PNN-curve: a new 2D graphical representation of DNA sequences and its application

We introduce a novel 2D graphical representation of DNA sequences based on the pairs of the neighboring nucleotides (PNNs). Then we get the PNNs' distributions and obtain a y-M. The construction of the PNN-curve has some important advantages (1) It avoids loss of information and the PNN-curve standing for DNA sequences does not overlap or intersect with itself. (2) The novel 2D representation is more sensitive. The utility of this method can be illustrated by the examination of similarities/dissimilarities among the coding sequences of the first exon of beta-globin gene of eleven different species in Table 2.     

2-D graphical representation of protein sequences and its application to coronavirus phylogeny

Based on a five-letter model of the 20 amino acids, we propose a new 2-D graphical representation of protein sequence. Then we transform the 2-D graphical representation into a numerical characterization that will facilitate quantitative comparisons of protein sequences. As an application, we construct the phylogenetic tree of 56 coronavirus spike proteins. The resulting tree agrees well with the established taxonomic groups.     

集合种群理论在生态恢复中的应用

环境问题的改善是生态与环境学家所面临的挑战之一 ,其核心是生态系统的稳定性和平衡性遭到极大的破坏 ,最明显的表现是生境破碎和栖息地丧失。本文探讨了集合种群理论的形成与成因 ,概述了该理论发展的最新成果及应用前景。在集合种群理论应用于生态恢复实践的论述中 ,阐述了一些原则性问题 ,包括集合种群平衡观、最小可存活集合种群、最适斑块密度以及高质量生境斑块等 ,以求在人们设计物种保护和恢复对策时 ,有一定的指导价值。     

蛋白质序列的一种新的三维图形表示及其应用

基于氨基酸的五字母模型,给出蛋白质序列的一种新的三维图形表示,然后构造一个12维向量来刻画蛋白质序列,这个向量的分量是与12个图形相对应的D／D矩阵的正规化的ALE-指标。最后基于s结构蛋白对冠状病毒进行系统发生分析来阐明该方法的有用性。     

A new method of quantitative affinity chromatography and its application to the study of myosin.

A new method of quantifying the interactions between two or three components of an interacting system, one of which is insoluble, is described. The method differs from those previously applied to affinity chromatography systems in that it does not require that elution volumes be measured, but is instead dependent on measurements of the quantity of affinity-bound material. Theoretical expressions are derived for systems in which the acceptor is immobilized. Examples presented to illustrate the validity of the theory are of the latter type and are from studies on the myosin-adenosine nucleotide-PPi system. With Sepharose-myosin columns (myosin covalently coupled to CNBr-activated Sepharose) a dissociation constant of 1.8 muM for ATP4- was found. Data were also obtained under conditions that closely approximate to those found in vivo, i.e. on columns packed with a slurry of Sephadex G-50 and precipitated myosin filaments formed at low ionic strength. The binding of MgATP2-, MgADP-, ATP4- and MgPPi2- to "filamentous" myosin in both two- (myosin and nucleotide) and three- (myosin, nucleotide and PPi) component systems at different temperatures was studied and the dissociation constants obtained agreed well with previously published values. Except for the binding of ATP4- to filamentous myosin at 4 degrees when 85% of the protein was interacting with the nucleotide, much lower values for the number of available sites occupied by the nucleotides were as a routine found in this system. Although this apparent discrepancy is difficult to explain, it is not an anomaly of the theoretical approach and may reflect the present state of understanding of the myosin system.     

On the application of the information concept to learning theory

A learning curve derived by H. D. Landahl (Bull. Math. Biophysics,3, 71–77, 1941) from postulated neurological structures is shown to be derivable from simplified assumptions by introducing the information measure of the uncertainty of response. The possible significance of this approach to learning theory is discussed.     

A new method of vesicle formation by salting-out and its application to the reconstitution of sarcoplasmic reticulum

This paper describes a new method of forming membrane vesicles. It was found that the addition of salt such as KCl into a solution containing lipid (asolectin) and a non-ionic surfactant, Triton X-114, led to the formation of closed membrane vesicles. The vesicles were separated from Triton X-114 by hydrophobic interaction chromatography. Electron microscopy revealed that the mean diameter of the vesicles was 110 nm +/- 69 nm (S.D.). Measurement of osmotic volume change showed that the permeability of the vesicle was very low to salts, sugar (glucose) and amphoteric ion (glycine), but very high to glycerol, ethylene glycol and water. Vesicle formation by this 'salting-out' method is very useful for reconstitution of transport systems in biomembranes because of its advantages: completion within a short time; high yield; and the possibility of utilizing samples in non-ionic surfactant solution. When we applied the method to the reconstitution of sarcoplasmic reticulum, Ca2+-ATPase was incorporated into the reconstituted vesicles and was enzymatically active in the membrane.     

2-D graphical representation for characteristic sequences of DNA and its application

DNA sequencing has resulted in an abundance of data on DNA sequences for various species. Hence, the characterization and comparison of sequences become more important but still difficult tasks. In this paper, we first give a 2-D ladderlike graphical representation for the characteristic sequences of a DNA sequence, and then construct a 3-component vector, in which the normalized ALE-indices extracted from such three 2-D graphs via D/D matrices are individual components, to characterize the DNA sequence. The examination of similarities/dissimilarities among sequences of the beta-globin genes of different species illustrates the utility of the approach.     

A new method for DNA surface-property display and its application to E. coli promoter sequences

A personal computer program to visualize and compare the property of double-stranded DNA surface has been developed. Comparison of the surface property between Watson-Crick base-pairs in B-form DNA has elucidated that the base-pair replacement between a "degenerated base-pairs" conserves the pattern of potential hydrogen-bonding sites in both major and minor grooves. The idea of the "degenerated base-pairs" was applied for the problem of the base-sequence variation from the consensus sequence in the -35 region of E. coli promoter. The sequence variation is found to have tendency to occur among the degenerated base-pairs.     

分形理论及其在土壤空间变异研究中的应用

土壤具有不同程度的空间变异性,土壤空间变异研究对于土壤管理有重要意义.本文简要综述了分形理论及其在土壤空间变异研究中的应用,重点讨论了利用矩方法计算土壤属性分形维,多重分形分析土壤空间变异性及基于多重分形谱参数的土壤属性尺度转换.早期研究验证了分形理论在分析土壤空间变异中的有效性和应用潜力,国内外近期研究则报道了利用分形及多重分形理论分析土壤空间变异的最新进展.分形理论可以成为量化土壤属性空间变异性及尺度转换的重要工具.     

A 2D graphical representation of the sequences of DNA based on triplets and its application

In this paper, we first present a new concept of ‘weight’ for 64 triplets and define a different weight for each kind of triplet. Then, we give a novel 2D graphical representation for DNA sequences, which can transform a DNA sequence into a plot set to facilitate quantitative comparisons of DNA sequences. Thereafter, associating with a newly designed measure of similarity, we introduce a novel approach to make similarities/dissimilarities analysis of DNA sequences. Finally, the applications in similarities/dissimilarities analysis of the complete coding sequences of β-globin genes of 11 species illustrate the utilities of our newly proposed method.