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Shaft seals and stuffing boxes of pumps
Pluskal, Tomáš ; Dobrovolný, Martin (referee) ; Štefan, David (advisor)
Pumps are an integral part of industry, agriculture, but also everyday life. One of the main elements that affect the proper function and reliability of these machines are shaft seals and gaskets. The first part of this work deals with individual types of shaft seals and gaskets, their design, application, function and used materials. In the second part, a suitable seal for the selected pump is dimensioned.
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Solution of flow and formation of vortex structures behind a free-standing pillar
Pluskal, Tomáš ; Pochylý, František (referee) ; Fialová, Simona (advisor)
The instability of the flow and the formation of vortices when surrounding free-standing pillars is a problem that has been solved for a long time. In most engineering applications we try to minimize their influence. However, some newer applications require them to be maximized. This deals with the study of these effects on the public street lamp using computer modelling in the Ansys Fluent and their use for the production of electricity. The information obtained in this way is then used for the design of a vibration generator, which is then used to transform the energy from mechanical vibrations to electricity.
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Terpene discovery combining in silico and molecular biology approaches
Smrčková, Helena ; Pluskal, Tomáš (advisor) ; Hodek, Petr (referee)
Terpenoids are the largest class of natural products with remarkable chemical and structural diversity, making them a significant source of compounds for drug discovery. Terpenoids are used as food flavours, therapeutics, cosmetics, hormones or fuel. The starting scaffolds for terpenoid biosynthesis are condensed and, in some cases, cyclic carbohydrates synthesized from linear isoprenyl pyrophosphate precursors by terpene synthases. The enzyme family of terpene synthases is extensive and possesses well-characterized motifs and function-determining domains that can be used to search for homologous proteins with unknown catalytical function that might produce new compounds. Thanks to a bioinformatic pipeline developed in the Pluskal Lab in the Institute of Organic Chemistry and Biochemistry CAS, candidate terpene synthases with the potential to produce new terpene scaffolds were mined in silico from large protein sequence repositories. I expressed nine selected proteins originating from plants, bacteria, and fungi in the engineered budding yeast strains JWY501 and ZX178-08 that overproduce isoprenyl pyrophosphates. I then analysed the resulting yeast cell culture extracts using gas chromatography- and liquid chromatography-mass spectrometry. Five out of nine proteins exhibited terpene synthase...
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Development and analysis of a database of reactions catalyzed by cytochrome P450 enzymes for machine learning applications
Komorníková, Natália ; Pluskal, Tomáš (advisor) ; Berka, Karel (referee)
Cytochrome P450 enzymes are hemoproteins showing extraordinary di- versity in the reactions they catalyze. We developed a database containing all the needed data to provide a comprehensive data source on reactions cat- alyzed by cytochrome P450 enzymes. This data mainly includes information about the substrates, products of characterized reactions, and the sequence of these enzymes. The database was developed by collecting data from reliable protein and reaction databases like UniProt and RHEA. The work presents an in-depth analysis of the created database of reactions catalyzed by cy- tochrome P450 enzymes. This database can be utilized for future machine learning approaches to predict the function of uncharacterized cytochrome P450s.
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Differential discovery of protein features using tandem mass spectrometry
Wybitul, Evžen ; Kratochvíl, Miroslav (advisor) ; Pluskal, Tomáš (referee)
Disulphide bonds are crucial to correct protein folding, and heavily influ- ence protein function. Tandem mass spectrometry protein analysis is often used for the determination of disulphide bond positions, in combination with manual or computational interpretation methods. In this thesis we devise a program for automatic disulphide bond characterization called Dibby. Dibby identifies protein fragments in the fragmentation spectra, and uses the iden- tified fragments to determine which cysteines were connected in the protein. The identification algorithm is able to identify even complex fragments with multiple disulphide bonds that are often missed by other methods. To re- duce the fragment search space, we employ divide and conquer and branch and bound techniques. We evaluate Dibby on both measured and in-silico generated datasets, and find that it correctly identifies large portion of the present disulphide bonds with minimal manual interventions. 1
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De novo transcriptomics and its use in non-model organisms
Čalounová, Tereza ; Pluskal, Tomáš (advisor) ; Svatoňová, Petra (referee)
The rise of second generation sequencing enabled the study of non-model organisms. Without the requirement of having a reference genome, de novo transcriptomics allows the study of functional elements of their genomes. That way, the great complexity of non-model organisms can be explored. This thesis gives a comprehensive overview of the de novo transcriptomics experiment workflow from a bioinformatics perspective. The emphasis was placed on both theoretical background and practical approaches. This work also highlights new methods in de novo transcriptomics which may start to dominate in the near future. The practical part of the work presents transXpress - a de novo transcriptome assembly and annotation pipeline. Its use is demonstrated on a non-model plant long pepper (Piper longum) with medicinal potential. Keywords: transcriptomics, de novo transcriptomics, transcriptome, RNA-Seq, non-model organism, assembly
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Shaft seals and stuffing boxes of pumps
Pluskal, Tomáš ; Dobrovolný, Martin (referee) ; Štefan, David (advisor)
Pumps are an integral part of industry, agriculture, but also everyday life. One of the main elements that affect the proper function and reliability of these machines are shaft seals and gaskets. The first part of this work deals with individual types of shaft seals and gaskets, their design, application, function and used materials. In the second part, a suitable seal for the selected pump is dimensioned.
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