Crystal structures of open and closed forms of D-serine deaminase from Salmonella typhimurium - implications on substrate specificity and catalysis

Metabolism of D-amino acids is of considerable interest due to their key importance in cell structure and function. Salmonella typhimurium D-serine deaminase (StDSD) is a pyridoxal 5' phosphate (PLP) dependent enzyme that catalyses degradation of D-Ser to pyruvate and ammonia. The first crystal structure of D-serine deaminase described here reveals a typical Foldtype II or tryptophan synthase beta subunit fold of PLP-dependent enzymes. Although holoenzyme was used for crystallization of both wild-type StDSD (WtDSD) and selenomethionine labelled StDSD (SeMetDSD), significant electron density was not observed for the cofactor, indicating that the enzyme has a low affinity for the cofactor under crystallization conditions. Interestingly, unexpected conformational differences were observed between the two structures. The WtDSD was in an open conformation while SeMetDSD, crystallized in the presence of isoserine, was in a closed conformation suggesting that the enzyme is likely to undergo conformational changes upon binding of substrate as observed in other Foldtype II PLP-dependent enzymes. Electron density corresponding to a plausible sodium ion was found near the active site of the closed but not in the open state of the enzyme. Examination of the active site and substrate modelling suggests that Thr166 may be involved in abstraction of proton from the C alpha atom of the substrate. Apart from the physiological reaction, StDSD catalyses a, b elimination of D-Thr, D-Allothr and L-Ser to the corresponding alpha-keto acids and ammonia. The structure of StDSD provides a molecular framework necessary for understanding differences in the rate of reaction with these substrates.

Biomonitoring of Lotic habitats through Diatoms

Freshwater ecosystems vary in size and composition and contain a wide range of organisms which interact with each other and with the environment. These interactions are between organisms and the environment as nutrient cycling, biomass formation and transfer, maintenance of internal environment and interactions with the external environment. The range of organisms present in aquatic communities decides the generation and transfer function of biomass, which defines and characterises the system. These organisms have distinct roles as they occupy particular trophic levels, forming an interconnected system in a food chain. Availability of resources and competition would primarily determine the balance of individual species within the food web, which in turn influences the variety and proportions of the different organisms, with important implications for the overall functioning of the system. This dynamic and diverse relationship decides the physical, chemical and biological elements across spatial and temporal scales in the aquatic ecosystem, which can be recorded by regular inventorying and monitoring to maintain the integrity and conserve the ecosystem. Regular environmental monitoring, particularly water quality monitoring allows us to detect, assess and manage the overall impacts on the rivers. The appreciation of water quality is in constant flux. Water quality assessments derived through the biotic indices, i.e. assessments based on observations of the resident floral and faunal communities has gained importance in recent years. Biological evaluations provide a description of the water quality that is often not achievable from elemental analyses alone. A biological indicator (or bioindicator) is a taxon or taxa selected based on its sensitivity to a particular attribute, and then assessed to make inferences about that attribute. In other words, they are a substitute for directly measuring abiotic features or other biota. Bioindicators are evaluated through presence or absence, condition, relative abundance, reproductive success, community structure (i.e. composition and diversity), community function (i.e. trophic structure), or any combination thereof.Biological communities reflect the overall ecological integrity by integrating various stresses, thus providing a broad measure of their synergistic impacts. Aquatic communities, both plants and animals, integrate and reflect the effects of chemical and physical disturbances that occur over extended periods of time. Monitoring procedures based on the biota measure the health of a river and the ability of aquatic ecosystems to support life as opposed to simply characterising the chemical and physical components of a particular system. This is the central purpose of assessing the biological condition of aquatic communities of a river.Diatoms (Bacillariophyceae), blue green algae (Cyanophyceae), green algae (Chlorophyceae), and red algae (Rhodphyceae) are the main groups of algae in flowing water. These organisms are widely used as biological indicators of environmental health in the aquatic ecosystem because algae occupy the most basic level in the transfer of energy through natural aquatic systems. The distribution of algae in an aquatic ecosystem is directly related to the fundamental factors such as physical, chemical and biological constituents. Soft algae (all the algal groups except diatoms) have also been used as indicators of biological integrity, but they may have less efficiency than diatoms in this respect due to their highly variable morphology. The diatoms (Bacillariophyceae) comprise a ubiquitous, highly successful and distinctive group of unicellular algae with the most obvious distinguishing characteristic feature being siliceous cell walls (frustules). The photosynthetic organisms living within its photic zone are responsible for about one-half of global primary productivity. The most successful organisms are thought to be photosynthetic prokaryotes (cyanobacteria and prochlorophytes) and a class of eukaryotic unicellular algae known as diatoms. Diatoms are likely to have arisen around 240 million years ago following an endosymbiotic event between a red eukaryotic alga and a heterotrophic flagellate related to the Oomycetes.The importance of algae to riverine ecology is easily appreciated when one considers that they are primary producers that convert inorganic nutrients into biologically active organic compounds while providing physical habitat for other organisms. As primary producers, algae transform solar energy into food from which many invertebrates obtain their energy. Algae also transform inorganic nutrients, such as atmospheric nitrogen into organic forms such as ammonia and amino acids that can be used by other organisms. Algae stabilises the substrate and creates mats that form structural habitats for fish and invertebrates. Algae are a source of organic matter and provide habitat for other organisms such as non-photosynthetic bacteria, protists, invertebrates, and fish. Algae's crucial role in stream ecosystems and their excellent indicator properties make them an important component of environmental studies to assess the effects of human activities on stream health. Diatoms are used as biological indicators for a number of reasons: 1. They occur in all types of aquatic ecosystems. 2. They collectively show a broad range of tolerance along a gradient of aquatic productivity, individual species have specific water chemistry requirements. 3. They have one of the shortest generation times of all biological indicators (~2 weeks). They reproduce and respond rapidly to environmental change and provide early measures of both pollution impacts and habitat restoration. 4. It takes two to three weeks before changes are reflected to a measurable extent in the assemblage composition.

Thermodynamics of oxide sulfate melts: The system PbO PbSO4

Activities in the PbO-PbSO4 melts at 1253 K have been measured by emf and gas-equilibration techniques. The activity of PbO was directly obtained from the emf of the solid oxide cell, Pt, Ni-NiO/CaO-ZrO2/Auo.92PbO.08, PbOx-PbSO4(1-x), Ir, Pt for 1.0 >XPbO > 0.6. The melt and the alloy were contained in closed zirconia crucibles. Since the partial pressure of SO2 gas in equilibrium with the melt and alloy was appreciable (>0.08 atm) atXPbO < 0.6, activities at lower PbO concentrations were derived from measurements of the weight gain of pure PbO under controlled gas streans of Ar + SO2 + O2. The partial and integral free energies of mixing at 1253 K were calculated and found to fit a subregular model: ΔGEPbO =X2PbSO4 {-42,450 + 20,000X2PbSO4} J mol-1 ΔGEPbO =X2pbSO {-12,450 - 20,000XPbS} J mol-1 ΔGEpbSOXPbSO4 {-32,450XPbS - 22,450XPbSO4 } J mol-1. The standard free energy of formation of liquid PbSO4 from pure liquid PbO and gaseous SO3 at 1 atm at 1253 K was evaluated as -88.02 (±0.72) kJ mol-1.

Thermodynamic study of Fe2O3 Fe2(SO4)3 equilibrium using an oxyanionic electrolyte (Na2SO4 I)

The emf of the cell, Pt, Ar + O2 + SO2 + SO3/Na2SO4-I/Fe2O2 + Fe2(SO4)3, Pt, has been measured in the temperature range 800 to 1000 K, using a gas mixture of known input composition as the reference electrode. The equilibrium composition of the reference gas at the measuring temperatures was computed using the thermodynamic data on the gaseous species reported in the literature. A mixture of ferric oxide and sulfate was kept in a closed system to ensure establishment of equilibrium partial pressure at the electrode. The cell was designed to avoid physical contact between Fe2(SO4)3 and Na2SO4 electrolyte. Uncertainties arising from the formation of sulfate solid solution were thus eliminated. The Gibbs’ energy of formation of ferric sulfate calculated from the emf is discussed in comparison with data reported in the literature. There is no evidence for the formation of oxysulfates in the Fe-S-0 system. Based on the results obtained in the present study for Fe2(SO4)3 and literature data for other phases, chemical potential diagrams have been constructed for the Fe-S-O system at 900 and 1100 K.

A new matched thermochemical diagram for vacuum refining of nickel and cupronickel alloys

Sulfur and oxygen dissolved in nickel and cupronickel melts can be remwed as gaseous oxides of sulfur by a vacuum treatment. Presented in this paper is a new matched thermcxhemical disgran~ that permit.. direct evaluation of the equilibrium partial pressure of SO, as a function of temperature wer an alloy of specified compition. The matched thermochemical diagram consists of a central plot which shows the integral Gibbs' energy of mixing for the binary system SO, at different temperatures. The central plot is flanked on either side by terminal plots of the chemical potentials of oxygen and sulfur, as functions of temperature, for different alloy compositions. By projecting the chemical wtentials of oxygen and sulfur from the terminal lots on to the central diagram, ihe equilibrium partial pressure of S0,can be directly ;cad on the nomograms on the central plot at different temperatures. The matched therrnochemical diagrams are useful in assuring the efficiency of vacuum refining.

Electrochemical oxidation of boron containing compounds on titanium carbide and its implications to direct fuel cells

Electrochemical oxidation of sodium borohydride (NaBH(4)) and ammonia borane (NH(3)BH(3)) (AB) have been studied on titanium carbide electrode. The oxidation is followed by using cyclic voltammetry, chronoamperometry and polarization measurements. A fuel cell with TiC as anode and 40 wt% Pt/C as cathode is constructed and the polarization behaviour is studied with NaBH(4) as anodic fuel and hydrogen peroxide as catholyte. A maximum power density of 65 mW cm(-2) at a load current density of 83 mA cm(-2) is obtained at 343 K in the case of borhydride-based fuel cell and a value of 85 mW cm(-2) at 105 mA cm(-2) is obtained in the case of AB-based fuel cell at 353 K. (C) 2011 Elsevier Ltd. All rights reserved.

Hydrogen generation fromammonia borane using nanocatalysts

The rapidly depleting petroleum feed stocks and increasing green house gas emissions around the world has necessitated a search for alternative renewable energy sources. Hydrogen with molecular weight of 2.016 g/mol and high chemical energy per mass equal to 142 MJ/kg has clearly emerged as an alternative to hydrocarbon fuels. Means for safe and cost effective storage are needed for widespread usage of hydrogen as a fuel.Chemical storage is the one of the safer ways to store hydrogen compared to compressed and liquefied hydrogen. It involves storing hydrogen in chemical bonds in molecules and materials where an on-board reaction is used to release hydrogen. Ammonia–borane, (AB,H3N·BH3) with a potential capacity of 19.6 wt% is considered a very promising solid state hydrogen storage material. It is thermally stable at ambient temperatures. There are two major routes for the generation of H2 from AB: catalytic hydrolysis/alcoholysis and catalytic thermal decomposition. There has been a flurry of research activity on the generation of H2 from AB recently. The present review deals with an overview of our efforts in developing cost-effective nanocatalysts for hydrogen generation from ammonia borane in protic solvents.

Viscous effects in the inception of cavitation

The inception of cavitation in the steady flow of liquids around bodies is seen to depend upon the real fluid flow around the bodies as well as the supply of nucleating cavitation sources—or nuclei—within the fluid. A primary distinction is made between bodies having a laminar separation or not having a laminar separation. The former group is relatively insensitive to the nuclei concentration whereas the latter is much more sensitive. Except for the case of fully separated wake flows and for gaseous cavitation by diffusion the cavitation inception index tends always to be less than the magnitude of the minimum pressure coefficient and only approaches that value for high Reynolds numbers in flows well supplied with nuclei.

Towards sustainability: a new, solid-state synthetic route for supported metal nanocatalysts

Noble metal ions like Pt(IV) and Pd(II) were impregnated on gamma-alumina and aerosol 300 silica surfaces. Reduction of these ions using ammonia borane in the solid state resulted in the formation of the respective metal nanoparticles embedded in BNHx polymer which is dispersed on the oxide support. Removal of the BNH polymer was accomplished by washing the samples repeatedly with methanol. In this process the polymer undergoes solvolysis to release H-2 accompanied by the formation of ammonium methoxy borate salt, which has been removed by repeated methanol washings. As a result, metal nanoparticles well dispersed on gamma-alumina and aerosol 300 silica were obtained. These samples have been characterized by a combination of techniques, including electron microscopy, powder X-ray diffraction, NMR spectroscopy and surface area analyser.

Catalyst-Packed Non-Thermal Plasma Reactor for Removal of Nitrogen Oxides

A single-stage plasma-catalytic reactor in which catalytic materials were packed was used to remove nitrogen oxides. The packing material was scoria being made of various metal oxides including Al2O3, MgO, TiO2, etc. Scoria was able to act not only as dielectric pellets but also as a catalyst in the presence of reducing agent such as ethylene and ammonia. Without plasma discharge, scoria did not work well as a catalyst in the temperature range of 100 °C to 200 °C, showing less than 10% of NOx removal efficiency. When plasma is produced inside the reactor, the NOx removal efficiency could be increased to 60% in this temperature range.

DeNOx Study in Diesel Engine Exhaust Using Barrier Discharge Corona Assisted by V2O5/TiO2 Catalyst

A plasma-assisted catalytic reactor was used to remove nitrogen oxides (NOx) from diesel engine exhaust operated under different load conditions. Initial studies were focused on plasma reactor (a dielectric barrier discharge reactor) treatment of diesel exhaust at various temperatures. The nitric oxide (NO) removal efficiency was lowered when high temperature exhaust was treated using plasma reactor. Also, NO removal efficiency decreased when 45% load exhaust was treated. Studies were then made with plasma reactor combined with a catalytic reactor consisting of a selective catalytic reduction (SCR) catalyst, V2O5/TiO2. Ammonia was used as a reducing agent for SCR process in a ratio of 1:1 to NOx. The studies were focused on temperatures of the SCR catalytic reactor below 200°C. The plasma-assisted catalytic reactor was operated well to remove NOx under no-load and load conditions. For an energy input of 96 J/l, the NOx removal efficiencies obtained under no-load and load conditions were 90% and 72% respectively at an exhaust temperature of 100°C.

Nonthermal-Plasma-Promoted Catalysis for the Removal of NOx From a Stationary Diesel-Engine Exhaust

A detailed study on the removal of oxides of nitrogen (NOx) from the exhaust of a stationary diesel engine was carried out using nonthermal-plasma (pulsed electrical-discharge plasma)-promoted catalytic process. In this paper, the filtered exhaust from the diesel engine is made to pass through a combination of nonthermal plasma reactor and a catalytic reactor connected in series. This combination is referred to as cascade. Two types of cascaded systems were studied. In one type, the plasma treating filtered exhaust was cascaded with a reduction catalyst V2O5/TiO2 using ammonia as reducing agent, and in the other type, the plasma treating filtered exhaust was cascaded with activated-alumina catalyst without any additive. Improved NOx-removal performance of both the cascaded processes and the role of nonthermal plasma in promoting catalysis are explained. Along with the NOx, total hydrocarbon and aldehydes were also removed. Furthermore, experiments were conducted at different temperatures and engine-loading conditions.

Atmospheric chemistry and climate

Atmospheric chemistry is a branch of atmospheric science where major focus is the composition of the Earth's atmosphere. Knowledge of atmospheric composition is essential due to its interaction with (solar and terrestrial) radiation and interactions of atmospheric species (gaseous and particulate matter) with living organisms. Since atmospheric chemistry covers a vast range of topics, in this article the focus is on the chemistry of atmospheric aerosols with special emphasis on the Indian region. I present a review of the current state of knowledge of aerosol chemistry in India and propose future directions.

Evaporation Heat Transfer Coefficient in a Capillary Pumped Loop and Loop Heat Pipe for Different Working Fluids

Capillary pumped loop (CPL) and loop heat pipe (LHP) are passive two-phase heat transport devices. They have been gaining importance as a part of the thermal control system of spacecraft. The evaporation heat transfer coefficient at the tooth-wick interface of an LHP or CPL has a significant impact on the evaporator temperature. It is also the main parameter in sizing of a CPL or LHP. Experimentally determined evaporation heat transfer coefficients from a three-port CPL with tubular axially grooved (TAG) evaporator and a TAG LHP with acetone, R-134A, and ammonia as working fluids are presented in this paper. The influences of working fluid, hydrodynamic blocks in the core, evaporator configuration (LHP or CPL), and adverse elevation (evaporator above condenser) on the heat transfer coefficient are presented.

Investigations on supersonic combustion in a combustion-driven shock tunnel

This article reports experimental results on supersonic combustion in a new facility. The facility is a combustion-driven shock tunnel, which is cheaper to build than the facilities in which such experiments are carried out conventionally. The observation region is a zone between two parallel flat plates with a 33 degrees wedge attached to the upstream end of the bottom plate. Gaseous hydrogen is injected at an angle of 45 degrees into an oncoming supersonic flow of Mach 2 (approximate) from a port on the bottom plate. The resulting flow field is visualized by a high speed camera in a dark background. Three different test gases, namely nitrogen, air, and oxygen-rich air are used, and the results are compared. A distinct luminosity due to combustion for oxygen-containing test gases is observed. Heat-transfer rates on a probe placed at the downstream end of the observation region and midway between the parallel plates are measured and compared for the three cases. Wall static pressure at 28 mm downstream of the injection port on the bottom plate is also presented.