Effect of disorder on the exponent in the coherence region in high temperature superconductors

Effect of disorder on the electrical resistance near the superconducting transition temperature in the paracoherence region of high temperature YBa2CU3O7-delta (YBCO) thin film superconductor is reported. For this, c-axis oriented YBa2Cu3O7-delta thin films having superconducting transition width varying between 0.27 K and 6 K were deposited using laser ablation and high pressure oxygen sputtering techniques. Disorder in these films was further created by using 100 MeV oxygen and 200 MeV silver ions with varying fluences. It is observed that the critical exponent in the paracoherence region for films with high transition temperature and small transition width is in agreement with the theoretically predicted value (gamma = 1.33) and is not affected by disorder, while for films with lower transition temperature and larger transition width the value of exponent is much larger as compared to that theoretically predicted and it varies from sample to sample and usually changes with disorder induced by radiation. This difference in the behaviour of the exponent has been explained on the basis of differences in the strength of weak links and the transition between temperatures T. and T, is interpreted as a percolation like transition with disorder. (c) 2006 Elsevier B.V. All rights reserved.

Genetic characterization of Indian type O FMD virus 3A region in context with host cell preference

The 3A region of foot-and-mouth disease virus has been implicated in host range and virulence. For example, amino acid deletions in the porcinophilic strain (O/TAW/97) at 93-102 aa of the 153 codons long 3A protein have been recognized as the determinant of species specificity. In the present study, 18 type 0 FMDV isolates from India were adapted in different cell culture systems and the 3A sequence was analyzed. These isolates had complete 3A coding sequence (153 aa) and did not exhibit growth restriction in cells based on species of origin. The 3A region was found to be highly conserved at N-terminal half (1-75 aa) but exhibited variability or substitutions towards C-terminal region (80-153). Moreover the amino acid substitutions were more frequent in recent Indian buffalo isolates but none of the Indian isolates showed deletion in 3A protein, which may be the reason for the absence of host specificity in vitro. Further inclusive analysis of 3A region will reveal interesting facts about the variability of FMD virus 3A region in an endemic environment. (C) 2010 Elsevier B.V. All rights reserved.

Changes to near-surface region of PTFE during dry sliding against steel

PTFE specimens were slid against an EN24 disc. The unworn and worn surfaces as well as the wear debris were examined by X-ray diffraction. Sliding was found to introduce (i) shrinkage of the unit cell, (ii) enlargement of crystallites and (iii) residual stresses in the slid PTFE surface. No conformational changes in the 157 helix could be observed due to sliding. The wear debris was found to be 1 mgrm thick warped laminates.

DNA Clasping by Mycobacterial HU: The C-Terminal Region of HupB Mediates Increased Specificity of DNA Binding

Background: HU a small, basic, histone like protein is a major component of the bacterial nucleoid. E. coli has two subunits of HU coded by hupA and hupB genes whereas Mycobacterium tuberculosis (Mtb) has only one subunit of HU coded by ORF Rv2986c (hupB gene). One noticeable feature regarding Mtb HupB, based on sequence alignment of HU orthologs from different bacteria, was that HupB(Mtb) bears at its C-terminal end, a highly basic extension and this prompted an examination of its role in Mtb HupB function. Methodology/Principal Findings: With this objective two clones of Mtb HupB were generated; one expressing full length HupB protein (HupB(Mtb)) and another which expresses only the N terminal region (first 95 amino acid) of hupB (HupB(MtbN)). Gel retardation assays revealed that HupBMtbN is almost like E. coli HU (heat stable nucleoid protein) in terms of its DNA binding, with a binding constant (K-d) for linear dsDNA greater than 1000 nM, a value comparable to that obtained for the HU alpha alpha and HU alpha beta forms. However CTR (C-terminal Region) of HupB(Mtb) imparts greater specificity in DNA binding. HupB(Mtb) protein binds more strongly to supercoiled plasmid DNA than to linear DNA, also this binding is very stable as it provides DNase I protection even up to 5 minutes. Similar results were obtained when the abilities of both proteins to mediate protection against DNA strand cleavage by hydroxyl radicals generated by the Fenton's reaction, were compared. It was also observed that both the proteins have DNA binding preference for A: T rich DNA which may occur at the regulatory regions of ORFs and the oriC region of Mtb. Conclusions/Significance: These data thus point that HupB(Mtb) may participate in chromosome organization in-vivo, it may also play a passive, possibly an architectural role.

Total risk rating and stability analysis of embankment dams in the Kachchh Region, Gujarat, India

A method for total risk analysis of embankment dams under earthquake conditions is discussed and applied to the selected embankment dams, i.e., Chang, Tapar, Rudramata, and Kaswati located in the Kachchh region of Gujarat, India, to obtain the seismic hazard rating of the dam site and the risk rating of the structures. Based on the results of the total risk analysis of the dams, coupled non-linear dynamic numerical analyses of the dam sections are performed using acceleration time history record of the Bhuj (India) earthquake as well as five other major earthquakes recorded worldwide. The objective of doing so is to perform the numerical analysis of the dams for the range of amplitude, frequency content and time duration of input motions. The deformations calculated from the numerical analyses are also compared with other approaches available in literature, viz, Makdisi and Seed (1978) approach, Jansen's approach (1990), Swaisgood's method (1995), Bureau's method (1997). Singh et al. approach (2007), and Saygili and Rathje approach (2008) and the results are utilized to foresee the stability of dams in future earthquake scenario. (C) 2010 Elsevier B.V. All rights reserved.

Superconductivity in the 100–120 K region in oxides of the Tl-Ca-Ba-Cu-O system

Oxides with different cation ratios 2122, 2212, 2213 and 2223 in the Ti-Ca-Ba-Cu-O system exhibit onset of superconductivity in the 110–125 K range with zero-resistance in the 95–105 K range. Electron microscopic studies show dislocations, layered morphology and other interesting features. These oxides absorb electromagnetic radiation (9.11 GHz) in the superconducting phase.

Functional Identification of Regulatory Elements within the Promoter Region of Platelet-Derived Growth Factor 2

Human platelet-derived growth factor (PDGF) is composed of two polypeptide chains, PDGF-1 and PDGF-2,the human homolog of the v-sis oncogene. Deregulation of PDGF-2 expression can confer a growth advantage to cells possessing the cognate receptor and, thus, may contribute to the malignant phenotype. We investigated the regulation of PDGF-2 mRNA expression during megakaryocytic differentiation of K562 cells. Induction by 12-O-tetradecanoylphorbol-13-acetate (TPA) led to a greater than 200-fold increase in PDGF-2 transcript levels in these cells. Induction was dependent on protein synthesis and was not enhanced by cycloheximide exposure.In our initial investigation of the PDGF-2 promoter, a minimal promoter region, which included sequences extending only 42 base pairs upstream of the TATA signal, was found to be as efficient as 4 kilobase pairs upstream of the TATA signal in driving expression of a reporter gene in uninduced K562 cells. We also functionally identified different regulatory sequence elements of the PDGF-2 promoter in TPA-induced K562 cells. One region acted as a transcriptional silencer, while another region was necessary for maximal activity of the promoter in megakaryoblasts. This region was shown to bind nuclear factors and was the target for trans-activation in normal and tumor cells. In one tumor cell line, which expressed high PDGF-2 mRNA levels, the presence of the positive regulatory region resulted in a 30-fold increase in promoter activity. However, the ability of the minimal PDGF-2 promoter to drive reporter gene expression in uninduced K562 cells and normal fibroblasts, which contained no detectable PDGF-2 transcripts, implies the existence of other negative control mechanisms beyond the regulation of promoter activity.

A monoclonal antibody recognizing the C-terminal region of chicken egg white riboflavin carrier protein terminates early pregnancy in mice

In order to identify the functionally relevant epitopes on chicken riboflavin carrier protein, we have raised monoclonal antibodies to the vitamin carrier. One of these, 6B2C12, was found to interact specifically with a synthetic oligopeptide corresponding to the C-terminal 17 amino acid residues of the chicken egg white riboflavin carrier protein, which is missing in part in the egg yolk riboflavin carrier protein. This epitope is conserved through evolution in mammals including humans. Administration of the ascites fluid of 6B2C12 to pregnant mice intraperitoneally, resulted in the termination of pregnancy indicating that this epitope is involved in or closely associated with the transplacental transport of the vitamin from the maternal circulation to the growing fetus.

Boundary-layer heights over the monsoon trough region during active and break phases

The thermodynamic structure and the heights of the boundary layer over the monsoon trough region of the Indian southwest monsoon are presented for the active and break phases of the monsoon. Results indicate significant and consistent variation in boundary-layer heights between the active and break phases.

Nucleotide sequence of the 3terminal region of belladonna mottle virus (renamed Physalis mottle virus) RNA and analysis of the evolutionary relationships among tymoviral coat proteins

The 3' terminal 1255 nt sequence of Physalis mottle virus (PhMV) genomic RNA has been determined from a set of overlapping cDNA clones. The open reading frame (ORF) at the 3' terminus corresponds to the amino acid sequence of the coat protein (CP) determined earlier except for the absence of the dipeptide, Lys-Leu, at position 110-111. In addiition, the sequence upstream of the CP gene contains the message coding for 178 amino acid residues of the C-terminus of the putative replicase protein (RP). The sequence downstream of the CP gene contains an untranslated region whose terminal 80 nucleotides can be folded into a characteristic tRNA-like structure. A phylogenetic tree constructed after aligning separately the sequence of the CP, the replicase protein (RP) and the tRNA-like structure determined in this study with the corresponding sequences of other tymoviruses shows that PhMV wrongly named belladonna mottle virus [BDMV(I)] is a separate tymovirus and not another strain of BDMV(E) as originally envisaged. The phylogenetic tree in all the three cases is identical showing that any subset of genomic sequence of sufficient length can be used for establishing evolutionary relationships among tymoviruses.

Rigid and flexible region in lysozyme and the invariant features in its hydration shell

Water-mediated transformations provide a useful handle for exploring the flexibility in protein molecules and the invariant features in their hydration shells. Low-humidity monoclinic hen egg white lysozyme, resulting from such a transformation, has perhaps the lowest solvent content observed in any protein crystal so far and has a well-ordered structure. A detailed comparison involving this structure, low-humidity tetragonal lysozyme, and the other available refined crystal structures of the enzyme permits the delineation of the relatively rigid, moderately flexible and highly flexible regions of the molecule. The relatively rigid region forms a contiguous structural unit close to the molecular centroid and encompasses parts of of the main beta-structure and three alpha-helices. The hydration shell of the protein contains 30 invariant water molecules. Many of them are involved in holding different parts of the molecule together or in stabilizing local structure. Five of the six invariant water molecules attached to the substrate-binding region form part of a water cluster contiguous with the side-chains of the catalytic residues Glu-35 and Asp-52.

Unsteady mixed convection flow in stagnation region adjacent to a vertical surface

The unsteady two-dimensional laminar mixed convection flow in the stagnation region of a vertical surface has been studied where the buoyancy forces are due to both the temperature and concentration gradients. The unsteadiness in the flow and temperature fields is caused by the time-dependent free stream velocity. Both arbitrary wall temperature and concentration, and arbitrary surface heat and mass flux variations have been considered. The Navier-Stokes equations, the energy equation and the concentration equation, which are coupled nonlinear partial differential equations with three independent variables, have been reduced to a set of nonlinear ordinary differential equations. The analysis has also been done using boundary layer approximations and the difference between the solutions has been discussed. The governing ordinary differential equations for buoyancy assisting and buoyancy opposing regions have been solved numerically using a shooting method. The skin friction, heat transfer and mass transfer coefficients increase with the buoyancy parameter. However, the skin friction coefficient increases with the parameter lambda, which represents the unsteadiness in the free stream velocity, but the heat and mass transfer coefficients decrease. In the case of buoyancy opposed flow, the solution does not exist beyond a certain critical value of the buoyancy parameter. Also, for a certain range of the buoyancy parameter dual solutions exist.

Communication pathways from the anti-codon region to the aminoacylation site in Methionyl tRNA Synthetase: Molecular dynamics simulations and the structure network analysis

The enzymes of the family of tRNA synthetases perform their functions with high precision by synchronously recognizing the anticodon region and the aminoacylation region, which are separated by ?70 in space. This precision in function is brought about by establishing good communication paths between the two regions. We have modeled the structure of the complex consisting of Escherichia coli methionyl-tRNA synthetase (MetRS), tRNA, and the activated methionine. Molecular dynamics simulations have been performed on the modeled structure to obtain the equilibrated structure of the complex and the cross-correlations between the residues in MetRS have been evaluated. Furthermore, the network analysis on these simulated structures has been carried out to elucidate the paths of communication between the activation site and the anticodon recognition site. This study has provided the detailed paths of communication, which are consistent with experimental results. Similar studies also have been carried out on the complexes (MetRS + activated methonine) and (MetRS + tRNA) along with ligand-free native enzyme. A comparison of the paths derived from the four simulations clearly has shown that the communication path is strongly correlated and unique to the enzyme complex, which is bound to both the tRNA and the activated methionine. The details of the method of our investigation and the biological implications of the results are presented in this article. The method developed here also could be used to investigate any protein system where the function takes place through long-distance communication.

Discriminating between natural and anthropogenic aerosol contributions to optical depth over Afro-Asian region

To accurately assess the impact of anthropogenic aerosols on climate, spatial and temporal distribution of its radiative properties is essential. The first step towards separating the radiative impact of natural aerosol from its anthropogenic counterparts is to gather information on natural aerosols. In this paper, we have used data from multiple satellites to derive the anthropogenic aerosol fraction (AAF) over the Afro-Asian region. The AAF was largest during the pre-monsoon season (May-June) and lowest during winter. We have shown that over desert locations the AAF was unexpectedly large (>0.4) and the regionally (and annually) averaged anthropogenic fraction over the Afro-Asian region was 0.54 +/- 0.12. Copyright (C) 2010 Royal Meteorological Society