Combining Bayes Classification and Point Group Symmetry under Boolean Framework for Enhanced Protein Quaternary Structure Inference

Our ability to infer the protein quaternary structure automatically from atom and lattice information is inadequate, especially for weak complexes, and heteromeric quaternary structures. Several approaches exist, but they have limited performance. Here, we present a new scheme to infer protein quaternary structure from lattice and protein information, with all-around coverage for strong, weak and very weak affinity homomeric and heteromeric complexes. The scheme combines naive Bayes classifier and point group symmetry under Boolean framework to detect quaternary structures in crystal lattice. It consistently produces >= 90% coverage across diverse benchmarking data sets, including a notably superior 95% coverage for recognition heteromeric complexes, compared with 53% on the same data set by current state-of-the-art method. The detailed study of a limited number of prediction-failed cases offers interesting insights into the intriguing nature of protein contacts in lattice. The findings have implications for accurate inference of quaternary states of proteins, especially weak affinity complexes.

Structure of diaquadichlorobis(hydrazinium)iron(II) dichloride

[Fe(N2H5)2(H2O)2Cl2].Cl2, M(r) = 299.65, monoclinic, P2(1)/c, a = 8.027 (1), b = 5.725 (2), c = 11.430 (2) angstrom, beta = 97.08 (1)-degrees, V = 521.3 (2) angstrom 3, Z = 2, D(m) = 1.92, D(x) = 1.910 g cm-3, lambda(Mo K-alpha) = 0.71069 angstrom, mu = 24.5 cm-1, F(000) = 304, T = 295 K, final R = 0.0242 and wR = 0.0292 for 1411 significant [F(o) > 5.0-sigma(F(o))] reflections. The crystal contains discrete Cl- ions and complex [Fe(N2H5)2(H2O)2Cl2]2+ cations. In the complex cation, the Fe atom is bonded to two hydrazinium cations, two Cl atoms and two water molecules. The coordinated atoms are trans to each other. The ions are connected by both N-H...Cl and O-H...Cl type hydrogen bonds.

Purification and characterization of DNA-dependent RNA polymerase II from Candida utilis

DNA-dependent RNA polymerase II from Candida utilis has been purified to near homogeneity. The purified enzyme resolved into three subforms, viz. IIO, IIA and IIB. On SDS-PAGE the enzyme showed ten polypeptides with molecular weights in the range of 205 kDa to 14 kDa. By two dimensional electrophoresis (IEF followed by SDS-PAGE) the presence of basic and acidic polypeptides has been demonstrated. The enzyme showed Km values of 5, 5.6 and 8 mu M for GTP, CTP and ATP, respectively, and the activity was inhibited by low levels of oc-amanitin and antibodies raised against bovine RNA polymerase II. By Western blot analysis the enzyme was found to cross-react with antibodies to bovine RNA polymerase II. RNA polymerase II from G. utilis is a phosphoprotein, the subunits RPB1 and RPB10 were found to be phosphorylated. Analysis of carboxy-terminal domain indicated that it was functionally redundant at least in case of nonspecific transcription, implicating its role in other nuclear processes, such as promoter specific initiation or transcription activation or RNA processing.

Lithium ion transport in Li2SO4-Li2O-B2O3 glasses

Electrical conductivity and dielectric relaxation studies with a wide range of compositions of lithium ion conducting glasses belonging to the ternary glass system Li2SO4-Li2O-B2-O3- have been carried out over the temperature range 150-450 K and between 10 - 10(7) Hz. DC conductivities exhibit two different activation regions. This seems to suggest the presence of a cluster tissue texture in these glasses with weakly ordered clusters of Li2SO4 and lithium berates being held together by a truly amorphous tissue of the same average composition as clusters. AC conductivity behaviour of these glasses has been analysed using both power law and stretched exponential relaxation functions. The variation of the power law exponent s and the stretched exponent beta with temperature seems to be consistent with the presence of a cluster tissue texture in these glasses.

Electron beam surface melting of model 1200 Al alloys

Electron beam surface melting has been used to characterise the phase content formed in a number of model 1200 series Al alloys with increasing solidification velocity in the range 2–50 mm s−1, typical of that experienced during continuous strip casting. Phases were extracted from the Al matrix and analysed by X-ray diffraction. A qualitative solidification microstructure selection map has been produced, showing that, for a given Fe content of 0.55 wt.%: with increasing solidification velocity the metastable aluminides FeAl6 and FeAlm displace equilibrium Fe4Al13 at Si contents 0.15 wt.%, and that α-AlFeSi is an equilibrium phase at a Si content ≥0.50 wt.%.

The influence of Fe3+ ions at tetrahedral sites on the magnetic properties of nanocrystalline ZnFe2O4

A systematic study on the variation of Mössbauer hyperfine parameters with grain size in nanocrystalline zinc ferrite is lacking. In the present study, nanocrystalline ZnFe2O4 ferrites with different grain sizes were prepared by ball-milling technique and characterised by X-ray, EDAX, magnetisation and Mössbauer studies. The grain size decreases with increasing milling time and lattice parameter is found to be slightly higher than the bulk value. Magnetisation at room temperature (RT) and at 77 K could not be saturated with a magnetic field of 7 kOe and the observed magnetisation at these temperatures can be explained on the basis of deviation of cation distribution from normal spinel structure. The Mössbauer spectra were recorded at different temperatures between RT and 16 K. The values of quadrupole splitting at RT are higher for the milled samples indicating the disordering of ZnFe2O4 on milling. The strength of the magnetic hyperfine interactions increases with grain size reduction and this can be explained on the basis of the distribution of Fe3+ ions at both tetrahedral and octahedral sites.

Unsteady mixed convection flow from a rotating vertical cone with a magnetic field

An analysis is developed to study the unsteady mixed convection flow over a vertical cone rotating in an ambient fluid with a time-dependent angular velocity in the presence of a magnetic field. The coupled nonlinear partial differential equations governing the flow have been solved numerically using an implicit finite-difference scheme. The local skin friction coefficients in the tangential and azimuthal directions and the local Nusselt number increase with the time when the angular velocity of the-cone increases, but the reverse trend is observed for decreasing angular velocity. However, these are not mirror reflection of each other. The magnetic field reduces the skin friction coefficient in the tangential direction and also the Nusselt number, but it increases the skin friction coefficient in the azimuthal direction. The skin friction coefficients and the Nusselt number increase with the buoyancy force.

Metallo beta lactamase producing Pseudomonas aeruginosa and Acinetobacter baumannii

This study aims in identifying MBLs particularly Zn requiring Molecular Class B enzymes produced by Pseudomonas aeruginosa and Acinetobacter baumannii. The resistance by these organisms are in a rise against all antibiotics including carbapenems and no prescribed CLSI guidelines is available for detecting them. Clinical isolates antibiotic susceptibility was determined by number of phenotypic tests by addition of 50mM of 10 mu l zinc as cofactor for metallo beta lactamase production along with 0.5M ETDA of 5 mu l (930 mu g per disk) plain disks. Increase in zone size of the meropenem -EDTA disk compared to the meropenem disk without EDTA was recorded positive. For Zn requiring MBLs zone towards both disks of EDTA and Zn along with meropenem is detected by DDST.

Supercapacitor studies on globular polypyrrole microstructures developed by a facile electrochemical route

Micrometre-scale polypyrrole (PPy) structures are synthesised for electrochemical supercapacitor applications by a facile electrochemical route. Globular polypyrrole microstructures of size < 5 μm are grown on stainless steel (SS-304) substrate by electro-polymerisation of pyrrole on oxygen microbubble templates electrochemically generated and stabilised in the presence of surfactant/supporting electrolyte/ dopant b-naphthalene sulfonic acid (b-NSA). Microstructures obtained with scan range of 0??1.6 V (against Ag/AgCl) are uniformly distributed over the surface with high coverage density of 5 x 105 to 8 x 10 cm-2. Fourier transform infrared spectroscopy and X-ray photoelectron spectroscopy revealed that the formed microstructures are of Β-NSA doped PPy. Scanning electron microscopy showed the uniform spread and good coverage of microstructures over the substrate. Supercapacitor properties of PPy films are investigated by cyclic voltammetry, electrochemical impedance spectroscopy and galvanostatic charge/discharge methods with 1.0 M KCl as electrolyte in a three-electrode electrochemical cell. Specific capacitance of 583 Fg-1 is obtained, which is greater than the values (350-400 Fg-1 highest) usually reported for this material. Electrochemical impedance spectroscopy proves the superc

Supercapacitor studies on globular polypyrrole microstructures developed by a facile electrochemical route

Micrometre-scale polypyrrole (PPy) structures are synthesised for electrochemical supercapacitor applications by a facile electrochemical route. Globular polypyrrole microstructures of size <5 mu m are grown on stainless steel (SS-304) substrate by electro-polymerisation of pyrrole on oxygen microbubble templates electrochemically generated and stabilised in the presence of surfactant/supporting electrolyte/dopant beta-naphthalene sulfonic acid (beta-NSA). Microstructures obtained with scan range of 0-1.6 V (against Ag/AgCl) are uniformly distributed over the surface with high coverage density of 5 x 10(5) to 8 x 10 cm(-2). Fourier transform infrared spectroscopy and X-ray photoelectron spectroscopy revealed that the formed microstructures are of beta-NSA doped PPy. Scanning electron microscopy showed the uniform spread and good coverage of microstructures over the substrate. Supercapacitor properties of PPy films are investigated by cyclic voltammetry, electrochemical impedance spectroscopy and galvanostatic charge/discharge methods with 1.0 M KCl as electrolyte in a three-electrode electrochemical cell. Specific capacitance of 583 Fg(-1) is obtained, which is greater than the values (350-400 Fg(-1) highest) usually reported for this material. Electrochemical impedance spectroscopy proves the supercapacitance behaviour and explains the special inductive component of impedance observed in the high-frequency regime because of the globular structures of PPy deposited

Structural characterisation of reaction zone for friction stir welded aluminium-stainless steel joint

In the present investigation, commercially pure Al has been joined with 304 stainless steel (SS) by friction stir welding. The assembly finds widespread application in the field of cryogenics, nuclear, structural industries and domestic appliances. Microstructural characterisation was carried out using scanning and transmission electron microscopes. It has been found that diffusion of Fe, Cr and Ni is substantial within Al; however, diffusion of Al within 304SS is limited. Owing to interdiffusion of chemical species across the bondline, discrete islands of Fe3Al intermetallic form within the reaction zone. The rubbing action of tool over the butting edge of 304SS removed fine particles from 304SS, which were embedded in the stirring zone of Al matrix. Subsequently, austenite underwent phase transformation to ferrite due to large strain within this grain. Fracture path mainly moves through stirring zone of Al alloy under tensile loading; however, in some places, presence of Fe3Al compound has been also found.

Synthesis dependent characteristics of Sr1-xMnxTiO3 (x=0.03, 0.05, 0.07 and 0.09)

Sr1-xMnxTiO3 (where x=0.03, 0.05, 0.07 and 0.09) was synthesized via different routes that include solid-state, oxalate precipitation and freeze drying. In oxalate precipitation technique, compositions corresponding to 3 and 5 mol% doping of Mn were monophasic whereas the higher compositions revealed the presence of the secondary phases such as MnO, Mn3O4 etc., as confirmed by high resolution X-ray diffraction (XRD) studies. The decomposition behavior of the precursors prepared using oxalate precipitation method corresponding to the above mentioned compositions was studied. Nanopowders of compositions pertaining to 5 to 9 mol% of Mn doping were obtained using freeze-drying technique. The average crystallite size of these nanopowders was found to be in the 35 to 65 nm range. The microstructural studies carried out on the sintered ceramics, fabricated using powders synthesized by different routes established the fine grained nature ( < 1 mu m) of the one obtained by freeze drying method. Raman scattering studies were carried out in order to complement the observations made from XRD regarding the phase purity. The dielectric properties of the ceramics obtained by different synthesis routes were studied in the 80-300 K temperature range at 100 kHz and the effect of grain size has been discussed. (C) 2012 Elsevier Inc. All rights reserved.

Growth of Polypyrrole-Horseradish Peroxidase Microstructures for H2O2 Biosensor

Conducting polymer microstructures for enzymatic biosensors are developed by a facile electrochemical route. Horseradish peroxide (HRP)-entrapped polypyrrole (PPy) films with bowl-shaped microstructures are developed on stainless steel (SS 304) substrates by a single-step process. Potentiodynamic scanning/cyclic voltammetry is used for generation of PPy microstructures using electrogenerated oxygen bubbles stabilized by zwitterionic surfactant/buffer N-2-hydroxyethylpiperazine N-2-ethanesulfonic acid as soft templates. Scanning electron microscopic images reveal the bowl-shaped structures surrounded by cauliflower-like fractal PPy films and globular nanostructures. Raman spectroscopy reveals the oxidized nature of the film. Sensing properties of PPy-HRP films for hydrogen peroxide (H2O2) are demonstrated. Electrochemical characterization of the sensor films is done by linear sweep voltammetry (LSV) and amperometry. LSV results indicated the reduction of H2O2 and linearity in response of the sensing film. The amperometric biosensor has a performance comparable to those in the literature with advantages of hard-template free synthesis procedure and a satisfactory sensitivity value of 12.8 mu A/(cm(2) . mM) in the range of 1-10 mM H2O2.

A comparative study of deglaciation in two neighbouring basins (Warwan and Bhut) of Western Himalaya

Glaciers of the Himalaya contribute significantly in the processes linking atmosphere, biosphere and hydrosphere, thus need to be monitored in view of the climatic variations. In this direction, many studies have been carried out during the last two decades and satellite-based multispectral data have been used extensively for this purpose throughout the world. The present study is aimed at mapping of glaciers in two adjacent basins (Warwan and Bhut) of the Western Himalaya with almost similar altitude and latitude and comparing the changes in the two time-frames with respect to three parameters, i.e. area, debris cover and area altitude distribution of glaciers. The two time-frames are topographical maps of 1962 and IRS LISS III images of 2001/02. Deglaciation was observed in both the basins with 19% and 9% loss in the glaciated area in Warwan and Bhut respectively. This difference may be due to: (i) the smaller size of the glaciers of the Warwan Basin (e.g. 164 glaciers having <1 sq. km area in comparison to 101 glaciers in the Bhut Basin), (ii) lower percentage of moraine cover in Warwan (18) than in the Bhut Basin (30) and (iii) higher percentage of glaciated area lying below 5100 m (80) in Warwan than in the Bhut Basin (70).

Phase relationships and magnetic properties of TbxDy1-xFe1.95 alloys

The effect of Tb/Dy ratio on the structural and magnetic properties of (Tb,Dy)Fe-2 class of alloys has been investigated using nine alloys of TbxDy1-xFe1.95 (x = 0-1) covering the entire range. Our results indicate that the three phases viz. (Tb,Dy)Fe-2 (major phase), (Tb,Dy)Fe-3 and(Tb,Dy)-solid solution (minor phases) coexist in all the alloys. The volume fraction of pro-peritectic (Tb,Dy)Fe-3 phase however, has a minimum at x = 0.4 and a maximum at x = 0.6 compositions. The volume fraction of this phase decreases upon heat treatment at 850 degrees C and 1000 degrees C. A Widmanstatten type precipitate of (Tb,Dy)Fe-3 was observed for Dy-rich compositions (0 <= x <= 0.5). The microstructural investigations indicate that the ternary phase equilibria of Tb-Dy-Fe are sensitive to Tb/Dy ratio including the expansion of (Tb,Dy)Fe-2 phase field which is in contrast to the pseudo-binary assumption that is followed in available literature to date. The lattice parameter, Curie temperature and coercivity are found to increase with Tb addition. Split of (440) peak of (Tb,Dy)Fe-2 observed in x >= 0.3 alloys indicate, a spin reorientation transition from 100] to 111] occurs with Tb addition. (C) 2012 Elsevier B. V. All rights reserved.