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Analysis of C. necator genome changes after evolutionary adaptation
Vojsovič, Matúš ; Šedrlová, Zuzana (referee) ; Brázda, Václav (advisor)
The p53 protein is a transcription factor that belongs to the group of the tumour suppressor proteins. p53 functions include cell cycle regulation, interaction with DNA, and responses to damaged DNA that may lead to apoptosis or even senescence may occur. The theoretical part summarizes the latest information about the chemical structure and functions of the protein p53 and allosteric modifications that the p53 protein may possess in cells. It also describes selected methods of isolation and characterizes proteins. The aim of the experimental part was to isolate and characterize -isoforms of the p53 protein, which were isolated from the microorganism E.coli. Protein production was preceded by preparation and transformation of plasmids into production cells. From the production cells, 4 -isoforms of p53 were isolated by affinity chromatography, due to the polyhistidine anchor that the proteins contain. The isolated proteins were subsequently characterized by SDS-PAGE and western blotting. Moreover, the transactivation potential in the yeast system was monitored by luciferase assay under conditions involving the use of various culture media, as well as expressed or coexpressed under the inducible GAL1 promoter and the constitutive GPD promoter.
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Molecular characterization of selected PHA producers
Kubáčková, Eliška ; Brázda, Václav (referee) ; Obruča, Stanislav (advisor)
This diploma thesis focuses on the molecular characterization of selected PHA producers. Within this work, the PHA producing thermophilic isolates originating from the samples of activated sludge and compost were identified and characterized using molecular biological methods. By sequencing the 16S rRNA gene, the thermophilic isolates were identified and taxonomically classified into the Firmicutes bacterial phylum. In these bacterial isolates, the ability to produce PHA at the genotype level was determined by conventional PCR detection of the phaC gene encoding PHA synthase, which is a key enzyme in PHA biosynthesis. Class I, II and IV PHA synthases were detected in most of the isolated bacteria, wherein class I and II PHA synthases are not characteristic for these bacterial genera. The largest proportion of isolates was identified for the species of thermophilic bacterium Aneurinibacillus thermoaerophilus, in which class IV PHA synthase was detected. In the second part of the diploma thesis, the RT-qPCR method was implemented to study the expression of selected genes of the bacterium Cupriavidus necator H16 involved in PHA metabolism. As part of the implementation of this method, PCR-based detection of selected genes was optimized and quantification of genes using real-time PCR was performed. The tested method included steps of RNA isolation, cDNA synthesis and quantification of gene segments for which the critical points of the method were determined based on the obtained data.
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Optimization of p53 mutant protein isolation and its DNA binding properties
Osadchuk, Olha ; Zemanová, Jana (referee) ; Brázda, Václav (advisor)
Protein p53 je jednou z nejdůležitějších molekul v lidském těle. P53 reguluje celou řadu procesů v buňce, jako je například oprava DNA, buněčný cyklus nebo indukce apoptózy. Protein p53 je známý i jako „strážce genomu“. DNA vazebné schopnosti proteinu p53 jsou důležité pro normální vývoj a růst buňky. Mutace genu pro p53 mohou vést ke ztrátě jeho DNA vazebných vlastností a funkce nádorového supresoru, což muže způsobit rozvoj rakoviny. Teoretická část této diplomové práce je zaměřena na popis vlastností, funkce a mechanismus aktivace proteinu p53 a popis lokálních sekundárních struktur DNA. Hlavním cílem experimentální části byla produkce čtyř mutantních forem proteinů p53 a wild-type p53 proteinu a studium jejich vazebných vlastnosti s různými lokálními sekundárními strukturami DNA. Pomoci Gateway klonovacího systému byly připraveny čtyři expresní vektory, které byly použity pro produkci proteinů v bakteriálním expresním systému. Celkem byly úspěšně připraveny čtyři mutantní formy a wild-type p53 protein. Jejich vazebné vlastnosti byly studovány gelovou retardační analýzu. Výsledky naznačují různé DNA-vazebné vlastnosti wild-type p53 a studovaných mutantních forem tohoto proteinu. Všechny mutantní proteiny ztratily schopnost sekvenčně specificky vázat DNA, zatímco nespecifická interakce s DNA byla pozorována u tří ze čtyř mutantních forem. Jeden ze studovaných mutantních proteinů se vázal jenom na superhelikální formu DNA.
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DNA Isolation and Analysis Focused on Microorganisms Important in Food Production
Čutová, Michaela ; Obruča, Stanislav (referee) ; Fojtová,, Miloslava (referee) ; Brázda, Václav (advisor)
Identification of bacterial DNA consists from several steps: cell lysis, isolation and purification of DNA, precipitation by ethanol, identification of bacterial strain by PCR or other molecular biology methods. Each step must be optimised. Nucleic acids can be isolated from cells using magnetic particles. The molecules of DNA are bound to the surface of magnetic carriers by electrostatic interaction, and then they are eluted into buffer. The aim of the work will be to optimize individual steps of identification of bacterial DNA: cell lysis, DNA isolation, characterization of solid magnetic carriers functionalized by amino groups for nucleic acids isolation. The presence of DNA will be verified using agarose gel electrophoresis and the amount of eluted DNA will be determined spectrophotometrically. The quality of isolated DNA will be proved by their amplification using polymerase chain reaction (PCR). Furthermore, the thesis focuses on the study of secondary structures of nucleic acids – cruciforms structures and quadruplexes. These structures are involved in the regulation of cellular processes and their appearance is associated with cancer development and neurodegenerative diseases. In silico genome analysis was performed on important food industry microorganisms. The microorganisms genomic sequences were obtained from the NCBI (National Center for Biotechnology) database. The Palindrome Analyzer and G4 Hunter software were used for the analysis.
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Comparison of biotechnological procedures for pure proteins preparation
Bušanski, Patrik ; Langová, Denisa (referee) ; Brázda, Václav (advisor)
The production of recombinant proteins is a biotechnological process during which proteins are produced in foreign organisms by gen manipulation. To form a recombinant plasmid the gene encoding the desired protein is isolated and inserted into an expression vector. The plasmid is then transformed using physical or chemical method into a suitable host, where the recombinant gene is translated into amino acid sequence in the newly synthetized protein. The theoretical part of this bachelor thesis includes characteristics of proteins, methods of recombinant protein preparation and compares individual expression systems. Three isoforms of the p53 protein, which were synthesized in the E. coli microorganism, were selected for processing the experimental part. The transformed recombinant plasmid contained two tags for purification, HIS-tag and GST-tag, making it possible to compare the efficacy of the two purification methods. HIS-tag purification was found to work for all three isoforms better, with concentrations of recombinant proteins were several times higher than those of the GST-tag. The p53 proteins are about 50 kDa long, what was confirmed by sodium dodecyl sulfate polyacrylamide gel electrophoresis.
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Optimization of plasmid DNA isolation by magnetic particles
Chlopková, Barbora ; Zemanová, Jana (referee) ; Brázda, Václav (advisor)
The theoretical part summarizes information on the isolation and purification of plasmid DNA and nucleic acids as. Plasmid DNA is often used in gene engineering as a vector for the transfer of a particular gene. Its insulation and transportation in sufficient quality is crucial for other processes associated with it. Isolation and survival of pDNA using magnetic carriers of different concentrations of PEG 8000 in combination with 1M NaCl was investigated in experimental parts. Furthermore, the isolation of pDNA using commercial kits was examined.
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The effects of chemicals on cell lines viability
Zemanová, Anita ; Obruča, Stanislav (referee) ; Brázda, Václav (advisor)
The subject of this diploma thesis is the influence of selected chemicals on cell lines viability. The theoretical part contains options of cancer treatment by using chemotherapeutics including their mechanism of action and side effects. Additionally, there are described alternative DNA structures with focus on G-quadruplexes and ligands that interact with G-quadruplexes. These compounds are promising drugs in cancer treatment due to their high specificity to G-quadruplexes, which are found in telomeres of chromosomes. G-quadruplex interacting ligands by stabilization of G-quadruplexes can inhibit the enzyme telomerase, which is necessary for telomere lengthening of rapidly dividing cancer cells. Additionally, the possibilities of viability assays are summarized in the theoretical part. The aim of the experimental part was comparing cytotoxic activity between commercially available chemotherapeutics and selected G-quadruplex interacting ligands. Another task was the study of apoptosis and necrosis after the treatment of selected chemicals on cell lines and after the localization of ligands interacting with G-quadruplexes in the cells of the breast cancer cell line. In the experimental part, G-quadruplex interacting ligands have been shown to exhibit similar cytotoxic activity to commercially available chemotherapeutic agents.
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Preparation and expression of p53 protein isoforms using the GATEWAY expression system
Wikarská, Monika ; Hrstka, Miroslav (referee) ; Brázda, Václav (advisor)
The TP53 gene can express protein p53 and 11 another isoform proteins N- and/or C-terminally truncated by using two promoters and alternative splicing. The p53 isoforms are found in both healthy and tumorous tissues, and are intensively studied in relation to cancer diagnosis, prognosis and treatment. In this work, the p53 isoforms were subcloned into expression vectors by LR reaction adapted from Gateway cloning system. The expression vectors were designed for protein production by bacteria E. coli strain BL-21. The constructs containing p53 isoforms were encoded together with two fusion proteins, glutathione-S-transferase and polyhistidine tag under the control of the same promotor for the affinity chromatography protein isolation. All the clones underwent Sanger sequencing for verification after homologous recombination. Sequencing confirmed the accuracy of the subcloned isoforms p53, 133p53, 160p53, p53 and 160p53 into an expression vector pDEST15-N6xHis-GST-GW-DEST. Protein 160p53 was expressed in BL-21 and isolated using both HIS and GST tag interacion. Isolation using HIS tag yielded in a higher protein concentration then the isolation mediated by the interaction of the glutathione-S-transferase.
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Use of high resolution melting analysis for the study of lactic acid bacteria
Knápková, Monika ; Němcová, Andrea (referee) ; Brázda, Václav (advisor)
Currently, there is a growing interest in the use of probiotic products, and there are many of them in the market. With the growing interest, greater emphasis is placed on the identification of declared probiotic microorganisms. Precise identification of microbial composition is often a difficult task and it requires more advanced methods especially in the field of molecular diagnostics. The diploma thesis was focused on the verification of the presence od declared probiotic microorganisms in probiotic food supplements GS Laktobacily Forte 21, Biopron 9 Premium and Linex® Forte. DNA was isolated from the complex matrices by phenol extraction, commercial kit and magnetic carriers F79/L3-PLL in the quality suitable for PCR. Subsequently, the isolated DNA was amplified by real-time polymerase chain reaction using genus- and species-specific primers. The specific PCR product was subjected to agarose gel electrophoresis, whereas species identification was not always in compliance with the data declared by producers. The next part of the thesis was focused on polymerase chain reaction with high-resolution melting analysis to distinguish bacterial strains belonging to the Lactobacillus group and to identify probiotic microorganisms present in the complex matrices of the probiotic food supplements. Eight primer sets were tested (V1F HRM a V1R-HRM, CHAU-V3F a CHAU-V3R, CHAU-V6F a CHAU-V6R, LAC2 a LAC4, LAC1 a LAC2, P1V1 a P2V1, poxcDNAFw a poxPromRVC, poxcDNAFw a poxPromRVT). Three primer pairs (V1F HRM a V1R-HRM, poxcDNAFw a poxPromRVC, poxcDNAFw a poxPromRVT) were evaluated as the most suitable for distinguishing Lactobacillus bacterial strains.
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Using different methods of DNA isolation of lactic acid bacteria in molecular biological methods
Chvalkovská, Eva ; Skoumalová, Petra (referee) ; Brázda, Václav (advisor)
This thesis focused on the probiotic bacteria, DNA isolated from these bacteria by three different methods and the effect of isolation on DNA identification using molecular biological methods. Probiotic bacteria are an important part of human intestinal tract. They have an important role in the function of the immune system due to adhesion to the mucosa of the intestinal flora. They create a inhostile environment for pathogens. Probiotic bacteria are commonly taken in the food like dairy products or food supplements. However, overuse of antibiotics is at risk of passing on the intrinsic resistance that probiotic bacteria have to the pathogenic bacteria. The intrinsic resistence they have to maintain the natural homeostasis of the intestinal tract. It is important to effectively identify risky probiotic bacteria that have the ability to transmit resistance to eliminate their presence in food and dietary supplements. Three methods of DNA isolation like phenol extraction method, magnetic particle isolation and commercial kit isolation were used in the experimental part. DNA was isolated from three dietary supplements, namely Biopron 9 premium, Linex forte and GS Lactobacily forte 21. The purity and concentration of the isolated DNA was detected spectrophotometrically. The presence of individual DNA strains in dietary supplements was confirmed by real-time polymerase chain reaction. The best method of isolation in terms of purity and concentration of isolated DNA was evaluated by RT-PCR and spectrophotometry using a commercial kit isolation method.
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