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Analyses of inverted repeats in human patogen genomes
Hanzlíková, Anna ; Nováčková, Ivana (referee) ; Brázda, Václav (advisor)
Pathogens are organisms that cause various host diseases. These include prions, viruses, bacteria, fungi, protozoa and animals. This bachelor thesis is focused specifically on viruses causing human diseases such as severe respiratory syndromes, liver diseases or cervical cancer. The aim of this bachelor thesis was to characterize the presence and location of inverted repeats in the genomes of organism using the web application Palindrome analyzer. Four viruses were selected, two of them are from the group of DNA viruses and two from the group of RNA viruses. In view of the outbreak of a pandemic in early 2020 caused by virus SARSCoV-2, is included in this bachelor thesis. Thus, SARS-CoV and SARS-CoV-2 were selected from RNA viruses and hepatitis B virus and human papillomavirus were selected from the DNA viruses. The sequences of the viral genomes were obtained from the NCBI (National Center for Biotechnology) database. Then, all four viruses were analyzed for the presence of inverse repeats, their location and size using the Palindrome analyzer, which is available online. The largest genome was SARS-CoV-2 of 29 903 bp, which also had the most inverse repeats.
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Anti-Malware Screensaver
Rebenda, Ivo ; Polášek, Petr (referee) ; Peringer, Petr (advisor)
The aim of this thesis is creating anti-malware screen saver and move hardware demanding anti-malware scanning, on time when the user doesn't work with computer. Application programming interface is AVG API, programming language C++. Target operating system is Microsoft Windows.
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Diagnostics of genom conditioned diseases with the use of micro- and nanoparticles
Mondeková, Věra ; Prášek, Jan (referee) ; Provazník, Ivo (advisor)
The bachelor´s thesis discusses possibilities of viral genome´s detection through use of biosensors, more specifically through use of magnetic particles. The introductory part consists of brief characteristic of viruses, mentioned as originator of genom conditioned diseases, followed by chapters related to selected methods of nucleic acid´s extraction and analysis. The main part is dedicated to magnetic particles. The practical part of thesis deals with possibility of use of biosensors in specific viral pathogen´s detection, selection of biocompatible molecules suitable for magnetic particle modification and description of specific DNA sequence isolation procedure through use of magnetic particles.
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Analysis of local structures in DNA molecules
Nyczová, Adéla ; Smetana, Jan (referee) ; Brázda, Václav (advisor)
Local DNA structures are alternative DNA conformations which can be formed aside from typical B-DNA conformation. These structures often play pivotal roles in regulation of basic biological processes, such as DNA replication, transcription or binding of specific ligands. This biological significance makes alternative DNA secondary structures a potential drug target. In this diploma thesis, local structures in genomes of viruses from Flaviviridae and Retroviridae families are analysed using bioinformatics tools. Furthermore, these structures are visualised using atomic force microscopy.
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Methodology to identify missing genetic resources in culture collections, strategy to fill the gaps
Komínek, Petr a kolektiv
The methodology was created under the National programme on conservation of microbial genetic resources of economical imortance. Its preparation was planned in the beginning of a current period of solving the National programme (2018-2022). The methodology describe procedures for the evaluation of specialization of individual collections from the point of view variability of genetic resources held on the collections. The goal of the methodology is to improve the work of microbial collections for the sustainable conservation of microbial genetic resources.
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Critical factors affecting pathogen development in sand flies
Jančářová, Magdaléna ; Volf, Petr (advisor) ; Ratinier, Maxime (referee) ; Bilej, Martin (referee)
This thesis deals with barriers and factors critical for development of viruses, leishmania and gregarines in sand flies. First, we focused on life cycle of sand fly-borne phleboviruses, especially possible routes of sand fly infection. As a laboratory model we chose Massilia virus (MASV), species closely related to Toscana virus, which is main causative agent of summer meningitis in Mediterranean area. We tested different ways of infection by MASV in various developmental stages of Phlebotomus perniciosus; infection of (i) first (L1) and fourth (L4) instar larvae through larval food, (ii) females by blood meal, (iii) both sexes by sugar meal. Infection of L1 and L4 by larval food and subsequent transstadial MASV transmission to adults were not efficient; from 875 adults only three were MASV-positive. Infection through bloodmeal led to high infection rate before defecation, nevertheless, post defecation the infection rate declined and only 5 out of 27 females were MASV-positive. The most efficient infection way was through the sugar meal: 72% of females (88 out of 122) and 51% of males (58 out of 113) were detected as MASV-positive. Moreover, both males and females infected by this way released MASV particles into the drop of sugar which stayed infectious for next 24 hours for other naïve sand...
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Impact of plant alkaloids on viral infection
Šnejdarová, Aneta ; Horníková, Lenka (advisor) ; Váňová, Jana (referee)
Plant products have been used to treat various diseases since ancient times thanks to the many active substances they contain. One such group of substances are alkaloids. Alkaloids are biologically active substances which, in addition to antimicrobial, anti-inflammatory, antioxidant and many other properties, also possess antiviral properties. As a result, they can help treat viral infections, which are still a major medical problem today. Alkaloids affect all steps of virus replication, both viral components but especially cellular processes, without which a successful progress of viral cycle is not possible. In connection with the treatment of viral infections, the tropane, troponol, purine and isoquinoline alkaloids have been best investigated, which are also the subject of this work. The tropane alkaloid atropine acts mainly on enveloped viruses due to its ability to change the properties of biological membranes. Purine alkaloid caffeine, thanks to its ability to inhibit the cellular enzyme phosphodiestrase, causes an increase in intracellular cAMP levels and it has an impact on viral replication. Its antioxidant and immunomodulatory properties are also beneficial for the treatment. The anti-inflammatory effects of the tropane alkaloid colchicine stem from its ability to inhibit the dynamics of...
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Analysis of local structures in DNA molecules
Nyczová, Adéla ; Smetana, Jan (referee) ; Brázda, Václav (advisor)
Local DNA structures are alternative DNA conformations which can be formed aside from typical B-DNA conformation. These structures often play pivotal roles in regulation of basic biological processes, such as DNA replication, transcription or binding of specific ligands. This biological significance makes alternative DNA secondary structures a potential drug target. In this diploma thesis, local structures in genomes of viruses from Flaviviridae and Retroviridae families are analysed using bioinformatics tools. Furthermore, these structures are visualised using atomic force microscopy.
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Critical factors affecting pathogen development in sand flies
Jančářová, Magdaléna
This thesis deals with barriers and factors critical for development of viruses, leishmania and gregarines in sand flies. First, we focused on life cycle of sand fly-borne phleboviruses, especially possible routes of sand fly infection. As a laboratory model we chose Massilia virus (MASV), species closely related to Toscana virus, which is main causative agent of summer meningitis in Mediterranean area. We tested different ways of infection by MASV in various developmental stages of Phlebotomus perniciosus; infection of (i) first (L1) and fourth (L4) instar larvae through larval food, (ii) females by blood meal, (iii) both sexes by sugar meal. Infection of L1 and L4 by larval food and subsequent transstadial MASV transmission to adults were not efficient; from 875 adults only three were MASV-positive. Infection through bloodmeal led to high infection rate before defecation, nevertheless, post defecation the infection rate declined and only 5 out of 27 females were MASV-positive. The most efficient infection way was through the sugar meal: 72% of females (88 out of 122) and 51% of males (58 out of 113) were detected as MASV-positive. Moreover, both males and females infected by this way released MASV particles into the drop of sugar which stayed infectious for next 24 hours for other naïve sand...
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