|
|
Enantioseparation and derivatization of selected amino acid.
Rozumová, Nela ; Loukotková, Lucie (referee) ; Bosáková, Zuzana (advisor)
The enantioseparation of native and derivatized form of D,L-valine was studied on chiral stationary phase, based on teicoplanin chiral selector. The most suitable mobile phase for the enantioseparation and quantification of underivatized D,L-valine was methanol/water 50/50 (v/v) and UV detection at 205 nm. LOD and LOQ for L- and D-enantiomers were evaluated, in order of hundredths of mg/ml. Derivatization of D,L-valine was done using 9-fluorenylmethylchloroformate (FMOC-Cl). For the enantioseparation of FMOC-D,L-valine the optimized mobile phase consisted of 37/63 (v/v) methanol/0,5% triethylamine acetate buffer (TEEA), pH 4,0. Quantification was carried out using fluorescence detection at the excitation wavelength of 254 nm and the emission wavelength of 314 nm. LOD and LOQ values for FMOC-L- and FMOC-D-valine were in the range from hundredths to tenths of μg/ml. The results show that much higher detection sensitivity was achieved after the derivatization procedure.
|
|
|
Biogenic amins in beer
Zima, Matěj ; Orsák, Matyáš (advisor) ; Braný, Pavel (referee)
One of the most popular and widely used alcoholic beverages is beer. There is a long-standing tradition of beer production in the Czech Republic and it is our significant export commodity. Hops, specifically the so called Saaz Late, is a typical ingredient in the production of bottom fermented a Pilsen kind of beer that has made us famous in the world.
Beer is a complicated beverage and its production is not an easy process, although it may seem differently at first glance. Apart from the convenient ingredients, for the production of beer are also needed technological facilities and most importantly the knowledge. The procedure itself consists of grinding malt, mixing it with water and mashing process, which includes a shortage of polysaccharide chains by influence of malt enzymes. The extracted product is called hopped wort and it is further boiled together with hops.
This process is in Czech language known as chmelovar (hereinafter referred to as wort). During the wort, there are some bitter substances coming to work (this is how mixture of ingredients and water is generally called during the whole process of production), the bitter substances are specifically alfa bitter acids and beta bitter acids.
The extracted product is called hopped wort. After fermenting the hopped wort, there comes a stage of main and secondary fermentation. During this phase two crucial ingredients of beer are produced. Alcohol and carbon dioxide. Traditional for Czech regions is the bottom fermentation in which yeasts are descending to the base of a container.
Biogenic amines are one of many components of the beer. However, they can be found not only in the beer, but also in almost all basic foods. We can find them in meat, fish, vegetables and fruits, and even in different concentrations. Their production is often associated with the fermentation process. Regarding the content of biogenic amines in beer, due to the research it is obvious that a part of them gets into the beer from the original raw materials. Another part arises during the fermentation process. Tyramine and histamine (among others), discovered in the beer, can have a serious impact on human health. During the consumption of large quantities of such a beer, but even other foods that contain a lot of these biogenic amines, it may affect the circulatory system, breathing, cause a facial flushing and in extreme cases even cerebral haemorrhage. The intoxication by histamine is often manifested as food poisoning or allergic reactions.
|
|
|
Analysis of the Tools for Detecting Similarities between Tertiary Protein Structures
Trlica, Jiří ; Vogel, Ivan (referee) ; Bendl, Jaroslav (advisor)
Alignment of the three-dimensional structures of proteins is an essential task in bioinformatics. Because there are many tools offering this functionality, only a limited subset of them was chosen for comparison (DALI, LOCK 2, SPALIGN, MUSTANG and CLICK). These tools vary in the principle of calculation. Their performance was measured on three proteins, which represent main protein classes (all-α, all-β, α/β). These proteins were tested against a subset of PDB database containing 2 357 records. The results were visualized by ROC curves and the tools were compared by their area under ROC curve (AUC metric). According to this metric, the best results were obtained for SPALIGN.
|
|
|
Hardware Acceleration of Algorithms for Approximate String Matching
Nosek, Ondřej ; Kořenek, Jan (referee) ; Martínek, Tomáš (advisor)
Methods for aproximate string matching of various sequences used in bioinformatics are crucial part of development in this branch. Tasks are of very large time complexity and therefore we want create a hardware platform for acceleration of these computations. Goal of this work is to design a generalized architecture based on FPGA technology, which can work with various types of sequences. Designed acceleration card will use especially dynamic algorithms like Needleman-Wunsch and Smith-Waterman.
|
|
|
Clustering of Protein Sequences Based on Primary Structure of Proteins
Jurásek, Petr ; Stryka, Lukáš (referee) ; Burgetová, Ivana (advisor)
This master's thesis consider clustering of protein sequences based on primary structure of proteins. Studies the protein sequences from they primary structure. Describes methods for similarities in the amino acid sequences of proteins, cluster analysis and clustering algorithms. This thesis presents concept of distance function based on similarity of protein sequences and implements clustering algorithms ANGES, k-means, k-medoids in Python programming language.
|
|
|
Prediction of Protein Stability upon Mutations Using Evolution Strategy
Pavlík, David ; Martínek, Tomáš (referee) ; Bendl, Jaroslav (advisor)
This master's thesis deals with the matter of predicting the effects of aminoacid substitutions on protein stability. The main aim is to design meta-classifier that combines the results of the selected prediction tools. An evolution strategy was used to find the best weights for each of the selected tools with the aim of achieving better prediction performance compared to that achieved by using these tools separately. Five different and obtainable prediction tools were selected and their prediction outputs were weighted. Two different approaches of evolution strategy are investigated and compared: evolution strategy with the 1/5-rule and evolution strategy with the type 2 of control parameters self-adaptation. Two independent datasets of mutations were created for training and evaluating the performance of designed meta-classifier. The performed experiments and obtained results suggest that the evolution strategy could be considered as a~beneficial approach for prediction of protein stability changes. However, the special attention must be paid to careful selection of tools for integration and compilation of training and testing datasets.
|
|
|
Techniques for Comparing Biological Sequences
Sladký, Roman ; Křivka, Zbyněk (referee) ; Burgetová, Ivana (advisor)
This work presents the building up of basic biological units DNA, RNA and proteins as well as their function. Provided data are kept in biological databases which are connected worldwide to supply preferable communication along with all kinds of available information to be used in the scientific research. The secret of alive is hidden in genes coded in sequences of nucleotides. Genes enable the creation of proteins which are made of sequences of amino-acids. The wide-spread methods of comparing these sequences are FASTA and BLAST algorithms. Their base is used for the PSProt program which is described in this work. PSProt program is the tool for comparing the sequences of proteins. First it is necessary to synthesise the protein from the DNA oligonucleotide because it codes the surveyed protein. The most similar proteins are searched out by heuristic of hitpoints, then their final score that is essential for aligning is modified by semiglobal alignment algorithm.
|
|
|
Mutual similarity of aminoacid sequences in different organisms
Vysoudil, Ladislav ; Provazník, Ivo (referee) ; Škutková, Helena (advisor)
The aim of this semestral project is to try to study and describe work with sequences of proteins of different organisms, namely above all alligment sequences and evaluation of similarities of sequences. At the beginning of this work we deal with biochemistry of proteins, their constitution and structure. Further text go on with theory for work with sequential data, global, local and multiple assignment. At the last part we investigate possibilities of programme Matlab for aforesaid assignment.
|
guest ::
