A family of interesting exact solutions of the sine-Gordon equation

By using AKNS [Phys. Rev. Lett. 31 (1973) 125] system and introducing the wave function, a family of interesting exact solutions of the sine-Gordon equation are constructed. These solutions seem to be some soliton, kink, and anti-kink ones respectively for the different choice of the spectrum, whereas due to the interaction between two traveling-waves they have some properties different from usual soliton, kink, and anti-kink solutions.

A scheme for multiple sequences alignment optimization-an improvement based on family representative mechanics features

As a basic tool of modern biology, sequence alignment can provide us useful information in fold, function, and active site of protein. For many cases, the increased quality of sequence alignment means a better performance. The motivation of present work is to increase ability of the existing scoring scheme/algorithm by considering residue–residue correlations better. Based on a coarse-grained approach, the hydrophobic force between each pair of residues is written out from protein sequence. It results in the construction of an intramolecular hydrophobic force network that describes the whole residue–residue interactions of each protein molecule, and characterizes protein's biological properties in the hydrophobic aspect. A former work has suggested that such network can characterize the top weighted feature regarding hydrophobicity. Moreover, for each homologous protein of a family, the corresponding network shares some common and representative family characters that eventually govern the conservation of biological properties during protein evolution. In present work, we score such family representative characters of a protein by the deviation of its intramolecular hydrophobic force network from that of background. Such score can assist the existing scoring schemes/algorithms, and boost up the ability of multiple sequences alignment, e.g. achieving a prominent increase (50%) in searching the structurally alike residue segments at a low identity level. As the theoretical basis is different, the present scheme can assist most existing algorithms, and improve their efficiency remarkably.

Generating artificial homologous proteins according to the representative family character in molecular mechanics properties - an attempt in validating an underlying rule of protein evolution

The molecular mechanics property is the foundation of many characters of proteins. Based on intramolecular hydrophobic force network, the representative family character underlying a protein’s mechanics property is described by a simple two-letter scheme. The tendency of a sequence to become a member of a protein family is scored according to this mathematical representation. Remote homologs of the WW-domain family could be easily designed using such a mechanistic signature of protein homology. Experimental validation showed that nearly all artificial homologs have the representative folding and bioactivity of their assigned family. Since the molecular mechanics property is the only consideration in this study, the results indicate its possible role in the generation of new members of a protein family during evolution.

小檗科：花发育形态学、胚胎学和系统学

小檗科是毛茛类的核心成员之一，属于较原始的被子植物类群。目前有关该科在毛茛类的系统位置还没有一致的意见。一种观点认为它与毛茛科有密切关系，属于本目中较原始的一支;另一些学者则根据小檗科与罂粟科在心皮结构上的相似性提出它们有较近的亲缘关系，并可能在毛茛类中处于较高的演化水平上。小檗科的范畴与科内系统至今仍存在着较大争论。自本世纪初以来已有若干系统发表，其中有的采取广义小檗科的概念，而有的则分别成立2-4个科。在生殖结构演化方面，有关小檗科植物花的一些形态学本质，如花基数、蜜腺来源、心皮性质等仍有待揭示。因此，有必要对该科的结构、分化和系统发育进行深入的研究。 本研究首次报导了小檗科9属植物的花部形态发生、10属植物胚胎发育、9属植物的种皮纹饰和八角莲属与桃儿七属的rbcL基因全序列。并综合已有的研究资料，对小檗科的系统学问题进行了讨论。主要实验结果及结论如下： 1花部形态发生 小檗科植物典型花部形态为三数轮列、雄蕊与花瓣对生、单生心皮、侧生胎座。花器官发育的独特性状包括雄蕊与花瓣以共同原基方式发生;心皮原基环形、周缘组织等速向上发育而建成瓶状心皮，不形成腹缝线。我们认为，三基数在小檗科植物中可能是共同起源的，为典型轮列花;花瓣（蜜腺叶）来源于花瓣一雄蕊共同原基，而小檗属、十大功劳属、兰山草属花瓣上的小囊状蜜腺是其本身的附属结构，与雄蕊无关;雄蕊与花瓣对生来源于雄蕊一花瓣共同原基的发生方式;小檗科的心皮发生方式在毛茛类中是独特的，它不同于Hell (1981，198 3)描述的囊状心皮． 2胚胎学 小檗科植物的主要胚胎学性状有：腺质绒毡层，药室内壁带状加厚，2细胞花粉粒，胚珠具双珠被、厚珠心，珠孔由内外珠被组成，直线型大孢子4分体，蓼型、稀待宵草型（红毛七属）或葱型（桃儿七属）胚囊，反足细胞宿存，核型胚乳，柳叶草型或茄型胚胎发生。根据小檗科各属植物的胚胎学与种皮表面雕纹性状的分化，小檗科可以划分为：南天竹属，小檗属一十大功劳属，红毛七属一牡丹草属一狮足草属，山荷叶属一八角莲属一桃儿七属一足叶草属，淫羊藿属一鲜黄连属5个属群。说明胚胎学性状对揭示本科植物属间及属群间系统关系有较大的价值。 3分子数据 利用本研究测得的八角莲属、桃儿七属rbcL基因序列，结合从GenBank中得到的小檗科其他9属、毛茛科（4属）、防己科（2属）和木通科（1属）的rbcL序列，用PAUP软件进行分支分析。支持广义小檗科是单系类群的观点;．山荷叶属、八角莲属和桃儿七属构成的分支得到Bootstrap分析的完全支持(100%)，3属植物是科内的一个自然类群;具x=6染色体基数的草本属间存在密切关系(90%);十大功劳属与兰山草属近缘(73%);南天竹属与红毛七属可能有一定联系(53%)。 4系统排列 广义小檗科(17属)为一单系类群得到本研究所获得的花形态发生、胚胎学和分子证据支持;综合各学科的研究结果提出小檗科分5族系统的建议．其系统排列为：1).南天竹族，含南天竹属1属．2).小檗族，分小檗亚族（小檗属、十大功劳属）和兰山草亚族（草本的兰山草属），共3属．3).狮足草族，含红毛七属、狮足草属和牡丹草属3属。4）．足叶草族，分足叶草亚族（足叶草属、八角莲属与桃儿七属）和山荷叶亚族（山荷叶属），共4属．5).淫羊藿族，分淫羊藿亚族(淫羊藿属、 Vancou ver ia、Jef fersonia、鲜黄连属与Bongardia)和裸花草亚族（裸花草属），共6属。 5系统位置 根据小檗科花形态发生的独特性状，如心皮瓶状发育、雄蕊一花瓣以共同原基发生、二者对生、花药瓣裂和分子系统学的结果，以及据已有资料比较，小檗科在毛茛目中的特征较独特，与毛茛科的关系较远。支持小檗科提升为目的处理。