FluxExplorer： A general platform for modeling and analyses of metabolic networks based on stoichiometry

An increasing number of genomic and biochemical data make it possible to reconstruct biochemical net-works, especially metabolic networks, of an organelle or even a whole cell. Some methods for metabolism modeling and analyses in this field have been deve…     

Bow-tie topological features of metabolic networks and the functional significance

Exploring the structural topology of genome-based large-scale metabolic network is essential for in- vestigating possible relations between structure and functionality.Visualization would be helpful for obtaining immediate information about structural organization.In this work,metabolic networks of 75 organisms were investigated from a topological point of view.A spread bow-tie model was proposed to give a clear visualization of the bow-tie structure for metabolic networks.The revealed topological pattern helps to design more efficient algorithm specifically for metabolic networks.This coarse- grained graph also visualizes the vulnerable connections in the network,and thus could have important implication for disease studies and drug target identifications.In addition,analysis on the reciprocal links and main cores in the GSC part of bow-tie also reveals that the bow-tie structure of metabolic networks has its own intrinsic and significant features which are significantly different from those of random networks.     

Global organization of metabolic fluxes in the bacterium Escherichia coli

Cellular metabolism, the integrated interconversion of thousands of metabolic substrates through enzyme-catalysed biochemical reactions, is the most investigated complex intracellular web of molecular interactions. Although the topological organization of individual reactions into metabolic networks is well understood, the principles that govern their global functional use under different growth conditions raise many unanswered questions. By implementing a flux balance analysis of the metabolism of Escherichia coli strain MG1655, here we show that network use is highly uneven. Whereas most metabolic reactions have low fluxes, the overall activity of the metabolism is dominated by several reactions with very high fluxes. E. coli responds to changes in growth conditions by reorganizing the rates of selected fluxes predominantly within this high-flux backbone. This behaviour probably represents a universal feature of metabolic activity in all cells, with potential implications for metabolic engineering.     

Relationship between topology and functions in metabolic network evolution

What is the relationship between the topological connections among enzymes and their functions during metabolic network evolution? Does this relationship show similarity among closely related organisms? Here we investigated the relationship between enzyme connectivity and functions in metabolic networks of chloroplast and its endosymbiotic ancestor, cyanobacteria (Synechococcus sp. WH8102). Also several other species, including E. coli, Arabidopsis thaliana and Cyanidioschyzon merolae, were used for the comparison. We found that the average connectivity among different functional pathways and enzyme classifications (EC) was different in all the species examined. However, the average connectivity of enzymes in the same functional classification was quite similar between chloroplast and one representative of cyanobacteria, syw. In addition, the enzymes in the highly conserved modules between chloroplast and syw, such as amino acid metabolism, were highly connected compared with other modules. We also discovered that the isozymes of chloroplast and syw often had higher connectivity, corresponded to primary metabolism and also existed in conserved module. In conclusion, despite the drastic re-organization of metabolism in chloroplast during endosymbiosis, the relationship between network topology and functions is very similar between chloroplast and its precursor cyanobacteria, which demonstrates that the relationship may be used as an indicator of the closeness in evolution.     

特种设备安全事故时间序列拓扑网络特征研究

 为揭示特种设备安全事故时间序列的非线性动力特征,以2005—2020年中国不同类型特种设备安全事故时间序列为对象,采用可视图法将特种设备安全事故时间序列转化为拓扑网络图,生成拓扑网络结构模型;利用拓扑网络理论分析节点度、网络密度、加权聚类系数、幂律指数、介数中心性等拓扑网络特征参数,挖掘特种设备事故发生的时间序列规律。结果表明：各类特种设备安全事故时间序列的拓扑网络具有小世界特性和无标度特性;拓扑网络的聚类系数均较大,社团结构明显;介数中心性越大的节点,对应年份发生事故概率越大。采用的拓扑网络分析方法能更简洁、直观地展示特种设备安全事故时间序列的拓扑网络结构,更全面地表征特种设备安全事故时间序列的非线性动力特征,可为特种设备安全事故预测提供理论基础。     

Expanded flux variability analysis on metabolic network of Escherichia coli

Flux balance analysis, based on the mass conservation law in a cellular organism, has been extensively employed to study the interplay between structures and functions of cellular metabolic networks. Consequently, the phenotypes of the metabolism can be well elucidated. In this paper, we introduce the Expanded Flux Variability Analysis （EFVA） to characterize the intrinsic nature of metabolic reactions, such as flexibility, modularity and essentiality, by exploring the trend of the range, the maximum and the minimum flux of reactions. We took the metabolic network of Escherichia coli as an example and analyzed the variability of reaction fluxes under different growth rate constraints. The average variability of all reactions decreases dramatically when the growth rate increases. Consider the noise effect on the metabolic system, we thus argue that the microorganism may practically grow under a suboptimal state. Besides, under the EFVA framework, the reactions are easily to be grouped into catabolic and anabolic groups. And the anabolic groups can be further assigned to specific biomass constitute. We also discovered the growth rate dependent essentiality of reactions.     

网络失效条件下的北京市城市道路交通网络统计特征分析

为获知城市道路交通网络的结构和网络特性,根据实际的拓扑和交通流数据,采用原始法进行建模,将路口抽象为节点,将路段抽象为网络的连边,构建城市道路交通网络模型。通过MATLAB和pajek计算,分析了道路抽象、基础设施和动态交通3种网络的统计特征。对基础设施和动态交通网络的强度分布的分析,证实了北京市城市道路网络中的这两种网络均为无标度网络;通过计算基础设施网络的节点强度和介数等特征指标,获知了北京市城市道路的重要路口和路段。最后,仿真分析了3种网络在不同网络失效条件下的重要统计特征,结果表明北京市城市道路基础设施和动态交通网络既具有鲁棒性又具有脆弱性。     

Expanded flux variability analysis on metabolic network of Escherichia coli

Flux balance analysis, based on the mass conservation law in a cellular organism, has been extensively employed to study the interplay between structures and functions of cellular metabolic networks. Consequently, the phenotypes of the metabolism can be well elucidated. In this paper, we introduce the Expanded Flux Variability Analysis (EFVA) to characterize the intrinsic nature of metabolic reactions, such as flexibility, modularity and essentiality, by exploring the trend of the range, the maximum and the...     

基于小波变换的代谢网络比较方法

针对集合论的全网络比较方法仅考虑节点本身的特性这一缺陷,提出了一种新的代谢网络比较方法,能同时考虑到节点在网络拓扑结构属性方面的差异.该方法综合了7种代谢网络拓扑中心性,应用主成分分析方法选取主成分,设计了主成分分量的序列化方法,运用小波变换来研究代谢网络结构特征曲线,建立模糊函数比较不同物种的代谢网络.该方法能定量地...     

Network Visualization in Cell Biology

Many of the processes known to take place in biological cells are analyzed in the form of different types of network.The complexity of these networks increases along with our knowledge of these processes,making their analysis more difficult.Network visualization is a powerful analysis method that will have to be developed further to deal with this complexity.This survey provides a brief overview of network visualization in general,followed by an in-depth discussion of its application to three network types specific to cell biology,namely gene regulatory,protein interaction,and metabolic networks.Finally,we discuss the difficulty of visually integrating these network types and trying to compare networks of cells that belong to different organisms.     

拓扑结构对网络承载能力的影响

 通过建立3 种典型的复杂网络模型及对应的输运模型,数值计算并仿真试验拓扑结构指标和网络承载能力的变化.结果显示:3 种网络承载能力的数值计算结果和仿真试验结果基本吻合;核心节点的存在使得无标度网络的节点最大介数值所占比重高于其他网络,导致网络的承载能力最小;随机网络的节点最大介数值所占比重低于其他网络,导致承载能力最大;随着平均度的增大,各类型网络承载能力增加明显,但各种拓扑结构指标对承载能力提升的贡献不同.     

溶氧控制对黄色短杆菌YILW合成L-异亮氨酸的影响

对黄色短杆菌YILW合成L-异亮氨酸的发酵溶氧条件进行了探索,构建了该菌合成上L-异亮氨酸的代谢网络和代谢流平衡模型.在30 L发酵罐中考察了不同溶氧浓度下L-异亮氨酸发酵过程.研究结果表明:高溶氧浓度有利于菌体生长,15%溶氧浓度下产酸速率高且维持的时间长,有利于L-异亮氨酸的积累.为此提出了分段控氧模式:在菌体生长...     

电话社会网络结构的实证分析

根据城市中的电话通话记录建立了一个大型的社会网络,研究了这个网络的有关结构特性.网络呈现了与相关社会网络相似的特性,如度分布的幂律特性、小世界效应、非平凡聚集或网络传递的特点等,同时该网络也表现出与其他社会网络不同的特性,如度的异向匹配.通过给边赋予权重,分析了网络在加权情况下的一些静态结构性质,其中,包括点强度分布、强度相关性及群聚系数等.     

探讨无标度网络(图)的平衡集

无标度网络的无标度性导致其各顶点之间的连接状况(度数)具有严重的不均匀分布性,无法给出无标度网络的具体结构,不能直接观察信息传播的具体路径。基于利用生成树来研究无标度网络(图)的拓扑结构思想,尝试寻找与时间和次要节点无关的无标度网络(图)的普适性结构,研究与生成树密切相关的平衡集,给出一个寻找具有较多叶子生成树的算法。     

班轮航运网络拓扑特性

为获得班轮航运网络的结构特点,对现实航线数据进行计算机仿真,并利用复杂网络理论对网络的拓扑特性进行统计与分析.结果表明,班轮航运网络有一定的小世界特性,具有较短的平均路径长度和较大的聚类系数;其度分布服从幂律分布且具有典型的无标度网络特性;班轮航运网络具有富人俱乐部特性;其同配性系数为0.0574,未体现出明显的同配性.     

Recognition algorithm of seabed pipeline defect inspection based on dynamic WBF neural networks

This paper describes a magnetic flux leak (MFL) model of pipeline defect inspection, and presents a recognition algorithm based on dynmnic wavelet basis function (WBF) neural network. The dynamic network utilizes multiscale and multireselution orthogonal wavelet, through signals backwards propagation:,has more significant advantages than BP or other neural networks used in MFL inspection. It also can control the accuracy of the predicted defect profiles, high-speed convergence possessing and well approaching feature. The perfonnance applying the algorithm based on the network to predict defect profile from experimental MFL signals is presented.     

高速铁路网络复杂特性及其传播动力学研究

结合高速铁路网络的拓扑结构分析,建立了基于传播动力学理论的模型,研究突发事件在网络上的传播扩散规律及其传播过程.运用复杂网络理论分别构建了我国高速铁路物理网络和运输网络两个网络模型,并计算复杂网络条件下的相关统计特性指标,从而判断高速铁路网络的类别和性质;同时基于高铁网络性质,建立了突发事件下列车晚点在网络上的传播动力学模型,分析不同参数取值情况下的晚点传播扩散过程,并提出控制突发事件下列车晚点在网络中传播蔓延的措施和策略.     

基于复杂网络的武汉市公交网络特性研究

基于复杂网络的思想,以Gephi软件为分析工具,对武汉市公共汽车交通系统建立了邻近站点、公交线路和公交换乘3种复杂网络,获得了这3种网络的拓扑结构和几个静态几何量参数,并分析了这些网络的拓扑结构特性。结果显示,武汉公交基本可以满足当前需求,但是仍存在分布不均、乘客候车时间过长、个别站点不能通过换乘到达等问题。针对此类问题提出了优化建议。     

丙酮酸铁氧化还原蛋白酶对蓝藻光合生长速率影响的仿真分析

光合生物通过光合作用,可将光能转化为储存在生物体内部的生物质能,生物质能的生成速率受光合生长速率的影响.研究影响光合生长速率的因素,有利于提高生物质能的生成速率.蓝藻是最早进行光合作用和释氧的原核生物,具有遗传背景简单、固碳效率高等特点.丙酮酸铁氧化还原蛋白酶(PFOR)是丙酮酸固碳代谢的关键酶,在丙酮酸异化过程中起着重要作用.首先根据蓝藻的代谢网络,模拟敲除其中的酶PFOR,并利用通量平衡分析、通量可变性分析和多目标优化方法研究基因敲除后的代谢网络.通过研究分析,推测出酶PFOR对蓝藻光合生长速率的影响.