Molecular characterization and subcellular localization of Carassius auratus interferon regulatory factor-1

Interferon (IFN)-regulatory transcription factor-1 (IRF-1) has been studied in mammals and fish but little is known about the relationship between its gene structure and nuclear 'ion of IRF-1 protein. In this study, a cDNA encoding Carassius auratus IRF-1 (CaIRF-1) was isolated from an interferon-producing cell line, C. ouratus blastulae embryonic (CAB) cells, exposed to UV-inactivated grass carp hemorrhagic virus (GCHV). The CaIRF-1 genomic locus exhibits exon-intron arrangements similar to those of other vertebrate IRF-1 loci, with nine exons and eight introns, although together with pufferfish IRF-1, CaIRF-1 distinguishes itself from other vertebrate IRF-1 genes by a relatively compact genomic size. Similar to the known IRF-1 genes, CaIRF-1 is ubiquitously expressed, and is upregulated in vitro and in vivo in response to virus, Poty I:C, or CAB INF-containing supernatant (ICS). Subcellular localization analysis confirms the nuclear distribution of CaIRF-1 protein, and reveals two nuclear localization signals (NILS), any one of which is sufficient for nuclear translocation of CaIRF-1. One NLS Locates to amino acids 117-146, and appears to be the structural and functional equivalent of the NLS in mammalian IRF-1. The second NLS (amino acids 73-115) is found within the DNA-binding domain (DBD) of CaIRF-1, and contains two regions rich in basic amino acids (''(KDKSINK101)-K-95" and ''(75)KTWKANFR(82)"). In comparison with mammalian IRF-1, in which the corresponding amino acid stretch does not seem to drive nuclear translocation, five conserved basic amino acids (K-75, K-78, R-82, K-95, and K-101) and one non-conserved basic amino acid (K-97) are present in this NLS from CaIRF-1. This observation suggests that K97 Of CaIRF-1 might be essential for the function of its second NLS, wherein the six basic aminoacids might cooperate to drive CaIRF-1 to the nucleus. Therefore, the current study has revealed a new nuclear localization motif in the DBD of a vertebrate IRF-1. (C) 2007 Elsevier Ltd. All rights reserved.

Characterization of complete genome sequence of the spring viremia of carp virus isolated from common carp (Cyprinus carpio) in China

The complete genome of spring viraemia of carp virus (SVCV) strain A-1 isolated from cultured common carp (Cyprinus carpio) in China was sequenced and characterized. Reverse transcription-polymerase chain reaction (RT-PCR) derived clones were constructed and the DNA was sequenced. It showed that the entire genome of SVCV A-1 consists of 11,100 nucleotide base pairs, the predicted size of the viral RNA of rhabdoviruses. However, the additional insertions in bp 4633-4676 and bp 4684-4724 of SVCV A-1 were different from the other two published SVCV complete genomes. Five open reading frames (ORFs) of SVCV A-1 were identified and further confirmed by RT-PCR and DNA sequencing of their respective RT-PCR products. The 5 structural proteins encoded by the viral RNA were ordered 3'-N-P-M-G-L-5'. This is the first report of a complete genome sequence of SVCV isolated from cultured carp in China. Phylogenetic analysis indicates that SVCV A-1 is closely related to the members of the genus Vesiculovirus, family Rhabdoviridae.

Isolation and characterization of Scophthalmus maximus rhabdovirus

A rhabdovirus associated with a lethal hemorrhagic disease in cultured turbot Scophthalm us maximus Linnaeus was isolated. The virus induced typical cytopathogenic effects (CPE) in 9 of 15 fish cell lines examined and was then propagated and isolated from infected carp leucocyte cells (CLC). Electron microscopy observations revealed that the negatively stained virions had a typical bullet-shaped morphology with one rounded end and one flat base end. The bullet-shaped morphology was more obvious and clear in ultrathin sections of infected cells. Experimental infections also indicated that the S. maximus rhabdovirus (SMRV) was not only a viral pathogen for cultured turbot, but also had the ability to infect other fish species, such as freshwater grass carp. A partial nucleotide sequence of the SMRV polymerase gene was determined by RT-PCR using 2 pairs of degenerate primers designed according to the conserved sequences of rhabdovirus polymerase genes. Homology analysis, amino acid sequence alignment, and phylogenetic relationship analysis of the partial SMRV polymerase sequence indicated that SMRV was genetically distinct from other rhabdoviruses. Sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE) analysis of the purified SMRV revealed 5 major structural proteins, and their molecular masses were estimated to be about 250, 58, 47, 42, and 28 kDa. Significant serological reactivity differences were also observed between SMRV and its nearest neighbor, spring viremia of carp virus (SVCV). The data suggest that SMRV is likely a novel fish rhabdovirus, although it is closely related to rhabdoviruses in the genus Vesiculovirus.

Cloning and characterization of a new multi-stress inducible metallothionein gene in Tetrahymena pyriformis

A new multi-stress-inducible metallothionein (MT) gene isoform has been cloned and characterized from the ciliate Tetrahymena pyriformis. Both the 5'- and 3'-UT regions of the Tp-MT2 gene are very different from the previously reported Tp-MT1 isoform in this organism and from other described MT genes in Tetrahymena pigmentosa and Tetrahymena thermophila. The putative protein sequence of Tp-MT2 contains cysteine clusters with characteristics of the typical Tetrahymena Cd-inducible MT genes. However, the sequence has a special feature of four intragenic tandem repeats within its first half, with a conserved structural pattern x(5/8)CCCx(6)CCx(6)CxCxNCxCCK. To investigate the transcriptional activities of both Tp-MT2 and Tp-MT1 genes toward heavy metals (Cd, Hg, Cu, Zn) and H2O2, the mRNA levels of these two isoforms were evaluated by means of real-time quantitative PCR. Results showed that Tp-MT2 had a higher basal expression level than Tp-MT1 and both genes were induced by Cd, Hg, Cu, and Zn ions after short exposure (I h), although to different extents. Cd was the most effective metal inducer of both two isoforms, but the relative expression level of Tp-MT2 was much lower than that of Tp-MT1. Different expression patterns were also shown between the two genes when treated with Cd over a period of 24 h. We suggest that TpMT-1 plays the role of a multi-inducible stress gene, while TpMT-2 may have a more specific function in basal metal homeostasis although it may have undergone a functional differentiation process. The putative functional significance and evolutionary mode of the TpMT-2 isoform are discussed. (c) 2006 Elsevier GmbH. All rights reserved.

Characterization of two genes encoding leucine-rich repeat-containing proteins in grass carp Ctenopharyngodon idellus

The cDNAs and genes of two different types of leucine- rich repeat-containing proteins from grass carp ( Ctenopharyngodon idellus) were cloned. Homology search revealed that the two genes, designated as GC-GARP and GC-LRG, have 37% and 32% deduced aminoacid sequence similarities with human glycoprotein A repetitions predominant precursor ( GARP) and leucine-rich alpha2-glycoprotein (LRG), respectively. The cDNAs of GC-GARP and GC-LRG encoded 664 and 339 amino acid residues, respectively. GC-GARP and GC-LRG contain many distinct structural and/or functional motifs of the leucine- rich repeat (LRR) subfamily, such as multiple conserved 11-residue segments with the consensus sequence LxxLxLxxN/CxL ( x can be any amino acid). The genes GC-GARP and GC-LRG consist of two exons, with 4,782 bp and 2,119 bp in total length, respectively. The first exon of each gene contains a small 5'-untranslated region and partial open reading frame. The putative promoter region of GC-GARP was found to contain transcription factor binding sites for GATA-1, IRF4, Oct-1, IRF-7, IRF-1, AP1, GATA-box and NFAT, and the promoter region of GC-LRG for MYC-MAX, MEIS1, ISRE, IK3, HOXA9 and C/EBP alpha. Phylogenetic analysis showed that GC-GARP and mammalian GARPs were clustered into one branch, while GC-LRG and mammalian LRGs were in another branch. The GC-GARP gene was only detected in head kidney, and GC-LRG in the liver, spleen and heart in the copepod ( Sinergasilus major)- infected grass carp, indicating the induction of gene expression by the parasite infection. The results obtained in the present study provide insight into the structure of fish LRR genes, and further study should be carried out to understand the importance of LRR proteins in host - pathogen interactions.

Characterization of development-related genes for the cestode Bothriocephalus acheilognathi

Differential gene expression of mature and immature Bothriocephalus acheilognathi cestodes was analyzed using the suppression subtractive hybridization technique. Five mature-associated cDNAs were isolated and characterized. Virtual Northern blot and RT-PCR analyses confirmed that four of the five genes were up-regulated in mature parasites. The sequence analysis revealed that one gene encoded the structural protein chorion precursor, and that three encoded functional proteins homologous to yolk ferritin, sodium/hydrogen exchanger and muscin-like protein. Another gene appeared to be specific to B. acheilognathi, encoding a putative metal-bound protein. Although results obtained in the present study are preliminary, the information about the five genes may provide clues for further investigation on the decline in parasite numbers during the maturation of B. acheilognathi.

Characterization of ZnMgO hexagonal-nanotowers/films on m-plane sapphire synthesized by metal organic chemical vapour deposition

ZnMgO hexagonal-nanotowers/films grown on m-plane sapphire substrates were successfully synthesized using a vertical low-pressure metal organic chemical vapour deposition system. The structural and optical properties of the as-obtained products were characterized using various techniques. They were grown along the non-polar [1 0 (1) over bar 0] direction and possessed wurtzite structure. The ZnMgO hexagonal-nanotowers were about 200 nm in diameter at the bottom and 120 nm in length. Photoluminescence and Raman spectra show that the products have good crystal quality with few oxygen vacancies. With Mg incorporation, multiple-phonon scattering becomes weak and broad, and the intensities of all observed vibrational modes decrease. The ultraviolet near band edge emission shows a clear blueshift (as much as 100 meV) and broadening compared with that of pure ZnO products.

Characterization of Thick GaN Films Directly Grown on Wet-Etching Patterned Sapphire by HVPE

Thick GaN films of high quality are directly grown on wet-etching patterned sapphire in a vertical hydride vapour phase epitaxy reactor. The optical and structural properties of GaN films are studied using scanning electronic microscopy and cathodoluminescence. Test results show that initial growth of hydride vapour phase epitaxy GaN occurs not only on the mesas but also on the two asymmetric sidewalls of the V-shaped grooves without selectivity. After the two-step coalescence near the interface, the GaN films near the surface keep on growing along the direction perpendicular to the long sidewall. Based on Raman results, GaN of the coalescence region in the grooves has the maximum residual stress and poor crystalline quality over the whole GaN film, and the coalescence process can release the stress. Therefore, stress-free thick GaN films are prepared with smooth and crack-free surfaces by this particular growth mode on wet-etching patterned sapphire substrates.

Characterization of InAs quantum dots on lattice-matched InAlGaAs/InP superlattice structures

Self-assembled InAs quantum dots (QDs) in an InAlGaAs matrix, lattice-matched to InP substrate, have been grown by molecular beam epitaxy (MBE). Transmission electron microscopy (TEM), double-crystal X-ray diffraction (DCXRD) and photoluminescence (PL) are used to study their structural and optical properties. In InAs/InAlGaAs/ InP system, we propose that when the thickness of InAs layer deposited is small, the random strain distribution of the matrix layer results in the formation of tadpole-shaped QDs with tails towards random directions, while the QDs begin to turn into dome-shaped and then coalesce to form islands with larger size and lower density to release the increasing misfit strain with the continuous deposition of InAs. XRD rocking curves showing the reduced strain with increasing thickness of InAs layer may also support our notion. The results of PL measurements are in well agreement with that of TEM images. (C) 2004 Elsevier B.V. All rights reserved.

Microstructure characterization of transition films from amorphous to nanocrocrystalline silicon

Hydrogenated silicon (Si:H) films near the threshold of crystallinity were prepared by very high-frequency plasma-enhanced chemical vapor deposition (VHF-PECVD) using a wide range of hydrogen dilution R-H = [H-2]/[SiH4] values of 2-100. The effects of H dilution R-H on the structural properties of the films were investigated using micro-Raman scattering and Fourier transform infrared (FTIR) absorption spectroscopy. The obtained Raman spectra show that the H dilution leads to improvements in the short-range order and the medium-range order of the amorphous network and then to the morphological transition from amorphous to crystalline states. The onset of this transition locates between R-H = 30 and 40 in our case, and with further increasing R-H from 40 to 100, the nanocrystalline volume fraction increases from similar to23% to 43%, and correspondingly the crystallite size enlarges from similar to2.8 to 4.4 nm. The FTIR spectra exhibit that with R-H increasing, the relative intensities of both the SiH stretching mode component at 2100 cm(-1) and wagging mode component at 620 cm(-1) increase in the same manner. We assert that these variations in IR spectra should be associated with the formation of paracrystalline structures in the low H dilution films and nanocrystalline structures in the high H dilution films. (C) 2003 Elsevier Science B.V. All rights reserved.

Structural and photoluminescent properties of ternary Zn1-xCdxO crystal films grown on Si(111) substrates

The ternary Zn1-xCdxO (0less than or equal toxless than or equal to0.6) alloying films with highly c-axis orientation have been deposited on Si(111) substrates by direct current reactive magnetron sputtering method. X-ray diffraction measurement indicates that the wurtzite-type structure of ZnO can be stabilized up to nominal Cd content x similar to 0.6 without cubic CdO phase separation. The lattice parameter c of Zn1-xCdxO increases almost linearly from 5.229 Angstrom (x = 0) to 5.247 Angstrom (x = 0.6), indicating that Cd substitution takes place on the Zn lattice sites. The photoluminescence spectra of the Zn1-xCdxO thin films measured at 12 K display a substantial red shift (similar to0.3 eV) in the near-band-edges (NBEs) emission of ZnO: from 3.39 eV of ZnO to 3.00 eV of Zn0.4Cd0.6O. The direct modulation of band gap caused by Zn/Cd substitution is responsible for the red shift effect in NBE emission of ZnO. (C) 2003 Elsevier Science B.V. All rights reserved.

Homoepitaxial growth and characterization of 4H-SiC epilayers by low-pressure hot-wall chemical vapor deposition

Horizontal air-cooled low-pressure hot-wall CVD (LP-HWCVD) system is developed to get high quality 4H-SiC epilayers. Homoepitaxial growth of 4H-SiC on off-oriented Si-face (0001) 4H-SiC substrates purchased from Cree is performed at a typical temperature of 1500 degrees C with a pressure of 40 Torr by using SiH4+C2H4+H-2 gas system. The surface morphologies and structural and optical properties of 4H-SiC epilayers are characterized with Nomarski optical microscope, atomic force microscopy (AFM), x-ray diffraction, Raman scattering, and low temperature photoluminescence (LTPL). The background doping of 32 pm-thick sample has been reduced to 2-5 x 10(15) cm(-3). The FWHM of the rocking curve is 9-16 arcsec. Intentional N-doped and B-doped 4H-SiC epilayers are obtained by in-situ doping of NH3 and B2H6, respectively. Schottky barrier diodes with reverse blocking voltage of over 1000 V are achieved preliminarily.

Investigation on the strain relaxation of InGaN layer and its effects on the InGaN structural and optical properties

The evolution of strain and structural properties of thick epitaxial InGaN layers grown on GaN with different thicknesses are investigated. It is found that, with increase in InGaN thickness, plastic relaxation via misfit dislocation generation becomes a more important strain relaxation mechanism. Accompanied with the relaxation of compressive strain, the In composition of InGaN layer increases and induces an apparent red-shift of the cathodoluminescence peak of the InGaN layer. On the other hand, the plastic relaxation process results in a high defect density, which degrades the structural and optical properties of InGaN layers. A transition layer region with both strain and In composition gradients is found to exist in the 450-nm-thick InGaN layer.

GSMBE growth and characterization of InxGa1-xAs/InP strained-layer MQWs in a P-i-N configuration

InxGa1-xAs/InP (0.39 less than or equal to x less than or equal to 0.68) strained-layer quantum wells having 20 wells with thickness of 50 Angstrom in a P-i-N configuration were grown by gas source molecular beam epitaxy (GSMBE). High-resolution X-ray diffraction rocking curves show the presence of up to seven orders of sharp and intense satellite reflection, indicative of the structural perfection of the samples. Low-temperature photoluminescence and low-temperature absorption spectra were used to determine the exciton transition energies as a function of strain. Good agreement is achieved between exciton transition energies obtained experimentally at low temperature with those calculated using the deformation potential theory.

Structural and Optical Performance of GaN Thick Film Grown by HVPE

Thick GaN films were grown on GaN/sapphire template in a vertical HVPE reactor. Various material characterization techniques,including AFM, SEM, XRD, RBS/Channeling, CL, PL, and XPS, were used to characterize these GaN epitaxial films. It was found that stepped/terraced structures appeared on the film surface,which were indicative of a nearly step-flow mode of growth for the HVPE GaN despite the high growth rate. A few hexagonal pits appeared on the surface, which have strong light emission. After being etched in molten KOH, the wavy steps disappeared and hexagonal pits with {1010} facets appeared on the surface. An EPD of only 8 ×10~6cm~(-2) shows that the GaN film has few dislocations. Both XRD and RBS channeling indicate the high quality of the GaN thick films. Sharp band-edge emission with a full width at half maximum（FWHM）of 67meV was observed, while the yellow and infrared emissions were also found. These emissions are likely caused by native defects and C and O impurities.