Solution nuclear magnetic resonance structure of the GATase subunit and structural Basis of the interaction between GATase and ATPPase subunits in a two-subunit-type GMPS from methanocaldococcus jannaschii

The solution structure of the monomeric glutamine amidotransferase (GATase) subunit of the Methanocaldococcus janaschii (Mj) guanosine monophosphate synthetase (GMPS) has been determined using high-resolution nuclear magnetic resonance methods. Gel filtration chromatography and N-15 backbone relaxation studies have shown that the Mj GATase subunit is present in solution as a 21 kDa (188-residue) monomer. The ensemble of 20 lowest-energy structures showed root-mean-square deviations of 0.35 +/- 0.06 angstrom for backbone atoms and 0.8 +/- 0.06 angstrom for all heavy atoms. Furthermore, 99.4% of the backbone dihedral angles are present in the allowed region of the Ramachandran map, indicating the stereochemical quality of the structure. The core of the tertiary structure of the GATase is composed of a seven-stranded mixed beta-sheet that is fenced by five alpha-helices. The Mj GATase is similar in structure to the Pyrococcus horikoshi (Ph) GATase subunit. Nuclear magnetic resonance (NMR) chemical shift perturbations and changes in line width were monitored to identify residues on GATase that were responsible for interaction with magnesium and the ATPPase subunit, respectively. These interaction studies showed that a common surface exists for the metal ion binding as well as for the protein-protein interaction. The dissociation constant for the GATase-Mg2+ interaction has been found to be similar to 1 mM, which implies that interaction is very weak and falls in the fast chemical exchange regime. The GATase-ATPPase interaction, on the other hand, falls in the intermediate chemical exchange regime on the NMR time scale. The implication of this interaction in terms of the regulation of the GATase activity of holo GMPS is discussed.

Characterizing drought using the reliability-resilience-vulnerability concept

This study borrows the measures developed for the operation of water resources systems as a means of characterizing droughts in a given region. It is argued that the common approach of assessing drought using a univariate measure (severity or reliability) is inadequate as decision makers need assessment of the other facets considered here. It is proposed that the joint distribution of reliability, resilience, and vulnerability (referred to as RRV in a reservoir operation context), assessed using soil moisture data over the study region, be used to characterize droughts. Use is made of copulas to quantify the joint distribution between these variables. As reliability and resilience vary in a nonlinear but almost deterministic way, the joint probability distribution of only resilience and vulnerability is modeled. Recognizing the negative association between the two variables, a Plackett copula is used to formulate the joint distribution. The developed drought index, referred to as the drought management index (DMI), is able to differentiate the drought proneness of a given area when compared to other areas. An assessment of the sensitivity of the DMI to the length of the data segments used in evaluation indicates relative stability is achieved if the data segments are 5years or longer. The proposed approach is illustrated with reference to the Malaprabha River basin in India, using four adjoining Climate Prediction Center grid cells of soil moisture data that cover an area of approximately 12,000 km(2). (C) 2013 American Society of Civil Engineers.

Higher-Dimensional Analogues of the Map Coloring Problem

After a brief discussion of the history of the problem, we propose a generalization of the map coloring problem to higher dimensions.

A Multicast Authentication Protocol (MAP) for Dynamic Multicast Groups in Wireless Networks

In this paper, we have proposed a centralized multicast authentication protocol (MAP) for dynamic multicast groups in wireless networks. In our protocol, a multicast group is defined only at the time of the multicasting. The authentication server (AS) in the network generates a session key and authenticates it to each of the members of a multicast group using the computationally inexpensive least common multiple (LCM) method. In addition, a pseudo random function (PRF) is used to bind the secret keys of the network members with their identities. By doing this, the AS is relieved from storing per member secrets in its memory, making the scheme completely storage scalable. The protocol minimizes the load on the network members by shifting the computational tasks towards the AS node as far as possible. The protocol possesses a membership revocation mechanism and is protected against replay attack and brute force attack. Analytical and simulation results confirm the effectiveness of the proposed protocol.

X-ray diffraction and Mossbauer spectroscopy studies of cementite dissolution in cold-drawn pearlitic steel

Cementite dissolution in cold-drawn pearlitic steel (0.8 wt.% carbon) wires has been studied by quantitative X-ray diffraction (XRD) and Mossbauer spectroscopy up to drawing strain 1.4. Quantification of cementite-phase fraction by Rietveld analysis has confirmed more than 50% dissolution of cementite phase at drawing strain 1.4. It is found that the lattice parameter of the ferrite phase determined by Rietveld refinement procedure remains nearly unchanged even after cementite dissolution. This confirms that the carbon atoms released after cementite dissolution do not dissolve in the ferrite lattice as Fe-C interstitial solid solution. Detailed analysis of broadening of XRD line profiles for the ferrite phase shows high density of dislocations (approximate to 10(15)/m(2)) in the ferrite matrix at drawing strain 1.4. The results suggest a dominant role of 111 screw dislocations in the cementite dissolution process. Post-deformation heat treatment leads to partial annihilation of dislocations and restoration of cementite phase. Based on these experimental observations, further supplemented by TEM studies, we have suggested an alternative thermodynamic mechanism of the dissolution process.

Incorporation of Interfacial Intermetallic Morphology in Fracture Mechanism Map for Sn-Ag-Cu Solder Joints

A fracture mechanism map (FMM) is a powerful tool which correlates the fracture behavior of a material to its microstructural characteristics in an explicit and convenient way. In the FMM for solder joints, an effective thickness of the interfacial intermetallic compound (IMC) layer (t (eff)) and the solder yield strength (sigma (ys,eff)) are used as abscissa and ordinate axes, respectively, as these two predominantly affect the fracture behavior of solder joints. Earlier, a definition of t (eff), based on the uniform thickness of IMC (t (u)) and the average height of the IMC scallops (t (s)), was proposed and shown to aptly explain the fracture behavior of solder joints on Cu. This paper presents a more general definition of t (eff) that is more widely applicable to a range of metallizations, including Cu and electroless nickel immersion gold (ENIG). Using this new definition of t (eff), mode I FMM for SAC387/Cu joints has been updated and its validity was confirmed. A preliminary FMM for SAC387/Cu joints with ENIG metallization is also presented.

Imaging cellular signalling: many `moving tales' in MAP kinase odyssey

Cellular signalling events are at the core of every adaptive response. Signalling events link environmental changes to physiological responses, consequently allowing cellular and organismal sustenance and survival. Classical approaches to study cellular signalling have relied on a variety of cell disruptive techniques which yield limited kinetic information, while the underlying events are much more complex. In this article, we discuss how modern live cell imaging microscopy has found increasing utilization in revealing spatio temporal dynamics of various signalling pathways. Utilizing the well studied mitogen-activated protein kinase (MAPK) signalling cascade as a template, the design, construction and utilization of `mobile' (translocation proficient) biosensors, suitable for studying MAPK signalling in living cells are described in detail. Experimental setup and results obtained from these biosensors, based on different proteins involved in the MAPK signalling cascade, have been described along with the setup of a microscope optimal for live cell imaging applications. Utilizing the ability to activate or deactivate signalling pathways using defined activators and specific pharmacological inhibitors, we also show how these sensors can yield unique spatial and temporal kinetic information of signalling in living cells.

Behaviour simulation in computer aided product concept sketching

In the product conceptualization phase of design, sketches are often used for exploration of diverse behaviour patterns of the components to achieve the required functionality. This paper presents a method to animate the sketch produced using a tablet interface to aid verification of the desired behaviour. A sketch is a spatial organization of strokes whose perceptual organization helps one to visually interpret its components and their interconnections. A Gestalt based segmentation followed by interactive grouping and articulation, presented in this paper, enables one to use a mechanism simulation framework to animate the sketch in a “pick and drag” mode to visualize different configurations of the product and gain insight into the product’s behaviour.

Representative seismic hazard map of Coimbatore, India

The seismic hazard value of any region depends upon three important components such as probable earthquake location, maximum earthquake magnitude and the attenuation equation. This paper presents a representative way of estimating these three important components considering region specific seismotectonic features. Rupture Based Seismic Hazard Analysis (RBSHA) given by Anbazhagan et al. (2011) is used to determine the probable future earthquake locations. This approach is verified on the earthquake data of Bhuj region. The probable earthquake location for this region is identified considering earthquake data till the year 2000. These identified locations match well with the reported locations after 2000. The further Coimbatore City is selected as the study area to develop a representative seismic hazard map using RBSHA approach and to compare with deterministic seismic hazard analysis. Probable future earthquake zones for Coimbatore are located considering the rupture phenomenon as per energy release theory discussed by Anbazhagan et at (2011). Rupture character of the region has been established by estimating the subsurface rupture length of each source and normalized with respect to the length of the source. Average rupture length of the source with respect to its total length is found to be similar for most of the sources in the region, which is called as the rupture character of the region. Maximum magnitudes of probable zones are estimated considering seismic sources close by and regional rupture character established. Representative GMPEs for the study area have been selected by carrying out efficacy test through an average log likelihood value (LLH) as ranking estimator and considering the Isoseismal map. New seismic hazard map of Coimbatore has been developed using the above regional representative parameters of probable earthquake locations, maximum earthquake magnitude and best suitable GMPEs. The new hazard map gives acceleration values at bedrock for maximum possible earthquakes. These results are compared with deterministic seismic hazard map and recently published probabilistic seismic hazard values. (C) 2014 Elsevier B.V. All rights reserved.

Division of Labor in Hand Usage in Free- Ranging Bonnet Macaques, Macaca radiata

Primates exhibit laterality in hand usage either in terms of (a) hand with which an individual solves a task or while solving a task that requires both hands, executes the most complex action, that is, hand preference, or (b) hand with which an individual executes actions most efficiently, that is, hand performance. Observations from previous studies indicate that laterality in hand usage might reflect specialization of the two hands for accomplishing tasks that require maneuvering dexterity or physical strength. However, no existing study has investigated handedness with regard to this possibility. In this study, we examined laterality in hand usage in urban free-ranging bonnet macaques, Macaca radiata with regard to the above possibility. While solving four distinct food extraction tasks which varied in the number of steps involved in the food extraction process and the dexterity required in executing the individual steps, the macaques consistently used one hand for extracting food (i.e., task requiring maneuvering dexterity)the maneuvering hand, and the other hand for supporting the body (i.e., task requiring physical strength)the supporting hand. Analogously, the macaques used the maneuvering hand for the spontaneous routine activities that involved maneuvering in three-dimensional space, such as grooming, and hitting an opponent during an agonistic interaction, and the supporting hand for those that required physical strength, such as pulling the body up while climbing. Moreover, while solving a task that ergonomically forced the usage of a particular hand, the macaques extracted food faster with the maneuvering hand as compared to the supporting hand, demonstrating the higher maneuvering dexterity of the maneuvering hand. As opposed to the conventional ideas of handedness in non-human primates, these observations demonstrate division of labor between the two hands marked by their consistent usage across spontaneous and experimental tasks requiring maneuvering in three-dimensional space or those requiring physical strength. Am. J. Primatol. 76:576-585, 2014. (c) 2013 Wiley Periodicals, Inc.

NON-GLYCINE RESIDUES IN THE DISALLOWED REGIONS OF THE RAMACHANDRAN MAP AND THEIR NEIGHBORHOOD PREFERENCES

The allowed and the ``disallowed'' regions in the celebrated Ramachandran map (phi-psi] map) was elegantly deduced by Ramachandran, Ramakrishnan and Sasisekharan even before the protein crystal structures became available. This powerful map was derived based on rigid geometry of the peptide group and later several investigations on protein crystal structures reported the occurrence of a small fraction of the phi-psi] torsion angles in the disallowed region. The question is what factors make these residues adopt disallowed conformations? Is it driven by the necessity to maintain the overall topology or is it associated with function or is it just that the disallowed conformations are extreme limits of the allowed conformations? Today, with the availability of a large number of high resolution crystal structures, we have revisited this problem. Apart from validating some of the earlier findings such as residue propensities, preferred location in the secondary structure, we have explored their spatial neighborhood preferences using the protein structure network PSN] approach developed in our lab. Finally, the structural and functional implications of the disallowed conformations are examined.

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.

Microscopic description of the evolution of the local structure and an evaluation of the chemical pressure concept in a solid solution

Extended x-ray absorption fine-structure studies have been performed at the Zn K and Cd K edges for a series of solid solutions of wurtzite Zn1-xCdxS samples with x = 0.0, 0.1, 0.25, 0.5, 0.75, and 1.0, where the lattice parameter as a function of x evolves according to the well-known Vegard's law. In conjunction with extensive, large-scale first-principles electronic structure calculations with full geometry optimizations, these results establish that the percentage variation in the nearest-neighbor bond distances are lower by nearly an order of magnitude compared to what would be expected on the basis of lattice parameter variation, seriously undermining the chemical pressure concept. With experimental results that allow us to probe up to the third coordination shell distances, we provide a direct description of how the local structure, apparently inconsistent with the global structure, evolves very rapidly with interatomic distances to become consistent with it. We show that the basic features of this structural evolution with the composition can be visualized with nearly invariant Zn-S-4 and Cd-S-4 tetrahedral units retaining their structural integrity, while the tilts between these tetrahedral building blocks change with composition to conform to the changing lattice parameters according to the Vegard's law within a relatively short length scale. These results underline the limits of applicability of the chemical pressure concept that has been a favored tool of experimentalists to control physical properties of a large variety of condensed matter systems.

Hot deformation behavior of Ni-Fe-Ga-based ferromagnetic shape memory alloy - A study using processing map

Ni-Fe-Ga-based alloys form a new class of ferromagnetic shape memory alloys (FSMAs) that show considerable formability because of the presence of a disordered fcc gamma-phase. The current study explores the deformation processing of this alloy using an off-stoichiometric Ni55Fe59Ga26 alloy that contains the ductile gamma-phase. The hot deformation behavior of this alloy has been characterized on the basis of its flow stress variation obtained by isothermal constant true strain rate compression tests in the 1123-1323 K temperature range and strain rate range of 10(-3)-10 s(-1) and using a combination of constitutive modeling and processing map. The dynamic recrystallization (DRX) regime for thermomechanical processing has been identified for this Heusler alloy on the basis of the processing maps and the deformed microstructures. This alloy also shows evidence of dynamic strain-aging (DSA) effect which has not been reported so far for any Heusler FSMAs. Similar effect is also noticed in a Ni-Mn-Ga-based Heusler alloy which is devoid of any gamma-phase. (C) 2014 Elsevier Ltd. All rights reserved.