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Methylation of viral RNA
Šimonová, Anna ; Macíčková Cahová, Hana (advisor) ; Sýkora, David (referee) ; Elleder, Daniel (referee)
Viruses are the major force that shapes the evolution of both pro- and eukaryotic organisms. They have a simple inner organization and contain only a few, usually well-described RNAs. In the case of +(ss)RNA viruses, their genomic RNA serves also as mRNA. This makes them a perfect model system for searching for new mRNA modifications as well as for understanding the role of already known modifications. In this work, Human Immunodeficiency Virus type 1 (HIV-1) from the Retroviridae family was used as a model system. In the following study, four representatives from the Picornaviridae family were tested for RNA methylation profile. To get the information, a combination of two techniques was developed, liquid chromatography- mass spectrometry (LC-MS) and sequencing techniques. Results of LC-MS reveal a surprisingly high amount of 1-methyladenosine (m1 A) in RNA isolated from HIV-1. Nevertheless, the m1 A mapping sequencing technique confirm m1 A position only in co-packed tRNA. This led to the recalculation of HIV-1 virion RNA composition. In the case of Picornaviridae, LC-MS revealed m1 A and 5-methylcytidine (m5 C) in two insect viruses (Sacbrood virus, SBV and Deformed wing virus, DWV). RNA seq techniques (m1 A mapping and bisulfite sequencing) confirmed the presence of m1 A and m5 C only in tRNA....
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Capillary monolithic columns based on copolymer of styrene, divinylbenzene and methacrylic acid and their application for separations of small molecules.
Musilová, Adéla ; Coufal, Pavel (advisor) ; Čabala, Radomír (referee) ; Sýkora, David (referee)
This work is focused on the preparation and characterization of capillary monolithic columns based on a copolymer of styrene, divinylbenzene and methacrylic acid for the chromatographic separation of small molecules. The capillary monolithic columns were prepared in the quartz capillaries by one-step radical copolymerization reaction of monomers of styrene, divinylbenzene and methacrylic acid in the presence of toluene and isooctane as porogenic solvents and azobisisobutyronitrile as an initiator. The effect of incorporation of methacrylic acid into the polymerization mixture on the separation behavior and efficiency in reversed phase capillary liquid chromatography (CLC) and capillary liquid electrochromatography (CEC) was studied using a test mixture of compounds containing thiourea, phenol, aniline, benzene, toluene, ethylbenzene, propylbenzene and butylbenzene. The Walters test for reversed stationary phases was employed to evaluate the hydrophobicity of the prepared columns. Based on the calculated value of hydrophobicity index of 10.76, the prepared monolithic columns can be classified as very hydrophobic. Excellent repeatability of measurements in CLC mode and very good repeatability of the monolithic column preparation were achieved. The effect of polymerization time on the chromatographic...
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Utilization of liquid chromatography-mass spectrometry for the analysis of psychoactive substances in unconventional matrices
Nemeškalová, Alžběta ; Sýkora, David (advisor) ; Vrkoslav, Vladimír (referee)
Utilization of liquid chromatography-mass spectrometry for the analysis of psychoactive substances in unconventional matrices Abstract The growing popularity of new products used as alternatives to the traditional illegal drugs represents a current challenge for toxicological laboratories, which are required to widen the range of analytical methods and aim at new analytes and matrices. This work focuses on two types of analytes, specifically, amphetamine-like stimulants and cannabinoids, and their analysis in a variety of complex matrices. An LC-MS/MS method suitable for the analysis of amphetamine-like stimulants in newborn meconium and breast milk was developed. The sample extraction was based on the principles of salting-out assisted liquid-liquid extraction, which can be considered a potential alternative to conventional extraction techniques. The analysis was performed using a reversed-phase chromatography coupled to tandem mass spectrometry in multiple reaction monitoring mode, and the method was validated for six analytes, namely amphetamine, methamphetamine, 3,4- methylendioxymethamphetamine, mephedrone, methylone and 3,4- methylenedioxypyrovalerone. Finally, the analysis of authentic meconium and breast milk samples confirmed the applicability of the method. An LC-UV-MS/MS method for the analysis...
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Polymethacrylate monolithic columns in capillary liquid chromatography
Grafnetter, Jan ; Coufal, Pavel (advisor) ; Pacáková, Věra (referee) ; Ventura, Karel (referee) ; Sýkora, David (referee)
3 Conclusions This Thesis gives chromatographic and structural characteristics of the butyl methacrylate monolithic columns prepared for the capillary liquid chromatography. Results of this Thesis clearly demonstrate the possibility of preparation of capillary monolithic columns with a good repeatability of the principal chromatographic parameters. A completely new technique for preparation of the monolithic columns for use in the on-column detection mode was introduced. Different photometric detection modes were applied to monolithic capillary columns in CLC. The advantages and disadvantages of the on-column detection mode in comparison to the additional detection capillary were studied and described. It was shown that the best separation and the most sensitive quantification in the short analysis time could be reached by using the monolithic columns with detection window placed directry on the separation capillary, just after the stationary phase or within the monolith. The attempts leading to preparation of chiral monolithic stationary phases, which would allow enantioseparation of selected chiral analýes' were not totally successful. No time was left to find the suitable chromatographic conditions for enantioseparations. \ I
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Analysis of biologically active substances by modern separation methods
Bierhanzl, Václav ; Čabala, Radomír (advisor) ; Pacáková, Věra (referee) ; Sýkora, David (referee)
The thesis is dedicated to the phospholipids and their polar headgroups analysis by gas chromatography, capillary electrophoresis and mass spectrometry. Phospholipids are the most important polar lipids and they are classified into phospholipid classes according to their phosphorylated groups. Phospholipids can be found in cell membranes and the changes in their ratio are monitored to research the impact of external conditions on cells. Actually thin layer chromatography is still used for phospholipid class ratio analyses. It is not suitable for microbiological research due to its time demandingness. The presented compendium of papers engaged in phospholipid classification is targeted on Bacillus subtilis strain, which produces potential antibiotics with detergent effect - surfactin. Published methods can be used for research of optimal conditions for producing microbe cultivation. Because non-polar parts of the phospholipid molecule (fatty acids) can affect the analysis methods on spliced polar headgroups have to be designed. Capillary electrophoresis and gas chromatography methods were developed and the latter one was further optimized for simultaneous analysis with fatty acids. Additional part deals with an alternative approach which consists in direct injection on mass spectrometer of intact...
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New procedures in metabolomic analysis of biofluids
Řimnáčová, Lucie ; Čabala, Radomír (advisor) ; Feltl, Ladislav (referee) ; Sýkora, David (referee)
The aim of this thesis has been the research on reactivity of protic metabolites with chloroformates and its application for GC-MS analysis of biofluids. The research was conducted in three separate studies and the results are three new, original methods for GC-MS determination of low- molecular protic metabolites in biological material especially in biofluids. The first study explores the discovery of fast derivatization of alicyclic hydroxyl groups by fluoroalkyl chloroformates (FCFs) under anhydrous conditions [1]. FCF fully converts the hydroxyl group into a corresponding carbonate and the step can easily be coupled with liquid-liquid microextraction (LLME) of the arising derivatives into organic phase. The reaction of the alicyclic OH group with FCFs was tested on 12 clinically relevant steroids and 4 tocopherols. The analytical properties of determined analytes were described and the method was validated for the GC-MS determination of 6 diagnostic sterols and 4 tocopherols in human serum and amniotic fluid. The new method was further successfully used for determination of sterols and tocopherols in tissues of the bug Pyrrhocoris apterus [2]. The second study was focused on the reactions of protic, particularly urinary metabolites with FCFs, mainly heptafluorobutyl chloroformate (HFBCF)....
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Characterization of new chiral separation systems for HPLC
Vozka, Jiří ; Tesařová, Eva (advisor) ; Sýkora, David (referee) ; Petr, Jan (referee)
The dissertation thesis is focused on the physico-chemical characterization of interaction mechanisms of chiral stationary phases based on derivatized cyclofructans. Correct interpretation of retention and enantiodiscrimination processes substantially facilitates the development and optimization of new enantioselective methods using cyclofructan-based chiral stationary phases. At first, the interaction mechanisms of three commercially available cyclofructan-based stationary phases were studied in normal-phase mode of liquid chromatography. Namely, systems using chiral stationary phases based on dimethylphenyl carbamate cyclofructan 7, R-naphtylethyl carbamate cyclofructan 6 and isopropyl carbamate cyclofructan 6 were studied. Linear free energy relationship model was used as a basic tool for characterization of interactions on the stationary phases. The mentioned model revealed that the main interactions contributing to retention in cyclofructan-based systems are hydrogen bond acidity and dipolarity/polarizibility, while dispersion interactions cause decrease of retention. The impact of oligosaccharide skeleton of the cyclofructan selector on the enantioselectivity was elucidated by the comparison with seemingly analogous cyclodextrin-based chiral stationary phases. Cyclofructan-based chiral...
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Modern separation and spectrometric techniques for biological sample lipidom investigation
Havelková, Eva ; Bosáková, Zuzana (advisor) ; Sýkora, David (referee)
Modern separation and spectrometric techniques for biological sample lipidom investigation Due recent progress in field of mass spectrometry the lipidomics, part of metabolomics, is increasing its importance for broad fields of biological study. The aim of this study is to test the lipid extraction techniques and to optimize the preseparation and separation of lipids suitable for mass spectrometry detection. The fragmentation patterns of four, the most abundant lipid classes of glycerolipids (PC, PE, TG, DG), were acquired for the proposed system. These patterns were compared with literature. The most appropriate method for extraction was declared technique according Folch based on methanol and chloroform solution. The preseparation due SPE method is very useful tool for lipid determination. The optimized were focused to reach higher recovery especially in polar lipid fraction. Proposed HPLC system is based on methanol with ammonium buffer, water and isopropanol. The testing was done on three columns with different type of sorbents (Gemini, Syncronis and Kinetex). The separation was evaluated according mass spectrometer response, shape and wide of particular analytes peaks. Composition contains 20% of water was determinate as the best and also the best separation was achieved by Kinetex column. The proposed...
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Atmospheric pressure chemical ionization mass spectrometry at low flows: construction and applications
Strmeň, Timotej ; Cvačka, Josef (advisor) ; Sýkora, David (referee) ; Polášek, Miroslav (referee)
(EN) The first part of the thesis describes the ionization reactions in the APCI source in the presence (enclosed configuration) and absence (open configuration) of the ion source housing. Commercial APCI source was modified and used in enclosed, as well as open configuration. All other parameters were kept the same (including the source geometry). In the positive mode, the biggest differences were observed for non-polar analytes dissolved in aprotic solvents like toluene, chloroform and carbon disulfide. Protonated species were dominant in the open configuration, while radical cations were mostly present in the enclosed configuration. The excessive protonation in open ion source was caused by the diffusion of water vapor molecules into the ionization region from the atmosphere. Water vapor molecules were also responsible for the formation of an ion [M + 19]+ from alkynes in the open configuration. The fragmentation study confirmed that the ion [M + 19]+ was a 2-methylketone formed by the addition reaction. The formation of such artifacts can pose problems in qualitative analysis. On the other hand, the ion [M + 55]+ was observed in the enclosed ion source as a reaction product of unsaturated compounds with acetonitrile solvent molecules. Its fragmentation can be used for the double bond...
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Analysis of biologically active substances by modern separation methods
Bierhanzl, Václav ; Čabala, Radomír (advisor) ; Pacáková, Věra (referee) ; Sýkora, David (referee)
The thesis is dedicated to the phospholipids and their polar headgroups analysis by gas chromatography, capillary electrophoresis and mass spectrometry. Phospholipids are the most important polar lipids and they are classified into phospholipid classes according to their phosphorylated groups. Phospholipids can be found in cell membranes and the changes in their ratio are monitored to research the impact of external conditions on cells. Actually thin layer chromatography is still used for phospholipid class ratio analyses. It is not suitable for microbiological research due to its time demandingness. The presented compendium of papers engaged in phospholipid classification is targeted on Bacillus subtilis strain, which produces potential antibiotics with detergent effect - surfactin. Published methods can be used for research of optimal conditions for producing microbe cultivation. Because non-polar parts of the phospholipid molecule (fatty acids) can affect the analysis methods on spliced polar headgroups have to be designed. Capillary electrophoresis and gas chromatography methods were developed and the latter one was further optimized for simultaneous analysis with fatty acids. Additional part deals with an alternative approach which consists in direct injection on mass spectrometer of intact...
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