Structure and properties of donor doped barium titanate prepared by citrate process

Niobium doped barium titanate was prepared using two procedures. First, doped barium titanate was prepared starting from citrate solutions of all components and second, pure barium titanate powder was obtained from the citrate solutions and after that doped. Besides niobium, a small amount of manganese, as acceptor dopant was added. Phase composition, crystal structure, microstructure and dielectric properties were reported. The influence of powder processing on the properties of niobium doped barium titanate was analysed. The grain growth and the concentration of dopants on the dielectric properties were considered. © 2002 Taylor & Francis.

Structure and weak hydrogen bonds in liquid acetaldehyde

Monte Carlo simulations have been performed to investigate the structure and hydrogen bonds formation in liquid acetaldehyde. An all atom model for the acetaldehyde have been optimized in the present work. Theoretical values obtained for heat of vaporisation and density of the liquid are in good agreement with experimental data. Graphics of radial distribution function indicate a well structured liquid compared to other similar dipolar organic liquids. Molecular mechanics minimization in gas phase leads to a trimer of very stable structure. The geometry of this complex is in very good agreement with the rdf. The shortest site-site correlation is between oxygen and the carbonyl hydrogen, suggesting that this correlation play a important role in the liquid structure and properties. The O⋯H average distance and the C-H⋯O angle obtained are characteristic of weak hydrogen bonds.

The plant energy-dissipating mitochondrial systems: Depicting the genomic structure and the expression profiles of the gene families of uncoupling protein and alternative oxidase in monocots and dicots

The simultaneous existence of alternative oxidases and uncoupling proteins in plants has raised the question as to why plants need two energy-dissipating systems with apparently similar physiological functions. A probably complete plant uncoupling protein gene family is described and the expression profiles of this family compared with the multigene family of alternative oxidases in Arabidopsis thaliana and sugarcane (Saccharum sp.) employed as dicot and monocot models, respectively. In total, six uncoupling protein genes, AtPUMP1-6, were recognized within the Arabidopsis genome and five (SsPUMP1-5) in a sugarcane EST database. The recombinant AtPUMP5 protein displayed similar biochemical properties as AtPUMP1. Sugarcane possessed four Arabidopsis AOx1-type orthologues (SsAOx1a-1d); no sugarcane orthologue corresponding to Arabidopsis AOx2-type genes was identified. Phylogenetic and expression analyses suggested that AtAOx1d does not belong to the AOx1-type family but forms a new (AOx3-type) family. Tissue-enriched expression profiling revealed that uncoupling protein genes were expressed more ubiquitously than the alternative oxidase genes. Distinct expression patterns among gene family members were observed between monocots and dicots and during chilling stress. These findings suggest that the members of each energy-dissipating system are subject to different cell or tissue/organ transcriptional regulation. As a result, plants may respond more flexibly to adverse biotic and abiotic conditions, in which oxidative stress is involved. © The Author [2006]. Published by Oxford University Press [on behalf of the Society for Experimental Biology]. All rights reserved.

Pyrearinus termitilluminans larval click beetle luciferase: Active site properties, structure and function relationships and comparison with other beetle luciferases

Several beetle luciferases have been cloned and sequenced. However, most studies on structure and function relationships and bioanalytical applications were done with firefly luciferases, which are pH sensitive. Several years ago we cloned Pyrearinus termitilluminans larval click beetle luciferase, which displays the most blue-shifted bioluminescence among beetle luciferases and is pH insensitive. This enzyme was expressed in E. coli, purified, and its properties investigated. This luciferase shows slower luminescence kinetics, KM values comparable to other beetle luciferases and high catalytic constant. Fluorescence studies with 8-anilino-1-naphtalene-sulfonic acid (1,8-ANS) and modeling studies suggest that the luciferin binding site of this luciferase is very hydrophobic, supporting the solvent and orientation polarizability effects as determining mechanisms for bioluminescence colors. Although pH insensitive in the range between pH 6-8, at pH 10 this luciferase displays a remarkable red-shift and broadening of the bioluminescence spectrum. Modeling studies suggest that the residue C312 may play an important role in bioluminescence color modulation. Compared to other beetle luciferases, Pyrearinus termitilluminans luciferase also displays higher thermostability and sustained luminescence in a bacterial cell environment, which makes this luciferase particularly suitable for in vivo cell analysis and bioimaging. © The Royal Society of Chemistry and Owner Societies 2009.

Analysis of agonist and antagonist effects on thyroid hormone receptor conformation by hydrogen/deuterium exchange

Thyroid hormone receptors (TRs) are ligand-gated transcription factors with critical roles in development and metabolism. Although x-ray structures of TR ligand-binding domains (LBDs) with agonists are available, comparable structures without ligand (apo-TR) or with antagonists are not. It remains important to understand apo-LBD conformation and the way that it rearranges with ligands to develop better TR pharmaceuticals. In this study, we conducted hydrogen/deuterium exchange on TR LBDs with or without agonist (T 3) or antagonist (NH3). Both ligands reduce deuterium incorporation into LBD amide hydrogens, implying tighter overall folding of the domain. As predicted, mass spectroscopic analysis of individual proteolytic peptides after hydrogen/ deuterium exchange reveals that ligand increases the degree of solvent protection of regions close to the buried ligand-binding pocket. However, there is also extensive ligand protection of other regions, including the dimer surface at H10-H11, providing evidence for allosteric communication between the ligand-binding pocket and distant interaction surfaces. Surprisingly, Cterminal activation helix H12, which is known to alter position with ligand, remains relatively protected from solvent in all conditions suggesting that it is packed against the LBD irrespective of the presence or type of ligand. T 3, but not NH3, increases accessibility of the upper part of H3-H5 to solvent, and we propose that TR H12 interacts with this region in apo-TR and that this interaction is blocked by T 3 but not NH3.Wepresent data from site-directed mutagenesis experiments and molecular dynamics simulations that lend support to this structural model of apo-TR and its ligand-dependent conformational changes. (Molecular Endocrinology 25: 15-31, 2011). Copyright © 2011 by The Endocrine Society.

Morphological and molecular analysis of the collagen fibers in inflammatory process

Collagen makes up one third of the total protein in humans, being formed by the connection of three polypeptide chains arranged in a triple helix. This protein has fundamental importance in the formation of extracellular matrix of connective tissue. This study aimed to analyze the structural changes of collagen, which are resulting from inflammatory processes in oral mucosa, and to make the comparative analysis between the histopathology and the Raman spectra. The samples of tissues with inflammatory fibrous hyperplasia (IFH) and normal mucosa (NM) were evaluated by Raman Spectroscopy, hematoxylin-eosin and Massons trichrome stain. The histological analysis in both stains showed differences in collagen fibers, which was presented as thin fibers and arranged in parallel direction in NM and as collagen fibers are thick, mature and not organized, showing that these types of stain show morphological changes of collagen in IFH. The Raman Spectroscopy discriminate the groups of NM and IFH based on vibrational modes of proline, hydroxiproline and CH3, CH2. The histological stains only shows information from morphological data, and can be complemented by Raman spectra. This technique could demonstrate that inflammatory process caused some changes in collagen structure which is related to aminoacids such as proline and hidroxyproline. © 2011 SPIE-OSA.

Electronic structure and magnetic properties of FeWO 4 nanocrystals synthesized by the microwave-hydrothermal method

This communication reports that FeWO 4 nanocrystals were successfully synthesized by the microwave-hydrothermal method at 443 K for 1 h. The structure and shape of these nanocrystals were characterized by X-ray diffraction, Rietveld refinement, and transmission electron microscopy. The experimental results and first principles calculations were combined to explain the electronic structure and magnetic properties. Experimental data were obtained by magnetization measurements for different applied magnetic fields. Theoretical calculations revealed that magnetic properties of FeWO 4 nanocrystals can be assigned to two magnetic orderings with parallel or antiparallel spins in adjacent chains. These factors are crucial to understanding of competition between ferro- and antiferromagnetic behavior. © 2012 Elsevier Inc.

Molecular Dynamics simulations of track formation at different ensembles

A series of Molecular Dynamics simulations of thermal spikes has been run in zircon. For two different ensembles: microcanonical one and a combination of microcanonical one acting on the simulation core with Langevin one on the side walls of simulation. Depending on the used ensemble, different track-formation threshold energies were found. When the combined ensemble is carried out, the total energy of the simulations varies with the temperature which can influence how annealing fission-track models should deal with the lattice recovery. A fission-track annealing model is tested with the simulation results. © 2012 Elsevier Ltd. All rights reserved.

On the unzipping mechanisms of carbon nanotubes: Insights from reactive molecular dynamics simulations

Unzipping carbon nanotubes (CNTs) is considered one of the most promising approaches for the controlled and large-scale production of graphene nanoribbons (GNR). These structures are considered of great importance for the development of nanoelectronics because of its dimensions and intrinsic nonzero band gap value. Despite many years of investigations some details on the dynamics of the CNT fracture/unzipping processes remain unclear. In this work we have investigated some of these process through molecular dynamics simulations using reactive force fields (ReaxFF), as implemented in the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) code. We considered multi-walled CNTs of different dimensions and chiralities and under induced mechanical stretching. Our preliminary results show that the unzipping mechanisms are highly dependent on CNT chirality. Well-defined and distinct fracture patterns were observed for the different chiralities. Armchair CNTs favor the creation of GNRs with well-defined armchair edges, while zigzag and chiral ones produce GNRs with less defined and defective edges. © 2012 Materials Research Society.

Biophysical characterization of the recombinant importin-α from neurospora crassa

Neurospora crassa has been widely used as a model organism and contributed to the development of biochemistry and molecular biology by allowing the identification of many metabolic pathways and mechanisms responsible for gene regulation. Nuclear proteins are synthesized in the cytoplasm and need to be translocated to the nucleus to exert their functions which the importin-α receptor has a key role for the classical nuclear import pathway. In an attempt to get structural information of the nuclear transport process in N. crassa, we present herein the cloning, expression, purification and structural studies with N-terminally truncated IMPα from N. crassa (IMPα-Nc). Circular dichroism analysis revealed that the IMPα-Nc obtained is correctly folded and presents a high structural conservation compared to other importins-α. Dynamic light scattering, analytical size-exclusion chromatography experiments and molecular dynamics simulations indicated that the IMPα-Nc unbound to any ligand may present low stability in solution. The IMPα-Nc theoretical model displayed high similarity of its inner concave surface, which binds the cargo proteins containing the nuclear localization sequences, among IMPα from different species. However, the presence of non-conserved amino acids relatively close to the NLS binding region may influence the binding specificity of IMPα-Nc to cargo proteins. Copyright © 2012 Bentham Science Publishers. All Rights Reserved.

The correlation between electronic structure and antimalarial activity of alkoxylated and hydroxylated chalcones

Chalcones have shown potential to several pharmacological applications including antimalarial properties. We employed multivariate data analysis to correlate the antimalarial activity with electronic structure descriptors obtained through quantum mechanical calculations. The results show high statistical significance and bring valuable insights in order to design new compounds. © 2013 Springer Science+Business Media New York.

Expression, purification and molecular analysis of the human ZNF706 protein

Background: The ZNF706 gene encodes a protein that belongs to the zinc finger family of proteins and was found to be highly expressed in laryngeal cancer, making the structure and function of ZNF706 worthy of investigation. In this study, we expressed and purified recombinant human ZNF706 that was suitable for structural analysis in Escherichia coli BL21(DH3). Findings. ZNF706 mRNA was extracted from a larynx tissue sample, and cDNA was ligated into a cloning vector using the TOPO method. ZNF706 protein was expressed according to the E. coli expression system procedures and was purified using a nickel-affinity column. The structural qualities of recombinant ZNF706 and quantification alpha, beta sheet, and other structures were obtained by spectroscopy of circular dichroism. ZNF706's structural modeling showed that it is composed of α-helices (28.3%), β-strands (19.4%), and turns (20.9%), in agreement with the spectral data from the dichroism analysis. Conclusions: We used circular dichroism and molecular modeling to examine the structure of ZNF706. The results suggest that human recombinant ZNF706 keeps its secondary structures and is appropriate for functional and structural studies. The method of expressing ZNF706 protein used in this study can be used to direct various functional and structural studies that will contribute to the understanding of its function as well as its relationship with other biological molecules and its putative role in carcinogenesis. © 2013 Colombo et al.; licensee BioMed Central Ltd.

Revisiting AFLP fingerprinting for an unbiased assessment of genetic structure and differentiation of taurine and zebu cattle

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Quantitative and qualitative dynamics of exotic and native blowflies ( Diptera: Calliphoridae) with migrations among municipalities

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Influence of monomeric and polymeric structure on the physical properties of thermoplastic polyesters derived from hydroxy fatty acids

The physical properties of three vegetable oil derived medium and long chain poly(-hydroxy fatty ester)s (P(Me--OHFA)s), namely poly(-hydroxynonanoate) [P(Me--OHC9)], poly(-hydroxytridecanoate) [P(Me--OHC13)] and poly(-hydroxyoctadecanoate) [P(Me--OHC18)] (n = 8, 12 and 17, respectively), of the [-(CH2)(n)-COO-](x) polyester homologous series are presented. The effect of M-n (M-n 10-40 kg mol(-1)) and n on the crystal structure and thermal and mechanical properties of the P(Me--OHFA)s were investigated by wide-angle X-ray diffraction (WAXD), TGA, DSC, dynamic mechanical analysis (DMA) and tensile analysis and are discussed in the context of the [-(CH2)(n)-COO-](x) polyester homologous series, contrasted with linear polyethylene (PE). For all P(Me--OHFA)s the WAXD data indicated an orthorhombic crystal phase reminiscent of linear PE with crystallinity (X-c = 50%-80%) depending strongly on M-n. The glass transition temperature and Young's modulus for P(Me--OHFA)s increased with X-c. The DSC, DMA and TGA studies for P(Me--OHFA)s (n = 8, 12 and 17) indicated strong correlations between the melting, glass transition and thermal degradation behavior and n. The established predictive structure relationships can be used for the custom engineering of polyester materials suitable for specialty and commodity applications. (c) 2014 Society of Chemical Industry