Serum proteomics of hepatitis C virus infection reveals retinol-binding protein 4 as a novel regulator

Persistent infection of hepatitis C virus (HCV) can lead to liver cirrhosis and hepatocellular carcinoma, which are currently diagnosed by invasive liver biopsy. Approximately 15-20% of cases of chronic liver diseases in India are caused by HCV infection. In North India, genotype 3 is predominant, whereas genotype 1 is predominant in southern parts of India. The aim of this study was to identify differentially regulated serum proteins in HCV-infected Indian patients (genotypes 1 and 3) using a two-dimensional electrophoresis approach. We identified eight differentially expressed proteins by MS. Expression levels of one of the highly upregulated proteins, retinol-binding protein 4 (RBP4), was validated by ELISA and Western blotting in two independent cohorts. We also confirmed our observation in the JFH1 infectious cell culture system. Interestingly, the HCV core protein enhanced RBP4 levels and partial knockdown of RBP4 had a positive impact on HCV replication, suggesting a possible role for this cellular protein in regulating HCV infection. Analysis of RBP4-interacting partners using a bioinformatic approach revealed novel insights into the possible involvement of RBP4 in HCV-induced pathogenesis. Taken together, this study provided information on the proteome profile of the HCV-infected Indian population, and revealed a link between HCV infection, RBP4 and insulin resistance.

Oscillation dynamics of sessile droplets subjected to substrate vibration

Sessile droplets on a vibrating substrate are investigated focusing on axisymmetric oscillations with pinned contact line. Proper orthogonal decomposition is employed to identify the different modes of droplet shape oscillation and quantitatively assess the droplet oscillation and spectral response. We offer the first experimental evidence for the analogy of an oscillating sessile droplet with a non-linear spring mass damper system. The qualitative and quantitative agreement of amplitude response and phase response curves and limit cycles of the model dynamical system with that observed experimentally suggest that the bulk oscillations in the fundamental mode of a sessile droplet can be very well modeled by a Duffing oscillator with a hard spring, especially near the resonance. The red shift of the resonance peak with an increase in the glycerol concentration is clearly evidenced by both the experimental and predicted amplitude response curves. The influence of various operational parameters such as excitation frequency and amplitude and fluid properties on the droplet oscillation characteristics is adequately captured by the model. (C) 2014 Elsevier Ltd. All rights reserved.

Mycobacterium tuberculosis Rho Is an NTPase with Distinct Kinetic Properties and a Novel RNA-Binding Subdomain

Two mechanisms - factor independent and dependent termination - ensure the completion of RNA synthesis in eubacteria. Factor-dependent mechanism relies on the Rho protein to terminate transcription by interacting with RNA polymerase. Although well studied in Escherichia coli, the properties of the Rho homologs from most bacteria are not known. The rho gene is unusually large in genus Mycobacterium and other members of actinobacteria, having,150 additional residues towards the amino terminal end. We describe the distinct properties of Rho from Mycobacterium tuberculosis. It is an NTPase with a preference for purine nucleoside triphosphates with kinetic properties different from E. coli homolog and an ability to use various RNA substrates. The N-terminal subdomain of MtbRho can bind to RNA by itself, and appears to contribute to the interaction of the termination factor with RNAs. Furthermore, the interaction with RNA induces changes in conformation and oligomerization of MtbRho.

Organic passivation layer on flexible Surlyn substrate for encapsulating organic photovoltaics

Barrier materials are required for encapsulating organic devices. A simple methodology based on organic passivation layer on a flexible substrate has been developed in this work. Stearyl stearate ( SS) was directly coated over the flexible Surlyn film. The barrier films with SS passivation layer exhibited much lower water vapor transmission rates compared to the neat Surlyn films. Moreover, the effect of the process of deposition of organic passivation layer on the resultant water vapor properties of the barrier films was evaluated. The accelerated lifetime studies conducted on encapsulated organic photovoltaics showed that the passivation layer improved the device performance by several fold compared to the non-passivated barrier films. (C) 2014 AIP Publishing LLC.

Numerical modeling of the non-isothermal liquid droplet impact on a hot solid substrate

The heat transfer from a solid phase to an impinging non-isothermal liquid droplet is studied numerically. A new approach based on an arbitrary Lagrangian-Eulerian (ALE) finite element method for solving the incompressible Navier Stokes equations in the liquid and the energy equation within the solid and the liquid is presented. The novelty of the method consists in using the ALE-formulation also in the solid phase to guarantee matching grids along the liquid solid interface. Moreover, a new technique is developed to compute the heat flux without differentiating the numerical solution. The free surface and the liquid solid interface of the droplet are represented by a moving mesh which can handle jumps in the material parameter and a temperature dependent surface tension. Further, the application of the Laplace-Beltrami operator technique for the curvature approximation allows a natural inclusion of the contact angle. Numerical simulation for varying Reynold, Weber, Peclet and Biot numbers are performed to demonstrate the capabilities of the new approach. (C) 2014 Elsevier Ltd. All rights reserved.

Simultaneous co-ordination of three cytosine ligands displaying different binding sites around the copper centres

We report the synthesis and structural characterization of a polymeric ternary copper-cytosine-phenanthroline complex, Cu-4(phen)(3)-(mu(3)-cyt)(2)(mu-OH)(cyt)(OH)Cl-3](n)center dot 16H(2)O, where three cytosine ligands with different binding sites have simultaneously complexed to the four copper metal centres. Interestingly, the complex exhibits two different coordination geometries around the metal centres.

Synthesis, DNA binding, docking and photocleavage studies of quinolinyl chalcones

A series of simple quinoline-chalcone conjugates have been synthesized by Claisen-Schmidt condensation reactions of substituted acetophenones with 2-chloro-3-formyl-quinoline and evaluated for their nucleolytic activity. The structures of the synthesized quinoline-chalcone conjugates were confirmed by IR, H-1 NMR, C-13 NMR and mass spectral analyses. Most of the prepared compounds showed significant DNA binding and photocleavage activities. The incorporation of an electron-donating group into ring A caused a moderate increase in the DNA binding and photocleavage activities. Compounds 3c and 3d exhibited promising DNA photocleavage against pUC 19 DNA with 85% inhibition at 100 mu M concentration. A structure-activity relationship analysis of these compounds was performed; compounds 3c and 3d are potential candidates for future drug discovery and development.

Hexamethylenetetramine mediated simultaneous nitrogen doping and reduction of graphene oxide for a metal-free SERS substrate

We report a one-pot hydrothermal synthesis of nitrogen doped reduced graphene oxide (N-rGO) and Ag nanoparticle decorated N-rGO hybrid nanostructures from graphene oxide (GO), metal ions and hexamethylenetetramine (HMT). HMT not only reduces GO and metal ions simultaneously but also acts as the source for the nitrogen (N) dopant. We show that the N-rGO can be used as a metal-free surface enhanced Raman spectroscopy (SERS) substrate, while the Ag nano-particles decorated N-rGO can be used as an effective SERS substrate as well as a template for decorating various other nanostructures on N-rGO.

Phenyl carbohydrazone conjugated 2-oxoindoline as a new scaffold that augments the DNA and BSA binding affinity and anti-proliferative activity of a 1,10-phenanthroline based copper(II) complex

A new type of copper(II) complex, CuL(phen)(2)](NO3) (CuIP), where L ((E)-N'-(2-oxoindolin-3-ylidene) benzohydrazide) is a N donor ligand and phen is the N, N-donor heterocyclic 1,10-phenanthroline, has been synthesized. The phenyl carbohydrazone conjugated isatin-based ligand L and CuIP were characterized by elemental analysis, infrared, UV-Vis, H-1 and C-13 NMR and ESI-mass spectral data, as well as single-crystal X-ray diffraction. The interaction of calf thymus DNA (CT DNA) with L and CuIP has been investigated by absorption, fluorescence and viscosity titration methods. The complex CuIP displays better binding affinity than the ligand L. The observed DNA binding constant (K-b = 4.15(+/- 0.18) x 10(5) M-1) and binding site size (s = 0.19), viscosity data together with molecular docking studies of CuIP suggest groove binding and/or a partial intercalative mode of binding to CT DNA. In addition, CuIP shows good binding propensity to the bovine serum albumin (BSA) protein, giving a K-BSA value of 1.25(+/- 0.24) x 10(6) M-1. In addition, the docking studies on DNA and human serum albumin (HSA) CuIP interactions are consistent with the consequence of binding experiments. The in vitro anti-proliferative study establishes the anticancer potency of the CuIP against the human cervical (HeLa) and breast (MCF7) cancer cells; noncancer breast epithelial (MCF10a) cells have also been investigated. CuIP shows better cytotoxicity and sensitivity towards cancer cells over noncancer ones than L under identical conditions, with the appearance of apoptotic bodies. (C) 2014 Elsevier B.V. All rights reserved.

Reduced graphene oxide-titania based platform for label-free biosensor

A label-free biosensor has been fabricated using a reduced graphene oxide (RGO) and anatase titania (ant-TiO2) nanocomposite, electrophoretically deposited onto an indium tin oxide coated glass substrate. The RGO-ant-TiO2 nanocomposite has been functionalized with protein (horseradish peroxidase) conjugated antibodies for the specific recognition and detection of Vibrio cholerae. The presence of Ab-Vc on the RGO-ant-TiO2 nanocomposite has been confirmed using electron microscopy, Fourier transform infrared spectroscopy and electrochemical techniques. Electrochemical studies relating to the fabricated Ab-Vc/RGO-ant-TiO2/ITO immunoelectrode have been conducted to investigate the binding kinetics. This immunosensor exhibits improved biosensing properties in the detection of Vibrio cholerae, with a sensitivity of 18.17 x 10(6) F mol(-1) L-1 m(-2) in the detection range of 0.12-5.4 nmol L-1, and a low detection limit of 0.12 nmol L-1. The association (k(a)), dissociation (k(d)) and equilibrium rate constants have been estimated to be 0.07 nM, 0.002 nM and 0.41 nM, respectively. This Ab-Vc/RGO-ant-TiO2/ITO immunoelectrode could be a suitable platform for the development of compact diagnostic devices.

Molecular Dissection of Mycobacterium tuberculosis Integration Host Factor Reveals Novel Insights into the Mode of DNA Binding and Nucleoid Compaction

Background: mIHF belongs to a subfamily of proteins, distinct from E. coli IHF. Results: Functionally important amino acids of mIHF and the mechanism(s) underlying DNA binding, DNA bending, and site-specific recombination are distinct from that of E. coli IHF. Conclusion: mIHF functions could contribute beyond nucleoid compaction. Significance: Because mIHF is essential for growth, the molecular mechanisms identified here can be exploited in drug screening efforts. The annotated whole-genome sequence of Mycobacterium tuberculosis revealed that Rv1388 (Mtihf) is likely to encode for a putative 20-kDa integration host factor (mIHF). However, very little is known about the functional properties of mIHF or the organization of the mycobacterial nucleoid. Molecular modeling of the mIHF three-dimensional structure, based on the cocrystal structure of Streptomyces coelicolor IHF duplex DNA, a bona fide relative of mIHF, revealed the presence of Arg-170, Arg-171, and Arg-173, which might be involved in DNA binding, and a conserved proline (Pro-150) in the tight turn. The phenotypic sensitivity of Escherichia coli ihfA and ihfB strains to UV and methyl methanesulfonate could be complemented with the wild-type Mtihf but not its alleles bearing mutations in the DNA-binding residues. Protein-DNA interaction assays revealed that wild-type mIHF, but not its DNA-binding variants, binds with high affinity to fragments containing attB and attP sites and curved DNA. Strikingly, the functionally important amino acid residues of mIHF and the mechanism(s) underlying its binding to DNA, DNA bending, and site-specific recombination are fundamentally different from that of E. coli IHF. Furthermore, we reveal novel insights into IHF-mediated DNA compaction depending on the placement of its preferred binding sites; mIHF promotes DNA compaction into nucleoid-like or higher order filamentous structures. We therefore propose that mIHF is a distinct member of a subfamily of proteins that serve as essential cofactors in site-specific recombination and nucleoid organization and that these findings represent a significant advance in our understanding of the role(s) of nucleoid-associated proteins.

Performance comparison for 12 V lead-carbon hybrid ultracapacitors with substrate-integrated and conventional pasted positive plates

Lead-carbon hybrid ultracapacitors comprise positive lead dioxide plates of the lead-acid battery and negative plates of carbon-based electrical double-layer capacitors (EDLCs). Accordingly, a lead-carbon hybrid ultracapacitor has the features of both the battery and that of an EDLC. In this study, the development and performance comparison between the two types of lead-carbon hybrid ultracapacitors, namely those with substrate-integrated and conventional pasted positive plates, is presented as such a study is lacking in the literature. The study suggests that the faradaic efficiencies for both types of lead-carbon hybrid ultracapacitors are comparable. However, their capacitance values as well as energy and power densities differ significantly. For substrate-integrated positive plate hybrid ultracapacitor, capacitance and energy density values are lower, but power density values are higher than pasted positive plate lead-carbon hybrid ultracapacitors due to their shorter response time. Accordingly, internal resistance values are also lower for substrate-integrated lead-carbon hybrid ultracapacitors. Both types of lead-carbon hybrid ultracapacitors exhibit good cycle life of 100,000 pulse charge-discharge cycles with only a nominal loss in their capacitance values.

Chemical specificity and conformational flexibility in proteinase-inhibitor interaction: Scaffolds for promiscuous binding

One of the most important roles of proteins in cellular milieu is recognition of other biomolecules including other proteins. Protein protein complexes are involved in many essential cellular processes. Interfaces of protein protein complexes are traditionally known to be conserved in evolution and less flexible than other solvent interacting tertiary structural surface. But many examples are emerging where these features do not hold good. An understanding of inter-play between flexibility and sequence conservation is emerging, providing a fresh dimension to the paradigm of sequence structure function relationship. The functional manifestation of the inter-relation between sequence conservation and flexibility of interface is exemplified in this review using proteinase inhibitor protein complexes. (C) 2014 Elsevier Ltd. All rights reserved.

Room Temperature Growth of Ultrathin Au Nanowires with High Areal Density over Large Areas by in Situ Functionalization of Substrate

Although ultrathin Au nanowires (similar to 2 nm diameter) are expected to demonstrate several interesting properties, their extreme fragility has hampered their use in potential applications. One way to improve the stability is to grow them on substrates; however, there is no general method to grow these wires over large areas. The existing methods suffer from poor coverage and associated formation of larger nanoparticles on the substrate. Herein, we demonstrate a room temperature method for growth of these nanowires with high coverage over large areas by in situ functionalization of the substrate. Using control experiments, we demonstrate that an in situ functionalization of the substrate is the key step in controlling the areal density of the wires on the substrate. We show that this strategy works for a variety of substrates ranging like graphene, borosil glass, Kapton, and oxide supports. We present initial results on catalysis using the wires grown on alumina and silica beads and also extend the method to lithography-free device fabrication. This method is general and may be extended to grow ultrathin Au nanowires on a variety of substrates for other applications.

Morphology controlled synthesis of Al doped ZnO nanosheets on Al alloy substrate by low-temperature solution growth method

We report the morphology-controlled synthesis of aluminium (Al) doped zinc oxide (ZnO) nanosheets on Al alloy (AA-6061) substrate by a low-temperature solution growth method without using any external seed layer and doping process. Doped ZnO nanosheets were obtained at low temperatures of 60-90 degrees C for the growth time of 4 hours. In addition to the synthesis, the effect of growth temperature on the morphological changes of ZnO nanosheets is also reported. As-synthesized nanosheets are characterized by FE-SEM, XRD TEM and XPS for their morphology, crystallinity, microstructure and compositional analysis respectively. The doping of Al in ZnO nanosheets is confirmed with EDXS and XPS. Furthermore, the effect of growth temperature on the morphological changes was studied in the range of 50 to 95 degrees C. It was found that the thickness and height of the nanosheets varied with respect to the growth temperature. The study has given an important insight into the structural morphology with respect to the growth temperature, which in turn enabled us to determine the growth temperature window for the ZnO nanosheets. These Al doped ZnO nanosheets have potential application possibilities in gas sensors, solar cells and energy harvesting devices like nanogenerators.