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Bacterial REP elements: origins, variability and application.
Nunvář, Jaroslav ; Lichá, Irena (advisor) ; Pačes, Jan (referee) ; Melter, Oto (referee)
4 ABSTRACT (English) This thesis is based on three published research papers studying bacterial REP (repetitive extragenic palindrome) elements. REP elements are one of the best-characterized groups of bacterial DNA repeats, distributed mostly in gammaproteobacteria, including enterobacteria. They are present in noncoding parts of host genomes, usually occurring in hundreds of copies. REPs are typically aggregated in higher order repeats. In the Gram-negative model Escherichia coli, interactions of several proteins important for cell's physiology with REPs were described, indicating significant role for these elements for host cells. The first work (Nunvar et al. 2010) presents the discovery of a protein class, related to IS200/IS605 transposases. These proteins, termed RAYTs (REP-associated tyrosine transposases), contain characteristic motifs in their amino acid sequences, which are absent in canonical IS200/IS605 transposases. Another attribute of RAYTs is the arrangement of their encoding genes. These are single copy genes, always flanked at both termini by at least two REPs in inverted orientation. Based on the similarity between the REP-rayt-REP unit and insertion sequences of the IS200/IS605 family, between RAYTs and tyrosine transposases and between REPs and subterminal sequences of the IS200/IS605...
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Bacterial REP elements: origins, variability and application.
Nunvář, Jaroslav
4 ABSTRACT (English) This thesis is based on three published research papers studying bacterial REP (repetitive extragenic palindrome) elements. REP elements are one of the best-characterized groups of bacterial DNA repeats, distributed mostly in gammaproteobacteria, including enterobacteria. They are present in noncoding parts of host genomes, usually occurring in hundreds of copies. REPs are typically aggregated in higher order repeats. In the Gram-negative model Escherichia coli, interactions of several proteins important for cell's physiology with REPs were described, indicating significant role for these elements for host cells. The first work (Nunvar et al. 2010) presents the discovery of a protein class, related to IS200/IS605 transposases. These proteins, termed RAYTs (REP-associated tyrosine transposases), contain characteristic motifs in their amino acid sequences, which are absent in canonical IS200/IS605 transposases. Another attribute of RAYTs is the arrangement of their encoding genes. These are single copy genes, always flanked at both termini by at least two REPs in inverted orientation. Based on the similarity between the REP-rayt-REP unit and insertion sequences of the IS200/IS605 family, between RAYTs and tyrosine transposases and between REPs and subterminal sequences of the IS200/IS605...
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Bacterial REP elements: origins, variability and application.
Nunvář, Jaroslav
4 ABSTRACT (English) This thesis is based on three published research papers studying bacterial REP (repetitive extragenic palindrome) elements. REP elements are one of the best-characterized groups of bacterial DNA repeats, distributed mostly in gammaproteobacteria, including enterobacteria. They are present in noncoding parts of host genomes, usually occurring in hundreds of copies. REPs are typically aggregated in higher order repeats. In the Gram-negative model Escherichia coli, interactions of several proteins important for cell's physiology with REPs were described, indicating significant role for these elements for host cells. The first work (Nunvar et al. 2010) presents the discovery of a protein class, related to IS200/IS605 transposases. These proteins, termed RAYTs (REP-associated tyrosine transposases), contain characteristic motifs in their amino acid sequences, which are absent in canonical IS200/IS605 transposases. Another attribute of RAYTs is the arrangement of their encoding genes. These are single copy genes, always flanked at both termini by at least two REPs in inverted orientation. Based on the similarity between the REP-rayt-REP unit and insertion sequences of the IS200/IS605 family, between RAYTs and tyrosine transposases and between REPs and subterminal sequences of the IS200/IS605...
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Bacterial REP elements: origins, variability and application.
Nunvář, Jaroslav ; Lichá, Irena (advisor) ; Pačes, Jan (referee) ; Melter, Oto (referee)
4 ABSTRACT (English) This thesis is based on three published research papers studying bacterial REP (repetitive extragenic palindrome) elements. REP elements are one of the best-characterized groups of bacterial DNA repeats, distributed mostly in gammaproteobacteria, including enterobacteria. They are present in noncoding parts of host genomes, usually occurring in hundreds of copies. REPs are typically aggregated in higher order repeats. In the Gram-negative model Escherichia coli, interactions of several proteins important for cell's physiology with REPs were described, indicating significant role for these elements for host cells. The first work (Nunvar et al. 2010) presents the discovery of a protein class, related to IS200/IS605 transposases. These proteins, termed RAYTs (REP-associated tyrosine transposases), contain characteristic motifs in their amino acid sequences, which are absent in canonical IS200/IS605 transposases. Another attribute of RAYTs is the arrangement of their encoding genes. These are single copy genes, always flanked at both termini by at least two REPs in inverted orientation. Based on the similarity between the REP-rayt-REP unit and insertion sequences of the IS200/IS605 family, between RAYTs and tyrosine transposases and between REPs and subterminal sequences of the IS200/IS605...
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Verification of the possibility of cancer therapy using bacteria Stenotrophomonas maltophilia. Optimization of this therapy, the effect of agonist of signaling receptors.
SVÁČKOVÁ, Petra
Cancerous disease or cancer is a very feared disease, old as the history of mankind itself. Cancer is understood as a lifestyle disease that affects increasing number of people. Statistical surveys show that the problem is more than current and should be paid close attention to. The main objectives of this thesis are to understand the issue of tumor therapy and to verify the possibilities of using a microorganism therapy. The bachelor thesis has a theoretical and an experimental part. The findings were verified in the experimental part and the hypotheses obtained from the research paper were verified in the theoretical part. The theoretical part is focused on understanding a broad topic of cancer, reaching from the definition of what cancer is, how it arises, up to the therapy options. The second section of the theoretical part is focused on tumorous disease therapy using microorganisms. A research has been made regarding the use of bacteria for cancer treatment. Further research has shown that at natural pH the tumor cells are of a negative charge. That means that if there is a bacteria of naturally positive charge and it is applied on the place of tumor, the positively charged bacteria is bound to the negatively charged cell. After such binding an immune response of the organism is followed, fighting not only against the inflammation caused by the bacteria, but also against the tumor cells. The bacterium S. maltophilia seems to be positively charged. To confirm this hypothesis it was necessary to find a bacteria with similar features, size and ability to move like those of S. maltophilia, but charged negatively . The bacterium S. marcescens is the most convenient, also forming part of Colley´s toxin. Experiments were carried out in female mice of inbred strain C57BL/6 from Charles River Laboratories, using cell line of B16-F10 mice melanoma. The cultivation method of the bacterium S. maltophilia and S. marcescens was introduced in the phase of the in vitro experiment. In the first in vivo experiment a hypothesis was confirmed that by the intratumoral application of the vaccine with the inactivated bacterium S. maltophilia the melanoma was affected. The second in vivo experiment verified the hypothesis concerning the negative charge of the tumor cell and the positive charge of the bacterium S. maltophilia. S. marcescens was used as a control bacteria with a negative charge. The experiments monitored both, the growth and the volume of the tumor. The tumors were measured once in two days by means of caliper, which determined the size of the tumor. The volume of the tumor was calculated. Statistical analysis of data was done using Student's t-test in MS Excel program. The survival of mice was evaluated using the Kaplan-Meier test in the Med Calc program. Performing the in vitro experiment the cultivation of both bacteria was introduced in the workplace. The first in vivo experiment where the bacterium S.maltophilia was used confirmed the hypotesis of the positive impact of the intratumorous application of the bacteria on the melanoma. 472 days on the 10.8.2013, after initiation of therapy - 26.4. 2012). The second in vivo experiment confirmed the hypothesis of the effect of the bacteria charge on the size of the tumor. By means of testing the bacterium S. maltophilia and S. marcescens it was confirmed that the bacterium S. maltophilia affects the reduction of the tumor growth much more than the bacterium S. marcescens. The experiments carried out in the thesis confirmed the hypothesis of the positive impact of bacteria charges on their antitumor effect in the treatment of B16-F10 melanoma.
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