Cloning, characterization and promoter analysis of common carp hairy/Enhancer-of-split-related gene, her6

Some members of hairy/Enhancer-of-split-related gene (HES) family have important effects on axial mesoderm segmentation and the establishment and maintenance of the somite fringe. In fishes. the her6 gene, a member of the HES family, is the homologue Of heS1 in mammals and chicken. In this study, the her6 gene and its full-length cDNA from the common carp (Cyprinus carpio) were isolated and characterized. The genomic sequence of common carp her6 is approximately 1.7 kb. with four exons and three introns, and the full-length cDNA of 1314 bp encodes a Putative polypeptide of 271 amino acids. To analyse the promoter sequence of common carp her6. sequences of various lengths upstream from the transcription initiation site of her6 were fused to enhanced green fluorescent. protein gene (eGFP) and introduced into zebrafish embryos by microinjection to generate transgenic embryos. Our results show that the upstream sequence of 500 bp can direct highly efficient and tissue-specific expression of eGFP in zebrafish embryos. whereas a fragment of 200 bp containing the TATA box and a partial suppressor of hairless paired site sequence (SPS) is not sufficient to drive eGFP expression in zebrafish embryos.

A preliminary phylogenetic analysis of Metapenaeopsis (Decapoda : Penaeidae) based on mitochondrial dna sequences of selected species from the Indo-West Pacific

Phylogenetic relationships within Metapenaeopsis remain largely unknown. The modern revision of the genus suggests that the shape of the petasma, followed by the presence of a stidulating organ, are the most important distinguishing taxonomic features. In the present study, phylogenetic relationships were studied among seven Metapenaeopsis species from the Indo-West Pacific based on partial sequences of mitochondrial 16S rRNA and cytochrome c oxidase I (COI) genes. Mean sequence divergence was 6.4% for 16S and 15.8% for COI. A strikingly large nucleotide distance (10.0% for 16S and 16.9% for COI) was recorded between M. commensalis, the only Indo-West Pacific species with a one-valved petasma, and the other species with a two-valved petasma. Phylogenetic analyses using neighbor-joining, maximum parsimony, and maximum likelihood generated mostly identical tree topologies in which M. commensalis is distantly related to the other species. Two clades were resolved for the remaining species, one with and the other without a stridulating organ, supporting the main groupings of the recent taxonomic revision. Results of the present study also indicate that the deep-water forms represent a relatively recent radiation in Metapenaeopsis.

Molecular phylogenetic systematics of twelve species of acipenseriformes based on mtDNA ND4L-ND4 gene sequence analysis

Acipenseriformes is an endangered primitive fish group, which occupies a special place in the history of ideas concerning fish evolution, even in vertebrate evolution. However, the classification and evolution of the fishes have been debated. The mitochondrial DNA (mtDNA) ND4L and partial ND4 genes were first sequenced in twelve species of the order Acipenseriformes, including endemic Chinese species. The following points were drawn from DNA sequences analysis: (i) the two species of Huso can be ascribed to Acipenser; (ii) A. dabryanus is the mostly closely related to A. sinensis, and most likely the landlocked form of A. sinensis; (iii) genus Acipenser in trans-Pacific region might have a common origin; (iv) mtDNA ND4L and ND4 genes are the ideal genetic markers for phylogenetic analysis of the order Acipenseriformes.

Quasi-thermo dynamic analysis of MOVPE growth of GaxAlyIn1-x-yN

A quasi-thermodynamic model of metalorganic vapor phase epitaxy (MOVPE) growth of GaxAlyIn1-x-yN alloys has been proposed. In view of the complex growth behavior of GaxAlyIn1-x-yN, we focus our attention on the galliumrich quaternary alloys that are lattice matched to GaN, In0.15Ga0.85N or Al0.15Ga0.85N, which are widely used in the GaN-based optoelectronic devices. The relationship between GaAlInN alloy composition and input molar ratio of group III metalorganic compounds at various growth conditions has been calculated. The influence of growth temperature, nitrogen fraction in the carrier gas, input partial pressure of group III metalorganics, reactor pressure, V/III ratio and the decomposition rate of ammonia on the composition of deposited alloys are studied systematically. Based on these calculated results, we can find out the appropriate growth conditions for the MOVPE growth of GaxAlyIn1-x-yN alloy lattice matched to GaN, In0.15Ga0.85N or Al0.15Ga0.85N. (C) 2002 Elsevier Science B.V. All rights reserved.

Thermodynamic analysis of GaSb-GaCl3 vapor phase epitaxy

A thermodynamic model for the GaSb-GaCl3 system in a closed quartz ampoule was proposed. The species in the gas phase are GaCl, GaCl3, Sb-4, Sb-2. The partial pressures of these species and total pressure in the ampoule have been calculated. The calculated results indicate that the equilibrium partial pressures of GaCl, GaCl3, Sb4, Sb2 and the total pressure in the ampoule have strong dependence on temperature, free volume inside the closed ampoule and amount of transport agent GaCl3. The total pressure will give strong influence not only on the flow pattern in the ampoule, but also on the uniformity of the epilayer.

Analysis of current induced by long internal solitary waves in stratified ocean

An approximate theoretical expression for the current induced by long internal solitary waves is presented when the ocean is continuously or two-layer stratified. Particular attention is paid to characterizing velocity fields in terms of magnitude, flow components, and their temporal evolution/spatial distribution. For the two-layer case, the effects of the upper/lower layer depths and the relative layer density difference upon the induced current are further studied. The results show that the horizontal components are basically uniform in each layer with a shear at the interface. In contrast, the vertical counterparts vary monotonically in the direction of the water depth in each layer while they change sign across the interface or when the wave peak passes through. In addition, though the vertical components are generally one order of magnitude smaller than the horizontal ones, they can never be neglected in predicting the heave response of floating platforms in gravitationally neutral balance. Comparisons are made between the partial theoretical results and the observational field data. Future research directions regarding the internal wave induced flow field are also indicated.

Phenomenological analysis of the double-pion production in nucleon-nucleon collisions up to 2.2 GeV

With an effective Lagrangian approach, we analyze several NN -> NN pi pi channels by including various resonances with mass up to 1.72 GeV. For the channels with the pion pair of isospin zero, we confirm the dominance of N*(1440) -> N sigma in the near-threshold region. At higher energies and for channels with the final pion pair of isospin one, we find large contributions from N*(1440) -> Delta pi, double-Delta, Delta(1600) -> N*(1440)pi, Delta(1600) -> Delta pi and Delta(1620) -> Delta pi. There are also sizable contributions from Delta -> Delta pi, Delta -> N pi, N -> Delta pi, and nucleon pole at energies close to the threshold. We give a good reproduction to the total cross sections up to beam energies of 2.2 GeV except for the pp -> pp pi(0)pi(0) channel at energies around 1.1 GeV and our results agree with the existing data of differential cross sections of pp -> pp pi(+)p pi(-), pp -> nn pi(+)pi(+), and pp -> pp pi(0)pi(0) which are measured at CELSIUS and COSY.

Comparison of steroid substrates and inhibitors of P-glycoprotein by 3D-QSAR analysis

Steroid derivatives show a complex interaction with P-glycoprotein (Pgp). To determine the essential structural requirements of a series of structurally related and functionally diverse steroids for Pgp-mediated transport or inhibition, a three-dimensional quantitative structure activity relationship study was performed by comparative similarity index analysis modeling. Twelve models have been explored to well correlate the physiochemical features with their biological functions with Pgp on basis of substrate and inhibitor datasets, in which the best predictive model for substrate gave cross-validated q(2) = 0.720, non-cross-validated r(2) = 0.998, standard error of estimate SEE = 0.012, F = 257.955, and the best predictive model for inhibitor gave q(2) = 0.536, r(2) = 0.950, SEE = 1.761 and F = 45.800. The predictive ability of all models was validated by a set of compounds that were not included in the training set. The physiochemical similarities and differences of steroids as Pgp substrate and inhibitor, respectively, were analyzed to be helpful in developing new steroid-like compounds. (C) 2004 Elsevier B.V. All rights reserved.

A New Method for Analysis of Disulfide-Containing Proteins by Matrix-Assisted Laser Desorption Ionization (MALDI) Mass Spectrometry

A simple and high-throughput method for the identification of disulfide-containing peptides utilizing peptide-matrix adducts is described. Some commonly used matrices in MALDI mass spectrometry were found to specifically react with sulfhydryl groups within peptide, thus allowing the observation of the peptide-matrix adduct ion [M + n + n' matrix + H](+) or [M + n + n' matrix + Na](+) (n = the number of cysteine residues, n' = 1, 2, ..., n) in MALDI mass spectra after chemical reduction of disulfide-linked peptides. Among several matrices tested, alpha-cyano-4-hydroxycinnamic acid (CHCA, molecular mass 189 Da) and alpha-cyano-3-hydroxycinnamic acid (3-HCCA) were found to be more effective for MALDI analysis of disulfide-containing peptides/proteins. Two reduced cysteines involved in a disulfide bridge resulted in a mass shift of 189 Da per cysteine, so the number of disulfide bonds could then be determined, while for the other matrices (sinapinic acid, ferulic acid, and caffeic acid), a similar addition reaction could not occur unless the reaction was carried out under alkaline conditions. The underlying mechanism of the reaction of the matrix addition at sulfhydryl groups is proposed, and several factors that might affect the formation of the peptide-matrix adducts were investigated.

Simultaneous spectrophotometric determination of zinc, cadmium and mercury with hybrid linear analysis

A new method for simultaneous spectrophotometric determination of Zn, Cd and Hg using 2-(5-Br-2-pyridylazo)-5-diethylaminophenol as the color developing reagent was proposed. The absorption spectra of these three complexes have similar features with severe overlap in visible spectral range. For resolving these spectra, hybrid linear analysis was used, and the pure spectrum of each component was obtained from the calibration mixtures by least squares method. The effects of reaction condition, selection of wavelengths, determination of pure spectrum and additivity of absorbances etc. on the determination were discussed. The proposed method offers the advantages of simple, rapid, and accuracy. It has been successfully applied to the simultaneous determination of Zn, Cd and Hg in synthetic sample. A comparison was also made with the partial least squares method.

Simultaneous spectrophotometric determination of trace iron (III) and aluminum (III) with hybrid linear analysis

Hybrid linear analysis (HLA) was applied to resolution of overlapping spectra of Fe3+-salicylfluorone and Al3+-salicylfluorone complexes and simultaneous spectrophotometric determination of Fe3+ and Al3+. The absorbance matrix of 7 standard mixtures at 41 measuring points ranged from the wavelength of 550 nm to 630 nm was used for calibration. To avoid the effect of interaction between the two components on the determination, the column vector of K matrix obtained from the standard mixtures with least squares was used as the pure spectrum of component. The recoveries of the two elements for the analysis of the synthetic samples were 93.3% similar to 107.5% in the range of the concentration ratio of Fe3+:Al3+ = 10:1 to 1:8. Comparing with the partial least squares (PIS) model, the HLA method was simple, accuracy and precise.

THERMAL ANALYSIS AND INFRARED SPECTRA OF DIALKYLAMMONIUM TETRAC HLOROCUPRATE

The thermal stability and the solid solid phase transitions in Ills compounds with n = 7-12 have been studied by DSC and TG methods. Comparision with CnZn compounds want made. The nature of three phases of CnCu has been discussed in terms of infrared spectroscopy and the assignment of the phase transitions has been given. The thermal stability of CnCu is lower than that of CnZn and presents an obvious odd even effect. All of these compounds exhibit two solid solid phase transitions in the temperature range of 248-337 K. The peak tempe nature of phase transitions changes regularly. The peak temperature or the main phase transition increases with the chain length. The total transition enthalpies and entropies increase with increasing chain length. When n <= 9, the high temperature phase exists in a partial disorder state. When n >= 10, the high temperature phase exists in a conformational disorder state. The main phase transition and the phase transition at 307.7 K of CnCu may mainly are from the change of the packing structure and the change of the partial conformational order-disorder of alkyl chain, respectively.

Domain analysis of the Edwardsiella tarda ferric uptake regulator

Recent studies have shown that the ferric uptake regulator (Fur) of Edwardsiella tarda (Fur(Et)) shares high sequence identity with the Escherichia coli Fur (Fur(Ec)) at the N-terminal DNA-binding region. In the present study, the functional importance of the C-terminal region of Fur(Et) was investigated. It was found that Fur(Et) bearing deletion of the C-terminal 12 residues still possesses most of the repressor activity, whereas Fur(Et) bearing deletions of the C-terminal 16 and more than 16 residues are severely affected in activity. Domain swapping analyses indicated that the chimeric Fur proteins (Et75Ec73 and Et75Vh74) consisting of the N-terminal 1-75 region of Fur(Et) fused to the C-terminal 76-148 region of Fur(Ec) and the C-terminal 76-149 region of the Vibrio harveyi Fur (Fur(Vh)), respectively, are fully active. C92 of Fur(Ec) and C137 of Fur(Vh), which are functionally essential in Fur(Ec) and Fur(Vh), respectively, are also essential in Et75Ec73 and Et75074, respectively. Further study identified an artificial Fur protein, EtMF54, which is composed of the N-terminal 49 residues of Fur(Et) and five artificial residues. Compared to Fur(Et), EtMF54 possesses partial Fur activity that is iron-dependent. These results (I) indicate that there exist certain functional/structural compatibilities among Fur(Et), Fur(Ec), and Fur(Vh) at the C-terminal region; (ii) provide insights to the potential location of the regulatory ion-binding site of Fur(Et).

Cloning, sequencing and expression analysis of cDNA encoding a constitutive heat shock protein 70 (HSC70) in Fenneropenaeus chinensis

The cDNA encoding hsc70 of Chinese shrimp Fenneropenaeus chinensis was cloned from hepatopancreas by RT-PCR based on its EST sequence. The full length cDNA of 2090 bp contained an open reading frame of 1956 nucleotides and partial 5'- and 3'-untranslated region(5'- and 3'-UTR). PCR amplification and sequencing analysis showed the existence of introns in the region of 1-547 bp, but they did not exist in the region of 548-2090 bp of hsc70 cDNA. When the deduced 652 amino acid sequence of HSC70 was compared with the members of HSP70 family from other organisms, the results showed 85.9% similarity with HSC71 from Oncorhynchus mykiss and HSC70 from Homo sapiens. It also exhibited 85.8% similarity with HSP70 from Mus musculu and 85.4% with HSC70 from Manduca sexta. Expression analysis showed that hsc70 mRNA was espressed constitutively in hepatopancreas, muscle, eyestalks, haemocytes, heart, ovary, intestine and gills in Fenneropenaeus chinensis. No difference could be detected on hsc70 mRNA level in muscle between heat-shocked and control animals.