Synthesis, biological studies of linear and branched arabinofuranoside-containing glycolipids and their interaction with surfactant protein A

Oligoarabinofuranoside-containing glycolipids relevant to mycobacterial cell wall components were synthesized in order to understand the functional roles of such glycolipids. A series of linear tetra-, hexa-, octa-and a branched heptasaccharide oligoarabinofuranosides, with 1 -> 2 and 1 -> 5 a-linkages between the furanoside residues, were synthesized by chemical methods from readily available monomer building blocks. Upon the synthesis of glycolipids, constituted with a double alkyl chain-substituted sn-glycerol core and oligosaccharide fragments, biological studies were performed to identify the effect of synthetic glycolipids on the biofilm formation and sliding motilities of Mycobacterium smegmatis. Synthetic glycolipids and arabinofuranosides displayed an inhibitory effect on the growth profile, but mostly on the biofilm formation and maturation. Similarly, synthetic compounds also influenced the sliding motility of the bacteria. Further, biophysical studies were undertaken, so as to identify the interactions of the glycolipids with a pulmonary surfactant protein, namely surfactant protein A (SP-A), with the aid of the surface plasmon resonance technique. Specificities of each glycolipid interacting with SP-A were thus evaluated. From this study, glycolipids were found to exhibit higher apparent association constants than the corresponding oligosaccharide portion alone, without the double alkyl group-substituted glycerol core.

Effect of ester chemical structure and peptide bond conformation in fragmentation pathways of differently metal cationized cyclodepsipeptides

Fragmentation behavior of two classes of cyclodepsipeptides, isariins and isaridins, obtained from the fungus Isaria, was investigated in the presence of different metal ions using multistage tandem mass spectrometry (MS(n)) with collision induced dissociation (CID) and validated by NMR spectroscopy. During MS(n) process, both protonated and metal-cationized isariins generated product ions belonging to the identical `b-ion' series, exhibiting initial backbone cleavage explicitly at the beta-ester bond. Fragmentation behavior for the protonated and metal-cationized acyclic methyl ester derivative of isariins was very similar. On the contrary, isaridins during fragmentation produced ions belonging to the `b' or/and the `y' ion series depending on the nature of interacting metal ions, due to initial backbone cleavages at the beta-ester linkage or/and at a specific amide linkage. Interestingly, independent of the nature of the interacting metal ions, the product ions formed from the acyclic methyl ester derivative of isaridins belonged only to the `y-type'. Complementary NMR data showed that, while all metal ions were located around the beta-ester group of isariins, the metal ion interacting sites varied across the backbone for isaridins. Combined MS and NMR data suggest that the different behavior in sequence specific charge-driven fragmentation of isariins and isaridins is predetermined because of the constituent beta-hydroxy acid residue in isariins and the cis peptide bond in isaridins.

Novel Algorithm for estimation of Swell Pressure of Fine Grained Soils Based on Diffuse Double Layer (DDL) Theory

Use of engineered landfills for the disposal of industrial wastes is currently a common practice. Bentonite is attracting a greater attention not only as capping and lining materials in landfills but also as buffer and backfill materials for repositories of high-level nuclear waste around the world. In the design of buffer and backfill materials, it is important to know the swelling pressures of compacted bentonite with different electrolyte solutions. The theoretical studies on swell pressure behaviour are all based on Diffuse Double Layer (DDL) theory. To establish a relation between the swell pressure and void ratio of the soil, it is necessary to calculate the mid-plane potential in the diffuse part of the interacting ionic double layers. The difficulty in these calculations is the elliptic integral involved in the relation between half space distance and mid plane potential. Several investigators circumvented this problem using indirect methods or by using cumbersome numerical techniques. In this work, a novel approach is proposed for theoretical estimations of swell pressures of fine-grained soil from the DDL theory. The proposed approach circumvents the complex computations in establishing the relationship between mid-plane potential and diffused plates’ distances in other words, between swell pressure and void ratio.

NETGEM: Network Embedded Temporal GEnerative Model for gene expression data

Background: Temporal analysis of gene expression data has been limited to identifying genes whose expression varies with time and/or correlation between genes that have similar temporal profiles. Often, the methods do not consider the underlying network constraints that connect the genes. It is becoming increasingly evident that interactions change substantially with time. Thus far, there is no systematic method to relate the temporal changes in gene expression to the dynamics of interactions between them. Information on interaction dynamics would open up possibilities for discovering new mechanisms of regulation by providing valuable insight into identifying time-sensitive interactions as well as permit studies on the effect of a genetic perturbation. Results: We present NETGEM, a tractable model rooted in Markov dynamics, for analyzing the dynamics of the interactions between proteins based on the dynamics of the expression changes of the genes that encode them. The model treats the interaction strengths as random variables which are modulated by suitable priors. This approach is necessitated by the extremely small sample size of the datasets, relative to the number of interactions. The model is amenable to a linear time algorithm for efficient inference. Using temporal gene expression data, NETGEM was successful in identifying (i) temporal interactions and determining their strength, (ii) functional categories of the actively interacting partners and (iii) dynamics of interactions in perturbed networks. Conclusions: NETGEM represents an optimal trade-off between model complexity and data requirement. It was able to deduce actively interacting genes and functional categories from temporal gene expression data. It permits inference by incorporating the information available in perturbed networks. Given that the inputs to NETGEM are only the network and the temporal variation of the nodes, this algorithm promises to have widespread applications, beyond biological systems. The source code for NETGEM is available from https://github.com/vjethava/NETGEM

Ferromagnetism Exhibited by Nanoparticles of Noble Metals

Gold nanoparticles with average diameters in the range 2.515 nm, prepared at the organic/aqueous interface by using tetrakis( hydroxymethyl) phosphonium chloride (THPC) as reducing agent, exhibit ferromagnetism whereby the saturation magnetization M(S) increases with decreasing diameter and varies linearly with the fraction of surface atoms. The value of M(S) is higher when the particles are present as a film instead of as a sol. Capping with strongly interacting ligands such as alkane thiols results in a higher M(S) value, which varies with the strength of the metal-sulfur bond. Ferromagnetism is also found in Pt and Ag nanoparticles prepared as sols, and the M(S) values vary as Pt > Au > Ag. A careful study of the temperature variation of the magnetization of Au nanoparticles, along with certain other observations, suggests that small bare nanoparticles of noble metals could indeed possess ferromagnetism, albeit weak, which is accentuated in the presence of capping agents, specially alkane thiols which form strong metal-sulfur bonds.

Spin State Selective Excitation of Single Quantum Transitions Using Multiple Quantum Spectroscopy- an Aid to Analyse Complex Proton NMR spectra of Oriented Molecules

NMR spectra of molecules oriented in liquid-crystalline matrix provide information on the structure and orientation of the molecules. Thermotropic liquid crystals used as an orienting media result in the spectra of spins that are generally strongly coupled. The number of allowed transitions increases rapidly with the increase in the number of interacting spins. Furthermore, the number of single quantum transitions required for analysis is highly redundant. In the present study, we have demonstrated that it is possible to separate the subspectra of a homonuclear dipolar coupled spin system on the basis of the spin states of the coupled heteronuclei by multiple quantum (MQ)−single quantum (SQ) correlation experiments. This significantly reduces the number of redundant transitions, thereby simplifying the analysis of the complex spectrum. The methodology has been demonstrated on the doubly 13C labeled acetonitrile aligned in the liquid-crystal matrix and has been applied to analyze the complex spectrum of an oriented six spin system.

A resource based game theoretical model for military conflicts

A resource interaction based game theoretical model for military conflicts is presented in this paper. The model includes both the spatial decision capability of adversaries (decision regarding movement and subsequent distribution of resources) as well as their temporal decision capability (decision regarding level of allocation of resources for conflict with adversary’s resources). Attrition is decided at present by simple deterministic models. An additional feature of this model is the inclusion of the possibility of a given resource interacting with several resources of the adversary.The decisions of the adversaries is determined by solving for the equilibrium Nash strategies given that the objectives of the adversaries may not be in direct conflict. Examples are given to show the applicability of these models and solution concepts.

Synthesis and characterization of some gold(I)-thiolate complexes having N-methylimidazole moiety

Antithyroid drugs inhibit the thyroid hormone synthesis by inactivating the thyroid peroxidase and/or iodothyronine deiodinase, which are involved in iodination and deiodination reactions. Gold(I) compounds also inhibit the thyroid hormone synthesis by interacting with the selenocysteine residue of iodothyronine deiodinase. However, the chemical reactions between these two different classes of compounds have not been studied. In this paper, we describe the interaction of therapeutic gold(I) compounds with the commonly used thiourea-based antithyroid drug, methimazole. It is observed that the gold(I) phosphine complexes (R(3)PAuCl, where R = Me, Et, Ph) react with methimazole only upon deprotonation to produce the corresponding gold(I)-thiolate complexes. Addition of PPh(3) to the gold(I)-thiolates produces (R(3)PAuPPh(3))(+) (R = Me or Et), indicating the possibility of ligand exchange reactions.

On the magnetization reversal of the oxide-based exchange spring magnet

The role of the soft phase (Ni0.8Zn0.2Fe2O4) on the magnetization reversal and coercivity mechanism of the Ni0.8Zn0.2Fe2O4/BaFe12O19 nanocomposite has been investigated. The presence of the interacting field and the disorder in the nanocomposite has been confirmed by the variation of Jr/Jr(∞) vs Jd/Jr(∞) and the irreversible magnetization. To understand the relative strength of the pinning and the nucleation, the magnetic viscosity measurement has been done and the thermal activation volume has been estimated. From the Barbier plot and the activation volume measurement, the dominant mechanism governing the magnetization reversal process has been proposed.

Oneand twodimensional single quantumand multiplequantumNMR methodologies: tools for chiral analyses

It is well known that enantiomers cannot be distinguished by NMR spectroscopy unless diastereomorphic interactions are imposed. Several chiral aligning media have therefore been reported for their visualization, although extensive studies are carried out using the liquid crystal made of polypeptide poly-γ-benzyl-L-glutamate (PBLG) in organic solvent. In PBLG medium the spin systems are weakly coupled and the first order analyses of the spectra are generally possible. But due to large number of pair wise interactions of nuclear spins resulting in many degenerate transitions the 1H NMR spectra are not only complex but also broad and featureless, in addition to an indistinguishable overlap of the spectra of enantiomers. This enormous loss of resolution severely hinders the analyses of proton spectra, even for spin systems with 5–6 interacting protons, thereby restricting itsroutine application. In this review we discuss our recently developed several one and multidimensional NMR experiments to circumvent these difficulties taking specific examples of the molecules containing a single chiral centre.

The spectral index-luminosity relationship for steep-spectrum cores in extra-galactic radio-sources

The spectral index-luminosity relationship for steep-spectrum cores in galaxies and quasars has been investigated, and it is found that the sample of galaxies supports earlier suggestions of a strong correlation, while there is weak evidence for a similar relationship for the quasars. It is shown that a strong spectral index-luminosity correlation can be used to set an upper limit to the velocities of the radio-emitting material which is expelled from the nucleus in the form of collimated beams or jets having relativistic bulk velocities. The data on cores in galaxies indicate that the Lorentz factors of the radiating material are less than about 2.

Vlbi observations of a mixed selection of extra-galactic objects

VLBI observations at 6 cm reported of several weak radio cores of normal and Seyfert galaxies, of radio sources which have jets or a head tail morphology as well as some stronger cores of flat spectrum galaxies from the NRAO-Bonn "S 4", survey. Nearly all sources were detected at an angular resolution of approximately 15 milli arc s. Some of the sources are resolved at this level.

Nonspecific Interaction between DNA and Protein allows for Cooperativity: A Case Study with Mycobacterium DNA Binding Protein

Different DNA-binding proteins have different interaction modes with DNA. Sequence-specific DNA protein interaction has been mostly associated with regulatory processes inside a cell, and as such extensive studies have been made. Adequate data is also available on nonspecific DNA protein interaction, as an intermediate to protein's search for its cognate partner. Multidomain nonspecific DNA protein interaction involving physical sequestering of DNA has often been implicated to regulate gene expression indirectly. However, data available on this type of interaction is limited. One such interaction is the binding of DNA with mycobacterium DNA binding proteins. We have used the Langmuir-Blodgett technique to evaluate for the first time the kinetics and thermodynamics of Mycobacterium smegmatis Dps 1 binding to DNA. By immobilizing one of the interacting partners, we have shown that, when a kinetic bottleneck is applied, the binding mechanism showed cooperative binding (n = 2.72) at lower temperatures, but the degree of cooperativity gradually reduces (n = 1.38) as the temperature was increased We have also compared the kinetics and thermodynamics of sequence-specific and nonspecific DNA protein interactions under the same set of conditions.

A density matrix renormalization group method study of optical properties of porphines and metalloporphines

The symmetrized density matrix renormalization group method is used to study linear and nonlinear optical properties of free base porphine and metalloporphine. Long-range interacting model, namely, Pariser-Parr-Pople model is employed to capture the quantum many-body effect in these systems. The nonlinear optical coefficients are computed within the correction vector method. The computed singlet and triplet low-lying excited state energies and their charge densities are in excellent agreement with experimental as well as many other theoretical results. The rearrangement of the charge density at carbon and nitrogen sites, on excitation, is discussed. From our bond order calculation, we conclude that porphine is well described by the 18-annulenic structure in the ground state and the molecule expands upon excitation. We have modeled the regular metalloporphine by taking an effective electric field due to the metal ion and computed the excitation spectrum. Metalloporphines have D(4h) symmetry and hence have more degenerate excited states. The ground state of metalloporphines shows 20-annulenic structure, as the charge on the metal ion increases. The linear polarizability seems to increase with the charge initially and then saturates. The same trend is observed in third order polarizability coefficients. (C) 2012 American Institute of Physics. [doi: 10.1063/1.3671946]