Overexpression and purification of Treponema pallidum rubredoxin; kinetic evidence for a superoxide-mediated electron transfer with the superoxide reductase neelaredoxin

J Biol Inorg Chem (2004) 9: 839–849 DOI 10.1007/s00775-004-0584-6

Impaired uptake of glutathione by hepatic mitochondria from chronic ethanol-fed rats. Tracer kinetic studies in vitro and in vivo and susceptibility to oxidant stress.

Isolated hepatocytes incubated with [35S]-methionine were examined for the time-dependent accumulation of [35S]-glutathione (GSH) in cytosol and mitochondria, the latter confirmed by density gradient purification. In GSH-depleted and -repleted hepatocytes, the increase of specific activity of mitochondrial GSH lagged behind cytosol, reaching nearly the same specific activity by 1-2 h. However, in hepatocytes from ethanol-fed rats, the rate of increase of total GSH specific radioactivity in mitochondria was markedly suppressed. In in vivo steady-state experiments, the mass transport of GSH from cytosol to mitochondria and vice versa was 18 nmol/min per g liver, indicating that the half-life of mitochondrial GSH was approximately 18 min in controls. The fractional transport rate of GSH from cytosol to mitochondria, but not mitochondria to cytosol, was significantly reduced in the livers of ethanol-fed rats. Thus, ethanol-fed rats exhibit a decreased mitochondrial GSH pool size due to an impaired entry of cytosol GSH into mitochondria. Hepatocytes from ethanol-fed rats exhibited a greater susceptibility to the oxidant stress-induced cell death from tert-butylhydroperoxide. Incubation with glutathione monoethyl ester normalized the mitochondrial GSH and protected against the increased susceptibility to t-butylhydroperoxide, which was directly related to the lowered mitochondrial GSH pool size in ethanol-fed cells.

Experiments on anisotropic radial viscous fingering

We observe dendritic patterns in fluid flow in an anisotropic Hele-Shaw cell and measure the tip shapes and trajectories of individual dendritic branches under conditions where the pattern growth appears to be dominated by surface tension anisotropy and also under conditions where kinetic effects appear dominant. In each case, the tip position depends on a power law in the time, but the exponent of this power law can vary significantly among flow realizations. Averaging many growth exponents a yields a =0.640.09 in the surface tension dominated regime and a =0.660.09 in the kinetic regime. Restricting the analysis to realizations when a is very close to 0.6 shows great regularity across pattern regimes in the coefficient of the temporal dependence of the tip trajectory.

Wet oxidation of recalcitrant lignin waters: Experimental and kinetic studies

The dissertation is based on four articles dealing with recalcitrant lignin water purification. Lignin, a complicated substance and recalcitrant to most treatment technologies, inhibits seriously pulp and paper industry waste management. Therefore, lignin is studied, using WO as a process method for its degradation. A special attention is paid to the improvement in biodegradability and the reduction of lignin content, since they have special importance for any following biological treatment. In most cases wet oxidation is not used as a complete ' mineralization method but as a pre treatment in order to eliminate toxic components and to reduce the high level of organics produced. The combination of wet oxidation with a biological treatment can be a good option due to its effectiveness and its relatively low technology cost. The literature part gives an overview of Advanced Oxidation Processes (AOPs). A hot oxidation process, wet oxidation (WO), is investigated in detail and is the AOP process used in the research. The background and main principles of wet oxidation, its industrial applications, the combination of wet oxidation with other water treatment technologies, principal reactions in WO, and key aspects of modelling and reaction kinetics are presented. There is also given a wood composition and lignin characterization (chemical composition, structure and origin), lignin containing waters, lignin degradation and reuse possibilities, and purification practices for lignin containing waters. The aim of the research was to investigate the effect of the operating conditions of WO, such as temperature, partial pressure of oxygen, pH and initial concentration of wastewater, on the efficiency, and to enhance the process and estimate optimal conditions for WO of recalcitrant lignin waters. Two different waters are studied (a lignin water model solution and debarking water from paper industry) to give as appropriate conditions as possible. Due to the great importance of re using and minimizing the residues of industries, further research is carried out using residual ash of an Estonian power plant as a catalyst in wet oxidation of lignin-containing water. Developing a kinetic model that includes in the prediction such parameters as TOC gives the opportunity to estimate the amount of emerging inorganic substances (degradation rate of waste) and not only the decrease of COD and BOD. The degradation target compound, lignin is included into the model through its COD value (CODligning). Such a kinetic model can be valuable in developing WO treatment processes for lignin containing waters, or other wastewaters containing one or more target compounds. In the first article, wet oxidation of "pure" lignin water was investigated as a model case with the aim of degrading lignin and enhancing water biodegradability. The experiments were performed at various temperatures (110 -190°C), partial oxygen pressures (0.5 -1.5 MPa) and pH (5, 9 and 12). The experiments showed that increasing the temperature notably improved the processes efficiency. 75% lignin reduction was detected at the lowest temperature tested and lignin removal improved to 100% at 190°C. The effect of temperature on the COD removal rate was lower, but clearly detectable. 53% of organics were oxidized at 190°C. The effect of pH occurred mostly on lignin removal. Increasing the pH enhanced the lignin removal efficiency from 60% to nearly 100%. A good biodegradability ratio (over 0.5) was generally achieved. The aim of the second article was to develop a mathematical model for "pure" lignin wet oxidation using lumped characteristics of water (COD, BOD, TOC) and lignin concentration. The model agreed well with the experimental data (R2 = 0.93 at pH 5 and 12) and concentration changes during wet oxidation followed adequately the experimental results. The model also showed correctly the trend of biodegradability (BOD/COD) changes. In the third article, the purpose of the research was to estimate optimal conditions for wet oxidation (WO) of debarking water from the paper industry. The WO experiments were' performed at various temperatures, partial oxygen pressures and pH. The experiments showed that lignin degradation and organics removal are affected remarkably by temperature and pH. 78-97% lignin reduction was detected at different WO conditions. Initial pH 12 caused faster removal of tannins/lignin content; but initial pH 5 was more effective for removal of total organics, represented by COD and TOC. Most of the decrease in organic substances concentrations occurred in the first 60 minutes. The aim of the fourth article was to compare the behaviour of two reaction kinetic models, based on experiments of wet oxidation of industrial debarking water under different conditions. The simpler model took into account only the changes in COD, BOD and TOC; the advanced model was similar to the model used in the second article. Comparing the results of the models, the second model was found to be more suitable for describing the kinetics of wet oxidation of debarking water. The significance of the reactions involved was compared on the basis of the model: for instance, lignin degraded first to other chemically oxidizable compounds rather than directly to biodegradable products. Catalytic wet oxidation of lignin containing waters is briefly presented at the end of the dissertation. Two completely different catalysts were used: a commercial Pt catalyst and waste power plant ash. CWO showed good performance using 1 g/L of residual ash gave lignin removal of 86% and COD removal of 39% at 150°C (a lower temperature and pressure than with WO). It was noted that the ash catalyst caused a remarkable removal rate for lignin degradation already during the pre heating for `zero' time, 58% of lignin was degraded. In general, wet oxidation is not recommended for use as a complete mineralization method, but as a pre treatment phase to eliminate toxic or difficultly biodegradable components and to reduce the high level of organics. Biological treatment is an appropriate post treatment method since easily biodegradable organic matter remains after the WO process. The combination of wet oxidation with subsequent biological treatment can be an effective option for the treatment of lignin containing waters.

Kinetic modeling of mechanisms of industrially important organic reactions in gas and liquid phase

This dissertation is based on 5 articles which deal with reaction mechanisms of the following selected industrially important organic reactions: 1. dehydrocyclization of n-butylbenzene to produce naphthalene 2. dehydrocyclization of 1-(p-tolyl)-2-methylbutane (MB) to produce 2,6-dimethylnaphthalene 3. esterification of neopentyl glycol (NPG) with different carboxylic acids to produce monoesters 4. skeletal isomerization of 1-pentene to produce 2-methyl-1-butene and 2-methyl-2-butene The results of initial- and integral-rate experiments of n-butylbenzene dehydrocyclization over selfmade chromia/alumina catalyst were applied when investigating reaction 2. Reaction 2 was performed using commercial chromia/alumina of different acidity, platina on silica and vanadium/calcium/alumina as catalysts. On all catalysts used for the dehydrocyclization, major reactions were fragmentation of MB and 1-(p-tolyl)-2-methylbutenes (MBes), dehydrogenation of MB, double bond transfer, hydrogenation and 1,6-cyclization of MBes. Minor reactions were 1,5-cyclization of MBes and methyl group fragmentation of 1,6- cyclization products. Esterification reactions of NPG were performed using three different carboxylic acids: propionic, isobutyric and 2-ethylhexanoic acid. Commercial heterogeneous gellular (Dowex 50WX2), macroreticular (Amberlyst 15) type resins and homogeneous para-toluene sulfonic acid were used as catalysts. At first NPG reacted with carboxylic acids to form corresponding monoester and water. Then monoester esterified with carboxylic acid to form corresponding diester. In disproportionation reaction two monoester molecules formed NPG and corresponding diester. All these three reactions can attain equilibrium. Concerning esterification, water was removed from the reactor in order to prevent backward reaction. Skeletal isomerization experiments of 1-pentene were performed over HZSM-22 catalyst. Isomerization reactions of three different kind were detected: double bond, cis-trans and skeletal isomerization. Minor side reaction were dimerization and fragmentation. Monomolecular and bimolecular reaction mechanisms for skeletal isomerization explained experimental results almost equally well. Pseudohomogeneous kinetic parameters of reactions 1 and 2 were estimated by usual least squares fitting. Concerning reactions 3 and 4 kinetic parameters were estimated by the leastsquares method, but also the possible cross-correlation and identifiability of parameters were determined using Markov chain Monte Carlo (MCMC) method. Finally using MCMC method, the estimation of model parameters and predictions were performed according to the Bayesian paradigm. According to the fitting results suggested reaction mechanisms explained experimental results rather well. When the possible cross-correlation and identifiability of parameters (Reactions 3 and 4) were determined using MCMC method, the parameters identified well, and no pathological cross-correlation could be seen between any parameter pair.

Time-resolved gas-phase kinetic and quantum chemical studies of reactions of silylene with chlorine-containing species. 1. HCl

Time-resolved kinetic studies of the reaction of silylene, SiH2, generated by laser flash photolysis of phenylsilane, have been carried out to obtain rate constants for its bimolecular reaction with HCL The reaction was studied in the gas phase at 10 Torr total pressure in SF6 bath gas, at five temperatures in the range of 296-611 K. The second-order rate constants fitted the Arrhenius equation: log(k/cm(3) molecule(-1) s(-1)) = (-11.51 +/- 0.06) + (1.92 +/- 0.47 kJ mol(-1))/RTIn10 Experiments at other pressures showed that these rate constants were unaffected by pressure in the range of 10-100 Torr, but showed small decreases in value of no more than 20% ( +/- 10%) at I Toff, at both the highest and lowest temperatures. The data are consistent with formation of an initial weakly bound donor-acceptor complex, which reacts by two parallel pathways. The first is by chlorine-to-silicon H-shift to make vibrationally excited chlorosilane, SiH3Cl*, which yields HSiCl by H-2 elimination from silicon. In the second pathway, the complex proceeds via H-2 elimination (4-center process) to make chlorosilylene, HSiCl, directly. This interpretation is supported by ab initio quantum calculations carried out at the G3 level which reveal the direct H-2 elimination route for the first time. RRKM modeling predicts the approximate magnitude of the pressure effect but is unable to determine the proportions of each pathway. The experimental data agree with the only previous measurements at room temperature. Comparisons with other reactions of SiH2 are also drawn.

Coupling aerosol surface and bulk chemistry with a kinetic double layer model (K2-SUB): oxidation of oleic acid by ozone

We present a kinetic double layer model coupling aerosol surface and bulk chemistry (K2-SUB) based on the PRA framework of gas-particle interactions (Poschl-Rudich-Ammann, 2007). K2-SUB is applied to a popular model system of atmospheric heterogeneous chemistry: the interaction of ozone with oleic acid. We show that our modelling approach allows de-convoluting surface and bulk processes, which has been a controversial topic and remains an important challenge for the understanding and description of atmospheric aerosol transformation. In particular, we demonstrate how a detailed treatment of adsorption and reaction at the surface can be coupled to a description of bulk reaction and transport that is consistent with traditional resistor model formulations. From literature data we have derived a consistent set of kinetic parameters that characterise mass transport and chemical reaction of ozone at the surface and in the bulk of oleic acid droplets. Due to the wide range of rate coefficients reported from different experimental studies, the exact proportions between surface and bulk reaction rates remain uncertain. Nevertheless, the model results suggest an important role of chemical reaction in the bulk and an approximate upper limit of similar to 10(-11) cm(2) s(-1) for the surface reaction rate coefficient. Sensitivity studies show that the surface accommodation coefficient of the gas-phase reactant has a strong non-linear influence on both surface and bulk chemical reactions. We suggest that K2-SUB may be used to design, interpret and analyse future experiments for better discrimination between surface and bulk processes in the oleic acid-ozone system as well as in other heterogeneous reaction systems of atmospheric relevance.

Night-time tropospheric chemistry of the unsaturated alcohols (Z)-pent-2-en-1-ol and pent-1-en-3-ol: Kinetic studies of reactions of NO3 and N2O5 with stress-induced plant emissions

The night-time tropospheric chemistry of two stress-induced volatile organic compounds (VOCs), (Z)-pent-2-en-1-ol and pent-1-en-3-ol, has been studied at room temperature. Rate coefficients for reactions of the nitrate radical (NO3) with these pentenols were measured using the discharge-flow technique. Because of the relatively low volatility of these compounds, we employed off-axis continuous-wave cavity-enhanced absorption spectroscopy for detection of NO3 in order to be able to work in pseudo first-order conditions with the pentenols in large excess over NO3. The rate coefficients were determined to be (1.53 +/- 0.23) x 10(-13) and (1.39 +/- 0.19) x 10(-14) cm(3) molecule(-1) s(-1) for reactions of NO3 with (Z)-pent-2-en-1-ol and pent-1-en-3-ol. An attempt to study the kinetics of these reactions with a relative-rate technique, using N2O5 as source of NO3 resulted in significantly higher apparent rate coefficients. Performing relative-rate experiments in known excesses of NO2 allowed us to determine the rate coefficients for the N2O5 reactions to be (5.0 +/- 2.8) x 10(-19) cm(3) molecule(-1) s(-1) for (Z)-pent-2-en-1-ol, and (9.1 +/- 5.8) x 10(-19) cm(3) molecule(-1) s(-1) for pent-1-en-3-ol. We show that these relatively slow reactions can indeed interfere with rate determinations in conventional relative-rate experiments.

Some numerical experiments on the effect of the variation of static stability in two-layer quasi-geostrophic models

A method to solve a quasi-geostrophic two-layer model including the variation of static stability is presented. The divergent part of the wind is incorporated by means of an iterative procedure. The procedure is rather fast and the time of computation is only 60–70% longer than for the usual two-layer model. The method of solution is justified by the conservation of the difference between the gross static stability and the kinetic energy. To eliminate the side-boundary conditions the experiments have been performed on a zonal channel model. The investigation falls mainly into three parts: The first part (section 5) contains a discussion of the significance of some physically inconsistent approximations. It is shown that physical inconsistencies are rather serious and for these inconsistent models which were studied the total kinetic energy increased faster than the gross static stability. In the next part (section 6) we are studying the effect of a Jacobian difference operator which conserves the total kinetic energy. The use of this operator in two-layer models will give a slight improvement but probably does not have any practical use in short periodic forecasts. It is also shown that the energy-conservative operator will change the wave-speed in an erroneous way if the wave-number or the grid-length is large in the meridional direction. In the final part (section 7) we investigate the behaviour of baroclinic waves for some different initial states and for two energy-consistent models, one with constant and one with variable static stability. According to the linear theory the waves adjust rather rapidly in such a way that the temperature wave will lag behind the pressure wave independent of the initial configuration. Thus, both models give rise to a baroclinic development even if the initial state is quasi-barotropic. The effect of the variation of static stability is very small, qualitative differences in the development are only observed during the first 12 hours. For an amplifying wave we will get a stabilization over the troughs and an instabilization over the ridges.

The reaction between silylene and ammonia: some gas-phase kinetic and quantum chemical studies

Time-resolved kinetic studies of the reaction of silylene, SiH2, generated by 193 nm laser flash photolysis of silacyclopent-3-ene, have been carried out in the presence of ammonia, NH3. Second order kinetics were observed. The reaction was studied in the gas phase at 10 Torr total pressure in SF6 bath gas at each of the three temperatures, 299, 340 and 400 K. The second order rate constants (laser pulse energy of 60 mJ/pulse) fitted the Arrhenius equation: log(k/cm3 molecule-1 s-1) = (-10.37 ± 0.17) + (0.36 ± 1.12 kJ mol-1)/RTln10 Experiments at other pressures showed that these rate constants were unaffected by pressure in the range 10-100 Torr, but showed small decreases in value at 3 and 1 Torr. There was also a weak intensity dependence, with rate constants decreasing at laser pulse energies of 30 mJ/pulse. Ab initio calculations at the G3 level of theory, show that SiH2 + NH3 should form an initial adduct (donor-acceptor complex), but that energy barriers are too great for further reaction of the adduct. This implies that SiH2 + NH3 should be a pressure dependent association reaction. The experimental data are inconsistent with this and we conclude that SiH2 decays are better explained by reaction of SiH2 with the amino radical, NH2, formed by photodissociation of NH3 at 193 nm. The mechanism of this previously unstudied reaction is discussed.

The Crystal Complex of Phosphofructokinase-2 of Escherichia coli with Fructose-6-phosphate KINETIC AND STRUCTURAL ANALYSIS OF THE ALLOSTERIC ATP INHIBITION

Substrate inhibition by ATP is a regulatory feature of the phosphofructokinases isoenzymes from Escherichia coli (Pfk-1 and Pfk-2). Under gluconeogenic conditions, the loss of this regulation in Pfk-2 causes substrate cycling of fructose-6-phosphate (fructose-6-P) and futile consumption of ATP delaying growth. In the present work, we have broached the mechanism of ATP-induced inhibition of Pfk-2 from both structural and kinetic perspectives. The crystal structure of Pfk-2 in complex with fructose-6-P is reported to a resolution of 2 angstrom. The comparison of this structure with the previously reported inhibited form of the enzyme suggests a negative interplay between fructose-6-P binding and allosteric binding of MgATP. Initial velocity experiments show a linear increase of the apparent K(0.5) for fructose-6-P and a decrease in the apparent k(cat) as a function of MgATP concentration. These effects occur simultaneously with the induction of a sigmoidal kinetic behavior (n(H) of approximately 2). Differences and resemblances in the patterns of fructose-6-P binding and the mechanism of inhibition are discussed for Pfk-1 and Pfk-2, as an example of evolutionary convergence, because these enzymes do not share a common ancestor.

Kinetic asymmetry in the gel-liquid crystalline state transitions of DDAB vesicles studied by differential scanning calorimetry

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Supercritical fluid extraction from fennel (Foeniculum vulgare): global yield, composition and kinetic data

Supercritical fluid extraction (SFE) from solids has proven to be technically feasible for almost any system; nonetheless, its economical viability has been proven for a restricted number of systems. A common practice is to compare the cost of manufacturing of vegetable extracts by a variety of techniques without deeply considering the huge differences in composition and functional properties among the various types of extracts obtained; under this circumstance, the cost of manufacturing do not favor SFE. Additionally, the influence of external parameters such as the agronomic conditions and the SFE system geometry are not considered. In the present work, these factors were studied for the system fennel seeds + CO2. The effects of the harvesting season and the degree of maturation on the global yields for the system fennel seeds + CO2 were analyzed at 300 bar and 40 degrees C. The effects of the pressure on the global yields were determined for the temperatures of 30 and 40 degrees C. Kinetics experiments were done for various ratios of bed height to bed diameter. Fennel extracts were also obtained by hydrodistillation and low-pressure solvent extraction. The chemical composition of the fennel extracts were determined by gas chromatography. The SFE maximum global yield (12.5%, dry basis) was obtained with dry harvested fennel seeds. Anethole and fenchone were the major constituents of the extract; the following fat acids palmitic (C16H32O2), palmitoleic stearic (C18H36O2), oleic (C18H34O2), linoleic (C18H32O2) and linolenic (C18H30O2) were also detected in the extracts. A relation between amounts of feed and solvent, bed height and diameter, and solvent flow rate was proposed. The models of Sovova, Goto et al. and Tan and Lion were capable of describing the mass transfer kinetics. (c) 2005 Elsevier B.V. All rights reserved.

A kinetic model of phosphorus metabolism in growing goats

The effect of increasing phosphorus (P) intake on P utilization was investigated in balance experiments using 12 Saanen goats, 4 to 5 mo of age and weighing 20 to 30 kg. The goats were given similar diets with various concentrations of P, and 32P was injected to trace the movement of P in the body. A P metabolism model with four pools was developed to compute P exchanges in the system. The results showed that P absorption, bone resorption, and excretion of urinary P and endogenous and fecal P all play a part in the homeostatic control of P. Endogenous fecal output was positively correlated to P intake (P < .01). Bone resorption of P was not influenced by intake of P, and P recycling from tissues to the blood pool was lesser for low P intake. Endogenous P loss occurred even in animals fed an inadequate P diet, resulting in a negative P balance. The extrapolated minimum endogenous loss in feces was .067 g of P/d. The minimum P intake for maintenance in Saanen goats was calculated to be .61 g of P/ d or .055 g of P/(kg.75·d) at 25 kg BW. Model outputs indicate greater P flow from the blood pool to the gut and vice versa as P intake increased. Intake of P did not significantly affect P flow from bone and soft tissue to blood. The kinetic model and regressions could be used to estimate P requirement and the fate of P in goats and could also be extrapolated to both sheep and cattle.

Kinetic study of pyrolysis of castor beans (Ricinuscommunis L) presscake: an alternative use for solid waste arising from the biodiesel production

This work investigated the effects of temperature and of rate of heating on the kinetic parameters of pyrolysis of castor beans presscake, a byproduct generated in the biodiesel production process. Pyrolysis process was investigated by thermogravimetric analysis, and parameters were obtained from nonisothermal experiments. The results obtained from the process of thermal decomposition indicated the elimination of humidity and the decomposition of organic components of the biomass. DTG curves showed that the heating rate affects the temperature of maximum decomposition of the material. Kinetic parameters such as activation energy and pre-exponential factor were obtained by model-free methods proposed by Flynn–Wall–Ozawa (FWO), Kissinger–Akahira–Sunose (KAS), and Kissinger. Experimental results showed that the kinetic parameters values of the FWO and KAS methods display good agreement and can be used to understand the mechanism of degradation of the cake. In a generalized way, the results contribute to better understanding of the processes of biomass pyrolysis.