Differential binding of ppGpp and pppGpp to E-coli RNA polymerase: photo-labeling and mass spectral studies

(p) ppGpp, a secondary messenger, is induced under stress and shows pleiotropic response. It binds to RNA polymerase and regulates transcription in Escherichia coli. More than 25 years have passed since the first discovery was made on the direct interaction of ppGpp with E. coli RNA polymerase. Several lines of evidence suggest different modes of ppGpp binding to the enzyme. Earlier cross-linking experiments suggested that the beta-subunit of RNA polymerase is the preferred site for ppGpp, whereas recent crystallographic studies pinpoint the interface of beta'/omega-subunits as the site of action. With an aim to validate the binding domain and to follow whether tetra-and pentaphosphate guanosines have different location on RNA polymerase, this work was initiated. RNA polymerase was photo-labeled with 8-azido-ppGpp/8-azido-pppGpp, and the product was digested with trypsin and subjected to mass spectrometry analysis. We observed three new peptides in the trypsin digest of the RNA polymerase labeled with 8-azido-ppGpp, of which two peptides correspond to the same pocket on beta'-subunit as predicted by X-ray structural analysis, whereas the third peptide was mapped on the beta-subunit. In the case of 8-azido-pppGpp-labeled RNA polymerase, we have found only one cross-linked peptide from the beta'-subunit. However, we were unable to identify any binding site of pppGpp on the beta-subunit. Interestingly, we observed that pppGpp at high concentration competes out ppGpp bound to RNA polymerase more efficiently, whereas ppGpp cannot titrate out pppGpp. The competition between tetraphosphate guanosine and pentaphosphate guanosine for E. coli RNA polymerase was followed by gel-based assay as well as by a new method known as DRaCALA assay.

Non-covalent C-Cl center dot center dot center dot pi interaction in acetylene-carbon tetrachloride adducts: Matrix isolation infrared and ab initio computational studies

Non-covalent halogen-bonding interactions between n cloud of acetylene (C2H2) and chlorine atom of carbon tetrachloride (CCl4) have been investigated using matrix isolation infrared spectroscopy and quantum chemical computations. The structure and the energies of the 1:1 C2H2-CCl4 adducts were computed at the B3LYP, MP2 and M05-2X levels of theory using 6-311++G(d,p) basis set. The computations indicated two minima for the 1:1 C2H2-CCl4 adducts; with the C-Cl center dot center dot center dot pi adduct being the global minimum, where pi cloud of C2H2 is the electron donor. The second minimum corresponded to a C-H...Cl adduct, in which C2H2 is the proton donor. The interaction energies for the adducts A and B were found to be nearly identical. Experimentally, both C-Cl center dot center dot center dot pi and C-H center dot center dot center dot Cl adducts were generated in Ar and N2 matrixes and characterized using infrared spectroscopy. This is the first report on halogen bonded adduct, stabilized through C-Cl center dot center dot center dot pi interaction being identified at low temperatures using matrix isolation infrared spectroscopy. Atoms in Molecules (AIM) and Natural Bond Orbital (NBO) analyses were performed to support the experimental results. The structures of 2:1 ((C2H2)(2)-CCl4) and 1:2 (C2H2-(CCl4)(2)) multimers and their identification in the low temperature matrixes were also discussed. (C) 2015 Elsevier B.V. All rights reserved.

Solution processed Cu2SnS3 thin films for visible and infrared photodetector applications

The Cu2SnS3 thin films were deposited using an economic, solution processible, spin coating technique. The films were found to possess a tetragonal crystal structure using X-ray diffraction. The film morphology and the particle size were determined using scanning electron microscopy. The various planes in the crystal were observed using transmission electron microscopy. The optimum band gap of 1.23 eV and a high absorption coefficient of 104 cm-1 corroborate its application as a photoactive material. The visible and infrared (IR) photo response was studied for various illumination intensities. The current increased by one order from a dark current of 0.31 mu A to a current of 1.78 mu A at 1.05 suns and 8.7 mu A under 477.7 mW/cm(2) IR illumination intensity, at 3 V applied bias. The responsivity, sensitivity, external quantum efficiency and specific detectivity were found to be 10.93 mA/W, 5.74, 2.47% and 3.47 x 10(10) Jones respectively at 1.05 suns and 16.32 mA/W, 27.16, 2.53% and 5.10 x 10(10) Jones respectively at 477.7 mW/cm(2) IR illumination. The transient photoresponse was measured both for visible and IR illuminations. (C) 2016 Author(s).

Transient potassium channels augment degeneracy in hippocampal active dendritic spectral tuning

Hippocampal pyramidal neurons express an intraneuronal map of spectral tuning mediated by hyperpolarization-activated cyclic-nucleotide-gated nonspecific-cation channels. Modeling studies have predicted a critical regulatory role for A-type potassium (KA) channels towards augmenting functional robustness of this map. To test this, we performed patch-clamp recordings from soma and dendrites of rat hippocampal pyramidal neurons, and measured spectral tuning before and after blocking KA channels using two structurally distinct pharmacological agents. Consistent with computational predictions, we found that blocking KA channels resulted in a significant reduction in resonance frequency and significant increases in input resistance, impedance amplitude and action-potential firing frequency across the somato-apical trunk. Furthermore, across all measured locations, blocking KA channels enhanced temporal summation of postsynaptic potentials and critically altered the impedance phase profile, resulting in a significant reduction in total inductive phase. Finally, pair-wise correlations between intraneuronal percentage changes (after blocking KA channels) in different measurements were mostly weak, suggesting differential regulation of different physiological properties by KA channels. Our results unveil a pivotal role for fast transient channels in regulating theta-frequency spectral tuning and intrinsic phase response, and suggest that degeneracy with reference to several coexisting functional maps is mediated by cross-channel interactions across the active dendritic arbor.

Infrared Magnitude-Redshift Relations for Luminous Radio Galaxies

Infrared magnitude-redshift relations for the 3CR and 6C samples of radio galaxies are presented for a wide range of plausible cosmological models, including those with non-zero cosmological constant OmegaLambda. Variations in the galaxy formation redshift, metallicity and star formation history are also considered. The results of the modelling are displayed in terms of magnitude differences between the models and no-evolution tracks, illustrating the amount of K-band evolution necessary to account for the observational data. Given a number of plausible assumptions, the results of these analyses suggest that: (i) cosmologies which predict T_0xH_0>1 (where T_0 denotes the current age of the universe) can be excluded; (ii) the star formation redshift should lie in the redshift interval 5

Monte Carlo filtering and smoothing with application to time-varying spectral estimation

We develop methods for performing filtering and smoothing in non-linear non-Gaussian dynamical models. The methods rely on a particle cloud representation of the filtering distribution which evolves through time using importance sampling and resampling ideas. In particular, novel techniques are presented for generation of random realisations from the joint smoothing distribution and for MAP estimation of the state sequence. Realisations of the smoothing distribution are generated in a forward-backward procedure, while the MAP estimation procedure can be performed in a single forward pass of the Viterbi algorithm applied to a discretised version of the state space. An application to spectral estimation for time-varying autoregressions is described.

Measurements of thermal radiation in ultralight metal foams with open cells

Highly porous ultralightweight cellular metal foams with open cells have attractive mechanical, thermal, acoustic and other properties and are currently being exploited for high-temperature applications (e.g. acoustic liners for combustion chambers). In such circumstances, thermal radiation in the metal foam becomes a significant mechanism of heat transfer. This paper presents results from experimental measurements on radiative transfer in Fe-Cr-Al-Y (a steel-based high-temperature alloy) foams having high porosity (95 per cent) and different cell sizes, manufactured at low cost from the sintering route. The spectral transmittance and reflectance are measured at different infrared wavelengths ranging from 2.5 to 50 μm, which are subsequently used to determine the extinction coefficient and foam emissivity. The results show that the spectral quantities are strongly dependent on the wavelength, particularly in the short-wavelength regime (less than 25 μm). While the extinction coefficient decreases with increasing cell size, the effect of cell size on foam reflectance is not significant. When the temperature is increased, the total extinction coefficient increases but the total reflectance decreases. The effective radiative conductivity of the metal foam is obtained by using the guarded hot-plate apparatus. With the porosity fixed, the effective radiative conductivity increases with increasing cell size and increasing temperature. © IMechE 2004.

Thermal radiation in ultralight metal foams with open cells

This paper presents results from experimental measurements on radiative transfer in FeCrAlY (a steel based high temperature alloy) foams having high porosity (95%) and different cell sizes, manufactured at low cost from the sintering route. The spectral transmittance and reflectance are measured at different infrared wavelengths ranging from 2.5 to 50 μm, which are subsequently used to determine the extinction coefficient and foam emissivity. The results show that the spectral quantities are strongly dependent on the wavelength, particularly in the short wavelength regime (<25 μm). Whilst the extinction coefficient decreases with increasing cell size, the effect of cell size on foam reflectance is not significant. When the temperature is increased, the total extinction coefficient increases but the total reflectance decreases. An analytical model based on geometric optics laws, diffraction theory and metal foam morphology is developed to predict the radiative transfer, with cell size (or cell ligament diameter) and porosity identified as the two key parameters that dictate the foam radiative properties. Close agreement between the predicted effective foam conductivity due to radiation alone and that measured is observed. At fixed porosity, the radiative conductivity of the metal foam increases with increasing cell size and temperature. © 2004 Elsevier Ltd.All rights reserved.

Towards a perceptually optimal spectral amplitude estimator for audio signal enhancement

We present a statistical model-based approach to signal enhancement in the case of additive broadband noise. Because broadband noise is localised in neither time nor frequency, its removal is one of the most pervasive and difficult signal enhancement tasks. In order to improve perceived signal quality, we take advantage of human perception and define a best estimate of the original signal in terms of a cost function incorporating perceptual optimality criteria. We derive the resultant signal estimator and implement it in a short-time spectral attenuation framework. Audio examples, references, and further information may be found at http://www-sigproc.eng.cam.ac.uk/~pjw47.

Rapidly Infrared-Assisted Cooperatively Self-Assembled Highly Ordered Multiscale Porous Materials

In this paper, cooperative self-assembly (CSA) of colloidal spheres with different sizes was studied. It was found that a complicated jamming effect makes it difficult to achieve an optimal self-assembling condition for construction of a well-ordered stacking of colloidal spheres in a relatively short growth time by CSA. Through the use of a characteristic infrared (IR) technique to significantly accelerate local evaporation on the growing interface without changing the bulk growing environment, a concise three-parameter (temperature, pressure, and IR intensity) CSA method to effectively overcome the jamming effect has been developed. Mono- and multiscale inverse opals in a large range of lattice scales can be prepared within a growth time (15-30 min) that is remarkably shorter than the growth times of several hours for previous methods. Scanning electron microscopy images and transmittance spectra demonstrated the superior crystalline and optical qualities of the resulting materials. More importantly, the new method enables optimal conditions for CSA without limitations on sizes and materials of multiple colloids. This strategy not only makes a meaningful advance in the applicability and universality of colloidal crystals and ordered porous materials but also can be an inspiration to the self-assembly systems widely used in many other fields, such as nanotechnology and molecular bioengineering.