基于非线性方法的DNA序列分析

以人类DNA序列为原始数据,对其进行数字编码。在利用功率谱分析编码DNA序列的基础上,利用Hurst指数进一步分析序列的自相似性。从分析结果看出,DNA序列中的确存在长程相关现象,而且这种长程相关现象与DNA的组成结构有关,表现为它的结构基团的Hurst指数大于其功能基团的Hurst指数。同时,从内含子含量的角度分析序列的长程相关程度,结果表明,同一序列中,内含子含量与不同的化学基团具有不同的关系。这表明不同的化学结构对DNA序列特征具有不同的贡献。这些结论从非线性方法的角度对DNA序列的分析提供了新的思路。     

外显子与内含子序列的分形尺度参数可分性研究

近年来, 关于ＤＮＡ 序列的分形尺度特性的研究引起了研究者广泛的兴趣, 许多研究表明,ＤＮＡ 序列的外显子和内含子区域具有不同的分形尺度特性,这有可能成为区别外显子和内含子序列的特征之一。文中应用ＷＴＭＭ（ Ｗａｖｅｌｅｔ Ｔｒａｎｓｆｏｒｍ Ｍｏｄｕｌｕｓ Ｍａｘｉｍ） 方法分析ＤＮＡ 序列的分形结构,计算表征分形结构尺度特性的量化参数 Ｈｌｄｅｒ 指数。考虑到外显子序列的三联体编码特性, 计算了ＤＮＡ 序列及三个不同的相位序列分别在三种ＤＮＡ ｗａｌｋ 方式下得到的序列的Ｈｌｄｅｒ 指数,并将每个Ｈｌｄｅｒ 指数作为一维特征,考察外显子与内含子序列的分布。计算结果表明,只按单个分形尺度参数来看,外显子与内含子不具有可分性。在此基础上,从模式识别的角度出发, 将外显子与内含子视为由此构成的多维特征空间中的两个模式类, 由此设计基于ＬＬＭ（ＬｏｃａｌＬｉｎｅａｒ Ｍａｐ） 神经网络的分类器,并对分类器的错误率进行估计,实验结果表明外显子序列与内含子序列在此特征空间中具有聚类特性,从而表明以这一组分形尺度参数作为序列特征,外显子与内含子具有可分性。这一结果为研究外显子与内含子序列的识别算法提供了新的线索     

基于分组码模型的DNA序列编码特性分析

基于差错控制原理,将遗传信息中由海量碱基构成的DNA序列看作经过编码而获得的具有某种编码特性的编码序列。在此基础上,将编码理论中分组码的分析方法用于对DNA序列进行分析,选用了（6,3）分组码对三种原核生物和两种真核生物DNA序列进行分析,在ORF起始端和结束端观察到明显的码间距离变化。证明该方法对DNA序列分析有较好的指导作用。     

乙型、丙型流感病毒的长记忆ARFIMA模型

用时间序列模型来分析乙型、丙型这两种流感病毒,对乙流、丙流病毒DNA序列提供了一种新的时间序列模型,即CGR弧度序列。利用CGR坐标将乙流、丙流病毒DNA序列转换成CGR弧度序列,且引入长记忆ARFIMA模型去拟合这两类序列。发现随机找来的10条乙流序列,10条丙流序列都具有长相关性且拟合很好,并且还发现这两种病毒序列可以尝试用不同的ARFIMA模型ARFIMA(0,d,4)模型,ARFIMA(1,d,1)模型去识别。     

杨树叶绿体3′rps12基因,rps7基因和ndhB基因片段的克隆及序列分析

通过烟草叶绿体相关序列设计引物 ,从杨树的叶绿体基因组中克隆出 2个相邻的DNA片段 .经分析发现 ,这 2个DNA片段包含核糖体蛋白 3′rps12、rps7基因和NADH脱氢酶第二亚基ndhB基因片段 .利用DNAMAN等软件 ,将扩增到的杨树叶绿体DNA片段与烟草、拟南芥、玉米和黑松的相关序列进行比较 ,证实所扩增的片段具有较高的保守性 ,尤其是在这 3个基因的编码区 ,同源性均在 90 %以上 .插入或缺失常发生在基因间隔区 ,同源性在 80 %左右 ;对其编码区所推导的氨基酸序列进行了比较 ,同源性均在 92 %以上 .首次克隆了杨树叶绿体的部分DNA序列 ,详细报道并分析了杨树 3′rps12、rps7基因和ndhB基因片段及其边界序列信息 .所报告的基因序列均已登录GenBank .     

在接种DNA小鼠中细胞介导的丙型肝炎病毒特异的基因型交叉反应性免疫的诱导

通用的丙型肝炎(HCV)疫苗应当激发多重抗原及基因型的应答,从而更易于保护机体抵御在社区中流传的基因型以及亚型范围内病毒的攻击。疫苗的混合使用以及编码HCV共有序列的疫苗是达到这一目的有吸引力的方法。因而,在一系列小鼠免疫研究中,研究者比较了一种编码HCV共有非结构5B(NS5B)蛋白与编码基因型1b(Gt1b)和Gt3aNS5B蛋白的DNA质粒混合物的免疫原性。为了完善这一研究,通过将编码Gt1b和Gt3aNS3、NS4以及NS5B蛋白的DNA疫苗混合物与单基因型NS3/4/5BDNA疫苗进行比较,评估机体对多重抗原性混合物配体的应答。     

天目山物种多样性尺度依赖及其与空间格局关系的多重分形

以浙江省天目山国家级自然保护区为例,采用多尺度分析思想,利用多重分形分析方法,研究了不同尺度下物种多样性的变化、空间分布格局以及多样性与空间格局之间的关系。研究主要得到3方面的结论：（1）物种多样性具有尺度依赖性,随着空间尺度的增大,Shannon-Wiener多样性指数Ⅳ增大,Margalef多样性指数足和均匀度指数E减小;（2）多重分形参数αmin。多重分形谱的变化范围SR等能够定量反映物种的空间分布特征,空间大尺度越大,物种越聚集,空间分布越不均匀;（3）物种多样性与空间格局存在线性或幂函数关系。研究表明多重分形分析定量描述物种空间格局是有效性的,多重分形参数与生物多样性之间的定量关系为研究物种空间格局、生态属性与尺度之间的关系奠定了基础。因此,分形结合传统方法,在生物多样性方面的研究将有很大的潜在价值。     

侧耳木霉T2-1植酸酶基因的序列分析及蛋白结构预测

利用GenBank发表的植酸酶A编码序列设计的引物,通过PCR的方法对侧耳木霉(Trichoderma pleuroticola)T2-1基因组DNA进行扩增,获得了一条长约1.7 kb的特异性DNA片段.序列测定结果表明,该DNA片段含有植酸酶编码基因的完整序列和3段内舍子序列,其中植酸酶基因全长1 443 bp,编码480个氨基酸,5'端有一段编码23个氨基酸的信号肤序列,其余的457个氨基酸残基为成熟植酸酶的氨基酸序列.对该基因编码的氨基酸序列进行三级结构预测,发现它为磷酸单酯酶.已将侧耳木霉T2-1植酸酶基因序列在GenBank中注册(登录号:GQ325590).这是目前中国在GenBank注册的第一个完整的木霉植酸酶编码基因.     

翻译起点的多样性可能决定着人开放阅读码组的高度复杂性

开放阅读码框（ORFs）是含有碱基的编码蛋白质的DNA,它们位于起始密码序列（ATG码）和终止密码序列之间。令人惊奇的是,一些顺序分析结果指出,某些cDNA在其编码序列之前的上游部分至少有一个ATG码,这表明在基因5＇端非翻译区域（UTRs）存在着潜在的编码区段。在本文中,作者运用同高分辨多重串联质谱仪偶联的自动双向液体色谱系统证实,在mRNAs非翻译区域存在这一些上游ORFs。     

基因组序列的长程关联

用快速付立叶变换的谱分析方法研究了多种类型的基因组序列的长程关联性质。结果表明,含有内含子的序列有明显的长程关联,ｃＤＮＡ和编码区则没有此种表现;人的２０余种基因组序列的长程关联随着内含子含量的增长呈正关联,而内含子含量超过８０％后呈负关联。内含子的序列位置对长程关联亦有效应。     

Fractal dimension of birds population sizes time series

Information about fractal dimension is collected so that it can be applied to time series interpreting Hurst coefficient. The population size of a species is modelled as a dynamic system. The Hurst coefficient is calculated for these times series. A computer programme has been elaborated to compute the Hurst exponent of time series using the algorithms of range increment, second order moment increment and local second order moment increment. It has been applied to time series of birds' populations.     

Persistent behavior in a phase-shift sequence of periodical biochemical oscillations

We present the analysis of a phase-shift sequence obtained from random transitions between periodic solutions of a biochemical dynamical model, formed by a system of three differential equations and which represent an instability-generating multienzymatic mechanism. The phase-shift series was studied in terms of Hurst’s rescaled range analysis. We found that the data were characterized by a Hurst exponent H = 0.69, which was clearly indicative of long-term trends. This result had a high significance level, as was confirmed through Monte Carlo simulations in which the data were scrambled in the series, destroying its original ordering. For these series we obtained a Hurst exponent which was consistent with the expectation of H = 0.5 for a random independent process. This clearly showed that, although the transitions between the periodic solutions were provoked randomly, the stochastic process obtained exhibited long-term persistence. The fractal dimension was also estimated and found to be consistent with the value of the Hurst exponent.     

Evaluation of Scaling Invariance Embedded in Short Time Series

Scaling invariance of time series has been making great contributions in diverse research fields. But how to evaluate scaling exponent from a real-world series is still an open problem. Finite length of time series may induce unacceptable fluctuation and bias to statistical quantities and consequent invalidation of currently used standard methods. In this paper a new concept called correlation-dependent balanced estimation of diffusion entropy is developed to evaluate scale-invariance in very short time series with length . Calculations with specified Hurst exponent values of show that by using the standard central moving average de-trending procedure this method can evaluate the scaling exponents for short time series with ignorable bias () and sharp confidential interval (standard deviation ). Considering the stride series from ten volunteers along an approximate oval path of a specified length, we observe that though the averages and deviations of scaling exponents are close, their evolutionary behaviors display rich patterns. It has potential use in analyzing physiological signals, detecting early warning signals, and so on. As an emphasis, the our core contribution is that by means of the proposed method one can estimate precisely shannon entropy from limited records.     

Assessment of cerebral hemodynamics during neurosurgical procedures using laser speckle image analysis

Aneurysmal subarachnoid hemorrhage (aSAH) is a severe medical condition associated with a significant cause of mortality throughout the world. Cisterna magna injection model is accepted widely to mimic clinical aSAH and is performed on small animal models to study aSAH during neurosurgery. Coherent light scattered from the surface of the rat brain is used to infer information about the variations in blood flow during this condition. We obtained speckle images from the exposed cortex during the entire experiment using an external tissue imaging system. Contrast and fractal analyses are carried out for the recorded speckle pattern time series. Correlation analysis based on Hurst exponent for these images is found to be a more sensitive tool in studying aSAH as compared to routinely used laser speckle contrast analysis for assessing the changes in blood flow velocity. Additionally, our studies provide improved blood flow detection sensitivity with image Hurst exponent in combination with computed fractal dimension, during an event of aSAH.     

Molecular structures of mitochondrial-DNA-like sequences in human nuclear DNA.

Two lambda phage clones carrying mitochondrial-DNA-like (mtDNA-like) sequences isolated from a human gene library were named Lm E-1 and Lm C-2, and their DNA structures were characterized. Lm E-1 contains about 0.4 kb DNA homologous to the 5' portion of the mitochondrial 16S ribosomal RNA (rRNA) gene and Lm C-2, a 1.6 kb DNA homologous to the 3' portion of the 12S rRNA gene and to almost all of the 16S rRNA gene. Comparisons of their nucleotide sequences with those of the corresponding regions of the human mtDNA revealed no detectable DNA rearrangement and their homologies to the human mtDNA are 84% and 80%, respectively. There are neither terminal repeats in the nuclear mtDNA-like sequences nor duplications of the nuclear DNAs flanking the mtDNA-like sequences. Evolutionary relationship between these two human nuclear mtDNA-like sequences and the human and bovine mtDNAs is discussed.     

Isolation and characterization of a 15-kilobase genomic sequence coding for part of the Pro alpha 2 chain of sheep type I collagen

DNA fragments, prepared by partial Eco RI digestion of fetal sheep liver genomic DNA, were used to prepare a "library" of amplified genomic sequences with the lambda vector Charon 4A. Several recombinant plaques were identified by their ability to hybridize to 32P-labeled cDNA prepared from fetal sheep tendon type I procollagen mRNA. Two of these recombinant DNA bacteriophages (SpC3 and SpC7) were identified as containing procollagen pro alpha 2 gene sequences by their ability to specifically anneal to procollagen pro alpha 2 mRNA. Restriction endonuclease and hybridization to a cloned pro alpha 2 cDNA demonstrated that approximately half (2.5 kilobases) of the pro alpha 2 mRNA sequence is distributed over 15 kilobases of genomic DNA. Restriction maps of SpC3 and SpC7 demonstrated that these two DNA fragments contain overlapping sequences of the pro alpha 2 gene. Electron microscopy and R-loop analysis of SpC3 revealed that at least 12 to 16 intervening sequences are distributed throughout the length of this gene fragment.     

麂属(Muntiacus)动物线粒体12S rRNA、细胞色素b基因和多药耐药基因序列分析及其分子进化关系

对麂属（Muntiacus)中的3种动物：赤麂（M.muntjak)(2n=6♀,7♂）,小麂（M.reevesi)(2n=46),黑麂（M.cri.nifrons)(2n=8♀,9♂）线粒体DNA 12S rRNA和细胞色素b基因784bp左右的片段和核基因－多药耐药基因（multidrug resistance,MDR1)的728bp左右的片段进行了序列分析,并根据序列信息建立了分子系统树,同时探讨了这3种动物的起源,分类地位及进化关系。