Liposome-mediated conformation transition of DNA detected by molecular probe: methyl green

Recent studies have focused on the structural features of DNA-lipid assemblies. In this paper, we take methyl green (MG) as a probe molecule to detect the conformational change of DNA molecule induced by dimethyldioctadecylammonium bromide (DDAB) liposomes before the condensation process of DNA begins. DDAB-induced DNA topology changes were investigated by cyclic voltammetry (CV), circular dichroism (CD) and UV-VIS spectrometry. We find that upon binding to DNA, positively charged liposomes induce a conformational transition of DNA molecules from the native B-form to the C motif. Conformational transition in DNA results in the binding modes of MG to DNA, changing and being isolated from DNA to the solution. More stable complexes are formed between DNA and DDAB. That is also proved by the melting study of DNA.

Synthesis and structure of a novel open-framework zincophosphate with intersecting three-dimensional helical channels

A new open-framework zincophosphate, Zn-0.5(H2PO4).0.5H(2)O (denoted as FJ-13), possessing intersecting three-dimensional helical channels, has been synthesized under solvothermal conditions.

自旋置换对称体系多脉冲及二维核磁共振实验的密度算符描述(Ⅱ)——多量子积算符方法

在对称化乘积算符(简称SAPO)方法基础上提出了多量子积算符(简称MQCPO)方法。改进的密度算符理论对I_nS(I=1/2,S=1/2;n为任意正整数)自旋体系多脉冲及二维核磁共振实验的描述普遍适用。MQCPO与SAPO从不同角度反映了自旋体系的对称性,故它们之间存在简单线性关系。文中给出I_n(I=1/2,n=2,3)自旋体系MQCPO的SAPO表示。MQCPO有利于自由演化过程的描述,而脉冲作用的描述则是SAPO为佳;利用MQCPO与SAPO的线性关系及SAPO笛卡儿分量的坐标轮换性质,“z”表象下脉冲作用的描述变得简单而直观。对异核谱剪辑及自旋拓扑滤波(spin topology filtration)等实验脉冲序列的分析,该方法是方便的。

A novel C1q-domain-containing protein from Zhikong scallop Chlamys farreri with lipopolysaccharide binding activity

The C1q-domain-containing (C1qDC) proteins are a family of proteins characterized by a globular C1q (gC1q) domain in their C-terminus. They are involved in various processes of vertebrates and supposed to be an important pattern recognition receptor in innate immunity of invertebrates. In this study, a novel member of C1q-domain-containing protein family was identified from Zhikong scallop Chlamys farreri (designated as CfC1qDC) by expressed sequence tag (EST) and rapid amplification of cDNA ends (RACE) approaches. The full-length cDNA of CfC1qDC was of 777 bp, consisting of a T-terminal untranslated region (UTR) of 62 bp and a 3' UTR of 178 bp with a polyadenylation signal sequence AATAAA and a poly (A) tail. The CfC1qDC cDNA encoded a polypeptide of 178 amino acids, including a signal peptide and a C1q-domain of 158 amino acids with the theoretical isoelectric point of 5.19 and the predicted molecular weight of 17.2 kDa. The C1q-domain in CfC1qDC exhibited homology with those in sialic acid binding lectin from mollusks and C1qDC proteins from higher vertebrates. The typical 10 beta-strand jelly-roll folding topology structure of C1q-domain and the residues essential for effective packing of the hydrophobic core were well conserved in CfC1qDC. By fluorescent quantitative real-time PCR, mRNA transcripts of CfC1qDC were mainly detected in kidney, mantle, adductor muscle and gill, and also marginally detectable in hemocytes. In the bacterial challenge experiment, after the scallops were challenged by Listonella anguillarum, there was a significant up-regulation in the relative expression level of CfC1qDC and at 6 h post-injection, the mRNA expression reached the maximum level and was 4.55-fold higher than that of control scallops. Similarly, the expression of CfC1qDC mRNA in mixed primary cultures of hemocytes stimulated by lipopolysaccharides (LPS) was up-regulated and reached the maximum level at 6 h post-stimulation, and then dropped back to the original level gradually. In order to investigate its function, the cDNA fragment encoding the mature peptide of CfC1qDC was recombined and expressed in Escherichia coli BL21 (DE3). The recombinant CfC1qDC protein displayed a significantly strong activity to bind LIDS from E. coli, although no obvious antibacterial or agglutinating activity toward Gram-negative bacteria E. coli JM109, L. anguillarum and Gram-positive bacteria Micrococcus luteus was observed. These results suggested that CfC1qDC was absolutely a novel member of the C1qDC protein family and was involved in the recognition of invading microorganisms probably as a pattern recognition molecule in mollusk. (c) 2008 Elsevier Ltd. All rights reserved.

Characterizing a monotopic membrane enzyme. Biochemical, enzymatic and crystallization studies on Aquifex aeolicus sulfide:quinone oxidoreductase

Monotopic membrane proteins are membrane proteins that interact with only one leaflet of the lipid bilayer and do not possess transmembrane spanning segments. They are endowed with important physiological functions but until now only few of them have been studied. Here we present a detailed biochemical, enzymatic and crystallographic characterization of the monotopic membrane protein sulfide:quinone oxidoreductase. Sulfide:quinone oxidoreductase is a ubiquitous enzyme involved in sulfide detoxification, in sulfide-dependent respiration and photosynthesis, and in heavy metal tolerance. It may also play a crucial role in mammals, including humans, because sulfide acts as a neurotransmitter in these organisms. We isolated and purified sulfide:quinone oxidoreductase from the native membranes of the hyperthermophilic bacterium Aquifex aeolicus. We studied the pure and solubilized enzyme by denaturing and non-denaturing polyacrylamide electrophoresis, size-exclusion chromatography, cross-linking, analytical ultracentrifugation, visible and ultraviolet spectroscopy, mass spectrometry and electron microscopy. Additionally, we report the characterization of its enzymatic activity before and after crystallization. Finally, we discuss the crystallization of sulfide:quinone oxidoreductase in respect to its membrane topology and we propose a classification of monotopic membrane protein crystal lattices. Our data support and complement an earlier description of the three-dimensional structure of A. aeolicus sulfide:quinone oxidoreductase (M. Marcia, U. Ermler, G. Peng, H. Michel, Proc Natl Acad Sci USA, 106 (2009) 9625-9630) and may serve as a reference for further studies on monotopic membrane proteins. (C) 2010 Elsevier B.V. All rights reserved.

AiC1qDC-1, a novel gC1q-domain-containing protein from bay scallop Argopecten irradians with fungi agglutinating activity

The globular C1q-domain-containing (C1qDC) proteins are a family of versatile pattern recognition receptors via their globular C1q (gC1q) domain to bind various ligands including several PAMPs on pathogens. In this study, a new gC1q-domain-containing protein (AiC1qDC-1) gene was cloned from Argopecten irradians by rapid amplification of cDNA ends (RACE) approaches and expressed sequence tag (EST) analysis. The full-length cDNA of AiC1qDC-1 was composed of 733 bp, encoding a signal peptide of 19 residues and a typical gC1q domain of 137 residues containing all eight invariant amino acids in human C1qDC proteins and seven aromatic residues essential for effective packing of the hydrophobic core of AiC1qDC-1. The gC1q domain of AiC1qDC-1, which possessed the typical 10-stranded beta-sandwich fold with a jelly-roll topology common to all C1q family members, showed high homology not only to those of Cl qDC proteins in mollusk but also to those of C1qDC proteins in human. The AiC1qDC-1 transcripts were mainly detected in the tissue of hepatopancreas and also marginally detectable in adductor, heart, mantle, gill and hemocytes by fluorescent quantitative real-time PCR. In the microbial challenge experiment, there was a significant up-regulation in the relative expression level of AiC1qDC-1 in hepatopancreas and hemocytes of the scallops challenged by fungi Pichia pastoris GS115, Gram-positive bacteria Micrococcus luteus and Gram-negative bacteria Listonella anguillarum. The recombinant AiC1qDC-1 (rAiC1qDC-1) protein displayed no obvious agglutination against M. luteus and L. anguillarum, but it aggregated P. pastoris remarkably. This agglutination could be inhibited by D-mannose and PGN but not by LPS, glucan or D-galactose. These results indicated that AiC1qDC-1 functioned as a pattern recognition receptor in the immune defense of scallops against pathogens and provided clues for illuminating the evolution of the complement classical pathway. (C) 2010 Elsevier Ltd. All rights reserved.

cDNA cloning and overexpression of acidic ribosomal phosphoprotein P1 gene (RPLP1) from the Giant Panda

RPLP1 is one of acidic ribosomal phosphoproteins encoded by RPLP1 gene, which plays an important role in the elongation step of protein synthesis. The cDNA of RPLP1 was cloned successfully for the first time from the Giant Panda (Ailuropoda melanoleuca) using RT-PCR technology, which was also sequenced, analyzed preliminarily and expressed in E. coli. The cDNA fragment cloned is 449bp in size, containing an open reading frame of 344bp encoding 114 amino acids. Alignment analysis indicated that the nucleotide sequence and the deduced amino acid sequence are highly conserved to other five species studied, including Homo sapiens, Mus musculus, Rattus norvegicus, Bos Taurus and Sus scrofa. The homologies for nucleotide sequences of Giant Panda PPLP1 to that of these species are 92.4%, 89.8%, 89.0%, 91.3% and 87.5%, while the homologies for amino acid sequences are 96.5%, 94.7%, 95.6%, 96.5% and 88.6%. Topology prediction showed there are three Casein kinase II phosphorylation sites and two N-myristoylation sites in the RPLP1 protein of the Giant Panda (Ailuropoda melanoleuca). The RPLP1 gene was overexpressed in E. coli and the result indicated that RPLP1 fusion with the N-terminally His-tagged form gave rise to the accumulation of an expected 18kDa polypeptide, which was in accordance with the predicted protein and could also be used to purify the protein and study its function.

Mitochondrial DNA phylogeny of two morphologically enigmatic fishes in the subfamily Schizothoracinae (Teleostei : Cyprinidae) in the Qinghai-Tibetan Plateau

The complete mitochondrial DNA (mtDNA) cytochrome b gene (1140 bp) was sequenced in Herzenstein macrocephalus and Gymnocypris namensis and in 13 other species and sub-species (n = 22), representing four closely related genera in the subfamily Schizothoracinae. Conflicting taxonomies of H. macrocephalus and G. namensis have been proposed because of the character instability among individuals. Parsimony, maximum likelihood and Bayesian methods produced phylogenetic trees with the same topology and resolved several distinctive clades. Previous taxonomic treatments, which variously placed these two species of separate genera or as sub-species, are inconsistent with the mtDNA phylogeny. Both H. macrocephalus and G. namensis appear in a well-supported clade, which also includes nine species of Schizopygopsis, and hence should be transferred to the genus Schizopygopsis. Morphological changes are further illustrated, and their adaptive evolution in response to the local habitat shifts during the speciation process appears to be responsible for conflicting views on the systematics of these two species and hence the contrasting taxonomic treatments. These species are endemic to the Qinghai-Tibetan Plateau, a region with a history of geological activity and a rich diversity of habitats that may have result in the parallel and reversal evolution of some morphological characters used in their taxonomies. Our results further suggest that speciation and morphological evolution of fishes in this region may be more complex than those previously expected. (c) 2007 The Authors Journal compilation (c) 2007 The Fisheries Society of the British Isles.

Molecular phylogeny and biogeography of the Qinghai-Tibet Plateau endemic Nannoglottis (Asteraceae)

All taxa endemic to the Qinghai-Tibet Plateau are hypothesized to have originated in situ or from immediately adjacent areas because of the relatively recent formation of the plateau since the Pliocene, followed by the large-scaled biota extinction and recession caused by the Quaternary ice sheet. However, identification of specific progenitors remains difficult for some endemics, especially some endemic genera. Nannoglottis, with about eight species endemic to this region, is one such genus. Past taxonomic treatments have suggested its relationships with four different tribes of Asteraceae. We intend to identify the closest relatives of Nannoglottis by evaluating the level of monophyly, tribal delimitation, and systematic position of the genus by using molecular data from ndhF gene, trnL-F, and ITS region sequences. We find that all sampled species of Nannoglottis are a well-defined monophyly. This supports all recent taxonomic treatments of Nannoglottis, in which all sampled species were placed in one broadly re-circumscribed genus. Nannoglottis is most closely related to the Astereae, but stands as an isolated genus as the first diverging lineage of the tribe, without close relatives. A tentative relationship was suggested for Nannoglottis and the next lineage of the tribe was based on the ITS topology, the "basal group," which consists of seven genera from the Southern Hemisphere. Such a relationship is supported by some commonly shared plesiomorphic morphological characters. Despite the very early divergence of Nannoglottis in the Astereae, the tribe must be regarded to have its origin in Southern Hemisphere rather than in Asia, because based on all morphological, molecular, biogeographical, and fossil data, the Asteraceae and its major lineages (tribes) are supposed to have originated in the former area. Long-distance dispersal using Southeast Asia as a steppingstone from Southern Hemisphere to the Qinghai-Tibet Plateau is the most likely explanation for this unusual biogeographic link of Nannoglottis. The 23-32-million-year divergence time between Nannoglottis and the other Astereae estimated by DNA sequences predated the formation of the plateau. This estimation is further favored by the fossil record of the Asteraceae and the possible time of origin of the Astereae. Nannoglottis seems to have reached the Qinghai-Tibet area in the Oligocene-Eocene and then re-diversified with the uplift of the plateau. The molecular infragenetic phylogeny of the genus identifies two distinct clades, which reject the earlier infrageneric classification based on the arrangement of the involucral bracts and the length of the ligules, but agree well with the habits and ecological preferences of its current species. The "alpine shrub" vs. "coniferous forest" divergence within Nannoglottis was estimated at about 3.4 million years ago when the plateau began its first large-scale uplifting and the coniferous vegetation began to appear. Most of the current species at the "coniferous forest" clade of the genus are estimated to have originated from 1.02 to 1.94 million years ago, when the second and third uprisings of the plateau occurred, the climate oscillated and the habitats were strongly changed. The assumed evolution, speciation diversity, and radiation of Nannoglottis based on molecular phylogeny and divergence times agree well with the known geological and paleobotanical histories of the Qinghai-Tibet Plateau. (C) 2002 Elsevier Science (USA). All rights reserved.

第十四章 WIA-PA:用于过程自动化的工业无线网络系统结构与通信规范

概要介绍工业无线网络的标准化进程,详细介绍了用于过程自动化的工业无线网络WIA规范的网络构成、拓扑结构、协议体系和关键技术,并将WIA-PA与WirelessHART、ISASP100两大工业无线标准进行了比较分析。

基于图论的无线传感器网络拓扑控制方法研究

传感器技术、通信技术和计算机技术的飞速发展，孕育了具有现代意义的无线传感器网络，带来了一项新的信息革命。无线传感器网络的出现改变了人与自然的交互方式，其应用领域已经深入到了社会生活的各个方面。 无线传感器网络是一种测控网络，网络设计一般侧重网络的节能性、生命周期的延长、网络的扩展性等方面。对于网络拓扑控制来说，由于网络中节点数量众多、能力有限，网络的拓扑结构相当复杂，同时节点易失效也导致了网络拓扑结构的频繁变化，所以拓扑控制是无线传感器网络中重要的研究问题。本文基于图论中的理论知识，对无线传感器网络中的拓扑控制进行了研究，主要内容和研究成果包括以下几个方面。  论述了无线传感器网络拓扑控制问题研究的基本内容、分类、评价指标，并且指出了前人研究的成果的不足之处。  为了对无线传感器网络中节点进行功率控制，以单位圆盘图为模型构造了一个几何支撑图结构。此支撑图满足连通性、平面性、t-支撑图以及稀疏性，并且构造此支撑图的通信开销相对于其它支撑图构造算法大大降低。  针对无线传感器网络中没有基础结构的特点，利用连通支配集理论构造了无线传感器网络的虚拟骨干结构，从而把无线传感器网络映射成一个层次型的骨干结构。  基于修剪策略提出了一种极小连通支配集构造算法。算法又分为集中式和分布式两个版本。集中式算法中不仅考虑了节点的度、节点id，还综合考虑了节点的剩余能量，从而平衡了网络中节点的能量消耗，延长了算法的稳定运行时间，减少了拓扑结构重构的频率，有利于延长网络的生存时间。分布式算法中，节点根据两条邻居信息，采用了一种本地化的启发式搜索策略，从而降低了整个算法的信息复杂度。此外，这种基于修剪策略的构造算法实现方法非常简单，且够在算法运行的任何时刻得到一个可行的解。  基于极大独立集技术提出了一种启发式的极小连通支配集构造算法。在求解极大独立集过程中只需要根据节点和一跳邻居节点之间的信息确定极大独立集，在求解连通集时，根据独立节点的性质采用了本地化的启发式算法，从而提高了算法的性能，构造算法的信息复杂度也相对较低。仿真结果表明，构造算法在整个过程中所需要的通信开销大大降低，从而节省了节点的能量，有利于延长网络的生存时间。  根据无线传感器网络中节点易失效的特点，提出了一个容错的虚拟骨干构造算法。算法基于极大独立集构造方法，首先构造一个连通支配集，然后基于本地化信息得到一个支配度为k的冗余连通支配集，最后再使用协商和贪心策略使得连通支配集的连通度为m，从而得到一个m-连通k-支配集。仿真结果表明算法信息复杂度低，构造算法所需要的数据通信量降低。 本文基于图论知识，针对无线传感器网络的特点，对无线传感器网络的拓扑结构控制方法进行了研究，各项研究成果可以为无线传感器网络设计者提供一些有益的指导。

含环路布局和运动副轴线方位特征的运动链拓扑结构描述

构造一种含环路布局、构件类型、运动副类型和运动副轴线方位信息的运动链的拓扑特征矩阵。构件的类型构成特定的环路布局,运动副的类型及其轴线的方位配置决定运动的状态特征,多副构件是联系环路间的桥梁。以运动链构成的独立环路为基础构建特征矩阵的行数,运动链的构件数目构建特征矩阵的列数;以独立环路的旋向确定构件及其排序;以代表运动副类型的符号或数字表达构件及环路间的连接关系;以同一构件上两个运动副的相对轴线方位描述运动副的方位特征。构造的运动链特征矩阵为(2l+2)×n,而单环运动链为3×n矩阵。实例表明,该特征矩阵可以描述各类运动链,与传统n×n拓扑矩阵相比,结构大大简化,而且拓扑信息量多。该矩阵特别便于由特征矩阵构造对应的机构简图,同时也为计算机辅助运动学和动力学建模提供了一种便捷途径。

基于状态构形矢量和状态构形矩阵的可重构模块星球机器人构形水

可重构模块星球机器人系统由母体和多个子机器人模块组成,单个模块可以独立运动和操作,多个模块可以重构组合成不同构形,模块采用非对称式轮手一体机构,具有姿态方位性和运动方向性,重构目的是组成在某种环境下更好地完成有向性运动的构形。基于此,提出矢量构形概念,将运动趋势方向和方位性融合到构形拓扑结构中。在模块矢量分析模型基础上,提出并构建状态构形矢量(State configuration vector,SCV)和状态构形矩阵(State configuration matrix,SCM),对非对称式单模块和整体构形的状态信息进行描述,同时支持预定义的数学变换操作,可以表达并触发模块的基础动作、构形重构。提出离散模块组合重构成目标构形的优化分析算法,通过实例仿真计算获得优化分析的选择结果。

模块化变形机器人非同构构形表达与计数

提出一种新型链式可重构模块机器人平台,该机器人平台具有手动可重构和自动变形的特点,介绍一种三模块变形机器人样机。组成机器人的单个模块可以简化为由模块本体、连接臂和偏置关节组成。模块的数量可以根据实际工作的需要进行选择,模块间的连接具有规则连接和非规则连接两种方式;同时,由连接模块的偏置关节的运动,模块间的相对位置可以改变。由于模块连接方式的不同和模块间相对位置的变化,变形机器人具有多种非同构构形;为此,根据模块的物理结构和邻接关系提出了用构形矩阵来表达机器人结构的拓扑信息,并在仿真环境下进行等效描述;提出基于组合计数原理的递归算法,用于多模块变形机器人的非同构构形的计数,并根据构形矩阵的拓扑信息对构形进行评价。最后根据仿真结果给出了一种三模块变形机器人样机对称构形的设计示例,验证了算法的可行性。

基于CAN的仿人机器人控制器的设计与实现

本文针对仿人机器人的结构和控制性能的要求,设计并实现了基于CAN的关节控制器,并利用CAN把各个关节和力传感器及上位机连接在一起,构成了有效可靠的控制系统。主要包括仿人机器人的总体结构、控制器的硬件与软件的设计实现、控制系统的拓扑结构等,并提出了一些设想以提高系统的性能。