Conformational basis for substrate recognition and regulation of catalytic activity in Staphylococcus aureus nucleoside di-phosphate kinase

Nucleoside diphosphate kinases (NDK) are characterized by high catalytic turnover rates and diverse substrate specificity. These features make this enzyme an effective activator of a pro-drug an application that has been actively pursued for a variety of therapeutic strategies. The catalytic mechanism of this enzyme is governed by a conserved histidine that coordinates a magnesium ion at the active site. Despite substantial structural and biochemical information on NDK, the mechanistic feature of the phospho-transfer that leads to auto-phosphorylation remains unclear. While the role of the histidine residue is well documented, the other active site residues, in particular the conserved serine remains poorly characterized. Studies on some homologues suggest no role for the serine residue at the active site, while others suggest a crucial role for this serine in the regulation and quaternary association of this enzyme in some species. Here we report the biochemical features of the Staphylococcus aureus NDK and the mutant enzymes. We also describe the crystal structures of the apo-NDK, as a transition state mimic with vanadate and in complex with different nucleotide substrates. These structures formed the basis for molecular dynamics simulations to understand the broad substrate specificity of this enzyme and the role of active site residues in the phospho-transfer mechanism and oligomerization. Put together, these data suggest that concerted changes in the conformation of specific residues facilitate the stabilization of nucleotide complexes thereby enabling the steps involved in the ping-pong reaction mechanism without large changes to the overall structure of this enzyme. (C) 2011 Elsevier B.V. All rights reserved.

Ecological Assessment of Lentic Water Bodies of Bangalore

The restoration, conservation and management of water resources require a thorough understanding of what constitutes a healthy ecosystem. Monitoring and assessment provides the basic information on the condition of our waterbodies. The present work details the study carried out at two waterbodies, namely, the Chamarajasagar reservoir and the Madiwala Lake. The waterbodies were selected on the basis of their current use and locations. Chamarajasagar reservoir serves the purpose of supplying drinking water to Bangalore city and is located on the outskirts of the city surrounded by agricultural and forest land. On the other hand, Madiwala lake is situated in the heart of Bangalore city receiving an influx of pollutants from domestic and industrial sewage. Comparative assessment of the surface water quality of both were carried out by instituting the various physico–chemical and biological parameters. The physico-chemical analyses included temperature, transparency, pH, electrical conductivity, dissolved oxygen, alkalinity, total hardness, calcium hardness, magnesium hardness, nitrates, phosphates, sodium, potassium and COD measurements of the given waterbody. The analysis was done based on the standard methods prescribed (or recommended) by (APHA) and NEERI. The biological parameter included phytoplankton analysis. The detailed investigations of the parameters, which are well within the tolerance limits in Chamarajasagar reservoir, indicate that it is fairly unpolluted, except for the pH values, which indicate greater alkalinity. This may be attributed to the natural causes and the agricultural runoff from the catchment. On the contrary, the limnology of Madiwala lake is greatly influenced by the inflow of sewage that contributes significantly to the dissolved solids of the lake water, total hardness, alkalinity and a low DO level. Although, the two study areas differ in age, physiography, chemistry and type of inflows, they still maintain a phytoplankton distribution overwhelmingly dominated by Cyanophyceae members,specifically Microcystis aeruginosa. These blue green algae apparently enter the waterbodies from soil, which are known to harbour a rich diversity of blue green flora with several species common to limnoplankton, a feature reported to be unique to the south Indian lakes.Chamarajasagar water samples revealed five classes of phytoplankton, of which Cyanophyceae (92.15 percent) that dominated other algal forms comprised of one single species of Microcystis aeruginosa. The next major class of algae was Chlorophyceae (3.752 percent) followed by Dinophyceae (3.51 percent), Bacillariophyceae (0.47 percent) and a sparsely available and unidentified class (0.12 percent).Madiwala Lake phytoplankton, in addition to Cyanophyceae (26.20 percent), revealed a high density of Chlorophyceae members (73.44 percent) dominated by Scenedesmus sp.,Pediastrum sp., and Euglena sp.,which are considered to be indicators of organic pollution. The domestic and industrial sewage, which finds its way into the lake, is a factor causing organic pollution. As compared to the other classes, Euglenophyceae and Bacillariophyceae members were the lowest in number. Thus, the analysis of various parameters indicates that Chamarajasagar reservoir is relatively unpolluted except for the high percentage of Microcystis aeruginosa, and a slightly alkaline nature of water. Madiwala lake samples revealed eutrophication and high levels of pollution, which is clarified by the physico–chemical analysis, whose values are way above the tolerance limits. Also, the phytoplankton analysis in Madiwala lake reveals the dominance of Chlorophyceae members, which indicate organic pollution (sewage being the causative factor).

Evaluation of the Quality of Drinking Water in Kerala State, India

The quality of tap water from water supplies from 14 districts of Kerala state, India was studied. Parameters like pH, water temperature, total dissolved solids, salinity, nitrates, chloride, hardness, magnesium, calcium, sodium, potassium, fluoride, sulphate, phosphates, and coliform bacteria were enumerated. The results showed that all water samples were contaminated by coliform bacteria. About 20% of the tap water samples from Alappuzha and 15% samples from Palakkad district are above desirable limits prescribed by Bureau of Indian Standards. The contamination of the source water (due to lack of community hygiene) and insufficient treatment are the major cause for the coliform contamination in the state. Water samples from Alappuzha and Palakkad have high ionic and fluoride content which could be attributed to the geology of the region. Water supplied for drinking in rural areas are relatively free of any contamination than the water supplied in urban area by municipalities, which may be attributed higher chances of contamination in urban area due to mismanagement of solid and liquid wastes. The study highlights the need for regular bacteriological enumeration along with water quality in addition to setting up decentralised region specific improved treatment system.

Novel Pentameric Structure of the Diarrhea-Inducing Region of the Rotavirus Enterotoxigenic Protein NSP4

A novel pentameric structure which differs from the previously reported tetrameric form of the diarrhea-inducing region of the rotavirus enterotoxin NSP4 is reported here. A significant feature of this pentameric form is the absence of the calcium ion located in the core region of the tetrameric structures. The lysis of cells, the crystallization of the region spanning residues 95 to 146 of NSP4 (NSP4(95-146)) of strain ST3 (ST3: NSP4(95-146)) at acidic pH, and comparative studies of the recombinant purified peptide under different conditions by size-exclusion chromatography (SEC) and of the crystal structures suggested pH-, Ca(2+)-, and protein concentration-dependent oligomeric transitions in the peptide. Since the NSP4(95-146) mutant lacks the N-terminal amphipathic domain (AD) and most of the C-terminal flexible region (FR), to demonstrate that the pentameric transition is not a consequence of the lack of the N- and C-terminal regions, glutaraldehyde cross-linking of the Delta N72 and Delta N94 mutant proteins, which contain or lack the AD, respectively, but possess the complete C-terminal FR, was carried out. The results indicate the presence of pentamers in preparations of these longer mutants. Detailed SEC analyses of Delta N94 prepared under different conditions, however, revealed protein concentration-dependent but metal ion-and pH-independent pentamer accumulation at high concentrations which dissociated into tetramers and lower oligomers at low protein concentrations. While calcium appeared to stabilize the tetramer, magnesium in particular stabilized the dimer. Delta N72 existed primarily in the multimeric form under all conditions. These findings of a calcium-free NSP4 pentamer and its concentration-dependent and largely calcium-independent oligomeric transitions open up a new dimension in an understanding of the structural basis of its multitude of functions.

Microstructure and texture evolution during accumulative roll bonding of aluminium alloy AA5086

In the present investigation, a strongly bonded strip of an aluminium-magnesium based alloy AA5086 is successfully produced through accumulative roll bonding (ARB). A maximum of up to eight passes has been used for the purpose. Microstructural characterization using electron backscatter diffraction (EBSD) technique indicates the formation of submicron sized (similar to 200-300 nm) subgrains inside the layered microstructure. The material is strongly textured where individual layers possess typical FCC rolling texture components. More than three times enhancement in 0.2% proof stress (PS) has been obtained after 8 passes due to grain refinement and strain hardening. (C) 2011 Elsevier B.V. All rights reserved.

Phase equilibria and thermodynamics of the system Dy-Mg-Cl at 1073 K

The phase relations in the system Dy–Mg–Cl at 1073 K have been established by isothermal equilibration and chemical analysis of quenched samples. Liquid Mg-rich alloy was found to be in equilibrium with molten DyCl2. Therefore, DyCl2 can be synthesized by reduction of MgCl2 with excess of metallic Dy at 1073 K. The Gibbs energy of formation of DyCl2 at 1073 K was evaluated by two different methods. From voltammetric determination of decomposition voltage, the upper limit for the standard Gibbs energy of formation of DyCl2 was estimated to be −505(±20) kJ mol−1. A value of −543(±10) kJ mol−1 was deduced from phase relations using Gibbs–Duhem integration. The value for the standard Gibbs energy of DyCl2 indicates that the Dy2+ ion has a potential capability for reducing TiCl4 to metal titanium. At the same time, Mg is a reductant for Dy3+ produced during the reduction of TiCl4. Thus, it is thermodynamically confirmed that reduction of TiCl4 by magnesium using a reaction mediator in the salt phase is feasible.

Role of Spectral Studies in Detection of Antibacterial Phytoelements and Phytochemicals of Moringa oleifera

This paper reports, the Laser Induced Breakdown Spectroscopy (LIBS) studies and structure elucidation of compounds isolated from the fruit extract of Moringa oleifera and also deals with their possible effects on some bacterial strains viz. Staphylococcus aureus, Klebsiella pneumonia, Escherichia coli and Pseudomonas aeruginosa. The extract was found to be active against all four microorganisms used. Extent of inhibitory effect of extract was assessed at different concentrations of 25, 50, 75 mg/ml by measuring diameter of inhibition zone (DIZ). Our results clearly showed that the 75 mg/ml concentration of the extract had 14, 12 and 18 mm of the DIZ against Staphylococcus aureus, Klebsiella pneumonia and Pseudomonas aeruginosa and 14 mm with 50 mg/ml concentration against Escherichia coli. The results were compared with the standard antibiotic `ampicillin' of 1 mg/ml concentration. LIBS was recorded with high power pulsed laser beam from Nd: YAG Laser (Continuum Surelite III-10), focused on the surface of the material, which was in liquid form, to generate plasma on the surface of the sample. LIBS data clearly demonstrate the presence of trace elements, magnesium and iron, in high concentration in the extract. Whereas, from the phytochemical profile reveals the presence of two new compounds, S-ethyl-N-{4-[(alpha-L-rhamnosyloxy) benzyl]} thiocarbamate and 2-acetoxy {4-[(2',3',4'-tri-O-acetyl-alpha-L-rhamnosyloxy) benzyl]} acetonitrile as the major constituents. This study is the first report on synergetic effect of the phytoconstituents and certain set of elements present in their defined role in bacterial management against different bacterial strains.

New metal-organic precursors for MOCVD applications: Synthesis, characterization, crystal structure and thermal properties of mixed-ligand Mg(II) complexes

In an effort to develop new MOCVD precursors, mixed-ligand metal-organic complexes, bis (acetylacetonato-k(2)O,O') (2,2'-bipyridine-k(2)N,N') magnesium(II), and his (acetylacetonato-k(2)O,O') (1,10-phenanthroline-k(2)N,N') magnesium(II) were synthesized. Spectroscopic characterization and crystal structures confirmed them to be monomeric and stable complexes. Crystal structure analysis suggests in each of the magnesium(II) complexes, the metal center has a distorted octahedral coordination geometry. Thermo-gravimetric analysis (TGA/DTA) suggests that these complexes are volatile and thermally stable. The thermal characteristics of newly designed complexes make them attractive precursors for MOCVD applications. (c) 2012 Elsevier B.V. All rights reserved.

Influence of anthropogenic contamination on groundwater chemistry in Mulbagal town, Kolar District, India

Geochemical studies are performed to examine the impact of leachate infiltration from on-site sewage disposal systems on the groundwater chemistry in Mulbagal town, Kolar District, Karnataka State, India. The leachate infiltration imposed nitrate concentrations ranging from 4 mg/L to 388 mg/L in the groundwater samples; it was observed that 79% of the samples exhibited nitrate concentrations in excess of drinking water permissible limit (45 mg/L). The average (of 43 measurements) E. coli levels in the groundwater samples corresponded to 189 MPN/100 mL and 55% of the samples tested exhibit pathogen contamination. Results also showed that the groundwater in the study area is characterized by acidic pH, large calcium + magnesium ion and Na/Cl ratios of < unity causing majority of the ground water samples to classify as Ca-Mg-Cl type and Na-Cl type. Saturation index (SI) computation using Visual MINTEQ program showed that the groundwater samples are under-saturated with respect to calcite. The theoretical SI values (of calcite) however suggested that the groundwater samples ought to be over-saturated with calcite. Under-saturation of the groundwater samples with calcite is attributed to increased dissolution of the mineral in the acidic environment of the groundwater.

Solution nuclear magnetic resonance structure of the GATase subunit and structural Basis of the interaction between GATase and ATPPase subunits in a two-subunit-type GMPS from methanocaldococcus jannaschii

The solution structure of the monomeric glutamine amidotransferase (GATase) subunit of the Methanocaldococcus janaschii (Mj) guanosine monophosphate synthetase (GMPS) has been determined using high-resolution nuclear magnetic resonance methods. Gel filtration chromatography and N-15 backbone relaxation studies have shown that the Mj GATase subunit is present in solution as a 21 kDa (188-residue) monomer. The ensemble of 20 lowest-energy structures showed root-mean-square deviations of 0.35 +/- 0.06 angstrom for backbone atoms and 0.8 +/- 0.06 angstrom for all heavy atoms. Furthermore, 99.4% of the backbone dihedral angles are present in the allowed region of the Ramachandran map, indicating the stereochemical quality of the structure. The core of the tertiary structure of the GATase is composed of a seven-stranded mixed beta-sheet that is fenced by five alpha-helices. The Mj GATase is similar in structure to the Pyrococcus horikoshi (Ph) GATase subunit. Nuclear magnetic resonance (NMR) chemical shift perturbations and changes in line width were monitored to identify residues on GATase that were responsible for interaction with magnesium and the ATPPase subunit, respectively. These interaction studies showed that a common surface exists for the metal ion binding as well as for the protein-protein interaction. The dissociation constant for the GATase-Mg2+ interaction has been found to be similar to 1 mM, which implies that interaction is very weak and falls in the fast chemical exchange regime. The GATase-ATPPase interaction, on the other hand, falls in the intermediate chemical exchange regime on the NMR time scale. The implication of this interaction in terms of the regulation of the GATase activity of holo GMPS is discussed.

Transition in subicular burst firing neurons from epileptiform activity to suppressed state by feedforward inhibition

The subiculum, a para-hippocampal structure positioned between the cornu ammonis 1 subfield and the entorhinal cortex, has been implicated in temporal lobe epilepsy in human patients and in animal models of epilepsy. The structure is characterized by the presence of a significant population of burst firing neurons that has been shown previously to lead epileptiform activity locally. Phase transitions in epileptiform activity in neurons following a prolonged challenge with an epileptogenic stimulus has been shown in other brain structures, but not in the subiculum. Considering the importance of the subicular burst firing neurons in the propagation of epileptiform activity to the entorhinal cortex, we have explored the phenomenon of phase transitions in the burst firing neurons of the subiculum in an in vitro rat brain slice model of epileptogenesis. Whole-cell patch-clamp and extracellular field recordings revealed a distinct phenomenon in the subiculum wherein an early hyperexcitable state was followed by a late suppressed state upon continuous perfusion with epileptogenic 4-aminopyridine and magnesium-free medium. The suppressed state was characterized by inhibitory post-synaptic potentials in pyramidal excitatory neurons and bursting activity in local fast-spiking interneurons at a frequency of 0.1-0.8Hz. The inhibitory post-synaptic potentials were mediated by GABA(A) receptors that coincided with excitatory synaptic inputs to attenuate action potential discharge. These inhibitory post-synaptic potentials ceased following a cut between the cornu ammonis 1 and subiculum. The suppression of epileptiform activity in the subiculum thus represents a homeostatic response towards the induced hyperexcitability. Our results suggest the importance of feedforward inhibition in exerting this homeostatic control.

SELF-ORGANIZATION AND FRICTION DURING SLIDING

In self-organized sliding processes, the surfaces align to each other during sliding. This alignment leads to a more ordered contact state and significantly influences the frictional behavior. To understand the self-organization sliding processes, experiments were conducted on a pin-on-plate reciprocating sliding tester for various numbers of cycles. In the experiments, soft magnesium pins were slid against hard steel plates of various surface textures (undirectional, 8-ground, and random). Experimental results showed that the transfer layer formation on the steel plates increased with increasing number of cycles for all surfaces textures under both dry and lubricated conditions. The friction also increased with the number of cycles under dry conditions for all of the textures studied. During lubricated conditions, the friction decreased for unidirectional and 8-ground surfaces and increased for random surfaces with the number of cycles. Furthermore, the friction and transfer layer formation depend on the surface textures under both dry and lubricated conditions during the first few sliding cycles. Later on, it is less dependent of surface textures. The variation in the coefficient of friction under both dry and lubrication conditions were attributed to the self-organization process that occurred during repeated sliding.

Off-site impacts of agricultural composting: role of terrestrially derived organic matter in structuring aquatic microbial communities and their metabolic potential

While considered as sustainable and low-cost agricultural amendments, the impacts of organic fertilizers on downstream aquatic microbial communities remain poorly documented. We investigated the quantity and quality of the dissolved organic matter leaching from agricultural soil amended with compost, vermicompost or biochar and assessed their effects on lake microbial communities, in terms of viral and bacterial abundances, community structure and metabolic potential. The addition of compost and vermicompost significantly increased the amount of dissolved organic carbon in the leachate compared with soil alone. Leachates from these additions, either with or without biochar, were highly bioavailable to aquatic microbial communities, although reducing the metabolic potential of the community and harbouring more specific communities. Although not affecting bacterial richness or taxonomic distributions, the specific addition of biochar affected the original lake bacterial communities, resulting in a strongly different community. This could be partly explained by viral burst and converging bacterial abundances throughout the samples. These results underline the necessity to include off-site impacts of agricultural amendments when considering their cascading effect on downstream aquatic ecosystems.

Exploring sand and bentonite - enhanced sand as filter media for nitrate removal

Increasing nitrate concentrations in ground water is deleterious to human health as ingestion of such water can cause methemoglobinemia in infants and even cancer in adults (desirable limit for nitrate as NO3 - 45 mg/L, IS code 10500-1991). Excess nitrate concentrations in ground water is contributed by reason being disposal of sewage and excessive use of fertilizers. Though numerous technologies such as reverse osmosis, ion exchange, electro-dialysis, permeable reactive barriers using zerovalent iron etc exists, nitrate removal continues to be one of challenging issue as nitrate ion is highly mobile within the soil strata. The tapping the denitrification potential of soil denitrifiers which are inherently available in the soil matrix is the most sustainable approach to mitigate accumulation of nitrate in ground water. The insitu denitrification of sand and bentonite enhanced sand (bentonite content = 5%) in presence of easily assimilable organic carbon such as ethanol was studied. Batch studies showed that nitrate reduction by sand follows first order kinetics with a rate constant 5.3x10(-2) hr(-1) and rate constant 4.3 x 10(-2) hr(-1) was obtained for bentonite-enhanced sand (BS) at 25 degrees C. Filter columns (height = 5 cm and diameter = 8.2 cm) were constructed using sand and bentonite-enhanced sand as filter media. The filtration rate through both the filter columns was maintained at average value of 2.60 cm/h. The nitrate removal rates through both the filter media was assessed for solution containing 22.6 mg NO3-N/L concentrations while keeping C/N mass ratio as 3. For sand filter column, the nitrate removal efficiency reached the average value of 97.6% after passing 50 pore volumes of the nitrate solution. For bentonite-enhanced sand filter column, the average nitrate removal efficiency was 83.5%. The time required for effective operation for sand filter bed was 100 hours, while bentonite-enhanced sand filter bed did not require any maturation period as that of sand filter bed for effective performance because the presence of micropores in bentonite increases the hydraulic retention time of the solution inside the filter bed.

Study of Microstructure Evolution during Semi-Solid Processing of an In-Situ Al Alloy Composite

In the present work, effect of pouring temperature (650 degrees C, 655 degrees C, and 660 degrees C) on semi-solid microstructure evolution of in-situ magnesium silicide (Mg2Si) reinforced aluminum (Al) alloy composite has been studied. The shear force exerted by the cooling slope during gravity driven flow of the melt facilitates the formation of near spherical primary Mg2Si and primary Al grains. Shear driven melt flow along the cooling slope and grain fragmentation have been identified as the responsible mechanisms for refinement of primary Mg2Si and Al grains with improved sphericity. Results show that, while flowing down the cooling slope, morphology of primary Mg2Si and primary Al transformed gradually from coarse dendritic to mixture of near spherical particles, rosettes, and degenerated dendrites. In terms of minimum grain size and maximum sphericity, 650 degrees C has been identified as the ideal pouring temperature for the cooling slope semi-solid processing of present Al alloy composite. Formation of spheroidal grains with homogeneous distribution of reinforcing phase (Mg2Si) improves the isotropic property of the said composite, which is desirable in most of the engineering applications.