Structures of new crystal forms of Mycobacterium tuberculosis peptidyl-tRNA hydrolase and functionally important plasticity of the molecule

The X-ray structures of new crystal forms of peptidyl-tRNA hydrolase from M.similar to tuberculosis reported here and the results of previous X-ray studies of the enzyme from different sources provide a picture of the functionally relevant plasticity of the protein molecule. The new X-ray results confirm the connection deduced previously between the closure of the lid at the peptide-binding site and the opening of the gate that separates the peptide-binding and tRNA-binding sites. The plasticity of the molecule indicated by X-ray structures is in general agreement with that deduced from the available solution NMR results. The correlation between the lid and the gate movements is not, however, observed in the NMR structure.

Use of Vertex Index in Structure-Activity Analysis and Design of Molecules

The last few decades have witnessed application of graph theory and topological indices derived from molecular graph in structure-activity analysis. Such applications are based on regression and various multivariate analyses. Most of the topological indices are computed for the whole molecule and used as descriptors for explaining properties/activities of chemical compounds. However, some substructural descriptors in the form of topological distance based vertex indices have been found to be useful in identifying activity related substructures and in predicting pharmacological and toxicological activities of bioactive compounds. Another important aspect of drug discovery e. g. designing novel pharmaceutical candidates could also be done from the distance distribution associated with such vertex indices. In this article, we will review the development and applications of this approach both in activity prediction as well as in designing novel compounds.

Current trends in modeling hostpathogen interactions

The rapid emergence of infectious diseases calls for immediate attention to determine practical solutions for intervention strategies. To this end, it becomes necessary to obtain a holistic view of the complex hostpathogen interactome. Advances in omics and related technology have resulted in massive generation of data for the interacting systems at unprecedented levels of detail. Systems-level studies with the aid of mathematical tools contribute to a deeper understanding of biological systems, where intuitive reasoning alone does not suffice. In this review, we discuss different aspects of hostpathogen interactions (HPIs) and the available data resources and tools used to study them. We discuss in detail models of HPIs at various levels of abstraction, along with their applications and limitations. We also enlist a few case studies, which incorporate different modeling approaches, providing significant insights into disease. (c) 2013 Wiley Periodicals, Inc.

A Novel Monte-Carlo-Sampling-Based Receiver for Large-Scale Uplink Multiuser MIMO Systems

In this paper, we propose low-complexity algorithms based on Monte Carlo sampling for signal detection and channel estimation on the uplink in large-scale multiuser multiple-input-multiple-output (MIMO) systems with tens to hundreds of antennas at the base station (BS) and a similar number of uplink users. A BS receiver that employs a novel mixed sampling technique (which makes a probabilistic choice between Gibbs sampling and random uniform sampling in each coordinate update) for detection and a Gibbs-sampling-based method for channel estimation is proposed. The algorithm proposed for detection alleviates the stalling problem encountered at high signal-to-noise ratios (SNRs) in conventional Gibbs-sampling-based detection and achieves near-optimal performance in large systems with M-ary quadrature amplitude modulation (M-QAM). A novel ingredient in the detection algorithm that is responsible for achieving near-optimal performance at low complexity is the joint use of a mixed Gibbs sampling (MGS) strategy coupled with a multiple restart (MR) strategy with an efficient restart criterion. Near-optimal detection performance is demonstrated for a large number of BS antennas and users (e. g., 64 and 128 BS antennas and users). The proposed Gibbs-sampling-based channel estimation algorithm refines an initial estimate of the channel obtained during the pilot phase through iterations with the proposed MGS-based detection during the data phase. In time-division duplex systems where channel reciprocity holds, these channel estimates can be used for multiuser MIMO precoding on the downlink. The proposed receiver is shown to achieve good performance and scale well for large dimensions.

Entropy of quantum states: Ambiguities

The von Neumann entropy of a generic quantum state is not unique unless the state can be uniquely decomposed as a sum of extremal or pure states. As pointed out to us by Sorkin, this happens if the GNS representation (of the algebra of observables in some quantum state) is reducible, and some representations in the decomposition occur with non-trivial degeneracy. This non-unique entropy can occur at zero temperature. We will argue elsewhere in detail that the degeneracies in the GNS representation can be interpreted as an emergent broken gauge symmetry, and play an important role in the analysis of emergent entropy due to non-Abelian anomalies. Finally, we establish the analogue of an H-theorem for this entropy by showing that its evolution is Markovian, determined by a stochastic matrix.

Spontaneous Lorentz violation in gauge theories

Frohlich, Morchio and Strocchi long ago proved that the Lorentz invariance is spontaneously broken in QED because of infrared effects. We develop a simple model where the consequences of this breakdown can be explicitly and easily calculated. For this purpose, the superselected U(1) charge group of QED is extended to a superselected ``Sky'' group containing direction-dependent gauge transformations at infinity. It is the analog of the Spi group of gravity. As Lorentz transformations do not commute with Sky, they are spontaneously broken. These Abelian considerations and model are extended to non-Abelian gauge symmetries. Basic issues regarding the observability of twisted non-Abelian gauge symmetries and of the asymptotic ADM symmetries of quantum gravity are raised.

A novel MCMC algorithm for near-optimal detection in large-scale uplink mulituser MIMO systems

In this paper, we propose a low-complexity algorithm based on Markov chain Monte Carlo (MCMC) technique for signal detection on the uplink in large scale multiuser multiple input multiple output (MIMO) systems with tens to hundreds of antennas at the base station (BS) and similar number of uplink users. The algorithm employs a randomized sampling method (which makes a probabilistic choice between Gibbs sampling and random sampling in each iteration) for detection. The proposed algorithm alleviates the stalling problem encountered at high SNRs in conventional MCMC algorithm and achieves near-optimal performance in large systems with M-QAM. A novel ingredient in the algorithm that is responsible for achieving near-optimal performance at low complexities is the joint use of a randomized MCMC (R-MCMC) strategy coupled with a multiple restart strategy with an efficient restart criterion. Near-optimal detection performance is demonstrated for large number of BS antennas and users (e.g., 64, 128, 256 BS antennas/users).

Mechanical properties of glasses and TiO2 nanocrystal glass composites in BaO-TiO2-B2O3 system

Glasses and glass-nanocrystal (anatase TiO2) composites in BaO-TiO2-B2O3 system were fabricated by conventional melt-quenching technique and controlled heat treatment respectively. Poisson's ratio and Young's moduli were predicted through Makishima-Mackenzie theoretical equation for the as-quenched glasses by taking the four and three coordinated borons into account. Mechanical properties of the glasses and glass-nanocrystal composites were investigated in detail through nanoindentation and microindentation studies. Predicted Young's moduli of glasses were found to be in reasonable agreement with nanoindentation Measurements. Hardness and Young's modulus were enhanced with increasing volume fraction of nanocrystallites of TiO2 in glass matrix whereas fracture toughness was found susceptible to the surface features. The results were correlated to the structural units and nanocrystals present in the glasses. (C) 2013 Elsevier B.V. All rights reserved.

Corticosterone targets distinct steps of synaptic transmission via concentration specific activation of mineralocorticoid and glucocorticoid receptors

Hippocampal neurons are affected by chronic stress and have a high density of cytoplasmic mineralocorticoid and glucocorticoid receptors (MR and GR). Detailed studies on the genomic effects of the stress hormone corticosterone at physiologically relevant concentrations on different steps in synaptic transmission are limited. In this study, we tried to delineate how activation of MR and GR by different concentrations of corticosterone affects synaptic transmission at various levels. The effect of 3-h corticosterone (25, 50, and 100nM) treatment on depolarization-mediated calcium influx, vesicular release and properties of miniature excitatory post-synaptic currents (mEPSCs) were studied in cultured hippocampal neurons. Activation of MR with 25nM corticosterone treatment resulted in enhanced depolarization-mediated calcium influx via a transcription-dependent process and increased frequency of mEPSCs with larger amplitude. On the other hand, activation of GR upon 100nM corticosterone treatment resulted in increase in the rate of vesicular release via the genomic actions of GR. Furthermore, GR activation led to significant increase in the frequency of mEPSCs with larger amplitude and faster decay. Our studies indicate that differential activation of the dual receptor system of MR and GR by corticosterone targets the steps in synaptic transmission differently.

Synthesis, characterization and spectroscopic investigation of Cr3+ doped wollastonite nanophosphor

This work explores the preparation of nanocrystalline Cr3+ (1-5 mol%) doped CaSiO3 phosphors by solution combustion process and study of its photoluminescence (PL) behavior. The nanopowders are well characterized by powder X-ray diffraction (PXRD), scanning electron microscopy (SEM), transmission electron microscopy (TEM) and Fourier transform infra-red (FTIR) spectroscopy. PXRD results confirm monoclinic phase upon calcination at 950 degrees C for 3 h. SEM micrographs indicates that the powder is highly porous and agglomerated. The TEM images show the powder to consist of spherical shaped particles of size similar to 30-60 nm. Upon 323 nm excitation, the emission profile of CaSiO3:Cr3+ exhibits a narrow red emission peak at 641 nm due to E-2 -> (4)A(2) transition and broad band at 722 nm due to T-4(2g) -> (4)A(2g). It is observed that PL intensity increases with increase in Cr3+ concentration and highest PL intensity is observed for 3 mol% doped sample. The PL intensity decreases with further increase in Cr3+ doping. This decrease in PL intensity beyond 3 mol% is ascribed to concentration quenching. Racah parameters are calculated to describe the effects of electron-electron repulsion within the crystal lattice. The parameters show 21% reduction in the Racah parameter of free ion and the complex, indicating the moderate nephelauxetic effect in the lattice. (C) 2014 Elsevier B.V. All rights reserved.

Gd1.96-xYxEu0.04O3 (x=0.0, 0.49, 0.98, 1.47, 1.96 mol%) nanophosphors: Propellant combustion synthesis, structural and luminescence studies

Gd1.96-xYxEu0.04O3 (x = 0.0, 0.49, 0.98, 1.47, 1.96 mol%) nanophosphors were synthesized by propellant combustion method at low temperature (400 degrees C). The powder X-ray diffraction patterns of as formed Gd1.96Eu0.04O3 showed monoclinic phase, however with the addition of yttria it transforms from monoclinic to pure cubic phase. The porous nature increases with increase of yttria content. The particle size was estimated from Scherrer's and W-H plots which was found to be in the range 30-40 nm. These results were in well agreement with transmission electron microscopy studies. The optical band gap energies estimated were found to be in the range 5.32-5.49 eV. PL emission was recorded under 305 nm excitation show an intense emission peak at 611 nm along with other emission peaks at 582, 641 nm. These emission peaks were attributed to the transition of D-5(0) —> F-7(J) (J = 0, 1, 2, 3) of Eu3+ ions. It was observed that PL intensity increases with increase of Y content up to x = 0.98 and thereafter intensity decreases. CIE color co-ordinates indicates that at x = 1.47 an intense red bright color can be achieved, which could find a promising application in flat panel displays. The cubic and monoclinic phases show different thermoluminescence glow peak values measured under identical conditions. The response of the cubic phase to the applied dose showed good linearity, negligible fading, and simple glow curve structure than monoclinic phase indicating that suitability of this phosphor in dosimetric applications. (C) 2014 Elsevier B.V. All rights reserved.

Synthesis and luminescence properties of Sm3+ doped CaTiO3 nanophosphor for application in white LED under NUV excitation

CaTiO3:Sm3+ (1-11 mol%) nanophosphors were successfully synthesized by a low temperature solution combustion method LCS]. The structural and morphological properties of the phosphors were studied by using Powder X-ray diffractometer (PXRD), Fourier transform infrared (FTIR), X-ray photo electron spectroscopy (XPS), scanning electron microscope (SEM) and transmission electron microscopy (TEM). TEM studies indicate that the size of the phosphor is similar to 20-35 nm. Photoluminescence (PL) properties of Sm3+ (1-11 mol%) doped CaTiO3 for NUV excitation (407 nm) was studied in order to investigate the possibility of its use in White light emitting diode (WLED) applications. The emission spectra consists of intra 4f transitions of Sm3+, such as (4)G(5/2) -> H-6(5/2) (561 nm), (4)G(5/2) -> H-6(7/2) (601-611 nm), (4)G(5/2) -> H-6(9/2) (648 nm) and (4)G(5/2) -> H-6(11/2) (703 nm) respectively. Further, the emission at 601-611 nm show strong orange-red emission and can be applied to the orange-red emission of phosphor for the application for near ultra violet (NUV) excitation. Thermoluminescence (TL) of the samples irradiated with gamma source in the dose range 100-500 Gy was recorded at a heating rate of 5 degrees C s(-1). Two well resolved glow peaks at 164 degrees C and 214 degrees C along with shouldered peak at 186 degrees C were recorded. TL intensity increases up to 300 Gy and thereafter, it decreases with further increase of dose. The kinetic parameters namely activation energy (E), frequency factor (s) and order of kinetics were estimated and results were discussed in detail. (C) 2014 Elsevier B.V. All rights reserved.

Voltammetric detection of arsenic on a bismuth modified exfoliated graphite electrode

We present the application of a bismuth modified exfoliated graphite electrode in the detection of arsenic in water. Bismuth film was electrodeposited onto an exfoliated graphite (EG) electrode at a potential of -600 mV. The modification of EG resulted in an increase in the electroactive surface area of the electrode and consequently peak current enhancement in Ru(NH3)(6)(2+/13+) redox probe. Square wave anodic stripping voltammetry was performed with the modified electrode (EG-Bi) in As (III) solutions at the optimum conditions of pH 6, deposition potential of -600 mV and pre-concentration time of 180s. The EG-Bi was able to detect As (III) to the limit of 5 mu g L-1 and was not susceptible to many interfering cations except Cu (II). The EG-Bi is low cost and easy to prepare. (C) 2013 Elsevier Ltd. All rights reserved.

PROPENSITIES OF AMINO ACID RESIDUES IN PROTEINS FOR DIFFERENT REGIONS OF THE RAMACHANDRAN MAP

Using a dataset of 1164 crystal structures of largely non-homologous proteins defined at a resolution of 1.5 angstrom or better, we have investigated the (phi,psi) preferences of 20 residue types by considering the residues which occur in loops. Propensities of residue types to occur in the loops with (phi,psi) values in the aa region of the Ramachandran map has a poor correlation coefficient of 0.48 to the Chou-Fasman propensities of the residue types to occur in the a-helical segments. However the correlation coefficient between propensities of residues in loops to adopt beta conformations and those in beta-sheet is much higher (0.95). These observations suggest that a-helix formation is well influenced by the local amino acid sequence while intrinsic preference of residue types for beta-sheet plays a major role in the formation of beta-sheet. The main chain polar groups of residues in loops, that can affect the (phi,psi) values, can be involved in intra-molecular hydrogen bonding. Therefore we investigated further by considering subset of residues in loops with low (0 to 2) number of intra-molecular hydrogen bonds per residue involving main chain polar atoms. For this subset, the correlation coefficients between propensities for alpha-helix and alpha(R) region and between beta-sheet and beta-region are 0.26 and 0.64 respectively. This reiterates higher intrinsic tendency of beta-region favouring residues to adopt beta-sheet than alpha(R) region favouring residues to adopt alpha-helical structure.

Fabrication and characterization of gold coated hollow silicon microneedle array for drug delivery

In this paper, we present the fabrication and characterization of Ti and Au coated hollow silicon microneedles for transdermal drug delivery applications. The hollow silicon microneedles are fabricated using isotropic etching followed by anisotropic etching to obtain a tapered tip. Silicon microneedle of 300 mu m in height, with 130 mu m outer diameter and 110 mu m inner diameter at the tip followed by 80 mu m inner diameter and 160 mu m outer diameter at the base have been fabricated. In order to improve the biocompatibility of microneedles, the fabricated microneedles were coated with Ti (500 nm) by sputtering technique followed by gold coating using electroplating. A breaking force of 225 N was obtained for the fabricated microneedles, which is 10 times higher than the skin resistive force. Hence, fabricated microneedles can easily be inserted inside the skin without breakage. The fluid flow through the microneedles was studied for different inlet pressures. A minimum inlet pressure of 0.66 kPa was required to achieve a flow rate of 50 mu l in 2 s with de-ionized water as a fluid medium. (C) 2014 Elsevier B.V. All rights reserved.