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Analysis of horizontal transfer of genetic components using static network analysis
Labanava, Anastasiya ; Jurečková, Kateřina (referee) ; Schwarzerová, Jana (advisor)
The bachelor's thesis focuses on the issue of horizontal genetic elements transfer between bacteria of different strains and the software analysis implementation that enables horizontally transferred genes identification. The packages and tools used were tested on a dataset of bacterial genomes from several strains. The thesis’ theoretical part provides a detailed description of the genetic components transfer between bacteria and describes modern laboratory techniques that enable genome sequencing in various ways. In the practical part, the thesis deals with the preprocessing of genomic files to obtain suitable data for annotation. To detect the horizontal transfer of genetic elements between bacteria, a script is introduced, which organizes annotated bacteria to tables and searches for the same genes in their genomes that, under theoretical assumptions, were horizontally transferred. Furthermore, the gene transfer is visualized using tools that graphically represent phylogenetic relations between bacteria. In the final step, bacterial genomes are connected into networks, and based on their static analysis, a discussion is conducted on the results accuracy and the success of the proposed analysis.
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Vliv kovů v potravinářství na bakteriální virulenci
Pavezka, Pavel
The bachelor's thesis deals with the issue of gene transfer of resistance of β-lactam antibiotics by means of horizontal gene transfer, specifically transformation. It deals with the transfer of resistance genes through the food chain, when Escherichia coli can subsequently cause foodborne illness. It also points to the current risks of resistance to β-lactam antibiotics and an alternative method of replacing antibiotics with an iron complex together with an antibiotic. The experimental part is demonstrating the antibacterial effect of the Fe16+AMP complex on the ampicillin-resistant bacterial strain E. coli CCM 4225 and the sensitive strain E. coli CCM 3953. The minimum inhibitory concentration was experimentally determined for these samples. Morphological changes upon exposure of the Fe16+AMP complex to E. coli CCM 3953 were also observed using a cryo-SEM scanning electron microscope. The development of resistance to the model bacterium E. coli TOP10 by transformation was also investigated and verified by polymerase chain reaction PCR and gel electrophoresis. Based on the results, it was proven that the Fe16+AMP complex has an inhibitory effect on the bacterium E. coli CCM 3953 and does not have a significant effect on the resistance spreading via transformation mechanism.
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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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Analysis of horizontal transfer of genetic components using static network analysis
Labanava, Anastasiya ; Jurečková, Kateřina (referee) ; Schwarzerová, Jana (advisor)
The bachelor's thesis focuses on the issue of horizontal genetic elements transfer between bacteria of different strains and the software analysis implementation that enables horizontally transferred genes identification. The packages and tools used were tested on a dataset of bacterial genomes from several strains. The thesis’ theoretical part provides a detailed description of the genetic components transfer between bacteria and describes modern laboratory techniques that enable genome sequencing in various ways. In the practical part, the thesis deals with the preprocessing of genomic files to obtain suitable data for annotation. To detect the horizontal transfer of genetic elements between bacteria, a script is introduced, which organizes annotated bacteria to tables and searches for the same genes in their genomes that, under theoretical assumptions, were horizontally transferred. Furthermore, the gene transfer is visualized using tools that graphically represent phylogenetic relations between bacteria. In the final step, bacterial genomes are connected into networks, and based on their static analysis, a discussion is conducted on the results accuracy and the success of the proposed analysis.
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Analýza repetic v genomech vybraných druhů modrásků rodů \kur{Polyommatus} a \kur{Lysandra}
HRUBÁ, Monika
This thesis focuses on the analysis of mobile elements in the genera Polyommatus and Lysandra (Lepidoptera) with a potential impact on karyotype fragmentation. The presence of selected mobile elements in genomes of 15 lycaenid species was tested by PCR. Moreover, the same method was used to detect these elements in 13 selected ant species, which may present a source for lateral gene transfer in myrmecophilous blue butterfly species. Selected transposable elements were localized in pachytene nuclei using fluorescence in situ hybridization. The results of this thesis suggest a patchy phylogenetic pattern of studied repeats which can be partly explained by mobile elements spread through interspecific hybridization and horizontal gene transfer among studied Polyommatus and Lysandra species.
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Enterococcus spp. as a reservoir of resistance genes.
Zajíčková, Adéla ; Lichá, Irena (advisor) ; Balíková Novotná, Gabriela (referee)
Bacteria of the genus Enterococcus are categorised among common nosocomial pathogens. They are a significant reservoir of resistance genes to a majority of antibiotics and exhibit an intrinsic resistance to low levels of beta-lactams, glycopeptides, aminoglycosides, streptogramines and lincosamides. The aim of this paper is to review the main resistance genes and other mechanisms involved in the resistance of bacteria of this genus to antibiotics. The paper is mainly focused on the resistance to beta-lactam antibiotics, which is provided by the expression and mutations of low-affinity PBPs, the individual van resistance types mediating resistance to vancomycin, and the expression of enzymes capable of modifying the functional groups of aminoglycoside antibiotics. The paper also describes the resistance to newer antibiotics that are used to treat vancomycin-resistant isolates. The resistance to individual antibiotics can arise from the coding of their own chromosomal genes or entire signaling pathways leading to a reduction in the effect of antibiotics, the acquisition of genetic mutations, and especially the spread of new resistance genes by horizontal transfer.
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