利用支持向量机和马氏判别式预测人类polⅡ启动子

通过选取人类启动子与非启动子序列中不同的k-mer作为预测算法的基础特征,分别以三个区域（-249～-1;0～＋50;-30～＋30）的6-mer频数作为离散源参数构建离散增量,同时选取24个位点（-31～-21;-4-＋2;＋25-＋29）的3-mer频数作为位置打分函数的参数,分别利用支持向量机和马氏判别式为判别函数对启动子进行预测。用10折叠交叉检验来衡量两种算法的预测能力,预测结果成功率分别达到87．0％和87．9％。对于独立检验集,敏感性分别为62．7％和76．0％,特异性分别为77．5％和66.8％。     

基于离散增量的支持向量机算法预测蛋白质中四类简单超二级结构

蛋白质超二级结构预测是三级结构预测的一个非常重要的中间步骤。本文从蛋白质的一级序列出发,对5793个蛋白质中的四类简单超二级结构进行预测,以位点氨基酸为参数,采用3种片段截取方式,分别用离散增量算法预测的结果不理想,将组合的离散增量值作为特征参数输入支持向量机,取得了较好的预测结果,5交叉检验的平均预测总精度达到83.0%,Matthew’s相关系数在0.71以上。     

用ID-SVM预测蛋白质的ATP结合位点

从蛋白质序列出发,对经Dr．G．P．S．Raghava整理和使用过的168条非冗余的ATP与蛋白质结合氨基酸序列进行分段,对ATP与蛋白质结合位点进行了统计分析。在此基础上,利用20种氨基酸的亲疏水性将20种氨基酸约化为6类。以氨基酸组分和6类亲疏水紧邻为参数,用多样性增量（ID）方法将氨基酸组分和6类亲疏水紧邻降维并将降维后的特征参数输入支持向量机中运算,本文运算结果显示用氨基酸组分ID值和6类亲疏水紧邻ID值共同作为特征参数结果最优,在七交叉检验下的预测总精度达到了99．67％,相关系数达到0．9934,好于前人的预测结果。     

利用分组重量编码预测细胞凋亡蛋白的亚细胞定位

从氨基酸的物化特性出发,利用物理学中“粗粒化”和“分组”的思想,提出了一种新的蛋白质序列特征提取方法——分组重量编码方法。采用组分耦合算法作为分类器,从蛋白质一级序列出发对细胞凋亡蛋白的亚细胞定位进行研究。针对Zhou和Doctor使用的数据集,Re—substitution和Jackknife检验总体预测精度分别为98、O％和85．7％,比基于氨基酸组成和组分耦合算法的总体预测精度提高了7．2％和13．2％;针对陈颖丽和李前忠使用的数据集,Re—substitution和Jackknife检验总体预测精度分别为94．0％和80、1％,比基于二肽组成和离散增量算法的总体预测精度提高了5．9％和2、0％。针对我们自己整理的最新数据集,通过Re—substitution和Jackknife检验,总体预测精度分别为97．33％和75、11％。实验结果表明蛋白质序列的分组重量编码对于细胞凋亡蛋白的定位研究是一种有效的特征提取方法。     

用离散量预测蛋白质的结构型

基于蛋白质的结构类型决定了它的二级结构序列的概念,用二级结构序列参数Nα,Nβ,Nβaβ,N(βαβ）构成离散源,并计算离散量D（Xα）,D（Xβ）,D（Xα＋β）,利用离散增量预测蛋白质的结构类型,它是由这个蛋白质的离散量D（Xn）与四个标准离散D（Xα）,D（Xβ）,D（Xα／β）,D（Xα＋β）之间离散增量的最小值所决定的,预测结果表明,准确率分别达到84．8％（标准集）和83．3％（检验集）。     

基于序列特征的人类PolⅡ启动子理论预测

基于已知的人类PolII启动子序列数据,综合选取启动子序列内容和序列信号特征,构建启动子的支持向量机分类器．分别以启动子序列的6-mer频数作为离散源参数构建序列内容特征。同时选取24个位点的3-mer频数作为序列信号特征构建PWM,将所得到的两类参数输入支持向量机对人类启动子进行预测．用10折叠交叉检验和独立数据集来衡量算法的预测能力,相关系数指标达到95％以上,结果显示结合了支持向量机的离散增量算法能够有效的提高预测成功率,是进行真核生物启动子预测的一种很有效的方法．     

用二次判别方法识别蛋白质β-发夹模体

基于氨基酸序列,用打分值、离散增量、自相关函数值和距离值来表示β-发夹模体信息,通过二次判别方法对上述信息进行融合,预测数据库ArchDB40和EVA中的β-发夹模体。文章使用的β-发夹模体包含的loop长为2～10个氨基酸,当序列模式长为17个氨基酸时,对两个数据库中β-发夹5交叉检验预测的总精度分别达到83.1%和80.7%,相关系数达到0.59和0.61,好于前人的预测结果。     

基于支持向量机和贝叶斯方法的蛋白质四级结构分类研究

用支持向量机和贝叶斯两种方法对蛋白质四级结构进行分类研究。结果表明,基于支持向量机的分类结果最好,其l0CV检验的总分类精度、正样本正确预测率、Matthes相关系数和假阳性率分别为74．2％、84．6％、0．474、38．9％;基于贝叶斯的分类结果没有支持向量机的分类结果好,但其l0CV检验的假阳性率最低(15．9％)．这些结果说明同源寡聚蛋白质一级序列包含四级结构信息,同时特征向量的确表示了埋藏在缔合亚基作用部位接触表面的基本信息。     

拟南芥和线虫基因序列及剪切位点的理论预测

将拟南芥(A．thaliana)和线虫(C．elegans)基因组按外显子、内含子及基因间序列区分为3类。分别选取64、40、20种三联体的概率作为信号参数构建离散源,根据离散增量预测序列所属类型。结果表明：拟南芥各条染色体标准集总预测成功率达到82．19％,检验集为87．95％;线虫各条染色体标准集总预测成功率达到79．67％,检验集达到81,93％。另外,将两种基因序列中的外显子分别划分成3类,用外显子剪切位点、翻译起始和结束位点附近的三联体的3个位点作为3条子链,以各条子链的12个参数构建离散源,用离散增量对3种序列类型进行预测,预测成功率都达80％以上。     

基于多样性指标的分枝杆菌蛋白质亚细胞定位预测

由于蛋白质亚细胞位置与其一级序列存在很强的相关性,利用多样性增量来描述蛋白质之间氨基酸组分和二肽组分的相似程度,采用修正的马氏判别式（这里称为IDQD方法）对分枝杆菌蛋白质的亚细胞位置进行了预测。利用Jackknife检验对不同序列相似度下的蛋白质数据集进行了预测研究,结果显示,当数据集的序列相似度小于等于70％时,算法的预测精度稳定在75％左右。在对整体852条蛋白质的预测成功率达到87．7％,这一结果优于已有算法的预测精度,说明IDQD是一种有效的分枝杆菌蛋白质亚细胞预测方法。     

Recent advances in the study of Kaposi's sarcoma-associated herpesvirus replication and pathogenesis

It has now been over twenty years since a novel herpesviral genome was identified in Kaposi's sarcoma biopsies. Since then, the cumulative research effort by molecular biologists, virologists, clinicians, and epidemiologists alike has led to the extensive characterization of this tumor virus, Kaposi's sarcoma-associated herpesvirus(KSHV; also known as human herpesvirus 8(HHV-8)), and its associated diseases. Here we review the current knowledge of KSHV biology and pathogenesis, with a particular emphasis on new and exciting advances in the field of epigenetics. We also discuss the development and practicality of various cell culture and animal model systems to study KSHV replication and pathogenesis.     

The structure, reproduction and taxonomy of Vidalia and Osmundaria (Rhodophyta, Rhodomelaceae)

Comprises species occurring mostly in subtidal habitats in tropical, subtropical and warm-temperate areas of the world. An analysis of the type species, V. spiralis (Sonder) Lamouroux ex J. Agardh, a species from Australia, establishes basic characters for distinguishing species in the genus. These characters are (1) branching patterns of thalli, (2) flat blades that may be spiralled on their axis, (3) width of the blade, (4) primary or secondary derivation of sterile and fertile branchlets and (5) position of sterile and fertile branchlets on the thalli. Application of the latter two characters provides an important basic method for separation of species into three major groups. Osmundaria , a genus known only in southern Australia, was studied in relation to Vidalia , and its separation from the Vidalia assemblage is not accepted. Species of Vidalia therefore are transferred to the older genus name, Osmundaria. Two new species, Osmundaria papenfussii and Osmundaria oliveae are described from Natal. Confusion in the usage of the epithet, Vidalia fimbriala Brown ex Turner has been clarified, and Vidalia gregaria Falkenberg, described as an epiphyte on Osmundaria pro/ifera Lamouroux, is revealed to be young branches of the host, Osmundaria prolifera.     

New or rare chromosome counts in Artemisia L. (Asteraceae, Anthemideae) and related genera from Kazakhstan

Fifteen chromosome counts of six Artemisia taxa and one species of each of the genera Brachanthemum, Hippolytia, Kaschgaria, Lepidolopsis and Turaniphytum are reported from Kazakhstan. Three of them are new reports, two are not consistent with previous counts and the remainder are confirmations of very scarce (one to four) earlier records. All the populations studied have the same basic chromosome number, x = 9, with ploidy levels ranging from 2x to 6x. Some correlations between ploidy level, morphological characters and distribution are noted.     

肝癌中HBV和HCV基因和抗原的分布及意义

采用原位分子杂交方法检测HCV RNA及HBV X基因;采用免疫组织化学方法研究HCV核心抗原,非结构区C33c抗原及HBxAg在肝细胞肝癌中的定位及分布.结果表明(1)HCV RNA、HBV X基因在肝细胞肝癌组织检出率分别为40%(55/136)和82%(112/136).HCV RNA定位于癌细胞的胞浆内,阳性细胞呈散在、灶状及弥漫分布三种形式;HBV X基因在肝癌细胞中的分布呈胞浆型、核型及核浆型,阳性细胞也呈上述三种分布形式;(2)HCV C33c抗原、核心抗原在肝细胞肝癌中的阳性率为81%(133/164)及86%(141/164).C33c抗原定位于癌细胞及肝细胞的胞浆内;核心抗原既定位于癌细胞核中,又可定位于胞浆中.C33c抗原阳性细胞以灶状分布为主;而核心抗原阳性细     

Selection with two alleles and complete dominance

For a plant selection model with frequency-independent viabilities, fertilities and selfing rates, it is shown that apart from global fixation, for certain parameter combinations a protected polymorphism and facultative fixation (either allele may become fixed according to initial frequencies) may both occur. Facultative fixation requires different selling rates for the dominant and recessive type. Protection of the polymorphism requires resource allocation for male and female function. In this connection the problem of purely genetically caused population extinction is discussed.
For general frequency dependence and regular segregation, the chances for establishment of a completely recessive gene are compared to those of a completely dominant gene. It is proven that the process of establishment of the recessive gene, despite a fitness advantage, may be considerably endangered by drift effects if random mating prevails. The recessive gene may reach the same effectivity in establishment as a dominant gene, only if the recessive homozygote mates exclusively with its own type during the period of establishment.