基于Z曲线的核酸序列可视化分析平台研究

随着Z曲线的提出,用几何学的方法研究DNA序列得到了发展。利用z曲线的思想对核酸序列的可视化分析平台的构建进行了研究,提出了基于包围盒的多精度抽稀算法,实现了从DNA序列到三维空间点和曲线的直接转换。     

Z曲线在基因组中应用的研究与展望

随着后基因组时代的到来,大规模分子数据的处理和分析的需求变得越来越重要,生物数据的处理方法也层出不穷。这里介绍了一种新的表示DNA序列的模型-Z曲线,并详细的介绍了它的数学原理、和它在识别基因、基因起始位点以及识别Isochore结构上的应用,最后展望了Z曲线在识别TFBS上的应用。     

RNA-Z曲线及其在病毒基因识别中的应用

20世纪90年代中期提出的Z曲线方法从几何学的角度阐明了如何识别基因,并取得了非常好的实验结果．但它是完全基于DNA序列结构构建的,对于识别RNA病毒基因效果并不理想,本文提出的RNA—Z曲线方法则弥补了这一缺陷．     

基于Z曲线方法重新注释脑膜炎奈瑟菌MC58株基因组

已测序的微生物基因组中包含的注释开放阅读框(open reading frames,ORFs)可以分为两大类:第一类对应于功能已知的蛋白质编码基因;第二类则为功能未知的假设ORFs,其中通常有一部分实际上不编码蛋白质。采用基于Z曲线的方法从属于第一类的功能已知基因出发训练参数,进而确定第二类ORFs中非编码的部分。通过支持向量机的学习及分类,结果显示十重交叉检验平均正确率为98.45%,说明Z曲线联合支持向量机是一种高度准确的基因识别方法。最终,确定216个假设ORFs实际上不编码蛋白质。通过采用Blastp进行序列比对,保留的假设ORFs中有341个在高可靠性的条件下获得了功能信息。根据蛋白质直系同源簇方法进行功能分类,分别有30、53、59和159个新注释的假设ORFs属于信息储存和加工类、细胞加工和信号传递类、新陈代谢类和特征不明显类。另外还有70个不属于其中的任何一类。注释结果比RefSeq及GenBank提供的原注释更加准确,更加完整。     

基于Z曲线的新城疫病毒基因组生物信息分析

Z曲线是DNA序列信息的一种几何学表示形式。利用Z曲线坐标所对应的生物学含义,可以对DNA序列的生物信息进行系统分析。本文对40株自测序和从GenBank下载的新城疫病毒(NDV)全基因组序列,利用网络提供和自开发的Z曲线分析系统,对NDV生物信息进行了比较分析,构建了NDV全基因组的X、Y、Z分量沿序列的分布曲线和三维Z曲线,比较了不同基因型NDV基因组Z曲线的特征。结果显示,在NDV全基因组中A、G碱基或A、C碱基是占优势的,在基因组的前1/3序列中,G、C含量大于A、T的含量。不同基因型NDV全基因组的Z曲线(从ClassI到ClassII的I-VIII型)有向Z轴靠拢的趋势。     

蛋白质特征曲线的研究

提出一种新颖的方案使蛋白质结构信息可视化。在滑动窗口方法基础上,每一个天然氨基酸采用从氨基酸索引数据库中挑选的48种特性参数描述,在某一特定窗口下的所有氨基酸残基的参数就组成一个矩阵,通过矩阵变换得到一个方矩阵,再经过窗口的滑动就得到基于整个蛋白质的所有这些窗口矩阵的本征值矩阵。对本征值矩阵元素作图得到一系列的本征值曲线,这种曲线的轮廓不随窗口的变化而变化,这些曲线被称为蛋白质的特征曲线。为选择合适的窗口宽度、对同一类型蛋白质不同窗口宽度及不同类型蛋白质相同窗口宽度下的本征值矩阵进行了比较研究,对其潜在的用途进行了讨论。     

正四面体晶格的计数、分布及其应用

本文引入正四面体晶格（简称D晶格）、D格点、D格点简并度等新概念,对正四面体晶格的计数及分布规律进行了系统地研究,从归纳法和组合数学两条途径均得出了正四面体的顶点、棱上、面上、体内及总的D格点数的一般公式,而且得到了其D格点简并度的表达式;归纳总结出了D格点碱基组分表及分布规律．解释了经验方程〔1〕;计算了人的46条染色体DNA分子的简并度,探讨了不同生物种类DNA的排序花样．     

运用遗传算法拟合Logistic曲线的研究

Logistic方程是研究有限空间内种群增长规律的重要工具之一．本文运用遗传算法拟合logistic曲线,并且比较了各种方法的拟合结果,证明遗传算法具有较强的拟合非线性方程的能力,对生物实验及生态、生理学中诸多非线性曲线的参数估计具有普遍意义．     

Z:ZCLA长爪沙鼠微卫星标记的遗传多态性研究

通过对9个微卫星座位的扩增,研究了Z：ZCLA长爪沙鼠的遗传多态性。结果表明,Z：ZCLA长爪沙鼠在其中1个位点上只有一个等位基因,在其它位点上均有2～4个等位基因,平均等位基因数2．6个。平均杂合度0．4684,平均多态信息量0．4166,平均有效等位基因数2．1756。全群基因纯合度从0．1111～0．5555,平均0．3389,提示目前本群遗传多样性水平处于中度多态。     

不同株型玉米光响应曲线的特征参数研究

以平展型品种高油115、中间型品种农大108和紧凑型品种郑单958为供试材料,利用LI-6400便携式光合测定系统测定了玉米吐丝期不同叶位的光响应曲线,并提取出曲线的特征参数。结果表明：不同株型玉米吐丝期光响应曲线的特征参数存在着差异,不同叶位的最大光合速率值均为农大108＞郑单958＞高油115;表观量子利用效率和暗呼吸速率均为郑单958＞农大108＞高油115,揭示了不同株型品种间光能利用特点差异的生理学基础。     

基于DNA弯曲度的H2A.Z核小体定位与修饰研究

在真核生物染色质中,H2A.Z是高度保守的组蛋白变异体,与转录调控、基因组的稳定性密切相关。为了探讨组蛋白修饰、DNA弯曲度与H2A.Z核小体定位三者之间的关联,在得到实验所测的相关数据后,利用MINE算法并结合皮尔逊相关系数在酵母全基因组的转录起始位点周围探讨了三者间的线性与非线性关系。其中MIC算法可以定量的得出数据之间关联度大小的值,用于衡量数据之间是否存在着关联,而皮尔逊相关系数则用于检查是否为线性关联。结果除了发现大部分组蛋白修饰种类和核小体定位之间存在着线性关联外,还探测到有两种组蛋白修饰数据(H4ac修饰与GCN4修饰)和核小体定位数据之间存在着以往未发现的非线性关系(大致呈正余弦函数),并从数据的生物背景(组蛋白修饰与核小体位置)上探讨了出现非线性现象的原因。     

Theoretical evaluation of the order of reactivity of transfer agents utilized in RAFT polymerization: group Z

In the present study we report theoretical calculations, by means of density functional theory (DFT), for 28 transfer agents used in reversible addition-fragmentation chain transfer (RAFT) polymerization. Functional PBE1PBE and 3–21G* theory levels with Gaussian 03 software were used to determine the order of reactivity of RAFT agents through the evaluation of reactivity parameters such as global softness, global hardness and global philicity. It was found that the global softness of the agent was more favored when it contained benzyl or phenyl groups as the Z group, than in RAFT agents with Z groups based on oxygen, nitrogen, or sulfur. On the one hand, when the Z group is based on oxygen or nitrogen, the tendency to form zwitterionic bonds with the adjacent radical center is very high, causing reactivity reduction in these kinds of compounds (e.g., dithiocarbamates) in comparison with compounds that do not experience this type of event; on the other hand, with Z groups based on sulfur, two fragmentation paths are possible, which reduces the fragmentation rate since both Z and R can function as leaving groups. With this investigation we contribute to the understanding of RAFT-mediated polymerization mechanisms by proposing an order of reactivity based on evaluating the importance of the Z group.     

组蛋白变异体H2A.Z的研究进展

H2A.Z是组蛋白H2A的变异体之一,是高度保守的组蛋白变异体,参与保护常染色体,防止形成异染色质;并且与转录调节、抗沉默、沉默和基因组稳定性有关。组蛋白变异体H2A.Z可能与染色体形成独立的结构域,从而调节染色质结构功能。但是,H2A.Z对染色体结构功能的作用机制还不是很清楚。组蛋白变异体H2A.Z和它的表观遗传修饰对染色体动态结构和功能起重要的作用。该文将对组蛋白变异体H2A.Z进行综述。     

Studies on the mechanism of formation of the 5S,12S-dihydroxy-6,8,10,14(E,Z,E,Z)-icosatetraenoic acid in leukocytes

Incubation of peripheral blood leukocytes with arachidonic acid (and ionophore A23187) led to the formation of leukotriene B₄, Δ⁶-trans-leukotriene B₄, Δ⁶-trans-12-epi-leukotriene B₄, 5-hydroxy-icosatetraenoic acid, 12-hydroxy-icosatetraenoic acid and of 5S,12S-dihydroxy-6,8,10,14-(E,Z,E,Z)-icosatetraenoic acid (5S,12S-DiHETE). Incubation of leukocytes with leukotriene A₄ resulted in the formation of leukotriene B₄ and of its two Δ⁶-trans-isomers but not of the 5S,12S-DiHETE. ¹⁸O₂ labeling experiments have shown that the hydroxyl groups at C5 and C12 in the 5S,12S-DiHETE are derived from molecular oxygen. The tetraacetylenic analog of arachidonic acid was found to be a potent inhibitor of the formation of the 5S,12S-DiHETE whereas it potentiated the synthesis of the 5-hydroxy acid and of leukotriene B₄. Addition of the 12-hydroxy-icosatetraenoic acid to leukocytes, or of the 5-hydroxy-icosatetraenoic acid to a suspension of platelets caused the formation of the 5S,12S-DiHETE. It is concluded that the 5S,12S-DiHETE is not derived from leukotriene A₄ but is a product of the successive reactions of arachidonic acid with two lipoxygenases of different positional specificities.     

Analysis of nucleotide distribution in the genome of Streptomyces coelicolor A3(2) using the Z curve method

The nucleotide distribution of all 33 527 open reading frames (ORFs) (≥300 bp) in the genome of Streptomyces coelicolor A3(2) has been analyzed using the Z curve method. Each ORF is mapped onto a point in a 9-dimensional space. To visualize the distribution of mapping points, the points are projected onto the principal plane based on principal component analysis. Consequently, the distribution pattern of the 33 527 points in the principal plane shows a flower-like shape, in which there are seven distinct regions. In addition to the central region, there are six petal-like regions around the center, one of which corresponds to 7172 coding sequences. The central region and the remaining five petal-like regions correspond to the intergenic sequences and out-of-frame non-coding ORFs, respectively. It is shown that selective pressure produces a remarkable bias of the G+C content among three codon positions, resulting in the interesting phenomenon observed. A similar phenomenon is also observed for other bacterial genomes with high genomic G+C content, such as Pseudomonas aeruginosa PA01 (G+C=66.6%). However, for the genomes of Bacillus subtilis (G+C=43.5%) and Clostridium perfringens (G+C=28.6%), no similar phenomenon was observed. The finding presented here may be useful to improve the gene-finding algorithms for genomes with high G+C content. A set of supplementary materials including the plots displaying the base distribution patterns of ORFs in 12 prokaryotes is provided on the website http://tubic.tju.edu.cn/highGC/.     

Identification of the New Hydrocarbon (Z,Z)-1,6,9-Heptadecatriene as the Secretory Component of Caloglyphus polyphyllae (Astigmata: Acaridae)

A new heptadecatriene was isolated from the acarid mite, Caloglyphus polyphyllae, as the major characteristic component which could be used to identify the species chemo-taxonomically. Its structure was elucidated as 1,6,9-heptadecatriene by partial hydrogenation and a subsequent GC/MS analysis of the dimethyldisulfide derivative, together with evidence of the terminal vinyl group and Z-configuration of double bonds that was provided by GC-FT/IR and NMR. The triene was identified as (Z,Z)-1,6,9-heptadecatriene by its synthesis and is revealed to be a new compound as a natural product.     

基于组蛋白甲基化信息的H2A.Z和H2A核小体识别

组蛋白H2A的变体H2A.Z在基因的表达过程中发挥着重要的作用。根据H2A.Z和H2A核小体中组蛋白甲基化修饰方式的不同,作者应用多样性增量二次判别方法(increment of diversity with quadratic discriminant,IDQD)成功地对H2A.Z和H2A核小体进行了识别,说明了以组蛋白甲基化信息作为特征参数的IDQD模型对H2A.Z和H2A核小体识别的有效性。通过计算DNA序列的柔性,发现H2A.Z核小体对应的DNA序列的平均柔性比常规H2A核小体对应的DNA序列的平均柔性弱。     

Molecular Dynamics Study of Zinc-Blende GaN,AIN and InN

Abstract

We present a result of the molecular dynamics calculations with used a three-body empirical Tersoff potential. The parameters of the Tersoff potential are determined for nitride compound semiconductors such as GaN, AlN and InN. The structural and thermodynamic properties of GaN, AlN and InN in zinc-blende structure are presented. We report the equilibrium lattice constants, the bulk moduli, the cubic clastic constants, thermal expansion coefficient and specific heat. Good agreement is obtained with recent experimental and theoretical results for all constants.