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Development and characterization of new dairy products with increased fiber and protein content
Smatana, Igor ; Punčochářová, Lenka (referee) ; Pořízka, Jaromír (advisor)
The bachelor thesis was focused on the production and characterization of new dairy products with increased protein and fiber content. Ground wheat bran was used as the fiber source and wheat bran protein extract was used as the protein source. From an ecological point of view, it would be ideal if 100% of the raw material was used and nothing was left as waste. We tried to approach this by using the waste (by-product) that arises during the production of flour as an additive to dairy products. The theoretical part focused on the characterization of fermented and unfermented dairy products and their production, the nutritional value of proteins and fiber and the composition and benefits for human health of wheat bran, protein isolation from wheat bran and common analytical methods to determine rheological properties, viable cell numbers. water binding and sensory acceptability. Two basic dairy products were created, one fermented and one unfermented, and subsequently fortified with a source of fiber (wheat bran) and a source of protein (protein concentrate from wheat bran). All products were subsequently characterized for characterization. Water binding, rheological and sensory properties were determined. The fermented dairy product was also subjected to cytometric analysis to determine the number of viable cells. The experimental part describes the methods we use to prepare and characterize new products. After evaluating the measured data, options for optimizing the acceptability of products by consumers were proposed. The results showed that the organoleptic properties were negatively affected by the addition of wheat bran and protein concentrate.
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Analysis of Genomic Data with the Assistance of Algorithm BLAST
Křížová, Martina ; Burgetová, Ivana (referee) ; Jaša, Petr (advisor)
This Bachelor Thesis describes analysis of genomic data with assistance of algorithm BLAST. In theoretic part, it describes genomes, their importance and structure. In this thesis, you can find a description of algorithm BLAST, Smith-Waterman and Needleman-Wunsch and with algorithm BLAST connected Karlin-Altschul statistics. This thesis is discussing types of databases such as spatial, deductive and relational which store genomic data. Second part is concerned with design and implementation of application which use mentioned algorithm and database Oracle 10g R2. Testing and confrontation output of algorithm is also a part of this work.
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The effect of proteins on friction of artificial articular cartilage
Plachý, Tomáš ; Nečas, David (referee) ; Rebenda, David (advisor)
This bachelor thesis deals with the influence of the composition of synovial fluid on the coefficient of friction of artificial cartilage. The effect of protein concentration and their combination with other components of synovial fluid on the coefficient of friction of CD hydrogels simulating artificial cartilage is observed. All experiments were performed at a constant load of 10 N, speed 10 mm / s, temperature 37 ° C. In experiments investigating the effect of a combination of hyaluronic acid and phospholipids together with proteins, concentrations corresponding to a healthy individual were used. In experiments where the effect of the proteins themselves and their own combinations was investigated, concentrations corresponding to both a healthy individual and patients with advanced osteoarthritis or patients with aseptic release of the prosthesis were used. The work shows that when using the proteins alone, or their combination, there is a decrease in concentration of friction coefficient with increasing concentration. However, if hyaluronic acid alone or phospholipids alone is added to the protein, the coefficient of friction increases. The reduction occurs only after the addition of the combination of acid and phospholipid.
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Clustering of Biological Sequences
Kubiš, Radim ; Burgetová, Ivana (referee) ; Martínek, Tomáš (advisor)
One of the main reasons for protein clustering is prediction of structure, function and evolution. Many of current tools have disadvantage of high computational complexity due to all-to-all sequence alignment. If any tool works faster, it does not reach accuracy as other tools. Further disadvantage is processing on higher rate of similarity but homologous proteins can be similar with less identity. The process of clustering often ends when reach the condition which does not reflect sufficient quality of clusters. Master's thesis describes the design and implementation of new tool for clustering of protein sequences. New tool should not be computationally demanding but it should preserve required accuracy and produce better clusters. The thesis also describes testing of designed tool, evaluation of results and possibilities of its further development.
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Barley Proteomic Studies Related to Beer Production
Benkovská, Dagmar ; Márová, Ivana (referee) ; Ehrenbergerová, Jaroslava (referee) ; Zdráhal, Zbyněk (referee) ; Bobáľová, Janette (advisor)
Tato práce se zabývá proteomickými studiemi ječmene v souvislosti s výrobou piva. Ječmen patří mezi nejvýznamnější plodiny na světě a je využíván hlavně pro sladovnické účely, nejčastěji pro pivovarnictví. Studium proteinů ječmene během sladování a výroby piva poskytuje informace o změnách v proteinovém složení nebo jejich posttranslačních modifikacích. Jelikož jsou proteiny v ječmeni a jejich změny zásadní pro kvalitu sladu a piva, proteomické studie ječmene mají potenciál pro zlepšení procesu sladování a pivovarnictví. Hlavním cílem této práce je studium ve vodě rozpustných proteinů ječmene a jejich změn, ke kterým dochází během sladování a výroby piva. Rozdíly v proteinovém složení byly sledovány pomocí gelové elektroforézy, kapalinové chromatografie na reverzní fázi, gelové chromatografie a MALDI-TOF hmotnostní spektrometrie. Během sladování se vlivem klíčení zrna zvyšuje množství některých proteinů a také jsou tvořeny nové proteiny. V průběhu vaření piva se naopak v důsledku vysoké teploty a enzymatické aktivity proteáz mnoho proteinů rozkládá. Těmto drsným podmínkám odolají jen některé proteiny, které přechází až do piva a mohou ovlivnit jeho kvalitu. Dále byly zkoumány různé odrůdy ječmene a jejich rozdíly. Byly porovnány odrůdy povolené pro výrobu certifikovaného Českého piva s jednou osvědčenou sladovnickou odrůdou a jednou nesladovnickou odrůdou ječmene. Kromě toho byly studovány v alkoholu rozpustné proteiny ječmene a jejich změny v průběhu sladování. Zvláštní pozornost byla věnována vybrané skupině posttranslačních modifikací proteinů: glykosylacím. Neenzymaticky glykosylované proteiny ječmene (neboli glykované proteiny) jsou tvořeny v průběhu sladování kvůli přítomnosti velkého množství glukózy uvolněné z rozkladu škrobu. Glykované proteiny ovlivňují stabilitu proteinů a kvalitu piva, obzvlášť pěnotvorný účinek. Enzymatické N-glykosylace představují nejčastěji studované posttranslační modifikace u rostlin, protože glykoproteiny hrají klíčovou roli v různých biologických funkcích. Glykoproteiny jsou často přítomny v malém množství, a proto je pro jejich analýzu potřebné obohacení glykoproteinů z komplexní směsi. Pro studium glykoproteinů byla využita afinitní chromatografie s lektinem concanavalin A. Kromě toho byla také optimalizována analýza sacharidové části glykoproteinů. Tato disertační práce přináší důležité informace o proteinech ječmene, jejich změnách a analýze, které budou užitečné pro další studium.
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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.
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Utilization of light scattering techniques in study on protein denaturation
Köbölová, Klaudia ; Kalina, Michal (referee) ; Sedláček, Petr (advisor)
This bachelor thesis is focused on verifying the use of light scattering techniques in the study of protein denaturation. The theoretical part of the thesis describes proteins, their general properties, the process of denaturation and it provides an insight into light scattering. In the experimental part of the study I investigated the denaturation effects of four selected potential denaturing agents – urea, guanidine hydrochloride, sodium dodecyl sulfate, copper (II) sulfate – on two model enzymes: lipase and lysosyme. The denaturation effects of these denaturants were studied with the help of the dynamic light scattering method (DLS). In order to describe the change in particle size during denaturation, I used Z-Average, Volume mean and intensity distribution which were determined by this method.
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Bioinformatics Tool for Prediction of Protein Solubility
Hronský, Patrik ; Burgetová, Ivana (referee) ; Martínek, Tomáš (advisor)
This master's thesis addresses the solubility of recombinant proteins and its prediction. It describes the subject of protein synthesis, as well as the process of recombinant protein creation. Recombinant protein synthesis is of great importance for example to pharmacologic industry. This synthesis is not a simple task and it does not always produce viable proteins. Protein solubility is an important factor, determining the viability of the resulting proteins. It is of course favourable for companies, that take part in recombinant protein synthesis, to focus their effort and their resources on proteins, that will be viable in the end. In this regard, bioinformatics is of great help, as it is capable, with the help of machine learning, of predicting the solubility of proteins, for example based on their sequences. This thesis introduces the reader to the basic principles of machine learning and presents several machine learning methods, used in the field of protein solubility prediction. It deals with the definition of a dataset, which is later used to test selected predictors, as well as to train the ensemble predictor, which is the main focus of this thesis. It also focuses on several specific protein solubility predictors and explains the basic principles upon which they are built, as well as the results of their testing. In the end, it presents the ensemble predictor of protein solubility.
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Geometry of protein moleculs
Novotný, Jan ; Maděránková, Denisa (referee) ; Škutková, Helena (advisor)
Objective of this work was to study the spatial arrangement of protein molecules, with their extraction, notations and variables used in the course descriptions. Prediction of protein structures is very important for determining the future function of proteins. Another objective was to create a function in MATLAB that will graphically represent the spatial arrangement of the backbone structure of the protein by form Ramachandran plot. Along with this function create another function to render the side-chains of amino acids and function to calculate the stereochemical quality. Finally, create a program for a complete assessment of the spatial arrangement of the protein molecules and calculating the stereochemical quality of and test program for protein structures from public databases RSCB PDB.
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Web Application for Bioinformatics Education - Genetic Code
Kilián, Martin ; Martínek, Tomáš (referee) ; Burgetová, Ivana (advisor)
This thesis briefly describes basic informations in moleculary biology. Thesis deals with a transfer of information from DNA into RNA through uprotein, are also briefly described the methods and algorithms dealing with the detection of genome. The larger part deals with the recognition cue coded signals and determination of sequences and their subsequent transcription and translation, which demonstration program was needed to create. The final result is s web application as the education system.
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