Role of PheE15 gate in ligand entry and nitric oxide detoxification function of Mycobacterium tuberculosis truncated hemoglobin N

The truncated hemoglobin N, HbN, of Mycobacterium tuberculosis is endowed with a potent nitric oxide dioxygenase (NOD) activity that allows it to relieve nitrosative stress and enhance in vivo survival of its host. Despite its small size, the protein matrix of HbN hosts a two-branched tunnel, consisting of orthogonal short and long channels, that connects the heme active site to the protein surface. A novel dual-path mechanism has been suggested to drive migration of O(2) and NO to the distal heme cavity. While oxygen migrates mainly by the short path, a ligand-induced conformational change regulates opening of the long tunnel branch for NO, via a phenylalanine (PheE15) residue that acts as a gate. Site-directed mutagenesis and molecular simulations have been used to examine the gating role played by PheE15 in modulating the NOD function of HbN. Mutants carrying replacement of PheE15 with alanine, isoleucine, tyrosine and tryptophan have similar O(2)/CO association kinetics, but display significant reduction in their NOD function. Molecular simulations substantiated that mutation at the PheE15 gate confers significant changes in the long tunnel, and therefore may affect the migration of ligands. These results support the pivotal role of PheE15 gate in modulating the diffusion of NO via the long tunnel branch in the oxygenated protein, and hence the NOD function of HbN.

Electric field distribution in silicon edgeless detector

This Master’s Thesis work reports about electric field distribution in recently developed silicon edgeless detector with a new current terminating structure. This structure enables the essential reduction of insensitive detector area as well as allows separation of the current flowing through the active area from the current flowing at the cut edge. The reliable operation of this detector is strongly needed due to the installation inside LHC. In accordance with formulated problems SEM was used as an investigation tool for collecting the data about electric field distribution.

Comparative effects of macro-sized aluminum oxide and aluminum oxide nanoparticles on erythrocyte hemolysis: influence of cell source, temperature and size

Al2O3 is the most abundantly produced nanomaterial and has been used in diverse fields, including the medical, military and industrial sectors. As there are concerns about the health effects of nanoparticles, it is important to understand how they interact with cells, and specifically with red blood cells. The hemolysis induced by three commercial nano-sized aluminum oxide particles (nanopowder 13 nm, nanopowder <50 nm and nanowire 2-6 nm × 200-400 nm) was compared to aluminum oxide and has been studied on erythrocytes from humans, rats and rabbits, in order to elucidate the mechanism of action and the influence of size and shape on hemolytic behavior. The concentrations inducing 50% hemolysis (HC50) were calculated for each compound studied. The most hemolytic aluminum oxide particles were of nanopowder 13, followed by nanowire and nanopowder 50. The addition of albumin to PBS induced a protective effect on hemolysis in all the nano-forms of Al2O3, but not on Al2O3. The drop in HC50 correlated to a decrease in nanomaterial size, which was induced by a reduction of aggregation Aluminum oxide nanoparticles are less hemolytic than other oxide nanoparticles, and behave differently depending on the size and shape of the nanoparticles. The hemolytic behavior of aluminum oxide nanoparticles differs from that of aluminum oxide.

Structure and dynamics of the membrane attaching nitric oxide transporter nitrophorin 7

Nitrophorins represent a unique class of heme proteins that are able to perform the delicate transportation and release of the free-radical gaseous messenger nitric oxide (NO) in a pH-triggered manner. Besides its ability to bind to phospholipid membranes, the N-terminus contains an additional Leu-Pro-Gly stretch, which is a unique sequence trait, and the heme cavity is significantly altered with respect to other nitrophorins. These distinctive features encouraged us to solve the X-ray crystallographic structures of NP7 at low and high pH and bound with different heme ligands (nitric oxide, histamine, imidazole). The overall fold of the lipocalin motif is well preserved in the different X-ray structures and resembles the fold of other nitrophorins. However, a chain-like arrangement in the crystal lattice due to a number of head-to-tail electrostatic stabilizing interactions is found in NP7. Furthermore, the X-ray structures also reveal ligand-dependent changes in the orientation of the heme, as well as in specific interactions between the A-B and G-H loops, which are considered to be relevant for the biological function of nitrophorins. Fast and ultrafast laser triggered ligand rebinding experiments demonstrate the pH-dependent ligand migration within the cavities and the exit route. Finally, the topological distribution of pockets located around the heme as well as from inner cavities present at the rear of the protein provides a distinctive feature in NP7, so that while a loop gated exit mechanism to the solvent has been proposed for most nitrophorins, a more complex mechanism that involves several interconnected gas hosting cavities is proposed for NP7.

Comparative effects of macro-sized aluminum oxide and aluminum oxide nanoparticles on erythrocyte hemolysis: influence of cell source, temperature and size

Al2O3 is the most abundantly produced nanomaterial and has been used in diverse fields, including the medical, military and industrial sectors. As there are concerns about the health effects of nanoparticles, it is important to understand how they interact with cells, and specifically with red blood cells. The hemolysis induced by three commercial nano-sized aluminum oxide particles (nanopowder 13 nm, nanopowder <50 nm and nanowire 2-6 nm × 200-400 nm) was compared to aluminum oxide and has been studied on erythrocytes from humans, rats and rabbits, in order to elucidate the mechanism of action and the influence of size and shape on hemolytic behavior. The concentrations inducing 50% hemolysis (HC50) were calculated for each compound studied. The most hemolytic aluminum oxide particles were of nanopowder 13, followed by nanowire and nanopowder 50. The addition of albumin to PBS induced a protective effect on hemolysis in all the nano-forms of Al2O3, but not on Al2O3. The drop in HC50 correlated to a decrease in nanomaterial size, which was induced by a reduction of aggregation Aluminum oxide nanoparticles are less hemolytic than other oxide nanoparticles, and behave differently depending on the size and shape of the nanoparticles. The hemolytic behavior of aluminum oxide nanoparticles differs from that of aluminum oxide.

Iron oxide and pyrocatechol: a spectroscopy study of the reaction products

The reaction of 1,2-dihydroxy-benzene (pyrocatechol) (C6H6O2) with iron oxide (Fe2O3) and sodium thiosulfate (Na2S2O3) in aqueous medium (pH 7) was investigated. Pyrocatechol suffers autoxidation and coordinates with Fe3+ in solution. The presence of S2O3(2-) in solution was fundamental to generate and stabilize the pyrocatechol oxidation products as o-semiquinones. This compound was isolated and its structure characterized using FT-IR, EPR and UV-Vis Spectroscopy as [CTA][Fe(SQ)2(Cat)]. A thermal mass loss mechanism was proposed based on Thermogravimetric Analysis (TG) to support the structural characterization.

Blackbody emission under laser excitation of silicon nanopowder produced by plasma-enhanced chemical-vapor deposition

Previous results concerning radiative emission under laser irradiation of silicon nanopowder are reinterpreted in terms of thermal emission. A model is developed that considers the particles in the powder as independent, so under vacuum the only dissipation mechanism is thermal radiation. The supralinear dependence observed between the intensity of the emitted radiation and laser power is predicted by the model, as is the exponential quenching when the gas pressure around the sample increases. The analysis allows us to determine the sample temperature. The local heating of the sample has been assessed independently by the position of the transverse optical Raman mode. Finally, it is suggested that the photoluminescence observed in porous silicon and similar materials could, in some cases, be blackbody radiation

Gas collisions and pressure quenching of the photoluminescence of silicon nanopowder grown by plasma-enhanced chemical vapor deposition

The quenching of the photoluminescence of Si nanopowder grown by plasma-enhanced chemical vapor deposition due to pressure was measured for various gases ( H2, O2, N2, He, Ne, Ar, and Kr) and at different temperatures. The characteristic pressure, P0, of the general dependence I(P)=I0exp(-P/P0) is gas and temperature dependent. However, when the number of gas collisions is taken as the variable instead of pressure, then the quenching is the same within a gas family (mono- or diatomic) and it is temperature independent. So it is concluded that the effect depends on the number of gas collisions irrespective of the nature of the gas or its temperature

Quantification of the bond-angle dispersion by Raman spectroscopy and the strain energy of amorphous silicon

A thorough critical analysis of the theoretical relationships between the bond-angle dispersion in a-Si, Δθ, and the width of the transverse optical Raman peak, Γ, is presented. It is shown that the discrepancies between them are drastically reduced when unified definitions for Δθ and Γ are used. This reduced dispersion in the predicted values of Δθ together with the broad agreement with the scarce direct determinations of Δθ is then used to analyze the strain energy in partially relaxed pure a-Si. It is concluded that defect annihilation does not contribute appreciably to the reduction of the a-Si energy during structural relaxation. In contrast, it can account for half of the crystallization energy, which can be as low as 7 kJ/mol in defect-free a-Si

Relaxation and derelaxation of pure and hydrogenated amorphous silicon during thermal annealing experiments

The structural relaxation of pure amorphous silicon (a-Si) and hydrogenated amorphous silicon (a-Si:H) materials, that occurs during thermal annealing experiments, has been analyzed by Raman spectroscopy and differential scanning calorimetry. Unlike a-Si, the heat evolved from a-Si:H cannot be explained by relaxation of the Si-Si network strain but it reveals a derelaxation of the bond angle strain. Since the state of relaxation after annealing is very similar for pure and hydrogenated materials, our results give strong experimental support to the predicted configurational gap between a-Si and crystalline silicon

Effect of the structure of commercial poly(ethylene oxide-b-propylene oxide) demulsifier bases on the demulsification of water-in-crude oil emulsions: elucidation of the demulsification mechanism

Water-in-crude oil emulsions are formed during petroleum production and asphaltenes play an important role in their stabilization. Demulsifiers are added to destabilize such emulsions,however the demulsification mechanism is not completely known. In this paper, the performances of commercial poly(ethylene oxide-b-propylene oxide) demulsifiers were studied using synthetic water-in-oil emulsions and model-systems (asphaltenes in organic solvent). No change in the asphaltene aggregate size induced by the demulsifier was observed. The demulsification performance decreased as the asphaltene aggregate size increased, so it can be suggested that the demulsification mechanism is correlated to the voids between the aggregates adsorbed on the water droplets surface.

Synthesis of quinoxaline 1,4-di-N-oxide derivatives on solid support using room temperature and microwave-assisted solvent-free procedures

We describe the synthesis of 12 new ethyl and methyl quinoxaline-7-carboxylate 1,4-di-N-oxide derivatives on solid supports with room temperature and microwave-assisted solvent-free procedures. Results show that solid supports have good catalytic activity in the formation of quinoxaline 1,4-di-N-oxide derivatives. We found that florisil and montmorillonite KSF and K10 could be used as new, easily available, inexpensive alternatives of catalysts. Additionally, room temperature and microwave-irradiation solvent-free synthesis was more efficient than a conventional procedure (Beirut reaction), reducing reaction time and increasing yield.

Synthesis of indium tin oxide nanoparticles by a nonhydrolytic sol-gel method

Indium tin oxide nanoparticles were synthesized in two different sizes by a nonhydrolytic sol-gel method. These powders were then transformed into ITO via an intermediate metastable state at between 300 and 600 ºC. The presence of characteristic O-In-O and O-Sn-O bands at 480 and 670 cm-1 confirmed the formation of ITO. The X-ray diffraction patterns indicated the preferential formation of metastable hexagonal phase ITO (corundum type) as opposed to cubic phase ITO when the reflux time was less than 3 h and the heat treatment temperature was below 600 ºC. Particle morphology and crystal size were examined by scanning electron microscopy.

Basic properties of potassium oxide supported on zeolite y studied by pyrrole-tpd and catalytic conversion of methylbutynol

ABSTRACT We report on the basic properties of zeolite NaY and potassium supported on NaY (K/NaY) assessed by pyrrole-TPD and MBOH transformation. Pyrrole-TPD revealed that impregnation of zeolite NaY with potassium promoted additional adsorption sites for pyrrole compared to parent zeolite. For zeolite with various potassium loadings, pyrrole adsorbed on K/NaY decreased with increased potassium loading. Reduction in pyrrole adsorption could be due to potassium hindering intrinsic basic sites (lattice oxygen), to oxide of potassium occluding in zeolite cavities restricting access for pyrrole, or to K2O reacting with pyrrole to form nondesorbed pyrrolate anions. On MBOH transformation, potassium almost completely suppressed NaY acid sites while K/NaY basicity increased with potassium loading.

Nitrous oxide emissions from an intermittent aeration activated sludge system of an urban wastewater treatment plant

This study investigated the emission of N2O during the sequential aerated (60-min) and non-aerated (30-min) stages of an intermittent aeration cycle in an activated sludge wastewater treatment plant (WWTP). N2O emission occurred during both stages; however, emission was much higher during aeration. Air stripping is the major factor controlling transfer of N2O from the sewage to the atmosphere. The N2O emissions exclusively from the aeration tank represented 0.10% of the influent total nitrogen load and the per capita emission factor was almost 3 times higher than that suggested by the IPCC for inventories of N2O emission from WWTPs.