LZ complexity distance of DNA sequences and its application in phylogenetic tree reconstruction

DNA sequences can be treated as finite-length symbol strings over a four-letter alphabet （A, C, T, G）. As a universal and computable complexity measure, LZ complexity is valid to describe the complexity of DNA sequences. In this study, a concept of conditional LZ complexity between two sequences is proposed according to the principle of LZ complexity measure. An LZ complexity distance metric between two nonnull sequences is defined by utilizing conditional LZ complexity. Based on LZ complexity distance, a phylogenetic tree of 26 species of placental mammals （Eutheria） with three outgroup species was reconstructed from their complete mitochondrial genomes. On the debate that which two of the three main groups of placental mammals, namely Primates, Ferungulates, and Rodents, are more closely related, the phylogenetic tree reconstructed based on LZ complexity distance supports the suggestion that Primates and Ferungulates are more closely related.     

一种用于蛋白质相似性分析的新的相对距离

本文论述了一种新的相对距离,用于分析不同蛋白质序列的相似性分析和构造进化树．此种距离基于Lempel-Zip复杂度,不需要进行序列比对和复杂性算法．为了说明这种距离的合理性,本文对8个物种进行了相似性分析并构造了其进化树．     

Comparison of protein secondary structures based on backbone dihedral angles

In this article, we propose a relatively similar measure to compare protein secondary structures. We first transform a protein secondary structure into a special sequence representation (angle sequence) based on a partition of the backbone φ,ψ-space. Then, pairwise sequence distance is evaluated on the basis of a symbolic sequence complexity. To illustrate our approach, we construct the similarity tree of 24 proteins from PDB.     

Phylogenetic analysis of DNA sequences based on the generalized pseudo-amino acid composition

The main work of this paper is to propose a new theory and method, which is based on the idea of the pseudo-amino acid composition, for phylogenetic analysis of DNA primary sequences. In our method, we revise the part of the occurrence frequency of 20 amino acids in the method of the pseudo-amino acid composition by replacing the frequency of 16 dinucleotides. And we select eight LZ complexity factors of eight (0,1) sequences of a DNA primary sequence as PseAA components. Finally, we characterize a DNA sequence with a 24-dimensional vector. We reconstruct the phylogenetic trees of two datasets. The results show that our method is efficient and significant.     

Protein-based phylogenetic analysis by using hydropathy profile of amino acids

So far, various approaches for phylogenetic analysis have been developed. Almost all of them put stress on analyzing nucleic acid sequences or protein primary structures. In this paper, we take the physicochemical properties of amino acids into account and introduce the hydropathy profile of amino acids into phylogenetic analysis. We find that this introduction is effectual and our method may be used to complement phylogenetic analysis.     

Evolution of structure,order and complexity in biological systems: Part III of a general theory

In this, Part III of a general theory, the large-scale features of evolution of structure, order, and complexity are considered as characteristic features of the biological state of matter. This starts with a rigorous formal definition of structure, classes of structural order, complexity, measures of complexity, and how these arise through evolution by a cumulative process of storing information in memory systems. Three such memory systems have evolved: the genetic memory, the immune memory, and the memories of the nervous system. The evolution, characteristic parameters and the limitations of these memory systems are explored. From these considerations emerge the large-scale features of the evolutionary pathways of biological structure, function, and complexity.     

Measurable notions of complexity and their relationship to biological complexity

Complexity is often invoked as a motivation for a systems approach to biology. We review three measurable notions of complexity from the areas of computation and data analysis. These measures have each led to mathematical theory and to further insight on the complexity of objects, demonstrating the benefits of having a well-defined measure of complexity. Each measure is applicable in the study of particular biological systems; however, none is satisfactory to serve as a universal measure of biological complexity. The study of biological systems will likely require numerous measures of complexity, each appropriate for analysis in specific settings.     

基于替代数据思想的复杂度归一化方法及其在心电信号分析中的应用

基于替代数据(Surrogate)思想的复杂度归一化方法,克服了一般复杂度对信号采样长度与采样频率的敏感性。文章对在生物医学信号复杂度分析中最有潜在应用价值的近似熵和C0复杂度进行了归一化。应用该方法可以有效地反映人体心脏某些病理状态之间的差别。同时,通过比较各种复杂度指标发现,C0复杂度和近似熵对采样长度的敏感性最弱,适用于短数据量的信号分析。     

Reducing the computational complexity of protein folding via fragment folding and assembly

Understanding, and ultimately predicting, how a 1-D protein chain reaches its native 3-D fold has been one of the most challenging problems during the last few decades. Data increasingly indicate that protein folding is a hierarchical process. Hence, the question arises as to whether we can use the hierarchical concept to reduce the practically intractable computational times. For such a scheme to work, the first step is to cut the protein sequence into fragments that form local minima on the polypeptide chain. The conformations of such fragments in solution are likely to be similar to those when the fragments are embedded in the native fold, although alternate conformations may be favored during the mutual stabilization in the combinatorial assembly process. Two elements are needed for such cutting: (1) a library of (clustered) fragments derived from known protein structures and (2) an assignment algorithm that selects optimal combinations to "cover" the protein sequence. The next two steps in hierarchical folding schemes, not addressed here, are the combinatorial assembly of the fragments and finally, optimization of the obtained conformations. Here, we address the first step in a hierarchical protein-folding scheme. The input is a target protein sequence and a library of fragments created by clustering building blocks that were generated by cutting all protein structures. The output is a set of cutout fragments. We briefly outline a graph theoretic algorithm that automatically assigns building blocks to the target sequence, and we describe a sample of the results we have obtained.     

The structural complexity of DNA templates—Implications on cellular complexity

A previously formulated procedure for the quantitative evaluation of the complexities of molecules and biostructures is applied to assess the complexities of selected genomic DNA sequences. These include: (1) Several E. coli genes, including lacI, as examples of DNA sequences which are nearly as complex as possible (relative complexity=∼1). This is verified by the Lempel-Ziv (LZ) complexity analysis. (2) The telomere of a yeast chromosome, which has a considerable number of regular features that reduce complexity; the telomere shows indeed a lower structural complexity value. (3) A segment of human DNA, gene p53, which has a certain number of regular features such as 29 interspersed alu elements; these features cause a certain reduction in the complexity of the p53 gene, but do not invalidate the (previous) overall conclusion that template complexity is very high. The close to maximal complexity of the transcribed regions of p53 is validated by the LZ compression analysis. The general conclusion is that DNA base sequence composition is the dominant factor determining cellular complexity. The high complexity of DNA arrived at is a direct consequence of the template character of DNA and reflects the role of genomic DNA as a principal regulating element of a cell. It will be a challenge to find systems of lower complexity with the ability to respond to challenges from the environment to the extent that DNA templated systems do. Cellular complexity and template directed activity are thus highly intertwined properties, at the heart of many developmental, behavioral and evolutionary processes.     

Herbicide effects on planktonic systems of different complexity

Bioassays of different complexity were compared with respect to their capability to predict the environmental impact of the herbicide atrazine in aquatic systems. Acute toxicity tests with Daphnia did not yield meaningful results. Sublethal tests with Daphnia (feeding inhibition, reduction of growth and reproduction) were more sensitive, but effective concentrations of atrazine were still rather high (2 mg/L). A relatively complicated artificial food chain system that incorporated direct and indirect effects on Daphnia yielded significant reduction of daphnid population growth at 0.1 mg/L. Enclosure experiments with natural communities were by far the most sensitive tools. Community responses could be measured at concentrations as low as 1 µg/L and 0.1 µg atrazine/L. At the lowest concentration, however, communities recovered after three weeks. We conclude that in complex systems indirect effects can be more important than direct effects, so that, contrary to the conditions in simple tests, non-target organisms may be the better indicators of herbicide stress to natural communities.     

Measuring complexity of environmental gradients

Analysis of vegetation response to environmental gradients should take into account the spatial complexity of the environmental property itself. Whether a gradient exists on the landscape or in abstract space, the spatial variability of environmental factors often invalidates the implicit assumption that the gradient is continuous. There is a need to know how variable the spatial pattern of a gradient is and how much deviation from the general trend may be expected. Geostatistics is shown to provide a useful method for analyzing spatial variability. If the assumptions for its use can be met, the fractal dimension can be used in combination with geostatistics to provide a quantitative index of gradient complexity. An example is given, showing that an hypothesized gradient of shoreline erosion disturbance along Delaware Bay either does not exist or is so complicated by short-range, local factors that any longer-range gradient is relatively unimportant. Such complex environmental patterns are thought to be common in nature. Geostatistics, fractals, or similar spatial methods can be utilized to detect and measure such complexity.This work was conducted while the author was a research assistant at the Center for Coastal and Environmental Studies, Rutgers University, New Brunswick, N.J. The support of the Center is gratefully acknowledged.     

MicroRNA对多细胞动物复杂性进化的影响

MicroRNA(miRNA)是一种长度约为22个碱基的非编码单链小分子RNA。作为一类重要的转录后基因表达调控因子,miRNA参与了广泛的生物学过程,如发育时程调控、细胞分化、凋亡、肿瘤以及病毒抵抗等。然而,除了在个体发生过程中的重要功能外,越来越多的研究表明,miRNA在系统发生中也扮演着关键的角色。基因表达模式的不同被广泛地认为是物种内和物种间表型差异的根源,动物物种间miRNA的保守性和多样性研究提示miRNA对物种间表型差异以及动物进化起着重要的作用。文章介绍了miRNA产生过程和作用机制,重点探讨了miRNA在动物进化过程中的作用,从miRNA的进化速度、miRNA表达的时空特异性、miRNA作用靶位点变异以及miRNA基因的扩增与丢失4个方面论述miRNA介导的基因调控网络对多细胞动物发育复杂性进化的影响,推测miRNA在多细胞动物进化过程中驱动了复杂性的增加。     

基于市政综合监管信息的城市生态系统复杂性分析

随着我国城市化进程的不断加快,城市结构日趋复杂,人类活动对生态系统过程和功能的干扰愈发严重,使城市生态系统更加的复杂.城市生态系统是城市居民与其环境相互作用而形成的统一整体,也是人类对自然环境的适应、加工、改造而建设起来的特殊的人工生态系统.城市生态系统的复杂性不但直接体现在其自然、经济和社会三个子系统的结构和过程中,也通过许多市政综合管理要素和对象呈现出来.通过对北京市东城区2009年6月至11月的城市综合监管信息平台立案数据的归类分析,结合东城区地形图和专题图矢量数据,从公用设施类、道路交通类、市容环境类、园林绿化类、房屋土地类、其他设施等因素,分析了东城区城市生态系统及其人类活动的相互关系.把从市政管理信息中提取出的城市管理部件问题与城市生态系统的水、土、气、噪声、视觉污染和固体废弃物等关键要素进行关联分析.通过挖掘东城区生态系统在组成和空间分布上的复杂性和规律性,阐明东城区城市生态系统与人类活动时空关系的复杂性,以期为城市生态系统管理提供借鉴.     

A weighted measure for the similarity analysis of DNA sequences

Here we propose a weighted measure for the similarity analysis of DNA sequences. It is based on LZ complexity and (0,1) characteristic sequences of DNA sequences. This weighted measure enables biologists to extract similarity information from biological sequences according to their requirements. For example, by this weighted measure, one can obtain either the full similarity information or a similarity analysis from a given biological aspect. Moreover, the length of DNA sequence is not problematic. The application of the weighted measure to the similarity analysis of β-globin genes from nine species shows its flexibility.     

Phenotypic noise and the cost of complexity

Experimental studies demonstrate the existence of phenotypic diversity despite constant genotype and environment. Theoretical models based on a single phenotypic character predict that during an adaptation event, phenotypic noise should be positively selected far from the fitness optimum because it increases the fitness of the genotype, and then be selected against when the population reaches the optimum. It is suggested that because of this fitness gain, phenotypic noise should promote adaptive evolution. However, it is unclear how the selective advantage of phenotypic noise is linked to the rate of evolution, and whether any advantage would hold for more realistic, multidimensional phenotypes. Indeed, complex organisms suffer a cost of complexity, where beneficial mutations become rarer as the number of phenotypic characters increases. Using a quantitative genetics approach, we first show that for a one-dimensional phenotype, phenotypic noise promotes adaptive evolution on plateaus of positive fitness, independently from the direct selective advantage on fitness. Second, we show that for multidimensional phenotypes, phenotypic noise evolves to a low-dimensional configuration, with elevated noise in the direction of the fitness optimum. Such a dimensionality reduction of the phenotypic noise promotes adaptive evolution and numerical simulations show that it reduces the cost of complexity.