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Database System for Biological Data Management
Drlík, Radovan ; Burgetová, Ivana (referee) ; Jaša, Petr (advisor)
This thesis describes the problems of storage and management of biological data, particularly of Haloalkane Dehalogenase enzymes. Furthermore, the thesis aims at project HADES (HAloalkane DEhalogenase databaSe) initiated by protein engineering group of Loschmidt Laboratories, Masaryk University in Brno. This is a project whose main goal is simply to store, preserve and display a wide variety of proteins data. The result of this work is a flexible database system allowing easy extensibility and maintainability, which is built on technologies Apache, PostgreSQL and PHP using the Zend Framework.
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Protein Domains Prediction
Valenta, Martin ; Martínek, Tomáš (referee) ; Burgetová, Ivana (advisor)
The work is focused on the area of the proteins and their domains. It also briefly describes gathering methods of the protein´s structure at the various levels of the hierarchy. This is followed by examining of existing tools for protein´s domains prediction and databases consisting of domain´s information. In the next part of the work selected representatives of prediction methods are introduced. These methods work with the information about the internal structure of the molecule or the amino acid sequence. The appropriate chapter outlines applied procedure of domains´ boundaries prediction. The prediction is derived from the primary structure of the protein, using a neural network The implemented procedure and its possibility of further development in the related thesis are introduced at the conclusion of this work.
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Monitoring the stability of the beer brewing process
Tichá, Anna ; Štursa, Václav (referee) ; Diviš, Pavel (advisor)
The bachelor thesis deals with the analysis of 3 samples of the same beer, brewed in different batches of the brewing process. The analyzed sample is Dalešická jedenáctka - light lager of 11% of the Stock Brewery Dalešice, a.s., which was taken directly from the lager tanks in the brewery. The aspect we have examined were total protein content, total carbohydrate content, maltose content, total polyphenol content and ethanol content. The Hartree-lowry method was used to analyzed the total protein content. Total carbohydrates were measured spectrophotometrically using anthrone reagent. The maltose content was analysed by HPLC with an ELSD detector. The total polyphenol content was analyzed by the Folin-Ciocaltau reagent method and measured spectrophotometrically. The ethanol content was analyzed on a HPLC using a refractometric detector. The aim of the work was to compare to what extent the process of beer production is stable and what parameters may change in the final product
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Dietary supplements with adaptogenic effects
Izraelová, Alexandra ; Vespalcová, Milena (referee) ; Souralová Popelková, Miriam (advisor)
The aim of this thesis was to design a recipe for the dietary supplements with adaptogenic effects, production, and subsequent analysis (proteins, lipids, carbohydrates), which led to the determination of the energetic value of preparation. Adaptogenic effects are the domain of plants and fungi, known as adaptogens. Adaptogens act non-specifically to the human body - improve the overall condition of the body, accelerate healing and regenerative processes, slow degenerative processes in the body and thus the aging process. As biogenic active stimulators, they affect not only in the physical but also in mental area. Dietary supplements have been designed in three different forms - capsules, syrup, drops. The analysis was also performed in tablets of Vietnamese origin supplied by supervizor, of which entry to our market is being considered. Protein content was determined by Kjeldahl method, lipids by Soxhlet extraction, saccharides by gravimetric method. Dietary supplements were analyzed for heavy metals (Pb, Cd, Hg), and in herbal drops ethanol content was determined.
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Comparison of growth and productivity of autotrophic algae and red yeasts
Kouřilová, Xenie ; Rapta, Marek (referee) ; Márová, Ivana (advisor)
The submitted bachelor thesis focuses on the comparison of growth and productivity of red yeasts Rhodotorula aurantiaca and Xanthophyllomyces dendrorhous and autotrophic algae Chlamydomonas reinhardtii and Chlorella vulgaris under different physical conditions. The theoretical part contains the characteristics of selected micro-organisms, stress factors caused by temperature, radiation, combination of aeration and radiation and osmotic stress. Furthermore, knowledge on metabolites and the possibilities of their analysis are mentioned. Physical stresses, namely 2%, 3%, 4% and 5% solution of sodium chloride, intense radiation, absence of lighting, 8°C and 30°C, were applied to selected strains in cultivation. Under these conditions, changes in production of carotenoids, fatty acids, ergosterol, ubiquinone and proteins were being observed. A significant inhibitive effect on all the above mentioned micro-organisms was brought about by the use of 5% solution NaCl. The highest production of metabolites with X. dendrorhous was discovered when 4% solution of NaCl was used. R. aurantiaca demonstrated higher substance utilization at 30°C. For the selected algae strains were the used stresses lethal. Within the cultivation process, the possibilities of co-cultivation of yeasts and algae were also tested, which will be the subject of further studies.
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Analysis of selected substances contained in the extract from elderberry twigs
Škeřík, Jan ; Flodrová, Dana (referee) ; Šalplachta, Jiří (advisor)
My diploma thesis deals with the optimization and verification of conditions for separation of proteins, which are contained in the twigs of elder (Sambucus nigra L.) using the technique RP-HPLC. The measurements were made with the use of a HPLC system with a UV-VIS detector. Column Zorbax 300SB-C18 300 4,6 x 250 mm and particles the size of 5 microns were used. The theoretical part describes the attributes and usage of elder and especially its proteins. The basic characteristic of the used HPLC technique is introduced. The possibilities of how to identify proteins are described. The practical part demonstrates the individual steps of optimization of the HPLC method applied to the mixture of standard proteins. The application of this method in the real sample is also reported. The final part of the diploma thesis is focused on the comparison of analysed samples taken in different seasons.
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Preparation and characterization of protein concentrates from wheat bran
Hubačová, Klára ; Diviš, Pavel (referee) ; Pořízka, Jaromír (advisor)
The diploma thesis deals with usage of wheat bran as a source of high-quality proteins. Every year mill industry produces large amounts of by-products. These by-products are constituted by wheat bran. There is a big effort to use these type of materials within a circular economy. Wheat bran contains about 14–18 % proteins which appears to be a good component for valorisation. It is possible to extract proteins from bran according to their behaviour in the range of pH. Proteins are soluble in alkaline pH and can be precipitated around their isoelectric point. The final treatment of precipitated proteins is lyophilisation. The next step is characterisation of the product. There are a few parameters to analyse: purity of the isolate, amino acid profile, composition of minerals, water contain etc. Interest in nutrition is on the rise not only by professional sportsman. This isolated product could serve as a potential protein supplement.
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Web Server for Protein Secondary Structure Prediction
Villem, Lukáš ; Očenášek, Pavel (referee) ; Burgetová, Ivana (advisor)
This master’s thesis deals with protein secondary structure prediction. There is a theoretical introduction followed by study of available tools, proposal and implementation of web application, which combines functionality of several web tools used to predict secondary structure. User is asked to choose prediction methods and insert input sequence as plain text or upload a file. Results collected from selected tools serve to convert data into common format, show the result and create new type of prediction. Finally, the testing is applied and influences of tools are adjusted in order to increase percentage of prediction. The output of application is a result of prediction also available as plain text or as a file.
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DNA Sequence Compression
Friedrich, Tomáš ; Burgetová, Ivana (referee) ; Martínek, Tomáš (advisor)
The increasing volume of biological data requires finding new ways to save these data in genetic banks. The target of this work is design and implementation of a novel algorithm for compression of DNA sequences. The algorithm is based on aligning DNA sequences agains a reference sequence and storing only diferencies between sequence and reference model. The work contains basic prerequisities from molecular biology which are needed for understanding of algorithm details. Next aligment algorithms and common compress schemes suitable for storing of diferencies agains reference sequence are described. The work continues with a description of implementation, which is follewed by derivation of time and space complexity and comparison with common compression algorithms. Further continuation of this thesis is discussed in conclusion.
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Study some active substances in Czech beer
Pařilová, Kateřina ; Vávrová, Milada (referee) ; Márová, Ivana (advisor)
The aim of this work was to study phenolics and other active compounds in 22 kinds of lager beer and especially to find some differences between Czech beer and beers made in foreign countries. In theoretical part the most useful methods for phenolic and protein analysis are discussed. Further, basic steps of brewery technology are introduced and main beer components with regard to Czech beer specificity are presented. Analysis of total phenolics, total flavonoids, antioxidant activity and most of basic technological characteristics was performed spectrophotometrically. To identification and quantitative analysis of individual phenolics on-line liquid chromatography with photo-diode array (PDA) and mass spectrometry (MS) detection was used. Protein analysis was performed by vertical electrophoresis SDS-PAGE and by Experion microfluidic electrophoresis (BioRad). From the total of 22 samples, 15 Czech beers and 7 beers of foreign marks were enrolled into this study. In these samples levels of brewery characteristics, group antioxidants and individual phenolics were compared. Flask and can beers as well as alcoholic and non-alcoholic beers were compared too. As a model comparative sample the Czech hop of Sládek variety was used. Finally, usefulness of tested parameters to differentiation composition and technology of individual beer samples was evaluated and parameters suitable for Czech beer authenticity analysis were proposed.
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