DNA序列全球对称群和多义密码子的对称性（I）

为了完善DNA序列对称理论,本文将12阶DNA群（D群）推广为24阶DNA全对称群（Dd群）。DNA全对称群被定义为特殊的交换群（S4）,其交换元素是DNA序列的4个碱基。DNA群与四面体群（T群）同构,DNA全对称群与正四面体全对称群（Td群）同内,D群是Dd群的一个子群。本文还推导出了Dd群12个新元素的矩阵表。Dd群的乘法表,得到了在Dd群操作四碱基A,C,G和T的变换表等。     

DNA序列全对称群和多义密码子的对称性(Ⅰ)

为了完善DNA序列对称理论,本文将12阶DNA群(D群)推广为24阶DNA全对称群(Dd群).DNA全对称群被定义为特殊的交换群(S4),其交换元素是DNA序列的4个碱基.DNA群与四面体群(T群)同构,DNA全对称群与正四面体全对称群(Td群)同构,D群是Dd群的一个子群.本文还推导出了Dd群12个新元素的矩阵表,Dd群的乘法表,得到了在Dd群操作下四碱基A,C,G和T的变换表等.     

子囊菌延长因子1 alpha基因密码子偏好性分析(英文)

文中对子囊菌代表类群的延伸因子1 alpha基因密码子的使用模式进行了研究。结果表明:该基因的密码子使用偏好性不仅与核酸碱基组成密切相关,也受到其他选择性压力的影响。统计分析揭示了子囊菌各类群该基因的密码子组成和编码特点,在同义密码子的选择模式上,酵母纲(Saccharomycetes)的成员具有较独特的偏好性。基于密码子用法分歧度的聚类分析方法较合理地反映了大部分类群的分类学地位,但在各个纲的内部,密码子偏好性的变化程度存在差异。     

无齿稻蝗和黄翅踵蝗线粒体基因组与系统发育分析

为了研究无齿稻蝗和黄翅踵蝗在蝗总科的系统发育地位,本研究采用基于长PCR的二次PCR方法对这两种蝗虫的线粒体基因组进行了测定和系统发育分析。结构显示:无齿稻蝗和黄翅踵蝗线粒体基因组全长分别是15 447 bp和15 598 bp,均含有典型的37个基因以及一个控制区,基因排序和数量与其他已知近缘昆虫相同;线粒体基因组A+T含量分别是75.4%、75.4%。两种蝗虫的蛋白质编码基因中均是除了COX1的起始密码子是ACC,其他都是典型的起始密码子ATN;所有蛋白质编码基因的终止密码子都是典型的TAA或TAG;两种蝗虫t RNA基因中,21个能形成三叶草结构,只有trn~(SAGN)缺少DHU臂;黄翅踵蝗控制区的N链出现一个tRNA-like的结构。由两个外群和24个蝗总科物种构建的系统树结果显示无齿稻蝗与小稻蝗为姐妹群,黄翅踵蝗与飞蝗属和车蝗属与小车蝗属组成的分支为姐妹群。     

中国石炭纪和二叠纪植物群

本文总结了和讨论了中国石炭纪和二叠纪植物群分布特征,在对植物群成分分析的基础上,认为中国早石炭世（杜内期、维宪期和纳缪尔A期）分布一个全球一致性的植物群,即拟鳞木植物群Lepidodendropsis flora。中国的晚石炭世（纳缪尔B-C期、维期发期和斯蒂分期）和二叠纪植物群为华夏植物群。本文还对北方华夏植物群亚区和南方华夏植物群亚区植物群进行了对比,并论述了这两个植物群在组成成分上的差异。     

遗传密码的高维空间对称性

对称性是由均衡比例产生的匀称美。对称性和对称破缺在自然界和生命现象中普遍存在。20种氨基酸和终止码共有64个遗传密码子,组成一个6维的编码空间。遗传密码空间以对称轴将空间分成对称的两大部分：嘌呤空间和嘧啶空间。遗传密码子的简并以对称轴为参考轴,呈平行排列。高简并度氨基酸（6,4,3,简并度）和低筒并度氨基酸（1,2简并度）的简并子空间近似呈周期性的双方错方式排列。遗传密码的简并与4种核苷酸的二进制数字编码,具有密切的关系。经过分析,可得出遗传密码的连通性λλ简并法则：“除丝氨酸的密码子分成两个与对称轴平行的,分离的子空间之外,其余氨基酸和终止密码的密码子,都通过与空间对称轴平行的λλ平面或λ边简并,组成独立的,单一的连通子空间。”并对氨基酸密码子的惯用率与编码空间的对称关系,以及数字生物学的意义进行了分析和讨论。     

霍乱弧菌O139群菌苗研究进展

本文综述了目前研制出的Ｏ１３９群口服菌苗,包括灭活菌苗,基因工程减毒活菌苗和基因工程加法菌苗;阐述了有关Ｏ１３９群菌苗的基础研究,包括Ｏ１群和Ｏ１３９群的分子遗传学关系。Ｏ１３９群感染的免疫机制和产生的保护机制。     

中国石炭纪和二叠纪植物群

本文总结和讨论了中国石炭纪和二叠纪植物群分布特征,在对植物群成分分析的基础上,认为中国早石炭世（杜内期、维宪期和纳缪尔A期）分布一个全球一致性的植物群,即拟鳞木植物群Lepidodendropsis flora。中国的晚石炭世（纳缪尔B_C期、维斯发期和斯蒂芬期）和二叠纪植物群为华夏植物群。本文还对北方华夏植物群亚区和南方华夏植物群亚区植物群进行了对比,并论述了这两个植物群在组成成分上的差异。     

新型粒子群优化算法在多序列联配中的应用

将粒子群优化算法应用于序列联配,提出了一种改进的粒子群优化算法,该算法在粒子群的进化过程中根据粒子的适应值动态地调整粒子群的惯性权重与粒子群飞行速度范围,提高了算法的收敛速度和收敛精度;针对PSO算法可能出现的早熟现象,引入重新初始化机制,增强了算法的搜索能力,实验表明该算法是有效的。     

樟树叶绿体基因组密码子偏好性分析

为分析樟树(Cinnamomum camphora)叶绿体基因组密码子偏好性使用模式,该研究利用CodonW、EMBOSS、R语言等软件和程序,对53条樟树叶绿体基因组密码子使用模式及偏好性进行了系统分析。结果表明:樟树叶绿体基因的有效密码子数(ENC)在36.82～59.30之间,表明密码子的偏好性较弱。相对同义密码子使用度(RSCU)分析发现RSCU>1的密码子有32个,其中28个以A、U结尾,表明第3位密码子偏好使用A和U碱基。中性绘图分析发现GC₃与GC₁₂的相关性不显著,回归曲线斜率为0.049,说明密码子偏好性主要受到自然选择的影响。ENC-plot分析发现大部分基因落在曲线的下方,同样表明选择是影响密码子偏好性的主要因素。该研究发现共有9个密码子(UUU、CUU、UCA、ACA、UAU、AAU、GAU、UGA、GGA)被鉴定为樟树叶绿体基因组的最优密码子。     

A Novel Constraint for Thermodynamically Designing DNA Sequences

Biotechnological and biomolecular advances have introduced novel uses for DNA such as DNA computing, storage, and encryption. For these applications, DNA sequence design requires maximal desired (and minimal undesired) hybridizations, which are the product of a single new DNA strand from 2 single DNA strands. Here, we propose a novel constraint to design DNA sequences based on thermodynamic properties. Existing constraints for DNA design are based on the Hamming distance, a constraint that does not address the thermodynamic properties of the DNA sequence. Using a unique, improved genetic algorithm, we designed DNA sequence sets which satisfy different distance constraints and employ a free energy gap based on a minimum free energy (MFE) to gauge DNA sequences based on set thermodynamic properties. When compared to the best constraints of the Hamming distance, our method yielded better thermodynamic qualities. We then used our improved genetic algorithm to obtain lower-bound DNA sequence sets. Here, we discuss the effects of novel constraint parameters on the free energy gap.     

A duplication of gcyc predates divergence within tribe Coronanthereae (Gesneriaceae): Phylogenetic analysis and evolution

Recent investigations in Gesneriaceae have indicated that the cycloidea homolog, gcyc, remains functional at the DNA level and rates of sequence divergence in this gene are not statistically different across all taxa regardless of floral symmetry. A duplication of gcyc has been detected within Coronanthereae, a tribe that has phylogenetic affinities to subfamily Gesnerioideae and includes two genera with radially symmetrical corollas. Duplication of gcyc has been detected in all Coronanthereae except Sarmienta. All paralogs appear functional at the DNA level. Likewise, there is no increased sequence divergence between the two copies, nor between species with radially symmetrical flowers to those with bilateral symmetry. The duplication of gcyc in Coronanthereae is most likely a result of polyploidy since Coronanthereae have the highest chromosome counts of all Gesneriaceae.     

Classification of Nucleotide Sequences Using Support Vector Machines

Species identification is one of the most important issues in biological studies. Due to recent increases in the amount of genomic information available and the development of DNA sequencing technologies, the applicability of using DNA sequences to identify species (commonly referred to as “DNA barcoding”) is being tested in many areas. Several methods have been suggested to identify species using DNA sequences, including similarity scores, analysis of phylogenetic and population genetic information, and detection of species-specific sequence patterns. Although these methods have demonstrated good performance under a range of circumstances, they also have limitations, as they are subject to loss of information, require intensive computation and are sensitive to model mis-specification, and can be difficult to evaluate in terms of the significance of identification. Here, we suggest a new DNA barcoding method in which support vector machine (SVM) procedures are adopted. Our new method is nonparametric and thus is expected to be robust for a wide range of evolutionary scenarios as well as multilocus analyses. Furthermore, we describe bootstrap procedures that can be used to test the significances of species identifications. We implemented a novel conversion technique for transforming sequence data to real-valued vectors, and therefore, bootstrap procedures can be easily combined with our SVM approach. In this study, we present the results of simulation studies and empirical data analyses to demonstrate the performance of our method and discuss its properties.     

鸡下丘脑cDNA文库的构建及部分克隆ESTs序列初步分析

以鸡下丘脑为实验材料,以λgt10为载体,构建了鸡下丘脑cDNA文库。结果表明,文库的滴度为3.8×10     

Analysis of Junction Sequences Resulting from Integration at Nonhomologous Loci in Neurospora Crassa

We have analyzed the junctions involved in two examples of ectopic integration of plasmids containing the am+ (glutamate dehydrogenase) gene into a strain of Neurospora crassa bearing a complete deletion of the am locus. In one transformed strain a single copy of plasmid DNA had been integrated into linkage group (LG) III DNA without the loss of chromosomal DNA. In contrast, 450 bp had been lost from plasmid sequences at the site of integration. The transforming DNA used was circular, so we postulate that the plasmid was linearized and truncated prior to its integration by end joining into a break in LG III DNA. There was no significant homology between the incoming DNA and DNA at the site of integration. The second transformed strain resulted from transformation with a linearized plasmid. It contained multiple integrated copies of plasmid DNA, one of which was recloned, together with adjacent chromosomal DNA, by plasmid rescue in Escherichia coli. Prior to integration into chromosomal DNA, the linear plasmid had been truncated by 64 bp on one end and 3.2 kbp on the other end. One end of the integrated DNA was adjacent to DNA from the right arm of LG I, while the other end was integrated into a copy of a repetitive sequence. Restriction fragment length polymerism mapping showed that integration was in a copy of the repetitive sequence that is linked to the previously unassigned telomere M11 and is distantly linked to the LG VI marker con-11. Genetic analysis revealed that a long segment of LG I containing all markers from un-1 to the right tip has been translocated to the right end of LG VI. Tetrad analysis showed that the integrated DNA was closely linked to the translocation. We conclude that the transforming DNA was truncated and joined to DNA from two different chromosomes by end joining during the formation of a quasiterminal translocation, T(IR----VIR) UK-T12. We also conclude that the previously unassigned telomere, M11, is the right end of LG VI.     

基于DTW距离的DNA序列相似性分析

在DNA序列相似性的研究中,通常采用的动态规划算法对空位罚分函数缺乏理论依据而带有主观性,从而取得不同的结果,本文提出了一种基于DTW（Dynamic Time Warping,动态时间弯曲）距离的DNA序列相似性度量方法可以解决这一问题．通过DNA序列的图形表示把DNA序列转化为时间序列,然后计算DTW距离来度量序列相似度以表征DNA序列属性,得到能够比较DNA序列相似性度量方法,并用这个方法比较分析了七种东亚钳蝎神经毒素（Buthusmartensi Karsch neurotoxin）基因序列的相似性,验证了该度量方法的有效性和准确性．     

The sequence of metK, the structural gene for S-adenosylmethionine synthetase in Escherichia coli

The DNA sequence of the Escherichia coli metK gene has been determined. Protein sequence data for purified S-adenosylmethionine synthetase have also been obtained and confirm that metK is the structural gene for S-adenosylmethionine synthetase in E. coli. The sequence of the amino-terminal 35 residues of purified S-adenosylmethionine synthetase localizes the beginning of the coding region of the DNA. The open reading frame extends 1152 bases and codes for a 384-residue protein of Mr = 41,941. The gene is transcribed clockwise on the E. coli chromosome. The DNA region 5' to the coding region was found to contain symmetrical sequences suggestive of operator structures and homologous to sequences upstream from other met genes sharing the same regulatory mechanism.