A multi-level multi-scale approach to study essential genes in Mycobacterium tuberculosis

Background: The set of indispensable genes that are required by an organism to grow and sustain life are termed as essential genes. There is a strong interest in identification of the set of essential genes, particularly in pathogens, not only for a better understanding of the pathogen biology, but also for identifying drug targets and the minimal gene set for the organism. Essentiality is inherently a systems property and requires consideration of the system as a whole for their identification. The available experimental approaches capture some aspects but each method comes with its own limitations. Moreover, they do not explain the basis for essentiality in most cases. A powerful prediction method to recognize this gene pool including rationalization of the known essential genes in a given organism would be very useful. Here we describe a multi-level multi-scale approach to identify the essential gene pool in a deadly pathogen, Mycobacterium tuberculosis. Results: The multi-level workflow analyses the bacterial cell by studying (a) genome-wide gene expression profiles to identify the set of genes which show consistent and significant levels of expression in multiple samples of the same condition, (b) indispensability for growth by using gene expression integrated flux balance analysis of a genome-scale metabolic model, (c) importance for maintaining the integrity and flow in a protein-protein interaction network and (d) evolutionary conservation in a set of genomes of the same ecological niche. In the gene pool identified, the functional basis for essentiality has been addressed by studying residue level conservation and the sub-structure at the ligand binding pockets, from which essential amino acid residues in that pocket have also been identified. 283 genes were identified as essential genes with high-confidence. An agreement of about 73.5% is observed with that obtained from the experimental transposon mutagenesis technique. A large proportion of the identified genes belong to the class of intermediary metabolism and respiration. Conclusions: The multi-scale, multi-level approach described can be generally applied to other pathogens as well. The essential gene pool identified form a basis for designing experiments to probe their finer functional roles and also serve as a ready shortlist for identifying drug targets.

Kinematic and Mechanical Profile of the Self-Actuation of Thermosalient Crystal Twins of 1,2,4,5-Tetrabromobenzene: A Molecular Crystalline Analogue of a Bimetallic Strip

A paradigm shift from hard to flexible, organic-based optoelectronics requires fast and reversible mechanical response from actuating materials that are used for conversion of heat or light into mechanical motion. As the limits in the response times of polymer-based actuating materials are reached, which are inherent to the less-than-optimal coupling between the light/heat and mechanical energy in them, 1 a conceptually new approach to mechanical actuation is required to leapfrog the performance of organic actuators. Herein, we explore single crystals of 1,2,4,5-tetrabromobenzene (TBB) as actuating elements and establish relations between their kinematic profile and mechanical properties. Centimeter-size acicular crystals of TBB are the only naturally twinned crystals out of about a dozen known materials that exhibit the thermosalient effect-an extremely rare and visually impressive crystal locomotion. When taken over a phase transition, crystals of this material store mechanical strain and are rapidly self-actuated to sudden jumps to release the internal strain, leaping up to several centimeters. To establish the structural basis for this colossal crystal motility, we investigated the mechanical profile of the crystals from macroscale, in response to externally induced deformation under microscope, to nanoscale, by using nanoindentation. Kinematic analysis based on high-speed recordings of over 200 twinned TBB crystals exposed to directional or nondirectional heating unraveled that the crystal locomotion is a kinematically complex phenomenon that includes at least six kinematic effects. The nanoscale tests confirm the highly elastic nature, with an elastic deformation recovery (60%) that is far superior to those of molecular crystals reported earlier. This property appears to be critical for accumulation of stress required for crystal jumping. Twinned crystals of TBB exposed to moderate directional heating behave as all-organic analogue of a bimetallic `strip, where the lattice misfit between the two crystal components drives reveriible deformation of the crystal.

Effect of choice of basis functions in neural network for capturing unknown function for dynamic inversion control

The basic requirement for an autopilot is fast response and minimum steady state error for better guidance performance. The highly nonlinear nature of the missile dynamics due to the severe kinematic and inertial coupling of the missile airframe as well as the aerodynamics has been a challenge for an autopilot that is required to have satisfactory performance for all flight conditions in probable engagements. Dynamic inversion is very popular nonlinear controller for this kind of scenario. But the drawback of this controller is that it is sensitive to parameter perturbation. To overcome this problem, neural network has been used to capture the parameter uncertainty on line. The choice of basis function plays the major role in capturing the unknown dynamics. Here in this paper, many basis function has been studied for approximation of unknown dynamics. Cosine basis function has yield the best response compared to any other basis function for capturing the unknown dynamics. Neural network with Cosine basis function has improved the autopilot performance as well as robustness compared to Dynamic inversion without Neural network.

Correlations between mechanical and photoluminescence properties in Eu doped sodium bismuth titanate

Nanoindentation technique is utilized to examine mechanical property variation in Eu doped Na0.5Bi0.5 TiO3 (NBT). Doping levels of Eu in NBT is systematically varied. Dilute doping results in a linear reduction in both modulus and hardness. At higher concentrations, a recovery of the mechanical properties (to undoped NBT values) is observed. These experimental trends mirror variations in the optical emission intensities with Eu concentration. Observed trends are rationalized on the basis of a model, which hypothesizes phase segregation beyond a critical Eu doping level. Such segregation leads to the formation of pure NBT, nano-Eu saturated NBT, and nano-mixed Eu oxides in the microstructure. Pure NBT is optically inactive, while saturated Eu:NBT is a much better emitter when compared to europium oxide. Hence beyond the critical concentration, luminescence signal comes primarily from the saturated Eu:NBT phase. The model presented is supported by nanoindentation, and spectroscopic results. (C) 2013 Elsevier Ltd. All rights reserved.

Size Control and Magnetic Property Trends in Cobalt Ferrite Nanoparticles Synthesized Using an Aqueous Chemical Route

Cobalt ferrite (CoFe2O4) is an engineering material which is used for applications such as magnetic cores, magnetic switches, hyperthermia based tumor treatment, and as contrast agents for magnetic resonance imaging. Utility of ferrites nanoparticles hinges on its size, dispersibility in solutions, and synthetic control over its coercivity. In this work, we establish correlations between room temperature co-precipitation conditions, and these crucial materials parameters. Furthermore, post-synthesis annealing conditions are correlated with morphology, changes in crystal structure and magnetic properties. We disclose the synthesis and process conditions helpful in obtaining easily sinterable CoFe2O4 nanoparticles with coercive magnetic flux density (H-c) in the range 5.5-31.9 kA/m and M-s in the range 47.9-84.9 A.m(2)Kg(-1). At a grain size of similar to 54 +/- 2 nm (corresponding to 1073 K sintering temperature), multi-domain behavior sets in, which is indicated by a decrease in H-c. In addition, we observe an increase in lattice constant with respect to grain size, which is the inverse of what is expected of in ferrites. Our results suggest that oxygen deficiency plays a crucial role in explaining this inverse trend. We expect the method disclosed here to be a viable and scalable alternative to thermal decomposition based CoFe2O4 synthesis. The magnetic trends reported will aid in the optimization of functional CoFe2O4 nanoparticles

Structural basis for the redox sensitivity of the Mycobacterium tuberculosis SigK-RskA sigma-anti-sigma complex

The host-pathogen interactions in Mycobacterium tuberculosis infection are significantly influenced by redox stimuli and alterations in the levels of secreted antigens. The extracyto-plasmic function (ECF) sigma factor sigma(K) governs the transcription of the serodominant antigens MPT70 and MPT83. The cellular levels of sigma(K) are regulated by the membrane-associated anti-sigma(K) (RskA) that localizes sigma(K) in an inactive complex. The crystal structure of M. tuberculosis sigma(K) in complex with the cytosolic domain of RskA (RskAcyto) revealed a disulfide bridge in the -35 promoter-interaction region of sigma(K). Biochemical experiments reveal that the redox potential of the disulfide-forming cysteines in sigma(K) is consistent with its role as a sensor. The disulfide bond in sigma(K) influences the stability of the sigma(K)-RskA(cyto) complex but does not interfere with sigma(K)-promoter DNA interactions. It is noted that these disulfide-forming cysteines are conserved across homologues, suggesting that this could be a general mechanism for redox-sensitive transcription regulation.

Molecular Basis for the Differential Quinolone Susceptibility of Mycobacterial DNA Gyrase

DNA gyrase is a type II topoisomerase that catalyzes the introduction of negative supercoils in the genomes of eubacteria. Fluoroquinolones (FQs), successful as drugs clinically, target the enzyme to trap the gyrase-DNA complex, leading to the accumulation of double-strand breaks in the genome. Mycobacteria are less susceptible to commonly used FQs. However, an 8-methoxy-substituted FQ, moxifloxacin (MFX), is a potent antimycobacterial, and a higher susceptibility of mycobacterial gyrase to MFX has been demonstrated. Although several models explain the mechanism of FQ action and gyrase-DNA-FQ interaction, the basis for the differential susceptibility of mycobacterial gyrase to various FQs is not understood. We have addressed the basis of the differential susceptibility of the gyrase and revisited the mode of action of FQs. We demonstrate that FQs bind both Escherichia coli and Mycobacterium tuberculosis gyrases in the absence of DNA and that the addition of DNA enhances the drug binding. The FQs bind primarily to the GyrA subunit of mycobacterial gyrase, while in E. coli holoenzyme is the target. The binding of MFX to GyrA of M. tuberculosis correlates with its effectiveness as a better inhibitor of the enzyme and its efficacy in cell killing.

Reduced Grobner bases and Macaulay-Buchberger Basis Theorem over Noetherian rings

In this paper, we extend the characterization of Zx]/(f), where f is an element of Zx] to be a free Z-module to multivariate polynomial rings over any commutative Noetherian ring, A. The characterization allows us to extend the Grobner basis method of computing a k-vector space basis of residue class polynomial rings over a field k (Macaulay-Buchberger Basis Theorem) to rings, i.e. Ax(1), ... , x(n)]/a, where a subset of Ax(1), ... , x(n)] is an ideal. We give some insights into the characterization for two special cases, when A = Z and A = ktheta(1), ... , theta(m)]. As an application of this characterization, we show that the concept of Border bases can be extended to rings when the corresponding residue class ring is a finitely generated, free A-module. (C) 2014 Elsevier B.V. All rights reserved.

Model-Resolution-Based Basis Pursuit Deconvolution Improves Diffuse Optical Tomographic Imaging

The image reconstruction problem encountered in diffuse optical tomographic imaging is ill-posed in nature, necessitating the usage of regularization to result in stable solutions. This regularization also results in loss of resolution in the reconstructed images. A frame work, that is attributed by model-resolution, to improve the reconstructed image characteristics using the basis pursuit deconvolution method is proposed here. The proposed method performs this deconvolution as an additional step in the image reconstruction scheme. It is shown, both in numerical and experimental gelatin phantom cases, that the proposed method yields better recovery of the target shapes compared to traditional method, without the loss of quantitativeness of the results.

Basis pursuit deconvolution for improving model-based reconstructed images in photoacoustic tomography

The model-based image reconstruction approaches in photoacoustic tomography have a distinct advantage compared to traditional analytical methods for cases where limited data is available. These methods typically deploy Tikhonov based regularization scheme to reconstruct the initial pressure from the boundary acoustic data. The model-resolution for these cases represents the blur induced by the regularization scheme. A method that utilizes this blurring model and performs the basis pursuit deconvolution to improve the quantitative accuracy of the reconstructed photoacoustic image is proposed and shown to be superior compared to other traditional methods via three numerical experiments. Moreover, this deconvolution including the building of an approximate blur matrix is achieved via the Lanczos bidagonalization (least-squares QR) making this approach attractive in real-time. (C) 2014 Optical Society of America

Design Aspects of Luminescent Organic Crystals

With the progress of modern material science and successful commercialisations of organic-electronics, the field of organic luminescent materials has gained much attention in recent years. For a long time, the concepts and knowledge of photoluminescence (i.e. fluorescence and phosphorescence) were restricted to the solution phase as the exceptions of fluorescence quenching in condensed state were yet to be discovered. However, in the last few decades, researchers around the globe have come up with a number of promising strategies and concepts to systematically design solid-state emissive organic materials. In particular, the manipulations of ordered solid state structures and intermolecular strong and weak interactions provide a basis for understanding structure-property relationship and serve as an important tool for the design of newer, better and more efficient luminescent materials. In this short review, recent developments in this field will be presented.

Discerning heat transfer in building materials

The function of a building is to ensure safety and thermal comfort for healthy living conditions. Buildings primarily comprise an envelope, which acts as an interface separating the external environment from the indoors environment. The building envelope is primarily responsible for regulating indoor thermal comfort in response to external climatic conditions. It usually comprises a configuration of building materials to thus far provide requisite structural performance. However, studies into building-envelope configurations to provide a particular thermal performance are limited. As the building envelope is exposed to the external environment there will be heat and moisture transfer to the indoor environment through it. The overall phenomenon of heat and moisture transfer depends on the microstructure and configuration within the building material. Further, thermal property of a material is generally dependent on its microstructure, which comprises a network of pores and particles arranged in a definite structure. Thermal behaviour of a building material thus depends on the thermal conductivities of the solid particles, pore micro-structure and its constituent fluid (air and/or moisture). The thermal response of a building envelope is determined by the thermal characteristics of the individual building materials and its configuration. Understanding the heat transfer influenced by the complex networks of pores and particles is a relatively new study in the area of building climatic-response. The current study reviews the heat-transfer mechanisms that determine the thermal performance of a building material attributed to its micro-structure. A theoretical basis for the same is being evolved and its relevance in regulating heat-transfer through building envelopes, walls in particular, is reviewed in this paper. (C) 2014 N.C. Balaji. Published by Elsevier Ltd. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/3.0/).

Properties of the chalcogenide-carbon nano tubes and graphene composite materials

Composite can deliver more than the individual elemental property of the material. Specifically chalcogenide- multi walled carbon nano tubes and chalcogenide- bilayer graphene composite materials could be interesting for the investigation, which have been less covered by the investigators. We describe micro structural properties of Se55Te25Ge20, Se55Te25Ge20 + 0.025% multi walled carbon nano tubes and Se55Te25Ge20 + 0.025% bilayer graphene materials. This gives realization of the alloying constituents inclusion/or diffusion inside the multi walled carbon nano tubes and bilayer graphene under the homogeneous parent alloy configuration. Raman spectroscopy, X-ray photoelectron spectroscopy, UV/Visible spectroscopy and Fourier transmission infrared spectroscopy have also been carried out under the discussion. A considerable core energy levels peak shifts have been noticed for the composite materials by the X-ray photoelectron spectroscopy. The optical energy band gaps are measured to be varied in between 1.2 and 1.3 eV. In comparison to parent (Se55Te25Ge20) alloy a higher infrared transmission has been observed for the composite materials. Subsequently, variation in physical properties has been explained on the basis of bond formation in solids. (C) 2014 Elsevier B. V. All rights reserved.

Faster computation of the Karhunen-Loeve expansion using its domain independence property

The goal of this work is to reduce the cost of computing the coefficients in the Karhunen-Loeve (KL) expansion. The KL expansion serves as a useful and efficient tool for discretizing second-order stochastic processes with known covariance function. Its applications in engineering mechanics include discretizing random field models for elastic moduli, fluid properties, and structural response. The main computational cost of finding the coefficients of this expansion arises from numerically solving an integral eigenvalue problem with the covariance function as the integration kernel. Mathematically this is a homogeneous Fredholm equation of second type. One widely used method for solving this integral eigenvalue problem is to use finite element (FE) bases for discretizing the eigenfunctions, followed by a Galerkin projection. This method is computationally expensive. In the current work it is first shown that the shape of the physical domain in a random field does not affect the realizations of the field estimated using KL expansion, although the individual KL terms are affected. Based on this domain independence property, a numerical integration based scheme accompanied by a modification of the domain, is proposed. In addition to presenting mathematical arguments to establish the domain independence, numerical studies are also conducted to demonstrate and test the proposed method. Numerically it is demonstrated that compared to the Galerkin method the computational speed gain in the proposed method is of three to four orders of magnitude for a two dimensional example, and of one to two orders of magnitude for a three dimensional example, while retaining the same level of accuracy. It is also shown that for separable covariance kernels a further cost reduction of three to four orders of magnitude can be achieved. Both normal and lognormal fields are considered in the numerical studies. (c) 2014 Elsevier B.V. All rights reserved.

Correlation between band propagation property and the nature of serrations in the Portevin-Le Chatelier effect

We investigate the correlation between the band propagation property and the nature and amplitude of serrations in the Portevin-Le Chatelier effect within the framework of the Ananthakrishna model. Several significant results emerge. First, we find that spatial and temporal correlations continuously increase with strain rate from type C to type A bands. Consequently, the nature of the bands also changes continuously from type C to A bands, and so do the changes in the associated serrations. Second, even the smallest extent of propagation induces small amplitude serrations. The spatial extent of band propagation is directly correlated with the duration of small amplitude serrations, a result that is consistent with recent experiments. This correspondence allows one to estimate the spatial extent of band propagation by just measuring the temporal stretch of small amplitude serrations. Therefore, this should be of practical value when only stress versus strain is recorded. Third, the average stress drop magnitude of the small amplitude serrations induced by the propagating bands remains small and nearly constant with strain rate. As a consequence, the fully propagating type A bands are in a state of criticality. We rationalize the increasing levels of spatial and temporal correlations found with increasing strain rates. Lastly, the model also predicts several band morphologies seen in experiments including the Luders-like propagating band. (C) 2015 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.