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.

Temperature gradient induced phase transitions and morphological changes in diamond thin film

The diamond films were deposited onto a wurtzite gallium nitride (GaN) thin film substrate using hot-filament chemical vapor deposition (HFCVD). During the film deposition a lateral temperature gradient was imposed across the substrate by inclining the substrate. As grown films predominantly showed the hexagonal phase, when no inclination was applied to the substrate. Tilting the substrate with respect to the heating filament by 6 degrees imposed a lateral temperature gradient across the substrate, which induced the formation of a cubic diamond phase. Diamond grains were predominantly oriented in the (100) direction. However, a further increase in the substrate tilt angle to 12 degrees, resulted in grains oriented in the (111) direction. The growth rate and hence the morphology of diamond grains varied along the inclined substrate. The present study focuses on the measurements of dominant phase formation and crystal orientation with varying substrate inclination using orientation-imaging microscopy (OIM). This technique enables direct examination of individual diamond grains and their crystallographic orientation. (C) 2012 Elsevier B.V. All rights reserved.

Increased time-dependent room temperature plasticity in metallic glass nanopillars and its size-dependency

Room temperature, uniaxial compression creep experiments were performed on micro-/nano-sized pillars (having diameters in the range of 250-2000 nm) of a Zr-based bulk metallic glass (BMG) to investigate the influence of sample size on the time-dependent plastic deformation behavior in amorphous alloys. Experimental results reveal that plastic deformation indeed occurs at ambient temperature and at stresses that are well below the nominal quasi-static yield stress. At a given stress, higher total strains accrue in the smaller specimens. In all cases, plastic deformation was found to be devoid of shear bands, i.e., it occurs in homogeneous manner. The stress exponent obtained from the slope of the linear relation between strain rate and applied stress also shows a strong size effect, which is rationalized in terms of the amount of free volume created during deformation and the surface-to-volume ratio of the pillar. (C) 2012 Elsevier Ltd. All rights reserved.

Optical, electrochemical and morphological investigations of poly (3,4-propylenedioxythiophene)-sultone (PProDOT-S) thin films

In this paper, we have carried out thin film characterization of poly(3,4-propylenedioxythiophene)-sultone (PProDOT-S), a derivative of electrochromic poly(3,4-propylenedioxythiophene) (PProDOT). PProDOT-S was deposited onto transparent conducting oxide coated glass substrates by solution casting method. Single wavelength spectrophotometry is used to monitor the switching speed and contrast ratio at maximum wavelength (lambda (max)). The percentage transmittance at the lambda (max) of the neutral polymer is monitored as a function of time when the polymer film is repeatedly switched. This experiment gives a quantitative measure of the speed with which a film is able to switch between the two states i.e. the coloured and the bleached states. PProDOT-S films were switched at a voltage of 1 center dot 9 V with a switching speed of 2 s at lambda (max) of 565 nm and showed a contrast of similar to 37%. Cyclic voltammetry performed at different scan rates have shown the characteristic anodic and cathodic peaks. The structural investigations of PProDOT-S films by IR spectra were in good agreement with previously reported results. Raman spectra of PProDOT-S showed a strong Raman peak at 1509 cm (-aEuro parts per thousand 1) and a weak peak at 1410 cm (-aEuro parts per thousand 1) due to the C = C asymmetric and symmetric stretching vibrations of thiophene rings. The morphological investigations carried out by using scanning electron microscope (SEM) of polymer films have shown that these polymers are found to be arranged in dense packed clusters with non-uniform distribution having an average width and length of 95 nm and 160 nm, respectively.

Crowding, molecular volume and plasticity: An assessment involving crystallography, NMR and simulations

The discrepancy between the X-ray and NMR structures of Mycobacterium tuberculosis peptidyl-tRNA hydrolase in relation to the functionally important plasticity of the molecule led to molecular dynamics simulations. The X-ray and the NMR studies along with the simulations indicated an inverse correlation between crowding and molecular volume. A detailed comparison of proteins for which X-ray and the NMR structures appears to confirm this correlation. In consonance with the reported results of the investigations in cellular compartments and aqueous solution, the comparison indicates that the crowding results in compaction of the molecule as well as change in its shape, which could specifically involve regions of the molecule important in function. Crowding could thus influence the action of proteins through modulation of the functionally important plasticity of the molecule. Selvaraj M, Ahmad R, Varshney U and Vijayan M 2012 Crowding, molecular volume and plasticity: An assessment involving crystallography, NMR and simulations. J. Biosci. 37 953-963] DOI 10.1007/s12038-012-9276-5

Variation in glass transition temperature of polymer nanocomposite films driven by morphological transitions

We report the variation of glass transition temperature in supported thin films of polymer nanocomposites, consisting of polymer grafted nanoparticles embedded in a homopolymer matrix. We observe a systematic variation of the estimated glass transition temperature T-g, with the volume fraction of added polymer grafted nanoparticles. We have correlated the observed T-g variation with the underlying morphological transitions of the nanoparticle dispersion in the films. Our data also suggest the possibility of formation of a low-mobility glass or gel-like layer of nanoparticles at the interface, which could play a significant role in determining T-g of the films provided. (C) 2013 American Institute of Physics. http://dx.doi.org/10.1063/1.4773442]

A Calcium-Dependent Plasticity Rule for HCN Channels Maintains Activity Homeostasis and Stable Synaptic Learning

Theoretical and computational frameworks for synaptic plasticity and learning have a long and cherished history, with few parallels within the well-established literature for plasticity of voltage-gated ion channels. In this study, we derive rules for plasticity in the hyperpolarization-activated cyclic nucleotide-gated (HCN) channels, and assess the synergy between synaptic and HCN channel plasticity in establishing stability during synaptic learning. To do this, we employ a conductance-based model for the hippocampal pyramidal neuron, and incorporate synaptic plasticity through the well-established Bienenstock-Cooper-Munro (BCM)-like rule for synaptic plasticity, wherein the direction and strength of the plasticity is dependent on the concentration of calcium influx. Under this framework, we derive a rule for HCN channel plasticity to establish homeostasis in synaptically-driven firing rate, and incorporate such plasticity into our model. In demonstrating that this rule for HCN channel plasticity helps maintain firing rate homeostasis after bidirectional synaptic plasticity, we observe a linear relationship between synaptic plasticity and HCN channel plasticity for maintaining firing rate homeostasis. Motivated by this linear relationship, we derive a calcium-dependent rule for HCN-channel plasticity, and demonstrate that firing rate homeostasis is maintained in the face of synaptic plasticity when moderate and high levels of cytosolic calcium influx induced depression and potentiation of the HCN-channel conductance, respectively. Additionally, we show that such synergy between synaptic and HCN-channel plasticity enhances the stability of synaptic learning through metaplasticity in the BCM-like synaptic plasticity profile. Finally, we demonstrate that the synergistic interaction between synaptic and HCN-channel plasticity preserves robustness of information transfer across the neuron under a rate-coding schema. Our results establish specific physiological roles for experimentally observed plasticity in HCN channels accompanying synaptic plasticity in hippocampal neurons, and uncover potential links between HCN-channel plasticity and calcium influx, dynamic gain control and stable synaptic learning.

Revision of the scolopendrid centipede digitipes Attems, 1930, from India (Chilopoda: Scolopendromorpha): reconciling molecular and morphological estimates of species diversity

Recent work on molecular phylogenetics of Scolopendridae from the Western Ghats, Peninsular India, has suggested the presence of six cryptic species of the otostigmine Digitipes Attems, 1930, together with three species described in previous taxonomic work by Jangi and Dass (1984). Digitipes is the correct generic attribution for a monophyletic group of Indian species, these being united with three species from tropical Africa (including the type) that share a distomedial process on the ultimate leg femur of males that is otherwise unknown in Otostigminae. Second maxillary characters previously used in the diagnosis of Digitipes are dismissed because Indian species do not possess the putatively diagnostic character states. Two new species from the Western Ghats that correspond to groupings identified based on monophyly, sequence divergence and coalescent analysis using molecular data are diagnosed based on distinct morphological characters. They are D. jangii and D. periyarensis n. spp. Three species named by Jangi and Dass (Digitipes barnabasi, D. coonoorensis and D. indicus) are revised based on new collections; D. indicus is a junior subjective synonym of Arthrorhabdus jonesii Verhoeff, 1938, the combination becoming Digitipes jonesii (Verhoeff, 1938) n. comb. The presence of Arthrorhabdus in India is accordingly refuted. Three putative species delimited by molecular and ecological data remain cryptic from the perspective of diagnostic morphological characters and are presently retained in D. barnabasi, D. jangii and D. jonesii. A molecularly-delimited species that resolved as sister group to a well-supported clade of Indian Digitipes is identified as Otostigmus ruficeps Pocock, 1890, originally described from a single specimen and revised herein. One Indian species originally assigned to Digitipes, D. gravelyi, deviates from confidently-assigned Digitipes with respect to several characters and is reassigned to Otostigmus, as O. gravelyi (Jangi and Dass, 1984) n. comb.

The Relationship of Solid-State Plasticity to Mechanochromic Luminescence in Difluoroboron Avobenzone Polymorphs

In solid-state mechanochromic luminescence (ML) materials, it remains a challenge to establish the origin of fluorescence color changes upon mechanical action and to determine why only some fluorophores exhibit ML behavior. The study of mechanical properties by nanoindentation, followed by ML experiments on green- and cyan-emitting polymorphs of difluoroboron avobenzone reveals that upon smearing, the plastically deformable cyan form shows a prominent color change to yellow, while in the harder green form the redshifted emission is barely detectable. Crystal structure analysis reveals the presence of slip planes in the softer cyan form that can facilitate the formation of recoverable and low energy defects in the structure. Hence, the cyan form exhibits prominent and reversible ML behavior. This suggests a potential design strategy for efficient ML materials.

Quantitative interactions between the A-type K+ current and inositol trisphosphate receptors regulate intraneuronal Ca2+ waves and synaptic plasticity

Key points center dot Active calcium signal propagation occurs when an initial calcium trigger elicits calcium release through endoplasmic reticulum (ER) receptors. A high concentration of the calcium trigger in thin-calibre dendrites would suppress release of calcium through hippocampal inositol trisphosphate receptors (InsP3Rs). center dot Could the high-density expression of A-type K+ channels in thin-calibre dendrites be a mechanism for inhibiting this suppression, thereby restoring the utility of the ER as a substrate for active calcium propagation? center dot Quantitative analyses involving experimentally constrained models reveal a bell-shaped dependence of calcium released through InsP3Rs on the A-type K+ channel density, during the propagation of a calcium wave. center dot A-type K+ channels regulated the relative contribution of ER calcium to the induction of synaptic plasticity in the presence of model metabotropic glutamate receptors. center dot These results identify a novel form of interaction between active dendrites and the ER membrane and suggest that A-type K+ channels are ideally placed for inhibiting the suppression of InsP3Rs in thin-calibre dendrites. Abstract The A-type potassium current has been implicated in the regulation of several physiological processes. Here, we explore a role for the A-type potassium current in regulating the release of calcium through inositol trisphosphate receptors (InsP3R) that reside on the endoplasmic reticulum (ER) of hippocampal pyramidal neurons. To do this, we constructed morphologically realistic, conductance-based models equipped with kinetic schemes that govern several calcium signalling modules and pathways, and constrained the distributions and properties of constitutive components by experimental measurements from these neurons. Employing these models, we establish a bell-shaped dependence of calcium release through InsP3Rs on the density ofA-type potassium channels, during the propagation of an intraneuronal calcium wave initiated through established protocols. Exploring the sensitivities of calcium wave initiation and propagation to several underlying parameters, we found that ER calcium release critically depends on dendritic diameter and that wave initiation occurred at branch points as a consequence of a high surface area to volume ratio of oblique dendrites. Furthermore, analogous to the role ofA-type potassium channels in regulating spike latency, we found that an increase in the density ofA-type potassium channels led to increases in the latency and the temporal spread of a propagating calcium wave. Next, we incorporated kinetic models for the metabotropic glutamate receptor (mGluR) signalling components and a calcium-controlled plasticity rule into our model and demonstrate thatthe presence of mGluRs induced a leftward shift in a BienenstockCooperMunro-like synaptic plasticity profile. Finally, we show that the A-type potassium current could regulate the relative contribution of ER calcium to synaptic plasticity induced either through 900 pulses of various stimulus frequencies or through theta burst stimulation. Our results establish a novel form of interaction between active dendrites and the ER membrane, uncovering a powerful mechanism that could regulate biophysical/biochemical signal integration and steer the spatiotemporal spread of signalling microdomains through changes in dendritic excitability.

Nanocomposites of crosslinked starch phthalate and silane modified nanoclay: Study of mechanical, thermal, morphological, and biodegradable characteristics

Biodegradable composites comprising of modified starch and modified nanoclay have been prepared. Starch has been modified by esterification and subsequently crosslinked. The thermal, mechanical, and biodegradation characteristics of the composites have been investigated. The compressive properties of the composites with the addition of nanoclay were twice that of crosslinked starch phthalate without addition of nanoclay. Predictive theories were used to analyze the obtained experimental results. SEM studies on fracture morphology indicated quasi-brittle fracture. Flexural properties showed considerable improvement due to nanoclay addition. The water uptake increased up to 6% nanoclay, beyond which the uptake decreased. Biodegradation studies showed an initial time lag prior to the onset of degradation.

Out of equilibrium plasticity dynamics and the annealing of supersolidity in solid He-4

We present a numerical study of a continuum plasticity field coupled to a Ginzburg-Landau model for superfluidity. The results suggest that a supersolid fraction may appear as a long-lived transient during the time evolution of the plasticity field at higher temperatures where both dislocation climb and glide are allowed. Supersolidity, however, vanishes with annealing. As the temperature is decreased, dislocation climb is arrested and any residual supersolidity due to incomplete annealing remains frozen. Our results may provide a resolution of many perplexing issues concerning a variety of experiments on bulk solid He-4.

Influence of annealing on structural, morphological, compositional and surface properties of magnetron sputtered nickel-titanium thin films

Thin films of NiTi were deposited by DC magnetron sputtering from an equiatomic alloy target (Ni/Ti: 50/50 at.%). The films were deposited without intentional heating of the substrates. The thickness of the deposited films was approximately 2 mu m. The structure and morphology of NiTi films annealed at different temperatures were analyzed in order to understand the effect of annealing on physical properties of the films. The compositional investigations of fresh and annealed films were also evaluated by energy dispersive X-ray spectroscopy (EDS) and X-ray photo-electron spectroscopy (XPS) techniques. X-ray diffraction (XRD) studies showed that as-deposited films were amorphous in nature whereas annealed films were found to poly-crystalline with the presence of Austenite phase as the dominant phase. AFM investigations showed higher grain size and surface roughness values in the annealed films. In annealed films, the grain size and film roughness values were increased from 10 to 85 nm and 2-18 nm. Film composition measured by EDS were found to 52.5 atomic percent of Ni and 47.5 atomic percent of Ti. XPS investigations, demonstrated the presence of Ni content on the surface of the films, in fresh films, whereas annealed films did not show any nickel. From HR-XPS investigations, it can be concluded that annealed NiTi films have higher tendency to form metal oxide (titanium dioxide) layer on the surface of the films than fresh NiTi films. (C) 2013 Elsevier B. V. All rights reserved.

Morphological and electrochemical characterization of electrodeposited Zn-Ag nanoparticle composite coatings

Silver nanoparticles with an average size of 23 nm were chemically synthesized and used to fabricate Zn-Ag composite coatings. The Zn-Ag composite coatings were generated by electrodeposition method using a simple sulfate plating bath dispersed with 0.5, land 1.5 g/l of Ag nanoparticles. Scanning electron microscopy, X-ray diffraction and texture co-efficient calculations revealed that Ag nanoparticles appreciably influenced the morphology, micro-structure and texture of the deposit. It was also noticed that agglomerates of Ag nanopartides, in the case of high bath load conditions, produced defects and dislocations on the deposit surface. Ag nanoparticles altered the corrosion resistance property of Zn-Ag composite coatings as observed from Tafel polarization, electrochemical impedance analysis and an immersion test. Reduction in corrosion rate with increased charge transfer resistance was observed for Zn-Ag composite coatings when compared to a pure Zn coating. However, the particle concentration in the plating bath and their agglomeration state directly influenced the surface morphology and the subsequent corrosion behavior of the deposits. (C) 2013 Elsevier Inc. All rights reserved.