Structural basis for the functional and inhibitory mechanisms of beta-hydroxyacyl-acyl carrier protein dehydratase (FabZ) of Plasmodium falciparum

The beta-hydroxyacyl-acyl carrier protein dehydratase of Plasmodium falciparum (PfFabZ) catalyzes the third and important reaction of the fatty acid elongation cycle. The crystal structure of PfFabZ is available in hexameric (active) and dimeric (inactive) forms. However, PfFabZ has not been crystallized with any bound inhibitors until now. We have designed a new condition to crystallize PfFabZ with its inhibitors bound in the active site, and determined the crystal structures of four of these complexes. This is the first report on any FabZ enzyme with active site inhibitors that interact directly with the catalytic residues. Inhibitor binding not only stabilized the substrate binding loop but also revealed that the substrate binding tunnel has an overall shape of ``U''. In the crystal structures, residue Phe169 located in the middle of the tunnel was found to be in two different conformations, open and closed. Thus, Phe169, merely by changing its side chain conformation, appears to be controlling the length of the tunnel to make it suitable for accommodating longer substrates. The volume of the substrate binding tunnel is determined by the sequence as well as by the conformation of the substrate binding loop region and varies between organisms for accommodating fatty acids of different chain lengths. This report on the crystal structures of the complexes of PfFabZ provides the structural basis of the inhibitory mechanism of the enzyme that could be used to improve the potency of inhibitors against an important component of fatty acid synthesis common to many infectious organisms. (C) 2011 Elsevier Inc. All rights reserved.

Hydrothermal synthesis of CdTe QDs: Their luminescence quenching in the presence of bio-molecules and observation of bistable memory effect in CdTe QD/PEDOT:PSS heterostructure

We report one-pot hydrothermal synthesis of nearly mono-disperse 3-mercaptopropionic acid capped water-soluble cadmium telluride (CdTe) quantum dots (QDs) using an air stable Te source. The optical and electrical characteristics were also studied here. It was shown that the hydrothermal synthesis could be tuned to synthesize nano structures of uniform size close to nanometers. The emissions of the CdTe QDs thus synthesized were in the range of 500-700 nm by varying the duration of synthesis. The full width at half maximum (FWHM) of the emission peaks is relatively narrow (40-90 nm), which indicates a nearly uniform distribution of QD size. The structural and optical properties of the QDs were characterized by transmission electron microscopy (TEM), photoluminescence (PL) and Ultraviolet-visible (UV-Vis) spectroscopy. The photoluminescence quenching of CdTe QDs in the presence of L-cysteine and DNA confirms its biocompatibility and its utility for biosensing applications. The room temperature current-voltage characteristics of QD film on ITO coated glass substrate show an electrically induced switching between states with high and low conductivities. The phenomenon is explained on the basis of charge confinement in quantum dots. (C) 2011 Elsevier B.V. All rights reserved.

A Kinematic Theory for Planar Hoberman and Other Novel Foldable Mechanisms

In this paper, we present a kinematic theory for Hoberman and other similar foldable linkages. By recognizing that the building blocks of such linkages can be modeled as planar linkages, different classes of possible solutions are systematically obtained including some novel arrangements. Criteria for foldability are arrived by analyzing the algebraic locus of the coupler curve of a PRRP linkage. They help explain generalized Hoberman and other mechanisms reported in the literature. New properties of such mechanisms including the extent of foldability, shape-preservation of the inner and outer profiles, multi-segmented assemblies and heterogeneous circumferential arrangements are derived. The design equations derived here make the conception of even complex planar radially foldable mechanisms systematic and easy. Representative examples are presented to illustrate the usage of the design equations and the kinematic theory.

An Objective Evaluation of Displacement-Amplifying Compliant Mechanisms for Sensor Applications

Displacement-amplifying compliant mechanisms (DaCMs) reported in literature are mostly used for actuator applications. This paper considers them for sensor applications that rely on displacement measurement, and evaluates them objectively. The main goal is to increase the sensitivity under constraints imposed by several secondary requirements and practical constraints. A spring-mass-lever model that effectively captures the addition of a DaCM to a sensor is used in comparing eight DaCMs. We observe that they significantly differ in performance criteria such as geometric advantage, stiffness, natural frequency, mode amplification, factor of safety against failure, cross-axis stiffness, etc., but none excel in all. Thus, a combined figure of merit is proposed using which the most suitable DaCM could be selected for a sensor application. A case-study of a micro machined capacitive accelerometer and another case-study of a vision-based force sensor are included to illustrate the general evaluation and selection procedure of DaCMs with specific applications. Some other insights gained with the analysis presented here were the optimum size-scale for a DaCM, the effect on its natural frequency, limits on its stiffness, and working range of the sensor.

Synthesis from zinc oxalate, growth mechanism and optical properties of ZnO nano/micro structures

We report the synthesis of various morphological micro to nano structured zinc oxide crystals via simple precipitation technique. The growth mechanisms of the zinc oxide nanostructures such as snowflake, rose, platelets, porous pyramid and rectangular shapes were studied in detail under various growth conditions. The precursor powders were prepared using several zinc counter ions such as chloride, nitrate and sulphate along with oxalic acid as a precipitating agent. The precursors were decomposed by heating in air resulting in the formation of different shapes of zinc oxide crystals. Variations in ZnO nanostructural shapes were possibly due to the counter ion effect. Sulphate counter ion led to unusual rose-shape morphology. Strong ultrasonic treatment on ZnO rose shows that it was formed by irregular arrangement of micro to nano size hexagonal zinc oxide platelets. The X-ray diffraction studies confirmed the wurzite structure of all zinc oxide samples synthesized using different zinc counter ions. Functional groups of the zinc oxalate precursor and zinc oxide were identified using micro Raman studies. The blue light emission spectra of the various morphologies were recorded using luminescence spectrometer. (C) 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim

Mechanisms of summer intraseasonal sea surface temperature oscillations in the Bay of Bengal

Intraseasonal variations (ISV) of sea surface temperature (SST) in the Bay of Bengal (BoB) is highest in its northwestern part. An Indian Ocean model forced by QuikSCAT winds and climatological river discharge (QR run) reproduces ISV of SST, albeit with weaker magnitude. Air-sea fluxes, in the presence of a shallow mixed layer, efficiently effect intraseasonal SST fluctuations. Warming during intraseasonal events is smaller (<1°C) for June - July period and larger (1.5° to 2°C) during September, the latter due to a thinner mixed layer. To examine the effect of salinity on ISV, the model was run by artificially increasing the salinity (NORR run) and by decreasing it (MAHA10 run). In NORR, both rainfall and river discharge were switched off and in MAHA10 the discharge by river Mahanadi was increased tenfold. The spatial pattern of ISV as well as its periodicity was similar in QR, NORR and MAHA10. The ISV was stronger in NORR and weaker in MAHA10, compared to QR. In NORR, both intraseasonal warming and cooling were higher than in QR, the former due to reduced air-sea heat loss as the mean SST was lower, and the latter due to enhanced subsurface processes resulting from weaker stratification. In MAHA10, both warming and cooling were lower than in QR, the former due to higher air-sea heat loss owing to higher mean SST, and the latter due to weak subsurface processes resulting from stronger stratification. These model experiments suggest that salinity effects are crucial in determining amplitudes of intraseasonal SST variations in the BoB.

Dislocation mechanisms for plastic flow of nickel in the temperature range 4.2 – 1200 K

The temperature ranges of thermal and athermal deformation behaviour of nickel are identified by employing the temperature-dependence of flow-stress and strain-rate cycling data. The results are used to present a unified view of dislocation mechanisms of glide encompassing the two thermally activated and the intermediate athermal regimes of plastic flow.In the low-temperature thermally activated region (<250 K) the strain rate is found to be controlled by the repulsive intersection of glide and forest dislocations, in accordance with current ideas. The athermal stress in this region can be attributed mainly to the presence of strong attractive junctions which are overcome by means of Orowan bowing, a small contribution also coming from the elastic interactions between dislocations. The values of activation area and activation energy obtained in the high-temperature region (> 750 K) negate the operation of a diffusion-controlled mechanism. Instead, the data support a thermal activation model involving unzipping of the attractive junctions. The internal (long-range) stress contribution here results solely from the elastic interactions between dislocations. This view concerning the high-temperature plastic flow is further supported by the observation that the Cottrell–Stokes law is obeyed over large strains in the range 750–1200 K.

Some mechanisms of tribofilm formation in metal/metal and ceramic/metal sliding interactions

Tribological interaction often generates new structures and materials which form the interface between the sliding pair. The new material designated tribofilm here may be protective or tribologically deleterious. The tribofilm plays a major role in determining the friction and wear of the interaction. Here, we give three examples: mechanically mixed, chemically generated and thermally activated, of tribofilms formed in three different tribological systems and speculate on the mechanism of their formation.

Solvent effect on the fluorescence quenching of biologically active carboxamide by aniline and carbon tetrachloride in different solvents using S-V plots

The fluorescence quenching studies of carboxamide namely (E)-N-(3-Chlorophenyl)-2-(3,4,5-trimethoxybenzylideneamino)-4,5,6,7 tetrahydrobenzob]thiophene-3-carboxamide ENCTTTC] by aniline and carbon tetrachloride in six different solvents namely toluene, cyclohexane, n-hexane, n-heptane, n-decane and n-pentane have been carried out at room temperature with a view to understand the quenching mechanisms. The Stern-Volmer (S-V) plots have been found to be nonlinear with a positive deviation for all the solvents studied. In order to interpret these results we have invoked the ground state complex formation and sphere of action static quenching models. Using these models various quenching rate parameters have been determined. The magnitudes of these parameters suggest that sphere of action static quenching model agrees well with the experimental results. Hence the positive deviation is attributed to the static and dynamic quenching. Further, with the use of Finite Sink approximation model, it was possible to check these bimolecular reactions as diffusion-limited and to estimate independently distance parameter R' and mutual diffusion coefficient D. Finally an effort has been made to correlate the values of R' and D with the values of the encounter distance R and the mutual coefficient D determined using the Edward's empirical relation and Stokes Einstein relation. (C) 2011 Elsevier B.V. All rights reserved.

A novel ``pro-sensitizer'' based sensing of enzymes using Tb(III) luminescence in a hydrogel matrix

Chemically synthesized ``pro-sensitizers'' release the sensitizer in the presence of lipase or beta-glucosidase, triggering a significant luminescence response from a lanthanide based hydrogel.

Synthesis of one-dimensional N-doped Ga2O3 nanostructures: different morphologies and different mechanisms

N-doped monoclinic Ga2O3 nanostructures of different morphologies have been synthesized by heating Ga metal in ambient air at 1150 degrees C to 1350 degrees C for 1 to 5 h duration. Neither catalyst nor any gas flow has been used for the synthesis of N-doped Ga2O3 nanostructures. The morphology was controlled by monitoring the curvature of the Ga droplet. Plausible growth mechanisms are discussed to explain the different morphology of the nanostructures. Elemental mapping by electron energy loss spectroscopy of the nanostructures indicate uniform distribution of Ga, O and N. It is interesting to note that we have used neither nitride source nor any gas flow but the synthesis was carried out in ambient air. We believe that ambient nitrogen acts as the source of nitrogen. Unintentional nitrogen doping of the Ga2O3 nanostructures is a straightforward method and such nanostructures could be promising candidates for white light emission.

Distinct mechanisms of DNA repair in mycobacteria and their implications in attenuation of the pathogen growth

About a third of the human population is estimated to be infected with Mycobacterium tuberculosis. Emergence of drug resistant strains and the protracted treatment strategies have compelled the scientific community to identify newer drug targets, and to develop newer vaccines. In the host macrophages, the bacterium survives within an environment rich in reactive nitrogen and oxygen species capable of damaging its genome. Therefore, for its successful persistence in the host, the pathogen must need robust DNA repair mechanisms. Analysis of M. tuberculosis genome sequence revealed that it lacks mismatch repair pathway suggesting a greater role for other DNA repair pathways such as the nucleotide excision repair, and base excision repair pathways. In this article, we summarize the outcome of research involving these two repair pathways in mycobacteria focusing primarily on our own efforts. Our findings, using Mycobacterium smegmatis model, suggest that deficiency of various DNA repair functions in single or in combinations severely compromises their DNA repair capacity and attenuates their growth under conditions typically encountered in macrophages. (C) 2011 Elsevier Ireland Ltd. All rights reserved.

Synthesis, luminescence and EPR studies on CaSiO 3: Pb, Mn-nano phosphors synthesized by the solution combustion method

Nano-ceramic phosphor CaSiO 3 doped with Pb and Mn was synthesized by the low temperature solution combustion method. The materials were characterized by Powder X-Ray Diffraction (XRD), Thermo-gravimetric and Differential Thermal Analysis (TG-DTA), Scanning Electron Microscopy (SEM) and Transmission Electron Microscopy (TEM). The Electron Paramagnetic Resonance (EPR) spectrum of the investigated sample exhibits a broad resonance signal centered at g=1.994. The number of spins participating in resonance (N) and its paramagnetic susceptibility (�) have been evaluated. Photoluminescence of doped CaSiO 3 was investigated when excited by UV radiation of 256 nm. The phosphor exhibits an emission peak at 353 nm in the UV range due to Pb 2+. Further, a broad emission peak in the visible range 550-625 nm can be attributed to 4T 1� 6A 1 transition of Mn 2+ ions. The investigation reveals that doping perovskite nano-ceramics with transition metal ions leads to excellent phosphor materials for potential applications. © 2012 Elsevier Ltd and Techna Group S.r.l.