|
|
Ultra-weak photon emission from biological samples
Vahalová, Petra ; Cifra, Michal (advisor) ; Rác, Marek (referee) ; Šachl, Radek (referee)
Oxidative processes are an inseparable part of the life of almost all living organisms. They help to maintain homeostasis but they can also stand behind various dysfunctions or diseases. Therefore, an effective method for monitoring oxidative processes in biosamples is an essential tool for medicine, agriculture, and food industry. In this thesis, an overview of available methods for monitoring oxidation in biosamples with a special focus on biological autoluminescence (BAL) is provided. This thesis uses the term BAL to encapsulate various synonyms including the commonly used term ultra-weak photon emission. BAL correlations with various physical, chemical, and biological factors (as original research and an overview from other authors) are also presented. Specifically, the relationships between spontaneous BAL of yeast Saccharomyces cerevisiae and the selected physical and chemical parameters (pH, oxygen partial pressure, and cell concentration) during cell growth were established. Additionally, the correlation of BAL intensity from yeast cells or protein bovine serum albumin (BSA) and the number of reactive oxygen species (ROS) that originated as a result of the Fenton reaction were measured. Physical enhancement of BAL from BSA by pulsed electric field was also studied and a basic reaction...
|
|
|
Tracking membrane permeabilization on single lipid vesicles - method development.
Gücklhorn, David ; Šachl, Radek (advisor) ; Heřman, Petr (referee)
Protein complexes are challenging systems to study, especially when these complexes form on lipid membranes only for a short period of time. This is also the case of fibroblast growth factor 2 (FGF2), a protein that has many physiological and pathological functions in the human organism. It plays major role in the development of cancer as it promotes cell survival and angiogenesis. It also serves as a basis for development of novel treatments of nerve injuries. Despite being heavily studied for many years, it remains unclear how the protein is translocated into the extracellular space where it performs its function. To study complex systems such as FGF2 that self-assembles on the membrane into membrane penetrating pores we decided to develop a simple and efficient fluorescent microscopy method. This method is called double leakage single GUV assay (DLSGA). It utilizes giant unilamellar vesicles (GUVs) mimicking native cellular membranes. In a single experiment, up to 300 individual GUVs are imaged for the content of a leakage dye that reports on the presence of FGF2 pores. During three measurements and under different conditions, detailed information about pore-opening dynamics is gained for each GUV. Results of these measurements are then used to divide GUVs into six groups based on formation and...
|
|
|
Multidimensional characterization of polyelectrolytes and interpolyelectrolyte complexes in aqueous solutions
Murmiliuk, Anastasiia ; Štěpánek, Miroslav (advisor) ; Šachl, Radek (referee) ; Hoffmann, Ingo (referee)
Multidimensional characterization of polyelectrolytes and interpolyelectrolyte complexes in aqueous solutions Abstract: This PhD thesis is dedicated to the study of polyelectrolytes and their self-assembly in aqueous solutions. The morphology and ionization state of individual polymer chains were investigated as well as their co-assembly with oppositely charged species. First, the charge regulation of short and long weak polyelectrolytes in aqueous solution was investigated to deeper understand their pH-responsive properties. The changes of ionization degree and charge of oligopeptides composed of 5 amino acids with acid side-chains and 5 with basic side chains were followed upon varying the pH in order to reveal the effect of interactions between the like-charged and oppositely charged groups. It was shown that intra-molecular electrostatic interactions and conformational flexibility caused the suppression of the total charge and enhancement of ionization of the peptides. To get an insight into the distribution of local H+ concentration in the proximity of a polyelectrolyte chain, a modified polyelectrolyte structure was used with a fluorescent pH- indicator, covalently attached at the end of the chain. Ionization of the pH-responsive fluorophore revealed its effective pK which was compared with the local...
|
|
|
The study of the self- and co-assembly of block copolymers and block polyelectrolytes
Raya, Rahul Kumar ; Procházka, Karel (advisor) ; Štěpánek, Petr (referee) ; Šachl, Radek (referee)
The Thesis describe my studies based on self-assembly and co-assembly of block copolymer micelles that I conducted at the Department of Physical and Macro- molecular Chemistry at the Charles University, Prague in the research group of my supervisor, Prof. Dr. Karel Procházka, DrSc. The Thesis based on my publications and consists of four parts. Here I studied the formation of polymeric nanoparticles in aqueous solutions formed by polyelectrolytes with hydrophobic backbones by a combination of several experimental methods. The achieved results enabled me to explain the structure and properties of studied self- and co-assembled nanoparticles and to outline the decisive trends of their behavior. The spontaneous formation, sol- ubility and stability of complex nanoparticles depend not only on the electrostatic attractive forces but also on the hydrophobic effects. As the enthalpy-to-entropy interplay is very complex, a number of external factors such as temperature, pH, salinity and concentration affect the assembling process and structure of formed nanoparticles. 1
|
|
| |
|
|
Multidimensional characterization of polyelectrolytes and interpolyelectrolyte complexes in aqueous solutions
Murmiliuk, Anastasiia ; Štěpánek, Miroslav (advisor) ; Šachl, Radek (referee) ; Hoffmann, Ingo (referee)
Multidimensional characterization of polyelectrolytes and interpolyelectrolyte complexes in aqueous solutions Abstract: This PhD thesis is dedicated to the study of polyelectrolytes and their self-assembly in aqueous solutions. The morphology and ionization state of individual polymer chains were investigated as well as their co-assembly with oppositely charged species. First, the charge regulation of short and long weak polyelectrolytes in aqueous solution was investigated to deeper understand their pH-responsive properties. The changes of ionization degree and charge of oligopeptides composed of 5 amino acids with acid side-chains and 5 with basic side chains were followed upon varying the pH in order to reveal the effect of interactions between the like-charged and oppositely charged groups. It was shown that intra-molecular electrostatic interactions and conformational flexibility caused the suppression of the total charge and enhancement of ionization of the peptides. To get an insight into the distribution of local H+ concentration in the proximity of a polyelectrolyte chain, a modified polyelectrolyte structure was used with a fluorescent pH- indicator, covalently attached at the end of the chain. Ionization of the pH-responsive fluorophore revealed its effective pK which was compared with the local...
|
|
| |
|
|
Computational modeling of diffusion in polymer solutions
Kubečka, Jakub ; Košovan, Peter (advisor) ; Šachl, Radek (referee)
We performed coarse-grained molecular dynamics simulations of fully dissociated polyelectrolytes in the presence of monovalent and multivalent counterions and charged oligomers. The dynamics of these systems has been studied to follow internal dynamics of polyelectrolyte and counterions. The dynamics is presented via the mean square displacement which we obtain from the simulation trajectory and, moreover, via curves of Fluorescence Correlation Spectroscopy (FCS) obtained also from the simulation trajectory. FCS is an experimental technique which can be used to study condensation of counterions on polyelectrolytes. Therefore, we analyze the FCS curves and investigate applicability of various analytical models to fit these FCS curves. The aim of this work is a discussion about the fitting of the FCS curves and presentation of our observations for dynamics of counterions during condensation on the polyelectrolyte.
|
|
| |
|
|
Localisation of Fluorescent Probes and the Estimation of Lipid Nanodomain Sizes by Modern Fluorescence Techniques
Šachl, Radek ; Hof, Martin (advisor) ; Obšil, Tomáš (referee) ; Almgren, Mats (referee)
iii Organizations Umeå University Department of Chemistry, Umeå, SE & Charles University in Prague, Faculty of Science, Prague, CZ Document name Doctoral thesis Date of issue February 2012 Author Radek Šachl Title Localisation of Fluorescent Probes and the Estimation of Lipid Nanodomain Sizes by Modern Fluorescence Techniques Abstract The thesis is divided into two major parts. The first part focuses on the localisation of probes in lipid/polymeric bilayers and in GM1 micelles. Included in this thesis is a new approach based on electronic energy transfer/migration (FRET/DDEM), which efficiently determines transversal positions of fluorescent molecules in lipid bilayers. This approach has been used to locate newly synthesized lipid probes in DOPC bilayers. The label was introduced at the end of sn-2 acyl chains of variable length. Analytical models accounting for FRET exist for a limited number of basic geometries. Here, a combination of FRET and Monte Carlo simulations enables the localisation of probes in bicelles and in bilayers containing pores, i.e. in lipid systems with variable curvature, or in non-homogenous lipid systems. This approach has been used to test whether conical-like fluorescence probes have an increased affinity to highly curved regions, which would enable preferential labelling of...
|
guest ::
