Studies on interactions between NKR-P1D and Clrb membrane receptors Interaction between murine NKR-P1D and Clrb receptors was originally described as a novel type of "MHC class-I independent missing-self recognition" and was shown to confer protection from killing by natural killer cells.[1] However, further study brought conflicting results suggesting that NKR-P1D does not binds Clrb strongly if it does at all.[2] In order to address the issues arising from these conflicting results, we have recombinantly expressed the extracellular domains of both receptors in E. coli cells and refolded the proteins in vitro. The quality of refolding was confirmed both by determining the disulphide bonding pattern using FTMS and measuring 1 H/15 N-HSQC spectra. By means of size exclusion chromatography and analytical ultracentrifuge we were unable to provide convincing results for the interaction itself. However, using SPR technique, a weak, specific, pH-dependent interaction was observed. Interaction between the proteins in solution was immobilized using chemical cross-linking technique. Three cross-linking reagents, EDC, DSG and DSS were used. The reaction mixture was separated by means of SDS-PAGE and protein bands corresponding to dimers were digested in gel. Using FT-MS we were able to find peptides from both...

Previously, selenium was known as an element with negative properties. However, in the last century, the significant positive effects on human health were detected. Currently, the function, behavior and toxicity of selenium are still not well known. The key to understand it is to do speciation analysis. The aim of this diploma thesis is to develop method for determination inorganic (sodium selenite and selenate) and organic (selenourea, selenocystine, selenomethionine) selenium compounds. Parameters of apparatus for electrochemical hydride generation with atomic absorption spectrometry detector were optimized, final conditions were set and optimal conditions for separation process using HPLC were investigated. Calibration dependences for selenium compounds were measured and analytical figures of merit were investigated. In conclusion, a coupled method HPLC- EcHG- QFAAS for determination of individual selenium compounds was proposed, and it was tested on urea samples. Calibrations for these measurements were investigated and analytic characteristics were calculated. Based on these comparisons it can be said that proposed method allows the determination of selected selenium compounds in both aqueous and urea matrices. Subject words: Spectroscopy, analytical chemistry Key words: Atomic absorption...

This study focuses on the recombinant cysteine peptidases - cathepsin B originating in the bird schistosome Trichobilharzia regenti that is unique across the whole family for its ability to migrate through the nerve tissue to the final localization. For invasion, migration, degradation of nutritional proteins and/or evasion of host immune responses, schistosome employs peptidases. This study follows the research done by researchers of Department of parasitology, Faculty of Natural Sciences, Charles University. The main goal of this study was to deepen the characteristics of recombinant cathepsins B originating in T. regenti. In T. regenti, two cysteine peptidases - cathepsins B1 (TrCB1) and B2 (TrCB2) - have been previously characterized. TrCB1 is located in the gut of schistosomula and involved in digestion. TrCB2 occurs in post-acetabular penetration glands of cercariae and probably facilitates penetration. The recombinant pro-cathepsin B (isoforms TrCB1.1, TrCB1.4 and also TrCB2) were expressed in Pichia pastoris yeast system. An attempt was made to produce in P. pastoris the recombinant isoform TrCB1.6, in which the active site cysteine is substituted by glycine. While TrCB2 underwent self-processing in the expression medium, TrCB1.1 and TrC1.4 zymogens were effectively activated only after the...

This Ph.D. thesis was focused on the application of Raman spectroscopy as the main analytical method for the characterization of neo-formed minerals, notably sulfates, from burning coal waste dumps. This environment associated with subsurface fires gives rise to a variety of uncommon and rare minerals. The specific features of these minerals (metastability, hygroscopy, mixed aggregates) causes that the mineralogical investigation is a challenging task using traditional laboratory-based techniques. Advantages such as the non-destructive nature, the sensitivity to the changes in the hydration degree of sulfates, little or none pretreatment, and the option of measurements directly in the field were the main reasons for applying this spectroscopy method. The scarce availability of spectroscopic data of most gas-vent minerals can be considered as the disadvantage. Therefore, artificial prepared samples of six anhydrous sulfates, which are rarely found in nature, were analyzed by Raman laboratory spectroscopy and a miniature a Raman spectrometer, and specific Raman features as well the differences with hydrated counterparts are shown. Laboratory investigation of two natural hydrated aluminum sulfates, alunogen and khademite, were carried out using Raman spectroscopy and other methods in order to obtain...

Proteomics as a modern comprehensive approach to the analysis of proteomes was applied in three projects aimed at diagnosis and therapy of cancer. The aim of the first the project was to find a new diagnostic biomarker for ovarian cancer. Two different comparative proteomic approaches were used for comparative analysis of sera from patients diagnosed with ovarian cancer and from healthy age-matched women. We identified -1-antitrypsin with increased concentration in patien sera, and apolipoprotein A4 and retinol-binding protein 4 (RBP4) with significantly decreased concentration in patients. The significantly decerased concentration of RBP4 in patients is a new observation. We propose that RBP4 is either decreased in ovarian cancer patients as a result of its reduced production by ovary or it may reflect less specific systemic changes, for instance early onset of cancer cachexia. The second project was focused on gaining insight into the molecular mechanism of cytarabine resistance in mantle cell lymphoma (MCL). Proteomic and transcriptomic analyses of cytarabine-resistant cells revealed marked downregulation of deoxycytidine kinase (DCK) - a protein essential to intracellular activation of purine and pyrimidine nucleosides and their analogues including cytarabine. The cytarabine-resistant MCL...

Historical pharmaceutical preparations analyzed in this thesis were a senna extract more than 200 years old, an ointment "Naso-Merfen" 75 years old, and an ointment "Sulfathiazol" 42 years old. The active substances in the analyzed samples were sennosides A and B (senna extract), ephedrine and menthol (the ointment "Naso-Merfen"), and sulfathiazole (the ointment "Sulfathiazol"). The senna extract was analyzed by RP-HPLC and HPLC-MS. Separation conditions were optimized, especially for separation of the sennoside A and B enantiomers. The active substances were not detected in the sample. One degradation product and substances characteristic for senna were identified. Their presence in the historical and contemporary sample was compared. Detailed ESI− -MSn fragmentation mechanisms of sennoside A and B have been proposed. The sample of the ointment "Naso-Merfen" was analyzed by HILIC-UV, HPLC-MS, GC-MS, and AAS. Separation conditions were optimized. The active substances were quantified. Degradation products of the active substances were not detected in the sample. The sample of the ointment "Sulfathiazol" was analyzed by RP-HPLC and HPLC-MS. Separation conditions were optimized. The active substance was quantified. Degradation products of the active substance were not detected. The authenticity of...

This diploma thesis is based on the current issue of the presence of pharmaceuticals in various components of the environment. Concerning the contamination by residues of pharmaceuticals the most affected environment is the aquatic environment where these substances leaks especially from wastewater treatment plants, which eliminate them during the cleaning process only partially. This work is focused on the selected group of pharmaceuticals, non-steroidal anti-inflammatory drugs (salicylic acid, ibuprofen, caffeine, naproxen, ketoprofen, diclofenac) in waste water. For analysis purposes two types of sampling were used and compared: the conventional spot sampling of wastewater and the sampling using passive samplers POCIS. The sampling took place at the inflow and outflow of the wastewater treatment plant in Brno Modřice. The solid phase extraction (SPE) using Oasis HLB columns was used as the extraction method. Extracted sample was derivatized then. Derivatization agents were: MSTFA (N-methyl-N-(trimethylsilyl)trifluoroacetamid) and BSTFA (N, O-bis(trimethylsilyl) trifluoroacetamid). The final analysis was performed using gas chromatography with mass spectrometric detection Time-of-Flight (GC/TOF-MS).

Master’s thesis deals with a determination problem of ignitable liquids from fire debris. The aim of this work is to introduce the properties of used fire accelerants and to give an overview and evaluation of the various techniques which can be conducive to the fire investigator. Determination of fire accelerants from fire debris was made by the technique of solid phase microextraction (SPME) with subsequent chemical analysis by GC/MS. Based on the chromatographic results were established the target compounds and reconstructed ion chromatograms which are typical for some kinds of flammable liquids. There were used gasoline, diesel, kerosene and technical gasoline (white spirit) as the fire accelerants. This work also deals with the influence of interfering products in fire debris analysis, including their identification and characterization. Different kinds of substrates were burned, extracted and analyzed in order to identify all the interfering products that they may release.

This diploma thesis deals with the conformation and molecular organization of humic acids in aqueous solutions. Humic substances have heterogeneous and polydisperse nature, therefore their secondary chemical structure has not yet been defined properly, neither has their conformational arrangement. The conformation of humic substances in the solutions is mainly stabilized by weak disperse forces, such as Van der Waals, -, CH- interactions and hydrogen bonds. Humic substances in the solutions tend to form aggregates that are held together mostly by the intermolecular hydrophobic interactions. Concentration series of humic acids were prepared in three different mediums of constant ionic strength: NaOH and NaCl (prepared either by neutralization NaOH by HCl or direct dilution by solution of NaCl). Several analytical methods have been used to determine conformation and molecular organization of humic acids: potentiometric determination of pH, direct conductometry, ultraviolet and visible spectroscopy, density measurement, dynamic light scattering, laser Doppler velocimetry and high resolution ultrasound spectrometry. It was confirmed that the conformation and molecular organization of humic acids in aqueous solutions depend not only on pH of medium, but they also depend on chemical nature and concentration with the same pH. Results showed that hydrodynamic diameter of particles is significantly increasing in NaCl medium prepared by neutralization NaOH by HCl, particularly at low concentrations, which corresponds to higher values of zeta potential obtained. Concentration dependencies of ultrasonic velocity and compressibility also indicate the changes in conformation and molecular organization corresponding with results from other methods used.

The goal of my diploma thesis was finding a suitable method for unifying score values from various protein identification search tools in MS/MS mass spectrometry into one single score value. Data coming from the output of mass spectrometer are processed in two independent search tools Mascot and X!Tandem. These were selected especially for their wide usage in proteomic labs. Both results are evaluated through newly designed function and unified by single valued score clearly identifying found proteins. Newly designed scoring value is called Matascore and function producing this score was implemented in MATLAB. Function and its results were successfully tested by real data available in public databases on the Internet.