CancerLectinDB: a database of lectins relevant to cancer

The role of lectins in mediating cancer metastasis, apoptosis as well as various other signaling events has been well established in the past few years. Data on various aspects of the role of lectins in cancer is being accumulated at a rapid pace. The data on lectins available in the literature is so diverse, that it becomes difficult and time-consuming, if not impossible to comprehend the advances in various areas and obtain the maximum benefit. Not only do the lectins vary significantly in their individual functional roles, but they are also diverse in their sequences, structures, binding site architectures, quaternary structures, carbohydrate affinities and specificities as well as their potential applications. An organization of these seemingly independent data into a common framework is essential in order to achieve effective use of all the data towards understanding the roles of different lectins in different aspects of cancer and any resulting applications. An integrated knowledge base (CancerLectinDB) together with appropriate analytical tools has therefore been developed for lectins relevant for any aspect of cancer, by collating and integrating diverse data. This database is unique in terms of providing sequence, structural, and functional annotations for lectins from all known sources in cancer and is expected to be a useful addition to the number of glycan related resources now available to the community. The database has been implemented using MySQL on a Linux platform and web-enabled using Perl-CGI and Java tools. Data for individual lectins pertain to taxonomic, biochemical, domain architecture, molecular sequence and structural details as well as carbohydrate specificities. Extensive links have also been provided for relevant bioinformatics resources and analytical tools. Availability of diverse data integrated into a common framework is expected to be of high value for various studies on lectin cancer biology.

Consistent quaternion interpolation for objective finite element approximation of geometrically exact beam

We explore an isoparametric interpolation of total quaternion for geometrically consistent, strain-objective and path-independent finite element solutions of the geometrically exact beam. This interpolation is a variant of the broader class known as slerp. The equivalence between the proposed interpolation and that of relative rotation is shown without any recourse to local bijection between quaternions and rotations. We show that, for a two-noded beam element, the use of relative rotation is not mandatory for attaining consistency cum objectivity and an appropriate interpolation of total rotation variables is sufficient. The interpolation of total quaternion, which is computationally more efficient than the one based on local rotations, converts nodal rotation vectors to quaternions and interpolates them in a manner consistent with the character of the rotation manifold. This interpolation, unlike the additive interpolation of total rotation, corresponds to a geodesic on the rotation manifold. For beam elements with more than two nodes, however, a consistent extension of the proposed quaternion interpolation is difficult. Alternatively, a quaternion-based procedure involving interpolation of relative rotations is proposed for such higher order elements. We also briefly discuss a strategy for the removal of possible singularity in the interpolation of quaternions, proposed in [I. Romero, The interpolation of rotations and its application to finite element models of geometrically exact rods, Comput. Mech. 34 (2004) 121–133]. The strain-objectivity and path-independence of solutions are justified theoretically and then demonstrated through numerical experiments. This study, being focused only on the interpolation of rotations, uses a standard finite element discretization, as adopted by Simo and Vu-Quoc [J.C. Simo, L. Vu-Quoc, A three-dimensional finite rod model part II: computational aspects, Comput. Methods Appl. Mech. Engrg. 58 (1986) 79–116]. The rotation update is achieved via quaternion multiplication followed by the extraction of the rotation vector. Nodal rotations are stored in terms of rotation vectors and no secondary storages are required.

Chemically Programmed Ultrahigh Density Two-Dimensional Semiconductor Superlattice Array

Designing an ultrahigh density linear superlattice array consisting of periodic blocks of different semiconductors in the strong confinement regime via a direct synthetic route remains an unachieved challenge in nanotechnology. We report a general synthesis route for the formulation of a large-area ultrahigh density superlattice array that involves adjoining multiple units of ZnS rods by prolate US particles at the tips. A single one-dimensional wire is 300-500 nm long and consists of periodic quantum wells with a barrier width of 5 nm provided by ZnS and a well width of 1-2 nm provided by CdS, defining a superlattice structure. The synthesis route allows for tailoring of ultranarrow laserlike emissions (fwhm approximate to 125 meV) originating from strong interwell energy dispersion along with control of the width, pitch, and registry of the superlattice assembly. Such an exceptional high-density superlattice array could form the basis of ultrahigh density memories in addition to offering opportunities for technological advancement in conventional heterojunction-based device applications.

Interaction of cationic amphiphilic drugs with lipid A: Implications for development of endotoxin antagonists

This report presents evidence for the interactions of several classes of cationic amphiphilic drugs including the phenothiazines, aminoquinolines, biguanides, and aromatic diamidines, with lipid A, the endotoxic principle of lipopolysaccharides. The interactions of the drugs were quantitatively assessed by fluorescence methods. The affinities of the drugs for lipid A parallel their endotoxin-antagonistic effects in the Limulus gelation assay. Dicationic compounds bind lipid A with greater affinity; the affinity of such molecules increases exponentially as a function of the distance between the basic moieties. The bis-amidine drug - pentamidine - examined in greater detail, binds lipid A with high affinity (apparent K-d: 0.12 mu M), and LPS, probably due to simultaneous interactions of the terminal amidine groups with the anionic phosphates on lipid A. The sequestration of endotoxin by pentamidine reduces its propensity to bind to cells, and the complex exhibits attenuated toxicity in biological assays. These results have implications in the development of therapeutic strategies against endotoxin-related disease states.

Disallowed Ramachandran Conformations of Amino Acid Residues in Protein Structures

An analysis of the nature and distribution of disallowed Ramachandran conformations of amino acid residues observed in high resolution protein crystal structures has been carried out. A data set consisting of 110 high resolution, non-homologous, protein crystal structures from the Brookhaven Protein Data Bank was examined. The data set consisted of a total of 18,708 non-Gly residues, which were characterized on the basis of their backbone dihedral angles (φ, ψ). Residues falling outside the defined “broad allowed limits” on the Ramachandran map were chosen and the reportedB-factor value of the α-carbon atom was used to further select well defined disallowed conformations. The conformations of the selected 66 disallowed residues clustered in distinct regions of the Ramachandran map indicating that specific φ, ψ angle distortions are preferred under compulsions imposed by local constraints. The distribution of various amino acid residues in the disallowed residue data set showed a predominance of small polar/charged residues, with bulky hydrophobic residues being infrequent. As a further check, for all the 66 cases non-hydrogen van der Waals short contacts in the protein structures were evaluated and compared with the ideal “Ala-dipeptide” constructed using disallowed dihedral angle (φ, ψ) values. The analysis reveals that short contacts are eliminated in most cases by local distortions of bond angles. An analysis of the conformation of the identified disallowed residues in related protein structures reveals instances of conservation of unusual stereochemistry.

Studies on the tryptophan residues of soybean agglutinin. Involvement in saccharide binding

Modification of tryptophan side chains of soybean agglutinin (SBA) with N-bromosuccinimide results in a loss of the hemagglutinating and carbohydrate binding activities of the protein. One residue/subunit is probably essential for the binding activity. Modification leads to a large decrease in the fluorescene of the protein accompained by a blue shift. Iodide ion quenching of the protein fluorescence shows that saccharide binding results in a decreased accessibility of some of the tryptophan side chains. These results strongly point towards the involvement of tryptophan residues in the active site of SBA.

Seeing is Believing: Electron Microscopy for Investigating Nanostructures

Controlling the properties of nanostructures requires a detailed understanding of structure, microstructure, and chemistry at ever-decreasing length scales. The modern day transmission electron microscope has thus become an indispensable tool in the study of nanostructures. In this Perspective, we present a brief account of the capabilities of the TEM with some typical examples for characterizing nanostructures. The modern-day TEM has moved from a simple characterization tool to a nanoscale laboratory enabling in situ observation of several fundamental processes at unprecedented resolution levels.

A generalized equation for diffusion in liquids

The association parameter in the diffuswn equaiior, dye fo Wiike one Chong has been interpreted in deferminable properties, thus permitting easily the calculation of the same for unknown systems. The proposed eqyotion a!se holds goods for water as soiute in organic solvenfs. The over-all percentage error remains the sarrse as that of the original equation.

An immunochemical study of ovine pituitary follicle-stimulating hormone (FSH)

An immunochemical study of ovine follicle-stimulating hormone and its antibody carried out by using precipitin, agglutinating and complement-fixation systems, has suggested that the follicle-stimulating hormone, possibly by virtue of it being a univalent antigen, forms a soluble complex with its specific antibody. This antiserum is species nonspecific in that it is able to neutralize the follicle-stimulating activity of rat, mouse, hamster, guinea pig pituitary extracts, and pregnant mare serum gonadotropin. Human chorionic gonadotropin, however, has been shown not to form a complex with the follicle-stimulating hormone specific antibody.

Flow of a maxwell liquid fluid between two rotating coaxial cones having the same vertex

We consider the secondary flows arising in the motion of a Maxwell fluid between two rotating coaxial cones having the same vertex. We find that in any meridian plane passing through the common axis of the cones, the flow field is divided into two regions. Such a division of flow field was first reported by Bhatnagar and Rathna.

Multi-criteria seismic hazard evaluation for Bangalore city, India

Different seismic hazard components pertaining to Bangalore city,namely soil overburden thickness, effective shear-wave velocity, factor of safety against liquefaction potential, peak ground acceleration at the seismic bedrock, site response in terms of amplification factor, and the predominant frequency, has been individually evaluated. The overburden thickness distribution, predominantly in the range of 5-10 m in the city, has been estimated through a sub-surface model from geotechnical bore-log data. The effective shear-wave velocity distribution, established through Multi-channel Analysis of Surface Wave (MASW) survey and subsequent data interpretation through dispersion analysis, exhibits site class D (180-360 m/s), site class C (360-760 m/s), and site class B (760-1500 m/s) in compliance to the National Earthquake Hazard Reduction Program (NEHRP) nomenclature. The peak ground acceleration has been estimated through deterministic approach, based on the maximum credible earthquake of M-W = 5.1 assumed to be nucleating from the closest active seismic source (Mandya-Channapatna-Bangalore Lineament). The 1-D site response factor, computed at each borehole through geotechnical analysis across the study region, is seen to be ranging from around amplification of one to as high as four times. Correspondingly, the predominant frequency estimated from the Fourier spectrum is found to be predominantly in range of 3.5-5.0 Hz. The soil liquefaction hazard assessment has been estimated in terms of factor of safety against liquefaction potential using standard penetration test data and the underlying soil properties that indicates 90% of the study region to be non-liquefiable. The spatial distributions of the different hazard entities are placed on a GIS platform and subsequently, integrated through analytical hierarchal process. The accomplished deterministic hazard map shows high hazard coverage in the western areas. The microzonation, thus, achieved is envisaged as a first-cut assessment of the site specific hazard in laying out a framework for higher order seismic microzonation as well as a useful decision support tool in overall land-use planning, and hazard management. (C) 2010 Elsevier Ltd. All rights reserved.

High efficiency infrared antireflection coatings (ARCs) for space optics

Simple ARC designs for germanium (Ge) optics useful in spaceborne electro-optical systems have been generated. It is seen that the designs which are non-quarterwave in nature are efficient in terms of spectral coverage and residual reflection loss. They have been realised experimentally and the resulting ARCs are found to have very good spectral and durability properties.

Liquid Limit Of Kaolinitic Soils

This paper elucidates the relative importance of soil structure and various compositional factors in influencing the liquid limit of natural kaolinitic soils. Earlier studies dealt with purified systems and anticipated that the liquid limit of the soils would increase with percentage clay size fraction and surface area, and that soils with a greater degree of paricle flocculation would possess a higher liquid limit than soils with a more parallel particle arrangement. The results revealed that the inter-particle attraction and repulsion forces have a prominent role in determining the liquid limit of kaolinitic soils. These forces determine the particle arrangement (clay fabric) which in turn regulates the liquid limit values. The influence of clay fabric was ascertained from the relationships of liquid limit with shrinkage limit and sediment volume (in water) values. It was anticipated that kaolinitic soils with a greater degree of particle flocculatin and a higher liquid limit would shrink less and occupy a higher sedimentation volume. As expected an increase in liquid limit was accompanied by an increase in shrinkage limit and sediment volume in water.

A novel supersecondary structure in globular proteins comprising the collagen-like helix and ?-turn

A structure consisting of the polyproline-II or collagen-like helix immediately succeeded by a ?-turn is seen in several synthetic peptides and has been suggested to be the conformational requirement for proline hydroxylation in nascent procollagen. Using a simple algorithm for detecting secondary structures, we have analysed crystal structure data on 40 globular proteins and have found eight examples of the collagen-helix + ?-turn supersecondary structure in 15 proteins that contain the collagen-like helical segments.