Affinity of a galactose-specific legume lectin from Dolichos lablab to adenine revealed by X-ray cystallography

Crystal structure analysis of a galactose-specific lectin from a leguminous food crop Dolichos lablab (Indian lablab beans) has been carried out to obtain insights into its quaternary association and lectin-carbohydrate interactions. The analysis led to the identification of adenine binding sites at the dimeric interfaces of the heterotetrameric lectin. Structural details of similar adenine binding were reported in only one legume lectin, Dolichos biflorus, before this study. Here, we present the structure of the galactose-binding D. lablab lectin at different pH values in the native form and in complex with galactose and adenine. This first structure report on this lectin also provides a high resolution atomic view of legume lectin-adenine interactions. The tetramer has two canonical and two DB58-like interfaces. The binding of adenine, a non-carbohydrate ligand, is found to occur at four hydrophobic sites at the core of the tetramer at the DB58-like dimeric interfaces and does not interfere with the carbohydrate-binding site. To support the crystallographic observations, the adenine binding was further quantified by carrying out isothermal calorimetric titration. By this method, we not only estimated the affinity of the lectin to adenine but also showed that adenine binds with negative cooperativity in solution.

Novel co-evaporation approach for the growth of Sb doped SnO2 nanowires

Antimony doped tin oxide (Sb:SnO2) nanowires were grown by thermal and e-beam assisted co-evaporation of Sb and Sn in the presence of oxygen at a low substrate temperature of 450 degrees C. The field emission scanning electron microscopy study revealed that the nanowires had a length and diameter of 2-4 mu m and 20-60 nm respectively. Transmission electron microscopy study revealed the single crystalline nature of the nanowires; energy dispersive X-ray spectroscopy (EDS) and EDS mapping on the nanowires confirmed the presence of Sb doping in the nanowires. UV light detection study on the doped SnO2 nanowire films exhibited fast response and recovery time compared to undoped SnO2 nanowire films. This is an innovative and simple method to grow doped SnO2 nanowires.

Generation of Ligand Specificity and Modes of Oligomerization in beta-Prism I Fold Lectins

beta-Prism I fold lectins constitute one of the five widely occurring structural classes of plant lectins. Each single domain subunit is made up of three Greek key motifs arranged in a threefold symmetric fashion. The threefold symmetry is not reflected in the sequence except in the case of the lectin from banana, a monocot, which carries two sugar-binding sites instead of the one in other lectins of known three-dimensional structure, all from dicots. This is believed to be a consequence of the different evolutionary paths followed by the lectin in monocots and dicots. The galactose-specific lectins among them have two chains produced by posttranslational proteolysis and contain three aromatic residues at the binding site. The extended binding sites of galactose- and mannose-specific lectins have been thoroughly characterized. Ligand binding at the sites involves both conformational selection and induced fit. Molecular plasticity of some of the lectins in the family has been characterized. The plasticity appears to be such as to promote variability in quaternary association which could be dimeric, tetrameric, or octameric. Structural and evolutionary reasons for the variability have been explored, and the relation of oligomerization to ligand binding and conformational selection investigated.

Identification and characterization of starvation induced msdgc-1 promoter involved in the c-di-GMP turnover

C-di-GMP Bis-(3'-5')-cyclic-dimeric-guanosine monophosphate], a second messenger is involved in intracellular communication in the bacterial species. As a result several multi-cellular behaviors in both Gram-positive and Gram-negative bacteria are directly linked to the intracellular level of c-di-GMP. The cellular concentration of c-di-GMP is maintained by two opposing activities, diguanylate cyclase (DGC) and phosphodiesterase (PDE-A). In Mycobacterium smegmatis, a single bifunctional protein MSDGC-1 is responsible for the cellular concentration of c-di-GMP. A better understanding of the regulation of c-di-GMP at the genetic level is necessary to control the function of above two activities. In this work, we have characterized the promoter element present in msdgc-1 along with the + 1 transcription start site and identified the sigma factors that regulate the transcription of msdgc-1. Interestingly, msdgc-1 utilizes SigA during the initial phase of growth, whereas near the stationary phase SigB containing RNA polymerase takes over the expression of msdgc-1. We report here that the promoter activity of msdgc-1 increases during starvation or depletion of carbon source like glucose or glycerol. When msdgc-1 is deleted, the numbers of viable cells are similar to 10 times higher in the stationary phase in comparison to that of the wild type. We propose here that msdgc-1 is involved in the regulation of cell population density. (C) 2013 Elsevier B.V. All rights reserved.

Optimisation of an asymmetric polymerase chain reaction assay for the amplification of single-stranded DNA from Wuchereria bancrofti for electrochemical detection

Single-stranded DNA (ssDNA) is a prerequisite for electrochemical sensor-based detection of parasite DNA and other diagnostic applications. To achieve this detection, an asymmetric polymerase chain reaction method was optimised. This method facilitates amplification of ssDNA from the human lymphatic filarial parasite Wuchereria bancrofti. This procedure produced ssDNA fragments of 188 bp in a single step when primer pairs (forward and reverse) were used at a 100:1 molar ratio in the presence of double-stranded template DNA. The ssDNA thus produced was suitable for immobilisation as probe onto the surface of an Indium tin oxide electrode and hybridisation in a system for sequence-specific electrochemical detection of W. bancrofti. The hybridisation of the ssDNA probe and target ssDNA led to considerable decreases in both the anodic and the cathodic currents of the system's redox couple compared with the unhybridised DNA and could be detected via cyclic voltammetry. This method is reproducible and avoids many of the difficulties encountered by conventional methods of filarial parasite DNA detection; thus, it has potential in xenomonitoring.

Photovoltaic structures using thermally evaporated SnS and CdS thin films

Polycrystalline tin sulfide thin films were prepared by thermal evaporation technique. The films grown at substrate temperature of 300 degrees C had an orthorhombic crystal structure with strong preferred orientation along (111) plane. Electrical resistivity of the deposited films was about 32.5 Omega cm with a direct optical band gap of 1.33 eV. Carrier concentration and mobility of charge carriers estimated from the Hall measurement were found to be 6.24 x 10(15) cm(-3) and 30.7 cm(2)V(-1) s(-1) respectively. Heterojunction solar cells were fabricated in superstrate configuration using thermally evaporated SnS as an absorber layer and CdS, In: CdS as window layer. The resistivity of pure CdS thin film of a thickness of 320 nm was about 1-2 Omega cm and was reduced to 40 x 10(-3) Omega cm upon indium doping. The fabricated solar cells were characterized using solar simulator. The solar cells with indium doped CdS window layer showed improved performance as compared to pure CdS window layer. The best device had a conversion efficiency of 0.4% and a fill factor of 33.5%. (C) 2013 Elsevier B.V. All rights reserved.

Mechanistic features of Salmonella typhimurium propionate kinase (TdcD): Insights from kinetic and crystallographic studies

Short-chain fatty acids (SCFAs) play a major role in carbon cycle and can be utilized as a source of carbon and energy by bacteria. Salmonella typhimurium propionate kinase (StTdcD) catalyzes reversible transfer of the gamma-phosphate of ATP to propionate during L-threonine degradation to propionate. Kinetic analysis revealed that StTdcD possesses broad ligand specificity and could be activated by various SCFAs (propionate > acetate approximate to butyrate), nucleotides (ATP approximate to GTP > CTP approximate to TTP; dATP > dGTP > dCTP) and metal ions (Mg2+ approximate to Mn2+ > Co2+). Inhibition of StTdcD by tricarboxylic acid (TCA) cycle intermediates such as citrate, succinate, alpha-ketoglutarate and malate suggests that the enzyme could be under plausible feedback regulation. Crystal structures of StTdcD bound to PO4 (phosphate), AMP, ATP, Ap4 (adenosine tetraphosphate), GMP, GDP, GTP, CMP and CTP revealed that binding of nucleotide mainly involves hydrophobic interactions with the base moiety and could account for the broad biochemical specificity observed between the enzyme and nucleotides. Modeling and site-directed mutagenesis studies suggest Ala88 to be an important residue involved in determining the rate of catalysis with SCFA substrates. Molecular dynamics simulations on monomeric and dimeric forms of StTdcD revealed plausible open and closed states, and also suggested role for dimerization in stabilizing segment 235-290 involved in interfacial interactions and ligand binding. Observation of an ethylene glycol molecule bound sufficiently close to the gamma-phosphate in StTdcD complexes with triphosphate nucleotides supports direct in-line phosphoryl transfer. (C) 2013 Elsevier B.V. All rights reserved.

Biological sulfate reduction of a sulfate-rich industrial waste liquor using sulfate reducing bacteria

An industrial waste liquor having high sulfate concentrations was subjected to biological treatment using the sulfate-reducing bacteria (SRB) Desulfovibrio desulfuricans. Toxicity levels of different sulfate, cobalt and nickel concentrations toward growth of the SRB with respect to biological sulfate reduction kinetics was initially established. Optimum sulfate concentration to promote SRB growth amounted to 0.8 - 1 g/L. The strain of D. desulfuricans used in this study initially tolerated up to 4 -5 g/L of sulfate or 50 mg/L of cobalt and nickel, while its tolerance could be further enhanced through adaptation by serial subculturing in the presence of increasing concentrations of sulfate, cobalt and nickel. From the waste liquor, more than 70% of sulfate and 95% of cobalt and nickel could be precipitated as sulfides, using a preadapted strain of D. desulfuricans. Probable mechanisms involving biological sulfide precipitation and metal adsorption onto precipitates and bacterial cells are discussed.

The effect of multisubstitution on the thermoelectric properties of chalcogenide-based Cu2.1Zn0.9Sn1-xInxSe4 (0 <= x <= 0.1)

Quinary chalcogenide compounds Cu2.1Zn0.9Sn1-xInxSe4 (0 <= x <= 0.1) were prepared by melting (1170K) followed by annealing (773 K) for 172 h. Powder X-ray diffraction (XRD) data accompanied by electron probe microanalysis (EPMA) and Raman spectra of all the samples confirmed the formation of a tetragonal kesterite structure with Cu2FeSnS4-type. The thermoelectric properties of all the samples were measured as a function of temperature in the range of 300-780K. The electrical resistivity of all the samples exhibits metallic-like behavior. The positive values of the Seebeck coefficient and the Hall coefficient reveal that holes are the majority charge carriers. The codoping of copper and indium leads to a significant increase of the electrical resistivity and the Seebeck coefficient as a function of temperature above 650 K. The thermal conductivity of all the samples decreases with increasing temperature. Lattice thermal conductivity is not significantly modified as the doping content may infer negligible mass fluctuation scattering for copper/zinc and indium/tin substitution. Even though, the power factors (S-2/rho) of indium-doped samples Cu2.1Zn0.9Sn1-xInxSe4 (x = 0.05, 0.075) are almost the same, the maximum zT = 0.45 at 773K was obtained for Cu2.1Zn0.9Sn0.925In0.075Se4 due to its smaller value of thermal conductivity. (C) 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim

Sensitivity of Water Dynamics to Biologically Significant Surfaces of Monomeric Insulin: Role of Topology and Electrostatic Interactions

In addition to the biologically active monomer of the protein insulin circulating in human blood, the molecule also exists in dimeric and hexameric forms that are used as storage. The insulin monomer contains two distinct surfaces, namely, the dimer forming surface (DFS) and the hexamer forming surface (HFS), that are specifically designed to facilitate the formation of the dimer and the hexamer, respectively. In order to characterize the structural and dynamical behavior of interfacial water molecules near these two surfaces (DFS and HFS), we performed atomistic molecular dynamics simulations of insulin with explicit water. Dynamical characterization reveals that the structural relaxation of the hydrogen bonds formed between the residues of DFS and the interfacial water molecules is faster than those formed between water and that of the HFS. Furthermore, the residence times of water molecules in the protein hydration layer for both the DFS and HFS are found to be significantly higher than those for some of the other proteins studied so far, such as HP-36 and lysozyme. In particular, we find that more structured water molecules, with higher residence times (similar to 300-500 ps), are present near HFS than those near DFS. A significant slowing down is observed in the decay of associated rotational auto time correlation functions of O-H bond vector of water in the vicinity of HFS. The surface topography and the arrangement of amino acid residues work together to organize the water molecules in the hydration layer in order to provide them with a preferred orientation. HFS having a large polar solvent accessible surface area and a convex extensive nonpolar region, drives the surrounding water molecules to acquire predominantly an outward H-atoms directed, clathrate-like structure. In contrast, near the DFS, the surrounding water molecules acquire an inward H-atoms directed orientation owing to the flat curvature of hydrophobic surface and the interrupted hydrophilic residual alignment. We have followed escape trajectory of several such quasi-bound water molecules from both the surfaces that reveal the significant differences between the two hydration layers.

Stable and low resistive zinc contacts for SnS based optoelectronic devices

The contact behavior of tin mono sulfide (SnS) nanocrystalline thin films with zinc (Zn) and silver (Ag) contacts was studied. SnS films have been deposited on glass substrates by thermal evaporation technique at a growth temperature of 300 degrees C. The as-grown SnS films composed of vertically aligned nanocrystallites with a preferential orientation along the < 010 > direction. SnS films exhibited excellent chemical stoichiometry and direct optical band gap of 1.96 eV. These films also exhibited excellent Ohmic characteristics and low electrical resistivity with Zn contacts. The observed electrical resistivity of SnS films with Zn contacts is 22 times lower than that of the resistivity with Ag contacts. The interfacing analysis reveals the formation of conductive Zn-S layer between SnS and Zn as interfacial layer. (C) 2014 Elsevier B. V. All rights reserved.

Titanium nitride thin film anode: chemical and microstructural evaluation during electrochemical studies

TIN thin films with (200) fibre texture are deposited on Cu substrate at room temperature using reactive magnetron sputtering. They exhibit a discharge capacity of 172 mu Ah cm(-2) mu m(-1) (300 mAh g(-1)) in a non-aqueous electrolyte containing a Li salt. There is a graded decrease in discharge capacity when cycled between 0.01 and 3.0 V. Electron microscopy investigations indicate significant changes in surface morphology of the cycled TiN electrodes in comparison with the as deposited TiN films. From XPS depth profile analysis, it is inferred that Li intercalated TIN films consist of lithium compounds, hydroxyl groups, titanium sub oxides and TiN. Lithium diffusivity and reactivity decrease with increase in depth and the major reaction with lithium takes place at film surface and grain boundaries. (C) 2014 Elsevier Ltd. All rights reserved.

FOLD TYPE II PYRIDOXAL 5 `-PHOSPHATE DEPENDENT ENZYMES: STRUCTURE, SUBSTRATE RECOGNITION AND CATALYSIS

Enzymes utilizing pyridoxal 5'-phosphate dependent mechanism for catalysis are observed in all cellular forms of living organisms. PLP-dependent enzymes catalyze a wide variety of reactions involving amino acid substrates and their analogs. Structurally, these ubiquitous enzymes have been classified into four major fold types. We have carried out investigations on the structure and function of fold type I enzymes serine hydroxymethyl transferase and acetylornithine amino transferase, fold type n enzymes catabolic threonine deaminase, D-serine deaminase, D-cysteine desulfhydrase and diaminopropionate ammonia lyase. This review summarizes the major findings of investigations on fold type II enzymes in the context of similar studies on other PLP-dependent enzymes. Fold type II enzymes participate in pathways of both degradation and synthesis of amino acids. Polypeptide folds of these enzymes, features of their active sites, nature of interactions between the cofactor and the polypeptide, oligomeric structure, catalytic activities with various ligands, origin of specificity and plausible regulation of activity are briefly described. Analysis of the available crystal structures of fold type II enzymes revealed five different classes. The dimeric interfaces found in these enzymes vary across the classes and probably have functional significance.

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.

Impacts of modern transitions on thermal comfort in vernacular dwellings in warm-humid climate of Sugganahalli (India)

Sugganahalli, a rural vernacular community in a warm-humid region in South India, is under transition towards adopting modern construction practices. Vernacular local building elements like rubble walls and mud roofs are given way to burnt brick walls and reinforced cement concrete (RCC)/tin roofs. Over 60% of Indian population is rural, and implications of such transitions on thermal comfort and energy in buildings are crucial to understand. Vernacular architecture evolves adopting local resources in response to the local climate adopting passive solar designs. This paper investigates the effectiveness of passive solar elements on the indoor thermal comfort by adopting modern climate-responsive design strategies. Dynamic simulation models validated by measured data have also been adopted to determine the impact of the transition from vernacular to modern material-configurations. Age-old traditional design considerations were found to concur with modern understanding into bio-climatic response and climate-responsiveness. Modern transitions were found to increase the average indoor temperatures in excess of 7 degrees C. Such transformations tend to shift the indoor conditions to a psychrometric zone that is likely to require active air-conditioning. Also, the surveyed thermal sensation votes were found to lie outside the extended thermal comfort boundary for hot developing countries provided by Givoni in the bio-climatic chart.