Proteome analysis in the bovine adrenal medulla using liquid chromatography with tandem mass spectrometry

Liquid chromatography/mass spectrometry (LC/MS)-based proteomics has been used to identify soluble proteins in the bovine adrenal medulla. This gland is a major source of hormones, opioids, neurotransmitters, and several vital proteins. The adrenal medulla proteins were first purified using ammonium sulfate precipitation. The resulting proteins were then pre-fractionated with a C-4 high-performance liquid chromatography (HPLC) column. Each 2-min HPLC fraction was digested with trypsin, and separated further and analyzed using capillary liquid chromatography/tandem mass spectrometry (capLC/nanospray-MS/MS) to map the proteome of the adrenal medulla. The parent mass and sequence ion information thus obtained for tryptic peptides was used to search the NCBInr database using the SEQUEST search engine. A total of 195 proteins were identified, of which 71 had good scores (delta correlation value greater than 0.1, preliminary score above 200, and cross-correlation value above 2.5). The prominent proteins thus identified are secretogranin I precursor, chromogranin A, proenkephalin A precursor, myosin X, hemoglobin beta chain, hemoglobin alpha chain, heat shock protein 10 kDa, and replicase.     

Motif structure and cooperation in real-world complex networks

Networks of dynamical nodes serve as generic models for real-world systems in many branches of science ranging from mathematics to physics, technology, sociology and biology. Collective behavior of agents interacting over complex networks is important in many applications. The cooperation between selfish individuals is one of the most interesting collective phenomena. In this paper we address the interplay between the motifs’ cooperation properties and their abundance in a number of real-world networks including yeast protein-protein interaction, human brain, protein structure, email communication, dolphins’ social interaction, Zachary karate club and Net-science coauthorship networks. First, the amount of cooperativity for all possible undirected subgraphs with three to six nodes is calculated. To this end, the evolutionary dynamics of the Prisoner’s Dilemma game is considered and the cooperativity of each subgraph is calculated as the percentage of cooperating agents at the end of the simulation time. Then, the three- to six-node motifs are extracted for each network. The significance of the abundance of a motif, represented by a Z-value, is obtained by comparing them with some properly randomized versions of the original network. We found that there is always a group of motifs showing a significant inverse correlation between their cooperativity amount and Z-value, i.e. the more the Z-value the less the amount of cooperativity. This suggests that networks composed of well-structured units do not have good cooperativity properties.     

<Emphasis Type="Italic">N</Emphasis>=2 de Sitter Super-symmetry Algebra

It was shown that N=1 super-symmetry algebra can be constructed in de Sitter space (Pahlavan et al. in Phys Lett. B 627:217–223, 2005), through calculation of charge conjugation in the ambient space notation (Moradi et al. in Phys. Lett. B 613:74, 2005; Phys. Lett. B 658:284, 2008). Calculation of N=2 super-symmetry algebra constitutes the main frame of this paper. N=2 super-symmetry algebra was presented in Pilch et al. (Commun. Math. Phys. 98:105, 1985). In this paper, we obtain an alternative N=2 super-symmetry algebra.     

Molecular dynamics simulations of hydrogen adsorption/desorption by palladium decorated single-walled carbon nanotube bundle

Utilising molecular dynamics simulations, the hydrogen molecules adsorption isotherms of the (8,?0) palladium decorated single-walled carbon nanotube (SWNT) were obtained. The hydrogen adsorption was studied on the external, interstial and internal surfaces of the SWNT bundle at several temperatures ranging from 77 to 400?K. The results were compared with the bare single-walled carbon nanotube bundle under the same conditions. The decorated carbon nanotube bundle hydrogen adsorption was significantly higher than that of the bare one. The hydrogen desorption and readsorption were studied using temperature as the readsorption/desorption variable. The rate constants were calculated for the hydrogen desorption at different temperatures. The calculated decorated SWNT bundle hydrogen desorption activation energy was higher than that for the bare SWNT bundle. The calculated activation energies for the hydrogen desorption in both nanotube bundles specified the temperature dependency of hydrogen desorption.     

Al-doped B80 fullerene as a suitable candidate for H2, CH4, and CO2 adsorption for clean energy applications

Dispersion-corrected density functional theory method was performed to report on a high-performance adsorbent for removal of CO₂ from the precombustion and natural gases. At first, the effect of Al atom impurity on the structural and electronic properties of B₈₀ fullerene is studied. Then, the adsorption geometries and energies of gases (H₂, CH₄, or CO₂) on the B₈₀ and AlB₇₉ (amphoteric adsorbents) are explored. The Al atom enhances reactivity of the cage toward the gases and the adsorption processes are more exothermic with low and high energy barriers for chemisorption of H₂ and CO₂, respectively. Stable chemisorption of CO₂ on the AlB₇₉ is validated by the high adsorption energy and large charge transfer, while the CH₄ is just physically adsorbed on the AlB₇₉. Further, the physisorbed gases can enhance field emission current of the AlB₇₉ and in the continuous capturing of the gases, the magnetic moment of the cage is quenched. Furthermore, dependency of the electronic structure of the adsorbent on the gas adsorption is intensively studied. We suggest that the AlB₇₉ could be a promising material for capture, storage, and separation of the gases and as a novel material for sustainable energy and sweetening process in the petroleum industry.     

Inhibitory effect of safranal and crocin,two principle compounds of <Emphasis Type="Italic">Crocus sativus</Emphasis>, on fibrillation of lysozyme

A key feature in more than twenty amyloid-related diseases is the aggregation of intra-and/or extracellular misfolded proteins as amyloid fibrils. Therefore, preventing or reversing amyloid aggregation by using of small molecules is considered as useful approaches to the treatment of these diseases. We have evaluated the ability of safranal and crocin, to inhibit amyloid self-assembly of hen egg white lysozyme (HEWL), as an in vitro model system. Structural properties of HEWL in the presence of these compounds were investigated individually using thioflavin T, anilinonaphthalene-8-sulfonic acid fluorescence assays, far-UV circular dichroism and scanning electron microscopy as well as docking method. Our results showed that incubation of HEWL with either crocin or safranal at various concentrations leads a significant inhibition in the rate of amyloid formation. Docking analysis revealed crocin and safranal interact with the central hydrophobic region of lysozyme through van der Waals interaction. Hydroxyl group in crocin through hydrogen bonds connected to the several hydrophilic amino acids of lysozyme, while in safranal there are just one aldehyde group that through hydrogen bonds connected to aspartic acid in lysozyme. It can be concluded that both hydrophobic and hydrophilic groups contribute to lower lysozyme fibril accumulation.     

Molecular dynamics simulation of the sliding of distamycin anticancer drug along DNA: interactions and sequence selectivity

Molecular dynamics simulations and umbrella sampling have been used to investigate the sliding of distamycin anticancer drug along the DNA minor groove. The potential energy surface calculated for the sliding of drug shows three minima. The global minimum corresponds to the binding of drug to the AT-rich region, which is the origin of sequence selectivity of distamycin. This selectivity originates from both structural factors and energy contributions. The analysis of energy contributions of binding was performed by the MM–PBSA method. The analysis of hydrogen bonds and van der Waals, electrostatic, and solvation interactions show that structural or steric factors are more important in the selectivity of distamycin than energetic factors. The results of this study can be applied in the design of new derivatives of distamycin anticancer drug with improved properties.     

Effects of fiber diameter and CO2 activation temperature on the pore characteristics of polyacrylonitrile based activated carbon nanofibers

The effects of fiber diameter and activation temperature on the pore characteristics of polyacrylonitrile based activated carbon nanofibers are investigated. It was found that lower fiber diameters as well as higher activation temperatures lead to a higher weight loss, specific surface area and total pore volume. The nitrogen adsorption capacity of activated carbon nanofibers is almost three times that of activated carbon fiber with a diameter of 10 µm. As far as the size of pores in activated carbon nanofibers is concerned, it is basically the micropores that dominate the scene. Moreover, tailoring the pore characteristics by adjusting the activation temperature and fiber diameter is plausible. Copyright © 2009 John Wiley & Sons, Ltd.     

Synthesis and characterization of copper(II) complexes incorporating pyrazolyl-derived N,S-donor bidentate ligands

The novel bidentate N,S-donor anionic ligands [PhNCSIndz]^?, [PhNCSImz]^?, [PhNCSPz^Me3]^?, and [EtNCSPz]^?, where Indz?=?indazole, Imz?=?imidazole, Pz^Me3?=?3,4,5-trimethylpyrazole, and Pz?=?pyrazole, were synthesized and used to prepare Cu(II) complexes of general formula [Cu(N^S)₂]. The ligands were synthesized via direct addition of phenylisothiocyanate or ethylisothiocyanate into THF suspensions of the corresponding sodium-pyrazolate salts. All of the synthesized compounds, including the ligands and the complexes, were characterized by physico-chemical and spectroscopic methods, and crystal structures of [Cu(EtNCSPz)₂] and [Cu(PhNCSPz^Me2)₂] were determined by X-ray diffraction analysis, showing a trans-square planar geometry for [Cu(EtNCSPz)₂] and a distorted tetrahedral geometry for [Cu(PhNCSPz^Me2)₂].