Lizards of the Thar Desert - Resource partitioning and community composition

How similar species co-exist in nature is a fundamental question in community ecology. Resource partitioning has been studied in desert lizard communities across four continents, but data from South Asia is lacking. We used area-constrained visual encounter surveys to study community composition and spatial and temporal resource partitioning in a lizard community during summer in the Thar Desert, western India, addressing an important biogeographic gap in knowledge. Twelve one-hectare grids divided into 25 m x 25 m plots were placed across four habitats barren dunes, stabilized dunes, grassland, and rocky hills. We recorded 1039 sightings of 12 species during 84 sampling sessions. Lizard abundance decreased in the order stabilized dunes > grassland > barren dunes > rocky hills; richness was in roughly the opposite order. Resource partitioning was examined for the seven commonest species. Overall spatial overlap was low (<0.6) between species pairs. Overlap was higher within habitats, but species showed finer separation through use of different microhabitat categories and specific spatial resources, as well as by positioning at different distances to vegetation. Diurnal species were also separated by peak time of activity. Space appears to be an important resource dimension facilitating coexistence in this desert lizard community. (C) 2015 Elsevier Ltd. All rights reserved.

Quench dynamics and parity blocking in Majorana wires

We theoretically explore quench dynamics in a finite-sized topological fermionic p-wave superconducting wire with the goal of demonstrating that topological order can have marked effects on such non-equilibrium dynamics. In the case studied here, topological order is reflected in the presence of two (nearly) isolated Majorana fermionic end bound modes together forming an electronic state that can be occupied or not, leading to two (nearly) degenerate ground states characterized by fermion parity. Our study begins with a characterization of the static properties of the finite-sized wire, including the behavior of the Majorana end modes and the form of the tunnel coupling between them; a transfer matrix approach to analytically determine the locations of the zero energy contours where this coupling vanishes; and a Pfaffian approach to map the ground state parity in the associated phase diagram. We next study the quench dynamics resulting from initializing the system in a topological ground state and then dynamically tuning one of the parameters of the Hamiltonian. For this, we develop a dynamic quantum many-body technique that invokes a Wick's theorem for Majorana fermions, vastly reducing the numerical effort given the exponentially large Hilbert space. We investigate the salient and detailed features of two dynamic quantities-the overlap between the time-evolved state and the instantaneous ground state (adiabatic fidelity) and the residual energy. When the parity of the instantaneous ground state flips successively with time, we find that the time-evolved state can dramatically switch back and forth between this state and an excited state even when the quenching is very slow, a phenomenon that we term `parity blocking'. This parity blocking becomes prominently manifest as non-analytic jumps as a function of time in both dynamic quantities.

First-principles study of the influence of different interfaces and core types on the properties of CdSe/CdS core-shell nanocrystals

With the expanding field of nanoengineering and the production of nanocrystals (NCs) with higher quality and tunable size, having reliable theoretical calculations to complement the experimental results is very important. Here we present such a study of CdSe/CdS core-shell NCs using density functional theory, where we focus on dependence of the properties of these NCs on core types and interfaces between the core and the shell, as well as on the core/shell ratio. We show that the density of states and the absorption indices depend rather weakly on the type of interface and core type. We demonstrate that the HOMO wavefunction is mainly localised in the core of the nanocrystal, depending primarily on the core/shell ratio. On the other hand the LUMO wavefunction spreads more into the shell of the nanocrystal, where its confinement in the core is almost the same in each of the studied structural models. Furthermore, we show that the radiative lifetimes decrease with increasing core sizes due to changes in the dipolar overlap integral of the HOMO and LUMO wavefunctions. In addition, the electron-hole Coulomb interaction energies follow a similar pattern as the localisation of the wavefunctions, with the smaller NCs having higher Coulomb interaction energies.

Interaction-induced singular Fermi surface in a high-temperature oxypnictide superconductor

In the family of iron-based superconductors, LaFeAsO-type materials possess the simplest electronic structure due to their pronounced two-dimensionality. And yet they host superconductivity with the highest transition temperature T-c approximate to 55K. Early theoretical predictions of their electronic structure revealed multiple large circular portions of the Fermi surface with a very good geometrical overlap (nesting), believed to enhance the pairing interaction and thus superconductivity. The prevalence of such large circular features in the Fermi surface has since been associated with many other iron-based compounds and has grown to be generally accepted in the field. In this work we show that a prototypical compound of the 1111-type, SmFe0.92Co0.08AsO, is at odds with this description and possesses a distinctly different Fermi surface, which consists of two singular constructs formed by the edges of several bands, pulled to the Fermi level from the depths of the theoretically predicted band structure by strong electronic interactions. Such singularities dramatically affect the low-energy electronic properties of the material, including superconductivity. We further argue that occurrence of these singularities correlates with the maximum superconducting transition temperature attainable in each material class over the entire family of iron-based superconductors.

Bioengineering of AAV2 Capsid at Specific Serine, Threonine, or Lysine Residues Improves Its Transduction Efficiency in Vitro and in Vivo

We hypothesized that the AAV2 vector is targeted for destruction in the cytoplasm by the host cellular kinase/ubiquitination/proteasomal machinery and that modification of their targets on AAV2 capsid may improve its transduction efficiency. In vitro analysis with pharmacological inhibitors of cellular serine/threonine kinases (protein kinase A, protein kinase C, casein kinase II) showed an increase (20-90%) on AAV2-mediated gene expression. The three-dimensional structure of AAV2 capsid was then analyzed to predict the sites of ubiquitination and phosphorylation. Three phosphodegrons, which are the phosphorylation sites recognized as degradation signals by ubiquitin ligases, were identified. Mutation targets comprising eight serine (S) or seven threonine (T) or nine lysine (K) residues were selected in and around phosphodegrons on the basis of their solvent accessibility, overlap with the receptor binding regions, overlap with interaction interfaces of capsid proteins, and their evolutionary conservation across AAV serotypes. AAV2-EGFP vectors with the wild-type (WT) capsid or mutant capsids (15 S/T -> alanine A] or 9 K -> arginine R] single mutant or 2 double K -> R mutants) were then evaluated in vitro. The transduction efficiencies of 11 S/T -> A and 7 K -> R vectors were significantly higher (similar to 63-90%) than the AAV2-WT vectors (similar to 30-40%). Further, hepatic gene transfer of these mutant vectors in vivo resulted in higher vector copy numbers (up to 4.9-fold) and transgene expression (up to 14-fold) than observed from the AAV2-WT vector. One of the mutant vectors, S489A, generated similar to 8-fold fewer antibodies that could be cross-neutralized by AAV2-WT. This study thus demonstrates the feasibility of the use of these novel AAV2 capsid mutant vectors in hepatic gene therapy.

Genetic diversity and proviral DNA load in different neural compartments of HIV-1 subtype C infection

In India, the low prevalence of HIV-associated dementia (HAD) in the Human immunodeficiency virus type 1 (HIV-1) subtype C infection is quite paradoxical given the high-rate of macrophage infiltration into the brain. Whether the direct viral burden in individual brain compartments could be associated with the variability of the neurologic manifestations is controversial. To understand this paradox, we examined the proviral DNA load in nine different brain regions and three different peripheral tissues derived from ten human subjects at autopsy. Using a highly sensitive TaqMan probe-based real-time PCR, we determined the proviral load in multiple samples processed in parallel from each site. Unlike previously published reports, the present analysis identified uniform proviral distribution among the brain compartments examined without preferential accumulation of the DNA in any one of them. The overall viral DNA burden in the brain tissues was very low, approximately 1 viral integration per 1000 cells or less. In a subset of the tissue samples tested, the HIV DNA mostly existed in a free unintegrated form. The V3-V5 envelope sequences, demonstrated a brain-specific compartmentalization in four of the ten subjects and a phylogenetic overlap between the neural and non-neural compartments in three other subjects. The envelope sequences phylogenetically belonged to subtype C and the majority of them were R5 tropic. To the best of our knowledge, the present study represents the first analysis of the proviral burden in subtype C postmortem human brain tissues. Future studies should determine the presence of the viral antigens, the viral transcripts, and the proviral DNA, in parallel, in different brain compartments to shed more light on the significance of the viral burden on neurologic consequences of HIV infection.

Simultaneous acquisition of three NMR spectra in a single experiment for rapid resonance assignments in metabolomics

NMR-based approach to metabolomics typically involves the collection of two-dimensional (2D) heteronuclear correlation spectra for identification and assignment of metabolites. In case of spectral overlap, a 3D spectrum becomes necessary, which is hampered by slow data acquisition for achieving sufficient resolution. We describe here a method to simultaneously acquire three spectra (one 3D and two 2D) in a single data set, which is based on a combination of different fast data acquisition techniques such as G-matrix Fourier transform (GFT) NMR spectroscopy, parallel data acquisition and non-uniform sampling. The following spectra are acquired simultaneously: (1) C-13 multiplicity edited GFT (3,2)D HSQC-TOCSY, (2) 2D H-1- H-1] TOCSY and (3) 2D C-13- H-1] HETCOR. The spectra are obtained at high resolution and provide high-dimensional spectral information for resolving ambiguities. While the GFT spectrum has been shown previously to provide good resolution, the editing of spin systems based on their CH multiplicities further resolves the ambiguities for resonance assignments. The experiment is demonstrated on a mixture of 21 metabolites commonly observed in metabolomics. The spectra were acquired at natural abundance of C-13. This is the first application of a combination of three fast NMR methods for small molecules and opens up new avenues for high-throughput approaches for NMR-based metabolomics.

Identification of dominant modes in random dynamical and aeroelastic systems

Identification of dominant modes is an important step in studying linearly vibrating systems, including flow-induced vibrations. In the presence of uncertainty, when some of the system parameters and the external excitation are modeled as random quantities, this step becomes more difficult. This work is aimed at giving a systematic treatment to this end. The ability to capture the time averaged kinetic energy is chosen as the primary criterion for selection of modes. Accordingly, a methodology is proposed based on the overlap of probability density functions (pdf) of the natural and excitation frequencies, proximity of the natural frequencies of the mean or baseline system, modal participation factor, and stochastic variation of mode shapes in terms of the modes of the baseline system - termed here as statistical modal overlapping. The probabilistic descriptors of the natural frequencies and mode shapes are found by solving a random eigenvalue problem. Three distinct vibration scenarios are considered: (i) undamped arid damped free vibrations of a bladed disk assembly, (ii) forced vibration of a building, and (iii) flutter of a bridge model. Through numerical studies, it is observed that the proposed methodology gives an accurate selection of modes. (C) 2015 Elsevier Ltd. All rights reserved.

Quantitative metabolic profiling of NMR spectral signatures of branched chain amino acids in blood serum

Branched Chain Amino Acids (BCAAs) are related to different aspects of diseases like pathogenesis, diagnosis and even prognosis. While in some diseases, levels of all the BCAAs are perturbed; in some cases, perturbation occurs in one or two while the rest remain unaltered. In case of ischemic heart disease, there is an enhanced level of plasma leucine and isoleucine but valine level remains unaltered. In `Hypervalinemia', valine is elevated in serum and urine, but not leucine and isoleucine. Therefore, identification of these metabolites and profiling of individual BCAA in a quantitative manner in body-fluid like blood plasma/serum have long been in demand. H-1 NMR resonances of the BCAAs overlap with each other which complicates quantification of individual BCAAs. Further, the situation is limited by the overlap of broad resonances of lipoprotein with the resonances of BCAAs. The widely used commercially available kits cannot differentially estimate the BCAAs. Here, we have achieved proper identification and characterization of these BCAAs in serum in a quantitative manner employing a Nuclear Magnetic Resonance-based technique namely T-2-edited Correlation Spectroscopy (COSY). This approach can easily be extended to other body fluids like bile, follicular fluids, saliva, etc.

Electronic structure origin of conductivity and oxygen reduction activity changes in low-level Cr-substituted (La, Sr)MnO3

The electronic structure of the (La0.8Sr0.2)(0.98)Mn1-xCrxO3 model series (x = 0, 0.05, or 0.1) was measured using soft X-ray synchrotron radiation at room and elevated temperature. O K-edge near-edge X-ray absorption fine structure (NEXAFS) spectra showed that low-level chromium substitution of (La, Sr)MnO3 resulted in lowered hybridisation between O 2p orbitals and M 3d and M 4sp valance orbitals. Mn L-3-edge resonant photoemission spectroscopy measurements indicated lowered Mn 3d-O 2p hybridisation with chromium substitution. Deconvolution of O K-edge NEXAFS spectra took into account the effects of exchange and crystal field splitting and included a novel approach whereby the pre-peak region was described using the nominally filled t(2g) up arrow state. 10% chromium substitution resulted in a 0.17 eV lowering in the energy of the t(2g) up arrow state, which appears to provide an explanation for the 0.15 eV rise in activation energy for the oxygen reduction reaction, while decreased overlap between hybrid O 2p-Mn 3d states was in qualitative agreement with lowered electronic conductivity. An orbital-level understanding of the thermodynamically predicted solid oxide fuel cell cathode poisoning mechanism involving low-level chromium substitution on the B-site of (La, Sr)MnO3 is presented. (C) 2015 AIP Publishing LLC.

General framework for acoustic emission during plastic deformation

Despite the long history, so far there is no general theoretical framework for calculating the acoustic emission spectrum accompanying any plastic deformation. We set up a discrete wave equation with plastic strain rate as a source term and include the Rayleigh-dissipation function to represent dissipation accompanying acoustic emission. We devise a method of bridging the widely separated time scales of plastic deformation and elastic degrees of freedom. While this equation is applicable to any type of plastic deformation, it should be supplemented by evolution equations for the dislocation microstructure for calculating the plastic strain rate. The efficacy of the framework is illustrated by considering three distinct cases of plastic deformation. The first one is the acoustic emission during a typical continuous yield exhibiting a smooth stress-strain curve. We first construct an appropriate set of evolution equations for two types of dislocation densities and then show that the shape of the model stress-strain curve and accompanying acoustic emission spectrum match very well with experimental results. The second and the third are the more complex cases of the Portevin-Le Chatelier bands and the Luders band. These two cases are dealt with in the context of the Ananthakrishna model since the model predicts the three types of the Portevin-Le Chatelier bands and also Luders-like bands. Our results show that for the type-C bands where the serration amplitude is large, the acoustic emission spectrum consists of well-separated bursts of acoustic emission. At higher strain rates of hopping type-B bands, the burst-type acoustic emission spectrum tends to overlap, forming a nearly continuous background with some sharp acoustic emission bursts. The latter can be identified with the nucleation of new bands. The acoustic emission spectrum associated with the continuously propagating type-A band is continuous. These predictions are consistent with experimental results. More importantly, our study shows that the low-amplitude continuous acoustic emission spectrum seen in both the type-B and type-A band regimes is directly correlated to small-amplitude serrations induced by propagating bands. The acoustic emission spectrum of the Luders-like band matches with recent experiments as well. In all of these cases, acoustic emission signals are burstlike, reflecting the intermittent character of dislocation-mediated plastic flow.

Physical Insights on the Ambiguous Metal-Graphene Interface and Proposal for Improved Contact Resistance

The ambiguous behavior of metal-graphene interface has been addressed in this paper using density functional theory and nonequilibrium Green's function formalism. For the first time, the fundamental chemistry of metal-graphene interface, in particular role of sp-hybridized and sp(2)-hybridized carbon atoms, has been emphasized and discussed in detail in this paper. It was discovered that the sp-hybridized sites at the edge of a graphene monolayer contribute to 40% of current conduction when compared with sp(2)-hybridized atom sites in the graphene-metal overlap region. Moreover, we highlighted the insignificance of an additional metal layer, i.e., sandwiched contact, due to lacking sp-hybridized carbon sites. A fundamental way of defining the contact resistance, while keeping chemical bonding in mind, has been proposed. The bonding insight has been further used to propose the novel ways of interfacing metal with graphene, which results in a 40% reduction in contact resistance.

Relative stabilities of condensed face sharing mono- and di-carboranes: CB20H18 and C2B19H18+

The relative energies of triangular face sharing condensed macro polyhedral carboranes: CB20H18 and C2B19H18+ derived from mono- and di-substitution of carbons in (4) B21H18- is calculated at B3LYP/6-31G* level. The relative energies, H center dot center dot center dot H non-bonding distances, NICS values, topological charge analysis and orbital overlap compatibility connotes the face sharing condensed macro polyhedral mono-carboranes, 8 (4-CB20H18) to be the lowest energy isomer. The di-carba- derivative, (36) 4,4'a-C2B19H18+ with carbons substituted in a different B-12 cage in (4) B21H18- in anti-fashion is the most stable isomer among 28 possibilities. This structure has less non-bonding H center dot center dot center dot H interaction and is in agreement with orbital-overlap compatibility, and these two have the pivotal role in deciding the stability of these clusters. An estimate of the inherent stability of these carboranes is made using near-isodesmic equations which show that CB20H18 (8) is in the realm of the possible. (C) 2015 Elsevier B.V. All rights reserved.

MS3ALIGN: an efficient molecular surface aligner using the topology of surface curvature

Background: Aligning similar molecular structures is an important step in the process of bio-molecular structure and function analysis. Molecular surfaces are simple representations of molecular structure that are easily constructed from various forms of molecular data such as 3D atomic coordinates (PDB) and Electron Microscopy (EM) data. Methods: We present a Multi-Scale Morse-Smale Molecular-Surface Alignment tool, MS3ALIGN, which aligns molecular surfaces based on significant protrusions on the molecular surface. The input is a pair of molecular surfaces represented as triangle meshes. A key advantage of MS3ALIGN is computational efficiency that is achieved because it processes only a few carefully chosen protrusions on the molecular surface. Furthermore, the alignments are partial in nature and therefore allows for inexact surfaces to be aligned. Results: The method is evaluated in four settings. First, we establish performance using known alignments with varying overlap and noise values. Second, we compare the method with SurfComp, an existing surface alignment method. We show that we are able to determine alignments reported by SurfComp, as well as report relevant alignments not found by SurfComp. Third, we validate the ability of MS3ALIGN to determine alignments in the case of structurally dissimilar binding sites. Fourth, we demonstrate the ability of MS3ALIGN to align iso-surfaces derived from cryo-electron microscopy scans. Conclusions: We have presented an algorithm that aligns Molecular Surfaces based on the topology of surface curvature. Awebserver and standalone software implementation of the algorithm available at http://vgl.serc.iisc.ernet. in/ms3align.

A dendrimer facilitates resonance energy transfer between hydrophobic aromatic guest molecules in water

A water soluble third generation poly(alkyl aryl ether) dendrimer was examined for its ability to solubilize hydrophobic polyaromatic molecules in water and facilitate non-radiative resonance energy transfer between them. One to two orders of magnitude higher aqueous solubilities of pyrene (PY), perylene (PE), acridine yellow (AY) and acridine orange (AO) were observed in presence of a defined concentration of the dendrimer. A reduction in the quantum yield of the donor PY* emission and a partial decrease in lifetime of the donor excited state revealed the occurrence of energy transfer from dendrimer solubilized excited PY to ground state PE molecules, both present within a dendrimer. The energy transfer efficiency was estimated to be similar to 61%. A cascade resonance energy transfer in a three component system, PY*-to-PE-to-AY and PY*-to-PE-to-AO, was demonstrated through incorporation of AY or AO in the two component PY-PE system. In the three-component system, excitation of PY resulted in emission from AY or AO via a cascade energy transfer process. Careful choice of dye molecules with good spectral overlap and the employment of dendrimer as the medium enabled us to expand absorption-emission wavelengths, from similar to 330 nm to similar to 600 nm in aqueous solution. (C) 2015 Elsevier B.V. All rights reserved.