Sesbania Mosaic Virus (SeMV) Infectious Clone: Possible Mechanism of 3 ` and 5 ` End Repair and Role of Polyprotein Processing in Viral Replication

Sesbania mosaic virus (SeMV) is a positive stranded RNA virus belonging to the genus Sobemovirus. Construction of an infectious clone is an essential step for deciphering the virus gene functions in vivo. Using Agrobacterium based transient expression system we show that SeMV icDNA is infectious on Sesbania grandiflora and Cyamopsis tetragonoloba plants. The efficiency of icDNA infection was found to be significantly high on Cyamopsis plants when compared to that on Sesbania grandiflora. The coat protein could be detected within 6 days post infiltration in the infiltrated leaves. Different species of viral RNA (double stranded and single stranded genomic and subgenomic RNA) could be detected upon northern analysis, suggesting that complete replication had taken place. Based on the analysis of the sequences at the genomic termini of progeny RNA from SeMV icDNA infiltrated leaves and those of its 3' and 5' terminal deletion mutants, we propose a possible mechanism for 3' and 5' end repair in vivo. Mutation of the cleavage sites in the polyproteins encoded by ORF 2 resulted in complete loss of infection by the icDNA, suggesting the importance of correct polyprotein processing at all the four cleavage sites for viral replication. Complementation analysis suggested that ORF 2 gene products can act in trans. However, the trans acting ability of ORF 2 gene products was abolished upon deletion of the N-terminal hydrophobic domain of polyprotein 2a and 2ab, suggesting that these products necessarily function at the replication site, where they are anchored to membranes.

Carrier concentration dependence of donor activation energy in n-type GaN epilayers grown on Si (111) by plasma-assisted MBE

The n-type GaN layers were grown by plasma-assisted MBE and either intentionally doped with Si or unintentionally doped. The optical characteristics of a donor level in Si-doped, GaN were studied in terms of photoluminescence (PL) spectroscopy as a function of electron concentration. Temperature dependent PL measurements allowed us to estimate the activation energy of a Si-related donor from temperature-induced decay of PL intensity. PL peak positions, full width at half maximum of PL and activation energies are found to be proportional to the cube root of carrier density. The involvement of donor levels is supported by the temperature-dependent electron concentration measurements. (C) 2012 Elsevier Ltd. All rights reserved.

Carbon Nanotube based Composite Fibers for Strain Sensing, Signal Processing and Computing

Carbon nanotubes dispersed in polymer matrix have been aligned in the form of fibers and interconnects and cured electrically and by UV light. Conductivity and effective semiconductor tunneling against reverse to forward bias field have been designed to have differentiable current-voltage response of each of the fiber/channel. The current-voltage response is a function of the strain applied to the fibers along axial direction. Biaxial and shear strains are correlated by differentiating signals from the aligned fibers/channels. Using a small doping of magnetic nanoparticles in these composite fibers, magneto-resistance properties are realized which are strong enough to use the resulting magnetostriction as a state variable for signal processing and computing. Various basic analog signal processing tasks such as addition, convolution and filtering etc. can be performed. These preliminary study shows promising application of the concept in combined analog-digital computation in carbon nanotube based fibers. Various dynamic effects such as relaxation, electric field dependent nonlinearities and hysteresis on the output signals are studied using experimental data and analytical model.

Valence band offset at GaN/beta-Si3N4 and beta-Si3N4/Si(111) heterojunctions formed by plasma-assisted molecular beam epitaxy

Ultra thin films of pure beta-Si3N4 (0001) were grown on Si (111) surface by exposing the surface to radio- frequency nitrogen plasma with a high content of nitrogen atoms. Using beta-Si3N4 layer as a buffer layer, GaN epilayers were grown on Si (111) substrate by plasma-assisted molecular beam epitaxy. The valence band offset (VBO) of GaN/beta-Si3N4/ Si heterojunctions is determined by X-ray photoemission spectroscopy. The VBO at the beta-Si3N4 /Si interface was determined by valence-band photoelectron spectra to be 1.84 eV. The valence band of GaN is found to be 0.41 +/- 0.05 eV below that of beta-Si3N4 and a type-II heterojunction. The conduction band offset was deduced to be similar to 2.36 eV, and a change of the interface dipole of 1.29 eV was observed for GaN/ beta-Si3N4 interface formation. (c) 2011 Elsevier B.V. All rights reserved.

Realization of thermally durable close-packed 2D gold nanoparticle arrays using self-assembly and plasma etching

Realization of thermally and chemically durable, ordered gold nanostructures using bottom-up self-assembly techniques are essential for applications in a wide range of areas including catalysis, energy generation, and sensing. Herein, we describe a modular process for realizing uniform arrays of gold nanoparticles, with interparticle spacings of 2 nm and above, by using RF plasma etching to remove ligands from self-assembled arrays of ligand-coated gold nanoparticles. Both nanoscale imaging and macroscale spectroscopic characterization techniques were used to determine the optimal conditions for plasma etching, namely RF power, operating pressure, duration of treatment, and type of gas. We then studied the effect of nanoparticle size, interparticle spacing, and type of substrate on the thermal durability of plasma-treated and untreated nanoparticle arrays. Plasma-treated arrays showed enhanced chemical and thermal durability, on account of the removal of ligands. To illustrate the application potential of the developed process, robust SERS (surface-enhanced Raman scattering) substrates were formed using plasma-treated arrays of silver-coated gold nanoparticles that had a silicon wafer or photopaper as the underlying support. The measured value of the average SERS enhancement factor (2 x 10(5)) was quantitatively reproducible on both silicon and paper substrates. The silicon substrates gave quantitatively reproducible results even after thermal annealing. The paper-based SERS substrate was also used to swab and detect probe molecules deposited on a solid surface.

Sliding wear behavior of plasma nitrided Austenitic Stainless Steel Type AISI 316LN in the temperature range from 25 to 400 degrees C at 10(-4) bar

There is a research knowledge gap for the dry wear data of nitride treated Stainless Steel in high temperature and high vacuum environment. In order to fill this gap, plasma nitriding was done on austenitic Stainless Steel type AISI 316LN (316LN SS) and dry sliding wear tests have been conducted at 25 degrees C, 200 degrees C and 400 degrees C in high vacuum of 1.6 x 10(-4) bar. The two different slider material (316LN SS and Colmonoy) and two different sliding speeds (0.0576 m/s and 0.167 m/s) have been used. The tribological parameters such as friction coefficient, wear mechanism and volume of metal loss have been evaluated. Scanning Electron Microscopy (SEM) was used to study the surface morphology of the worn pins and rings. Electronic balancing machine was used to record the mass of metal loss during wear tests. The 2D optical profilometer was used to measure the depth of the wear track. The Plasma Nitride treated 316LN SS rings (PN rings) exhibit excellent wear resistance against 316LN SS pin and Colmonoy pin at all temperatures. However, PN ring vs. Colmonoy pin Pair shows better wear resistance than PN ring vs. 316LN SS pin Pair at higher temperature. (C) 2012 Elsevier B.V. All rights reserved.

Synthesis and characterization of nano silicon and titanium nitride powders using atmospheric microwave plasma technique

We have demonstrated a simple, scalable and inexpensive method based on microwave plasma for synthesizing 5 to 10 g/h of nanomaterials. Luminescent nano silicon particles were synthesized by homogenous nucleation of silicon vapour produced by the radial injection of silicon tetrachloride vapour and nano titanium nitride was synthesized by using liquid titanium tetrachloride as the precursor. The synthesized nano silicon and titanium nitride powders were characterized by XRD, XPS, TEM, SEM and BET. The characterization techniques indicated that the synthesized powders were indeed crystalline nanomaterials.

A Novel Property of DNA - As a Bioflotation Reagent in Mineral Processing

Environmental concerns regarding the use of certain chemicals in the froth flotation of minerals have led investigators to explore biological entities as potential substitutes for the reagents in vogue. Despite the fact that several microorganisms have been used for the separation of a variety of mineral systems, a detailed characterization of the biochemical molecules involved therein has not been reported so far. In this investigation, the selective flotation of sphalerite from a sphalerite-galena mineral mixture has been achieved using the cellular components of Bacillus species. The key constituent primarily responsible for the flotation of sphalerite has been identified as DNA, which functions as a bio-collector. Furthermore, using reconstitution studies, the obligatory need for the presence of non-DNA components as bio-depressants for galena has been demonstrated. A probable model involving these entities in the selective flotation of sphalerite from the mineral mixture has been discussed.

Equal channel angular pressing processing routes and associated structure modification: a differential scanning calorimetry and X-ray line profile analysis

The effectiveness of different routes of equal channel angular pressing (A, B-c, and C) is studied for commercially pure copper. The stored energy and the activation energy of recrystallization for the deformed samples were quantified using differential scanning calorimetry and X-ray diffraction line profile analysis. Results of the study revealed that the dislocation density and the stored energy are higher in the case of route B-c deformed sample. The activation energy for recrystallization is lower for route B-c. (C) 2012 International Centre for Diffraction Data doi:10.1017/S0885715612000310]

Microstructure and dry sliding wear resistance evaluation of plasma nitrided austenitic stainless steel type AISI 316LN against different sliders

In this work, Plasma Nitriding was carried out at a temperature of 570 degrees C on nuclear grade austenitic stainless steel type AISI 316 LN (316LN SS) in a gas mixture of 20% N-2-80% H-2 to improve the surface hardness and thereby sliding wear resistance. The Plasma Nitride (PN) treated surface has been characterized by Vickers microhardness measurements, Scanning Electron Microscopic (SEM) examination, X-ray Diffraction (XRD) and sliding wear assessment. The average thickness of the PN layer was found to be 70 mu m. Microhardness measurements showed a significant increase in the hardness from 210 HV25g (unnitrided sample) to 1040 HV25g (Plasma Nitrided sample). The XRD reveals that PN layer consists of CrN, Fe4N and Fe3N phases along with austenite phase. The tribological parameters such as the friction coefficient and wear mechanism have been evaluated at ambient conditions for PN treated ring (PN ring) vs. ASTM A453 grade 660 pin (ASTM pin), PN ring vs. Nickel based alloy hard faced pin (Colmonoy pin), PN ring vs. 316LN SS pin and 316LN SS ring vs. 316LN SS pin. The wear tracks have been analyzed by SEM, Energy Dispersive X-ray Analysis (EDX) and Optical Profilometry. The untreated 316LN SS ring vs. 316LN SS pin produced severe wear and was characterized by a combination of delamination and adhesion wear mechanism, whereas wear mechanism of the PN rings reveals mild abrasion and a transfer layer from pin materials. (C) 2012 Elsevier B.V. All rights reserved.

Is saccade averaging determined by visual processing or movement planning?

Bhutani N, Ray S, Murthy A. Is saccade averaging determined by visual processing or movement planning? J Neurophysiol 108: 3161-3171, 2012. First published September 26, 2012; doi:10.1152/jn.00344.2012.-Saccadic averaging that causes subjects' gaze to land between the location of two targets when faced with simultaneously or sequentially presented stimuli has been often used as a probe to investigate the nature of computations that transform sensory representations into an oculomotor plan. Since saccadic movements involve at least two processing stages-a visual stage that selects a target and a movement stage that prepares the response-saccade averaging can either occur due to interference in visual processing or movement planning. By having human subjects perform two versions of a saccadic double-step task, in which the stimuli remained the same, but different instructions were provided (REDIRECT gaze to the later-appearing target vs. FOLLOW the sequence of targets in their order of appearance), we tested two alternative hypotheses. If saccade averaging were due to visual processing alone, the pattern of saccade averaging is expected to remain the same across task conditions. However, whereas subjects produced averaged saccades between two targets in the FOLLOW condition, they produced hypometric saccades in the direction of the initial target in the REDIRECT condition, suggesting that the interaction between competing movement plans produces saccade averaging.

Low-thermal-budget solution processing of thin films of zinc ferrite and other complex oxides

Further miniaturization of magnetic and electronic devices demands thin films of advanced nanomaterials with unique properties. Spinel ferrites have been studied extensively owing to their interesting magnetic and electrical properties coupled with stability against oxidation. Being an important ferrospinel, zinc ferrite has wide applications in the biological (MRI) and electronics (RF-CMOS) arenas. The performance of an oxide like ZnFe2O4 depends on stoichiometry (defect structure), and technological applications require thin films of high density, low porosity and controlled microstructure, which depend on the preparation process. While there are many methods for the synthesis of polycrystalline ZnFe2O4 powder, few methods exist for the deposition of its thin films, where prolonged processing at elevated temperature is not required. We report a novel, microwave-assisted, low temperature (<100°C) deposition process that is conducted in the liquid medium, developed for obtaining high quality, polycrystalline ZnFe2O4 thin films on technologically important substrates like Si(100). An environment-friendly solvent (ethanol) and non-hazardous oxide precursors (β-diketonates of Zn and Fe in 1:2 molar ratio), forming a solution together, is subjected to irradiation in a domestic microwave oven (2.45 GHz) for a few minutes, leading to reactions which result in the deposition of ZnFe2O4 films on Si (100) substrates suspended in the solution. Selected surfactants added to the reactant solution in optimum concentration can be used to control film microstructure. The nominal temperature of the irradiated solution, i.e., film deposition temperature, seldom exceeds 100°C, thus sharply lowering the thermal budget. Surface roughness and uniformity of large area depositions (50x50 mm2) are controlled by tweaking the concentration of the mother solution. Thickness of the films thus grown on Si (100) within 5 min of microwave irradiation can be as high as several microns. The present process, not requiring a vacuum system, carries a very low thermal budget and, together with a proper choice of solvents, is compatible with CMOS integration. This novel solution-based process for depositing highly resistive, adherent, smooth ferrimagnetic films on Si (100) is promising to RF engineers for the fabrication of passive circuit components. It is readily extended to a wide variety of functional oxide films.

Efficient post-processing techniques for speech enhancement

We address the problem of speech enhancement in real-world noisy scenarios. We propose to solve the problem in two stages, the first comprising a generalized spectral subtraction technique, followed by a sequence of perceptually-motivated post-processing algorithms. The role of the post-processing algorithms is to compensate for the effects of noise as well as to suppress any artifacts created by the first-stage processing. The key post-processing mechanisms are aimed at suppressing musical noise and to enhance the formant structure of voiced speech as well as to denoise the linear-prediction residual. The parameter values in the techniques are fixed optimally by experimentally evaluating the enhancement performance as a function of the parameters. We used the Carnegie-Mellon university Arctic database for our experiments. We considered three real-world noise types: fan noise, car noise, and motorbike noise. The enhancement performance was evaluated by conducting listening experiments on 12 subjects. The listeners reported a clear improvement (MOS improvement of 0.5 on an average) over the noisy signal in the perceived quality (increase in the mean-opinion score (MOS)) for positive signal-to-noise-ratios (SNRs). For negative SNRs, however, the improvement was found to be marginal.

A post processing technique for improved harmonic/percussion separation in polyphonic speech

In this paper we propose a postprocessing technique for a spectrogram diffusion based harmonic/percussion decom- position algorithm. The proposed technique removes har- monic instrument leakages in the percussion enhanced out- puts of the baseline algorithm. The technique uses median filtering and an adaptive detection of percussive segments in subbands followed by piecewise signal reconstruction using envelope properties to ensure that percussion is enhanced while harmonic leakages are suppressed. A new binary mask is created for the percussion signal which upon applying on the original signal improves harmonic versus percussion separation. We compare our algorithm with two recent techniques and show that on a database of polyphonic Indian music, the postprocessing algorithm improves the harmonic versus percussion decomposition significantly.

Processing of DNA double-stranded breaks and intermediates of recombination and repair by saccharomyces cerevisiae Mre11 and its stimulation by Rad50, Xrs2, and Sae2 proteins

Saccharomyces cerevisiae RAD50, MRE11, and XRS2 genes are essential for telomere length maintenance, cell cycle checkpoint signaling, meiotic recombination, and DNA double-stranded break (DSB) repair via nonhomologous end joining and homologous recombination. The DSB repair pathways that draw upon Mre11-Rad50-Xrs2 subunits are complex, so their mechanistic features remain poorly understood. Moreover, the molecular basis of DSB end resection in yeast mre11-nuclease deficient mutants and Mre11 nuclease-independent activation of ATM in mammals remains unknown and adds a new dimension to many unanswered questions about the mechanism of DSB repair. Here, we demonstrate that S. cerevisiae Mre11 (ScMre11) exhibits higher binding affinity for single-over double-stranded DNA and intermediates of recombination and repair and catalyzes robust unwinding of substrates possessing a 3' single-stranded DNA overhang but not of 5' overhangs or blunt-ended DNA fragments. Additional evidence disclosed that ScMre11 nuclease activity is dispensable for its DNA binding and unwinding activity, thus uncovering the molecular basis underlying DSB end processing in mre11 nuclease deficient mutants. Significantly, Rad50, Xrs2, and Sae2 potentiate the DNA unwinding activity of Mre11, thus underscoring functional interaction among the components of DSB end repair machinery. Our results also show that ScMre11 by itself binds to DSB ends, then promotes end bridging of duplex DNA, and directly interacts with Sae2. We discuss the implications of these results in the context of an alternative mechanism for DSB end processing and the generation of single-stranded DNA for DNA repair and homologous recombination.