How Effective Is The Data On Co-Occurrence Of Domains In Multi-Domain Proteins In Prediction Of Protein-Protein Interactions?

We explore the fuse of information on co-occurrence of domains in multi-domain proteins in predicting protein-protein interactions. The basic premise of our work is the assumption that domains co-occurring in a polypeptide chain undergo either structural or functional interactions among themselves. In this study we use a template dataset of domains in multidomain proteins and predict protein-protein interactions in a target organism. We note that maximum number of correct predictions of interacting protein domain families (158) is made in S. cerevisiae when the dataset of closely related organisms is used as the template followed by the more diverse dataset of bacterial proteins (48) and a dataset of randomly chosen proteins (23). We conclude that use of multi-domain information from organisms closely-related to the target can aid prediction of interacting protein families.

A tropical oviparous lizard, Calotes versicolor, exhibiting a potentially novel FMFM pattern of temperature-dependent sex determination

Among squamate reptiles, lizards exhibit an impressive array of sex-determining modes viz. genotypic sex determination, temperature-dependent sex determination, co-occurrence of both these and those that reproduce parthenogenetically. The oviparous lizard, Calotes versicolor, lacks heteromorphic sex chromosomes and there are no reports on homomorphic chromosomes. Earlier studies on this species presented little evidence to the sex-determining mechanism. Here we provide evidences for the potential role played by incubation temperature that has a significant effect (P<0.01) on gonadal sex and sex ratio. The eggs were incubated at 14 different incubation temperatures. Interestingly, 100% males were produced at low (25.5 +/- 0.5 degrees C) as well as high (34 +/- 0.5 degrees C) incubation temperatures and 100% females were produced at low (23.5 +/- 0.5 degrees C) and high (31.5 +/- 0.5 degrees C) temperatures, clearly indicating the occurrence of TSD in this species. Sex ratios of individual clutches did not vary at any of the critical male-producing or female-producing temperatures within as well as across the seasons. However, clutch sex ratios were female- or male-biased at intermediate temperatures. Thermosensitive period occurred during the embryonic stages 3033. Three pivotal temperatures operate producing 1:1 sex ratio. Histology of gonad and accessory reproductive structures provide additional evidence for TSD. The sex-determining pattern, observed for the first time in this species, that neither compares to Pattern I [Ia (MF) and Ib (FM)] nor to Pattern II (FMF), is being referred to as FMFM pattern of TSD. This novel FMFM pattern of sex ratio exhibited by C. versicolor may have an adaptive significance in maintaining sex ratio. J. Exp. Zool. 317:3246, 2012. (c) 2011 Wiley Periodicals, Inc.

The Contribution of Rare Species to Community Phylogenetic Diversity across a Global Network of Forest Plots

Niche differentiation has been proposed as an explanation for rarity in species assemblages. To test this hypothesis requires quantifying the ecological similarity of species. This similarity can potentially be estimated by using phylogenetic relatedness. In this study, we predicted that if niche differentiation does explain the co-occurrence of rare and common species, then rare species should contribute greatly to the overall community phylogenetic diversity (PD), abundance will have phylogenetic signal, and common and rare species will be phylogenetically dissimilar. We tested these predictions by developing a novel method that integrates species rank abundance distributions with phylogenetic trees and trend analyses, to examine the relative contribution of individual species to the overall community PD. We then supplement this approach with analyses of phylogenetic signal in abundances and measures of phylogenetic similarity within and between rare and common species groups. We applied this analytical approach to 15 long-term temperate and tropical forest dynamics plots from around the world. We show that the niche differentiation hypothesis is supported in six of the nine gap-dominated forests but is rejected in the six disturbance-dominated and three gap-dominated forests. We also show that the three metrics utilized in this study each provide unique but corroborating information regarding the phylogenetic distribution of rarity in communities.

Integration of speckle de-noising and image segmentation using synthetic aperture radar image for flood extent extraction

Flood is one of the detrimental hydro-meteorological threats to mankind. This compels very efficient flood assessment models. In this paper, we propose remote sensing based flood assessment using Synthetic Aperture Radar (SAR) image because of its imperviousness to unfavourable weather conditions. However, they suffer from the speckle noise. Hence, the processing of SAR image is applied in two stages: speckle removal filters and image segmentation methods for flood mapping. The speckle noise has been reduced with the help of Lee, Frost and Gamma MAP filters. A performance comparison of these speckle removal filters is presented. From the results obtained, we deduce that the Gamma MAP is reliable. The selected Gamma MAP filtered image is segmented using Gray Level Co-occurrence Matrix (GLCM) and Mean Shift Segmentation (MSS). The GLCM is a texture analysis method that separates the image pixels into water and non-water groups based on their spectral feature whereas MSS is a gradient ascent method, here segmentation is carried out using spectral and spatial information. As test case, Kosi river flood is considered in our study. From the segmentation result of both these methods are comprehensively analysed and concluded that the MSS is efficient for flood mapping.

Prevalence and clinical correlates of obsessive-compulsive disorder in schizophrenia

Obsessive compulsive symptoms frequently occur in a substantial proportion of patients with schizophrenia. The term schizoobsessive has been proposed to delineate this subgroup of schizophrenia patients who present with obsessive compulsive symptoms/disorder. However, whether this co-occurrence is more than just co-morbidity and represents a distinct subgroup remains controversial. A striking variation is noted across studies examining prevalence of obsessive compulsive symptoms/disorder in schizophrenia patients and their impact on clinical profile of schizophrenia. Hence, in this study, we examined the prevalence of obsessive compulsive symptoms/disorder in a large sample of consecutively hospitalized schizophrenia patients and compared the clinical and functional characteristics of schizophrenia patients with and without obsessive compulsive symptoms/disorder. We evaluated 200 consecutive subjects with the DSM-IV diagnosis of schizophrenia using the Structured Clinical Interview for DSM-IV Axis I disorders, Positive and Negative Syndrome Scale, Yale Brown Obsessive Compulsive Scale, Brown Assessment of Beliefs Scale, Clinical Global Impression-Severity scale, Global Assessment of Functioning Scale, Family Interview for Genetic Studies and World Health Organization Quality of Life scale. The prevalence of obsessive compulsive symptoms in patients with schizophrenia was 24% (n = 48); 37 of them had obsessive compulsive disorder (OCD) and II had obsessive compulsive symptoms not amounting to a clinical diagnosis of OCD (OCS). Schizophrenia patients with OCS/OCD had an earlier age at onset of schizophrenia symptoms, lower positive symptoms score, higher co-morbidity with Axis II disorders, higher occurrence of OCD in family and better quality of life. Findings of the study indicate a higher prevalence of OCS/OCD in schizophrenia. Schizophrenia patients with and without OCS/OCD have comparable clinical profile with few exceptions. High rates of OCD in first degree relatives suggest possible genetic contributions and differences in neurobiology. Finally, evidence to consider schizoobsessive as a distinct diagnostic entity is inconclusive and warrants further studies. (C) 2014 Elsevier Inc. All rights reserved.

Relation between high-tc superconductivity and structure - a study of la3-xba3+xcu6o14+delta and yba2cu3o7-delta systems

Superconductivity is found in tetragonal La3−x Ba3+x Cu6O14+δ and La, Ba)6−x Sr x Cu6O14+δ even though they do not possess Cu-O chains or the K2NiF4 structure. Resistivity measurements confirm the occurrence of a transformation from chain-superconductivity to sheet-superconductivity in YBa2Cu3O7−δ as δ is varied in the range 0.0–0.5.

Spinel-Corundum Phase Equilibria in the Systems Mn-Cr-Al-O and Co-Cr-Al-O at 1373 K

The tie lines delineating ion-exchange equilibria between MCr2O4-MAl2O4 spinel solid solution, where M is either Mn or Co, and Cr2O3-Al2O3 solid solution with the corundum structure were determined at 1373 K by electron microprobe and E0AX point count analysis of the oxide phases equilibrated with metallic Co and Au-5% Mn. The component activities in the spinel solid solutions are derived from the tie lines and the thernodynamic data for Cr2O3-Al2O3 soiid solutions available hi the literature. The Gibbs free energies of mixing calculated from the experimental data are discussed in relation to the values derived from the cation distribution a.odel based on the site preference energies and assuming random mixing on both tetrahedral and octahedral sites. Positive deviations from ideality observed in this study suggest a miscibility gap for both series of spinel solid solutions at low temperatures in the absence of oxidation.

Chemical-shift of the X-ray K-absorption edge of Co in some compounds, complexes and minerals

The chemical-shift of the X-ray K-absorption edge of Co was studied in a large number of compounds, complexes (spinels) and minerals of Co in its different oxidation states having widely different crystal structures and containing different types of bonding and various types of ligands, and were reported collectively, for the first time, in a single paper. A quadratic relationship was established on the basis of least-squares regression analysis to hold between the chemical-shift and the effective charge on the absorbing atom, but the dominance of the linear term was shown. This relation was utilized in evaluating the charge on the Co-ion in a number of minerals. The effect on chemical-shift of oxidation states of the absorbing atom, of the bond length, crystal structure and higher shell atoms of the molecule, and of electronegativity, atomic number and ionic radius of the ligand was discussed.

Protein Hydration and Water Structure: X-ray Analysis of a Closely Packed Protein Crystal with Very Low Solvent Content

Low-humidity monoclinic lysozyme, resulting from a water-mediated transformation, has one of the lowest solvent contents (22% by volume) observed in a protein crystal. Its structure has been solved by the molecular replacement method and refined to an R value of 0.175 for 7684 observed reflections in the 10–1.75 Å resolution shell. 90% of the solvent in the well ordered crystals could be located. Favourable sites of hydration on the protein surface include side chains with multiple hydrogen-bonding centres, and regions between short hydrophilic side chains and the main-chain CO or NH groups of the same or nearby residues. Major secondary structural features are not disrupted by hydration. However, the free CO groups at the C terminii and, to a lesser extent, the NH groups at the N terminii of helices provide favourable sites for water interactions, as do reverse turns and regions which connect β-structure and helices. The hydration shell consists of discontinuous networks of water molecules, the maximum number of molecules in a network being ten. The substrate-binding cleft is heavily hydrated, as is the main loop region which is stabilized by water interactions. The protein molecules are close packed in the crystals with a molecular coordination number of 14. Arginyl residues are extensively involved in intermolecular hydrogen bonds and water bridges. The water molecules in the crystal are organized into discrete clusters. A distinctive feature of the clusters is the frequent occurrence of three-membered rings. The protein molecules undergo substantial rearrangement during the transformation from the native to the low-humidity form. The main-chain conformations in the two forms are nearly the same, but differences exist in the side-chain conformation. The differences are particularly pronounced in relation to Trp 62 and Trp 63. The shift in Trp 62 is especially interesting as it is also known to move during inhibitor binding.

An XPS study on oxidation states of Pt and its alloys with Co and Cr and its relevance to electroreduction of oxygen

Cathodic reduction of oxygen in fuel cells is known to be enhanced on platinum alloys in relation to the platinum metal. The higher performance of the platinum alloys is as a result of the improved oxygen-reduction kinetics on the alloys but there is hardly any increase in the electrode platinum-surface-areas for the platinum alloys as compared to the platinum metal, and thus the higher performance is solely due to the enhanced electrocatalytic activity of the alloys as compared to the platinum metal. The present X-ray photoelectron spectroscopic (XPS) study on carbon-supported Pt, Pt–Co and Pt–Co–Cr electrocatalysts suggests the presence of a relatively lower Pt-oxide content on the alloys. The X-ray powder diffraction patterns for these electrocatalysts show that while the carbon-supported platinum electrocatalyst has a face-centered cubic (fcc) phase, carbon-supported Pt–Co and Pt–Co–Cr electrocatalysts exhibit a face-centered tetragonal (fct) phase. But, Pt electrocatalyst has a lower particle-size and, hence, a higher dispersion. Previous studies have shown higher activities on the Pt-alloys than on Pt, and have attributed it to changes in the electronic and structural characteristics of Pt. These changes can be correlated with the lower oxidation-state of Pt sites, as found in this study.

Electrical and magneto-resistance of Co/CNT/epoxy thin film for strain and magnetic field sensing

Cobalt and iron nanoparticles are doped in carbon nanotube (CNT)/polymer matrix composites and studied for strain and magnetic field sensing properties. Characterization of these samples is done for various volume fractions of each constituent (Co and Fe nanoparticles and CNTs) and also for cases when only either of the metallic components is present. The relation between the magnetic field and polarization-induced strain are exploited. The electronic bandgap change in the CNTs is obtained by a simplified tight-binding formulation in terms of strain and magnetic field. A nonlinear constitutive model of glassy polymer is employed to account for (1) electric bias field dependent softening/hardening (2) CNT orientations as a statistical ensemble and (3) CNT volume fraction. An effective medium theory is then employed where the CNTs and nanoparticles are treated as inclusions. The intensity of the applied magnetic field is read indirectly as the change in resistance of the sample. Very small magnetic fields can be detected using this technique since the resistance is highly sensitive to strain. Its sensitivity due to the CNT volume fraction is also discussed. The advantage of this sensor lies in the fact that it can be molded into desirable shape and can be used in fabrication of embedded sensors where the material can detect external magnetic fields on its own. Besides, the stress-controlled hysteresis of the sample can be used in designing memory devices. These composites have potential for use in magnetic encoders, which are made of a magnetic field sensor and a barcode.

Phase equilibria in the Co Ni F system and activities in (CoxNi1 x)F2 solid solutions at 1373 K

The tie-lines delineating equilibria between CoF2-NiF2 and Co-Ni solid solutions in the ternary Co-Ni-F system at 1373 K have been determined by electron microprobe and EDAX point count analysis of the equilibrated phases. Activities in the fluoride solid solution have been derived from the knowledge of activitycomposition relation in the metallic solid solution and tie-line data,using a modified form of the Gibbs-Duhem integration. The fluorine potentials corresponding to the tie-line compositions have been calculated.The excess Gibbs' energy of mixing for the fluoride solid solution derived from the present data can be represented by the expression

Relation between Local Structure and Glass Forming Ability of Liquid Alloys

An attempt has been made to describe the glass forming ability (GFA) of liquid alloys, using the concepts of the short range order (SRO) and middle range order (MRO) characterizing the liquid structure.A new approach to obtain good GFA of liquid alloys is based on the following four main factors: (1) formation of new SRO and competitive correlation with two or more kinds of SROs for crystallization, (2) stabilization of dense random packing by interaction between different types of SRO, (3) formation of stable cluster (SC) or middle range order (MRO) by harmonious coupling of SROs, and (4) difference between SRO characterizing the liquid structure and the near-neighbor environment in the corresponding equilibrium crystalline phases. The atomic volume mismatch estimated from the cube of the atomic radius was found to be a close relation with the minimum solute concentration for glass formation. This empirical guideline enables us to provide the optimum solute concentration for good GFA in some ternary alloys. Model structures, denoted by Bernal type and the Chemical Order type, were again tested in the novel description for the glass structure as a function of solute concentration. We illustrated the related energetics of the completion between crystal embryo and different types of SRO. Recent systematic measurements also provide that thermal diffusivity of alloys in the liquid state may be a good indicator of their GFA.

Water treatment potential in relation to phytoplankton dynamics in tropical sewage-fed urban water bodies

Urban water bodies frequently receive untreated sewage and water levels in such water bodies are maintained by daily inputs of sewage. They function as “variable-zone” anaerobic-aerobic lagoons suffering several macrophyte, biotic and abiotic stresses. We have studied two such lakes in Bangalore (Bellandur-360 ha and Varthur-220 ha) to understand whether such an occurrence could be made beneficial (maintaining water levels as well as treatment). Such hypertrophic water body receives sewage at 180-250mg/L and is discharged at 25-80mg/L COD/BOD in different seasons. In an earlier study we reported macrophyte altering the purification function of the water body. In this paper we studied the impact of phytoplankton dynamics and macrophyte cover on the functions such as organic load removal. Algal community analysis, algal biomass, macrophyte cover, water quality, nutrient status was studied seasonally during 2009-2010. Oxygen deficiency and sometimes anoxia, recorded from surface samples resulted in high quantities of NH4+-N (30-40mg/L) and phosphate (0.5-4mg/L)-characteristics of anoxic hypertrophic urban lakes. The productiveness favoured high phytoplanktonic community characterized by small cells (<10μm; Chlorella sp. - highest numbers). The lake could be clearly demarcated into an initial anaerobic zone (40% area), a facultative zone (20%) and an aerobic zone (40%) based on redox values and GIS/bathymetry. During summer the lake is covered by floating macrophytes converting the lake into an anoxic/anaerobic water pool subduing the water purification function as well as aesthetics. When macrophytes are controlled such sewage fed water bodies can be used for treating urban wastewater while also maintaining water sustainability in these semi-arid ecosystems. This paper reports the community dynamics of phytoplankton, their function and competition with macrophytes.

Transition and acoustic response of recirculation structures in an unconfined co-axial isothermal swirling flow

This paper reports the first observations of transition from a pre-vortex breakdown (Pre-VB) flowreversal to a fully developed central toroidal recirculation zone in a non-reacting, double-concentric swirling jet configuration and its response to longitudinal acoustic excitation. This transition proceeds with the formation of two intermediate, critical flow regimes. First, a partially penetrated vortex breakdown bubble (VBB) is formed that indicates the first occurrence of an enclosed structure as the centre jet penetration is suppressed by the growing outer roll-up eddy; resulting in an opposed flow stagnation region. Second, a metastable transition structure is formed that marks the collapse of inner mixing vortices. In this study, the time-averaged topological changes in the coherent recirculation structures are discussed based on the non-dimensional modified Rossby number (Ro(m)) which appears to describe the spreading of the zone of swirl influence in different flow regimes. Further, the time-mean global acoustic response of pre-VB and VBB is measured as a function of pulsing frequency using the relative aerodynamic blockage factor (i.e., maximum radial width of the inner recirculation zone). It is observed that all flow modes except VBB are structurally unstable as they exhibit severe transverse radial shrinkage (similar to 20%) at the burner Helmholtz resonant modes (100-110 Hz). In contrast, all flow regimes show positional instability as seen by the large-scale, asymmetric spatial shifting of the vortex core centres. Finally, the mixing transfer function M (f) and magnitude squared coherence lambda(2)(f) analysis is presented to determine the natural couplingmodes of the system dynamic parameters (u', p'), i.e., local acoustic response. It is seen that the pre-VB flow mode exhibits a narrow-band, low pass filter behavior with a linear response window of 100-105 Hz. However, in the VBB structure, presence of critical regions such as the opposed flow stagnation region alters the linearity range with the structure showing a response even at higher pulsing frequencies (100-300 Hz). (C) 2013 AIP Publishing LLC.