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Analysis of C. necator genome changes after evolutionary adaptation
Kroupa, Štěpán ; Obruča, Stanislav (referee) ; Brázda, Václav (advisor)
This bachelor’s thesis deals with analysis of mutations in bacterial populations of Cupriavidus necator H16 evolved in distinct stress conditions. This analysis was performed by processing data from the genome sequencing method „Next Generation Sequencing“, outsourced through the company DNALink. A list of mutations for each adapted population was constructed through bioinformatic methods. These mutations were then associated with specific areas of the reference Cupriavidus necator H16 genome from NCBI and analysed according to available information. Finally, the effect of these mutations on production of storage polymers polyhydroxyalkanoates was discussed.
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Stability of PHA-based particles and fibres in different environments
Tarageľ, Matej ; Skoumalová, Petra (referee) ; Márová, Ivana (advisor)
The aim of this diploma thesis is the preparation of liposome nanoparticles enriched with PHA and PHA nanofibers. The nanostructures served to encapsulate extracts of lipophilic and hydrophilic nature. The characterization of the properties of nanostructures such as polydispersity, size, colloidal stability, long-term stability after exposure to various environments such as seawater, water from the Brno dam and tap water, and finally the cytotoxicity of fibers with extracts was addressed. The theoretical part is focused on different types of water, human skin, coffee and subsequently carotenoids. It continues by describing of possibilities of extraction and preparation of lipophilic and hydrophilic extracts and possibilities of their determination is discussed. Finally, it describes the possibilities of preparation and characterization of PHA based nanomaterials. The practical part deals with the preparation of liposome particles and fibers enriched with PHA with encapsulated extracts, their characterization, and their subsequent exposure to various environments. Monitoring of their long-term stability was carried out, but the release of the encapsulated extracts into the environment to which the nanoparticles and nanofibers were exposed was also measured. Finally, the interaction of nanofibers with live HaCaT cells was monitored, and cytotoxicity assays determined the viability of the cells after interaction with the nanofibers.
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Analytical methods for qualitative and quantitative determination of PHA in cyanobacteria
Černayová, Diana ; Samek, Ota (referee) ; Sedláček, Petr (advisor)
The diploma thesis is confused to verify the applicability of selected physicochemical and spectroscopic methods for characterization of cyanobacteria, with special emphasis on possibilities of qualitative and quantitative analysis of polyhydroxyalkanoates (specifically polyhydroxybutyrate (PHB)) accumulated in cyanobacterial cells. The sample basis of the work was formed by cultures of cyanobacterial strains of Synechocystis sp. PCC 6803 and Synechocystis salina CCALA 192. The cultures were were cultivated in several ways to cover the widest possible range of physiological conditions and PHB contents, in particular using an autotrophic way of cultivation on shakers and multicultural culture method in a basic culture medium,and in media enriched with 2% salt (NaCl ) as well as mixotrophic culture media with different types of the carbon substrate. After few weeks of cultivation, cyanobacterial cultures were obtained and complexly analyzed by following techniques- cell suspensions were analyzed by flow cytometry and UV-VIS spectrometry (transmission and diffusion transmission mode), dry cell biomass was characterised by gas chromatography to obtain a exact amount of PHB, and then FT-IR spectrometry and thermogravimetric analysis. The work aimed to assess whether any of these methods can be a quick and affordable alternative to the determination of PHB content to the most commonly used method of gas chromatography, but also to assess what additional information about the physiological state of cyanobacterial cells can provide test methods. The highest correlation on PHB content was determined for the parameters determined by infrared spectroscopy, in which specific peaks from the characteristic wavelengths for polyhydroxybutyrate were important. Weak correlations on PHB content were achieved in thermogravimetric analysis and cytometry, using the hydrophobic fluorescent probe BODIPY 439/503, which bound to lipophilic parts of cells. In addition to the determination of PHB, it was possible to determine pigments present in cyanobacteria (such as chlorophyll, phycocyanin and carotenoids) by flow cytometry and UV-VIS diffusion transmission spectrometry. In the end, results from all used techniques were compared by PCA analysis to determine the similarity of all analyzed samples.
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production of PHA by selected extremophilic bacteria
Šarköziová, Patrícia ; Slaninová, Eva (referee) ; Obruča, Stanislav (advisor)
This bachelor´s thesis deals with production of polyhydroxyalkanoates (PHA) by thermophilic bacterial strains of Chelatococcus composti and Chelatococcus sambhunathii. We were finding out the best conditions for production of PHA granules inside the cells. In the beginning of the experiment we employed PCR to detect the phaC gene, encoding for PHA synthase, which is requisite for production of PHA. We also analyse the best source of carbon, optimal temperature for production of polyhydroxyalkanoates and influence of chosen precursors to grow of biomass and production of copolymers. The last part of this experimental thesis deals with research utilization of selected model hydrolysates. Glucose was the best source of carbon for both bacteria Chelatococcus composti and Chelatococcus sambhunathii and optimal temperature for grow and production of P(3HB) was 45°C. The applied precursors inhibited cell grow, but both bacterial strains Chelatococcus composti and Chelatococcus sambhunathii could produce copolymer P(3HB-co-3HV) after additiong of precursors sodium propionate and valeric acid. For both bacterial strains was the most useful model hydrolysates, which contains the biggest part of glucose. Morever, bacterial cells containing PHA granules were observed by fluorescence and transmission electron microscopy.
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Utilization of physicochemical and spectroscopic techniques in study of stress-response of cyanobacteria
Skoryk, Maksym ; Šedrlová, Zuzana (referee) ; Sedláček, Petr (advisor)
Tato bakalářská práce je soustředěná na zkoumaní cyanobakterií, vystavených hyper a hyposmotickým stresům. Na základě literární rešerše byly navžené vhodné analytické metody určené ke studiu dvou modelových organismu - Synechocystis sp. PCC 6803 a Synechocystis sp. salina Wislouch CCALA 192. Celkem čtyři metody byly použité k charakterizaci osmoticky zatížených bakterií. Průtoková cytometrie byla použita k vyhodnocení viability. Fluorescenční sonda SYTOX Blue poskytla důvěryhodnou informaci ohledně viability bakterií. Propidium jodid naopak poskytl nezřetelnou informaci. Optické vlastnosti cyanobakterií byly prozkoumané pomoci UV-VIS absorpčních a turbidimetrických měření. Termogravimetrická analýza byla použita pro mapování změn obsahu vody v osmoticky stresovaných buňkách. Tato metoda ukazala. že PHB-positivní Synechocystis sp. PCC 6803 jsou pravděpodobně vice odolné vůči hyperosmotickým stresům než PHB-negativní. Plynová chromatografie byla použita ke kvantifikaci vnitrobuněčného PHB, který činil přibližně 1-2 % suché hmoty PHB-positivních buněk.
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Isolation, characterization and application of biomedically important polymer P(3HB-co-4HB)
Krupičková, Kristýna ; Přikryl, Radek (referee) ; Obruča, Stanislav (advisor)
This diploma thesis deals with the isolation and characterization of copolymer P(3HB-co-4HB). The teoretical part was prepared as a literature search which describe polyhydroxyalkanoates in general, their structure, synthesis, degradation and isolation. Furthermore, copolymers containing 4HB units are mentioned in this thesis and there is also no mentioned of the biosynthesis and biodegradation of copolymer P(3HB-co-4HB). The first aim of this diploma thesis was to find out which solvent is the best for copolymer extraction and then characterize obtained copolymer P(3HB-co-4HB). The isolated copolymer was characterized by gas chromatography, SEC-MALS, thermal analysis and SEM. In the second part of the thesis, release of model biologically active substance from the PHA films was studied. Rhodamine 6G dye was selected for the simulation, which was used to stain the copolymer films and the P(3HB) films. It was observed that film prepared from P(3HB-co-4HB) copolymer released entrapped substance much faster than film made from P3HB homopolymer, and, in addition, the copolymer was substantially more susceptible to enzyme degradation.
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Biodegradation of bioplasts in compost environment
Vodička, Juraj ; Kovalčík, Adriána (referee) ; Obruča, Stanislav (advisor)
This master’s thesis focuses on biodegradation of polyhydroxybutyrate (PHB) and polylactic acid (PLA). The theoretical part discusses an origin, properties and applications of investigated biopolyesters, and so the enzymology of their biodegradation. The experimental part deals with biodegradation of these polymers in liquid medium using several pure thermophilic bacteial strains and controlled composting of these bioplastics. Amongst six tested thermophilic bacterial strains only one showed PHB-biodegradation activity – strain Schlegelella thermodepolymerans. No degradation degree of amorphous or semi-crystalline PLA was observed. Mainly disintegration of both forms of PLA articles was observed in compost environment, thus the abiotic mechanism of its decomposition was indicated. After 4 weeks of composting, the relative weight loss of 99 % and 63 % was detected in amorphous and semi-crystalline PLA respectively. On the contrary, the weight loss of PHB after 4 weeks of composting reached 36 %, moreover, a half decrease of molar mass was observed using SEC. The surface erosive mechanism of PHB-biodegradation was stated using SEM. By monitoring of esterase, lipase and protease activities, no influence on the compost by polymer presence was concluded at statistical significance.
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Isolation of lignin from grape seeds and its application as filler for polyhydroxyalkanoates (PHA)
Vostrejš, Pavel ; Vítová, Eva (referee) ; Kovalčík, Adriána (advisor)
This diploma thesis deals with 1) the preparation of biodegradable polymer films based on polyhydroxyalkanoates (PHA) and 2) their modification by lignin as an active additive. The motivation for this work was to prepare active packaging material for food packaging. Polymer films were prepared by blending of neat crystalline poly(3hydroxybutyrate) (P3HB) and amorphous polyhydroxyalkanoate (PHA). The lignin was isolated from grape seeds derived from grape pomace. The solubility of lignin in chloroform was improved by acetylation. The properties of the isolated lignin were determined by elemental analysis, ash content, and infrared spectroscopy (FTIR). Lignin was used as an active additive for the modification of polymeric films prepared by solution casting of P3HB or P3HB blended with amorphous polyhydroxyalkanoate. The effect of different concentrations of lignin in the range of 1 to 10 % was tested. The lignin type and concentration had a different influence on the final thermal and mechanical behaviour of polymeric films. Lignin increased the values of the Young modulus and tensile strength of the prepared films. Differential scanning calorimetry data confirmed that lignin positively modified crystallization kinetics of P3HB. Thermogravimetry was used to analyse the thermal stability of PHA films. Lignin markedly increased the thermal stability of PHA films. However, acetylated lignin harms the mechanical properties of films. Moreover, this work showed that lignin isolated from grape seeds and added into PHA films proved its high antioxidant capacity. PHA films with lignin displayed much better gas barrier properties compared with PHA films without lignin. The prepared bioactive PHA films fulfil the requirements for sustainable food packaging with high antioxidant capacity and excellent gas barrier properties.
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Metabolism of Bacterial Cells and the Effect of Stress on Biosynthesis of PHA
Kučera, Dan ; Kráčmar, Stanislav (referee) ; Ondrejovič,, Miroslav (referee) ; Obruča, Stanislav (advisor)
This thesis deals with the study of polyhydroxyalkanoate biosynthesis as a microbial product with the potential to replace current conventional plastics made from petroleum. The dissertation thesis is elaborated in the form of a discussed set of already published publications, which are then part of the thesis in the form of appendices. The work builds on relatively extensive knowledge in the field of polyhydroxyalkanoate production and brings new facts and possible strategies. Various possibilities of analysis of polyhydroxyalkanoates using modern methods were tested in this work, which brings especially speed, which can be crucial in real-time evaluation of production biotechnological process. Raman spectroscopy has proven to be a very promising technique for rapid quantification of PHA. Furthermore, the work deals with valorisation of waste of food and agricultural origin. Emphasis is placed on methods of detoxification of lignocellulose hydrolysates. In this context, adsorption of inhibitors to lignin was first used as an alternative to other detoxification techniques. Due to detoxification, selected production strains Burkholederia cepacia and B. sacchari were able to utilize softwood hydrolyzate for PHA production. In the next part of the work was also tested the possibility of using chicken feathers as a complex source of nitrogen. Evolutionary engineering was also used as a possible strategy to eliminate the inhibitory effect of levulic acid as a microbial inhibitor that results from the hydrolysis of lignocellulosic materials. Adaptation experiments were used to develop strains exhibiting higher resistance to levulic acid and the ability to accumulate a higher 3HV copolymer from the original wild-type C. necator strain. Another promising approach tested in the work was the use of extremophilic microbial strain, which leads to a reduction in the cost of biotechnological production. Selected Halomonas species have shown high potential as halophilic PHA producers. The final part of the thesis was devoted to the selection of the production strain with regard to the properties of the resulting PHA. The Cupriavidus malaysiensis strain was selected to produce a P(3HB-co-3HV-co-4HB) terpolymer which revealed significant differences in material properties over P3HB.
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Evolutionary engineering of PHA producing bacterium Halomonas halophila
Ikrényiová, Terézia ; Kovalčík, Adriána (referee) ; Obruča, Stanislav (advisor)
This bachelor thesis deals with evolutionary engineering of PHA producing bacteria, the principle of PHA production and solution of this production’s disadvantages, but also applications of these biopolymers in the theoretical part. The production of polyhydroxyalkanoates by bacteria Halomonas halophila, which is focused on gaining the maximus amount of 3-hydroxyvalerate in formed copolymer, is described in the experimental part. The precursor valeric acid was added to bacteria due to gain the amount of 3HV. It was found that the concentrations over 3 g/l aren´t usable for production sufficient concentration of PHA. The very low concentrations of valeric acid led to low amount of 3HV in PHA. The available concentration of this precursor for production sufficient concentration of PHA by bacterial cell is 3 g/l. Moreover, it was found that the valeric acid should be added after 24 hours of cultivation in mineral production medium. The thesis is also concentred on comparison the original bacterial strains of Halomonas halophila to strains, which were adapted on valeric acid as stress factor for bacteria. The assumption, that the adapted strains can better utilize valeric acid and the incorporation to copolymer of it is higher like the original strains, was affirmed.
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