Phylogenetic analysis of the family Thermaceae with an emphasis on signature position and secondary structure of 16S rRNA

The sequences of the 16S rRNA genes from 38 strains of the family Thermaceae were compared by alignment analysis. The genus-specific and species-specific base substitutions or base deletions (signature positions) were found in three hypervariable regions (in the helices 6, 10 and 17). The differentiation of secondary structures of the high variable regions in the 5' end (38-497) containing several signature positions further supported the concept. Based on the comparisons of the secondary structures in the segments of 16S rRNAs, a key to the species of the family Thermaceae was proposed. (C) 2003 Published by Elsevier Science B.V. on behalf of the Federation of European Microbiological Societies.

Gene structure of an antimicrobial peptide from mandarin fish, Siniperca chuatsi (Basilewsky), suggests that moronecidins and pleurocidins belong in one family: the piscidins

The gene of piscidin, an antimicrobial peptide, has been cloned from the mandarin fish, Siniperca chuatsi. From the first transcription initiation site, the mandarin fish piscidin gene extends 1693 nucleotides to the end of the 3' untranslated region and contains four exons and three introns. A predicted 79-residue prepropeptide consists of three domains: a signal peptide (22 aa), a mature peptide (22 aa) and a C-terminal prodomain (35 aa). The shortage of XQQ motif in the prodomain of mandarin fish piscidin and the similar gene structure between moronecidins (piscidins) and pleurocidins may indicate that they are derived from the same ancestor gene. We thus suggest that piscidin should be used as a terminology for these antimicrobial peptides in the future. The mandarin fish piscidin mRNA was abundant in intestine, spleen, pronephros and kidney analysed by real-time polymerase chain reaction. After stimulation with lipopoly saccharides (LPS), a marked increase in transcripts was observed in most tissues, indicating that piscidin is not only a constitutively expressed molecule, but also has an increased response to bacterial infection. The synthetic, amidated mandarin fish piscidin exhibited different antimicrobial activity against different fish bacterial pathogens, especially against species of Aeromonas, which may to certain extent reflect the pathogenicity of these bacteria.

Shock-Induced Near-Wall Two-Phase Flow Structure Over a Micron-Sized Particles Bed

The present paper studies numerical modelling of near-wall two-phase flows induced by a normal shock wave moving at a constant speed, over a micronsized particles bed. In this two-fluid model, the possibility of particle trajectory intersection is considered and a full Lagrangian formulation of the dispersed phase is introduced. The finiteness of the Reynolds and Mach numbers of the flow around a particle as well as the fineness of the particle sizes are taken into account in describing the interactions between the carrier- and dispersed- phases. For the small mass-loading ratio case, the numerical simulation of flow structure of the two phases is implemented and the profiles of the particle number density are obtained under the constant-flux condition on the wall. The effects of the shock Mach number and the particle size and material density on particle entrainment motion are discussed in detail.The obtained results indicate that interphase non-equilibrium in the velocity and temperature is a common feature for this type of flows and a local particle accumulation zone may form near the envelope of the particle trajectory family.

A novel family of antimicrobial peptides from the skin of Amolops loloensis

While conducting experiments to investigate antimicrobial peptides of amphibians living in the Yunnan-Sichuan region of southwest China, a new family of antimicrobial peptides was identified from skin secretions of the rufous-spotted torrent frog, Amolops loloensis. Members of the new peptide family named amolopins are composed of 18 amino acids with a unique sequence, for example, NILSSIVNGINRALSFFG. By BLAST search, amolopins did no show similarity to any known peptides. Among the tested microorganisms, native and synthetic peptides only showed antimicrobial activities against Staphylococcus aureus ATCC2592 and Bacillus pumilus, no effects on other microorganisms. The CD spectroscopy showed that it adopted a structure of random combined with beta-sheet in water, Tris-HCl or Tris-HCl-SDS. Several cDNAs encoding amolopins were cloned from the skin cDNA library of A. loloensis. The precursors of amolopin are composed of 62 amino acid residues including predicted signal peptides, acidic propieces, and mature antimicrobial peptides. The preproregion of amolopin precursor comprises a hydrophobic signal peptide of 22 residues followed by an 18 residue acidic propiece which terminates by a typical prohormone processing signal Lys-Arg. The preproregions of precursors are very similar to other amphibian antimicrobial peptide precursors but the mature amolopins are different from other antimicrobial peptide families. The remarkable similarity of preproregions of precursors that give rise to very different antimicrobial peptides in distantly related frog species suggests that the corresponding genes form a multigene family originating from a common ancestor. (C) 2008 Elsevier Masson SAS. All rights reserved.

Phylogenetic analyses of Fringillidae (Aves : Passeriformes) using mitochondrial tRNA gene sequences and secondary structure

Fringillidae is a large and diverse family of Passeriformes. So far, however, Fringillidae relationships deduced from morphological features and by a number of molecular approaches have remained unproven. Recently, much attention has been attracted to mitochondrial tRNA genes, whose sequence and secondary structural characteristics have shown to be useful for Acrodont Lizards and deep-branch phylogenetic studies. In order to identify useful phylogenetic markers and test Fringillidae relationships, we have sequenced three major clusters of mitochondrial tRNA genes from 15 Fringillidae, taxa. A coincident tree, with coturnix as outgroup, was obtained through Maximum-likelihood method using combined dataset of 11 mitochondrial tRNA gene sequences. The result was similar to that through Neighbor-joining but different from Maximum-parsimony methods. Phylogenetic trees constructed with stem-region sequences of 11 genes had many different topologies and lower confidence than with total sequences. On the other hand, some secondary structural characteristics may provide phylogenetic information on relatively short internal branches at under-genus level. In summary, our data indicate that mitochondrial tRNA genes can achieve high confidence on Fringillidae phylogeny at subfamily level, and stem-region sequences may be suitable only at above-family level. Secondary structural characteristics may also be useful to resolve phylogenetic relationship between different genera of Fringillidae with good performance.

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

Natural killer (NK) cell enhancing factor (NKEF) belongs to the newly defined peroxiredoxin (Prx) family. Its functions are to enhance NK cell cytotoxicity and to protect DNA and proteins from oxidative damage. In this study, a partial cDNA sequence of carp NKEF-B was isolated from thymus cDNA library. Subsequently, the full-length cDNA of carp NKEF-B was obtained by means of 3' and 5' RACE, respectively. The full-length cDNA of carp NKEF-B was 1022 bp, consisting of a 73 bp 5'-terminal untranslated region (UTR), a 355 bp T-terminal UTR, and a 594 bp open reading frame coding for a protein of 197 amino acids. Carp NKEF-B contained two consensus Val-Cys-Pro (VCP) motifs and three consensus cysteine (Cys-51, Cys-70 and Cys-172) residues. Sequence comparison showed that the deduced amino acid sequence of carp NKEF-B had an overall similarity of 74-96% to that of other species homologues. Phylogenetic analysis revealed that carp NKEF-B forms a cluster with other known teleost NKEF-Bs. Then, by PCR we obtained a 5.1 -k long genomic DNA of carp NKEF-B containing six exons and five introns. Realtime RT-PCR results showed that carp NKEF-B gene was predominantly detected in kidney and head kidney under un-infected conditions. Whereas under SVCV-infection condition, the expression of NKEF-B gene was significantly increased in blood cells, gill, intestine and spleen, but maintained in liver, and decreased significantly in kidney and head kidney. Finally, the rNKEF-B was constructed and expressed in Escherichia coli. By using an antibody against carp rNKEF-B, immunohistochemical study further indicated that NKEF-B positive cells are mainly some RBCs and a few epithelial cells in gill and intestine, and that under SVCV-infection condition, these positive cells or positive products in their cytoplasm were mainly increased in gill and spleen sections of carp. The results obtained in the present study will help to understand the function of NKEF-B in teleost innate immunity. (C) 2008 Elsevier Ltd. All rights reserved.

Bead-probe complex capture a couple of SINE and LINE family from genomes of two closely related species of East Asian cyprinid directly using magnetic separation

Background: Short and long interspersed elements (SINEs and LINEs, respectively), two types of retroposons, are active in shaping the architecture of genomes and powerful tools for studies of phylogeny and population biology. Here we developed special protocol to apply biotin-streptavidin bead system into isolation of interspersed repeated sequences rapidly and efficiently, in which SINEs and LINEs were captured directly from digested genomic DNA by hybridization to bead-probe complex in solution instead of traditional strategy including genomic library construction and screening. Results: A new couple of SINEs and LINEs that shared an almost identical 3'tail was isolated and characterized in silver carp and bighead carp of two closely related species. These SINEs (34 members), designated HAmo SINE family, were little divergent in sequence and flanked by obvious TSD indicated that HAmo SINE was very young family. The copy numbers of this family was estimated to 2 x 10(5) and 1.7 x 10(5) per haploid genome by Real-Time qPCR, respectively. The LINEs, identified as the homologs of LINE2 in other fishes, had a conserved primary sequence and secondary structures of the 3'tail region that was almost identical to that of HAmo SINE. These evidences suggest that HAmo SINEs are active and amplified recently utilizing the enzymatic machinery for retroposition of HAmoL2 through the recognition of higher-order structures of the conserved 42-tail region. We analyzed the possible structures of HAmo SINE that lead to successful amplification in genome and then deduced that HAmo SINE, SmaI SINE and FokI SINE that were similar in sequence each other, were probably generated independently and created by LINE family within the same lineage of a LINE phylogeny in the genomes of different hosts. Conclusion: The presented results show the advantage of the novel method for retroposons isolation and a pair of young SINE family and its partner LINE family in two carp fishes, which strengthened the hypotheses containing the slippage model for initiation of reverse transcription, retropositional parasitism of SINEs on LINEs, the formation of the stem loop structure in 3'tail region of some SINEs and LINEs and the mechanism of template switching in generating new SINE family.

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.

ELECTRONIC AND MAGNETIC-STRUCTURE OF THE TERNARY COMPOUND ND2FE17N

The electronic and the magnetic structure of the Nd2Fe17N1 phase in the family of Nd-Fe-N ternary compounds have been calculated using the first-principles, spin-polarized orthogonalized linear-combination-of-atomic-orbitals method. Results are presented in the form of site-decomposed and spin-projected partial density of states. The occupation sites of the three N atoms are determined by an average radial distribution of all possible N site configurations. Both cases of N occupying the 3b and the 18g sites are studied. The results indicate that the 6c Fe sites have the maximum and the 18h Fe sites have the minimum local moments. This is in good agreement with experiment. It is concluded that the influence on the local moment due to lattice expansion is less important compared to that due to interatomic interaction between the N atom and its neighbors. The results also show the important role of N atoms in raising the Curie temperature of this compound.

Synthesis, structure, and optical properties of a contorted (110)-oriented layered hybrid perovskite: C3H11SN3PbBr4

The < 110 >-oriented perovskite is very rare in the hybrid perovskites family. In this work, an unusual layered < 110 >-oriented hybrid perovskite, which is stabilized by a special organic ligand, 2-(aminoethyl)isothiourea, has been obtained. This ligand combines a primary amine and a formamidine on the two ends of one molecule. Introduction of the special ligand brings about contorted inorganic sheets in the hybrid perovskite structure. The optical properties of the new < 110 >-oriented perovskite were studied.

A new family of Ce6MoO15 as fast oxide ion conductor

A novel solid solution Ce6MoO15 was achieved. Their structure and oxide ionic conductivity were studied. Based on Ce6MoO15, rare earth element substitution on cerium site shows that all resulting oxides enhance the conductivity further, and have high oxide-ion conductivity, which may be a kind of promising material for SOFCs.

Phase behavior of BaLn(2)Mn(2)O(7) (Ln = rare earth) with a layered perovskite structure

Many phases appear in BaLn(2)Mn(2)O(7) family (Ln = rare earth) belonging to one of the Ruddlesden-Popper type compounds, depending upon the experimental conditions such as heating conditions when prepared and composition. Some of these phases were characterized by powder X-ray diffraction method using Rietveld analysis. These phases have only a little difference in crystal structure which has fundamentally K2NiF4 type structure, although the X-ray diffraction patterns are clearly different: a little deformation or tilting of the oxygen octahedron surrounding a central manganese ion composing the main frame of this structure induce these different diffraction patterns. Phase behavior of these compounds, mainly the detailed relation between various phases in BaTb2Mn2O7, was refined including the data of high temperature X-ray diffractometry.

Hydrothermal synthesis and crystal structure of [{Cu(2,2 '-bpy)(2)}(2)Mo8O26]: a beta-octamolybdate cluster covalently bonded to two {Cu(2,2 '-bpy)(2)}(2+) coordination complexes via bridging oxo groups

An organic-inorganic hybrid solid, (Cu(2,2'-bpy)(2))(2)Mo8O26, has been hydrothermally synthesized and structurally characterized by single-crystal X-ray diffraction. Dark green crystals crystallize in the orthorhombic system, space group Pna21, a = 24.164(5), b = 18.281(4), c = 11.877(2) Angstrom, alpha = 90 degrees, beta = 90 degrees, gamma = 90 degrees, V= 5247(2) Angstrom (3), Z = 4, lambda (MoK alpha) = 0.71073 Angstrom (R(F) = 0.0331 for 5353 reflections). Data were collected on a Siemens P4 four-circle diffractometer at 293 K in the range 1.69 degrees < theta < 25.04 degrees using the omega -scan technique. The structure was solved by the direct method and refined by full-matrix least squares on F-2 using SHELXL-93. The structure of this compound consists of discrete (Cu(2,2'-bpy)(2))(2)Mo8O26 clusters, constructed from beta -octamolybdate subunits ((Mo8O26)(4-)) covalently bonded to two (Cu(2,2'-bpy)(2))(2+) coordination complexes via bridging oxo groups that connect two adjacent molybdenum sites. (C) 2001 Academic Press.