Structural analysis of SNARE motifs from sea perch, Lateolabrax japonicus by computerized approaches

Three cDNA sequences encoding four SNARE (N-ethylmaleimide-sensitive fusion protein attachment protein receptors) motifs were cloned from sea perch, and the deduced peptide sequences were analyzed for structural prediction by using 14 different web servers and softwares. The "ionic layer" structure, the three dimensional extension and conformational characters of the SNARE 7S core complex by using bioinformatics approaches were compared respectively with those from mammalian X-ray crystallographic investigations. The result suggested that the formation and stabilization of fish SNARE core complex might be driven by hydrophobic association, hydrogen bond among R group of core amino acids and electrostatic attraction at molecular level. This revealed that the SNARE proteins interaction of the fish may share the same molecular mechanism with that of mammal, indicating the universality and solidity of SNARE core complex theory. This work is also an attempt to get the protein 3D structural information which appears to be similar to that obtained through X-ray crystallography, only by using computerized approaches. (C) 2007 Elsevier Ltd. All rights reserved.

Structure analysis of the SECRAL superconducting magnet system

An advanced superconducting ECR ion source named SECRAL has been constructed at Institute of Modern Physics of Chinese Academy of Sciences, whose superconducting magnet assembly consists of three axial solenoid coils and six sextupole coils with a cold iron structure as field booster and clamp. In order to investigate the structure of sextupole coils and to increase the structural reliabilities of the magnet system, global and local structural analysis have been performed in various operation scenarios. Winding pack and support structure design of magnet system, mechanical calculation and stress analysis are given in this paper. From the analysis results, it has been found that the magnet system is safe in the referential operation scenarios and the configuration of the magnet complies with design requirements of the SECRAL.

Researches on essential mechanics issues for submerged floating tunnel

Since 2001, a research group in the Institute of Mechanics, Chinese Academy of Sciences, has been devoted to the research of essential mechanics issues for submerged floating tunnel (SFT). In addition to the structural design of the SFT prototype in Qiandao Lake, the relevant researches cover a number of topics. This paper briefly describes the research procedure and results, including dynamic response of SFT due to surface wave, vortex-induced vibration of anchoring system, structural analysis of curved SFT, temperature effects of curved SFT, structural dynamic response due to accidental load, and effects of structural parameters (buoyancy-weight ratio, tunnel length，tether stiffness，etc.) on dynamic response.

棕榈藤茎结构的研究

本文通过棕榈藤茎13属50余种的比较解剖观察，系统地比较了棕榈藤茎的解剖特征，评价其在各种棕榈藤茎鉴别中的作用，并在此基础上，解决了棕榈藤茎属一级的鉴定问题。除此之外，还讨论了棕榈藤茎的解剖特征与地理分布、系统分类和演化的关系。主要研究结果如下： （1）应用棕榈藤茎的解剖特征，可以区分到属（见分属检索表），但鉴定到种仍较困难。对棕榈藤茎的鉴定有重要价值的特征有：后生木质部导管和韧皮部的数目，基本薄壁组织细胞的类型，表皮细胞表面观的形状及排列样式，表皮细胞表面有无反射体等，对棕榈藤茎的鉴定有辅助意义的特征有：韧皮部中筛管和伴胞的排列方式，针晶囊的多少和大小等。 （2）依据表皮细胞的形状、排列样式和反射体的有无，可将棕榈藤茎的表皮细胞分为以下5种类型和3种亚型：1.针叶藤型：表皮细胞为长方形，细胞交错排列成砖墙状（如Plectocomia, Laccosperma, Retispatha, Plectocomiopsis）.2.黄藤型：表皮细胞为不规则的四边形，细胞排列成斜向网状（如Daemonorops）。3.省藤型：A亚型：表皮细胞六边形，细胞排列成网状，表皮表面有反射体，气孔平列型或四轮列型。B亚型：表皮细胞四边型，细胞交错排列如砖墙状，细胞长轴平行于茎轴，孔梭形四轮列型。C亚型：表皮细胞四边形，细胸垂周壁呈波浪形，细胞交错排列如砖墙状，细胞长轴平行于茎轴。4.Eremospatha型：表皮细胞六边形，细胞排列成网状，表皮表面无反射体，气孔平列型或四轮列型。5.Calsopatha型：表皮细胞近四边形，细胞排列成不规则网状，细胞长轴几乎垂直于茎轴。表皮表面无反射体。 （3）对白藤（Calamus tetradactylus Hance）茎纤维的成熟模式研究表明，纤维细胞壁的加厚可持续3年以上时间，但在细胞壁加厚的早期和末基匀较缓慢，细胞壁加厚的顺序通常由藤茎的基部向基本向顶部，藤茎的外部向内部以及纤维鞘的内部向外部。 （4）产于西部非洲棕榈藤的种类，其茎的结构特征明显地不同于分布在东南亚的种类，如前者的表皮层表面一般覆盖着膜质，而后者表面常覆盖一层硅质。另外，典型的双后生木质部导管仅见于西部非洲的种类。 （5）棕榈藤茎的后生木质部导管分子为单的平直穿孔板，管间纹孔式为对列式，直径大等于，故属进化类型。而棕榈藤茎韧皮部的演化趋势为：单韧皮部较原始，双韧皮部较进化。 （6）从棕榈藤的生长性看，直立棕榈藤的导管直径较爬行棕榈藤的大小，这可能与自立棕榈藤茎需要更大的机械支持力有关。 （7）通过对棕榈藤茎的结构研究，支持Uhl和Dansfield（1987）对棕榈藤的分类处理，即：将Calamus, Calospatha Ceratolobus, Daemonorops, Pogonotium, Retispatha放在Calamnieae亚族中;另将Korthalsia与Myrialepis, Plectocomia, Plectocomiopsis分别置于Metroxylinae和Plectocomiinae亚族中。

Accelerated evolution of the pituitary adenylate cyclase-activating polypeptide precursor gene during human origin

Pituitary adenylate cyclase-activating polypeptide (PACAP) is a neuropeptide abundantly expressed in the central nervous system and involved in regulating neurogenesis and neuronal signal transduction. The amino acid sequence of PACAP is extremely conserved across vertebrate species, indicating a strong functional constraint during the course of evolution. However, through comparative sequence analysis, we demonstrated that the PACAP precursor gene underwent an accelerated evolution in the human lineage since the divergence from chimpanzees, and the amino acid substitution rate in humans is at least seven times faster than that in other mammal species resulting from strong Darwinian positive selection. Eleven human-specific amino acid changes were identified in the PACAP precursors, which are conserved from murine to African apes. Protein structural analysis suggested that a putative novel Deuropeptide might have originated during human evolution and functioned in the human brain. Our data suggested that the PACAP precursor gene underwent adaptive changes during human origin and may have contributed to the formation of human cognition.

Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome

Understanding the dynamics of eukaryotic transcriptome is essential for studying the complexity of transcriptional regulation and its impact on phenotype. However, comprehensive studies of transcriptomes at single base resolution are rare, even for modern organisms, and lacking for rice. Here, we present the first transcriptome atlas for eight organs of cultivated rice. Using high-throughput paired-end RNA-seq, we unambiguously detected transcripts expressing at an extremely low level, as well as a substantial number of novel transcripts, exons, and untranslated regions. An analysis of alternative splicing in the rice transcriptome revealed that alternative cis-splicing occurred in similar to 33% of all rice genes. This is far more than previously reported. In addition, we also identified 234 putative chimeric transcripts that seem to be produced by trans-splicing, indicating that transcript fusion events are more common than expected. In-depth analysis revealed a multitude of fusion transcripts that might be by-products of alternative splicing. Validation and chimeric transcript structural analysis provided evidence that some of these transcripts are likely to be functional in the cell. Taken together, our data provide extensive evidence that transcriptional regulation in rice is vastly more complex than previously believed.

H5N2亚型禽流感病毒血凝素裂解位点碱性氨基酸对应mRNA核苷酸的二级结构分析

以H5N2亚型禽流感病毒毒株血凝素蛋白裂解位点碱性氨基酸为研究对象,对其密码子偏好性和对应mRNA序列的折叠二级结构特点进行研究和分析.旨在探讨裂解位点氨基酸对应mRNA核苷酸片段的二级结构与病毒致病力的关系,希望能对禽流感病毒的研究提供一些基础性信息.将mRNA样本按照序列等步长递增的方法,用RNAstructure 4.1程序预测这些样本的动态延伸折叠二级结构.序列和结构的分析结果:裂解位点的碱性氨基酸对富含腺嘌呤的密码子有强烈偏好;与碱性氨基酸对应的mRNA片段上的核苷酸主要位于折叠二级结构的单链环区,少数位于配对螺旋区.结果表明:裂解位点氨基酸对应的mRNA核苷酸形成发夹端环的大小与其碱性氨基酸的多少具有正相关性.

Five supramolecular compounds of water-soluble sulfonylcalix[4]arenetetrasulfonate showing two calixarene conformations

Five new compounds of sulfonylcalix[4]arenetetrasulfonate (SC4AS), [H7Na(H2O)(3)(SC4AS)(phen)(5)](H2O)(11.9) (1), [H6Mn(H2O)(4)(SC4AS)(phen)(5)] (H2O)(12.7) (2), [Cu-4(SC4AS) (phen)(6)] (H2O)(4.5) (3), {[Cu (2)(SC4AS) (bpy)(2)][Cu(bpy)(2)(H2O)](2)} (H2O)(6.6) (4), and {[Zn-2(SC4AS) (phen)(2)][Zn(phen)(2)(H2O)(2)](2)} (H2O)(7) (5) (where phen 1,10-phenanthroline and bpy = 2,2'-bipyridine), were synthesized by a hydrothermal method and structurally determined by single crystal X-ray diffraction. The SC4AS ligand adopts partial cone conformation in compounds 1 and 2 and 1,2-alternate form in compounds 3-5. According to the structural analysis and density functional theory (DFT) calculations, we suggest that the metal can affect the conformation of SC4AS.

Multiple-stage tandem mass spectrometry for differentiation of isomeric saponins

Four isomers of steroidal saponins were differentiated using multiple-stage tandem mass spectrometry combined with electrospray ionization (ESI-MSn). With the addition of lithium salt, the [M+Li](+) ions of saponins were observed in the ESI spectra. MSn spectra of these [M+Li](+) ions provided detailed structural information and allowed differentiation of the four isomeric saponins. The cross-ring cleavage ions from the saccharide chains of the saponins could be used as diagnostic ions for information concerning the linkage of the sugar moieties of the saponins. The masses of the X, A, Y and C type fragment ions formed from [M+Li](+) ions of the isomeric saponins provided information defining the methyl group locations.

Syntheses, crystal structures and magnetic properties of two heterometallic coordination polymers

Two heterometallic chain coordination polymers with the chemical formula {[Cu2Mn2L2(CH3OH)(H2O)] center dot 0.5CH(3)OH center dot 0.5CH(3)CH(2)OH}(n) (1) and {[Cu2Co2L2(H2O)(2)] center dot H2O}(n) (2) have been synthesized and characterized by IR, UV spectroscopy and single-crystal X-ray structural analysis, where H4L = 2-hydroxy-3-[(E)-({2-[(2-hydroxybetizoyl)amino]ethyl}imino)methyl] benzoic acid. Magnetic measurements showed that the two compounds exhibit antiferromagnetic coupling exchange interactions, and satisfactory fittings to the observed magnetic susceptibility data were obtained by assuming a linear four-spin arrangement with two isotropic magnetic exchange interactions.

Assignment of absolute configuration of cyclic secondary amines by NMR techniques using Mosher's method: a general procedure exemplified with (-)-isoanabasine

A general procedure to determine the absolute configuration of cyclic secondary amines with Mosher's NMR method is demonstrated, with assignment of absolute configuration of isoanabasine as an example. Each Mosher amide can adopt two stable conformations (named rotamers) caused by hindered rotation around amide C-N bond. Via a three-step structural analysis of four rotamers, the absolute configuration of (-)-isoanabasine is deduced to be (R) on the basis of Newman projections, which makes it easy to understand and clarify the application of Mosher's method to cyclic secondary amines. Furthermore, it was observed that there was an unexpected ratio of rotamers of Mosher amide derived from (R)-isoanabasine and (R)-Mosher acid. This phenomenon implied that it is necessary to distinguish the predominant rotamer from the minor one prior to determining the absolute configuration while using this technique.

Novel hydrogen-bonded three-dimensional networks encapsulating one-dimensional covalent chains: [M(4,4 '-bipy)(H2O)4](4-abs)2 center dot nH(2)O (4,4 '-bipy=4,4 '-Bipyridine; 4-abs=4-aminobenzenesulfonate) (M=Co, n=1; M=Mn, n=2)

Two novel compounds, [Co(4,4'-bipy)(H2O)(4)](4-abS)(2).H2O (1) and [Mn(4,4'-bipy)(H2O)(4)](4-abs)(2).2H(2)O (2) (4,4'-bipy = 4,4'-bipyridine; 4-abs = 4-aminobenzenesulfonate), have been synthesized in aqueous solution and characterized by single-crystal X-ray diffraction, elemental analyses, UV-vis and IR spectra, and TG analysis. X-ray structural analysis revealed that 1 and 2 both possess unusual hydrogen-bonded three-dimensional (3-D) networks encapsulating one-dimensional (1-D) covalently bonded infinite [M(4,4'-bipy)(H2O)(4)](2+) (M = Co, Mn) chains. The 4-abs anions in 1 form 1-D zigzag chains through hydrogen bonds. These chains are further extended through crystallization water molecules into 3-D hydrogen-bonded networks with 1-D channels, in which the [Co(4,4'-bipy)(H2O)(4)](2+) linear covalently bonded chains are located. Crystal data for 1: C22H30CoN4O11S2, monoclinic P2(1), a = 11.380(2) Angstrom, b = 8.0274(16) Angstrom, c = 15.670(3) Angstrom, alpha = gamma = 90degrees, beta = 92.82(3)degrees, Z = 2. Compound 2 contains interesting two-dimensional (2-D) honeycomb-like networks formed by 4-abs anions and lattice water molecules via hydrogen bonding, which are extended through other crystallization water molecules into three dimensions with 1-D hexagonal channels. The [Mn(4,4'-bipy)(H2O)(4)](2+) linear covalent chains exist in these channels. Crystal data for 2: C22H32WN4O12S2, monoclinic P2(1)/c, a = 15.0833(14) Angstrom, b = 8.2887(4) Angstrom, c = 23.2228(15) Angstrom, alpha = gamma = 90degrees, beta = 95.186(3)degrees, Z = 4.

Synthesis, characterization and molecular structure of a novel asymmetrical half-sandwich binuclear iron carborane complex Cp ' Fe-2(2)(CO)(3)(Se2C2B10H10)

The half-sandwich methylcyclopentadlenyl iron carbonyl complex reacted with 1,2-dilithium diselenolate carborane Li2Se2C2B10H10 (1) which was produced by the insertion of element Se into 1, 2-dilithium carborane to give a half-sandwich binuclear iron carborane complex Cp'Fe-2(2)(CO) 3Se2C2B10H10 (3). X-ray structural analysis of complex 3 reveals that one of the iron atoms is chiral.

Syntheses and crystalline structures of clusters Co-3(CO)(7)(mu(3)-S)(mu, eta(2)-SCNR2)

Through the reaction of Co-2(CO)(8) with four thiuram [R2NC(S)S](2), four new sulfur-capped trinuclear cobalt carbonyl clusters Co-3 (CO)(7) (mu(3)-S) (mu, eta(2)-S* C* NR2) ( I : R = Me; I : R = Et; II : R = i-Pr; IV : NR= -N [GRAPHICS] were prepared and characterized by elementary analysis, IR,H-1 NMR and MS spectroscopy. The crystal structure of the cluster Co-3(CO)(7)(mu(3)-S)[mu, eta(2)-S*C*N (i-Pr)(2)]( III) was determined by X-ray single crystal diffraction method. The crystal of m is monoclinic, belonging to space group P2(1)/n, and the cell parameters are as follows: a = 1, 145 2(2) nm, b = 1. 502 8(3) nm, c = 1, 214 4(2) nmj alpha = 90 degrees, beta = 92, 15(3)degrees, gamma = 90 degrees; V = 2. 088 5(7) nm(3) , Z = 4, F (000) = 1 096, D-c = 1. 747 mg . m(-3), mu = 2. 588 mm(-1), R=0. 040 7, R-w=0. 062 4, The structural analysis shows that cluster II has a pyrimidal Co3S framework and contains a heterocylic bridging bidentate ligand [mu, eta(2)-S* C* N (i-Pr)(2)] linked to the Co2 and Co3 atoms of the cluster by a cobalt-carbon and a cobalt-sulfur bond respectively.