Functional characterization of UvrD helicases from Haemophilus influenzae and Helicobacter pylori

Haemophilus influenzae and Helicobacter pylori are major bacterial pathogens that face high levels of genotoxic stress within their host. UvrD, a ubiquitous bacterial helicase that plays important roles in multiple DNA metabolic pathways, is essential for genome stability and might, therefore, be crucial in bacterial physiology and pathogenesis. In this study, the functional characterization of UvrD helicase from Haemophilus influenzae and Helicobacter pylori is reported. UvrD from Haemophilus influenzae (HiUvrD) and Helicobacter pylori (HpUvrD) exhibit strong single-stranded DNA-specific ATPase and 3'5' helicase activities. Mutation of highly conserved arginine (R288) in HiUvrD and glutamate (E206) in HpUvrD abrogated their activities. Both the proteins were able to bind and unwind a variety of DNA structures including duplexes with strand discontinuities and branches, three- and four-way junctions that underpin their role in DNA replication, repair and recombination. HiUvrD required a minimum of 12 nucleotides, whereas HpUvrD preferred 20 or more nucleotides of 3'-single-stranded DNA tail for efficient unwinding of duplex DNA. Interestingly, HpUvrD was able to hydrolyze and utilize GTP for its helicase activity although not as effectively as ATP, which has not been reported to date for UvrD characterized from other organisms. HiUvrD and HpUvrD were found to exist predominantly as monomers in solution together with multimeric forms. Noticeably, deletion of distal C-terminal 48 amino acid residues disrupted the oligomerization of HiUvrD, whereas deletion of 63 amino acids from C-terminus of HpUvrD had no effect on its oligomerization. This study presents the characteristic features and comparative analysis of Haemophilus influenzae and Helicobacter pylori UvrD, and constitutes the basis for understanding the role of UvrD in the biology and virulence of these pathogens.

Dual functional performance of fiber Bragg gratings coated with metals using flash evaporation technique

Metallic and other type of coatings on fiber Bragg grating (FBG) sensors alter their sensitivity with thermal and mechanical stress while protecting the fragile optical fiber in harsh sensing surroundings. The behavior of the coated materials is unique in their response to thermal and mechanical stress depending on the thickness and the mode of coating. The thermal stress during the coating affects the temperature sensitivity of FBG sensors. We have explored the thermal response of FBGs coated with Al and Pb to an average thickness of 80 nm using flash evaporation technique where the FBG sensor is mounted in a region at room temperature in an evacuated chamber having a pressure of 10(6) Torr which will minimize any thermal stress during the coating process. The coating thickness is chosen in the nanometer region with the aim to study thermal behavior of nanocoatings and their effect on FBG sensitivity. The sensitivity of FBGs is evaluated from the wavelengths recorded using an optical sensing interrogator sm 130 (Micron Optics) from room temperature to 300 degrees C both during heating and cooling. It is observed that the sensitivity of the metal coated fibers is better than the reference FBG with no coating for the entire range of temperature. For a coating thickness of 80 nm, Al coated FBG is more sensitive than the one coated with Pb up to 170 degrees C and it reverses at higher temperatures. This point is identified as a reversible phase transition in Pb monolayers as the 2-dimensional aspects of the metal layers are dominant in the nanocoatings of Pb. On cooling, the phase transition reverses and the FBGs return to the original state and for repeated cycles of heating and cooling the same pattern is observed. Thus the FBG functions as a sensor of the phase transitions of the coatings also. (C) 2012 Elsevier Inc. All rights reserved.

Functional Analysis of the Genes Encoding Diaminopropionate Ammonia Lyase in Escherichia coli and Salmonella enterica Serovar Typhimurium

Diaminopropionate ammonia lyase (DAPAL) is a pyridoxal-5'phosphate (PLP)-dependent enzyme that catalyzes the conversion of diaminopropionate (DAP) to pyruvate and ammonia and plays an important role in cell metabolism. We have investigated the role of the ygeX gene of Escherichia coli K-12 and its ortholog, STM1002, in Salmonella enterica serovar Typhimurium LT2, presumed to encode DAPAL, in the growth kinetics of the bacteria. While Salmonella Typhimurium LT2 could grow on DL-DAP as a sole carbon source, the wild-type E. coli K-12 strain exhibited only marginal growth on DL-DAP, suggesting that DAPAL is functional in S. Typhimurium. The expression of ygeX in E. coli was low as detected by reverse transcriptase PCR (RT-PCR), consistent with the poor growth of E. coli on DL-DAP. Strains of S. Typhimurium and E. coli with STM1002 and ygeX, respectively, deleted showed loss of growth on DL-DAP, confirming that STM1002 (ygeX) is the locus encoding DAPAL. Interestingly, the presence of DL-DAP caused a growth inhibition of the wild-type E. coli strain as well as the knockout strains of S. Typhimurium and E. coli in minimal glucose/glycerol medium. Inhibition by DL-DAP was rescued by transforming the strains with plasmids containing the STM1002 (ygeX) gene encoding DAPAL or supplementing the medium with Casamino Acids. Growth restoration studies using media lacking specific amino acid supplements suggested that growth inhibition by DL-DAP in the absence of DAPAL is associated with auxotrophy related to the inhibition of the enzymes involved in the biosynthetic pathways of pyruvate and aspartate and the amino acids derived from them.

Adsorption on Edge-Functionalized Bilayer Graphene Nanoribbons: Assessing the Role of Functional Groups in Methane Uptake

A combination of ab initio and classical Monte Carlo simulations is used to investigate the effects of functional groups on methane binding. Using Moller-Plesset (MP2) calculations, we obtain the binding energies for benzene functionalized with NH2, OH, CH3, COOH, and H2PO3 and identify the methane binding sites. In all cases, the preferred binding sites are located above the benzene plane in the vicinity of the benzene carbon atom attached to the functional group. Functional groups enhance methane binding relative to benzene (-6.39 kJ/mol), with the largest enhancement observed for H2PO3 (-8.37 kJ/mol) followed by COOH and CH3 (-7.77 kJ/mol). Adsorption isotherms are obtained for edge-functionalized bilayer graphene nanoribbons using grand canonical Monte Carlo simulations with a five-site methane model. Adsorbed excess and heats of adsorption for pressures up to 40 bar and 298 K are obtained with functional group concentrations ranging from 3.125 to 6.25 mol 96 for graphene edges functionalized with OH, NH2, and COOH. The functional groups are found to act as preferred adsorption sites, and in the case of COOH the local methane density in the vicinity of the functional group is found to exceed that of bare graphene. The largest enhancement of 44.5% in the methane excess adsorbed is observed for COOH-functionalized nanoribbons when compared to H terminated ribbons. The corresponding enhancements for OH- and NH2-functionalized ribbons are 10.5% and 3.7%, respectively. The excess adsorption across functional groups reflects the trends observed in the binding energies from MP2 calculations. Our study reveals that specific site functionalization can have a significant effect on the local adsorption characteristics and can be used as a design strategy to tailor materials with enhanced methane storage capacity.

Functional maps within a single neuron

Narayanan R, Johnston D. Functional maps within a single neuron. J Neurophysiol 108: 2343-2351, 2012. First published August 29, 2012; doi:10.1152/jn.00530.2012.-The presence and plasticity of dendritic ion channels are well established. However, the literature is divided on what specific roles these dendritic ion channels play in neuronal information processing, and there is no consensus on why neuronal dendrites should express diverse ion channels with different expression profiles. In this review, we present a case for viewing dendritic information processing through the lens of the sensory map literature, where functional gradients within neurons are considered as maps on the neuronal topograph. Under such a framework, drawing analogies from the sensory map literature, we postulate that the formation of intraneuronal functional maps is driven by the twin objectives of efficiently encoding inputs that impinge along different dendritic locations and of retaining homeostasis in the face of changes that are required in the coding process. In arriving at this postulate, we relate intraneuronal map physiology to the vast literature on sensory maps and argue that such a metaphorical association provides a fresh conceptual framework for analyzing and understanding single-neuron information encoding. We also describe instances where the metaphor presents specific directions for research on intraneuronal maps, derived from analogous pursuits in the sensory map literature. We suggest that this perspective offers a thesis for why neurons should express and alter ion channels in their dendrites and provides a framework under which active dendrites could be related to neural coding, learning theory, and homeostasis.

Design and Synthesis of a Functional Derivative of the Triazinium Cation and Its Rhodium Complex that Shows Photoinduced DNA Cleavage Activity and Photocytotoxicity

The design and synthesis of an intensely blue rhodium(III) complex 3]+ of a new N,N-donor ligand, 8-(quinolin-8-ylamino)pyrido2,1-c]1,2,4]benzotriazin-11-ium, 2]+, which contains a planar pendant triazinium arm, is described. Structural characterization for 3]+ was carried out by using various spectroscopic techniques and single-crystal X-ray crystallography. The organometallic rhodium(III) compound shows a ligand-based reversible reduction at 0.65 V. The electrochemically reduced compound displays a single-line EPR spectrum that signifies the formation of ligand-based free radicals. Compound 3]+ shows a binding propensity to calf thymus DNA to give a Kapp value of 6.05X105 M1. The parent triazinium salt, pyrido2,1-c]1,2,4]benzotriazin-11-ium 1]+ and the ligand salt 2]+ exhibit photoinduced cleavage of DNA in UV-A light, whereas the reference Rh complex 3]+ photocleaves DNA with red light (647.1 nm). The compounds show photonuclease activities under both aerobic and anaerobic conditions. Mechanistic investigations under aerobic conditions with several inhibitors indicate the formation of hydroxyl radicals by means of a photoredox pathway. Under anaerobic conditions, it is believed that a photoinduced oxidation of DNA mechanism is operative. Compound 3]+ exhibits photocytotoxicity in HeLa cervical cancer cells to give IC50 values of (12+/-0.9) mu M in UV-A light at 365 nm and (31.4+/-1.1) mu M in the dark.

Vaporization dynamics of functional droplets in a hot laminar air jet

The vaporization characteristics of pendant droplets of various chemical compositions (like conventional fuels, alternative fuels and nanosuspensions) subjected to convective heating in a laminar air jet have been analyzed. Different heating conditions were achieved by controlling the air temperature and velocity fields around the droplet. A hybrid timescale has been proposed which incorporates the effects of latent heat of vaporization, saturation vapor pressure and thermal diffusivity. This timescale in essence encapsulates the different parameters that influence the droplet vaporization rate. The analysis further permits the evaluation of the effect of various parameters such as surrounding temperature, Reynolds number, far-field vapor presence, impurity content and agglomeration dynamics (nanosuspensions) in the droplet. Flow visualization has been carried out to understand the role of internal recirculation on the vaporization rate. The visualization indicates the presence of a single vortex cell within the droplet on account of the rotation and oscillation of the droplet due to aerodynamic load. External heating induced agglomeration in nanofluids leads to morphological changes during the vaporization process. These morphological changes and alteration in vaporization behavior have been assessed using high speed imaging of the diameter regression and Scanning Electron Microscopy images of the resultant precipitate. (C) 2012 Elsevier Ltd. All rights reserved.

q-Gaussian based Smoothed Functional Algorithms for Stochastic Optimization

The q-Gaussian distribution results from maximizing certain generalizations of Shannon entropy under some constraints. The importance of q-Gaussian distributions stems from the fact that they exhibit power-law behavior, and also generalize Gaussian distributions. In this paper, we propose a Smoothed Functional (SF) scheme for gradient estimation using q-Gaussian distribution, and also propose an algorithm for optimization based on the above scheme. Convergence results of the algorithm are presented. Performance of the proposed algorithm is shown by simulation results on a queuing model.

Functional characterization, homology modeling and docking studies of beta-glucosidase responsible for bioactivation of cyanogenic hydroxynitrile glucosides from Leucaena leucocephala (subabul)

Glycosyl hydrolase family 1 beta-glucosidases are important enzymes that serve many diverse functions in plants including defense, whereby hydrolyzing the defensive compounds such as hydroxynitrile glucosides. A hydroxynitrile glucoside cleaving beta-glucosidase gene (Llbglu1) was isolated from Leucaena leucocephala, cloned into pET-28a (+) and expressed in E. coli BL21 (DE3) cells. The recombinant enzyme was purified by Ni-NTA affinity chromatography. The optimal temperature and pH for this beta-glucosidase were found to be 45 A degrees C and 4.8, respectively. The purified Llbglu1 enzyme hydrolyzed the synthetic glycosides, pNPGlucoside (pNPGlc) and pNPGalactoside (pNPGal). Also, the enzyme hydrolyzed amygdalin, a hydroxynitrile glycoside and a few of the tested flavonoid and isoflavonoid glucosides. The kinetic parameters K (m) and V (max) were found to be 38.59 mu M and 0.8237 mu M/mg/min for pNPGlc, whereas for pNPGal the values were observed as 1845 mu M and 0.1037 mu M/mg/min. In the present study, a three dimensional (3D) model of the Llbglu1 was built by MODELLER software to find out the substrate binding sites and the quality of the model was examined using the program PROCHEK. Docking studies indicated that conserved active site residues are Glu 199, Glu 413, His 153, Asn 198, Val 270, Asn 340, and Trp 462. Docking of rhodiocyanoside A with the modeled Llbglu1 resulted in a binding with free energy change (Delta G) of -5.52 kcal/mol on which basis rhodiocyanoside A could be considered as a potential substrate.

Eulerian two-phase flow simulation and experimental validation of semisolid slurry generation process using cooling slope

Experimental and numerical studies of slurry generation using a cooling slope are presented in the paper. The slope having stainless steel body has been designed and constructed to produce semisolid A356 Al alloy slurry. The pouring temperature of molten metal, slope angle of the cooling slope and slope wall temperature were varied during the experiment. A multiphase numerical model, considering liquid metal and air, has been developed to simulate the liquid metal flow along the cooling channel using an Eulerian two-phase flow approach. Solid fraction evolution of the solidifying melt is tracked at different locations of the cooling channel following Schiel's equation. The continuity, momentum and energy equations are solved considering thin wall boundary condition approach. During solidification of the melt, based on the liquid fraction and latent heat of the alloy, temperature of the alloy is modified continuously by introducing a modified temperature recovery method. Numerical simulations has been carried out for semisolid slurry formation by varying the process parameters such as angle of the cooling slope, cooling slope wall temperature and melt superheat temperature, to understand the effect of process variables on cooling slope semisolid slurry generation process such as temperature distribution, velocity distribution and solid fraction of the solidifying melt. Experimental validation performed for some chosen cases reveals good agreement with the numerical simulations.

Smoothed functional and Quasi-Newton algorithms for routing in multi-stage queueing network with constraints

We consider the problem of optimal routing in a multi-stage network of queues with constraints on queue lengths. We develop three algorithms for probabilistic routing for this problem using only the total end-to-end delays. These algorithms use the smoothed functional (SF) approach to optimize the routing probabilities. In our model all the queues are assumed to have constraints on the average queue length. We also propose a novel quasi-Newton based SF algorithm. Policies like Join Shortest Queue or Least Work Left work only for unconstrained routing. Besides assuming knowledge of the queue length at all the queues. If the only information available is the expected end-to-end delay as with our case such policies cannot be used. We also give simulation results showing the performance of the SF algorithms for this problem.

Vibrational spectroscopy and density functional theory analysis of 3-O-caffeoylquinic acid

Density functional theory (DFT) calculations are being performed to investigate the geometric, vibrational, and electronic properties of the chlorogenic acid isomer 3-CQA (1R,3R,4S,5R)-3-{(2E)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]oxy}-1,4, 5-trihydroxycyclohexanecarboxylic acid), a major phenolic compound in coffee. DFT calculations with the 6-311G(d,p) basis set produce very good results. The electrostatic potential mapped onto an isodensity surface has been obtained. A natural bond orbital analysis (NBO) has been performed in order to study intramolecular bonding, interactions among bonds, and delocalization of unpaired electrons. HOMO-LUMO studies give insights into the interaction of the molecule with other species. The calculated HOMO and LUMO energies indicate that a charge transfer occurs within the molecule. (C) 2012 Elsevier B.V. All rights reserved.

Multi-component, Self-assembled, Functional Soft Materials

Supramolecular chemistry is an emerging tool for devising materials that can perform specified functions. The self-assembly of facially amphiphilic bile acid molecules has been extensively utilized for the development of functional soft materials. Supramolecular hydrogels derived from the bile acid backbone act as useful templates for the intercalation of multiple components. Based on this, synthesis of gel-nanoparticle hybrid materials, photoluminescent coating materials, development of a new enzyme assay technique, etc. were achieved in the author's laboratory. The present account highlights some of these achievements.

A practical approach for cross-functional vehicle body weight optimization

The goal of optimization in vehicle design is often blurred by the myriads of requirements belonging to attributes that may not be quite related. If solutions are sought by optimizing attribute performance-related objectives separately starting with a common baseline design configuration as in a traditional design environment, it becomes an arduous task to integrate the potentially conflicting solutions into one satisfactory design. It may be thus more desirable to carry out a combined multi-disciplinary design optimization (MDO) with vehicle weight as an objective function and cross-functional attribute performance targets as constraints. For the particular case of vehicle body structure design, the initial design is likely to be arrived at taking into account styling, packaging and market-driven requirements. The problem with performing a combined cross-functional optimization is the time associated with running such CAE algorithms that can provide a single optimal solution for heterogeneous areas such as NVH and crash safety. In the present paper, a practical MDO methodology is suggested that can be applied to weight optimization of automotive body structures by specifying constraints on frequency and crash performance. Because of the reduced number of cases to be analyzed for crash safety in comparison with other MDO approaches, the present methodology can generate a single size-optimized solution without having to take recourse to empirical techniques such as response surface-based prediction of crash performance and associated successive response surface updating for convergence. An example of weight optimization of spaceframe-based BIW of an aluminum-intensive vehicle is given to illustrate the steps involved in the current optimization process.