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.

Optimal design of multiproduct batch chemical plant using NSGA-II

The optimal design of a multiproduct batch chemical plant is formulated as a multiobjective optimization problem, and the resulting constrained mixed-integer nonlinear program (MINLP) is solved by the nondominated sorting genetic algorithm approach (NSGA-II). By putting bounds on the objective function values, the constrained MINLP problem can be solved efficiently by NSGA-II to generate a set of feasible nondominated solutions in the range desired by the decision-maker in a single run of the algorithm. The evolution of the entire set of nondominated solutions helps the decision-maker to make a better choice of the appropriate design from among several alternatives. The large set of solutions also provides a rich source of excellent initial guesses for solution of the same problem by alternative approaches to achieve any specific target for the objective functions

Cluster based core vector machine

Core Vector Machine(CVM) is suitable for efficient large-scale pattern classification. In this paper, a method for improving the performance of CVM with Gaussian kernel function irrespective of the orderings of patterns belonging to different classes within the data set is proposed. This method employs a selective sampling based training of CVM using a novel kernel based scalable hierarchical clustering algorithm. Empirical studies made on synthetic and real world data sets show that the proposed strategy performs well on large data sets.

Room temperature ferromagnetism in ZnO (core)/graphite (shell) nanowires fabricated by a one-step method

ZnO (core)/graphitic (shell) nanowires were successfully fabricated by a one-step method. Morphology of the as-grown nanowires was studied in detail by scanning electron microscopy, transmission electron microscopy (TEM), and energy dispersive X-ray analysis (EDS). High resolution TEM micrographs and selected area electron diffraction patterns reveal the core/shell morphology of the nanowires that grew along the c-axis of ZnO. EDS study of the nanowires confirms that there are no impurities within the detectable limit. Superconducting quantum interference device magnetometer measurements show room temperature ferromagnetic ordering in these core/shell nanowires. (C) 2010 Elsevier Ltd. All rights reserved.

A core-level photoemission spectroscopic study of the electron-doped superconductor, Nd2-xCexCuO4-δ

A photoemission study of superconducting Nd1.85Ce0.15CuO4-δ shows that Ce in the cuprate is essentially in the 4+ state. While the electron donated by Ce does not appear to affect the Cu 3d band, we still find evidence for the presence of considerable Cu1+ - related configurations due to covalency effects. A role for oxygen holes and Cu1+ species is indicated just as in other cuprate superconductors.

Amido binding to ReO3+ core: Synthesis, structure and intermolecular interactions

The light green coloured complexes of general formula [(ReO)-O-V(L)CI(OH2)]Cl have been synthesised in good yields by reacting [RcvOCl(3)(AsPh3)21 with HL in dichloromethane in dinitrogen atmosphere. Here, L- is the deprotonated form of N',N'-bis(2-pyridylmethyl)amine (HL1); N-(2-pyridylmethyl)-N',N'-dimethylethylenediamine (HL2) and N-(2-pyridylmethyl)-N',N-diethylethylenediamine (HL3). Single crystal X-ray structure determination of [(ReO)-O-V(L-1)Cl(OH2)Cl confirms the amido binding of ReO3+ species. In the solid state of [(ReO)-O-V(L-1)Cl(OH2)]Cl, the coordinated and counter chloride ions are engaged in Re-Cl... H-C(ring), Cl...H-C(ring) and Re(OH2)...Cl hydrogen bonding and forming of a supramolecular network in the solid state. The subunit of the supramolecular network consists of one eight-membered and two nine-membered hydrogen bonded rings. The average diameters of eight-membered and nine-membered rings are similar to 3.70 and similar to 5.26 angstrom, respectively.

Biphenyl ethers conjugated CdSe/ZnS core/shell quantum dots and interpretation of the mechanism of amyloid fibril disruption

The biphenyl ethers (BPEs) are the potent inhibitors of TTR fibril formation and are efficient fibril disrupter. However, the mechanism by which the fibril disruption occurs is yet to be fully elucidated. To gain insight into the mechanism, we synthesized and used a new QD labeled BPE to track the process of fibril disruption. Our studies showed that the new BPE-QDs bind to the fiber uniformly and has affinity and specificity for TTR fiber and disrupted the pre-formed fiber at a relatively slow rate. Based on these studies we put forth the probable mechanism of fiber disruption by BPEs. Also, we show here that the BPE-QDs interact with high affinity to the amyloids of A beta(42), lysozyme and insulin. The potential of BPE-QDs in the detection of senile plaque in the brain of transgenic Alzheimer's mice has also been explored. (C) 2010 Elsevier Ltd. All rights reserved.

Reducing the babel in plant volatile communication: using the forest to see the trees

While plants of a single species emit a diversity of volatile organic compounds (VOCs) to attract or repel interacting organisms, these specific messages may be lost in the midst of the hundreds of VOCs produced by sympatric plants of different species, many of which may have no signal content. Receivers must be able to reduce the babel or noise in these VOCs in order to correctly identify the message. For chemical ecologists faced with vast amounts of data on volatile signatures of plants in different ecological contexts, it is imperative to employ accurate methods of classifying messages, so that suitable bioassays may then be designed to understand message content. We demonstrate the utility of `Random Forests' (RF), a machine-learning algorithm, for the task of classifying volatile signatures and choosing the minimum set of volatiles for accurate discrimination, using datam from sympatric Ficus species as a case study. We demonstrate the advantages of RF over conventional classification methods such as principal component analysis (PCA), as well as data-mining algorithms such as support vector machines (SVM), diagonal linear discriminant analysis (DLDA) and k-nearest neighbour (KNN) analysis. We show why a tree-building method such as RF, which is increasingly being used by the bioinformatics, food technology and medical community, is particularly advantageous for the study of plant communication using volatiles, dealing, as it must, with abundant noise.

Multiferroic and magnetoelectric properties of core-shell CoFe2O4@BaTiO3 nanocomposites

Core-shell CoFe2O4@BaTiO3 nanoparticles and nanotubes have been prepared using a combination of solution processing and high temperature calcination. Both the core-shell nanostructures exhibit magnetic and dielectric hysteresis at room temperature and magnetoelectric effect. The dielectric constant of both the nanocomposites decreases upon application of magnetic field. The core-shell nanoparticles exhibit 1.7% change in magnetocapacitance around 134 K at 1 T, while the core-shell nanotubes show a remarkable 4.5% change in magnetocapacitance around 310 K at 2 T.(C) 2010 American Institute of Physics. [doi:10.1063/1.3478231].

Electronic structure of high-Tc superconductors from core-level spectroscopies

Using the configuration-interaction approach, we show that various core-level spectroscopic observations on the high-Tc superconducting oxides can be consistently described in terms of mixing between d9 and d10 configurations, with a negligible amount of the d8 (Cu3+) state. From our analysis of the existing experimental data, we provide evidence of a wide and continuous valence transition in these systems as a function of temperature. The changes in the hybridization strengths deduced here are indicative of structural modifications of the square-planar CuO4 clusters with decreasing temperature.

Interaction of rat testis protein, TP, with nucleosome core particle

Circular dichroism studies have revealed that addition of testis specific protein, TP in vitro, to rat testes nucleosome core particle resulted in a decrease in the compaction of the core particle DNA. This was also corroborated by thermal denaturation analysis. Addition of TP to nucleosome core particle resulted in the conversion of a biphasic transition towards a single phase. However, at the same time there was a 20% reduction in the overall hyperchromicity of core particle DNA at core particle to TP molar ratios of 1:2 and 1:3. These observations along with our earlier report, showing the DNA melting properties of TP, suggest that TP may play an important role in the disassembly process of nucleosome core particle during spermiogenesis.

An Eventful Synthetic Approach Towards the Biologically Potent Natural Product Ottelione A: Enantio-, Regio- and Stereoselective Construction of the Bicyclic Core

A novel synthetic approach towards the recently reported anti-tumor and anti-tuberculor natural product ottelione A from the readily available Diels-Alder adduct of cyclopentadiene and p-benzoquinone is delineated. Our short strategy, besides being enantio-, regio- and stereoselective, charts an eventful course and is inherently well-suited for adaptation towards diverse synthetic analogues of this biologically potent natural product.

Genome-wide analysis and experimentation of plant serine/threonine/tyrosine-specific protein kinases

Protein tyrosine phosphorylation plays an important role in cell growth, development and oncogenesis. No classical protein tyrosine kinase has hitherto been cloned from plants. Does protein tyrosine kinase exist in plants? To address this, we have performed a genomic survey of protein tyrosine kinase motifs in plants using the delineated tyrosine phosphorylation motifs from the animal system. The Arabidopsis thaliana genome encodes 57 different protein kinases that have tyrosine kinase motifs. Animal non-receptor tyrosine kinases, SRC, ABL, LYN, FES, SEK, KIN and RAS have structural relationship with putative plant tyrosine kinases. In an extended analysis, animal receptor and non-receptor kinases, Raf and Ras kinases, mixed lineage kinases and plant serine/threonine/tyrosine (STY) protein kinases, form a well-supported group sharing a common origin within the superfamily of STY kinases. We report that plants lack bona fide tyrosine kinases, which raise an intriguing possibility that tyrosine phosphorylation is carried out by dual-specificity STY protein kinases in plants. The distribution pattern of STY protein kinase families on Arabidopsis chromosomes indicates that this gene family is partly a consequence of duplication and reshuffling of the Arabidopsis genome and of the generation of tandem repeats. Genome-wide analysis is supported by the functional expression and characterization of At2g24360 and phosphoproteomics of Arabidopsis. Evidence for tyrosine phosphorylated proteins is provided by alkaline hydrolysis, anti-phosphotyrosine immunoblotting, phosphoamino acid analysis and peptide mass fingerprinting. These results report the first comprehensive survey of genome-wide and tyrosine phosphoproteome analysis of plant STY protein kinases.