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Intensity Normalization of Raman Spectra by Means of Various Internal Standards
Sláma, Vladislav ; Mojzeš, Peter (advisor) ; Procházka, Marek (referee)
The work deals with the testing of selected inorganic anions as internal standards for intensity normalization of Raman spectra. Using the concentration and temperature series of aqueous solutions of PO4 3- , (CH3)2AsO2 - , NO3 - a SO4 2- , impact of the spectral changes of the standard bands for reliability and accuracy of the intensity calibration was studied. Temperature and concentration series of the anion Raman spectra are then used to test normalization by means of the bands of stretching and deformation vibrations of water molecules. In addition, reliability and robustness of the calibration procedures exploiting different spectral parameters present in the Raman spectra of standards was tested. Results of the study reveal possible sources of artifacts and misinterpretations arising from insufficient understanding of the standard behavior due to changes of the physical and chemical parameters, or due to improper calibration procedure applied.
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Monitoring of surface reactions on plasmon nanoparticles by surface-enhanced Raman spectroscopy
Kožíšek, Jan ; Šloufová, Ivana (advisor) ; Procházka, Marek (referee)
The presented diploma thesis is focused on finding conditions suitable for the study of surface reactions, especially Suzuki-Miyaura cross-coupling reaction (SMCR), by the surface- enhanced Raman scattering (SERS) method. The first part of the work deals with the optimization of the conditions of individual reactions using the classical synthetic Schlenk technique. Traditional, published, conditions for SMCR were gradually modified during the work so that the reactions could be performed in aqueous media and at room temperature, i.e., under conditions suitable for SERS spectroscopy. The following catalysts were tested: (i) PEPPSI - the traditional SMCR catalyst; (ii) palladium ions; (iii) Pd colloids; (iv) bimetallic colloids of Pd and plasmonic metal (Ag, Au) in the form of core-shell and alloy; (v) Ag and Au colloids with additions of palladium salt or N- heterocyclic carbenes (NHC-catalysts). Two groups of substrates were used: substrates with functional groups with high affinity for the surfaces of metal nanoparticles (NPs) and substrates without these anchoring functional groups. Substrates without the anchoring functional groups can be expected to enter the SMCR reaction from solution. In the second part of this diploma thesis selected reaction mixtures for SMCR were performed in septum...
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Sirtuin 3 and its function in cardiac metabolism
Procházka, Marek ; Horníková, Daniela (advisor) ; Koňaříková, Eliška (referee)
SIRT3 is a NAD+ -dependent deacetylase, that is abundant in the heart and essentially regulates cellular processes in cardiomyocytes. SIRT3 positively modulates most of the enzymes and proteins in the intermediate metabolism in mitochondria, which supply the necessary ATP energy for the heart muscle and that are centers of metabolism in cardiomyocytes. In the mitochondria SIRT3 inhibits the formation of ROS by activating an antioxidant system. SIRT3 has significant anti-apoptotic, anti-hypertrophic and anti-fibrotic cardioprotective effects. Its activation is based on several drugs and natural substances that could be a promising therapeutic approach to the treatment of cardiovascular diseases, which are currently the leading cause of death of more than a half of the European population. However, more studies are required for better understanding the processes in which SIRT3 is involved. The aim of this work is to summarize the function of SIRT3 in mitochondrial metabolism and cardiac physiology. Key words: sirtuin 3, cardioprotection, metabolism, heart, mitochondria
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Optical responses of biomolecules on regular metal plasmonic nanostructures
Šubr, Martin ; Procházka, Marek (advisor)
Title: Optical Responses of Biomolecules on Regular Metal Plasmonic Nanostructures Author: Martin Šubr Department: Institute of Physics of Charles University Supervisor of the doctoral thesis: prof. RNDr. Marek Procházka, Dr., Institute of Physics of Charles University Abstract: Adsorption of molecules on metal plasmonic nanostructures leads to significant enhancement of many optical processes, such as Raman scattering (surface-enhanced Raman scattering - SERS) or fluorescence (surface-enhanced fluorescence - SEF). Two groups of substrates were tested within this thesis: (i) Silver nanorods prepared by oblique angle vapor deposition, and (ii) silver and gold nanoislands growing on magnetron-sputtered polytetrafluoroethylene film. Step-by- step optimization process was performed on the nanoislands in order to obtain optimum SERS sensitivity and reproducibility. Detailed SERS intensity profiles were obtained using gradient nanostructures with the localized surface plasmon resonance (LSPR) condition varying across the sample and three different excitation wavelengths. It was also found that spectral position and height of the LSPR band can be controlled simultaneously using mixed gold/silver nanoislands. Detailed investigation of polarization- and angular- dependences of anisotropic silver nanorods was...
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Functional biomolecular coatings for affinity biosensors for medical diagnostics
Hemmerová, Erika ; Homola, Jiří (advisor) ; Procházka, Marek (referee) ; Skládal, Petr (referee)
OF THE DOCTORAL THESIS Title: Functional biomolecular coatings for affinity biosensors for medical diagnostics Author: Erika Hemmerová Department: Institute of Photonics and Electronics of the Czech Academy of Sciences Chaberská 1014/57, 182 51 Prague, Czech Republic Supervisor: Prof. Ing. Jiří Homola, CSc., DSc. Institute of Photonics and Electronics of the Czech Academy of Sciences Chaberská 1014/57, 182 51 Prague, Czech Republic Abstract: Detection and identification of diseases in their early stages represents one of the major goals of the contemporary medical diagnostics. This need drives a research of biomolecular processes behind the particular diseases and development of analytical devices for routine and long-term monitoring of the individuals' health. Surface plasmon resonance biosensors (SPR) have potential to contribute to addressing both of these challenges. This work aims at advancing multiple aspects of SPR biosensor method. It involves study and optimization of selected functional biomolecular coatings in order to improve the performance characteristics of SPR biosensors. It demonstrates utilization of these coatings in novel detection platforms for sensitive monitoring of multiple analytes, and in research of selected biomolecular interactions related to Alzheimer's disease. The...
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Optical responses of biomolecules on regular metal plasmonic nanostructures
Šubr, Martin ; Procházka, Marek (advisor)
Title: Optical Responses of Biomolecules on Regular Metal Plasmonic Nanostructures Author: Martin Šubr Department: Institute of Physics of Charles University Supervisor of the doctoral thesis: prof. RNDr. Marek Procházka, Dr., Institute of Physics of Charles University Abstract: Adsorption of molecules on metal plasmonic nanostructures leads to significant enhancement of many optical processes, such as Raman scattering (surface-enhanced Raman scattering - SERS) or fluorescence (surface-enhanced fluorescence - SEF). Two groups of substrates were tested within this thesis: (i) Silver nanorods prepared by oblique angle vapor deposition, and (ii) silver and gold nanoislands growing on magnetron-sputtered polytetrafluoroethylene film. Step-by- step optimization process was performed on the nanoislands in order to obtain optimum SERS sensitivity and reproducibility. Detailed SERS intensity profiles were obtained using gradient nanostructures with the localized surface plasmon resonance (LSPR) condition varying across the sample and three different excitation wavelengths. It was also found that spectral position and height of the LSPR band can be controlled simultaneously using mixed gold/silver nanoislands. Detailed investigation of polarization- and angular- dependences of anisotropic silver nanorods was...
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Surface-enhanced Raman spectral detection of bilirubin and temporally synchronized monitoring of its photochemical transformations in selected solvents by SERS and electronic absorption spectroscopy
Hrnčířová, Jana ; Vlčková, Blanka (advisor) ; Procházka, Marek (referee)
Surface-enhanced Raman scattering (SERS)-active systems based on macroscopic Ag nanosponge aggregates as well as the conditions of SERS spectral measurements were optimized for selective and sensitive detection of a biomedically important, amphiphilic bile pigment bilirubin (BR) in alkaline aqueous solutions and in its solutions in a selected water miscible solvent, namely dimethylsulfoxide (DMSO) and/or water-immiscible solvent, namely CH2Cl2. Ag nanosponges assembled by using HCl as a pre-aggregation agent were found to be the optimal SERS-active systems for a reliable detection of BR in all the above-mentioned solvents. In all cases, the protonated form of adsorbed BR has been detected upon BR incorporation into Ag nanosponges, and its marker bands have been established by SERS spectral probing at excitation wavelengths in the 445-780 nm range. The sensitivity of SERS spectral detection was evaluated in terms of the concentration values of SERS spectral detection limits (SERS LODs) of BR incorporated into Ag nanosponges. In particular, the SERS LOD for BR incorporated from its alkaline aqueous solution is 1 x 10-8 M (at 532 nm excitation), for BR incorporated from its solution in DMSO, its value is also 1 x 10-8 M (at 532 and/or 633 nm excitations), and for incorporation from the solution of BR...
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The Analysis of Senior's Opinions on Self-treatment by non-steroidal anti-inflamatory drugs III
Procházka, Marek ; Doseděl, Martin (advisor) ; Kostřiba, Jan (referee)
The Analysis of Seniors' Opinions on Self-treatment by Non-steroidal Anti-inflamatory Drugs III Charles University, Faculty of Pharmacy in Hradec Králové Department of: Social and Clinical Pharmacy Candidate: Marek Procházka Consultant: PharmDr.Martin Doseděl, Ph.D. Background: Self-treatment is one of the approaches in managing pain which is still gaining higher level of importance even amongst seniors. One of the most favourite over the counter (OTC) analgesics is ibuprofen, however its use can be associated with certain drug related problems (DRP). The potential of DRPs is increasing with age which makes seniors more sensitive to them. Aim of study: 1) To create an overview of DRPs of OTC analgesics, focusing on paracetamol (acetaminophen). 2) Through the survey find out the knowledge and experience of seniors with self-treatment by OTC analgesics. The other aim was to evaluate their sources of information concerning ibuprofen and their preferences to each product. Methods: The observable cross-sectional study was made through social media and in Královéhradecký region. In the first case the questionnaire was spread through social media- Facebook. In the second case standardised conversation with questionnaire lists was applied with seniors above 60 years of age. The research was anonymous and...
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Influence of the surface hydrophobicity and charge of the molecule for drop coating deposition Raman spectroscopy
Bura, Radek ; Kočišová, Eva (advisor) ; Procházka, Marek (referee)
Raman spectroscopy is an optical vibrational spectroscopic technique suited for a study of biomolecules and their interactions. In contrast to classical Raman spectroscopy, Drop-Coating Deposition Raman spectroscopy (DCDR) enables due to a preconcentration of the sample dried on a special hydrophobic surface to acquire a high-quality spectrum even in case of low concentrated samples. In collaboration with Department of Macromolecular Physics of the Faculty of Mathematics and Physics at Charles University, the three special surfaces - substrates - with different wettability (hydrophobicity) and roughness on the basis of silvers nanoparticles have been prepared. Solutions of methylene blue and glutamic acid at different concentrations and pH were dropped on these substrates. Nanoparticles size was determined. It was shown, that with increasing number of sputtered nanoparticles, the roughness of the substrates increased also. More roughened substrates show a higher static contact angle. The dynamics of droplet drying and the preconcentration of substances in the dried deposit were monitored. The preconcentration was assessed from the first subspectrum obtained from a factor analysis performed on series of measured Raman spectra from dried deposits. There was none among the substrates on which there would...
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Multifunctional biomolecular assemblies for parallelized analysis of biomolecular interactions
Bocková, Markéta ; Homola, Jiří (advisor) ; Brynda, Eduard (referee) ; Procházka, Marek (referee)
Title: Multifunctional biomolecular assemblies for parallelized analysis of biomolecular interactions Author: Markéta Bocková Department / Institute: Institute of Physics, Charles University Supervisor of the doctoral thesis: Prof. Jiří Homola, Ph.D., DSc., Institute of Photonics and Electronics, The Czech Academy of Sciences Abstract: Surface plasmon resonance (SPR) biosensors represent the most advanced optical method for the direct, real-time monitoring of biomolecular interactions without the need for labelling. This doctoral thesis aims to advance the SPR biosensor method and to expand its utility in the investigation of biomolecular interactions. This encompasses activities on two major fronts of SPR biosensor research - immobilization methods and biosensing methodologies. Methods for the immobilization of biomolecules were researched with the aim of enabling the immobilization of a broad range of biomolecules on the SPR biosensor surface in a spatially controlled manner. The development of novel biosensing methodologies was pursued in order to address the current limitations of SPR biosensors associated with non-specific adsorption and limited analyte transport, and thus to improve the accuracy and robustness of SPR biosensor measurements. Finally, advances in the development of immobilization...
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