Structure of Sesbania mosaic virus at 3 angstrom resolution

Sesbania mosaic virus (SMV) is an isometric, ss-RNA plant virus found infecting Sesbania grandiflora plants in fields near Tirupathi, South India. The virus particles, which sediment at 116 S at pH 5.5, swell upon treatment with EDTA at pH 7.5 resulting in the reduction of the sedimentation coefficient to 108 S. SMV coat protein amino acid sequence was determined and found to have approximately 60% amino acid sequence identity with that of southern bean mosaic virus (SBMV). The amino terminal 60 residue segment, which contains a number of positively charged residues, is less well conserved between SMV and SBMV when compared to the rest of the sequence. The 3D structure of SMV was determined at 3.0 Å resolution by molecular replacement techniques using SBMV structure as the initial phasing model. The icosahedral asymmetric unit was found to contain four calcium ions occurring in inter subunit interfaces and three protein subunits, designated A, B and C. The conformation of the C subunit appears to be different from those of A and B in several segments of the polypeptide. These observations coupled with structural studies on SMV partially depleted of calcium suggest a plausible mechanisms for the initiation of the disassembly of the virus capsid.

Study of fracture behaviour of bond coats on nickel superalloy by three-point bending of microbeams

A microbeam testing geometry is designed to study the variation in fracture toughness across a compositionally graded NiAl coating on a superalloy substrate. A bi-material analytical model of fracture is used to evaluate toughness by deconvoluting load-displacement data generated in a three-point bending test. It is shown that the surface layers of a diffusion bond coat can be much more brittle than the interior despite the fact that elastic modulus and hardness do not display significant variations. Such a gradient in toughness allows stable crack propagation in a test that would normally lead to unstable fracture in a homogeneous, brittle material. As the crack approaches the interface, plasticity due to the presence of Ni3Al leads to gross bending and crack bifurcation.

Cellular and molecular regulation of mammalian blastocyst hatching

In mammals including humans, failure in blastocyst hatching and implantation leads to early embryonic loss and infertility. Prior to implantation, the blastocyst must hatch out of its acellular glycoprotein coat, the zona pellucida (ZP). The phenomenon of blastocyst hatching is believed to be regulated by (i) dynamic cellular components such as actin-based trophectodermal projections (TEPs), and (ii) a variety of autocrine and paracrine molecules such as growth factors, cytokines and proteases. The spatio-temporal regulation of zona lysis by blastocyst-derived cellular and molecular signaling factors is being keenly investigated. Our studies show that hamster blastocyst hatching is acelerated by growth factors such as heparin binding-epidermal growth factor and leukemia inhibitory factor and that embryo-derived, cysteine proteases including cathepsins are responsible for blastocyst hatching. Additionally, we believe that cyclooxygenase-generated prostaglandins, estradiol-17 beta mediated estrogen receptor-alpha signaling and possibly NF kappa B could be involved in peri-hatching development. Moreover, we show that TEPs are intimately involved with lysing ZP and that the TEPs potentially enrich and harbor hatching-enabling factors. These observations provide new insights into our understanding of the key cellular and molecular regulators involved in the phenomenon of mammalian blastocyst hatching, which is essential for the establishment of early pregnancy.

Structure and assembly of Sesbania mosaic virus

Sesbania mosaic virus (SeMV) is a ss-RNA (4149 nt) plant sobemovirus isolated from farmer's field around Tirupathi, Andhra Pradesh. The viral capsid (30 nm diameter) consists of 180 copies of protein subunits (MW 29 kDa) organized with icosahedral symmetry. In order to understand the mechanism of assembly of SeMV, a large number of deletion and substitution mutants of the coat protein (CP) were constructed. Recombinant SeMV CP (rCP) as well as the N-terminal rCP deletion mutant Delta N22 were found to assemble in E. coli into virus-like particles (VLPs). Delta N36 and Delta N65 mostly formed smaller particles consisting of 60 protein subunits. Although particlem assembly was not affected due to the substitution of aspartates (D14 and D149) that coordinate calcium ions by asparagines, the stability of the resulting capsids was drastically reduced. Deletion of residues forming a characteristic beta-annulus at the icosahedral 3-folds did not affect the assembly of VLPs. Mutation of a single tryptophan, which occurs near the icosahedral fivefold axis to glutamate or lysine, resulted in the disruption of the capsid leading to soluble dimers that resembled the quasi-dimer structure of the native virus. Replacement of positively charged residues in the amino terminal segment of CP resulted in the formation of empty shells. Based on these observations, a plausible mechanism of assembly is proposed.

Conformational characteristics of asparaginyl residues in proteins

Backbone conformations at 1064 asparaginyl residues in 123 non-homologous, high-resolution X-ray structures of proteins were analysed. Asn adopts conformations in left-handed x-helical region and other partially allowed regions in the Ramachandran map more readily than any other non-glycyl residue. Asn conformational clusters in the (phi,psi) regions of left-handed alpha-helix, right-handed alpha-helix and extended (beta) strands were investigated in detail for their occurrence in various secondary structures, especially in beta-turn regions. Preferences were observed for Asn conformations in different positions in various beta-turn types, including the first and fourth positions of the turn. Asparaginyl residues with extended conformations are found to occur frequently in irregular regions, although they are expected to occur predominantly in extended strands or in the third position of type II beta-turns. Asn conformations at the N-cap positions of helices strongly prefer extended conformation than alpha(L), which seems to be characteristic of non-glycyl residues at that position. In the linkers connecting two extended strands and those connecting an alpha-helix and an extended strand, Asn with alpha(L) or alpha(R) conformation is more favoured than Asn with the beta-conformation. Analysis of Asn-Asn doublets and Asn-X-Asn triplets permitted identification of conformational families in such sequences. Results of this investigation provide useful hints in modelling Asn-rich regions in proteins such as malaria parasite coat protein. (C) Munksgaard 1994.

Structure-function relationships of icosahedral plant

X-ray diffraction studies on single crystals of a few viruses have led to the elucidation of their three dimensional structure at near atomic resolution. Both the tertiary structure of the coat protein subunit and the quaternary organization of the icosahedral capsid in these viruses are remarkably similar. These studies have led to a critical re-examination of the structural principles in the architecture of isometric viruses and suggestions of alternative mechanisms of assembly. Apart from their role in the assembly of the virus particle, the coat proteins of certian viruses have been shown to inhibit the replication of the cognate RNA leading to cross-protection. The coat protein amino acid sequence and the genomic sequence of several spherical plant RNA viruses have been determined in the last decade. Experimental data on the mechanisms of uncoating, gene expression and replication of several classes of viruses have also become available. The function of the non-structural proteins of some viruses have been determined. This rapid progress has provided a wealth of information on several key steps in the life cycle of RNA viruses. The function of the viral coat protein, capsid architecture, assembly and disassembly and replication of isometric RNA plant viruses are discussed in the light of this accumulated knowledge.

High temperature mechanical properties of thermal barrier coated superalloy applied to combustor liner of aero engines

High temperature load controlled fatigue, hot tensile and accelerated creep properties of thermal barrier coated (TBC) Superni C263 alloy used as a candidate material in combustor liner of aero engines are highlighted in this paper. Acoustic emission technique has been utilised to characterise the ductile-brittle transition teperature the bond coat. Results revealed that the DBTT (ductile to brittle transition temperature) of this bond coat is around 923 K, which is in close proximity to the value reported for CoCrAlY type of bond coat. Finite element technique, used for analysing the equivalent stresses in the bond coat well within the elastic limit, revealed the highest order of equivalent stress at 1073 K as the bond coat is ductile above 923 K. The endurance limit in fatigue and the life of TBC coated composite under accelerated creep conditions are substantially higher than those of the substrate material. Fractographic features at high stresses under fatigue showed intergranular cleavage whereas those at low stresses were transgranular and ductile in nature. Delamination of the bond coat and spallation of the TBC at high stresses during fatigue was evident. Unlike in the case of fatigue, the mode of fracture in the substrate at very high stresses was transgranular whereas that at low stresses was intergranular in creep.

Nanomechanical Characterization of Indium Nano/Microwires

Nanomechanical properties of indium nanowires like structures fabricated on quartz substrate by trench template technique, measured using nanoindentation. The hardness and elastic modulus of wires were measured and compared with the values of indium thin film. Displacementburst observed while indenting the nanowire. `Wire-only hardness' obtained using Korsunsky model from composite hardness. Nanowires have exhibited almost same modulus as indium thin film but considerable changes were observed in hardness value.

A novel fiber-coated strong base-type anion exchanger with superfast kinetics. Removal and recovery of silver thiosulfate from aqueous solutions

A commercial acrylic fiber with 92% (w/w) acrylonitrile content was partially hydrolyzed converting a fraction of the nitrile (-CN) groups to carboxylic acid (-COOH) groups, to coat the fiber with polyethylenimine (PEI) resin, which was then crosslinked with glutaraldehyde and further quaternized with ethyl chloroacetate to produce a novel strong-base anionic exchanger in the form of fiber. Designated as PAN(QPEI.XG)(Cl-), the fibrous sorbent was compared with a commercial bead-form resin Amberlite IRA-458(Cl-) in respect of sorption capacity, selectivity, and kinetics for removal of silver thiosulfate complexes from aqueous solutions. Though the saturation level of [Ag(S2O3)(2)](3-) on PAN(QPEI.XG)(Cl-) is considerably less than that on IRA-458(Cl-), the gel-coated fibrous sorbent exhibits, as compared to the bead-form sorbent, a significantly higher sorption selectivity for the silver thiosulfate complex in the presence of excess of other anions Such as S2O32-, SO42-, and Cl-, and a remarkably faster rate of both sorption and stripping. The initial uptake of the sorbate by the fibrous sorbent is nearly instantaneous, reaching up to similar to 80% of the saturation capacity within 10 s, as compared to only similar to 12% on the bead-form sorbent. The high initial rate of uptake fits a shell-core kinetic model for sorption on fiber of cylindrical geometry. With 4M HCl, the stripping of the sorbed silver complex from the fibrous sorbent is clean and nearly instantaneous, while, in contrast, a much slower rate of stripping on the bead-form sorbent leads to its fouling due to a slow decomposition of the silver thiosulfate complex in the acidic medium.

Nature of corrosive and abrasive wear in ball mill grinding

Laboratory results of marked-ball wear tests are used to discuss the relative significance of corrosive and abrasive wear in wet grinding. The electrochemical mechanism was investigated by correlating the corrosive wear with the corrosion current obtained from polarization curves under abrasion. Slurry rheology governs the manner in which ground slurries coat grinding balls, thereby influencing not only the grinding efficiency but also abrasive wear. The effects of percent solids and a grinding aid are illustrated.

Magnetic fabrics indicating Late Quaternary seismicity in the Himalayan foothills

The anisotropy of magnetic susceptibility (AMS) study was performed on soft sediment samples from a trenched fault zone across the Himalayan frontal thrust (HFT), western Himalaya. AMS orientation of K-min axes in the trench sediments is consistent with lateral shortening revealed by geometry of deformed regional structures and recent earthquakes. Well-defined vertical magnetic foliation parallel to the flexure cleavage in which a vertical magnetic lineation is developed, high anisotropy, and triaxial ellipsoids suggest large overprinting of earth-quake- related fabrics. The AMS data suggest a gradual variation from layer parallel shortening (LPS) at a distance from the fault trace to a simple shear fabric close to the fault trace. An abrupt change in the shortening direction (K-min) from NE-SW to E-W suggests a juxtaposition of pre-existing layer parallel shortening fabric, and bending-related flexure associated with an earthquake. Hence the orientation pattern of magnetic susceptibility axes helps in identifying co-seismic structures in Late Holocene surface sediments.

Development of a probe-based blotting technique for the detection of Tobacco streak virus

Digoxigenin (DIG)-labeled DNA probe was developed for a sensitive and rapid detection of the Tobacco streak virus (TSV) isolates in India by dot-blot and tissue print hybridization techniques. DIG-labeled DNA probe complementary to the coat protein (CP) region of TSV sunflower isolate was designed and used to detect the TSV presence at field levels. Dot-blot hybridization was used to check a large number of TSV isolates with a single probe. In addition, a sensitivity of the technique was examined with the different sample extraction methods. Another technique, the tissue blot hybridization offered a simple, reliable procedure and did not require a sample processing. Thus, both non-radioactively labeled probe techniques could facilitate the sample screening during TSV outbreaks and offer an advantage in quarantine services.

In vitro expression of belladonna mottle virus genome

In vitro translation of belladonna mottle virus BDMV(I) genomic RNA in a rabbit reticulocyte lysate system produced proteins of Mr 210,000, 150,000 and 78,000 which form the non-structural proteins. The coat protein, on the other hand, was expressed from a subgenomic RNA which was found to be encapsidated in the empty capsids forming the top component viral particles. The implications of subgenomic RNA encapsidation in viral replication and assembly are discussed.

Mechanistic evaluation of mitigation of petroleum hydrocarbon contamination by soil medium

Present in situ chemical treatment technologies for mitigation of petroleum hydrocarbon contamination are in the developmental stage or being tested. To devise efficient strategies for restricting the movement of petroleum hydrocarbon (PHC) molecules in the contaminated soil, it is proposed to utilize the sorption–interaction relationships between the petroleum contaminants and the soil substrate. The basic questions addressed in this paper are as follows (i) What are the prominent chemical constituents of the various petroleum fractions that interact with the soil substrate? (ii) What are the functional groups of a soil that interact with the contaminants? (iii) What are the bonding mechanisms possible between the soil functional groups and the PHC contaminants? (iv) What are the consequent changes brought about the soil physical properties on interaction with PHC's? (v) What are the factors influencing the interactions between PHC molecules and clay particles of the soil substrate? (vi) What is the possibility of improving the soil's attenuation ability for PHC's? The development of answers to the basic questions reveal that petroleum hydrocarbons comprise a mixture of nonpolar alkanes and aromatic and polycyclic hydrocarbons, that have limited solubility in water. The bonding mechanism between the nonpolar PHC's and the clay surface is by way of van der Waals attraction. The adsorption of the nonpolar hydrocarbons by the clay surface occurs only when their (i.e., the hydrocarbon molecules) solubility in water is exceeded and the hydrocarbons exist in the micellar form. Dilute solutions of hydrocarbons in water, i.e., concentrations of hydrocarbons at or below the solubility limit, have no effect on the hydraulic conductivity of clay soils. Permeation with pure hydrocarbons invariably influences the clay hydraulic conductivity. To improve the attenuation ability of soils towards PHC's, it is proposed to coat the soil surface with "ultra" heavy organic polymers. Adsorption of organic polymers by the clay surface may change the surface properties of the soil from highly hydrophilic (having affinity for water molecules) to organophilic (having affinity for organic molecules). The organic polymers attached to the clay surface are expected to attenuate the PHC molecules by van der Waals attraction, by hydrogen bonding, and also by adsorption into interlayer space in the case of soils containing swelling clays.

Structure-function relationships of icosahedral plant viruses

X-ray diffraction studies on single crystals of a few viruses have led to the elucidation of their three dimensional structure at near atomic resolution. Both the tertiary structure of the coat protein subunit and the quaternary morganization of the icosahedral capsid in these viruses are remarkably similar. These studies have led to a critical re-examination of the structural principles in the architecture of isometric viruses and suggestions of alternative mechanisms of assembly. Apart from their role in the assembly of the virus particle, the coat proteins of certian viruses have been shown to inhibit the replication of the cognate RNA leading to cross-protection. The coat protein amino acid sequence and the genomic sequence of several spherical plant RNA viruses have been determined in the last decade. Experimental data on the mechanisms of uncoating, gene expression and replication of several classes of viruses have also become available. The function of the non-structural proteins of some viruses have been determined. This rapid progress has provided a wealth of information on several key steps in the life cycle of RNA viruses. The function of the viral coat protein, capsid architecture, assembly and disassembly and replication of isometric RNA plant viruses are discussed in the light of this accumulated knowledge.