Modeling of angiogenin-3 '-NMP complex

Angiogenin belongs to the Ribonuclease superfamily and has a weak enzymatic activity that is crucial for its biological function of stimulating blood vessel growth. Structural studies on ligand bound Angiogenin will go a long way in understanding the mechanism of the protein as well as help in designing drugs against it. In this study we present the first available structure of nucleotide ligand bound Angiogenin obtained by computer modeling. The importance of this study in itself notwithstanding, is a precursor to modeling a full dinucleotide substrate onto Angiogenin. Bovine Angiogenin, the structure of which has been solved at a high resolution, was earlier subjected to Molecular Dynamics simulations for a nanosecond. The MD structures offer better starting points for docking as they offer lesser obstruction than the crystal structure to ligand binding. The MD structure with the least serious short contacts was modeled to obtain a steric free Angiogenin - 3' mononucleotide complex structure. The structures were energetically minimized and subjected to a brief spell of Molecular Dynamics. The results of the simulation show that all the li,ligand-Angiogenin interactions and hydrogen bonds are retained, redeeming the structure and docking procedure. Further, following ligand - protein interactions in the case of the ligands 3'-CMP and 3'-UMP we were able to speculate on how Angiogenin, a predominantly prymidine specific ribonuclease prefers Cytosine to Uracil in the first base position.

Mutations in beta ` subunit of Escherichia coli RNA polymerase perturb the activator polymerase functional interaction required for promoter clearance

P>Transcription activator C employs a unique mechanism to activate mom gene of bacteriophage Mu. The activation process involves, facilitating the recruitment of RNA polymerase (RNAP) by altering the topology of the promoter and enhancing the promoter clearance by reducing the abortive transcription. To understand the basis of this multi-step activation mechanism, we investigated the nature of the physical interaction between C and RNAP during the process. A variety of assays revealed that only DNA-bound C contacts the beta' subunit of RNAP. Consistent to these results, we have also isolated RNAP mutants having mutations in the beta' subunit which were compromised in C-mediated activation. Mutant RNAPs show reduced productive transcription and increased abortive initiation specifically at the C-dependent mom promoter. Positive control (pc) mutants of C, defective in interaction with RNAP, retained the property of recruiting RNAP to the promoter but were unable to enhance promoter clearance. These results strongly suggest that the recruitment of RNAP to the mom promoter does not require physical interaction with C, whereas a contact between the beta' subunit and the activator, and the subsequent allosteric changes in the active site of the enzyme are essential for the enhancement of promoter clearance.

Plate-shaped transformation products in zirconium-base alloys

Plate-shaped products resulting from martensitic, diffusional, and mixed mode transformations in zirconium-base alloys are compared. in the present study. These alloys are particularly suitable for the comparison in view of the fact that the lattice correspondence between the parent beta (bcc) and the product alpha (hcp) or gamma-hydride (fct) phases are remarkably similar for different types of transformations. Crystallographic features such as orientation relations, habit planes, and interface structures associated with these transformations have been compared:, with a view toward examining whether the transformation mechanisms have characteristic imprints on these experimental observables. Martensites exhibiting dislocated lath, internally twinned plate, and self-accommodating three-plate cluster morphologies have been encountered in Zr-2.5Nb alloy. Habit planes corresponding to all these morphologies have been found to be consistent with the predictions based on the invariant plane strain (IFS) criterion. Different morphologies have been found to reflect the manner in which the neighboring martensite variants are assembled. Lattice-invariant shears (LISs) for all these cases have been identified to be either {10 (1) over bar 1}(alpha) ((1) over bar 123)(alpha) slip or twinning on (10 (1) over bar 1)(alpha) planes. Widmanstatten alpha precipitates, forming in a step-quenching treatment, have been shown to have a lath morphology, the alpha/beta interface being decorated with a periodic array of (c + a) dislocations at a spacing of 8 to 10 nm. The line vectors of these dislocations are nearly parallel to the invariant lines. The alpha precipitates, forming in the retained beta phase on aging, exhibit an internally twinned structure with a zigzag habit plane. Average habit planes for the morphologies have been found to lie near the {103}(beta) - {113}(beta) poles, which are close to the specific variant of the {112}(beta) plane, which transforms into a prismatic plane of the type {1 (1) over bar 00}(alpha). The crystallography of the formation of the gamma-hydride phase (fct) from both the alpha and beta phases is seen to match the IFS predictions. While the beta-gamma transformation can be treated approximately as a simple shear on the basal plane involving a change in the stacking sequence, the alpha-gamma transformation call be conceptually broken into a alpha --> beta transformation following the Burgers correspondence and the simple beta-gamma shear process. The active eutectoid decomposition in the Zr-Cu system, beta --> alpha + beta', has been described in terms of cooperative growth of the alpha phase from the beta phase through the Burgers correspondence and of the partially ordered beta' (structurally similar to the equilibrium Zr2Cu phase) through an ordering process. Similarities and differences in crystallographic features of these transformations have been discussed. and the importance of the invariant line vector in deciding the geometry of the corresponding habit planes has been pointed out.

Syntheses, Transfection Efficacy and Cell Toxicity Properties of Novel Cholesterol-based Gemini Lipids having Hydroxyethyl Head group

We have synthesized five new cholesterol based gemini cationic lipids possessing hydroxyethyl (-CH2CH2OH) function on each head group, which differ in the length of the polymethylene spacer chain. These gemini lipids are important for gene delivery processes as they possess pre-optimized molecular features, e. g., cholesterol backbone, ether linkage and a variable spacer chain between both the headgroups of the gemini lipids. Cationic liposomes were prepared from each of these lipids individually and as a mixture of individual cationic gemini lipid and 1,2-dioleoyl phosphatidylethanolamine (DOPE). Each gemini lipid based formulation induced better transfection activity than that of their monomeric counterpart. One such gemini lipid with a -(CH2)(12)-spacer, HG-12, showed dramatic increase in the mean fluorescence intensity due to the expression of green-fluorescence protein (GFP) in the presence of 10% FBS compared to the conditions where there was no serum. Other gemini lipids retained their gene transfection efficiency without any marked decrease in the presence of serum. The only exception was seen with the gemini with a -(CH2)(3)-spacer, HG-3, which on gene transfection in the presence of 10% FBS lost similar to 70% of its transfection efficiency. Overall the gemini lipid with a -(CH2)(5)-spacer, HG-5, showed the highest transfection activity at N/P (lipid/DNA) ratio of 0.5 and lipid : DOPE molar ratio of 2. Upon comparison of the relevant parameters, e. g., %-transfected cells, the amount of DNA transfected to each cell and %-cell viability all together against Lipofectamine 2000, one of the best commercial transfecting agents, the optimized lipid formulation based on DOPE/HG-5 was found to be comparable. In terms of its ability to induce gene-transfer in the presence of serum and shelf-life DOPE/HG-5 liposome was found to be superior to its commercial counterpart. Confocal imaging analysis confirmed that in the presence of 10% serum using a Lipid : DOPE of 1 : 4 and N/P charge ratio of 0.75 with 1.2 mu g DNA per well, HG-5 is better than Lipofectamine 2000.

Studies of ternary Li2SO4-Li2O-P2O5 glasses

Glasses in a wide range of compositions in the ternary system xLi(2)SO(4-y)Li(2)O-zP(2)O(5) where x ranges from 0 to 30 mol%, y ranges from 35 to 55 mol% and z ranges from 25 to 50 mol% have been prepared and their properties measured using infra-red, Raman, and P-31 magic angle spinning nuclear magnetic resonance spectroscopic techniques. We conclude that a random close packing of phosphate and sulphate ions which also leads to formation of connected voids in the structure is consistent with our data. There is also evidence for formation of condensed sulphate-phosphate species in the liquid which may be retained in the glass structure. (C) 1999 Elsevier Science B.V. All rights reserved.

Studies on the Effect of Li2SO4 on the Structure of Lithium Borate Glasses

Thermal and spectroscopic investigations have been carried out on a number of glasses with a wide range of compositions in the pseudoternary glass system, Li2SO4-Li2O-B2O3, to understand the role of sulfate ions in modifying the borate glass structure. Both nuclear magnetic resonance (NMR) and infrared (IR) spectroscopic results indicate that four-coordinate boron atoms are retained in the glass structure to a greater extent in sulfate-containing glasses than in pure lithium borate glasses. There seems to be some evidence for the existence of sulfoborate-type units in Raman spectra in the region of 800-960 cm(-1). These conclusions are supported by the observed behavior of glass transition temperatures and molar volumes. The possibility of formation of sulfoborate-type units is discussed from bonding and thermodynamic points of view.

Synthesis of metastable, wurzite-based zinc oxide-cobalt(II) oxide solid solutions by spray pyrolysis

Aqueous solutions of acetates and nitrates of zinc and cobalt have been spray decomposed to study the production of extended solid solutions in the ZnO-CoO system. Examination of the products of a variety of synthesis conditions indicates that up to 70% CoO may be retained in the solid solution in the wurzite phase, even though a comparison of the equilibrium solubility in the phase diagram might be expected to favor the formation of a rock-salt-based solid solution.

Durable electrocatalytic-activity of Pt-Au/C cathode in PEMFCs

Longevity remains as one of the central issues in the successful commercialization of polymer electrolyte membrane fuel cells (PEMFCs) and primarily hinges on the durability of the cathode. Incorporation of gold (Au) to platinum (Pt) is known to ameliorate both the electrocatalytic activity and stability of cathode in relation to pristine Pt-cathodes that are currently being used in PEMFCs. In this study, an accelerated stress test (AST) is conducted to simulate prolonged fuel-cell operating conditions by potential cycling the carbon-supported Pt-Au (Pt-Au/C) cathode. The loss in performance of PEMFC with Pt-Au/C cathode is found to be similar to 10% after 7000 accelerated potential-cycles as against similar to 60% for Pt/C cathode under similar conditions. These data are in conformity with the electrochemical surface-area values. PEMFC with Pt-Au/C cathode can withstand > 10 000 potential cycles with very little effect on its performance. X-ray diffraction and transmission electron microscopy studies on the catalyst before and after AST suggest that incorporating Au with Pt helps mitigate aggregation of Pt particles during prolonged fuel-cell operations while X-ray photoelectron spectroscopy reflects that the metallic nature of Pt is retained in the Pt-Au catalyst during AST in comparison to Pt/C that shows a major portion of Pt to be present as oxidic platinum. Field-emission scanning electron microscopy conducted on the membrane electrode assembly before and after AST suggests that incorporating Au with Pt helps mitigating deformations in the catalyst layer.

Phase transformation and semiconductor-metal transition in thin films of VO2 deposited by low-pressure metalorganic chemical vapor deposition

Thin films of the semiconducting, monoclinic vanadium dioxide, VO2(M) have been prepared on ordinary glass by two methods: directly by low-pressure metalorganic chemical vapor deposition (MOCVD), and by argon-annealing films of the VO2(B) phase deposited by MOCVD. The composition and microstructure of the films have been examined by x-ray diffraction, scanning electron microscopy, and transmission electron microscopy. Films made predominantly of either the B or the M phase, as deposited, can only be obtained over a narrow range of deposition temperatures. At the lower end of this temperature range, the as-deposited films are strongly oriented, although the substrate is glass. This can be understood from the drive to minimize surface energy. Films of the B phase have a platelet morphology, which leads to an unusual microstructure at the lower-deposition temperatures. Those grown at similar to370 degreesC convert to the metallic, rutile (R) phase when annealed at 550 degreesC, whereas those deposited at 420 degreesC transform to the R phase only at 580 degreesC. (When cooled to room temperature, the annealed films convert reversibly from the R phase to the M phase.) Electron microscopy shows that annealing leads to disintegration of the single crystalline VO2(B) platelets into small crystallites of VO2(R), although the platelet morphology is retained. When the annealing temperature is relatively low, these crystallites are nanometer sized. At a higher-annealing temperature, the transformation leads to well-connected and similarly oriented large grains of VO2(R), enveloped in the original platelet. The semiconductor-metal transition near 68 degreesC leads to a large jump in resistivity in all the VO2(M) films, nearly as large as in epitaxial films on single-crystal substrates. When the annealed films contain well-connected large grains, the transition is very sharp. Even when preferred orientation is present, the transition is not as sharp in as-deposited VO2(M), because the crystallites are not densely packed as in annealed VO2(B). However, the high degree of orientation in these films leads to a narrow temperature hysteresis. (C) 2002 American Institute of Physics.

Synthesis of acicular hydrogoethite (alpha-FeOOH center dot xH(2)O; 0.1 < x < 0.22) particles using morphology controlling cationic additives and magnetic properties of maghemite derived from hydrogoethite

A method for the preparation of acicular hydrogoethite (alpha -FeOOH.xH(2)O, 0.1 < x < 0.22) particles of 0.3-1 mm length has been optimized by air oxidation of Fe( II) hydroxide gel precipitated from aqueous (NH4)(2)Fe(SO4)(2) solutions containing 0.005-0.02 atom% of cationic Pt, Pd or Rh additives as morphology controlling agents. Hydrogoethite particles are evolved from the amorphous ferrous hydroxide gel by heterogeneous nucleation and growth. Preferential adsorption of additives on certain crystallographic planes thereby retarding the growth in the perpendicular direction, allows the particles to acquire acicular shapes with high aspect ratios of 8-15. Synthetic hydrogoethite showed a mass loss of about 14% at similar to 280 degreesC, revealing the presence of strongly coordinated water of hydration in the interior of the goethite crystallites. As evident from IR spectra, excess H2O molecules (0.1- 0.22 per formula unit) are located in the strands of channels formed in between the double ribbons of FeO6 octahedra running parallel to the c- axis. Hydrogoethite particles constituted of multicrystallites are formed with Pt as additive, whereas single crystallite particles are obtained with Pd (or Rh). For both dehydroxylation as well as H-2 reduction, a lower reaction temperature (similar to 220 degreesC) was observed for the former (Pt treated) compared to the latter (Pd or Rh) (similar to 260 degreesC). Acicular magnetite (Fe3O4) was prepared either by reducing hydrogoethite (magnetite route) or dehydroxylating hydrogoethite to hematite and then reducing it to magnetite (hematite- magnetite route). According to TEM studies, preferential dehydroxylation of hydrogoethite along < 010 > leads to microporous hematite. Maghemite (gamma -Fe2O3 (-) (delta), 0 < < 0.25) was obtained by reoxidation of magnetite. The micropores are retained during the topotactic transformation to magnetite and finally to maghemite, whereas cylindrical mesopores are formed due to rearrangement of the oxygen sublattice from hexagonal to cubic close packing during the conversion of hydrogoethite to magnetite and then to maghemite. Accordingly, three different types of maghemite particles are realized: strongly oriented multicrystalline particles, single crystalline acicular particles with micropores or crystallites having mesopores. Higher values of saturation magnetization ((s) = 74 emu g(-1)) and coercivity (H-c = 320 Oe) are obtained for single crystalline mesoporous particles. In the other cases, the smaller size of particles and larger distribution of micropores decreases sigma (s) considerably ( < 60 emu g(-1)) due to relaxation effects of spins on the surface atoms as revealed by Mossbauer spectroscopy.

Time Evolution of the Microstructure of VO2(B) Films Deposited on Glass by MOCVD

Thin films of VO2(B), a metastable polymorph of vanadium dioxide, have been grown on glass by low-pressure metalorganic chemical vapor deposition (MOCVD). The films grown for 90 minutes have atypical microstructure, comprising micrometer-sized, island-like entities made up of numerous small, single-crystalline platelets (≅1 μm) emerging orthogonally from larger ones at the center. Microstructure evolution as a function of deposition time has been examined by X-ray diffraction, scanning electron microscopy, and transmission electron microscopy. The metastable VO2(B) transforms to the stable rutile (R) phase at 550°C in inert ambient, which on cooling convert reversibly to M phase. Electron microscopy shows that annealing leads to the disintegration of the VO2(B) platelets into small crystallites of the rutile phase VO2(R), although the platelet morphology is retained. The magnitude of the jump in resistance at the semiconductor-to-metal, VO2(M)→VO2(R) phase transition depends on the arrangement of polycrystalline platelets in the films.

Self-organization of multiple components in a steroidal hydrogel matrix: design, construction and studies on novel tunable luminescent gels and xerogels

The present work combines two rapidly growing research areas-functional supramolecular gels and lanthanide based hybrid materials. Facile hydrogel formation from several lanthanide(III) cholates has been demonstrated. The morphological and mechanical properties of these cholate gels were investigated by TEM and rheology. The hydrogel matrix was subsequently utilized for the sensitization of Tb(III) by doping a non-coordinating chromophore, 2,3-dihydroxynaphthalene (DHN), at micromolar concentrations. In the mixed gels of Tb(III)-Eu(III), an energy transfer pathway was found to operate from Tb(III) to Eu(III) and by utilizing this energy transfer, tunable multiple-color luminescent hydrogels were obtained. The emissive properties of the hydrogels were also retained in the xerogels and their suspensions in n-hexane were used for making luminescent coating on glass surface.

Present status of Gottigere Tank : Indicator of Decision maker’s apathy

Gottigere lake with a water spread area of about 14.98 ha is located in the Bellandur Lake catchment of the South Pennar River basin. In recent years, this lake catchment has been subjected to environmental stress mainly due to the rampant unplanned developmental activities in the catchment. The functional ability of the ecosystem is impaired due to structural changes in the ecosystem. This is evident from poor water quality, breeding of disease vectors, contamination of groundwater in the catchment, frequent flooding in the catchment due to topography alteration, decline in groundwater table, erosion in lake bed, etc. The development plans of the region (current as well as the proposed) ignore the integrated planning approaches considering all components of the ecosystem. Serious threats to the sustainability of the region due to lack of holistic approaches in aquatic resources management are land use changes (removal of vegetation cover, etc.), point and non-point sources of pollution impairing water quality, dumping of solid waste (building waste, etc.). Conservation of lake ecosystem is possible only when the physical and chemical integrity of its catchment is maintained. Alteration in the catchment either due to land use changes (leading to paved surface area from vegetation cover), alteration in topography, construction of roads in the immediate vicinity are detrimental to water yield in the catchment and hence, the sustenance of the lake. Open spaces in the form of lakes and parks aid as kidney and lung in an urban ecosystem, which maintain the health of the people residing in the locality. Identification of core buffer zones and conservation of buffer zones (500 to 1000 m from shore) is to be taken up on priority for conservation and sustainable management of Bangalore lakes. Bangalore is located over a ridge delineating four watersheds, viz. Hebbal, Koramangala, Challaghatta and Vrishabhavathi. Lakes and tanks are an integral part of natural drainage and help in retaining water during rainfall, which otherwise get drained off as flash floods. Each lake harvests rainwater from its catchment and surplus flows downstream spilling into the next lake in the chain. The topography of Bangalore has uniquely supported the creation of a large number of lakes. These lakes form chains, being a series of impoundments across streams. This emphasises the interconnectivity among Bangalore lakes, which has to be retained to prevent Bangalore from flooding or from water scarcity. The main source of replenishment of groundwater is the rainfall. The slope of the terrain allows most of the rainwater to flow as run-off. With the steep gradients available in the major valleys of Bangalore, the rainwater will flow out of the city within four to five hours. Only a small fraction of the rainwater infiltrates into the soil. The infiltration of water into the subsoil has declined with more and more buildings and paved road being constructed in the city. Thus the natural drainage of Bangalore is governed by flows from the central ridge to all lower contours and is connected with various tanks and ponds. There are no major rivers flowing in Bangalore and there is an urgent need to sustain these vital ecosystems through proper conservation and management measures. The proposed peripheral ring road connecting Hosur Road (NH 7) and Mysore Road (SH 17) at Gottigere lake falls within the buffer zone of the lake. This would alter the catchment integrity and hence water yield affecting flora, fauna and local people, and ultimately lead to the disappearance of Gottigere lake. Developmental activities in lake catchments, which has altered lake’s ecological integrity is in violation of the Indian Fisheries Act – 1857, the Indian Forest Act – 1927, Wildlife (Protection) Act – 1972, Water (Prevention and Control of Pollution) Act – 1974, Water (Prevention and Control of Pollution) Act – 1977, Forest (Conservation Act) – 1980, Environmental (Protection) Act – 1986, Wildlife (Protection) Amendment Act – 1991 and National Conservation Strategy and Policy Statement on Environment and Development – 1992. Considering 65% decline of waterbodies in Bangalore (during last three decades), decision makers should immediately take preventive measures to ensure that lake ecosystems are not affected. This report discusses the impacts due to the proposed infrastructure developmental activities in the vicinity of Gottigere tank.

Thermally induced phase separation in P alpha MSAN/PMMA blends in presence of functionalized multiwall carbon nanotubes: Rheology, morphology and electrical conductivity

The focus of this work is the evaluation and analysis of the state of dispersion of functionalized multiwall carbon nanotubes (CNTs), within different morphologies formed, in a model LCST blend (poly[(alpha-methylstyrene)-co-(acrylonitrile)]/poly(methyl-methacryla te), P alpha MSAN/PMMA). Blend compositions that are expected to yield droplet-matrix (85/15 P alpha MSAN/PMMA and 15/85 P alpha MSAN/PMMA, wt/wt) and co-continuous morphologies (60/40 P alpha MSAN/PMMA, wt/wt) upon phase separation have been combined with two types of CNTs; carboxylic acid functionalized (CNTCOOH) and polyethylene modified (CNTPE) up to 2 wt%. Thermally induced phase separation in the blends has been studied in-situ by rheology and dielectric (conductivity) spectroscopy in terms of morphological evolution and CNT percolation. The state of dispersion of CNTs has been evaluated by transmission electron microscopy. The experimental results indicate that the final blend morphology and the surface functionalization of CNT are the main factors that govern percolation. In presence of either of the CNTs, 60/40 P alpha MSAN/PMMA blends yield a droplet-matrix morphology rather than co-continuous and do not show any percolation. On the other hand, both 85/15 P alpha MSAN/PMMA and 15/85 P alpha MSAN/PMMA blends containing CNTPEs show percolation in the rheological and electrical properties. Interestingly, the conductivity spectroscopy measurements demonstrate that the 15/85 P alpha MSAN/PMMA blends with CNTPEs that show insulating properties at room temperature for the miscible blends reveal highly conducting properties in the phase separated blends (melt state) as a result of phase separation. By quenching this morphology, the conductivity can be retained in the blends even in the solid state. (C) 2011 Elsevier Ltd. All rights reserved.

Impact of Sulphate counter ion in the migration of sodium ion through soils

Laboratory advection-diffusion tests are performed on two regional soils-Brown Earth and Red Earth-in order to assess their capacity to control contaminant migration with synthetic contaminant solution of sodium sulphate with sodium concentration of 1000 mg/L. The test was designed to study the transport/attenuation behaviour of sodium in the presence of sulphate. Effective diffusion coefficient (De) that takes into consideration of attenuation processes is used. Cation exchange capacity is an important factor for the attenuation of cationic species. Monovalent sodium ion cannot usually replace other cations and the retention of sodium ion is very less. This is particularly true when chloride is anion is solution. However, sulphate is likely to play a role in the attenuation of sodium. Cation exchange capacity and type of exchangeable ions of soils are likely to play an important role. The effect of sulphate ions on the effective diffusion coefficient of sodium, in two different types of soils, of different cation exchange capacity has been studied. The effective diffusion coefficients of sodium ion for both the soils were calculated using Ogata Bank’s equation. It was shown that effective diffusion coefficient of sodium in the presence of sulphate is lower for Brown Earth than for Red Earth due to exchange of sodium with calcium ions from the exchangeable complex of clay. The soil with the higher cation exchange retained more sodium. Consequently, the breakthrough times and the number of pore volumes of sodium ion increase with the cation exchange capacity of soil.