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Analysis of NGS data for study of transposon activity in cancer cells
Hrazdilová, Ivana ; Čegan,, Radim (referee) ; Eduard, Kejnovský (advisor)
Theoretical part of this diploma thesis gives a brief characteristic of human mobile elements (transposons), which represents nearly 50% of human genome. It provides basic transposon clasification and describes types of transposons present in hunam genome, as well as mobilization, activation and regulation mechanisms. The work also deals with the domestication of transposons, describes the ways in which TE contribute to DNA damage and summarizes the diseases caused by mutagenic activity of transposons in the human genome. Conclusion of theoretical part describes next-generation sequencing technologies (NGS). As practical part, data from RNA-seq experimet were analyzed in order to compare differen transposon activity in normal and cancer cells from prostate and colorectal tissues. As like as publicly available sophisticated tools (TopHat), new scripts were created to analyze these data. The results show that cancer cells exhibit overexpression of transposons. This corresponds with the published results and suggests a connection of transposon activation with cancer development.
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Mobile genetic elements detection by genomic signal processing
Nováková, Jarmila ; Sedlář, Karel (referee) ; Škutková, Helena (advisor)
Mobile genetic elements are occupied by this project. It is aimed at their features, which can be used for their detection. It also deals with issue of conversion of symbolic sequence into numerical form. Classifications of mobile genetic elements are explained, basic types of mobile genetic sequences are described, and principles of numerical maps and detection in symbolic represetation are also clarified. Conversion of symbolic genetical sequences by chosen numerical map and calculation of normalized correlation values for set of mobile genetic elements are compiled. Analysis of the mobile genetic elements properties is performed for design of detector. The library of themes is created at the end for usage by designed detector.
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Detail analysis on antibiotic and heavy-metal resistance genes and horizontal gene transfer traits in anaerobic bacteria
Vancová, Kateřina ; Schwarzerová, Jana (referee) ; Čejková, Darina (advisor)
This thesis deals with a detail analysis on antibiotic and heavy-metal resistance genes and horizontal gene transfer traits in anaerobic bacteria. Antimicrobial resistance (AMR) in bacteria is a growing threat to public health globally. In these bacteria, AMR genes are often associated with mobile genetic elements (MGEs), which promote their mobility, enabling them to rapidly spread throughout a bacterial community. The work describes the horizontal gene transfer, the issue of antimicrobial resistance and the database for the detection of AMR genes and MGEs. After that, the detection and analysis of AMR genes and MGEs in anaerobic bacteria was done. Almost half of them contained at least 1 gene coding for antibiotic or heavy-metal resistance, 112 different genes overall. Then, 66 different MGEs were detected, 4 of which carried 6 different AMR detected genes.
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Detail analysis on antibiotic and heavy-metal resistance genes and horizontal gene transfer traits in anaerobic bacteria
Vancová, Kateřina ; Schwarzerová, Jana (referee) ; Čejková, Darina (advisor)
This thesis deals with a detail analysis on antibiotic and heavy-metal resistance genes and horizontal gene transfer traits in anaerobic bacteria. Antimicrobial resistance (AMR) in bacteria is a growing threat to public health globally. In these bacteria, AMR genes are often associated with mobile genetic elements (MGEs), which promote their mobility, enabling them to rapidly spread throughout a bacterial community. The work describes the horizontal gene transfer, the issue of antimicrobial resistance and the database for the detection of AMR genes and MGEs. After that, the detection and analysis of AMR genes and MGEs in anaerobic bacteria was done. Almost half of them contained at least 1 gene coding for antibiotic or heavy-metal resistance, 112 different genes overall. Then, 66 different MGEs were detected, 4 of which carried 6 different AMR detected genes.
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Genetic basis of multidrug resistance in Acinetobacter baumannii
Křížová, Lenka ; Nemec, Alexandr (advisor) ; Higgins, Paul (referee) ; Šmajs, David (referee)
Charles University in Prague, Faculty of Science Department of Genetics and Microbiology Ph.D. study program: Molecular and Cellular Biology, Genetics and Virology Genetic basis of multidrug resistance in Acinetobacter baumannii Lenka Křížová Supervisor: Doc. RNDr. Alexandr Nemec, Ph.D. Supervisor-consultant: RNDr. Lubomír Janda, Ph.D. Prague 2014 SUMMARY Acinetobacter baumannii has emerged as a significant bacterial pathogen pre-eminently associated with hospital-acquired infections. Strains of this species may currently exhibit resistance to nearly all or even all clinically relevant drugs. The vast majority of epidemic and multidrug-resistant A. baumannii strains belong to a few globally spread lineages, in particular to the so-called European (EU) clones I, II, and III. Complex resistance patterns displayed by these strains result from their marked capacity to develop, acquire, and combine secondary resistance mechanisms against originally effective agents. The aim of this thesis was to broaden our knowledge on the genetic basis and epidemiology of multidrug resistance in A. baumannii. The obtained results have been published in the form of six studies which are part of this thesis. In the first study, we analysed the epidemiology of carbapenem resistance among hospital strains of Acinetobacter in the...
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SCCmec and other mobile genetic elements associated with methicillin resistance in staphylococci.
Kubištová, Lucie ; Lichá, Irena (advisor) ; Plocek, Vítězslav (referee)
Staphylococci are common part of human flora but also they are a dangerous pathogen. Among staphylococci strains, methicillin resistance is widespread. The mecA gene, organized in mec complex, is responsible for methicillin resistance. The mec complex is part of mobile genetic element - staphylococcal chromosome cassette SCCmec. SCCmec is large variable mobile genetic element and it is always composed of three parts - mec complex, ccr complex and J regions. Complex mec consists of mecA gene and its regulatory genes mecR1 and mecI. Complex ccr encodes recombinase genes, they are responsible for excision and insertion of SCCmec. J regions are remaining parts of SCCmec, which include other mobile genetic elements that directly influence methicillin resistance genes expression or carry genes for resistance to other antimicrobial agents. SCCmec or its parts can be transferred by horizontal gene transfer between staphylococci both intraspecific and interspecific, although mechanism of its transfer is still unknown. Eleven types of SCCmec have been described so far. In this thesis, I summarized the findings about molecular composition of SCCmec, horizontal gene transfer of the genes encoding methicillin resistance and molecular evolution of SCCmec. Mobile genetic elements play a key role in evolution and...
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Mobile genetic elements detection by genomic signal processing
Nováková, Jarmila ; Sedlář, Karel (referee) ; Škutková, Helena (advisor)
Mobile genetic elements are occupied by this project. It is aimed at their features, which can be used for their detection. It also deals with issue of conversion of symbolic sequence into numerical form. Classifications of mobile genetic elements are explained, basic types of mobile genetic sequences are described, and principles of numerical maps and detection in symbolic represetation are also clarified. Conversion of symbolic genetical sequences by chosen numerical map and calculation of normalized correlation values for set of mobile genetic elements are compiled. Analysis of the mobile genetic elements properties is performed for design of detector. The library of themes is created at the end for usage by designed detector.
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Analysis of NGS data for study of transposon activity in cancer cells
Hrazdilová, Ivana ; Čegan,, Radim (referee) ; Eduard, Kejnovský (advisor)
Theoretical part of this diploma thesis gives a brief characteristic of human mobile elements (transposons), which represents nearly 50% of human genome. It provides basic transposon clasification and describes types of transposons present in hunam genome, as well as mobilization, activation and regulation mechanisms. The work also deals with the domestication of transposons, describes the ways in which TE contribute to DNA damage and summarizes the diseases caused by mutagenic activity of transposons in the human genome. Conclusion of theoretical part describes next-generation sequencing technologies (NGS). As practical part, data from RNA-seq experimet were analyzed in order to compare differen transposon activity in normal and cancer cells from prostate and colorectal tissues. As like as publicly available sophisticated tools (TopHat), new scripts were created to analyze these data. The results show that cancer cells exhibit overexpression of transposons. This corresponds with the published results and suggests a connection of transposon activation with cancer development.
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