Identification of an exported heat shock protein 70 in Plasmodium falciparum

Host cell remodelling is a hallmark of malaria pathogenesis. It involves protein folding, unfolding and trafficking events and thus participation of chaperones such as Hsp70s and Hsp40s is well speculated. Until recently, only Hsp40s were thought to be the sole representative of the parasite chaperones in the exportome. However, based on the re-annotated Plasmodium falciparum genome sequence, a putative candidate for exported Hsp70 has been reported, which otherwise was known to be a pseudogene. We raised a specific antiserum against a C-terminal peptide uniquely present in PfHsp70-x. Immunoblotting and immunofluorescence-based approaches in combination with sub-cellular fractionation by saponin and streptolysin-O have been taken to determine the expression and localization of PfHsp70-x in infected erythrocyte. The re-annotated sequence of PfHsp70-x reveals it to be a functional protein with an endoplasmic reticulum signal peptide. It gets maximally expressed at the schizont stage of intra-erythrocytic life cycle. Majority of the protein localizes to the parasitophorous vacuole and some of it gets exported to the erythrocyte compartment where it associates with Maurer's clefts. The identification of an exported parasite Hsp70 chaperone presents us with the fact that the parasite has evolved customized chaperones which might be playing crucial roles in aspects of trafficking and host cell remodelling.

Synthon identification in co-crystals and polymorphs with IR spectroscopy. Primary amides as a case study

IR spectroscopy has been widely employed to distinguish between different crystal forms such as polymorphs, clathrates, hydrates and co-crystals. IR has been used to monitor co-crystal formation and single synthon detection. In this work, we have developed a strategy to identify multiple supramolecular synthons in polymorphs and co-crystals with this technique. The identification of multiple synthons in co-crystals with IR is difficult for several reasons. In this paper, a four step method involving well assigned IR spectral markers that correspond to bonds in a synthon is used. IR spectra of three forms of the co-crystal system, 4-hydroxybenzoic acid: 4,4'-bipyridine (2 : 1), show clear differences that may be attributed to differences in the synthon combinations existing in the forms (synthon polymorphism). These differences were picked out from the three IR spectra and the bands analysed and assigned to synthons. Our method first identifies IR marker bands corresponding to (covalent) bonds in known/model crystals and then the markers are mapped in known co-crystals having single synthons. Thereafter, the IR markers are queried in known co-crystals with multiple synthons. Finally they are queried in unknown co-crystals with multiple synthons. In the last part of the study, the N-H stretching absorptions of primary amides that crystallize with the amide dimers linked in a ladder like chain show two specific absorptions which are used as marker absorptions and all variations of this band structure have been used to provide details on the environment around the dimer. The extended dimer can accordingly be easily distinguished from the isolated dimer.

A novel filtering framework through Girsanov correction for the identification of nonlinear dynamical systems

Using a Girsanov change of measures, we propose novel variations within a particle-filtering algorithm, as applied to the inverse problem of state and parameter estimations of nonlinear dynamical systems of engineering interest, toward weakly correcting for the linearization or integration errors that almost invariably occur whilst numerically propagating the process dynamics, typically governed by nonlinear stochastic differential equations (SDEs). Specifically, the correction for linearization, provided by the likelihood or the Radon-Nikodym derivative, is incorporated within the evolving flow in two steps. Once the likelihood, an exponential martingale, is split into a product of two factors, correction owing to the first factor is implemented via rejection sampling in the first step. The second factor, which is directly computable, is accounted for via two different schemes, one employing resampling and the other using a gain-weighted innovation term added to the drift field of the process dynamics thereby overcoming the problem of sample dispersion posed by resampling. The proposed strategies, employed as add-ons to existing particle filters, the bootstrap and auxiliary SIR filters in this work, are found to non-trivially improve the convergence and accuracy of the estimates and also yield reduced mean square errors of such estimates vis-a-vis those obtained through the parent-filtering schemes.

Effect of temperature and strain rate on the deformation behavior and microstructure of a homogenized AZ31 magnesium alloy

The plastic deformation behavior and dynamic recrystallization (DRX) in homogenized AZ31 Mg alloy was investigated in uniaxial compression in the temperature range between 150 and 400 degrees C with strain rates ranging from 10(-3) to 10(2) s(-1). Twinning was found to contribute significantly during the early stages of deformation. The onset of twinning was examined in detail by recourse to the examination of the appearance of first local maxima before peak strain in the stress-strain responses and the second derivative of stress with strain. High strain hardening rate was observed immediately after the onset of twinning and was found to increase with the Zener-Hollomon parameter. DRX was observed at temperatures above 250 degrees C whereas deformation at lower temperatures (< 250 degrees C) leads to extensive twinning at all the strain rates. At intermediate temperatures of 250-300 degrees C, plastic strains tend to localize near grain/twin boundaries, confining DRX only to these regions. Increase in the temperature promotes non-basal slip, which, in turn, leads to uniform deformation; DRX too becomes uniform. Deformation behavior in three different regimes of temperature is discussed. The dependence of critical stress for the onset of DRX and peak flow stress on temperature and strain rate are also described. (C) 2013 Elsevier B.V. All rights reserved.

Identification of fault location in power distribution system with distributed generation using support vector machines

This paper presents a multi-class support vector machine (SVMs) approach for locating and diagnosing faults in electric power distribution feeders with the penetration of Distributed Generations (DGs). The proposed approach is based on the three phase voltage and current measurements which are available at all the sources i.e. substation and at the connection points of DG. To illustrate the proposed methodology, a practical distribution feeder emanating from 132/11kV-grid substation in India with loads and suitable number of DGs at different locations is considered. To show the effectiveness of the proposed methodology, practical situations in distribution systems (DS) such as all types of faults with a wide range of varying fault locations, source short circuit (SSC) levels and fault impedances are considered for studies. The proposed fault location scheme is capable of accurately identify the fault type, location of faulted feeder section and the fault impedance. The results demonstrate the feasibility of applying the proposed method in practical in smart grid distribution automation (DA) for fault diagnosis.

Identification of immuno-dominant antigens of Trypanosoma evansi for detection of chronic trypanosomosis using experimentally infected equines

Trypanosoma evansi is the most extensively distributed trypanosome responsible for disease called surra in livestock in many countries including frequent outbreaks in India. The prevalence of this disease is most commonly reported by standard parasitological detection methods (SPDM); however, antibody ELISA is being in practice by locally produced whole cell lysate (WCL) antigens in many countries. In the present investigation, we attempted to identify and purify immuno dominant, infection specific trypanosome antigens from T. evansi proteome using experimentally infected equine serum by immuno blot. Three immuno dominant clusters of proteins i.e. 62-66 kDa, 52-55 kDa and 41-43 kDa were identified based on their consistent reactivity with donkey sequential serum experimentally infected T. evansi up to 280 days post infection (dpi). The protein cluster of 62-66 kDa was purified in bulk in native form and comparatively evaluated with whole cell lysate antigen (WCL). ELISA and immuno blot showed that polypeptide of this cluster is 100% sensitive in detection of early and chronic infection. Further, this protein cluster was also found immuno reactive against hyper immune serum raised against predominantly 66 kDa exo antigen, revealed that this is a common immunodominant moieties in proteome and secretome of T. evansi.

Combining indentation and diffusion couple techniques for combinatorial discovery of high temperature shape memory alloys

We demonstrate the possibility of accelerated identification of potential compositions for high-temperature shape memory alloys (SMAs) through a combinatorial material synthesis and analysis approach, wherein we employ the combination of diffusion couple and indentation techniques. The former was utilized to generate smooth and compositionally graded inter-diffusion zones (IDZs) in the Ni-Ti-Pd ternary alloy system of varying IDZ thickness, depending on the annealing time at high temperature. The IDZs thus produced were then impressed with an indenter with a spherical tip so as to inscribe a predetermined indentation strain. Subsequent annealing of the indented samples at various elevated temperatures, T-a, ranging between 150 and 550 degrees C allows for partial to full relaxation of the strain imposed due to the shape memory effect. If T-a is above the austenite finish temperature, A(f), the relaxation will be complete. By measuring the depth recovery, which serves as a proxy for the shape recovery characteristic of the SMA, a three-dimensional map in the recovery temperature composition space is constructed. A comparison of the published Af data for different compositions with the Ta data shows good agreement when the depth recovery is between 70% and 80%, indicating that the methodology proposed in this paper can be utilized for the identification of promising compositions. Advantages and further possibilities of this methodology are discussed.

Identification and characterization of starvation induced msdgc-1 promoter involved in the c-di-GMP turnover

C-di-GMP Bis-(3'-5')-cyclic-dimeric-guanosine monophosphate], a second messenger is involved in intracellular communication in the bacterial species. As a result several multi-cellular behaviors in both Gram-positive and Gram-negative bacteria are directly linked to the intracellular level of c-di-GMP. The cellular concentration of c-di-GMP is maintained by two opposing activities, diguanylate cyclase (DGC) and phosphodiesterase (PDE-A). In Mycobacterium smegmatis, a single bifunctional protein MSDGC-1 is responsible for the cellular concentration of c-di-GMP. A better understanding of the regulation of c-di-GMP at the genetic level is necessary to control the function of above two activities. In this work, we have characterized the promoter element present in msdgc-1 along with the + 1 transcription start site and identified the sigma factors that regulate the transcription of msdgc-1. Interestingly, msdgc-1 utilizes SigA during the initial phase of growth, whereas near the stationary phase SigB containing RNA polymerase takes over the expression of msdgc-1. We report here that the promoter activity of msdgc-1 increases during starvation or depletion of carbon source like glucose or glycerol. When msdgc-1 is deleted, the numbers of viable cells are similar to 10 times higher in the stationary phase in comparison to that of the wild type. We propose here that msdgc-1 is involved in the regulation of cell population density. (C) 2013 Elsevier B.V. All rights reserved.

Strain-controlled fatigue in B-modified Ti-6Al-4V alloys

The strain-controlled fatigue behaviour of Ti-6Al-4V alloy with up to 0.11 wt.% B addition was investigated. Results show significant softening when the strain amplitudes, Delta epsilon(T)/2, are >= 0.75%. B addition was found to improve the fatigue life for Delta epsilon(T)/2 <= 0.75% as it corresponds to the elastic regime and hence is strength dominated. At Delta epsilon(T)/2 = 1%, in contrast, the base alloy exhibits higher fatigue life as TiB particle cracking due to strain incompatibility causes easy crack nucleation in the B-modified alloys. (C) 2013 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Examining the Effectiveness of Discriminant Function Analysis and Cluster Analysis in Species Identification of Male Field Crickets Based on Their Calling Songs

Traditional taxonomy based on morphology has often failed in accurate species identification owing to the occurrence of cryptic species, which are reproductively isolated but morphologically identical. Molecular data have thus been used to complement morphology in species identification. The sexual advertisement calls in several groups of acoustically communicating animals are species-specific and can thus complement molecular data as non-invasive tools for identification. Several statistical tools and automated identifier algorithms have been used to investigate the efficiency of acoustic signals in species identification. Despite a plethora of such methods, there is a general lack of knowledge regarding the appropriate usage of these methods in specific taxa. In this study, we investigated the performance of two commonly used statistical methods, discriminant function analysis (DFA) and cluster analysis, in identification and classification based on acoustic signals of field cricket species belonging to the subfamily Gryllinae. Using a comparative approach we evaluated the optimal number of species and calling song characteristics for both the methods that lead to most accurate classification and identification. The accuracy of classification using DFA was high and was not affected by the number of taxa used. However, a constraint in using discriminant function analysis is the need for a priori classification of songs. Accuracy of classification using cluster analysis, which does not require a priori knowledge, was maximum for 6-7 taxa and decreased significantly when more than ten taxa were analysed together. We also investigated the efficacy of two novel derived acoustic features in improving the accuracy of identification. Our results show that DFA is a reliable statistical tool for species identification using acoustic signals. Our results also show that cluster analysis of acoustic signals in crickets works effectively for species classification and identification.

Support vector clustering-based direct coherency identification of generators in a multi-machine power system

This study investigates the application of support vector clustering (SVC) for the direct identification of coherent synchronous generators in large interconnected multi-machine power systems. The clustering is based on coherency measure, which indicates the degree of coherency between any pair of generators. The proposed SVC algorithm processes the coherency measure matrix that is formulated using the generator rotor measurements to cluster the coherent generators. The proposed approach is demonstrated on IEEE 10 generator 39-bus system and an equivalent 35 generators, 246-bus system of practical Indian southern grid. The effect of number of data samples and fault locations are also examined for determining the accuracy of the proposed approach. An extended comparison with other clustering techniques is also included, to show the effectiveness of the proposed approach in grouping the data into coherent groups of generators. This effectiveness of the coherent clusters obtained with the proposed approach is compared in terms of a set of clustering validity indicators and in terms of statistical assessment that is based on the coherency degree of a generator pair.

Identification of key amino acid residues in the catalytic mechanism of diaminopropionate ammonialyase from Salmonella typhimurium

Diaminopropionate ammonialyase (DAPAL), a fold-typeII pyridoxal 5-phosphate-dependent enzyme, catalyzes the ,-elimination of diaminopropionate (DAP) to pyruvate and ammonia. DAPAL was able to utilize both d- and l-DAP as substrates with almost equal efficiency. Mutational analysis of functionally important residues such as Thr385, Asp125 and Asp194 was carried out to understand the mechanism by which the isomers are hydrolyzed. Further, the putative residues involved in the formation of disulfide bond Cys271 and Cys299 were also mutated. T385S, T385D sDAPAL were as active with dl-DAP as substrate as sDAPAL, whereas the later exhibited a threefold increase in catalytic efficiency with d-Ser as substrate. Further analysis of these mutants suggested that DAPAL might follow an anti-E-2 mechanism of catalysis that does not involve the formation of a quinonoid intermediate. Of the two mutants of Asp125, D125E showed complete loss of activity with d-DAP as substrate, whereas the reaction with l-DAP was not affected significantly, demonstrating that Asp125 was essential for abstraction of protons from the d-isomer. By contrast, mutational analysis of Asp194 showed that the residue may not be directly involved in proton abstraction from l-DAP. sDAPAL does not form a disulfide bond in solution, although the position of Cys299 and Cys271 in the modeled structure of sDAPAL favored the formation of a disulfide bond. Further, unlike eDAPAL, sDAPAL could be activated by monovalent cations. Mutation of the cysteine residues showed that Cys271 may be involved in coordinating the monovalent cation, as observed in the case of other fold-typeII enzymes.

A DNA methylation prognostic signature of glioblastoma: identification of NPTX2-PTEN-NF-kappa B nexus

Glioblastoma (GBM) is the most common, malignant adult primary tumor with dismal patient survival, yet the molecular determinants of patient survival are poorly characterized. Global methylation profile of GBM samples (our cohort; n = 44) using high-resolution methylation microarrays was carried out. Cox regression analysis identified a 9-gene methylation signature that predicted survival in GBM patients. A risk-score derived from methylation signature predicted survival in univariate analysis in our and The Cancer Genome Atlas (TCGA) cohort. Multivariate analysis identified methylation risk score as an independent survival predictor in TCGA cohort. Methylation risk score stratified the patients into low-risk and high-risk groups with significant survival difference. Network analysis revealed an activated NF-kappa B pathway association with high-risk group. NF-kappa B inhibition reversed glioma chemoresistance, and RNA interference studies identified interleukin-6 and intercellular adhesion molecule-1 as key NF-kappa B targets in imparting chemoresistance. Promoter hypermethylation of neuronal pentraxin II (NPTX2), a risky methylated gene, was confirmed by bisulfite sequencing in GBMs. GBMs and glioma cell lines had low levels of NPTX2 transcripts, which could be reversed upon methylation inhibitor treatment. NPTX2 overexpression induced apoptosis, inhibited proliferation and anchorage-independent growth, and rendered glioma cells chemosensitive. Furthermore, NPTX2 repressed NF-kappa B activity by inhibiting AKT through a p53-PTEN-dependent pathway, thus explaining the hypermethylation and downregulation of NPTX2 in NF-kappa B-activated high-risk GBMs. Taken together, a 9-gene methylation signature was identified as an independent GBM prognosticator and could be used for GBM risk stratification. Prosurvival NF-kappa B pathway activation characterized high-risk patients with poor prognosis, indicating it to be a therapeutic target. (C) 2013 AACR.

Nanoindentation behavior of nanotwinned Cu: Influence of indenter angle on hardness, strain rate sensitivity and activation volume

The influence of strain on the mechanical properties and deformation kinetic parameters of nanotwinned (at) copper is investigated by a series of nanoindentation experiments, which were performed by employing sharp indenters with five varying centerline-to-face angles (psi). Comparison experiments were also conducted on (1 1 0) single crystalline Cu. Experimental results indicate that, unlike coarsegrained materials, nt-Cu is prone to plastic flow softening with large material pile-up around the indentation impression at high levels of strains. Localized detwinning becomes more significant with decreasing psi, concomitant with reduced strain-rate sensitivity (m) and enhanced activation volume (V*). The m of nt-Cu is found to depend sensitively on psi with a variation of more than a factor of 3, whereas V* exhibits a much less sensitive trend. This paper discusses the validation of the experimental techniques and the implications of various deformation kinetic parameters on the underlying deformation mechanisms of nt-Ca. 2013 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Design and development of Fiber Bragg Grating sensing plate for plantar strain measurement and postural stability analysis

This paper describes an ab initio design and development of a novel Fiber Bragg Grating (FBG) sensor based strain sensing plate for the measurement of plantar strain distribution in human foot. The primary aim of this work is to study the feasibility of usage of FBG sensors in the measurement of plantar strain in the foot; in particular, to spatially resolve the strain distribution in the foot at different regions such as fore-foot, mid-foot and hind-foot. This study also provides a method to quantify and compare relative postural stability of different subjects under test; in addition, traditional accelerometers have been used to record the movements of center of gravity (second lumbar vertebra) of the subject and the results obtained have been compared against the outcome of the postural stability studies undertaken using the developed FBG plantar strain sensing plate. (C) 2013 Elsevier Ltd. All rights reserved.