Crystallization and preliminary X-ray diffraction studies of sortase A from Streptococcus pneumoniae

Sortases are cell-membrane-anchored cysteine transpeptidases that are essential for the assembly and anchoring of cell-surface adhesins in Gram-positive bacteria. Thus, they play critical roles in virulence, infection and colonization by pathogens. Sortases have been classified into four types based on their primary sequence and the target-protein motifs that they recognize. All Gram-positive bacteria express a class A housekeeping sortase (SrtA). Sortase A from Streptococcus pneumoniae (NP_358691) has been crystallized in two crystal forms. Diamond-shaped crystals of Delta N(59)SrtA diffracted to 4.0 angstrom resolution and belonged to a tetragonal system with unit-cell parameters a = b = 122.8, c = 86.5 angstrom, alpha = beta = gamma = 90 degrees, while rod-shaped crystals of Delta N(81)SrtA diffracted to 2.91 angstrom resolution and belonged to the monoclinic space group P2(1) with unit-cell parameters a = 66.8, b = 103.47, c = 74.79 angstrom, alpha = gamma = 90, beta = 115.65 degrees. The Matthews coefficient (V(M) = 2.77 angstrom(3) Da(-1)) with similar to 56% solvent content suggested the presence of four molecules in the asymmetric unit for Delta N(81)SrtA. Also, a multi-copy search using a monomer as a probe in the molecular-replacement method resulted in the successful location of four sortase molecules in the asymmetric unit, with statistics R = 41.61, R(free) = 46.44, correlation coefficient (CC) = 64.31, CC(free) = 57.67.

Influence of Tempered Microstructures on the Transformation Behaviour of Cold Deformed and Intercritically Annealed Medium Carbon Low Alloy Steel

This research is focused on understanding the role of microstructural variables and processing parameters in obtaining optimised dual phase structures in medium carbon low alloy steels. Tempered Martensite structures produced at 300, 500, and 650 degrees C, were cold rolled to varied degrees ranging from 20 to 80% deformation. Intercritical annealing was then performed at 740, 760, and 780 degrees C for various time duration ranging from 60 seconds to 60 minutes before quenching in water. The transformation behaviour was studied with the aid of optical microscopy and hardness curves. From the results, it is observed that microstructural condition, deformation, and intercritical temperatures influenced the chronological order of the competing stress relaxation and decomposition phase reactions which interfered with the rate of the expected alpha -> gamma transformation. The three unique transformation trends observed are systematically analyzed. It was also observed that the 300 and 500 degrees C tempered initial microstructures were unsuitable for the production of dual structures with optimized strength characteristics.

Spatio-temporal landscape modelling for natural hazard vulnerability analysis in select watersheds of Central Western Ghats

Natural hazards such as landslides are triggered by numerous factors such as ground movements, rock falls, slope failure, debris flows, slope instability, etc. Changes in slope stability happen due to human intervention, anthropogenic activities, change in soil structure, loss or absence of vegetation (changes in land cover), etc. Loss of vegetation happens when the forest is fragmented due to anthropogenic activities. Hence land cover mapping with forest fragmentation can provide vital information for visualising the regions that require immediate attention from slope stability aspects. The main objective of this paper is to understand the rate of change in forest landscape from 1973 to 2004 through multi-sensor remote sensing data analysis. The forest fragmentation index presented here is based on temporal land use information and forest fragmentation model, in which the forest pixels are classified as patch, transitional, edge, perforated, and interior, that give a measure of forest continuity. The analysis carried out for five prominent watersheds of Uttara Kannada district– Aganashini, Bedthi, Kali, Sharavathi and Venkatpura revealed that interior forest is continuously decreasing while patch, transitional, edge and perforated forest show increasing trend. The effect of forest fragmentation on landslide occurrence was visualised by overlaying the landslide occurrence points on classified image and forest fragmentation map. The increasing patch and transitional forest on hill slopes are the areas prone to landslides, evident from the field verification, indicating that deforestation is a major triggering factor for landslides. This emphasises the need for immediate conservation measures for sustainable management of the landscape. Quantifying and describing land use - land cover change and fragmentation is crucial for assessing the effect of land management policies and environmental protection decisions.

An operator-splitting finite element method for the efficient parallel solution of multidimensional population balance systems

A finite element method for solving multidimensional population balance systems is proposed where the balance of fluid velocity, temperature and solute partial density is considered as a two-dimensional system and the balance of particle size distribution as a three-dimensional one. The method is based on a dimensional splitting into physical space and internal property variables. In addition, the operator splitting allows to decouple the equations for temperature, solute partial density and particle size distribution. Further, a nodal point based parallel finite element algorithm for multi-dimensional population balance systems is presented. The method is applied to study a crystallization process assuming, for simplicity, a size independent growth rate and neglecting agglomeration and breakage of particles. Simulations for different wall temperatures are performed to show the effect of cooling on the crystal growth. Although the method is described in detail only for the case of d=2 space and s=1 internal property variables it has the potential to be extendable to d+s variables, d=2, 3 and s >= 1. (C) 2011 Elsevier Ltd. All rights reserved.

Immunotherapeutic efficacy of Mycobacterium indicus pranii in eliciting anti-tumor T cell responses: Critical roles of IFN gamma

Mycobacterium indicus pranii (MIP) is approved for use as an adjuvant (Immuvac/Cadi-05) in the treatment of leprosy. In addition, its efficacy is being investigated in clinical trials on patients with tuberculosis and different tumors. To evaluate and delineate the mechanisms by which autoclaved MIP enhances anti-tumor responses, the growth of solid tumors consisting of Sp2/0 (myeloma) and EL4 (thymoma) cells was studied in BALB/c and C57BL/6 mice, respectively. Treatment of mice with a single intra-dermal (i.d.) injection of MIP 3 days after Sp2/0 implantation greatly suppresses tumor growth. MIP treatment of tumor bearing mice lowers Interleukin (IL)6 but increases IL12p70 and IFN? amounts in sera. Also, increase in CD8+ T cell mediated lysis of specific tumor targets and production of high amounts of IL2 and IFN? by CD4+ T cells upon stimulation with specific tumor antigens in MIP treated mice is observed. Furthermore, MIP is also effective in reducing the growth of EL4 tumors; however, this efficacy is reduced in Ifn?-/- mice. In fact, several MIP mediated anti-tumor responses are greatly abrogated in Ifn?-/- mice: increase in serum Interleukin (IL)12p70 amounts, induction of IL2 and lysis of EL4 targets by splenocytes upon stimulation with specific tumor antigens. Interestingly, tumor-induced increase in serum IL12p70 and IFN? and reduction in growth of Sp2/0 and EL4 tumors by MIP are not observed in nonobese diabetic severe combined immunodeficiency mice. Overall, our study clearly demonstrates the importance of a functional immune network, in particular endogenous CD4+ and CD8+ T cells and IFN?, in mediating the anti-tumor responses by MIP.

Time Series Classification for Online Tamil Handwritten Character Recognition – A Kernel Based Approach

In this paper, we consider the problem of time series classification. Using piecewise linear interpolation various novel kernels are obtained which can be used with Support vector machines for designing classifiers capable of deciding the class of a given time series. The approach is general and is applicable in many scenarios. We apply the method to the task of Online Tamil handwritten character recognition with promising results.

Growth of InSb(1-x)Bix crystals by Rotatary Bridgman method and their characterization

The Rotatary Bridgman method was used to grow ternary InSb(1-x)SBix, crystals. In this method the ampoule was subjected to reversible rotation at a rate of 60rpm. High quality crystals of 8mm diameter and 25mm length were grown with 6.5 atomic percentage of Bi. The grown crystals were characterized employing various techniques such as energy dispersive spectroscopy, x-ray diffraction, differential scanning calorimetery, infrared spectroscopy and Hall measurement.

Appraisal of Bishop's method of slope stability analysis

The stability of slopes is a major problem in geotechnical engineering. Of the methods available for the analysis of soil slopes such as limit equilibrium methods, limit analysis and numerical methods such as FEM and FDM, limit equilibrium methods are popular and generally used, owing to their simplicity in formulation and in evaluating the overall factor of safety of slope. However limit equilibrium methods possess certain disadvantages. They do not consider whether the slope is an embankment or natural slope or an excavation and ignore the effect of incremental construction, initial stress, stress strain behavior etc. In the work reported in this paper, a comparative study of actual state of stress and actual factor of safety and Bishop's factor of safety is performed. The actual factor of safety is obtained by consideration of contours of mobilised shear strains. Using Bishop's method of slices, the critical slip surfaces of a number of soil slopes with different geometries are determined and both the factors of safety are obtained. The actual normal stresses and shear stresses are determined from finite difference formulation using FLAG (Fast Lagrangian Analysis of Continuaa) with Mohr-Coulomb model. The comparative study is performed in terms of parameter lambda(c phi) (= gamma H tan phi/c). I is shown that actual factor of safety is higher than Bishop's factor of safety depending on slope angle and lambda(c phi).

Thermoluminescence response in gamma and UV irradiated Dy2O3 nanophosphor

Low temperature solution combustion method was employed to synthesize Dy2O3 nanophosphors using two different fuels (sugar and oxalyl dihydrazine (ODH)). Powder X-ray diffraction confirm pure cubic phase and the estimated particle size from Scherrer's method in sugar and ODH fuel was found to be 26 and 78 nm, respectively, and are in close agreement with those obtained using TEM and W-H plot analysis. SEM micrographs reveal porous, irregular shaped particles with large agglomeration in both the fuels. An optical band gap of 5.24 eV and 5.46 eV was observed for Dy2O3 for sugar and ODH fuels, respectively. The blueshift observed in sugar fuel is attributed to the particles size effect. Thermoluminescence (TL) response of cubic Dy2O3 nanophosphors prepared by both fuels was examined using gamma and UV radiations. The thermoluminescence of sugar used samples shows a single glow peak at 377 degrees C for 1-4 kGy gamma irradiations. When dose is increased to 5 kGy, two more shouldered peaks were observed at 245 and 310 degrees C. However, in TL of ODH used samples, a single glow peak at 376 degrees C was observed. It is observed that TL intensity is found to be more in sugar used samples. In UV irradiated samples a single glow peak at 365 degrees C was recorded in both the fuels with a little variation in TL intensity. The trapping parameters were estimated by different methods and the results are discussed. (C) 2012 Elsevier B.V. All rights reserved.

Dilations of Gamma-contractions by solving operator equations

For a contraction P and a bounded commutant S of P. we seek a solution X of the operator equation S - S*P = (1 - P* P)(1/2) X (1 - P* P)(1/2) where X is a bounded operator on (Ran) over bar (1 - P* P)(1/2) with numerical radius of X being not greater than 1. A pair of bounded operators (S, P) which has the domain Gamma = {(z(1) + z(2), z(2)): vertical bar z(1)vertical bar < 1, vertical bar z(2)vertical bar <= 1} subset of C-2 as a spectral set, is called a P-contraction in the literature. We show the existence and uniqueness of solution to the operator equation above for a Gamma-contraction (S, P). This allows us to construct an explicit Gamma-isometric dilation of a Gamma-contraction (S, P). We prove the other way too, i.e., for a commuting pair (S, P) with parallel to P parallel to <= 1 and the spectral radius of S being not greater than 2, the existence of a solution to the above equation implies that (S, P) is a Gamma-contraction. We show that for a pure F-contraction (S, P), there is a bounded operator C with numerical radius not greater than 1, such that S = C + C* P. Any Gamma-isometry can be written in this form where P now is an isometry commuting with C and C. Any Gamma-unitary is of this form as well with P and C being commuting unitaries. Examples of Gamma-contractions on reproducing kernel Hilbert spaces and their Gamma-isometric dilations are discussed. (C) 2012 Elsevier Inc. All rights reserved.

Structural, EPR, photo and thermoluminescence properties of ZnO:Fe nanoparticles

Zn(1-x)Fe(x)O(1+0.5x) (x = 0.5-5 mol%) nanoparticles were synthesized by a low temperature solution combustion route. The structural characterization of these nanoparticles by PXRD, SEM and TEM confirmed the phase purity of the samples and indicated a reduction in the particle size with increase in Fe content. A small increase in micro strain in the Fe doped nanocrystals is observed from W-H plots. EPR spectrum exhibits an intense resonance signal with effective g values at g approximate to 2.0 with a sextet hyperfine structure (hfs) besides a weak signal at g approximate to 4.13. The signal at g approximate to 2.0 with a sextet hyperfine structure might be due to manganese impurity where as the resonance signal at g approximate to 4.13 is due to iron. The optical band gap E-g was found to decrease with increase of Fe content. Raman spectra exhibit two non-polar optical phonon (E-2) modes at low and high frequencies at 100 and 435 cm(-1) in Fe doped samples. These modes broaden and disappear with increase of Fe do pant concentration. TL measurements of gamma-irradiated (1-5 kGy) samples show a main glow peak at 368 degrees C at a warming rate of 6.7 degrees Cs-1. The thermal activation parameters were estimated from Glow peak shape method. The average activation energy was found to be in the range 0.34-2.81 eV. (C) 2012 Elsevier B.V. All rights reserved.

Photoresist functionalisation method for high-density protein microarrays using photolithography

Since the last decade, there is a growing need for patterned biomolecules for various applications ranging from diagnostic devices to enabling fundamental biological studies with high throughput. Protein arrays facilitate the study of protein-protein, protein-drug or protein-DNA interactions as well as highly multiplexed immunosensors based on antibody-antigen recognition. Protein microarrays are typically fabricated using piezoelectric inkjet printing with resolution limit of similar to 70-100 mu m limiting the array density. A considerable amount of research has been done on patterning biomolecules using customised biocompatible photoresists. Here, a simple photolithographic process for fabricating protein microarrays on a commercially available diazo-naphthoquinone-novolac-positive tone photoresist functionalised with 3-aminopropyltriethoxysilane is presented. The authors demonstrate that proteins immobilised using this procedure retain their activity and therefore form functional microarrays with the array density limited only by the resolution of lithography, which is more than an order of magnitude compared with inkjet printing. The process described here may be useful in the integration of conventional semiconductor manufacturing processes with biomaterials relevant for the creation of next-generation bio-chips.

Temperature Dependent Photoluminescence Studies in Hg0.2Cd0.8Te Nanorods Synthesized by Solvothermal Method

Hg0.2Cd0.8Te nanorods were synthesized via solvothermal route using an air-stable Na2Te-O-3. The structural and morphological studies were done by X-ray diffraction (XRD) and scanning electron microscopy (SEM). The diameters of the nanorods were found to be 20-50 nm. The growth of the nanorods were facilitated due to the use of CTAB as surfactant. The temperature dependent photoluminescence (PL) studies between 10-300 K show three prominent PL bands in 0.5-0.7 eV and are attributed to defect centers. The features like temperature independent peak energy and quite sensitive PL intensity which shows a thermal quenching behavior indicate that the defects are related to the compositional disorder.

SPLIT-STEP FORWARD MILSTEIN METHOD FOR STOCHASTIC DIFFERENTIAL EQUATIONS

In this paper, we consider the problem of computing numerical solutions for stochastic differential equations (SDEs) of Ito form. A fully explicit method, the split-step forward Milstein (SSFM) method, is constructed for solving SDEs. It is proved that the SSFM method is convergent with strong order gamma = 1 in the mean-square sense. The analysis of stability shows that the mean-square stability properties of the method proposed in this paper are an improvement on the mean-square stability properties of the Milstein method and three stage Milstein methods.

State Dependent Attempt Rate modeling of single cell IEEE 802.11 WLANs with homogeneous nodes and Poisson packet arrivals

We study a State Dependent Attempt Rate (SDAR) approximation to model M queues (one queue per node) served by the Carrier Sense Multiple Access with Collision Avoidance (CSMA/CA) protocol as standardized in the IEEE 802.11 Distributed Coordination Function (DCF). The approximation is that, when n of the M queues are non-empty, the (transmission) attempt probability of each of the n non-empty nodes is given by the long-term (transmission) attempt probability of n saturated nodes. With the arrival of packets into the M queues according to independent Poisson processes, the SDAR approximation reduces a single cell with non-saturated nodes to a Markovian coupled queueing system. We provide a sufficient condition under which the joint queue length Markov chain is positive recurrent. For the symmetric case of equal arrival rates and finite and equal buffers, we develop an iterative method which leads to accurate predictions for important performance measures such as collision probability, throughput and mean packet delay. We replace the MAC layer with the SDAR model of contention by modifying the NS-2 source code pertaining to the MAC layer, keeping all other layers unchanged. By this model-based simulation technique at the MAC layer, we achieve speed-ups (w.r.t. MAC layer operations) up to 5.4. Through extensive model-based simulations and numerical results, we show that the SDAR model is an accurate model for the DCF MAC protocol in single cells. (C) 2012 Elsevier B.V. All rights reserved.