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Bioinformatics Tool for the Analysis of Gene Neighbourhoods
Hřebíček, Ondřej ; Kameník, Zdeněk (advisor) ; Větrovský, Tomáš (referee)
The discovery of novel biosynthetic gene clusters (BGCs), particularly in Actinobacteria, is key for the development of new antimicrobials and other bioactive compounds derived from bacterial specialized metabolites. BGC database-independent BGC-finding software represents a largely-unexplored avenue of research capable of finding BGCs missed by mainstream software due to its dependence on databases of published BGCs. In this work, a bioinformatics tool is presented, which seeks to unite the fragmented functions of database-independent BGC-finding software into a single comprehensive package and make it accessible to non-expert users through an easy-to-use graphical user interface. The software utilizes the output of NCBI BLAST containing user-selected marker proteins to identify points of co-localization, and then displays the results through a fully- interactive graphical interface which allows users to further analyse the data. The software's capabilities and limitations have been tested on L-tyrosine-derived and L-leucine-derived 4-alkyl-L- proline biosynthetic gene subclusters. The software was able to find 120 out of 121 manually-found biosynthetic gene subclusters, showcasing the reliability of the core algorithm. In addition, a further 131 putative L-leucine-derived 4-alkyl-L-proline...
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Applications of flow cytometry in the study of microbial subpopulations.
Hřebíček, Ondřej ; Lichá, Irena (advisor) ; Sudzinová, Petra (referee)
This work reviews common flow cytometric methods and applications for the study of bacterial organisms. Flow cytometry is fluorescent method capable of both quantitative and qualitative analysis at the single cell level. It can offer insights about bacterial population dynamics, phenotypic heterogeneity and more. This work features a basic introduction to flow cytometry and presents some of the commonly measured variables, such as viability or membrane potential with an emphasis on the fluorescent probes used to visualize them. The difficulties of adapting flow cytometry to bacterial physiology are discussed, as well as the advantages and disadvantages of the particular probes and methods. Finally, this work seeks to demonstrate the flexibility as well as the shortcomings of flow cytometry using examples of practical applications in basic research, environmental microbiology, biotechnology, clinical practice. Keywords: flow cytometry, microbial subpopulations, fluorescent labelling, bacterial physiology, bacterial viability
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Sport and spirituality
Hřebíček, Ondřej ; Bednář, Miloš (advisor) ; Jebavá, Jana (referee)
Name of work: Sport and Spirituality Objectives of work: Look at consistency and coherence between the two at first sight different phenomenas, which are sport and spirituaity and show that these two aspects of human life may be significantly linked. Method: This dissertation is a theoretical work. The main part of information is drawn from literature, then from our own experience. In the first part we put the necessary information base based on the study of literature, in the second part we compare different views obtained by reading, which we connect and eke out with our own thoughts and insights. Results: Work on the mental and spiritual sphere is for sport currently. Physically, people reach the threshold, that why is needed to engage in training and overall approach to sport another aspect that moves the individual performance one step further. This aspect is currently developing mental and spiritual qualities. Key words: spirituality, sport, philosophy, religion, buddhismus 6
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