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Simulation of processes in cellular membranes
Melcr, Josef ; Jungwirth, Pavel (advisor)
Simulation of processes in cellular membranes Abstract Many important processes in cells involve ions, e.g., fusion of synaptic vesi- cles with neuronal cell membranes is controlled by a divalent cation Ca2+ ; and the exchange of Na+ and K+ drives the the fast electrical signal transmis- sion in neurons. We have investigated model phospholipid membranes and their interactions with these biologically relevant ions. Using state-of-the-art molecular dynamics simulations, we accurately quantified their respective affinites towards neutral and negatively charged phospholipid bilayers. In order to achieve that, we developed a new model of phospholipids termed ECC-lipids, which accounts for the electronic polarization via the electronic continuum correction implemented as charge rescaling. Our simulations with this new force field reach for the first time a quantitative agreement with the experimental lipid electrometer concept for POPC as well as for POPS with all the studied cations. We have also examined the effects of transmembrane voltage on phospholipid bilayers. The electric field induced by the voltage exists exclusively in the hydrophobic region of the membrane, where it has an almost constant strength. This field affects the structure of nearby water molecules highlighting its importance in electroporation. 1
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Potassium in plant osmoregulation
Kholová, Kateřina ; Tylová, Edita (advisor) ; Konrádová, Hana (referee)
Potassium is very mobile in plants and is transported across membranes using transporters and channels. It is present in the ionic form K+ in plants. Also, in the form of this ion, K+ is taken up by plants from the soil solution. The uptake is mediated by the transporter HAK5 and by the channel AKT1. The transfer of K+ to the xylem is provided by the channel SKOR and the transporter KUP7. The role of potassium as an osmotically active element is crucial. K+ helps to regulate the amount of water in the cells and thus to maintain the turgor. Turgor is important for maintaining the shape of the plant cells and for its growth. Stomatal guard cells are used as a model system for describing processes related to the K+ osmotic function. Movement of K+ is involved in the regulation of opening and closing of stomata on the principle of turgor changes. Transport of K+ into guard cells is provided by channels KAT1, KAT2, AKT1 and AKT2. On the contrary, K+ release is mediated by the channel GORK on the plasma membrane and TPK1 on the tonoplast. K+ supports also the transport of assimilates in the phloem, where the channel AKT2 plays a role. The osmotic functions of K+ are the main topic of this bachelor thesis, which summarizes current knowledge about transport mechanisms necessary for the function of K+ as osmotically...
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Simulation of processes in cellular membranes
Melcr, Josef ; Jungwirth, Pavel (advisor) ; Otyepka, Michal (referee) ; Tarek, Mounir (referee)
Simulation of processes in cellular membranes Abstract Many important processes in cells involve ions, e.g., fusion of synaptic vesi- cles with neuronal cell membranes is controlled by a divalent cation Ca2+ ; and the exchange of Na+ and K+ drives the the fast electrical signal transmis- sion in neurons. We have investigated model phospholipid membranes and their interactions with these biologically relevant ions. Using state-of-the-art molecular dynamics simulations, we accurately quantified their respective affinites towards neutral and negatively charged phospholipid bilayers. In order to achieve that, we developed a new model of phospholipids termed ECC-lipids, which accounts for the electronic polarization via the electronic continuum correction implemented as charge rescaling. Our simulations with this new force field reach for the first time a quantitative agreement with the experimental lipid electrometer concept for POPC as well as for POPS with all the studied cations. We have also examined the effects of transmembrane voltage on phospholipid bilayers. The electric field induced by the voltage exists exclusively in the hydrophobic region of the membrane, where it has an almost constant strength. This field affects the structure of nearby water molecules highlighting its importance in electroporation. 1
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Influence of the pre-analytical phase on glucose and potassium blood examination
ČERNÁ, Iva
This bachelor thesis deals with the stability of glucose and potassium in blood. The main objective of this work was to test the stability of both analytes with regard to the prolonged time from sampling to separation and the temperature conditions of sample storage before the actual analysis. For glucose, stability was tested in two different materials, both in serum and plasma, with the addition of a glycolysis inhibitor.
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Characterization of native and heterologously expressed membrane transporters in yeast using fluorescent probes
Zahumenský, Jakub ; Gášková, Dana (advisor) ; Cebecauer, Marek (referee) ; Krůšek, Jan (referee)
Yeast plasma membrane transporters play crucial roles in many cellular processes, including detoxification and build-up and maintenance of the plasma membrane potential (ΔΨ). The former development of the diS-C3(3) fluorescence assay by the Biophysics Group of the Institute of Physics, Charles University, enabled us to conveniently study both, including their changes, using a simple fluorescent probe diS-C3(3). Many studies carried out on both animal and yeast cells have revealed that ethanol and other alcohols inhibit the functions of various membrane channels, receptors and solute transport proteins, and a direct interaction of alcohols with these membrane proteins has been proposed. Using the diS- C3(3) assay for multidrug-resistance pump inhibitors in a set of isogenic yeast pdr5 and snq2 deletion mutants we found that n-alcohols (from ethanol to hexanol) exhibit an inhibitory effect on both pumps, increasing with the length of the alcohol carbon chain. The inhibition is not connected with loss of plasma membrane structural or functional integrity and is fully reversible. This supports a notion that the inhibitory action does not necessarily involve only changes in the lipid matrix of the membrane but may entail a direct interaction of the alcohols with the pump proteins. Tok1p is a highly specific...
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Potassium deficiency in plants - signs and responses
Štočková, Hana ; Tylová, Edita (advisor) ; Konrádová, Hana (referee)
Plants receive K+ mainly from the soil through the root system. In soil, K+ occurs primarily in minerals such as mica and potassium feldspar. The availability of K+ for plant uptake depends on the form in which K+ occurs in soil. There are forms directly available, slowly available, and unavailable for plant and the transition of K+ between these pools may occur. In plant, K+ is very mobile and it occurs in high amount in cells. It is the most prominent cytoplasmic cation. It affects high number of metabolic processes, including photosynthesis, osmoregulation, and activation of enzymes. K+ shortage can cause changes in plant morphology, anatomy and metabolism. K+ deficiency can be manifested by leaf deformation, decreased leaf area, necrosis, short internodes, reduced rate of photosynthesis, etc. K+ deficient plant is also more vulnerable to pathogens and its resistance to abiotic stress factors such as drought, low temperatures, or salinity is decreased. Deficiency of K+ reduces the biomass and overall yield in agricultural crops, so K+ fertilizers, both soil and foliar, are needed. The thesis focuses on the manifestations of K+ deficiency in plants and summarizes the recent findings on mechanisms of K+ deficiency perception and signal pathways leading to the response to this deficiency. Key...
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Involvement of AtKT/HAK/KUP high-affinity transporters in plant K+ and Cs+ uptake
Šustr, Marek ; Tylová, Edita (advisor) ; Maršík, Petr (referee)
Potassium is essential macroelement and large amount of potassium is taken up by plants, because it's the major osmotic of plant cell. Due to various potassium availability in different kinds of soil, plants have evolved transport system that can maintain sufficient K+ uptake between several orders of magnitude of potassium concentration. In Arabidopsis thaliana mechanism of K+ acquisition is well understood and it's known that AtHAK5 is mainly involved in K+ uptake in its very low concentrations. AtHAK5 belongs to KT/HAK/KUP family that consist 13 members in A. thaliana. There's known function for some members for example in auxin transport in root tip (TRH1) or in K+ efflux in stomatal closure (KUP6). In this thesis possible involvement of yet unstudied transporters KUP5, KUP7, KUP9 and KUP10 in K+ acquisition and homeostasis in A. thaliana was investigated. In vitro cultivation showed that kup9 mutant has very short lateral roots in K+ deficiency. On the other hand kup5 mutant showed significantly higher dry weight in K+ deficiency than Col-0. Kup9 phenotype was successfully replicated in subsequent cultivations and anatomy of lateral root apical meristems was investigated. Root tips of kup9 were differently organized in K+ deficiency and they showed signs of early termination of meristems. To...
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Application of Atomic Absorption Spectrometry for Determination of Selected Elements from Potential Ecological Burden Area
Juránková, Lada ; Hraníček, Jakub (advisor) ; Šíma, Jan (referee)
This work is focused on the determination of selected (chemical) elements (Fe, Mn, Zn, Cr, Na, K, Mg a Ca) in a potential ecological burden area using flame atomic absorption spectrometry as a detection technique. A potential ecological burden is represented by tires which are used as a construction material or as an environment surrounding for growing decorative and consumable plants. Analytes were determined in plant origin samples. Firstly, the samples were dried in a laboratory electric dryer. The weighted amount of a dried sample (approximately 0.2 g) was digested inside a microwave decomposition device with an addition of nitric acid and hydrogen peroxide. An optimization of experimental parameters was done for each of the elements before sample measuring. A burner height was optimized and 8 mm height was chosen as a optimum for most elements. Under the optimum condition basic characteristics were measured for each element separately. These characteristics included limits of detection that were: 0.05; 0.01; 0.08; 0.21; 0.02; 0.01; 0.01; 0.01 mg L-1 for the following elements: Fe, Mn, Zn, Cr, K, Ca, Mg and Na, respectively. The limits of quantification, sensitivity and repeatability were determined for each element as well. A significant attention was paid to the content of zinc in the studied...
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Determination of selected elements in plant extracts by atomic absorption spectrometry
Rydlová, Lenka ; Hraníček, Jakub (advisor) ; Kratzer, Jan (referee)
The aim of this bachelor thesis was to determine selected elements (Na, Mg, K, Ca, Zn, Se) in plant extracts and juices by atomic absorption spectrometry using different types of atomization. Each method has been optimized for determination of the mentioned elements. For flame atomization it has been used optimization of height of the primary radiation from the hollow cathode lamp over the edge of the burner. The height was generally between 6.0 and 8.0 mm. Then there have been optimized flow of each component of the flame (acetylene, air, nitrous oxide) and it has been set location of the hollow cathode lamp and the flame. Under the optimized conditions basic characteristics describing the method of the determination of mentioned elements have been measured (LOD for sodium 2.13 µg L-1 , for magnesium 2.44 µg L-1 , for potassium 11.3 µg L-1 , for calcium 15.6 µg L-1 , for zinc 6.04 µg L-1 , for selenium 0.34 µg L-1 ). In the next part of the thesis the optimized methods have been used for measuring concentration of all elements in real samples. After the preparation of the samples including dilution, addition of various reagents etc., they have been atomized by flame in an atomic absorption spectrometer (Na, Mg, K, Ca, Zn) and determined, or converted to a volatile compound (Se) and determined by...
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Uptake and metabolism of 137Cs in plants
Šustr, Marek ; Tylová, Edita (advisor) ; Maršík, Petr (referee)
Plants are able to uptake radiocesium from soil, which is the potential route to enter the food chain. Cesium mobility in soil is determined by clay particles. Cesium can be reversibly ad- sorbed on their surface or can be fixed between layers. Mineral illit has the highest selectivity for cesium due to its frayed edges. Organic matter determines cesium mobility only in soil with organic matter content above 90 %. Cesium is more available for plants in this soil. Cesium uptake varies among species. Many plant species accumulating big amounts of cesium belong to family Chenopodiaceae. Cesium uptake is affected by other cations in soil solution. Potassium is the most effective one. Increasing of external potassium concentration from 50 μM to 250 μM decreased cesium uptake thirty-fold. Potassium affects cesium mobili- ty in soil and plant uptake. Due to chemical similarities of cesium and potassium some potassium transporters efficiently transport both cations. Potassium transporters are therefore considered the main entrance site in plant roots. Great contribution to cesium uptake is dedi- cated to high-affinity potassium transporter HAK5. Another great part of cesium uptake is mediated by non-selective cation channels. Plants can uptake up to 80 % of cesium applied on shoot surface. Cesium is highly...
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