Structure and magnetic properties of CoNiP nanowire arrays embedded in AAO template

Ternary CoNiP nanowire (NW) arrays have been synthesized by electrochemical deposition inside the nanochannels of anodic aluminum oxide (AAO) template. The CoNiP NWs deposited at room temperature present soft magnetic properties, with both parallel and perpendicular coercivities less than 500 Oe. In contrast, as the electrolyte temperature (T-elc) increases from 323 to 343 K, the NWs exhibit hard magnetic properties with coercivities in the range of 1000-2500 Oe. This dramatic increase in coercivities can be attributed to the domain wall pinning that is related to the formation of Ni and Co nanocrystallites and the increase of P content. The parallel coercivity (i.e. the applied field perpendicular to the membrane surface) maximum as high as 2500 Oe with squareness ratio up to 0.8 is achieved at the electrolyte temperature of 328 K. It has been demonstrated that the parallel coercivity of CoNiP NWs can be tuned in a wide range of 200-2500 Oe by controlling the electrolyte temperature, providing an easy way to control magnetic properties and thereby for their integration with magnetic-micro-electromechanical systems (MEMS). (C) 2008 Elsevier B.V. All rights reserved.

A novel short neurotoxin, cobrotoxin c, from monocellate cobra (Naja kaouthia) venom: isolation and purification, primary and secondary structure determination, and tertiary structure modeling

A novel short neurotoxin, cobrotoxin c (CBT C) was isolated from the venom of monocellate cobra (Naja kaouthia) using a combination of ion-exchange chromatography and FPLC. Its primary structure was determined by Edman degradation. CBT C is composed of 61 amino acid residues. It differs from cobrotoxin b (CBT B) by only two amino acid substitutions, Thr/Ala11 and Arg/Thr56, which are not located on the functionally important regions by sequence similarity. However, the LD50 is 0.08 mg/g to mice, i.e. approximately five-fold higher than for CBT B. Strikingly, a structure-function relationship analysis suggests the existence of a functionally important domain on the outside of Loop III of CBT C. The functionally important basic residues on the outside of Loop III might have a pairwise interaction with alpha subunit, instead of gamma or delta subunits of the nicotinic acetylcholine receptor (nAChR). (C) 2002 Elsevier Science Inc. All rights reserved.

A new protein structure of P-II class snake venom metalloproteinases: it comprises metalloproteinase and disintegrin domains

A new metalloproteinase-disintegrin, named Jerdonitin, was purified from Trimeresurus jerdonii venom with a molecular weight of 36 kDa on SDS-PAGE. It dose-dependently inhibited ADP-induced human platelet aggregation with IC50 of 120 nM. cDNA cloning and sequencing revealed that Jerdonitin belonged to the class II of snake venom metalloproteinases (SVMPs) (P-II class). Different from other P-II class SVMPs, metalloproteinase and disintegrin domains of its natural protein were not separated, confirmed by internal peptide sequencing. Compared to other P-II class SVMPs, Jerdonitin has two additional cysteines (Cys219 and Cys238) located in the spacer domain and disintegrin domain, respectively. They probably form a disulfide bond and therefore the metalloproteinase and disintegrin domains cannot be separated by posttranslationally processing. In summary, comparison of the amino acid sequences of Jerdonitin with those of other P-II class SVMPs by sequence alignment and phylogenetic analysis, in conjunction with natural protein structure data, suggested that it was a new type of P-II class SVMPs. (C) 2003 Elsevier Inc. All rights reserved.

Structure analysis of CCR5 from human and primates

It is well known that the chemokine receptor CCR5 plays very important roles in HIV-1 virus infection. A three-dimensional molecular model of human CCR5 was generated by SYBYL, a distance geometry-based homologous modeling package, using the corresponding transmembrane domain of bacteriorhodopsin as the template. On the basis of human CCR5 model, we also built 18 3D molecular models of CCR5 in primates from Pongo pygmaeus, Pygathrix nemaeus, Macaca assameniss, Trachy-pithecus phayrei, T. francoisi, M. arotoides, Rhinopithecus roxellance, R, bieti, R. avunculus, Hylobates leucogenys, Pan troglodytes, Gorilla gorilla, Cercopithecus aethiops 1, C. aethiops 2, Papio hamadryas M. mulatta, M. fascicularis and M. nemestrina. Structural analyses and statistics results suggested that the main-chains of the primate CCR5 were similar to that of the human CCR5 and that the fit-RMS deviation values of these primate CCR5 were less than 0.1 Angstrom. Moreover, the structures of these CCR5 proteins, except those of the African green monkey 1 (C.aet1), do not have a remarkable difference. It is proved that the 14th residue is possibly very important in the inhibition infections by M-tropic HIV-1, and it is also demonstrated that the 13th residue of human CCR5 was changed from asparagine into aspartic acid in all these primates. It means that the primate CCR5 no longer depend on CD4 for efficient entry, but human CCR5 may have evolved subsequently due to the use of CD4 as a receptor, allowing the high-affinity chemokine receptor-binding site of HIV to be sequestered from host immune surveillance. (C) 2000 Elsevier Science B.V. All rights reserved.

Molecular modeling on some human interleukins sharing gamma c of interleukin-2 receptor, and structure-function relationships

Five models for human interleukin-7 (HIL-7), HIL-9, HIL-13, HIL-15 and HIL-17 have been generated by SYBYL software package. The primary models were optimized using molecular dynamics and molecular mechanics methods. The final models were optimized using a steepest descent algorithm and a subsequent conjugate gradient method. The complexes with these interleukins and the common gamma chain of interleukin-2 receptor (IL-2R) were constructed and subjected to energy minimization. We found residues, such as Gln127 and Tyr103, of the common gamma chain of IL-2R are very important. Other residues, e.g. Lys70, Asn128 and Glu162, are also significant. Four hydrophobic grooves and two hydrophilic sites converge at the active site triad of the gamma chain. The binding sites of these interleukins interaction with the common gamma chain exist in the first helical and/or the fourth helical domains. Therefore, we conclude that these interleukins binds to the common gamma chain of IL-2R by the first and the fourth helix domain. Especially at the binding sites of some residues (lysine, arginine, asparagine, glutamic acid and aspartic acid), with a discontinuous region of the common gamma chain of IL-2R, termed the interleukins binding sites (103-210). The study of these sites can be important for the development of new drugs. (C) 2000 Elsevier Science B.V. All rights reserved.

Structure, organization and expression of common carp (Cyprinus carpio L.) SLP-76 gene

SLP-76 is an important member of the SLP-76 family of adapters, and it plays a key role in TCR signaling and T cell function. Partial cDNA sequence of SLP-76 of common carp (Cyprinus carpio L.) was isolated from thymus cDNA Library by the method of suppression subtractive hybridization (SSH). Subsequently, the full length cDNA of carp SLP-76 was obtained by means of 3' RACE and 5' RACE, respectively. The full Length cDNA of carp SLP-76 was 2007 bp, consisting of a T-terminal untranslated region (UTR) of 285 bp, a T-terminal. UTR of 240 bp, and an open reading frame of 1482 bp. Sequence comparison showed that the deduced amino acid sequence of carp SLP-76 had an overall similarity of 34-73% to that of other species homotogues, and it was composed of an NH2-terminal domain, a central proline-rich domain, and a C-terminal SH2 domain. Amino acid sequence analysis indicated the existence of a Gads binding site R-X-X-K, a 10-aa-long sequence which binds to the SH3 domain of LCK in vitro, and three conserved tyrosine-containing sequence in the NH2-terminal domain. Then we used PCR to obtain a genomic DNA which covers the entire coding region of carp SLP-76. In the 9.2 k-long genomic sequence, twenty one exons and twenty introns were identified. RT-PCR results showed that carp SLP-76 was expressed predominantly in hematopoietic tissues, and was upregulated in thymus tissue of four-month carp compared to one-year old carp. RT-PCR and virtual northern hybridization results showed that carp SLP-76 was also upregulated in thymus tissue of GH transgenic carp at the age of four-months. These results suggest that the expression level of SLP-76 gene may be related to thymocyte development in teleosts. (c) 2007 Published by Elsevier Ltd.

Bioinformatic identification of genes encoding C1q-domain-containing proteins in zebrafish

C1q is the first subcomponent of classical pathway in the complement system and a major link between innate and acquired immunities. The globular (gC1q) domain similar with C1q was also found in many non-complement C1q-domain-containing (C1qDC) proteins which have similar crystal structure to that of the multifunctional tumor necrosis factor (TNF) ligand family, and also have diverse functions. In this study, we identified a total of 52 independent gene sequences encoding C1q-domain-containing proteins through comprehensive searches of zebrafish genome, cDNA and EST databases. In comparison to 31 orthologous genes in human and different numbers in other species, a significant selective pressure was suggested during vertebrate evolution. Domain organization of C1q-domain-containing (C1qDC) proteins mainly includes a leading signal peptide, a collagen-like region of variable length, and a C-terminal C1q domain. There are 11 highly conserved residues within the C1q domain, among which 2 are invariant within the zebrafish gene set. A more extensive database searches also revealed homologous C1qDC proteins in other vertebrates, invertebrates and even bacterium, but no homologous sequences for encoding C1qDC proteins were found in many species that have a more recent evolutionary history with zebrafish. Therefore, further studies on C1q-domain-containing genes among different species will help us understand evolutionary mechanism of innate and acquired immunities.

Zebraflsh z-otu, a novel Otu and Tudor domain-containing gene, is expressed in early stages of oogenesis and embryogenesis

Several studies have suggested that Otu domain had de-ubiquitinating activity and Tudor domain was important for the formation of germ cells. Here, we reported a novel zebrafish ovary-specific gene containing Otu and Tudor domain, z-otu, which was expressed at stages I-III oocytes and embryonic stages from zygotes to early blastula during embryonic cells maintained their totipotency. Therefore, z-otu might link the ubiquitin signaling pathway to early oogenesis and maintaining the totipotency of embryonic cell. (c) 2005 Elsevier B.V. All rights reserved.

Wavelength Coded Optical Time-Domain Reflectometry

This paper presents a wavelength coded optical timedomain reflectometry based on optical heterodyne technique. In this scheme, the probe and reference optical pulses have different wavelengths. This enables optical heterodyne detection to be used to improve the system performances significantly. We demonstrate a spatial resolution of 2.5 m within a range of 60 km in weak-reflection signal detection and direct observation of Brillouin scattering over a long optical fiber, suggesting online fiber sensing possible. The principle of wavelength coding is applicable to other systems like lidar and radar to increase receiver sensitivity and simplify system structure.

Dynamics of spin-dependent tunneling through a semiconductor double-barrier structure

The dynamics of spin-dependent tunneling through a nonmagnetic semiconductor double-barrier structure is studied including the k(3) Dresselhaus spin orbit coupling is solved by the time-dependent Schrodinger equation with a developed method for the finite-difference relaxation. The resonant peak and quasibound level lifetime are determined by the in-plane wave vector and the applied electric field. The buildup time and decay lifetime of resonant probability amplitude are different for the spin-down and spin-up electrons due to the Dresselhaus spin-orbit coupling. Further investigation shows that the steady spin-polarization in both the well and collector regions has been obtained in the time domain. (C) 2007 American Institute of Physics.

Suppression of self-sustained field domain oscillation in GaAs/AlAs superlattice by hydrostatic pressure at room temperature

The behavior of room temperature self-sustained current oscillations resulting from sequential resonance tunneling in a doped weakly-coupled GaAs/AlAs superlattice (SL) is investigated under hydrostatic pressure. From atmosphere pressure to 6.5 kbar, oscillations exist in the whole plateau of the I-V curve and oscillating characteristics are affected by the pressure. When hydrostatic pressure is higher than 6.5 kbar, the current oscillations are completely suppressed although a current plateau still can be seen in the I-V curve. The plateau disappears when the pressure is close to 13.5 kbar. As the main effect of hydrostatic pressure is to lower the X point valley with respect to Gamma point valley, the disappearance of oscillation and the plateau shrinkage before Gamma - X resonance takes place are attributed to the increases of thermoionic emission and nonresonant tunneling components determined by the lowest Gamma - X barrier height in GaAs/AlAs SL structure.

The Category-Theoretic Solution of Recursive Domain Equations

Recursive specifications of domains plays a crucial role in denotational semantics as developed by Scott and Strachey and their followers. The purpose of the present paper is to set up a categorical framework in which the known techniques for solving these equations find a natural place. The idea is to follow the well-known analogy between partial orders and categories, generalizing from least fixed-points of continuous functions over cpos to initial ones of continuous functors over $\omega $-categories. To apply these general ideas we introduce Wand's ${\bf O}$-categories where the morphism-sets have a partial order structure and which include almost all the categories occurring in semantics. The idea is to find solutions in a derived category of embeddings and we give order-theoretic conditions which are easy to verify and which imply the needed categorical ones. The main tool is a very general form of the limit-colimit coincidence remarked by Scott. In the concluding section we outline how compatibility considerations are to be included in the framework. A future paper will show how Scott's universal domain method can be included too.

Surface transformation and inversion domain boundaries in gallium nitride nanorods

Phase transformation and subdomain structure in [0001]-oriented gallium nitride (GaN) nanorods of different sizes are studied using molecular dynamics simulations. The analysis concerns the structure of GaN nanorods at 300 K without external loading. Calculations show that a transformation from wurtzite to a tetragonal structure occurs along {0110} lateral surfaces, leading to the formation of a six-sided columnar inversion domain boundary (IDB) in the [0001] direction of the nanorods. This structural configuration is similar to the IDB structure observed experimentally in GaN epitaxial layers. The transformation is significantly dependent on the size of the nanorods.

DYNAMIC SCALING OF THE STRUCTURE-FUNCTION FOR SPINODAL DECOMPOSITION IN CRITICAL AND NONCRITICAL MIXTURES OF POLY(VINYL ACETATE) POLY(METHYL METHACRYLATE)

The dynamics of phase separation in a binary polymer blend of poly(vinyl acetate) with poly(methyl methacrylate) was investigated by using a time-resolved light-scattering technique. In the later stages of spinodal decomposition, a simple dynamic scaling law was found for the scattering function S(q, t)(S(q, t) approximately I(q, t)): S(q, t)q(m)-3 S approximately (q/q(m)). The scaling function determined experimentally was in good agreement with that predicted by Furukawa, S approximately (X) approximately X2/(3 + X8) for critical concentration, and approximately in agreement with that predicted by Furukawa, S approximately (X) approximately X2/(3 + X6) for non-critical mixtures. The light-scattering invariant shows that the later stages of the spinodal decomposition were undergoing domain ripening.

The structure of Aquifex aeolicus sulfide:quinone oxidoreductase, a basis to understand sulfide detoxification and respiration

Sulfide: quinone oxidoreductase (SQR) is a flavoprotein with homologues in all domains of life except plants. It plays a physiological role both in sulfide detoxification and in energy transduction. We isolated the protein from native membranes of the hyperthermophilic bacterium Aquifex aeolicus, and we determined its X-ray structure in the "as-purified,'' substrate-bound, and inhibitor-bound forms at resolutions of 2.3, 2.0, and 2.9 angstrom, respectively. The structure is composed of 2 Rossmann domains and 1 attachment domain, with an overall monomeric architecture typical of disulfide oxidoreductase flavoproteins. A. aeolicus SQR is a surprisingly trimeric, periplasmic integral monotopic membrane protein that inserts about 12 angstrom into the lipidic bilayer through an amphipathic helix-turn-helix tripodal motif. The quinone is located in a channel that extends from the si side of the FAD to the membrane. The quinone ring is sandwiched between the conserved amino acids Phe-385 and Ile-346, and it is possibly protonated upon reduction via Glu-318 and/or neighboring water molecules. Sulfide polymerization occurs on the re side of FAD, where the invariant Cys-156 and Cys-347 appear to be covalently bound to polysulfur fragments. The structure suggests that FAD is covalently linked to the polypeptide in an unusual way, via a disulfide bridge between the 8-methyl group and Cys-124. The applicability of this disulfide bridge for transferring electrons from sulfide to FAD, 2 mechanisms for sulfide polymerization and channeling of the substrate, S2-, and of the product, S-n, in and out of the active site are discussed.