Force Biased Molecular Dynamics Simulation Study of Effect of Dendrimer Generation on Interaction with DNA

We have studied the effect of dendrimer generation on the interaction between dsDNA and the PAMAM dendrimer using force biased simulation of dsDNA with three generations of dendrimer: G3, G4, and G5. Our results for the potential of mean force (PMF) and the dendrimer asphericity along the binding pathway, combined with visualization of the simulations, demonstrate that dendrimer generation has a pronounced impact on the interaction. The PMF increases linearly with increasing generation of the dendrimer. While, in agreement with previous results, we see an increase in the extent to which the dendrimer bends the dsDNA with increasing dendrimer generation, we also see that the deformation of the dendrimer is greater with smaller generation of the dendrimer. The larger dendrimer forces the dsDNA to conform to its structure, while the smaller dendrimer is forced to conform to the structure of the dsDNA. Monitoring the number of bound cations at different values of force bias distance shows the expected effect of ions being expelled when the dendrimer binds dsDNA.

Effect of iodine concentration on the photovoltaic properties of dye sensitized solar cells for various I-2/LiI ratios

In the present study, the effect of iodine concentration on the photovoltaic properties of dye sensitized solar cells (DSSC) based on TiO2 nanoparticles for three different ratios of lithium iodide (LiI) and iodine (I-2) has been investigated. The electron transport properties and interfacial recombination kinetics have been evaluated by electrochemical impedance spectroscopy (EIS). It is found that increasing the concentration of lithium iodide for all ratios of iodine and lithium iodide decreases the open-circuit voltage (V-oc) whereas short circuit current density (J(sc)) and fill factor (FF) shows improvement. The reduction in V-oc and increment in J(sc) is ascribed to the higher concentration of absorptive Li+ cations which shifts the conduction band edge of TiO2 positively. The increase in FF is due to the reduction in electron transport resistance (R-omega) of the cell. In addition for all the ratios of LiI/I-2 increasing the concentration of I-2 decreases the V-oc which is attributed to the increased recombination with tri-iodide ions (I-3(-)) as verified from the low recombination resistance (R-k) and electron lifetime (tau) values obtained by EIS analysis. (C) 2012 Elsevier Ltd. All rights reserved.

A dynamic bandwidth allocation scheme for interactive multimedia applications over cellular networks

Cellular networks played key role in enabling high level of bandwidth for users by employing traditional methods such as guaranteed QoS based on application category at radio access stratum level for various classes of QoSs. Also, the newer multimode phones (e.g., phones that support LTE (Long Term Evolution standard), UMTS, GSM, WIFI all at once) are capable to use multiple access methods simulta- neously and can perform seamless handover among various supported technologies to remain connected. With various types of applications (including interactive ones) running on these devices, which in turn have different QoS requirements, this work discusses as how QoS (measured in terms of user level response time, delay, jitter and transmission rate) can be achieved for interactive applications using dynamic bandwidth allocation schemes over cellular networks. In this work, we propose a dynamic bandwidth allocation scheme for interactive multimedia applications with/without background load in the cellular networks. The system has been simulated for many application types running in parallel and it has been observed that if interactive applications are to be provided with decent response time, a periodic overhauling of policy at admission control has to be done by taking into account history, criticality of applications. The results demonstrate that interactive appli- cations can be provided with good service if policy database at admission control is reviewed dynamically.

Micro-shock wave assisted bacterial transformation

A gene is a unit of heredity in a living organism. It normally resides on a stretch of DNA that codes for a type of protein or for an RNA chain that has a function in the organism. All living things depend on genes, as they specify all proteins and functional RNA chains. Genes hold the information to build and maintain an organism’s cells and pass genetic traits to offspring. The gene has to be transferred to bacteria or eukaryotic cells for basic and applied molecular biology studies. Bacteria can uptake exogenous genetic material by three ways: conjugation, transduction and transformation. Genetic material is naturally transferred to bacteria in case of conjugation and transferred through bacteriophage in transduction. Transformation is the acquisition of exogenous genetic material through cell wall. The ability of bacteria of being transformed is called competency and those bacteria which have competency are competent cells. Divalent Calcium ions can make the bacteria competent and a heat shock can cause the bacteria to uptake DNA. But the heat shock method cannot be used for all the bacteria. In electroporation, a brief electric shock with an electric field of 10-20kV/cmmakes pores in the cell wall, facilitates the DNA to enter into the bacteria. Microprecipitates, microinjection, liposomes, and biological vectors are also used to transfer polar molecules like DNA into host cells.

Hydrothermal synthesis and characterization of bis(4,4 `-bipyridinium) dodecatungstosilicate dihydrate

Hydrothermal synthesis and structural characterization of a new organic polyoxometalate, namely, bis(4,4'-bipyridinium) dodecatungstosilicate dihydrate, 4,4'-bipyH(2)](2)SiW12O40]center dot 2H(2)O (1) is reported. The crystal structure of (1) consists of a SiW12O40](4-) Keggin anion situated on a two-fold axis, two unique 4,4'-bipyridinium cations, one of which is situated on a two-fold axis, and two independent lattice water molecules. The cations and anions are linked by H-bonding.

Hydrodynamic energy harvesting using an ionic polymer-metal composite stack for underwater applications

Ionic Polymer Metal Composites (IPMCs) are a class of Electro-Active Polymers (EAPs) consisting of a base polymer (usually Nafion), sandwiched between thin films of electrodes and an electrolyte. Apart from fuel cell like proton exchange process in Nafion, these IPMCs can act both as an actuator and a sensor. Typically, IPMCs have been known for their applications in fuel cell technology and in artificial muscles for robots. However, more recently, sensing properties of IPMC have opened up possibilities of mechanical energy harvesting. In this paper, we consider a bi-layer stack of IPMC membranes where fluid flow induced cyclic oscillation allows collection of electronic charge across a pair of functionalized electrode on the surface of IPMC layers/stacks. IPMCs work well in hydrated environment; more specifically, in presence of an electrolyte, and therefore, have great potential in underwater applications like hydrodynamic energy harvesting. Hydrodynamic forces produce bending deformation, which can induce transport of cations via polymer chains of the base polymer of Nafion or PTFE. In our experimental set-up, the deformation is induced into the array of IPMC membranes immersed in electrolyte by water waves caused by a plunger connected to a stepper motor. The frequency and amplitude of the water waves is controlled by the stepper motor through a micro-controller. The generated electric power is measured across a resistive load. Few orders of magnitude increase in the harvested power density is observed. Analytical modeling approach used for power and efficiency calculations are discussed. The observed electro-mechanical performance promises a host of underwater energy harvesting applications.

Imaging Intracellular Zinc by Using a Glyoxal Bis(4-methyl-4-phenyl-3-thiosemicarbazone) Ligand

The ligand glyoxal bis(4-methyl-4-phenyl-3-thiosemicarbazone) (GTSCH2) is shown to be a selective fluorescence turn-on sensor for zinc ions (Zn2+). This sensor is easy to synthesize, exhibits excellent sensitivity and selectivity towards Zn2+ over other physiologically relevant cations, and has sub-nanomolar binding affinity. It displays maximum fluorescence response to Zn2+ when the metal/ligand ratio is 1:1 and displays stable fluorescence over a broad pH range. The potential of GTSCH2 to image Zn2+ inside the cell was demonstrated in MCF-7 cells (human breast cancer cell line) by using flow cytometry and confocal fluorescence microscopy. Cell viability studies reveal that the probe is biocompatible and suitable for cellular applications.

Identification of key amino acid residues in the catalytic mechanism of diaminopropionate ammonialyase from Salmonella typhimurium

Diaminopropionate ammonialyase (DAPAL), a fold-typeII pyridoxal 5-phosphate-dependent enzyme, catalyzes the ,-elimination of diaminopropionate (DAP) to pyruvate and ammonia. DAPAL was able to utilize both d- and l-DAP as substrates with almost equal efficiency. Mutational analysis of functionally important residues such as Thr385, Asp125 and Asp194 was carried out to understand the mechanism by which the isomers are hydrolyzed. Further, the putative residues involved in the formation of disulfide bond Cys271 and Cys299 were also mutated. T385S, T385D sDAPAL were as active with dl-DAP as substrate as sDAPAL, whereas the later exhibited a threefold increase in catalytic efficiency with d-Ser as substrate. Further analysis of these mutants suggested that DAPAL might follow an anti-E-2 mechanism of catalysis that does not involve the formation of a quinonoid intermediate. Of the two mutants of Asp125, D125E showed complete loss of activity with d-DAP as substrate, whereas the reaction with l-DAP was not affected significantly, demonstrating that Asp125 was essential for abstraction of protons from the d-isomer. By contrast, mutational analysis of Asp194 showed that the residue may not be directly involved in proton abstraction from l-DAP. sDAPAL does not form a disulfide bond in solution, although the position of Cys299 and Cys271 in the modeled structure of sDAPAL favored the formation of a disulfide bond. Further, unlike eDAPAL, sDAPAL could be activated by monovalent cations. Mutation of the cysteine residues showed that Cys271 may be involved in coordinating the monovalent cation, as observed in the case of other fold-typeII enzymes.

Increasing cleavage specificity and activity of restriction endonuclease KpnI

Restriction enzyme KpnI is a HNH superfamily endonuclease requiring divalent metal ions for DNA cleavage but not for binding. The active site of KpnI can accommodate metal ions of different atomic radii for DNA cleavage. Although Mg2+ ion higher than 500 mu M mediates promiscuous activity, Ca2+ suppresses the promiscuity and induces high cleavage fidelity. Here, we report that a conservative mutation of the metal-coordinating residue D148 to Glu results in the elimination of the Ca2+-mediated cleavage but imparting high cleavage fidelity with Mg2+. High cleavage fidelity of the mutant D148E is achieved through better discrimination of the target site at the binding and cleavage steps. Biochemical experiments and molecular dynamics simulations suggest that the mutation inhibits Ca2+-mediated cleavage activity by altering the geometry of the Ca2+-bound HNH active site. Although the D148E mutant reduces the specific activity of the enzyme, we identified a suppressor mutation that increases the turnover rate to restore the specific activity of the high fidelity mutant to the wild-type level. Our results show that active site plasticity in coordinating different metal ions is related to KpnI promiscuous activity, and tinkering the metal ion coordination is a plausible way to reduce promiscuous activity of metalloenzymes.

Combustion synthesis approach for spectral tuning of Eu doped CaAl2O4 phosphors

Despite being a particularly good emitter, use of divalent Eu has been seriously limited. This is because severe reducing environments or special hosts are needed during synthesis of divalent Eu containing phosphors. In this work we stabilize Eu in its 2+ state (in CaAl2O4) using an open-air solution combustion reaction. The impact of fuel (F) to oxidizer (O) molar ratios (F/O = 0.5-2.0) on luminescence properties is explored. Chromaticity of Eu:CaAl2O4 depends sensitively on the F/O ratio. In general, higher F/O inhibits Eu3+ and promotes Eu2+ formation, which in turn improves the quality of the blue phosphor. EPR spectra show inhomogeneous broadening effects with the increase in F/O ratio, which suggests that disorder creation is promoted when F/O is increase. This is also confirmed by an increase in emission line width in PL spectra, when F/O is increased. (C) 2013 Elsevier B.V. All rights reserved.

Rv1027c-Rv1028c encode functional KdpDE two - Component system in Mycobacterium tuberculosis

In Mycobacterium tuberculosis Rv1027c-Rv1028c genes are predicted to encode KdpDE two component system, which is highly conserved across all bacterial species. Here, we show that the system is functionally active and KdpD sensor kinase undergoes autophosphorylation and transfers phosphoryl group to KdpE, response regulator protein. We identified His(642) and Asp(52) as conserved phosphorylation sites in KdpD and KdpE respectively and by SPR analysis confirmed the physical interaction between them. KdpD was purified with prebound divalent ions and their importance in phosphorylation was established using protein refolding and ion chelation approaches. Genetically a single transcript encoded both KdpD and KdpE proteins. Overall, we report that M. tuberculosis KdpDE system operates like a canonical two component system. (C) 2014 Elsevier Inc. All rights reserved.

Voltammetric detection of arsenic on a bismuth modified exfoliated graphite electrode

We present the application of a bismuth modified exfoliated graphite electrode in the detection of arsenic in water. Bismuth film was electrodeposited onto an exfoliated graphite (EG) electrode at a potential of -600 mV. The modification of EG resulted in an increase in the electroactive surface area of the electrode and consequently peak current enhancement in Ru(NH3)(6)(2+/13+) redox probe. Square wave anodic stripping voltammetry was performed with the modified electrode (EG-Bi) in As (III) solutions at the optimum conditions of pH 6, deposition potential of -600 mV and pre-concentration time of 180s. The EG-Bi was able to detect As (III) to the limit of 5 mu g L-1 and was not susceptible to many interfering cations except Cu (II). The EG-Bi is low cost and easy to prepare. (C) 2013 Elsevier Ltd. All rights reserved.

Differentially Selective Chemosensor with Fluorescence Off-On Responses on Cu2+ and Zn2+ Ions in Aqueous Media and Applications in Pyrophosphate Sensing, Live Cell Imaging, and Cytotoxicity

A new benzoyl hydrazone based chemosensor R is synthesized by Schiff base condensation of 2,6-diformyl-4-methylphenol and phenyl carbohydrazide and acts as a highly selective fluorescence sensor for Cu2+ and Zn2+ ions in aqueous media. The reaction of R with CuCl2 or ZnCl2 forms the corresponding dimeric dicopper(II) Cu-2(R)(CH3O)-(NO3)](2)(CH3O)(2) (R-Cu2+) and dizinc(1) Zn-2(R)(2)](NO3)(2) (R-Zn2+) complexes, which are characterized, as R, by conventional techniques including single-crystal X-ray analysis. Electronic absorption and fluorescence titration studies of R with different metal cations in a CH3CN/0.02 M HEPES buffer medium (pH = 7.3) show a highly selective binding affinity only toward Cu(2+)and Zn2+ ions even in the presence of other commonly coexisting ions such as Ne+, K+, Mg2+, Ca2+, Mn2+, Fe2+, Fe3+, Co2+, Ni2+, Cd2+, and Hg2+. Quantification of the fluorescence titration analysis shows that the chemosensor R can indicate the presence of Cu2+ and Zn2+ even at very low concentrations of 17.3 and 16.5 ppb, respectively. R-Zn2+ acts as a selective metal-based fluorescent sensor for inorganic pyrophosphate ion (PPi) even in the presence of other common anions such as F-, Cl-, Br-, I-, CH3COO-, CO32-, HCO3-, N-3(-), SO42-, PPi, AMP, ADP, and ATP in an aqueous medium. The propensity of R as a bioimaging fluorescent probe to detect Cu2+ and Zn2+ ions in human cervical HeLa cancer cell lines and their cytotoxicity against human cervical (HeLa), breast cancer (MCF7), and noncancer breast epithelial (MCF10a) cells have also been investigated. R-Cu2+ shows better cytotoxicity and sensitivity toward cancer cells over noncancer cells than R and R-Zn2+ under identical conditions, with the appearance of apoptotic bodies.

Sodium-ion battery cathodes Na2FeP2O7 and Na2MnP2O7: diffusion behaviour for high rate performance

Na-ion batteries are currently the focus of significant research activity due to the relative abundance of sodium and its consequent cost advantages. Recently, the pyrophosphate family of cathodes has attracted considerable attention, particularly Li2FeP2O7 related to its high operating voltage and enhanced safety properties; in addition the sodium-based pyrophosphates Na2FeP2O7 and Na2MnP2O7 are also generating interest. Herein, we present defect chemistry and ion migration results, determined via atomistic simulation techniques, for Na2MP2O7 (where M = Fe, Mn) as well as findings for Li2FeP2O7 for direct comparison. Within the pyrophosphate framework the most favourable intrinsic defect type is found to be the antisite defect, in which alkali-cations (Na/Li) and M ions exchange positions. Low activation energies are found for long-range diffusion in all crystallographic directions in Na2MP2O7 suggesting three-dimensional (3D) Na-ion diffusion. In contrast Li2FeP2O7 supports 2D Li-ion diffusion. The 2D or 3D nature of the alkali-ion migration pathways within these pyrophosphate materials means that antisite defects are much less likely to impede their transport properties, and hence important for high rate performance.

Eco-friendly green synthesis, structural and photoluminescent studies of CeO2:Eu3+ nanophosphors using E. tirucalli plant latex

The investigation involves preparation and photoluminescence properties of CeO2:Eu3+ (1-11 mol%) nano phosphors by eco-friendly green combustion route using Euphorbia tirucalli plant latex as fuel. The final product was characterized by powder X-ray diffraction (PXRD), Scanning electron microcopy (SEM) and Transmission electron microscopy (TEM). The PXRD and SEM results reveals cubic fluorite phase with flaky structure. The crystallite size obtained from TEM was found to be similar to 20-25 nm, which was comparable to W-H plots and Scherrer's method. Photoluminescence (PL) emission of all the Eu3+ doped samples shows characteristic bands arising from the transitions of D-5(0) -> F-5(J) (J = 0, 1, 2, 3, 4) manifolds under excitation at 373 and 467 nm excitation. The D-5(0) -> F-7(2) (613 nm) transition often dominate the emission spectra, indicating that the Eu3+ cations occupy a site without inversion center. The highest PL intensity was recorded for 9 mol% Eu3+ ions with 5 ml latex. PL quenching was observed upon further increase in Eu3+ concentration. The international commission on illumination (CIE) chromaticity co-ordinates were calculated from emission spectra, the values (x, y) were very close to national television system committee (NTSC) standard values of pure red emission. The results demonstrate that the synthesized phosphor material could be very useful for display applications. Further, the phosphor material prepared by this method was found to be non toxic, environmental friendly and could be a potential alternative to economical routes. (C) 2014 Elsevier B.V. All rights reserved.