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Operon structures inference in genome-wide analysis
Nejezchlebová, Julie ; Jurečková, Kateřina (referee) ; Schwarzerová, Jana (advisor)
The bachelor thesis is devoted to the problem of derivation of operon structures and creation of a software tool that allows prediction of operon structures. The tool both predicts operons based on gene expression information, but also refines already predicted operons with gene expression information. The tool is tested on the bacteria Escherichia coli BW25113 and Clostridium beijerinckii NRRL B-598. The theoretical part is devoted to description of operon structure and function, genome sequencing, transcriptome analysis, Clostridium beijerinckii NRRL B-598, Escherichia coli BW25113 and already available online tools for inferring operon structures. In the practical part of the thesis, the pre-processing of raw transcriptomic data to obtain a suitable format for the prediction of operon structures, testing of online tools and the actual implementation of the tool itself are discussed.
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Operon structures inference in genome-wide analysis
Nejezchlebová, Julie ; Jurečková, Kateřina (referee) ; Schwarzerová, Jana (advisor)
The bachelor thesis is devoted to the problem of derivation of operon structures and creation of a software tool that allows prediction of operon structures. The tool both predicts operons based on gene expression information, but also refines already predicted operons with gene expression information. The tool is tested on the bacteria Escherichia coli BW25113 and Clostridium beijerinckii NRRL B-598. The theoretical part is devoted to description of operon structure and function, genome sequencing, transcriptome analysis, Clostridium beijerinckii NRRL B-598, Escherichia coli BW25113 and already available online tools for inferring operon structures. In the practical part of the thesis, the pre-processing of raw transcriptomic data to obtain a suitable format for the prediction of operon structures, testing of online tools and the actual implementation of the tool itself are discussed.
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Making Transgenic \kur{C. elegans} with Polycistronic mCherry Vector
FARKA, Dominik
Creation of transgenic animals has become a popular method to analyse gene function. In the nematode Ceanorhabditis elegans transformation is widely used and can be achieved by microinjection. For functional analyses, transgene constructs typically contain a promoter driving the expression of the protein of interest that is fused to a fluorescent protein. However, as this fusion of proteins can lead to misfolding of the protein of interest and may not reflect proper function, a modification of the expression vector has been developed; introducing a short sequence of non-coding DNA in-between the sequences of the two proteins and making the construct compatible with a polycistronic operon system. In this study, four different polycistronic constructs were introduced into C. elegans by means of microinjection in order to provide new tools for the analyses of gene function. Tissue specific promoters wrt-2 (seam cells), grl-21 (hyp7), and egl-17 (vulval precursor cells) were used to over-express either NHR-25 or SMO-1 in the corresponding tissues and the expression was visualized by independently translated mCherry red fluorescent. 10 independent transformed C. elegans strains were established and corresponding tissue-specific promoter activities were confirmed. Furthermore, in some cases, ectopic behaviour was observed e.g. ectopic mCherry expression in different tissues or specific cell differentiation defects that was most likely caused by the overexpression of NHR-25 or SMO-1. This study was the first case in our laboratory to generate transformed C. elegans utilizing the polycistronic mCherry vector system. New genetic tools were introduced in the laboratory useful for further analyses of gene function.
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