MODELING AND SIMULATION OF HYDRODYNAMIC INTERACTION OF DNA IN A MICRO-FLUIDIC CHANNEL

The motion of DNA (in the bulk solution) and the non-Newtonian effective fluid behavior are considered separately and self-consistently with the fluid motion satisfying the no-slip boundary condition on the surface of the confining geometry in the presence of channel pressure gradients. A different approach has been developed to model DNA in the micro-channel. In this study the DNA is assumed as an elastic chain with its characteristic Young's modulus, Poisson's ratio and density. The force which results from the fluid dynamic pressure, viscous forces and electromotive forces is applied to the elastic chain in a coupled manner. The velocity fields in the micro-channel are influenced by the transport properties. Simulations are carried out for the DNAs attached to the micro-fluidic wall. Numerical solutions based on a coupled multiphysics finite element scheme are presented. The modeling scheme is derived based on mass conservation including biomolecular mass, momentum balance including stress due to Coulomb force field and DNA-fluid interaction, and charge transport associated to DNA and other ionic complexes in the fluid. Variation in the velocity field for the non-Newtonian flow and the deformation of the DNA strand which results from the fluid-structure interaction are first studied considering a single DNA strand. Motion of the effective center of mass is analyzed considering various straight and coil geometries. Effects of DNA statistical parameters (geometry and spatial distribution of DNAs along the channel) on the effective flow behavior are analyzed. In particular, the dynamics of different DNA physical properties such as radius of gyration, end-to-end length etc. which are obtained from various different models (Kratky-Porod, Gaussian bead-spring etc.) are correlated to the nature of interaction and physical properties under the same background fluid environment.

Interaction of Silver Nanoparticles with Serum Proteins Affects Their Antimicrobial Activity In Vivo

The emergence of multidrug-resistant bacteria is a global threat for human society. There exist recorded data that silver was used as an antimicrobial agent by the ancient Greeks and Romans during the 8th century. Silver nanoparticles (AgNPs) are of potential interest because of their effective antibacterial and antiviral activities, with minimal cytotoxic effects on the cells. However, very few reports have shown the usage of AgNPs for antibacterial therapy in vivo. In this study, we deciphered the importance of the chosen methods for synthesis and capping of AgNPs for their improved activity in vivo. The interaction of AgNPs with serum albumin has a significant effect on their antibacterial activity. It was observed that uncapped AgNPs exhibited no antibacterial activity in the presence of serum proteins, due to the interaction with bovine serum albumin (BSA), which was confirmed by UV-Vis spectroscopy. However, capped AgNPs with citrate or poly(vinylpyrrolidone)] exhibited antibacterial properties due to minimized interactions with serum proteins. The damage in the bacterial membrane was assessed by flow cytometry, which also showed that only capped AgNPs exhibited antibacterial properties, even in the presence of BSA. In order to understand the in vivo relevance of the antibacterial activities of different AgNPs, a murine salmonellosis model was used. It was conclusively proved that AgNPs capped with citrate or PVP exhibited significant antibacterial activities in vivo against Salmonella infection compared to uncapped AgNPs. These results clearly demonstrate the importance of capping agents and the synthesis method for AgNPs in their use as antimicrobial agents for therapeutic purposes.

Dinuclear zinc bis(thiosemicarbazone) complexes: Synthesis, in vitro anticancer activity, cellular uptake and DNA interaction study

Four dinucleating bis(thiosemicarbazone) ligands and their zinc complexes have been synthesized and characterized by multinuclear NMR (H-1 and C-13), IR, UV-Vis, ESI-MS and fluorescence spectroscopic techniques. Their purity was assessed by elemental analysis. Cytotoxicity was tested against five human cancer cell lines using the sulphorhodamine B (SRB) assay, where one of the complexes, 1,3-bis{biacetyl-2'-(4 `'-N-pyrrolidinylthiosemicarbazone)-3'-(4 `'-N-pyrrolidinylthiosemicarbazone) zinc(II)} propane (6), was found to be quite cytotoxic against MCF-7 (breast cancer) and HepG2 (hepatoma cancer) cell lines, with a potency similar to that of the well known anticancer drug adriamycin. It is evident from the cellular uptake studies that the uptake is same for the active complex 6 and the inactive complex 8 (1,6-bis{biacetyl- 2'-(4 `'-N-pyrrolidinylthiosemicarbazone)-3'-(4 `'-N-pyrrolidinylthiosemicarbazone) zinc(II)} hexane) in MCF-7 and HepG2 cell lines. In vitro DNA binding and cleavage studies revealed that all complexes bind with DNA through electrostatic interaction, and cause no significant cleavage of DNA. (C) 2'13 Elsevier B. V. All rights reserved.

Energy Hyperspace for Stacking Interaction in AU/AU Dinucleotide Step: Dispersion-Corrected Density Functional Theory Study

Double helical structures of DNA and RNA are mostly determined by base pair stacking interactions, which give them the base sequence-directed features, such as small roll values for the purine-pyrimidine steps. Earlier attempts to characterize stacking interactions were mostly restricted to calculations on fiber diffraction geometries or optimized structure using ab initio calculations lacking variation in geometry to comment on rather unusual large roll values observed in AU/AU base pair step in crystal structures of RNA double helices. We have generated stacking energy hyperspace by modeling geometries with variations along the important degrees of freedom, roll, and slide, which were chosen via statistical analysis as maximally sequence dependent. Corresponding energy contours were constructed by several quantum chemical methods including dispersion corrections. This analysis established the most suitable methods for stacked base pair systems despite the limitation imparted by number of atom in a base pair step to employ very high level of theory. All the methods predict negative roll value and near-zero slide to be most favorable for the purine-pyrimidine steps, in agreement with Calladine's steric clash based rule. Successive base pairs in RNA are always linked by sugar-phosphate backbone with C3-endo sugars and this demands C1-C1 distance of about 5.4 angstrom along the chains. Consideration of an energy penalty term for deviation of C1-C1 distance from the mean value, to the recent DFT-D functionals, specifically B97X-D appears to predict reliable energy contour for AU/AU step. Such distance-based penalty improves energy contours for the other purine-pyrimidine sequences also. (c) 2013 Wiley Periodicals, Inc. Biopolymers 101: 107-120, 2014.

Molecular Insights Revealing Interaction of Tim23 and Channel Subunits of Presequence Translocase

Tim23 is an essential channel-forming subunit of the presequence translocase recruiting multiple components for assembly of the core complex, thereby regulating the protein translocation process. However, understanding of the precise interaction of subunits associating with Tim23 remains largely elusive. Our findings highlight that transmembrane helix 1 (TM1) is required for homodimerization of Tim23, while, together with TM2, it is involved in preprotein binding within the channel. Based on our evidence, we predict that the TM1 and TM2 from each dimer are involved in the formation of the central translocation pore, aided by Tim17. Furthermore, TM2 is also involved in the recruitment of Tim21 and the presequence-associated motor (PAM) subcomplex to the Tim23 channel, while the matrix-exposed loop L1 generates specificity in their association with the core complex. Strikingly, our findings indicate that the C-terminal sequence of Tim23 is dispensable for growth and functions as an inhibitor for binding of Tim21. Our model conceptually explains the cooperative function between Tam41 and Pam17 subunits, while the antagonistic activity of Tim21 predominantly determines the bound and free forms of the PAM subcomplex during import.

Protumorigenic actions of S100A2 involve regulation of PI3/Akt signaling and functional interaction with Smad3

S100 family of calcium-binding proteins is commonly upregulated in a variety of tumor types and is often associated with tumor progression. Among several S100 members, altered expression of S100A2 is a potential diagnostic and prognostic marker in cancer. Several reports suggest a role for S100A2 in metastasis. Earlier, our studies established regulation of S100A2 by transforming growth factor- (TGF-) and its involvement in TGF--mediated cancer cell invasion and migration. However, the molecular mechanisms of S100A2 protumorigenic actions remain unexplored. In the present study, we demonstrate that overexpression of S100A2 in A549 lung cancer cells induced epithelialmesenchymal transition (EMT) followed by increased invasion, loose colony morphology in soft agar and enhanced Akt phosphorylation (Ser-473). Furthermore, overexpression of S100A2 led to increased tumor growth in immunocompromised mice. In agreement, immunohistochemical examination of resected xenograft tumors established inverse correlation between S100A2 and E-cadherin expression together with activated Akt signaling. Interestingly, our study demonstrates a strong dependence of S100A2 and Smad3 in TGF--induced Hep3B cell EMT and invasion. Most importantly, we demonstrate that these effects of S100A2 are manifested through functional interaction with Smad3, which is enhanced in the presence of high calcium and TGF-. S100A2 stabilizes Smad3 and binds to its C-terminal MH2 domain. Additionally, loss of S100A2 attenuates the transcription of TGF-/Smad3 target genes involved in tumor promotion, such as PA1-1 and vimentin. Collectively, our findings present the first mechanistic details of S100A2 protumorigenic actions and its involvement in TGF--mediated cancer cell invasion and EMT.

Shock-boundary layer interaction and transonic flutter

The transonic flutter dip of an aeroelastic system is primarily caused by compressibility of the flowing fluid. Viscous effects are not dominant in the pre-transonic dip region. In fact, an Euler solver can predict this flutter boundary with considerable accuracy. However with an increase in Mach number the shock moves towards the trailing edge causing shock induced separation. This shock-boundary layer interaction changes the flutter boundary in the transonic and post-transonic dip region significantly. We discuss the effect of viscosity in changing the flutter boundary in the post-transonic dip region using a RANS solver coupled to a two-degree of freedom model of the structural dynamics of a wing.

mu-Oxamido binuclear copper (II) complexes: Synthesis, crystal structure, DNA interaction and antibacterial studies

Four binuclear copper (II) complexes Cu(oxpn)Cu(B)](2+) (2-5) bridged by N, N'-bis3-(methylamino) propyl] oxamide (oxpn), where, B is N, N-donor heterocyclic bases (viz. 2,2'-bipyridine (bpy, 2), 1,10-phenathroline (phen, 3), dipyrido3,2-d:2',3'-f]quinoxaline (dpq, 4) and dipyrido3,2-a:2',3'-c]phenazine (dppz, 5) are synthesized, characterized by different spectroscopic and single crystal X-ray data technique. The phen (3) and dpq (4) complexes were structurally characterized by X-ray data analysis. Their DNA binding, oxidative cleavage and antibactirial activities were studied. The dpq (4) and dppz (5) complexes are avid binders to the Calf thymus DNA (CT-DNA). The phen (3), dpq (4) and dppz (5) complexes show efficient oxidative cleavage of supercoiled DNA (SC DNA) through hydroxyl radical ((OH)-O-center dot) pathway in the presence of Mercaptopropionic acid (MPA). (C) 2013 Elsevier Ltd. All rights reserved.

Synthesis, crystal structure, DNA interaction and cleavage activities of mononuclear and trinuclear copper(II) complexes

Mono- and trinuclear copper(II) complexes with 2-1-(2-dimethylamino-ethylamino)-ethyl]-phenol (HL) have been synthesized and structurally characterized. The mononuclear complex Cu(L)(H2O)(ONO2)] (1) crystallizes in monoclinic space group P2(1) /n with a square pyramidal Cu(II) center coordinated by the tridentate Schiff base (L) and a water ligand in the equatorial plane and an oxygen atom from nitrate in the axial position. The trinuclear complex (CuL)(3)(mu(3)-OH)](ClO4)(2)center dot H2O (2) crystallizes in hexagonal space group P6(3); all three copper atoms are five-coordinate with square pyramidal geometries. The interactions of these complexes with calf-thymus DNA have been investigated using absorption spectrophotometry. The mononuclear complex binds more strongly than the trinuclear complex. The DNA cleavage activity of these complexes has been studied on double-stranded pBR 322 plasmid DNA by gel electrophoresis experiments in the absence and in the presence of added oxidant (H2O2). The trinuclear complex cleaves DNA more efficiently than the mononuclear complex in the presence of H2O2.

Simulation of inhomogeneous distributions of ultracold atoms in an optical lattice via a massively parallel implementation of nonequilibrium strong-coupling perturbation theory

We present a nonequilibrium strong-coupling approach to inhomogeneous systems of ultracold atoms in optical lattices. We demonstrate its application to the Mott-insulating phase of a two-dimensional Fermi-Hubbard model in the presence of a trap potential. Since the theory is formulated self-consistently, the numerical implementation relies on a massively parallel evaluation of the self-energy and the Green's function at each lattice site, employing thousands of CPUs. While the computation of the self-energy is straightforward to parallelize, the evaluation of the Green's function requires the inversion of a large sparse 10(d) x 10(d) matrix, with d > 6. As a crucial ingredient, our solution heavily relies on the smallness of the hopping as compared to the interaction strength and yields a widely scalable realization of a rapidly converging iterative algorithm which evaluates all elements of the Green's function. Results are validated by comparing with the homogeneous case via the local-density approximation. These calculations also show that the local-density approximation is valid in nonequilibrium setups without mass transport.

Electronic band structure and Fermi surfaces of the quasi-two-dimensional monophosphate tungsten bronze, P4W12O44

The electronic structure of quasi-two-dimensional monophosphate tungsten bronze, P4W12O44, has been investigated by high-resolution angle-resolved photoemission spectroscopy and density functional theoretical calculations. Experimental electron-like bands around Gamma point and Fermi surfaces have similar shapes as predicted by calculations. Fermi surface mapping at different temperatures shows a depletion of density of states at low temperature in certain flat portions of the Fermi surfaces. These flat portions of the Fermi surfaces satisfy the partial nesting condition with incommensurate nesting vectors q(1) and q(2), which leads to the formation of charge density waves in this phosphate tungsten bronzes. The setting up of charge density wave in these bronzes can well explain the anomaly observed in its transport properties. Copyright (C) EPLA, 2014

PLIC: protein-ligand interaction clusters

Most of the biological processes are governed through specific protein-ligand interactions. Discerning different components that contribute toward a favorable protein-ligand interaction could contribute significantly toward better understanding protein function, rationalizing drug design and obtaining design principles for protein engineering. The Protein Data Bank (PDB) currently hosts the structure of similar to 68 000 protein-ligand complexes. Although several databases exist that classify proteins according to sequence and structure, a mere handful of them annotate and classify protein-ligand interactions and provide information on different attributes of molecular recognition. In this study, an exhaustive comparison of all the biologically relevant ligand-binding sites (84 846 sites) has been conducted using PocketMatch: a rapid, parallel, in-house algorithm. PocketMatch quantifies the similarity between binding sites based on structural descriptors and residue attributes. A similarity network was constructed using binding sites whose PocketMatch scores exceeded a high similarity threshold (0.80). The binding site similarity network was clustered into discrete sets of similar sites using the Markov clustering (MCL) algorithm. Furthermore, various computational tools have been used to study different attributes of interactions within the individual clusters. The attributes can be roughly divided into (i) binding site characteristics including pocket shape, nature of residues and interaction profiles with different kinds of atomic probes, (ii) atomic contacts consisting of various types of polar, hydrophobic and aromatic contacts along with binding site water molecules that could play crucial roles in protein-ligand interactions and (iii) binding energetics involved in interactions derived from scoring functions developed for docking. For each ligand-binding site in each protein in the PDB, site similarity information, clusters they belong to and description of site attributes are provided as a relational database-protein-ligand interaction clusters (PLIC).

NaOsO3: A high Neel temperature 5d oxide

The origin of a high Neel temperature in a 5d oxide, NaOsO3, has been analyzed within the mean-field limit of a multiband Hubbard model and compared with the analogous 4d oxide, SrTcO3. Our analysis shows that there are a lot of similarities in both of these oxides on the dependence of the effective exchange interaction strength (J(0)) on the electron-electron interaction strength ( U). However, the relevant value of U in each system puts them in different portions of the parameter space. Although the Neel temperature for NaOsO3 is less than that for SrTcO3, our results suggest that there could be examples among other 5d oxides that have a higher Neel temperature. We have also examined the stability of the G-type antiferromagnetic state found in NaOsO3 as a function of electron doping within GGA + U calculations and find a robust G-type antiferromagnetic metallic state stabilized. The most surprising aspect of the doped results is the rigid bandlike evolution of the electronic structure, which indicates that the magnetism in NaOsO3 is not driven by Fermi surface nesting.

Context dependency of rewards and services in an Indian ant-plant interaction: southern sites favour the mutualism between plants and ants

Protection-based ant-plant mutualisms may vary in strength due to differences in ant rewards, abundance of protective ants and herbivory pressure. We investigated geographical and temporal variation in host plant traits and herbivory pressure at five sites spanning the distribution range of the myrmecophyte Humboldtia brunonis (Fabaceae) in the Indian Western Ghats. Southern siteshad, onaverage, 2.4 times greater abundance of domatia-bearing individuals, 1.6 times greater extrafloral nectary numbers per leaf, 1.2 times larger extrafloral nectary sizes, 2.2 times greater extrafloral nectar (EFN) volumes and a two-fold increase in total amino acid and total sugar concentrations in EFN compared with northern sites. Astrong protection-based mutualismwith ants occurred at only one southern site where herbivory was highest, suggesting that investments in attracting ants correlate with anti-herbivore benefits gained from the presence of protective ants. Our results confirm a temporally stable north-south gradient in myrmecophytic traits in this ant-plant as several of these traits were re-sampled after a 5-y interval. However, the chemical composition of EFN varied at both spatial and short-term temporal scales suggesting that only repeated measurements of rewards such as EFN can reveal the real spectrum of trait variation in an ant-plant mutualistic system.