Density Functional Theoretical Modeling, Electrostatic Surface Potential and Surface Enhanced Raman Spectroscopic Studies on Biosynthesized Silver Nanoparticles: Observation of 400 pM Sensitivity to Explosives

Interaction of adsorbate on charged surfaces, orientation of the analyte on the surface, and surface enhancement aspects have been studied. These aspects have been explored in details to explain the surface-enhanced Raman spectroscopic (SERS) spectra of 2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazaisowurtzitane (HNIW or CL-20), a well-known explosive, and 2,4,6-trinitrotoluene (TNT) using one-pot synthesis of silver nanoparticles via biosynthetic route using natural precursor extracts of clove and pepper. The biosynthesized silver nanoparticles (bio Ag Nps) have been characterized using UV-vis spectroscopy, scanning electron microscopy and atomic force microscopy. SERS studies conducted using bio Ag Nps on different water insoluble analytes, such as CL-20 and TNT, lead to SERS signals at concentration levels of 400 pM. The experimental findings have been corroborated with density functional computational results, electrostatic surface potential calculations, Fukui functions and potential measurements.

Mahogany seed - a step forward in deciphering autorotation

This article presents an experimental approach for evaluating the various flight characteristics of a mahogany seed in its autorotative descent. Analytical formulae proposed by Yasuda and Azuma are used to interpret the results. The findings are used in the development of a sophisticated blade element computational model, primarily to analyse planar autorotating systems. This approximate computational approach is then used to predict the flight performance of mahogany seeds and the results are compared with experimental data. The potential use of the computational model in the design of autorotating systems is then brought to light.

A performance-based framework for assessing liquefaction potential based on CPT data

This article describes a new performance-based approach for evaluating the return period of seismic soil liquefaction based on standard penetration test (SPT) and cone penetration test (CPT) data. The conventional liquefaction evaluation methods consider a single acceleration level and magnitude and these approaches fail to take into account the uncertainty in earthquake loading. The seismic hazard analysis based on the probabilistic method clearly shows that a particular acceleration value is being contributed by different magnitudes with varying probability. In the new method presented in this article, the entire range of ground shaking and the entire range of earthquake magnitude are considered and the liquefaction return period is evaluated based on the SPT and CPT data. This article explains the performance-based methodology for the liquefaction analysis – starting from probabilistic seismic hazard analysis (PSHA) for the evaluation of seismic hazard and the performance-based method to evaluate the liquefaction return period. A case study has been done for Bangalore, India, based on SPT data and converted CPT values. The comparison of results obtained from both the methods have been presented. In an area of 220 km2 in Bangalore city, the site class was assessed based on large number of borehole data and 58 Multi-channel analysis of surface wave survey. Using the site class and peak acceleration at rock depth from PSHA, the peak ground acceleration at the ground surface was estimated using probabilistic approach. The liquefaction analysis was done based on 450 borehole data obtained in the study area. The results of CPT match well with the results obtained from similar analysis with SPT data.

Ferroelectric and optical properties of Ba5Li2Ti2Nb8O30 ceramics potential for memory applications

Giant grained (42 mu m) translucent Ba5Li2Ti2Nb8O30 ceramic was fabricated by conventional sintering technique using the powders obtained via solid state reaction route. These samples were confirmed to possess tetragonal tungsten bronze structure (P4bm) at room temperature. The scanning electron microscopy established the average grain size to be close to 20 mu m. The photoluminescence studies carried out on these ceramics indicated sharp emission bands around 433 and 578 nm at an excitation wavelength of 350 nm which were attributed to band-edge emission as the band gap was 2.76 eV determined by Kubelka-Munk function. The dielectric properties of these ceramics were studied over wide frequency range (100-1 MHz) at room temperature. The decrease in dielectric constant with frequency could be explained on the basis of Koops theory. The dielectric constant and the loss were found to decrease with increasing frequency. The Curie temperature was confirmed to be similar to 370 A degrees C based on the dielectric anomaly observed when these measurements were carried out over a temperature range of 30-500 A degrees C. This shows a deviation from Curie-Weiss behaviour and hence an indicator of the occurrence of disordering in the system, the gamma = 1.23 which confirms the diffuse ferroelectric transition. These ceramics at room temperature exhibited P-E hysteresis loops, though not well saturated akin to that of their single crystalline counterparts. These are the suitable properties for ferroelectric random access memory applications.

Biotechnological potential of plant-associated endophytic fungi:hope versus hype

The potential of endophytes, particularly endophytic fungi, capable of demonstrating desirable functional traits worth exploitation using red biotechnology is well established. However, these discoveries have not yet translated into industrial bioprocesses for commercial production of biopharmaceuticals using fungal endophytes. Here, we define the current challenges in transforming curiosity driven discoveries into industrial scale endophyte biotechnology. The possible practical, feasible, and sustainable strategies that can lead to harnessing fungal endophyte-mediated pharmaceutical products are discussed.

Suramin is a potent and selective inhibitor of Mycobacterium tuberculosis RecA protein and the SOS response: RecA as a potential target for antibacterial drug discovery

In eubacteria, RecA is essential for recombinational DNA repair and for stalled replication forks to resume DNA synthesis. Recent work has implicated a role for RecA in the development of antibiotic resistance in pathogenic bacteria. Consequently, our goal is to identify and characterize small-molecule inhibitors that target RecA both in vitro and in vivo. We employed ATPase, DNA strand exchange and LexA cleavage assays to elucidate the inhibitory effects of suramin on Mycobacterium tuberculosis RecA. To gain insights into the mechanism of suramin action, we directly visualized the structure of RecA nucleoprotein filaments by atomic force microscopy. To determine the specificity of suramin action in vivo, we investigated its effect on the SOS response by pull-down and western blot assays as well as for its antibacterial activity. We show that suramin is a potent inhibitor of DNA strand exchange and ATPase activities of bacterial RecA proteins with IC50 values in the low micromolar range. Additional evidence shows that suramin inhibits RecA-catalysed proteolytic cleavage of the LexA repressor. The mechanism underlying such inhibitory actions of suramin involves its ability to disassemble RecA-single-stranded DNA filaments. Notably, suramin abolished ciprofloxacin-induced recA gene expression and the SOS response and augmented the bactericidal action of ciprofloxacin. Our findings suggest a strategy to chemically disrupt the vital processes controlled by RecA and hence the promise of small molecules for use against drug-susceptible as well as drug-resistant strains of M. tuberculosis for better infection control and the development of new therapies.

Heat shock protein 90 as a potential drug target against surra

Trypanosomiasis is caused by Trypanosoma species which affect both human and animal populations and pose a major threat to developing countries. The incidence of animal trypanosomiasis is on the rise. Surra is a type of animal trypanosomiasis, caused by Trypanosoma evansi, and has been included in priority list B of significant diseases by the World Organization of Animal Health (OIE). Control of surra has been a challenge due to the lack of effective drugs and vaccines and emergence of resistance towards existing drugs. Our laboratory has previously implicated Heat shock protein 90 (Hsp90) from protozoan parasites as a potential drug target and successfully demonstrated efficacy of an Hsp90 inhibitor in cell culture as well as a pre-clinical mouse model of trypanosomiasis. This article explores the role of Hsp90 in the Trypanosoma life cycle and its potential as a drug target. It appears plausible that the repertoire of Hsp90 inhibitors available in academia and industry may have value for treatment of surra and other animal trypanosomiasis.

Synthesis of novel beta-aryl-beta-(methylthio)acroleins via Vilsmeier-Haack protocol as potential 1,3-dielectrophilic three-carbon building blocks

A new general route for the synthesis of novel beta-aryl-beta-(methylthio)acroleins, a class of stable potential 1,3-dielectrophilic synthons, has been reported. The overall protocol involves treatment of either beta-chloroacroleins or their precursor iminium salts (generated in situ from the corresponding active methylene ketones under Vilsmeier-Haack reaction conditions) with S,S-dimethyldithiocarbonates (DDC)/aqueous KOH in either a one-pot or two-step process. The dimethyldithiocarbonate (DDC)/30% aqueous KOH has been shown to be an excellent source of methylthiolate anion. (C) 2014 Elsevier Ltd. All rights reserved.

High Value of Proton Relaxivity Achieved by Graphene Oxide-Cobalt Ferrite Nanoparticle Composite: A Potential Contrast Agent in Magnetic Resonance Imaging

This work investigates the potential of graphene oxide-cobalt ferrite nanoparticle (GO-CoFe2O4) composite as image contrast enhancing material in Magnetic Resonance Imaging (MRI). In the preset work, GO-CoFe2O4 composites were produced by a two-step synthesis process. In the first step, graphene oxide (GO) was synthesized, and in the second step CoFe2O4 nanoparticles were synthesized in a reaction mixture containing GO to yield graphene GO-CoFe2O4 composite. Proton relaxivity value obtained from the composite was 361 mM(-1)s(-1). This value of proton relaxivity is higher than a majority of reported relaxivity values obtained using several ferrite based contrast agents.

High-conductance states and A-type K+ channels are potential regulators of the conductance-current balance triggered by HCN channels

An increase in the hyperpolarization-activated cyclic nucleotide-gated (HCN) channel conductance reduces input resistance, whereas the consequent increase in the inward h current depolarizes the membrane. This results in a delicate and unique conductance-current balance triggered by the expression of HCN channels. In this study, we employ experimentally constrained, morphologically realistic, conductance-based models of hippocampal neurons to explore certain aspects of this conductance-current balance. First, we found that the inclusion of an experimentally determined gradient in A-type K+ conductance, but not in M-type K+ conductance, tilts the HCN conductance-current balance heavily in favor of conductance, thereby exerting an overall restorative influence on neural excitability. Next, motivated by the well-established modulation of neuronal excitability by synaptically driven high-conductance states observed under in vivo conditions, we inserted thousands of excitatory and inhibitory synapses with different somatodendritic distributions. We measured the efficacy of HCN channels, independently and in conjunction with other channels, in altering resting membrane potential (RMP) and input resistance (R-in) when the neuron received randomized or rhythmic synaptic bombardments through variable numbers of synaptic inputs. We found that the impact of HCN channels on average RMP, R in, firing frequency, and peak-to-peak voltage response was severely weakened under high-conductance states, with the impinging synaptic drive playing a dominant role in regulating these measurements. Our results suggest that the debate on the role of HCN channels in altering excitability should encompass physiological and pathophysiological neuronal states under in vivo conditions and the spatiotemporal interactions of HCN channels with other channels.

On the Two-Step Mechanism for Synthesis of Transition-Metal Nanoparticles

The two-step particle synthesis mechanism, also known as the Finke-Watzky (1997) mechanism, has emerged as a significant development in the field of nanoparticle synthesis. It explains a characteristic feature of the synthesis of transition metal nanoparticles, an induction period in precursor concentration followed by its rapid sigmoidal decrease. The classical LaMer theory (1950) of particle formation fails to capture this behavior. The two-step mechanism considers slow continuous nucleation and autocatalytic growth of particles directly from precursor as its two kinetic steps. In the present work, we test the two-step mechanism rigorously using population balance models. We find that it explains precursor consumption very well, but fails to explain particle synthesis. The effect of continued nucleation on particle synthesis is not suppressed sufficiently by the rapid autocatalytic growth of particles. The nucleation continues to increase breadth of size distributions to unexpectedly large values as compared to those observed experimentally. A number of variations of the original mechanism with additional reaction steps are investigated next. The simulations show that continued nucleation from the beginning of the synthesis leads to formation of highly polydisperse particles in all of the tested cases. A short nucleation window, realized with delayed onset of nucleation and its suppression soon after in one of the variations, appears as one way to explain all of the known experimental observations. The present investigations clearly establish the need to revisit the two-step particle synthesis mechanism.

Antimicrobial Peptides with Potential for Biofilm Eradication: Synthesis and Structure Activity Relationship Studies of Battacin Peptides

We report on the first chemical syntheses and structureactivity analyses of the cyclic lipopeptide battacin which revealed that conjugation of a shorter fatty acid, 4-methyl-hexanoic acid, and linearization of the peptide sequence improves antibacterial activity and reduces hemolysis of mouse blood cells. This surprising finding of higher potency in linear lipopeptides than their cyclic counterparts is economically beneficial. This novel lipopeptide was membrane lytic and exhibited antibiofilm activity against Pseudomonas aeruginosa, Staphylococcus aureus, and, for the first time, Pseudomonas syringe pv. actinidiae. The peptide was unstructured in aqueous buffer and dimyristoylphosphatidylcholine-polymerized diacetylene vesicles, with 12% helicity induced in 50% v/v of trifluoroethanol. Our results indicate that a well-defined secondary structure is not essential for the observed antibacterial activity of this novel lipopeptide. A truncated pentapeptide conjugated to 4-methyl hexanoic acid, having similar potency against Gram negative and Gram positive pathogens was identified through alanine scanning.

B-Spline potential function for maximum a-posteriori image reconstruction in fluorescence microscopy

An iterative image reconstruction technique employing B-Spline potential function in a Bayesian framework is proposed for fluorescence microscopy images. B-splines are piecewise polynomials with smooth transition, compact support and are the shortest polynomial splines. Incorporation of the B-spline potential function in the maximum-a-posteriori reconstruction technique resulted in improved contrast, enhanced resolution and substantial background reduction. The proposed technique is validated on simulated data as well as on the images acquired from fluorescence microscopes (widefield, confocal laser scanning fluorescence and super-resolution 4Pi microscopy). A comparative study of the proposed technique with the state-of-art maximum likelihood (ML) and maximum-a-posteriori (MAP) with quadratic potential function shows its superiority over the others. B-Spline MAP technique can find applications in several imaging modalities of fluorescence microscopy like selective plane illumination microscopy, localization microscopy and STED. (C) 2015 Author(s).

Achieving Highly Efficient, Selective, and Stable CO2 Reduction on Nitrogen-Doped Carbon Nanotubes

The challenge in the electrosynthesis of fuels from CO2 is to achieve durable and active performance with cost-effective catalysts. Here, we report that carbon nanotubes (CNTs), doped with nitrogen to form resident electron-rich defects, can act as highly efficient and, more importantly, stable catalysts for the conversion of CO2 to CO. The unprecedented overpotential (-0.18 V) and selectivity (80%) observed on nitrogen-doped CNTs (NCNTs) are attributed to their unique features to facilitate the reaction, including (i) high electrical conductivity, (ii) preferable catalytic sites (pyridinic N defects), and (iii) low free energy for CO2 activation and high barrier for hydrogen evolution. Indeed, DFT calculations show a low free energy barrier for the potential-limiting step to form key intermediate COOH as well as strong binding energy of adsorbed CON and weak binding energy for the adsorbed CO. The highest selective site toward CO production is pyridinic N, and the NCNT-based electrodes exhibit no degradation over 10 h of continuous operation, suggesting the structural stability of the electrode.

Snaps and mends: DNA breaks and chromosomal translocations

Integrity in entirety is the preferred state of any organism. The temporal and spatial integrity of the genome ensures continued survival of a cell. DNA breakage is the first step towards creation of chromosomal translocations. In this review, we highlight the factors contributing towards the breakage of chromosomal DNA. It has been well-established that the structure and sequence of DNA play a critical role in selective fragility of the genome. Several non-B-DNA structures such as Z-DNA, cruciform DNA, G-quadruplexes, R loops and triplexes have been implicated in generation of genomic fragility leading to translocations. Similarly, specific sequences targeted by proteins such as Recombination Activating Genes and Activation Induced Cytidine Deaminase are involved in translocations. Processes that ensure the integrity of the genome through repair may lead to persistence of breakage and eventually translocations if their actions are anomalous. An insufficient supply of nucleotides and chromatin architecture may also play a critical role. This review focuses on a range of events with the potential to threaten the genomic integrity of a cell, leading to cancer.