The Escherichia coli Phosphotyrosine Proteome Relates to Core Pathways and Virulence

While phosphotyrosine modification is an established regulatory mechanism in eukaryotes, it is less well characterized in bacteria due to low prevalence. To gain insight into the extent and biological importance of tyrosine phosphorylation in Escherichia coli, we used immunoaffinity-based phosphotyrosine peptide enrichment combined with high resolution mass spectrometry analysis to comprehensively identify tyrosine phosphorylated proteins and accurately map phosphotyrosine sites. We identified a total of 512 unique phosphotyrosine sites on 342 proteins in E. coli K12 and the human pathogen enterohemorrhagic E. coli (EHEC) O157:H7, representing the largest phosphotyrosine proteome reported to date in bacteria. This large number of tyrosine phosphorylation sites allowed us to define five phosphotyrosine site motifs. Tyrosine phosphorylated proteins belong to various functional classes such as metabolism, gene expression and virulence. We demonstrate for the first time that proteins of a type III secretion system (T3SS), required for the attaching and effacing (A/E) lesion phenotype characteristic for intestinal colonization by certain EHEC strains, are tyrosine phosphorylated by bacterial kinases. Yet, A/E lesion and metabolic phenotypes were unaffected by the mutation of the two currently known tyrosine kinases, Etk and Wzc. Substantial residual tyrosine phosphorylation present in an etk wzc double mutant strongly indicated the presence of hitherto unknown tyrosine kinases in E. coli. We assess the functional importance of tyrosine phosphorylation and demonstrate that the phosphorylated tyrosine residue of the regulator SspA positively affects expression and secretion of T3SS proteins and formation of A/E lesions. Altogether, our study reveals that tyrosine phosphorylation in bacteria is more prevalent than previously recognized, and suggests the involvement of phosphotyrosine-mediated signaling in a broad range of cellular functions and virulence.

Analysis of size quantization and temperature effects on the threshold voltage of thin silicon film double-gate metal-oxide-semiconductor field-effect transistor (MOSFET)

In this paper, we analyze the combined effects of size quantization and device temperature variations (T = 50K to 400 K) on the intrinsic carrier concentration (n(i)), electron concentration (n) and thereby on the threshold voltage (V-th) for thin silicon film (t(si) = 1 nm to 10 nm) based fully-depleted Double-Gate Silicon-on-Insulator MOSFETs. The threshold voltage (V-th) is defined as the gate voltage (V-g) at which the potential at the center of the channel (Phi(c)) begins to saturate (Phi(c) = Phi(c(sat))). It is shown that in the strong quantum confinement regime (t(si) <= 3nm), the effects of size quantization far over-ride the effects of temperature variations on the total change in band-gap (Delta E-g(eff)), intrinsic carrier concentration (n(i)), electron concentration (n), Phi(c(sat)) and the threshold voltage (V-th). On the other hand, for t(si) >= 4 nm, it is shown that size quantization effects recede with increasing t(si), while the effects of temperature variations become increasingly significant. Through detailed analysis, a physical model for the threshold voltage is presented both for the undoped and doped cases valid over a wide-range of device temperatures, silicon film thicknesses and substrate doping densities. Both in the undoped and doped cases, it is shown that the threshold voltage strongly depends on the channel charge density and that it is independent of incomplete ionization effects, at lower device temperatures. The results are compared with the published work available in literature, and it is shown that the present approach incorporates quantization and temperature effects over the entire temperature range. We also present an analytical model for V-th as a function of device temperature (T). (C) 2013 AIP Publishing LLC.

Novel procedure for the estimation of swelling pressures of compacted bentonites based on diffuse double layer theory

Bentonite clays are proven to be attractive as buffer and backfill material in high-level nuclear waste repositories around the world. A quick estimation of swelling pressures of the compacted bentonites for different clay-water-electrolyte interactions is essential in the design of buffer and backfill materials. The theoretical studies on the swelling behavior of bentonites are based on diffuse double layer (DDL) theory. To establish theoretical relationship between void ratio and swelling pressure (e versus P), evaluation of elliptic integral and inverse analysis are unavoidable. In this paper, a novel procedure is presented to establish theoretical relationship of e versus P based on the Gouy-Chapman method. The proposed procedure establishes a unique relationship between electric potentials of interacting and non-interacting diffuse clay-water-electrolyte systems. A procedure is, thus, proposed to deduce the relation between swelling pressures and void ratio from the established relation between electric potentials. This approach is simple and alleviates the need for elliptic integral evaluation and also the inverse analysis. Further, application of the proposed approach to estimate swelling pressures of four compacted bentonites, for example, MX 80, Febex, Montigel and Kunigel V1, at different dry densities, shows that the method is very simple and predicts solutions with very good accuracy. Moreover, the proposed procedure provides continuous distributions of e versus P and thus it is computationally efficient when compared with the existing techniques.

Plasmons in spatially separated rolled-up electron-hole double-layer systems

Using the two-component random phase approximation, we report the collective mode spectrum of a quasi-one-dimensional spatially separated electron-hole double-layer system characterized by rolled-up type-II band aligned quantum wells. We find two intra-subband collective excitations, which can be classified into optic and acoustic plasmon branches, and several inter-subband plasmon modes. At the long wavelength limit and up to a given wave vector, our model predicts and admits an undamped acoustic branch, which always lies in the gap between the intra-subband electron and hole continua, and an undamped optic branch residing within the gap between the inter-subband electron and hole continua, for all values of the electron-hole charge separations. This theoretical investigation suggests that the low-energy and Landau-undamped plasmon modes might exist based on quasi-one-dimensional, two-component spatially separated electron-hole plasmas, and their possibility could be experimentally examined. (C) 2013 AIP Publishing LLC.

Microwave, infrared-microwave double resonance, and theoretical studies of C2H4 center dot center dot center dot H2S complex

In this manuscript, rotational spectra of four new isotopologues of the S-H center dot center dot center dot pi bonded C2H4 center dot center dot center dot H2S complex, i.e., C2D4 center dot center dot center dot H2S, C2D4 center dot center dot center dot D2S, C2D4 center dot center dot center dot HDS, and (CCH4)-C-13 center dot center dot center dot H2S have been reported and analyzed. All isotopologues except C2D4 center dot center dot center dot HDS show a four line pattern whereas a doubling of the transition frequencies was observed for C2D4 center dot center dot center dot HDS. These results together with our previous report on the title complex M. Goswami, P. K. Mandal, D. J. Ramdass, and E. Arunan, Chem. Phys. Lett. 393(1-3), 22-27 (2004)] confirm that both subunits (C2H4 and H2S) are involved in large amplitude motions leading to a splitting of each rotational transition to a quartet. Further, the results also confirm that the motions which are responsible for the observed splittings involve both monomers. Molecular symmetry group analysis, considering the interchange of equivalent H atoms in H2S and C2H4 could explain the observed four line pattern and their intensities in the microwave spectrum. In addition, hydride stretching fundamentals of the complex were measured using coherence-converted population transfer Fourier Transform Microwave-infrared (IR-MW double resonance) experiments in the S-H and C-H stretch regions. Changes in the tunneling splittings upon vibrational excitation are consistent with the isotopic dependence of pure rotational transitions. A complexation shift of 2.7-6.5 cm(-1) has been observed in the two fundamental S-H stretching modes of the H2S monomer in the complex. Vibrational pre-dissociation in the bound S-H stretch has been detected whereas the instrument-limited line-shapes in other S-H and C-H stretches indicate slower pre-dissociation rate. Some local perturbations in the vibrational spectra have been observed. Two combination bands have been observed corresponding to both the S-H stretching fundamentals and what appears to be the intermolecular stretching mode at 55 cm(-1). The tunneling splitting involved in the rotation of C2H4 unit has been deduced to be 1.5 GHz from the IR-MW results. In addition, ab initio barrier heights derived for different motions of the monomers support the experimental results and provide further insight into the motions causing the splitting. (C) 2013 AIP Publishing LLC.

The Modified Selenenyl Amide, M-hydroxy Ebselen, Attenuates Diabetic Nephropathy and Diabetes-Associated Atherosclerosis in ApoE/GPx1 Double Knockout Mice

Seleno-organic glutathione peroxidase (GPx) mimetics, including ebselen (Eb), have been tested in in vitro studies for their ability to scavenge reactive oxygen and nitrogen species, including hydrogen peroxide and peroxynitrite. In this study, we investigated the efficacies of two Eb analogues, m-hydroxy ebselen (ME) and ethanol-ebselen (EtE) and compared these with Eb in cell based assays. We found that ME is superior in attenuating the activation of hydrogen peroxide-induced pro-inflammatory mediators, ERK and P38 in human aortic endothelial cells. Consequently, we investigated the effects of ME in an in vivo model of diabetes, the ApoE/GPx1 double knockout (dKO) mouse. We found that ME attenuates plaque formation in the aorta and lesion deposition within the aortic sinus of diabetic dKO mice. Oxidative stress as assessed by 8-OHdG in urine and nitrotyrosine immunostaining in the aortic sinus and kidney tubules, was reduced by ME in diabetic dKO mice. ME also attenuated diabetes-associated renal injury which included tubulointerstitial fibrosis and glomerulosclerosis. Furthermore, the bioactivity of the pro-fibrotic cytokine transforming growth factor-beta (TGF-beta) as assessed by phospho-Smad2/3 immunostaining was attenuated after treatment with ME. TGF-beta-stimulated increases in collagen I and IV gene expression and protein levels were attenuated by ME in rat kidney tubular cells. However, in contrast to the superior activity of ME in in vitro and cell based assays, ME did not further augment the attenuation of diabetes-associated atherosclerosis and renal injury in our in vivo model when compared with Eb. In conclusion, this study strengthens the notion that bolstering GPx-like activity using synthetic mimetics may be a useful therapeutic strategy in lessening the burden of diabetic complications. However, these studies highlight the importance of in vivo analyses to test the efficacies of novel Eb analogues, as in vitro and cell based assays are only partly predictive of the in vivo situation.

Frustration induced oscillator death on networks

An array of identical maps with Ising symmetry, with both positive and negative couplings, is studied. We divide the maps into two groups, with positive intra-group couplings and negative inter-group couplings. This leads to antisynchronization between the two groups which have the same stability properties as the synchronized state. Introducing a certain degree of randomness in signs of these couplings destabilizes the anti-synchronized state. Further increasing the randomness in signs of these couplings leads to oscillator death. This is essentially a frustration induced phenomenon. We explain the observed results using the theory of random matrices with nonzero mean. We briefly discuss applications to coupled differential equations. (C) 2013 AIP Publishing LLC.

Modeling and analysis of MOS capacitor controlled by independent double gates

This paper, for the first time, explores the charcatersictics of MOS capacitor controlled by independent double gates by numerical simulation and analytical modeling for its possible use in RF circuit design as a varactor. By numerical simulation it is shown how the quasi-static and non-quasi-static characteristics of the first gate capacitance could be tuned by the second gate biases. Effect of body doping and energy quantization are also discussed in this regard. A semi-empirical quasi-static model is also developed by using the existing incomplete Poisson solution of independent double gate transistors. Proposed model, which is valid from accumulation to inversion, is shown to have excellent agreement with numerical simulation for practical bias conditions.

Environments of extended radio sources in the Australia Telescope Low-Brightness Survey

We present a study of the environments of extended radio sources in the Australia Telescope Low-Brightness Survey (ATLBS). The radio sources were selected from the ATLBS Extended Source Sample, which is a well defined sample containing the most extended of radio sources in the ATLBS sky survey regions. The environments were analysed using 4-m Cerro-Tololo Inter-American Observatory Blanco telescope observations carried out for ATLBS fields in the Sloan Digital Sky Survey r(') band. We have estimated the properties of the environments using smoothed density maps derived from galaxy catalogues constructed using these optical imaging data. The angular distribution of galaxy density relative to the axes of the radio sources has been quantified by defining anisotropy parameters that are estimated using a new method presented here. Examining the anisotropy parameters for a subsample of extended double radio sources that includes all sources with pronounced asymmetry in lobe extents, we find good evidence for environmental anisotropy being the dominant cause for lobe asymmetry in that higher galaxy density occurs almost always on the side of the shorter lobe, and this validates the usefulness of the method proposed and adopted here. The environmental anisotropy parameters have been used to examine and compare the environments of Fanaroff-Riley Class I (FRI) and Fanaroff-Riley Class II (FRII) radio sources in two redshift regimes (z < 0.5 and z > 0.5). Wide-angle tail sources and head-tail sources lie in the most overdense environments. The head-tail source environments (for the HT sources in our sample) display dipolar anisotropy in that higher galaxy density appears to lie in the direction of the tails. Excluding the head-tail and wide-angle tail sources, subsamples of FRI and FRII sources from the ATLBS appear to lie in similar moderately overdense environments, with no evidence for redshift evolution in the regimes studied herein.

Design of double toggle switching mechanisms

Toggle mechanisms are ubiquitous in electrical switches. However, literature for their mechanical design is scarce. This paper defines and classifies the toggle phenomena observed during switching. The concept of double toggle introduced in this paper enables a systematic screening of kinematic structure for the suitability in high performance switches. Seven structural and three kinematic criteria are identified for this purpose. It is also demonstrated that each such feasible kinematic structure lends itself to multiple physical embodiments. Therefore, the theory and procedure presented in this work can be used for design of numerous kinematically distinct mechanisms. One representative mechanical embodiment for a novel double toggle switch, including mass and geometric shape of links has been included in the paper. The switching behavior of the design is validated using Pro/Mechanism (TM). (C) 2013 Elsevier Ltd. All rights reserved.

Compressibility behaviour of bentonite and organically modified bentonite slurry

Bentonite in slurry walls needs to be amended with organo-clay to control the migration of organic contaminants. Consolidation behaviour of the slurry is important because it will reduce the total effective stress owing to mobilisation of frictional force between the side wall of the trench and the slurry. Compressibility of the slurry of bentonite is expected to undergo significant changes owing to amendment with organo-clay and according to the nature of the fluid. Standard one-dimensional consolidation tests were carried out on slurries of bentonite, organo-clay and their mixtures by remoulding them to their respective liquid limit consistency with water as well as fluids of low polarity, such as carbon tetrachloride, and inundating with different fluids. Organo-clay and its mixture with bentonite when moulded with water exhibit lower compressibility than bentonite in any pore fluid, but their compressibility increases when moulded with carbon tetrachloride and inundated with the same fluid. These changes in the compressibility of bentonite amended with organo-clay are explained by particle rearrangements, changes in the development of the diffuse double layer and contribution from the water adsorbed in the inter-lamellar space of the clay.

Glassy dielectric response in Tb2NiMnO6 double perovskite with similarities to a Griffiths phase

Results of frequency-dependent and temperature-dependent dielectric measurements performed on the double-perovskite Tb2NiMnO6 are presented. The real (epsilon(1)(f,T)) and imaginary (epsilon(2)(f,T)) parts of dielectric permittivity show three plateaus suggesting dielectric relaxation originating from the bulk, grain boundaries and the sample-electrode interfaces, respectively. The epsilon(1)(f,T) and epsilon(2)(f,T) are successfully simulated by a RC circuit model. The complex plane of impedance, Z'-Z `', is simulated using a series network with a resistor R and a constant phase element. Through the analysis of epsilon(f,T) using the modified Debye model, two different relaxation time regimes separated by a characteristic temperature, T*, are identified. The temperature variation of R and C corresponding to the bulk and the parameter alpha from modified Debye fit lend support to this hypothesis. Interestingly, the T* compares with the Griffiths temperature for this compound observed in magnetic measurements. Though these results cannot be interpreted as magnetoelectric coupling, the relationship between lattice and magnetism is markedly clear. We assume that the observed features have their origin in the polar nanoregions which originate from the inherent cationic defect structure of double perovskites. Copyright (C) EPLA, 2013

Quantum chemical study on influence of intermolecular hydrogen bonding on the geometry, the atomic charges and the vibrational dynamics of 2,6-dichlorobenzonitrile

FT-IR (4000-400 cm(-1)) and FT-Raman (4000-200 cm(-1)) spectral measurements on solid 2,6-dichlorobenzonitrile (2,6-DCBN) have been done. The molecular geometry, harmonic vibrational frequencies and bonding features in the ground state have been calculated by density functional theory at the B3LYP/6-311++G (d,p) level. A comparison between the calculated and the experimental results covering the molecular structure has been made. The assignments of the fundamental vibrational modes have been done on the basis of the potential energy distribution (PED). To investigate the influence of intermolecular hydrogen bonding on the geometry, the charge distribution and the vibrational spectrum of 2,6-DCBN; calculations have been done for the monomer as well as the tetramer. The intermolecular interaction energies corrected for basis set superposition error (BSSE) have been calculated using counterpoise method. Based on these results, the correlations between the vibrational modes and the structure of the tetramer have been discussed. Molecular electrostatic potential (MEP) contour map has been plotted in order to predict how different geometries could interact. The Natural Bond Orbital (NBO) analysis has been done for the chemical interpretation of hyperconjugative interactions and electron density transfer between occupied (bonding or lone pair) orbitals to unoccupied (antibonding or Rydberg) orbitals. UV spectrum was measured in methanol solution. The energies and oscillator strengths were calculated by Time Dependent Density Functional Theory (TD-DFT) and matched to the experimental findings. TD-DFT method has also been used for theoretically studying the hydrogen bonding dynamics by monitoring the spectral shifts of some characteristic vibrational modes involved in the formation of hydrogen bonds in the ground and the first excited state. The C-13 nuclear magnetic resonance (NMR) chemical shifts of the molecule were calculated by the Gauge independent atomic orbital (GIAO) method and compared with experimental results. Standard thermodynamic functions have been obtained and changes in thermodynamic properties on going from monomer to tetramer have been presented. (C) 2013 Elsevier B.V. All rights reserved.

Laser- induced optical properties change in Sb10S40Se50 chalcogenide thin films: An investigation through FTIR and XPS measurements

Chalcogenide glasses are interesting materials for their infrared transmitting properties and photo-induced effects. This paper reports the influence of light on the optical properties of Sb10S40Se50 thin films. The amorphous nature and chemical composition of the deposited film was studied by X-ray diffraction and energy dispersive X-ray analysis (EDAX). The optical constants, i.e., refractive index, extinction coefficient, and optical band gap as well as film thickness are determined from the measured transmission spectra using the Swanepoel method. The dispersion of the refractive index is discussed in terms of the single-oscillator Wemple-DiDomenico model. The dispersion energy parameter was found to be less for the laser-irradiated film, which indicates the laser-irradiated film is more microstructurally disordered as compared to the as-prepared film. It is observed that laser-irradiation of the films leads to decrease in optical band gap (photo-darkening) while increase in refractive index. The decrease in the optical band gap is explained on the basis of change in nature of films due to chemical disorderness and the increase in refractive index may be due to the densification of films with improved grain structure because of microstructural disorderness in the films. The optical changes are supported by X-ray photoelectron spectroscopy data. (C) 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim

Temperature dependent magnetic, dielectric and Raman studies of partially disordered La2NiMnO6

We report a detailed magnetic, dielectric and Raman studies on partially disordered and biphasic double perovskite La2NiMnO6. DC and AC magnetic susceptibility measurements show two magnetic anomalies at T-C1 similar to 270 K and T-C2 similar to 240 K, which may indicate the ferromagnetic ordering of the monoclinic and rhombohedral phases, respectively. A broad peak at a lower temperature (T-sg similar to 70 K) is also observed indicating a spin-glass transition due to partial anti-site disorder of Ni2+ and Mn4+ ions. Unlike the pure monoclinic phase, the biphasic compound exhibits a broad but a clear dielectric anomaly around 270 K which is a signature of magneto-dielectric effect. Temperature-dependent Raman studies between the temperature range 12-300 K in a wide spectral range from 220 cm(-1) to 1530 cm(-1) reveal a strong renormalization of the first as well as second-order Raman modes associated with the (Ni/Mn)O-6 octahedra near T-C1 implying a strong spin-phonon coupling. In addition, an anomaly is seen in the vicinity of spin-glass transition temperature in the temperature dependence of the frequency of the anti-symmetric stretching vibration of the octahedra. (C) 2014 Elsevier Ltd. All rights reserved.