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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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Analyses of inverted repeats localization in bacterial genomes
Šedý, Michal ; Zemanová, Jana (referee) ; Brázda, Václav (advisor)
Inverted repeats (IR) are common part of DNA of all living prokaryotic and eukaryotic organisms. Inverted repeats plays an important role in the regulation of basics cells processes. They are responsible for formation of cruciform structures. Inverted repeats also cause genomic instability and can be a source of numerous mutations. Cruciform structures can be recognized by DNA-binding proteins and can also act as a transcriptional regulators. Using the Palindrome Analyser tool, the frequency of IR and localization of inverted repeats in bacterial genomes was analyzed. The frequency of IR across the bacterial genome is variable. The frequency of short inverted repeats shows an approximately quadratic dependence on the %GC content in the genome with a minimum of about 50% of GC content. The localization of inverted repeats with respect to “annotated features” show a non-random distribution. The frequency of IR for most features is higher “outside” than “inside”.
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Presence and localization of local DNA structures in papillomavirus genomes
Vyoralová, Andrea ; Kollerová, Silvia (referee) ; Brázda, Václav (advisor)
Papillomaviruses are sexually transmitted pathogens with a genome length of about 8 kbp. The probability that an adult person will suffer from a papillomavirus infection is up to 80–90%. In most cases, the immune system will eliminate the infection. However, in women it can lead to the development of cervical cancer. That is caused by the high-risk human papillomaviruses, against which vaccination is available. Sequences rich in guanine have been found in the genomes of papillomaviruses, in these sequences the formation of G-quadruplexes occur. They are formed by stacked G-tetrads and are stabilized by monovalent cations, most often K+ and Na+. They are found e.g. in telomeres, oncogene promoters, transcription factor binding sites and recombination sites. Inverted repeats (IR) are also found in the genomes of these viruses. They consist of sequences of nucleotides followed by its reverse complement. Inverted repeats are being referred to as hotspots of genomic instability because they fold into hairpin or cruciform structures that disrupt DNA replication. G4Hunter and Palindrome analyzer were used to analyze the genomes. The analysis revealed that the presence of PQS (Potential Quadruplex-forming Sequence) is higher in papillomaviruses infecting vertebrates than in viruses infecting humans due to the higher content of guanine and cytosine which are connected to the formation of PQS. A higher frequency of PQS presence was found in the genomes of papillomaviruses than in Archaea, Bacteria and Homo sapiens. IR analysis showed that the shortest IRs (6 bases) are the mostly present in the genome and also that IRs formed of 25–30 bases are found in only a few genomes.
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Analyses of inverted repeats localization in bacterial genomes
Šedý, Michal ; Zemanová, Jana (referee) ; Brázda, Václav (advisor)
Inverted repeats (IR) are common part of DNA of all living prokaryotic and eukaryotic organisms. Inverted repeats plays an important role in the regulation of basics cells processes. They are responsible for formation of cruciform structures. Inverted repeats also cause genomic instability and can be a source of numerous mutations. Cruciform structures can be recognized by DNA-binding proteins and can also act as a transcriptional regulators. Using the Palindrome Analyser tool, the frequency of IR and localization of inverted repeats in bacterial genomes was analyzed. The frequency of IR across the bacterial genome is variable. The frequency of short inverted repeats shows an approximately quadratic dependence on the %GC content in the genome with a minimum of about 50% of GC content. The localization of inverted repeats with respect to “annotated features” show a non-random distribution. The frequency of IR for most features is higher “outside” than “inside”.
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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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