Use of a structural alphabet to find compatible folds for amino acid sequences

The structural annotation of proteins with no detectable homologs of known 3D structure identified using sequence-search methods is a major challenge today. We propose an original method that computes the conditional probabilities for the amino-acid sequence of a protein to fit to known protein 3D structures using a structural alphabet, known as Protein Blocks (PBs). PBs constitute a library of 16 local structural prototypes that approximate every part of protein backbone structures. It is used to encode 3D protein structures into 1D PB sequences and to capture sequence to structure relationships. Our method relies on amino acid occurrence matrices, one for each PB, to score global and local threading of query amino acid sequences to protein folds encoded into PB sequences. It does not use any information from residue contacts or sequence-search methods or explicit incorporation of hydrophobic effect. The performance of the method was assessed with independent test datasets derived from SCOP 1.75A. With a Z-score cutoff that achieved 95% specificity (i.e., less than 5% false positives), global and local threading showed sensitivity of 64.1% and 34.2%, respectively. We further tested its performance on 57 difficult CASP10 targets that had no known homologs in PDB: 38 compatible templates were identified by our approach and 66% of these hits yielded correctly predicted structures. This method scales-up well and offers promising perspectives for structural annotations at genomic level. It has been implemented in the form of a web-server that is freely available at http://www.bo-protscience.fr/forsa.

Improved design methodology for the development of electrically actuated MEMS structures

A comprehensive design flow is proposed for the design of Micro Electro Mechanical Systems that are fabricated using SOIMUMPs process. Many of the designers typically do not model the temperature dependency of electrical conductivity, thermal conductivity and convection coefficient, as it is very cumbersome to create/incorporate the same in the existing FEM simulators. Capturing these dependencies is very critical particularly for structures that are electrically actuated. Lookup tables that capture the temperature dependency of electrical conductivity, thermal conductivity and convection coefficient are created. These look up tables are taken as inputs for a commercially available FEM simulator to model the semiconductor behavior. It is demonstrated that when temperature dependency for all the above mentioned parameters is not captured, then the error in estimation of the maximum temperature (for a given structure) could be as high as 30%. Error in the estimated resistance value under the same conditions is as high as 40%. When temperature dependency of the above mentioned parameters is considered then error w.r.t the measured values is less than 5%. It is evident that error in temperature estimates leads to erroneous results from mechanical simulations as well.

Studies on Carbon Mediated Paste Screen Printed Sensors for Blood Glucose Sensing Application

Ready-to-use screen printed glucose sensors are fabricated using Prussian Blue (PB) and Cobalt Phthalocyanine (CoPC) mediated carbon inks as working electrodes. The reference and counter electrodes are screen printed using silver/silver chloride and graphitic carbon paste respectively. The screen printed reference electrodes (internal reference electrode (IRE)) are found to be stable for more than 60 minutes when examined with saturated calomel electrode. Optimal operating voltage for PB and CoPC screen printed sensors are determined by hydrodynamic voltammetric technique. Glucose oxidase is immobilized on the working electrodes by cross-linking method. PB mediated glucose sensor exhibits a sensitivity of 5.60 mA cm(-2)/mM for the range, 10 to 1000 mu M. Sensitivity of CoPC mediated glucose sensor is found to be 5.224 mu A cm(-2)/mM and amperometeric response is linear for the range, 100 to 1500 mu M. Interference studies on the fabricated glucose sensors are conducted with species like uric acid and ascorbic acid. PB mediated sensors showed a completely interference-free behavior. The sensing characteristics of PB mediated glucose sensors are also studied in diluted human serum samples and the results are compared with the values obtained through standard clinical method. The co-efficient of variation is found to be less than 5%. (C) 2015 The Electrochemical Society. All rights reserved.

Thermodynamics of ligand (substrate end product) binding to endoxylanase from Chainia sp. (NCL-82-5-1): isothermal calorimetry and fluorescence titration studies

The binding of xylo-oligosaccharides to Chainia endoxylanase resulted in a decrease in fluorescence intensity of the enzyme with the formation of 1:1 complex. Equilibrium and thermodynamic parameters of ligand binding were determined by fluorescence titrations and titration calorimetry. The affinity of xylanase for the oligosaccharides increases in the order X-2 < X-3 < X-4 less than or equal to X-5. Contributions from the enthalpy towards the free energy change decreased with increasing chain length from X-2 to X-4, whereas an increase in entropy was observed, the change in enthalpy and entropy of binding being compensatory. The entropically driven binding process suggested that hydrophobic interactions as well as hydrogen bonds play a predominant role in ligand binding.

Magnetic properties of rare earth nickelates of the Ln(2)BaNiO(5) family

Rare-earth nickelates Ln(2)BaNi(1-x)Cu(2)O(5), Ln = Nd and Dy, and Dy2-xYxBaNiO5 have been synthesized in order to investigate the effect of substitution of Ni by Cu and Dy by nonmagnetic Y on the magnetic properties of the nickelates. In Ln(2)BaNi(1-x)Cu(x)O(5), the nickelate structure (x=0.0) changes to the cuprate structure (x=1.0) at a specific composition (x=0.3). The Neel temperature of Nd2BaNi1-xCuxO5 decreases continuously with increase in x upto x=0.3 (T-N = 18K); when x > 0.3, the materials are paramagnetic down to 20K. The mu(eff) in Nd2BaNi1-xCxO5 essentially corresponds to the contribution of the Nd ions. In Dy2-xYxBaNiO5, the Neel temperature decreases from 40K when x=0.0 to 24K when x=1.5. The compositions with 1.5 less than or equal to x less than or equal to 2 (including the x=1.95 composition) are paramagnetic down to 20K, unlike Y2BaNiO5 (x=2.0) which exhibits a T-N of 370K. Even the smallest concentration of paramagnetic Dy seems to destroy the antiferromagnetic Ni-O-Ni chains in Y2BaNiO5.

SrB4O7:Bi2VO5.5 - A novel nanocomposite

Glass composites of strontium tetraborate, SrB4O7 (SBO) with bismuth vanadate, Bi2VO5.5 (BiV) of the composition (1-x) SBO-x BN (0 less than or equal to x less than or equal to 0.75), have been synthesized. X-ray powder diffraction and electron microscopy indicate as-quenched composites to be amorphous and the annealed samples showed the presence of nanometer sized particles of BN dispersed in the glassy matrix of SBO. The dielectric constant of these composites increases with increase in the volume fraction of BiV, at 300 K. The measured dielectric constant of the composite very nearly obeys the Maxwell's relationship. Optical transmission studies confirm a steady shirt in the optical absorption edge towards longer wavelengths with increase in x

Magnetocaloric effect in La1-xSrxCoO3 (0.05 <= x <= 0.40)

We report studies of magnetocaloric effect in lanthanum cobaltate doped with different Sr-concentrations, La1-xSrxCoO3 (0.05 less than or equal to x less than or equal to 0.4). The study has revealed that La0.6Sr0.4CoO3, which exhibits a moderately large value of maximum entropy change of about 1.45 J/kg/K in 1.5 T DC-fieid around its Curie temperature (of 235 K), can be used as an active magnetic refrigerant (AMR) material at similar to 2.35 K. (C) 1999 Elsevier Science B.V. Al rights reserved.

Universality in the fast orientational relaxation near isotropic-nematic transition

Detailed molecular dynamics simulations of Lennard-Jones ellipsoids have been carried out to investigate the emergence of criticality in the single-particle orientational relaxation near the isotropic-nematic (IN) phase transition. The simulations show a sudden appearance of a power-law behavior in the decay of the second-rank orientational relaxation as the IN transition is approached. The simulated value of the power-law exponent is 0.56, which is larger than the mean-field value (0.5) but less than the observed value (0.63) and may be due to the finite size of the simulated system. The decay of the first-rank orientational time correlation function, on the other hand, is nearly exponential but its decay becomes very slow near the isotropic-nematic transition, The zero-frequency rotational friction, calculated from the simulated angular Velocity correlation function, shows a marked increase near the IN transition.

Growth and study of antiferroelectric lead zirconate thin films by pulsed laser ablation

Antiferroelectric lead zirconate (PZ) thin films were deposited by pulsed laser ablation on platinum-coated silicon substrates. Films showed a polycrystalline pervoskite structure upon annealing at 650 degrees C for 5-10 min. Dielectric properties were investigated as a function of temperature and frequency. The dielectric constant of PZ films was 220 at 100 kHz with a dissipation factor of 0.03. The electric field induced transformation from the antiferroelectric phase to the ferroelectric phase was observed through the polarization change, using a Sawyer-Tower circuit. The maximum polarization value obtained was 40 mu C/cm(2). The average fields to excite the ferroelectric state, and to reverse to the antiferroelectric state were 71 and 140 kV/cm, respectively. The field induced switching was also observed through double maxima in capacitance-voltage characteristics. Leakage current was studied in terms of current versus time and current versus voltage measurements. A leakage current density of 5x10(-7) A/cm(2) at 3 V, for a film of 0.7 mu m thickness, was noted at room temperature. The trap mechanism was investigated in detail in lead zirconate thin films based upon a space charge limited conduction mechanism. The films showed a backward switching time of less than 90 ns at room temperature.

Distribution of black nodes at various levels in a linear quadtree

The distribution of black leaf nodes at each level of a linear quadtree is of significant interest in the context of estimation of time and space complexities of linear quadtree based algorithms. The maximum number of black nodes of a given level that can be fitted in a square grid of size 2n × 2n can readily be estimated from the ratio of areas. We show that the actual value of the maximum number of nodes of a level is much less than the maximum obtained from the ratio of the areas. This is due to the fact that the number of nodes possible at a level k, 0≤k≤n − 1, should consider the sum of areas occupied by the actual number of nodes present at levels k + 1, k + 2, …, n − 1.

Short-lived triplets of aliphatic thioketenes

The photophysical behavior of the triplets of three aliphatic thioketenes, namely di-tert-butylthioketene (1), 2,6-di-tert-butylcyclohexylthioketene (2) and 2,2,6,6-tetramethylcyclohexylthioketene, has been studied in fluid solutions at room temperature by nanosecond laser flash photolysis. Upon 532 nm laser excitation into the S1 state, the thioketenes in concentrated benzene solutions produce very short-lived transient absorptions (τ < 5 ns; λmax ≈ 450 nm) attributable to their triplets. The photogeneration of the latter under S1 excitation has also been established by energy transfer to all-trans-1,6-diphenyl-1,3,5-hexatriene. The factors which render the triplet lifetimes short are shown to be intrinsic in origin (rather than self-quenching). Unlike thiocarbonyl compounds in general, the thioketenes posses low intersystem crossing yields (less than 0.1 in benzene). From the kinetics of the quenching of a series of sensitizer triplets by 1 and 2, the thioketene triplet energies are estimated to be 43 – 44 kcal mol−1.

Laser flash photolysis study of triplets of cyclobutanethiones

Five cyclobutanethiones with different chromophores at the 3-position were examined for triplet state behaviour in benzene using laser excitation into their low lying nπ*1 band systems. A weak transient absorption attributable to the triplet state is observed in all these cases. Results concerning triplet lifetimes, intersystem crossing yields (S1 → T1), self-quenching kinetics and kinetics of energy transfer to all-trans-1,6-diphenyl-1,3,5-hexatriene and oxygen and quenching by di-t-butyl nitroxide (DTBN) are presented. Intersystem crossing yields estimated with reference to p,p′-dimethoxythiobenzophenone are roughly unity in all five cases. Self-quenching rates are found to be less than diffusion limited and this is attributed to steric crowding at the α positions (dimethyl group). The rates of oxygen and DTBN quenching compare well with those reported for several other thiones in the literature. No transients other than the triplet were detected in the above cyclobutane-thiones.

Generation of hydrogen peroxide on oxidation of NADH by hepatic plasma membranes

The oxidation of NADH by mouse liver plasma membranes was shown to be accompanied by the formation of H2O2. The rate of H2O2 formation was less than one-tenth the rate of oxygen uptake and much slower than the rate of reduction of artificial electron acceptors. The optimum pH for this reaction was 7.0 and theK m value for NADH was found to be 3×10–6 M. The H2O2-generating system of plasma membranes was inhibited by quinacrine and azide, thus distinguishing it from similar activities in endoplasmic reticulum and mitochondria. Both NADH and NADPH served as substrates for plasma membrane H2O2 generation. Superoxide dismutase and adriamycin inhibited the reaction. Vanadate, known to stimulate the oxidation of NADH by plasma membranes, did not increase the formation of H2O2. In view of the growing evidence that H2O2 can be involved in metabolic control, the formation of H2O2 by a plasma membrane NAD(P)H oxidase system may be pertinent to control sites at the plasma membrane.

A comprehensive study of interference and clearance fit pins in large plates

Pin joints in structures are designed for interference, push or clearance fits. That is, the diameter of the pin is made greater than, equal to or less than the hole diameter. Consider an interference fit pin in a plate subjected to a continuously increasing in-plane load.

Significance of Branching Angles in Streamer Discharges

The phenomenon of branching at specific angles in streamer breakdown studies is found to be more universal than was ever thought. The angles measured in the breakdown of gases show that the coefficient of field distortion, K, lies in the range from 1 to less than 0.1. The values of K, so obtained agree well with those envisaged in the criterion of the streamer mechanism. It is hoped that branching angles observed in various types of breakdown may, possibly, be explained similarly.