This master's thesis deals with optimization of conditions of chemical hydride generation of tellurium and conditions of its atomization, specifically in three types of atomizers - in a diffusion flame (DF), in a heated multiple microflame quartz tube atomizer (MMQTA) and in a dielectric barrier discharge (DBD) atomizer. Tellurium hydride was generated in a flow injection arrangement and a high-resolution continuum source atomic absorption spectrometer was used for detection. As hydride generation can be only done from tetravalent species of tellurium, at first a simple procedure of pre-reduction of hexavalent species of tellurium by heating a standard in hydrochloric acid at 6 mol dm-3 was verified. Further, conditions of chemical generation were optimized with a goal to achieve as high generation efficiency as possible, namely, concentration of hydrochloric acid and sodium tetrahydroborate, volume of the reaction coil and a flow rate of carrier gas. Subsequently, conditions of atomization of tellurium hydride were examined with chosen optimal generation conditions. In the case of DF, it was an amount of hydrogen in the flame, a total flow rate of gases and observation height. In the case of MMQTA, temperature of the atomizer, a flow rate of carrier gas and a flow rate of air or oxygen needed for...

Cardiovascular diseases (CVD) are the leading cause of morbidity and mortality in Europe. Over 4 million people die from CVDs annually and another 11 million people develops CVDs every year. These numbers show that there is a need for better diagnostic, prognostic and predictive biomarkers and, more importantly, a need for new and more efficient drugs. Integral membrane proteins (IMPs) are ideal candidates for new drug targets. However, a study of IMPs represents a major challenge in current proteomics. This challenge is associated with the low abundance of IMPs, their low solubility in aqueous solvents and the absence of trypsin cleavage sites in their transmembrane segments. To overcome these issues, methods that selectively target either N-glycosylated extra-membrane segments (CSC, SPEG, N-glyco-FASP) or transmembrane segments (hpTC) were developed. In this thesis we employed a combination of two N-glyco-capture methods (SPEG and N-glyco-FASP) performed on two different samples (membrane-enriched fraction and total tissue lysate) with analysis of membrane-embedded IMP segments by hpTC and with standard non-targeted "detergent+trypsin" approach to analyze rat myocardial membrane proteome. We also performed an evaluation of employed methods for preparation of membrane fraction by western blot...

Endosymbiotic gain and transfer of plastids is a widespread evolutionary phenomenon and a major driving force of eukaryotic evolution. The integration of a new organelle is accompanied by changes in its structure, gene content, molecular mechanisms for biogenesis and transport, and re-wiring of the host and organelle metabolic pathways. To understand the course and underlying mechanisms of plastid evolution, it is important to study these processes in variety of secondary algae and notice their differences and similarities. Euglenophytes gained their plastids from green eukaryotic algae after a long history of heterotrophic lifestyle. In my thesis, I participated in analyses of newly generated sequence datasets: transcriptomes of Euglena gracilis and Euglena longa and mass spectrometry-determined proteome of E. gracilis plastid with especial regard to the potential novelties associated with plastid gain and incorporation. In the resulting publications we particularly focus on plastid protein import machinery and targeting signals and report extremely reduced TIC and completely absent TOC in euglenophyte plastid. Using the proteomic dataset, we predict potential novel plastid protein translocases recruited from ER/Golgi and re-analyze plastid signal domains, characterizing previously overlooked...

Structural proteomic methods such as an ion mobility mass spectrometry, chemical cross- linking or covalent labeling have been established as powerful tools for structural studies of biomolecules in general. These methods have significantly contributed to the expansion of our knowledge about biomolecular functions, their dynamics and molecular interactions and therefore led to the understanding of important biological processes occurring in a cell. We decided to spread these methods and we developed a new radical labeling technique relaying on Fluor-alkyl radicals that does not require a laser dissociation pf hydrogen peroxide. We exploited the potential of Togni reagents to form Fluor-alkyl radicals by reducing agent under native conditions. The induction of Fluor-alkyl radicals was triggered by ascorbic acid and the labeling pulse was stopped by tryptophan. The modified proteins were analyzed by top down or bottom up approach using high resolution mass spectrometry. In case of top down approach, several fragmentation techniques (CID-ECD, ETD) were tested for protein analysis while in case of bottom up approach the analyzed proteins were digested by trypsin and separated on reverse phase column online coupled to mass spectrometer. As the model biomolecules we chose a 20 proteinogenic amino acids...

(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...

Lipidomics is a rapidly expanding research field that has captured extensive attention worldwide in the past few years due to the increasing awareness of the crucial roles of lipids in biological systems. The aim of lipidomics is to comprehensively analyze all lipids, to study their structure, biological function within the cell as well as interactions of lipids with other molecules. A combination of advanced analytical techniques, such as extraction, chromatography and mass spectrometry, is an effective tool for studying all aspects of lipidomics. This dissertation thesis is based on two journal publications and presents application of analytical strategies based on chromatography and mass spectrometry for investigation and characterization of new lipid classes of vernix caseosa. Firstly, the applicability of nonaqueous reversed-phase liquid chromatography atmospheric pressure ionization tandem mass spectrometry (LC- APCI-MS2 ) for structural characterization of cholesteryl esters of ω-(O-acyl)-hydroxy fatty acids (Chl-ωOAHFAs) in vernix caseosa was investigated. For this purpose, a TLC chromatography method for the isolation of neutral Chl-ωOAHFAs from vernix caseosa was developed. Their general structure was established using multi-step mass spectrometric approach requiring transesterification...

Light is one of the main environmental factors largely determining plant life. Light provides energy resources for photosynthesis and it is also the most important medium of perception as it represents the main source of information about plant surroundings. My diploma thesis entitled “Light and its effect on plant proteome” briefly summarizes present knowledge about the light perception in plants, its interpretation of light quality, quantity, and direction via photoreceptors. These components trigger a whole range of changes, both on molecular and developmental levels, but the complex molecular mechanisms regulating system of light signalling in plants are far from being resolved. Here, I followed effects of different light parameters on plant proteome, namely, diurnal variations, low- and high-light intensity, spectral composition, and a change in the light period duration. To study these effects two model organisms were selected (i) Arabidopsis thaliana as a representative plant model with the most annotated genome/proteome and (ii) Solanum lycopersicum as a representative plant model significant for agriculture and biotechnology. Proteome changes in response to different light factors were analyzed by LC-MS. In total, the analyses revealed over 100 and 300 light-responsive proteins in Arabidopsis and S. lycopersicum, respectively. Proteomics provided highly sensitive snapshots of protein abundance in response to light and selected experiments have been complemented with a GC-MS metabolite profiling, conductivity measurements, and fluorescence microscopy.

Title: Study of C-C coupling of dienes catalyzed by ruthenium (II) complexes. Author: Bc. Eva Hanikýřová Department: Department of Organic Chemistry Supervisor: Mgr. Jana Roithová, Ph.D. Abstract Transition metal catalyzed cycloadditions have contributed extensively to organic synthesis. The use of ruthenium complexes in those reactions gain importance due to their demonstrated ability in the catalytic carbon-carbon bond formations via ruthenacycle intermediates. In our studies, we have concentrated on the interaction between ruthenium (II) and alkenes using mass spectrometry with electrospray ionization. This technique allows to investigate ruthenium complexes in the ionized states, and allows to investigate these structures by using MS/MS analyse. Our experimental research was complemented by quantum chemical calculations using Density functional theory. The research leads to a more detailed understanding to Ruthenium complexes with unsaturated hydrocarbons reaction mechanism. Key words Gas-phase chemistry, Reaction mechanisms, Electrospray Ionization, Catalyst, [CpRu(CH3CN)3]PF6, Mass Spectrometry

Natural killer (NK) cells represent indispensable part of the innate immunity as they are capable of promptly identifying virally infected or tumor cells and participating in the regulation of adaptive immune responses. These functions are ensured by the interplay between NK receptors, creating a complex regulatory system. Solving the receptors' structure may contribute to an overall understanding of NK cell biology. Presented thesis describes an elucidation of the structure of the inhibitory C-type lectin-like receptor (CTLR) Nkrp1b with an emphasis toward structural features (stalk, loop and oligomerization state) which might affect conformation or interactions of this receptor. The interaction of Nkrp1b with its ligand, Clr-b protein, is immunologically significant as it regulates NK cells' activity independently and monitors changes that are not visible to cytotoxic T lymphocytes. To study individual structural aspects of Nkrp1b, two protein variants were recombinantly prepared in bacterial expression system: entire ectodomain and ligand-binding domain lacking the stalk. Using a range of mass spectrometric techniques in combination with homology modeling and molecular dynamics, we proposed the Nkrp1b structure including its monomeric and dimeric arrangements. In addition, the oligomerization...

Title: Implementation of ion imaging technique in experiments with free molecules, clusters and nanoparticles Author: Jaroslav Kočišek Department: Department of Surface and Plasma Science Supervisor: Mgr. Michal Fárník, PhD., DSc., Ústav fyzikální chemie J. Hey- rovského, AV ČR, v.v.i. Abstract: The experimental work is focused on implementation of novel tech- niques to study clusters and nanoparticles in molecular beams. A new exper- imental system was tested, which combines the technique of velocity map ion imaging with pulsed molecular beam source. The same method and new mass spectrometer were implemented on the apparatus with molecular beam of size selected clusters. The new methods were used to study environmental effects on photo and electron induced chemistry. The most important results concerns on influence of expansion conditions on the structure of formed neutral clusters of HBr and C2H2. Results of experiments with HNO3 and CF2Cl2 molecules are then crucial for understanding heterogeneous processes in the Stratosphere. Keywords: ion imaging, mass spectrometry, molecular beams, photochemistry, nanoparticles