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Shiv Nadar University

(SoNS) School of Natural Sciences

Measurement of gene expression can provide important clues about gene function and molecular basis of developmental processes. Here, we have analysed the chickpea transcriptome in vegetative and flower tissues by exploiting the potential of high-throughput sequencing to measure gene expression. We mapped more than 295 million reads to quantify the transcript abundance during flower development. We detected the expression of more than 90% genes in at least one tissue analysed. We found quite a large number of genes were differentially expressed during flower development as compared to vegetative tissues. Further, we identified several genes expressed in a stage-specific manner. Various transcription factor families and metabolic pathways involved in flower development were elucidated. The members of MADS-box family were most represented among the transcription factor genes up-regulated during various stages of flower development. The abundant expression of several well-known genes implicated in flower development in chickpea flower development stages confirmed our results. In addition, we detected the expression specificities of lineage-specific genes during flower development. The expression data presented in this study is the most comprehensive dataset available for chickpea as of now and will serve as resource for unraveling the functions of many specific genes involved in flower development in chickpea and other legumes. © 2013 Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.

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Life Sciences

Fulltext

Plant Biotechnology Journal

A global view of transcriptome dynamics during flower development in chickpea by deep sequencing

Temperature dependent steady state and time resolved fluorescence measurements have been performed to explore the interaction and dynamics in polymer-electrolyte composite of the following general formula: 0.85 PEG 0.15{f KNO3 (1-f) LiNO3}, with f denoting fraction of potassium ion in the 0.15 mol electrolyte present in the medium. Poly(ethylene glycol) with number-averaged molecular weight of 300 (PEG300) has been employed as polymer and C153 as the fluorescent probe. Substantial excitation wavelength dependence of probe fluorescence emission in presence of electrolyte suggests presence of spatial heterogeneity which vanishes either upon raising temperature or removing the electrolyte. This has been interpreted as arising from the cation-induced arrest of polymer segmental motion. Temporal heterogeneity in these composites is manifested via fractional viscosity dependence of average solvation and rotation rates of the dissolved probe. Viscosity decoupling of these rates in composites is found to depend on cation identity and is also reflected via the corresponding activation energies. The degree of decoupling differs between solvation and rotation, inducing an analogy to the observations made in deeply supercooled liquids. In addition, conformity to hydrodynamic predictions is recovered by measuring f dependent solute rotation at higher temperatures. Several complimentary but different experiments are suggested to re-examine the mechanism proposed here, based on the fluorescence results, for the emergence of spatio-temporal heterogeneity in these composites and its disappearance either in the absence of any electrolyte or at higher temperatures. © 2013 American Institute of Physics.

Chemistry

Journal of Chemical Physics

Ionic arrest of segmental motion and emergence of spatio-temporal heterogeneity: A fluorescence investigation of (polyethylene glycol electrolyte) composites

Physics

Confronting Precision Cosmology with the Minimal Supersymmetric Standard Model

Computational techniques are one of the most emerging topics in structural and molecular biology. Molecular dynamics (MD) simulations are used not only to explore the conformational aspects of biological systems but also to have significant scope in protein-ligand interactions. Then the binding free energy calculations are readily applied to the simulated systems in order to predict the binding affinities. The thermodynamic properties are directly related to protein-ligand interactions which are dependent upon a few specific parameters. In the present review, we highlight some facts related to protein-ligand complexes, by starting with a survey of MD simulations and binding free energy calculations and ending with some successful implementations of these computational techniques. © 2013 Bentham Science Publishers.

Current Computer-Aided Drug Design

Recent advances in protein-ligand interactions: Molecular dynamics simulations and binding free energy

75As and 31P NMR studies are performed in PrCoAsO and NdCoPO respectively. The Knight shift data in PrCoAsO indicate the presence of an antiferromagnetic interaction between the 4f moments along the c axis in the ferromagnetic state of Co 3d moments. We propose a possible spin structure in this system. The 75As quadrupolar coupling constant, $\nu$Q, increases continuously with decrease of temperature and is found to vary linearly with the intrinsic spin susceptibility, Kiso. This indicates the possibility of the presence of a coupling between charge density and spin density fluctuations. Further, the 31P NMR Knight shift and spin-lattice relaxation rate (1/T1) in the paramagnetic state of NdCoPO indicate that the differences of LaCoPO and NdCoPO from SmCoPO are due to the decrement of the interlayer separation and not due to the moments of the 4f electrons. The nuclear spin-lattice relaxation time (T1) in NdCoPO shows weak anisotropy at 300 K. Using the self-consistent renormalization (SCR) theory of itinerant ferromagnets, it is shown that in the ab plane, the spin fluctuations are three-dimensional ferromagnetic in nature. From SCR theory the important spin-fluctuation parameters (T0, T A, ) are evaluated. The similarities and dissimilarities of the NMR results in As and P based systems with different rare earths are also discussed. {\textcopyright} 2013 IOP Publishing Ltd.

Journal of Physics Condensed Matter

Local electromagnetic properties of magnetic pnictides: A comparative study probed by NMR measurements

We report resistivity, magnetization and 19F NMR results in a polycrystalline sample of SmFeAsO0.86F0.14. The resistivity and magnetization data show a sharp drop at 48 K indicating a superconducting transition. The nuclear spin-lattice rate (1/T1) and spin-spin relaxation rate (1/T2) clearly show the existence of a structural phase transition near 163 K in the sample, which also undergoes a superconducting transition. This finding creates interest in exploring whether this is unique for Sm based systems or is also present in other rare-earth based 1111 superconductors. {\textcopyright} 2013 IOP Publishing Ltd.

Evidence of a structural phase transition in superconducting SmFeAsO 1-xFx from 19F NMR

Background: Members of the periplasmic binding protein (PBP) superfamily utilize a highly conserved inter-domain ligand binding site that adapts to specifically bind a chemically diverse range of ligands. This paradigm of PBP ligand binding specificity was recently altered when the structure of the Thermotoga maritima cellobiose-binding protein (tmCBP) was solved. The tmCBP binding site is bipartite, comprising a canonical solvent-excluded region (subsite one), adjacent to a solvent-filled cavity (subsite two) where specific and semi-specific ligand recognition occur, respectively. Results: A molecular level understanding of binding pocket adaptation mechanisms that simultaneously allow both ligand specificity at subsite one and promiscuity at subsite two has potentially important implications in ligand binding and drug design studies. We sought to investigate the determinants of ligand binding selectivity in tmCBP through biophysical characterization of tmCBP in the presence of varying β-glucan oligosaccharides. Crystal structures show that whilst the amino acids that comprise both the tmCBP subsite one and subsite two binding sites remain fixed in conformation regardless of which ligands are present, the rich hydrogen bonding potential of water molecules may facilitate the ordering and the plasticity of this unique PBP binding site. Conclusions: The identification of the roles these water molecules play in ligand recognition suggests potential mechanisms that can be utilized to adapt a single ligand binding site to recognize multiple distinct ligands. © 2013 Munshi et al.; licensee BioMed Central Ltd.

BMC Structural Biology

Molecular details of ligand selectivity determinants in a promiscuous β-glucan periplasmic binding protein

Here a combined dynamic fluorescence and all-atom molecular dynamics simulation study of aqueous pool-size dependent solvation energy and rotational relaxations of a neutral dipolar solute, C153, trapped in AOT (charged) and IGPAL (neutral) reverse micelles (RMs) at 298 K, is described. RMs in simulations have been represented by a reduced model where SPC/E water molecules interact with a trapped C153 that possesses realistic charge distributions for both ground and excited states. In large aqueous pools, measured average solvation and rotation rates are smaller for the neutral RMs than those in charged ones. Interestingly, while the measured average solvation and rotation rates increase with pool size for the charged RMs, the average rotation rates for the neutral RMs exhibit a reverse dependence. Simulations have qualitatively reproduced this experimental trend and suggested interfacial location for the solute for all cases. The origin for the subnanosecond Stokes shift dynamics has been investigated and solute-interface interaction contribution quantified. Simulated layer-wise translational and rotational diffusions of water molecules re-examine the validity of the core-shell model and provide a resolution to a debate regarding the origin of the subnanosecond solvation component in dynamic Stokes shift measurements with aqueous RMs but not detected in ultrafast IR measurements. © 2013 American Chemical Society.

Journal of Physical Chemistry B

Solute and solvent dynamics in confined equal-sized aqueous environments of charged and neutral reverse micelles: A combined dynamic fluorescence and all-atom molecular dynamics simulation study

We propose a mechanism to obtain the generation of matter in the standard model. We start from the analysis of the T2/ZN shifted orbifold with magnetic flux, which imposes a ZN symmetry on torus. We also consider several orbifolds such as (T2×T2)/ZN, (T2×T2×T2)/ (ZN×ZN') and (T2×T2×T2)/(Z N×ZN'×ZN'). On such orbifolds, we study the behavior of fermions in two different means - the operator formalism and the explicit analysis of wave functions. For an interesting result, it is found that the number of zero-mode fermions is related to N of the ZN symmetry. In other words, the generation of matter relates to the type of orbifolds. Moreover, we find that shifted orbifold models are severely restricted from realizing three generations. For example, the three-generation model on the type of M4×(T2×T2)/ZN is unique. One can also construct other types of three-generation orbifold models with rich flavor structure. Those results may bring us a realistic model with desired Yukawa structure. © 2013 American Physical Society.

Physical Review D - Particles, Fields, Gravitation and Cosmology

Shifted orbifold models with magnetic flux

In this paper, we discuss a one parameter family of complex Born-Infeld solitons arising from a one parameter family of minimal surfaces. The process enables us to generate a new solution of the B-I equation from a given complex solution of a special type (which are abundant). We illustrate this with many examples. We find that the action or the energy of this family of solitons remains invariant in this family and find that the well-known Lorentz symmetry of the B-I equations is responsible for it. © Indian Academy of Sciences.