|
|
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.
|
|
|
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.
|
|
|
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.
|
|
|
Study of interactions of the surfactant component of Septonex with selected proteins
Bohunská, Miroslava ; Pekař, Miloslav (referee) ; Krouská, Jitka (advisor)
The study of protein and surfactant interactions is of great significance in a number of applications, such as the cosmetic, food or pharmaceutical industries and many others. However, they require further study due to their compositional complexity and the limitations of current analytical approaches. In this thesis, the cationic surfactant septonex in combination with two differently charged proteins lysozyme and bovine serum albumin under different physiological conditions (temperature, surfactant concentration, environment and others) was selected to study the interactions. Characterization of protein-surfactant interactions is a very important but challenging task, therefore it is essential to use appropriate approaches to explore the nature of these interactions. In order to unify the information to provide rational models, calorimetric methods (DSC, ITC) and dynamic light scattering were used. Isothermal titration calorimetry monitors the evidence for the formation of the system of the mentioned substances and information on aggregation behavior, differential scanning calorimetry characterizes the thermal stability of proteins and dynamic light scattering made it possible to monitor changes in particle size. Both proteins have been proven to interact with positive septonex, even if the lysozyme molecule is also positively charged. However, significant differences were found between the two proteins. From the obtained results it is evident that the identical charge of the protein with the surfactant has an effect on the intensity of the measurement, although all measured interactions showed an endothermic character.
|
|
|
Tisknutelné matrice na bázi složek mléka
Němec, Jan
The aim of the thesis is to introduce to the topic of 3D printing, milk components and their mutual connection. It explains individual technologies from the most common to the less well-known. Furthermore, the thesis deals with a review of current studies on this topic and their conclusions, progresses and complications. It focuses on individual components of milk, such as casein, micellar casein concentrate, milk protein concentrate, whey proteins and lactose, which have potential in 3D food printing. The thesis aims to provide a review of the information needed to understand 3D printing as it is used in other industries, as well as to understand the complexity of food 3D printing with a focus on milk. The main contribution of the work consists in providing comprehensible information and in the summarization of the indicated paths where 3D printing of milk has gone. Alternatively, it also reveals gaps that can be addressed and thus move development forward.
|
|
|
Metody ošetření čerstvého ovoce a zeleniny na bázi ochranných povrchových aplikací
Bůšek, Filip
This bachelor's thesis elaborates an overview of protective surface applications on fresh fruits and vegetables based on biocompatible polymers, which can be abbreviated as edible coatings, which can be made of polysaccharides, proteins or lipids, or a combination of several materials, referred to as composite coatings. It also deals with the method of their application to the surface of food, where the basic ones include dipping, spraying and brushing. The properties of edible coatings can be improved by incorporating active substances such as antimicrobial agents, texture improvers or nutraceuticals. The next part of the work summarizes the positives, but also the shortcomings of edible coatings and some materials applied to individual types of food. The final part deals with current research and perspectives in the field of edible coatings.
|
|
|
Vliv vazného ustájení na parametry mléčné užitkovosti dojnic ve vybraném chovu
Skoupý, Roman
The aim of this work was to find out the influence of bonded housing on the parameters of milk productivity of dairy cows in a selected farm. The work took place in one calendar year 2022 from January to December. Among the monitored parameters were fat content (%), protein (%), lactose (%), amount of milk produced (kg), stage of lactation (days) and order of lactation (n). The samples were obtained from our own breeding and evaluated in the Laboratory of Applied Lactology at the Institute of Animal Breeding and Breeding, Faculty of Agriculture, Mendel University in Brno using the Julie C5 Automatic device. A total of 12 samples from 4 cows of two breeds, namely Holstein and Czech Spotted cattle, were processed. The results show that bonded housing has a significant effect on the milk production of a dairy cow. The fat content is influenced by the method of breeding but also the feeding technique and the health status of dairy cows, when the fat content was very different in individual months. The protein content was influenced by the order of lactation, where the higher the lactation, the lower the protein content. Lactose was not affected by any factor and was constant.
|
|
|
Study of the effect of biomolecules on the solubility of poorly soluble drugs
Kheirabadi, Fatemeh ; Holas, Ondřej (advisor) ; Vraníková, Barbora (referee)
Charles University, Faculty of Pharmacy in Hradec Králové Department of Pharmaceutical Technology Supervisor: Dr. Ondrej Holas, Ph.D. Consultant: prof. Anette Müllertz, Ph.D. Student: Fatemeh Kheirabadi Title of thesis: Effects of Proteins on Apparent Drug solubility in Fasted State Stimulated Colonic Fluids This thesis investigates the influence of proteins on the apparent solubility of drugs in fasted state stimulated colonic fluids. The investigation was conducted on a selection of compounds with varying physicochemical and plasma protein binding properties. Precisely, three different compounds named as Nilotinib, Carvedilol and Ritonavir were analyzed for their apparent solubility in three distinct protein sources: bovine serum albumin, mucin from dehydrated porcine gastric mucin type II, and collected porcine intestinal mucus. Accurate reversed-phase high-performance liquid chromatography was developed and employed as the analytical method to determine the concentration of the apparent drug solubility of the investigated compounds. The research on the solubility of poorly soluble compounds in simulated colonic fluids has been restricted. Additionally, factors such as the impact of proteins remains unexplored in biorelevant media, which could be critical for enhancing our understanding of drug...
|
|
|
Synthesis and delivery of novel fluorescently-labelled nucleotides and their nucleic acids for bio-analytical applications
Güixens Gallardo, Pedro ; Hocek, Michal (advisor) ; Zimčík, Petr (referee) ; Klán, Petr (referee)
1 Abstract The goals of the thesis were to synthesise novel fluorescently labelled nucleotides and the corresponding nucleic acids for bio-analytical applications as well as their delivery into cells. The thesis also aimed at the development of an effective method to inhibit non-templated incorporation of nucleotides. The problematic non-templated enzymatic incorporation of nucleotides is addressed by using several commercially available 5'-modified-oligonucleotides. The oligonucleotides (ONs) that we tested bore ortho twisted intercalating nucleic acid (oTINA), a trityl group, or biotin at the 5'-end. The modified ONs were used as templates in the enzymatic primer extension (PEX) experiments in the presence of either modified nucleotides or only natural deoxynucleoside triphosphates (dNTPs). The oTINA templates underwent PEX reaction using natural dNTPs and different DNA polymerases of the A or B family. In parallel, two types of fluorescent nucleoside derivatives were independently designed and synthesised. Firstly, we envisaged new fluorescent nucleotide tags containing the hexamethylated BODIPY moiety as a bright fluorescent label. Conversely, we focused on the improvement of fluorescent nucleotide probes sensitive to the viscosity or polarity. The fluorescently labelled methylated BODIPY nucleotides...
|
|
|
Comprehensive chemical analysis of blood coatings
Matěcha, Tadeáš ; Kučková, Štěpánka (advisor) ; Kolář, Karel (referee)
This thesis deals with the comprehensive chemical analysis of blood coatings using mass spectrometry and infrared spectroscopy. The theoretical part focuses first on the history of use, properties, and formulations of blood coatings, then on their composition, which is divided into protein and non-protein components, as well as on selected analytical methods used for their identification. In the experimental part, 41 model samples and 2 real samples are evaluated and discussed. Liquid chromatography with tandem mass spectrometry (nano-LC-ESI-Q-TOF MS) was used to identify the protein component in all samples. Determination of the quantitative abundance of each type of protein additive in the blood coatings was performed based on the number of peptides found originating from proteins typical for specific protein additives. Furthermore, it was possible to identify the amino acid sequences that allow to determine the animal origin of the blood used. The non-protein components of all samples were identified by infrared spectroscopy, specifically by the attenuated total reflection and diffuse reflectance techniques. The quantitative analyses based on the change of the intensities of the measured spectra was also discussed. A special chapter is devoted to the identification of animal glue and to the...
|
guest ::
