditary tumor syndromes are known and targeted next generation sequencing (NGS) has become a standard approach for their analysis. NGS allows rapid acceleration diagnostics of causal mutation in high-risk individuals. To identify mutations in genes predisposing to hereditary cancers, we designed a panel NGS analysis including subsequent bioinformatics analysis allowing a reliable identification of single nucleotide variants, insertions/deletions, and large intragenic rearrangements. The bioinformatics procedures described in this thesis were used for panel NGS validation, but also for identification of alterations associating with so far undescribed hereditary tumor types. Bioinformatics analyzes have become the basis for the unified processing of large datasets from the CZECANCA consortium and enable the construction of a population-specific database of genotypes that serve to improve clinical diagnostics of cancer predisposition in Czech patients. The versatility of NGS also allows its use for RNA (cDNA-based) analyzes of splicing variants in the...
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Bioinformatic analysis of PHA synthases of thermophilic bacteria
Brondová, Zuzana ; Brázda, Václav (referee) ; Obruča, Stanislav (advisor)
The thesis deals with bioinformatics analysis, the aim of which was to find a suitable producer of PHA for new generation industrial biotechnologies from the collection of found thermophilic bacteria. Part of experiments was the finding of several thermophilic bacteria based on the similarity of the protein sequence of the phaC gene of the bacterium Cupriavidus necator. The next part of thesis was a literature search of the abilities of these thermophilic bacteria focused on culture conditions and the spectrum of usable substrates. Subsequently, five bacteria were selected for use in NGBI based on the information obtained. Freely available databases were used during the experimental work, and evolutionary analysis were performed in MEGA X and Operon-mapper. Rubrobacter xylanophilus with collection number DSM 9941 was selected from the collection of bacterial strains as the most promising PHA producer for NGIB. The high culture temperature of up to 70 ° C and a large amount of utilized carbohydrate substrates were considered decisive. An interesting result of the analysis was to find the gene sequences of two classes of PHA synthase – I. and III. class, as for a single bacterial strain from the entire collection. Additional genes linked to PHA metabolism were found in genome analysis.
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Analysis of local structures in DNA molecules
Nyczová, Adéla ; Smetana, Jan (referee) ; Brázda, Václav (advisor)
Local DNA structures are alternative DNA conformations which can be formed aside from typical B-DNA conformation. These structures often play pivotal roles in regulation of basic biological processes, such as DNA replication, transcription or binding of specific ligands. This biological significance makes alternative DNA secondary structures a potential drug target. In this diploma thesis, local structures in genomes of viruses from Flaviviridae and Retroviridae families are analysed using bioinformatics tools. Furthermore, these structures are visualised using atomic force microscopy.
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