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SARS-CoV-2 methyltransferases as druggable targets
Kocek, Hugo ; Nencka, Radim (advisor) ; Bouřa, Evžen (referee)
Novel coronavirus (earlier referred to as "nCoV2019") became part of our lives in March 2020 and overnight turned everything upside-down. This virus is transmitted via respiratory droplets and causes respiratory diseases COVID-19 which can be severe and even fatal. So far, no effective treatment has been discovered and vaccination is our biggest hope thanks to its high efficacy. It is important to point out, that new mutations may possess problems and escape immunity induced by the vaccination. During the whole pandemic, many approved drugs were tested against SARS-CoV-2 (for example favipiravir, toremifene, and hydroxychloroquine) but none of those drugs showed to be effective against SARS-CoV-2 in clinical trials. The only approved antiviral drug is nucleotide analog remdesivir which showed significant efficacy against SARS-CoV-2 in clinical trials. However, timing and overall patient's health condition play a key role. Development of new antiviral drugs is necessary given the fact that this is the third time we face coronavirus with the potential to cause pandemic since the beginning of the 21st century. Therefore, it is likely that another new coronavirus will emerge. This thesis focuses on S-adenosylmethionine-dependent methyltransferases nsp14 and nsp16 from SARS-CoV-2 because they play a key...
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Splicing Factors in the Regulation of Gene Expression - the Relationship Between Splicing and Transcription in Saccharomyces cerevisiae
Hálová, Martina
Transcription and pre-mRNA processing, e.g., splicing, occur at the same place and time in the context of chromatin. A growing amount of evidence supports the hypothesis that these processes are interconnected. Prp45/SKIP is one of the factors which are believed to mediate the interconnection. The human ortholog, SKIP, is known for affecting mRNA formation on the levels of transcription initiation and elongation. Moreover, it interacts with chromatin modifiers and it is a splicing factor, too. The function of the Saccharomyces cerevisiae ortholog, Prp45, has been so far connected only to pre-mRNA splicing. In this work, we characterized the role of Prp45 in splicing and elaborated the results connecting Prp45 to transcription and chromatin modifications. RNA-seq results showed that pre-mRNA is accumulated in prp45(1-169) cells. This accumulation is not caused by the reduced activity of pathways responsible for RNA degradation. The extent of the splicing inefficiency in prp45(1-169) cells did not depend on either the canonicity of the 5' splice site and branch site or the distance between the branch site and the 3' splice site. Using chromatin immunoprecipitation, we found that prp45(1-169) mutation causes delay in U2 snRNP recruitment to assembling spliceosome. This delay transfers to the later...
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Splicing Factors in the Regulation of Gene Expression - the Relationship Between Splicing and Transcription in Saccharomyces cerevisiae
Hálová, Martina
Transcription and pre-mRNA processing, e.g., splicing, occur at the same place and time in the context of chromatin. A growing amount of evidence supports the hypothesis that these processes are interconnected. Prp45/SKIP is one of the factors which are believed to mediate the interconnection. The human ortholog, SKIP, is known for affecting mRNA formation on the levels of transcription initiation and elongation. Moreover, it interacts with chromatin modifiers and it is a splicing factor, too. The function of the Saccharomyces cerevisiae ortholog, Prp45, has been so far connected only to pre-mRNA splicing. In this work, we characterized the role of Prp45 in splicing and elaborated the results connecting Prp45 to transcription and chromatin modifications. RNA-seq results showed that pre-mRNA is accumulated in prp45(1-169) cells. This accumulation is not caused by the reduced activity of pathways responsible for RNA degradation. The extent of the splicing inefficiency in prp45(1-169) cells did not depend on either the canonicity of the 5' splice site and branch site or the distance between the branch site and the 3' splice site. Using chromatin immunoprecipitation, we found that prp45(1-169) mutation causes delay in U2 snRNP recruitment to assembling spliceosome. This delay transfers to the later...
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Splicing Factors in the Regulation of Gene Expression - the Relationship Between Splicing and Transcription in Saccharomyces cerevisiae
Hálová, Martina ; Folk, Petr (advisor) ; Pospíšek, Martin (referee) ; Staněk, David (referee)
Transcription and pre-mRNA processing, e.g., splicing, occur at the same place and time in the context of chromatin. A growing amount of evidence supports the hypothesis that these processes are interconnected. Prp45/SKIP is one of the factors which are believed to mediate the interconnection. The human ortholog, SKIP, is known for affecting mRNA formation on the levels of transcription initiation and elongation. Moreover, it interacts with chromatin modifiers and it is a splicing factor, too. The function of the Saccharomyces cerevisiae ortholog, Prp45, has been so far connected only to pre-mRNA splicing. In this work, we characterized the role of Prp45 in splicing and elaborated the results connecting Prp45 to transcription and chromatin modifications. RNA-seq results showed that pre-mRNA is accumulated in prp45(1-169) cells. This accumulation is not caused by the reduced activity of pathways responsible for RNA degradation. The extent of the splicing inefficiency in prp45(1-169) cells did not depend on either the canonicity of the 5' splice site and branch site or the distance between the branch site and the 3' splice site. Using chromatin immunoprecipitation, we found that prp45(1-169) mutation causes delay in U2 snRNP recruitment to assembling spliceosome. This delay transfers to the later...
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The relationship between splicing and posttranslational modifications of chromatin in Saccharomyces cerevisiae
Kovaľová, Libuša ; Folk, Petr (advisor) ; Čáp, Michal (referee)
Protein Prp45, the yeast ortholog of the human transcription coregulator SNW1/SKIP, has been previously associated only with the regulation of pre-mRNA splicing. However, our laboratory found that protein Prp45 genetically interacts not only with the proteins involved in pre-mRNA splicing, but also with factors important for transcription elongation and with chromatin modifying enzymes. Our data and the information about the human ortholog SNW1/SKIP suggest that Prp45 could serve as a regulator coupling splicing, transcription and chromatin state in S. cerevisiae. The main aim of this diploma thesis was to find out whether the protein Prp45, which is essential for cotranscriptional assembly of the spliceosome, affects posttranslational modifications of chromatin on transcribed genes. Using chromatin immunoprecipitation, the influence of prp45(1-169) mutation on trimethylation of histone H3 at lysine 4 and acetylation of histone H3 at lysines 9, 14 and 18 on transcriptionally active genes was not confirmed. The other aim was to analyse the behavior of cells synchronized by α-factor by using flow cytometry. According to our results, prp45(1-169) mutation leads to the prolongation of the cell cycle. For the purpose of monitoring the dynamics of nucleosomes in S. cerevisiae strains, the system of...
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Preparation and characterization of hydrogels based on cationic biopolymer
Tesařová, Barbora ; Mravec, Filip (referee) ; Smilek, Jiří (advisor)
Presented thesis deals with the preparation and characterization of hydrogels based on positively-charged biopolymer and negatively-charged tenside. As an appropriate representative of positively-charged polymer was chosen chitosan, because of his biocompatibility and biodegrability, and N,N,N-trimethylchitosan, which was synthetised from chitosan in this diploma thesis. The final product of synthesis was characterised by SEC-MALS, elemental analysis, infrared spectroscopy and nuclear magnetic rezonation. Interactions between these polymers and representatives of negatively-charged tensides, which are sodium dodecylsuphate and sodium tetradecylsulphate, were investigated. The main method used in this thesis was rheology, through it were investigated prepared hydrogels based on chitosan and tensides and also prepared microgels based on N,N,N-trimethylchitosan and tensides. The interactions between polymers and tensides have been proved.
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Impact of the rRNA modifications on protein synthesis
Kročová, Eliška ; Pospíšek, Martin (advisor) ; Holá, Dana (referee)
A ribosome is a supramolecular structure, which mediates synthesis of all cellular proteins, and therefore is essential for cell life. The fact, that some nucleotides of ribosomal RNA are modified, is known for forty years. However only recently, successful deeper studies on how the individual modifications are synthesized and what is their effect on ribosome synthesis and function appear. Some particular nucleotide modifications are important for the ribosome formation (like m1 acp3 Ψ1191 SSU), some others influence proper function of the ribosome (e.g. Um2921, Gm2922, Ψ2923 LSU, m1 acp3 Ψ1191 SSU). Majority of modified nucleotides in eukaryotic rRNA is being recognized by small nucleolar RNA (snoRNA). Few nucleotides is, however, recognized and subsequently modified by specific proteins. These proteins also play crucial role in ribosome maturation. In thesis presented, current knowledge on the role of ribosomal RNA nucleotide modifications during their formation and maturation, and on their function is summarized and overviewed.
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Utilization of Diffusive Techniques in Study on Reactivity of Biocolloids
Kalina, Michal ; Maršálek, Roman (referee) ; Mráček, Aleš (referee) ; Klučáková, Martina (advisor)
The main aim of this thesis is the utilization of simple diffusion techniques for the study on transport properties of copper ions in the systems containing humic acids with respect to the other parameters, which can affect the process (the structure of diffusion environment, the interactions between transported specie and diffusion matrices, selective blocking of binding sites of humic acids). The first part of experimental works was focused on characterization of studied materials (humic acids, humic sol and humic hydrogel). The main part of the thesis was dealing with the optimization of simple diffusion techniques, which were suitable for the study on transport of copper ions in matrices containing humic acids, taking into account the mutual interactions between studied components in the system. The obtained diffusion characteristics were compared to the data determined using sorption experiments. Consequently, the minor goal of the experimental works of this thesis was also the assessment of the influence of basic physico-chemical parameters of studied materials on transport phenomenon.
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Characterization of methylated humic acids
Solná, Irena ; Kislinger, Jiří (referee) ; Klučáková, Martina (advisor)
The main concern of this bachelor thesis was a characterization of the properties of methylated humic acids. Retrieval on modifications of acidic functional groups of humic substances was done. In addition appropriate experimental methods for assessing the impact of methylation of carboxylic groups of humic acids were selected. Methylation of formentioned carboxylic groups is used to improve stability of humic acids while working with them. The sample of methylated humic acids, produced by the University of Poitiers in France, was investigated by the following methods: UV-Vis spectroscopy, FT-IR spectroscopy, fluorescence spectroscopy and thermal analysis - TGA, DSC. The degree of methylation of carboxylic functional groups of methylated humic acids was considered using an indirect titration. Results were trade-off with the sample without methylation. The impact of gelation on properties of methylated and non-methylated humic acids was also studied.
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