基于基因互作网络熵量化细胞分化状态

细胞动态过程的研究表明,细胞在动态过程中会发生状态变化,主要由细胞内部的基因表达情况控制.随着高通量测序技术的发展,大量的基因表达数据能够在单细胞水平上获得细胞真实的基因表达信息.然而,现有大多数研究方法需要使用除基因表达以外其他的信息,带来了额外的复杂度和不确定性.此外,普遍存在的"缺失值"事件更是影响了对细胞动态发...     

太白红杉种群邻体范围与邻体竞争强度的研究

采用逐步扩大范围的方法探讨了不同径级基株所受的邻体竞争强度 平均竞争强度和总竞争强度 与影响范围的关系 ,结果发现 : 1 邻体的平均竞争强度随影响范围的增加而降低 ,在一定的范围内下降较快 ,而超出该范围后下降的幅度变小 ,可以此为依据来确定邻体范围 ; 2 不同径级的基株 ,邻体范围有一定的差异 ; 3 邻体总的竞争强度和影响范围的关系服从对数函数关系 CI=Aln C+B .结果表明采用逐步扩大范围的方法能有效地确定邻体范围 ,提出了确定邻体范围的新方法     

Functional gene diversity of soil microbial communities from five oil-contaminated fields in China

To compare microbial functional diversity in different oil-contaminated fields and to know the effects of oil contaminant and environmental factors, soil samples were taken from typical oil-contaminated fields located in five geographic regions of China. GeoChip, a high-throughput functional gene array, was used to evaluate the microbial functional genes involved in contaminant degradation and in other major biogeochemical/metabolic processes. Our results indicated that the overall microbial community structures were distinct in each oil-contaminated field, and samples were clustered by geographic locations. The organic contaminant degradation genes were most abundant in all samples and presented a similar pattern under oil contaminant stress among the five fields. In addition, alkane and aromatic hydrocarbon degradation genes such as monooxygenase and dioxygenase were detected in high abundance in the oil-contaminated fields. Canonical correspondence analysis indicated that the microbial functional patterns were highly correlated to the local environmental variables, such as oil contaminant concentration, nitrogen and phosphorus contents, salt and pH. Finally, a total of 59% of microbial community variation from GeoChip data can be explained by oil contamination, geographic location and soil geochemical parameters. This study provided insights into the in situ microbial functional structures in oil-contaminated fields and discerned the linkages between microbial communities and environmental variables, which is important to the application of bioremediation in oil-contaminated sites.     

基于相邻木排列关系的混交度研究

混交度是反映森林群落中树种相互隔离状况的一个重要指标,目前已提出多种混交度指数.Mg考虑了对象木与最近相邻木的树种异同,Mv和Ms进一步考虑了最近相邻木(空间结构单元)树种数,但仍不能准确描述树种隔离程度.基于相邻木排列关系的混交度Mp,利用“1+4”结构的17个不同空间结构单元和天目山常绿阔叶林数据对Mg、Mv、Ms和Mp4个混交度进行了比较分析.结果表明:Mp的区分能力最强,Mv和Ms次之,Mg最差.Mp最适用于分析混交结构复杂的林分.在天目山常绿阔叶林分析中,混交度水平为中度,4个最近邻体中有2个相同种顺序排列的空间结构单元个数明显多于交错排列的个数.基于相邻木排列关系的混交度Mp能准确区分树种隔离程度,提高了混交度的区分度,可反映森林实际混交状况.     

黄山松种群邻体范围与邻体竞争强度的研究

当环境中可利用的资源低于种群最佳生长需要时,种群内个体之间就会产生竞争。竞争常发生在邻近植物之间,植物地上部分和地下部分的竞争范围是不同的。目前,有很多度量竞争强度和确定竞争范围的方法,能否对这些方法进行改进,提出更具有说服力的方法,是本研究的出发点。黄山松是常见的针叶树种,分布范围广,生存能力强,是亚热带中部中山地区代表群系的建群种,也是较高海拔地区重要的造林树种,具有较强的代表性。对黄山松的邻体竞争研究发现:(1)改进的竞争指数有更强的说服力;(2)逐步扩大范围的方法能很好地确定植株间的竞争范围;(3)邻体竞争强度随影响范围的增加而增加,在一定的范围内增加的较快,而超出该范围后增加的幅度变小,可以此为依据来确定邻体范围;(4)不同径级的基株,邻体范围有一定的差异;(5)邻体竞争强度和影响范围的关系服从对数函数关系(CI=AlnC+B)。结果表明,改进的竞争指数能很好地度量竞争强度,采用逐步扩大范围的方法能有效地确定邻体范围。     

A common neighbor based technique to detect protein complexes in PPI networks

Detection of protein complexes by analyzing and understanding PPI networks is an important task and critical to all aspects of cell biology. We present a technique called PROtein COmplex DEtection based on common neighborhood (PROCODE) that considers the inherent organization of protein complexes as well as the regions with heavy interactions in PPI networks to detect protein complexes. Initially, the core of the protein complexes is detected based on the neighborhood of PPI network. Then a merging strategy based on density is used to attach proteins and protein complexes to the core-protein complexes to form biologically meaningful structures. The predicted protein complexes of PROCODE was evaluated and analyzed using four PPI network datasets out of which three were from budding yeast and one from human. Our proposed technique is compared with some of the existing techniques using standard benchmark complexes and PROCODE was found to match very well with actual protein complexes in the benchmark data. The detected complexes were at par with existing biological evidence and knowledge.     

Reshaping of global gene expression networks and sex-biased gene expression by integration of a young gene

New genes originate frequently across diverse taxa. Given that genetic networks are typically comprised of robust, co-evolved interactions, the emergence of new genes raises an intriguing question: how do new genes interact with pre-existing genes? Here, we show that a recently originated gene rapidly evolved new gene networks and impacted sex-biased gene expression in Drosophila. This 4–6 million-year-old factor, named Zeus for its role in male fecundity, originated through retroposition of a highly conserved housekeeping gene, Caf40. Zeus acquired male reproductive organ expression patterns and phenotypes. Comparative expression profiling of mutants and closely related species revealed that Zeus has recruited a new set of downstream genes, and shaped the evolution of gene expression in germline. Comparative ChIP-chip revealed that the genomic binding profile of Zeus diverged rapidly from Caf40. These data demonstrate, for the first time, how a new gene quickly evolved novel networks governing essential biological processes at the genomic level.     

Effects of asexual reproduction on the neighborhood area of cyclical parthenogens

The habitat occupied by a subpopulation and withinwhich there is random mating is known as itsneighborhood area. Neighborhood area is dependenton dispersal rates and organisms with low rates ofdispersal are expected to have small neighborhoodareas. In the absence of evolutionary forces,neighborhood areas under sexual reproduction will beconstant in size as long as dispersal patterns do notchange. This scenario differs when reproduction is bycyclical parthenogenesis since recombination anddispersal may occur in different generations. Ingeneral, dispersal distances increase with the numberof parthenogenetic generations. We show that cyclicalparthenogenesis increases neighborhood area which,concomitantly, decreases the potential for geneticsubdivision. It is noteworthy, however, that theincrease in neighborhood area is a decreasing functionof the number of parthenogenetic generations.This mechanism may have important implications for thepopulation structure of planktonic rotifers living ina horizontally undifferentiated habitat. In suchhabitats organisms are effectively unrestricted intheir lateral movements. Because rotifers typicallyhave low dispersal rates spatial geneticdiscontinuities may develop that divide the populationinto genetically distinct subpopulations. Counteringthis tendency is the increased neighborhood areaproduced by dispersal during the parthenogeneticphase. Thus cyclical parthenogenesis in organismslike rotifers may have important and previouslyunreported effects on the population's geneticstructure.     

概率布尔型基因调节网络的分解方法研究

基于Iyla Shumlevich等提出的概率布尔型网络(PBN)模型,计算网络中任意两基因之间量化了的相互影响,给出相应的有向带权图模型。通过对模型的标准化分析,找出关键节点,以各关键节点为中心,对网络划分,通过计算子网络间交互信息,确定各子网络边界,以达到对网络的最优分解。     

Modeling DNA sequence-based cis-regulatory gene networks

Gene network analysis requires computationally based models which represent the functional architecture of regulatory interactions, and which provide directly testable predictions. The type of model that is useful is constrained by the particular features of developmentally active cis-regulatory systems. These systems function by processing diverse regulatory inputs, generating novel regulatory outputs. A computational model which explicitly accommodates this basic concept was developed earlier for the cis-regulatory system of the endo16 gene of the sea urchin. This model represents the genetically mandated logic functions that the system executes, but also shows how time-varying kinetic inputs are processed in different circumstances into particular kinetic outputs. The same basic design features can be utilized to construct models that connect the large number of cis-regulatory elements constituting developmental gene networks. The ultimate aim of the network models discussed here is to represent the regulatory relationships among the genomic control systems of the genes in the network, and to state their functional meaning. The target site sequences of the cis-regulatory elements of these genes constitute the physical basis of the network architecture. Useful models for developmental regulatory networks must represent the genetic logic by which the system operates, but must also be capable of explaining the real time dynamics of cis-regulatory response as kinetic input and output data become available. Most importantly, however, such models must display in a direct and transparent manner fundamental network design features such as intra- and intercellular feedback circuitry; the sources of parallel inputs into each cis-regulatory element; gene battery organization; and use of repressive spatial inputs in specification and boundary formation. Successful network models lead to direct tests of key architectural features by targeted cis-regulatory analysis.     

MADS-box基因家族基因重复及其功能的多样性

基因的重复(duplication)及其功能的多样性(diversification)为生物体新的形态进化提供了原材料。MADS-box基因在植物(特别是被子植物)的进化过程中发生了大规模的基因重复事件而形成一个多基因家族。MADS-box基因家族的不同成员在植物生长发育过程中起着非常重要的作用,在调控开花时间、决定花分生组织和花器官特征以及调控根、叶、胚珠及果实的发育中起着广泛的作用。探讨MADS-box基因家族的进化历史有助于深入了解基因重复及随后其功能分化的过程和机制。本文综述了MADS-box基因家族基因重复及其功能分化式样的研究进展。     

基于双聚类挖掘癌症共享的基因功能模块

基因多效性是癌症遗传机制中的普遍现象, 但罕见系统性的分析。文章提出采用双聚类挖掘基因功能模块的新思路探索癌症的共享分子机制和不同癌症间的关系。获取20种癌症的基因表达数据, 应用改良t检验和倍数法筛选出至少在两种癌症中差异表达的基因, 得到10417×20的数据矩阵; 采用双聚类方法获得22个癌症共享的基因簇; 进一步富集分析得到17个基因功能模块(Bonferroni校正后P<0.05), 主要参与有丝分裂染色单体分离的调控、细胞分化、免疫和炎症反应、胶原纤维组织等生物过程; 主要执行ATP结合和微管活动、MHCⅡ类受体活性、肽链内切酶抑制活性等分子功能; 活动区域主要在细胞骨架、染色体、MHCⅡ蛋白质复合体、中间丝蛋白、胶原纤维等。基于模块构建癌症相关网络, 显示胃癌、卵巢腺癌、宫颈鳞癌和间皮瘤等之间相关程度较高, 而两种血液系统癌症(急性髓细胞性白血病与多发性骨髓瘤)分子机制与其他癌症存在较大差异。可见癌症共享的基因功能模块与多种生物机制有关, 癌症之间相似性可能与组织起源、共同的致癌机制等有关。文章提出的基因多效性分析方法有助于解释人类复杂性疾病的共享分子机制。     

鼎湖山南亚热带常绿阔叶林不同树种存活对邻体组成的响应差异

理解群落结构和动态的主导机制是生态学研究的基本目标之一。群落内树种的存活受到其邻近树木的显著影响。为探究不同树种的存活对邻体组成的响应差异, 本研究基于鼎湖山南亚热带阔叶林20 ha森林动态监测样地中常见的90个树种的存活监测数据和功能性状数据, 建立了一系列关于邻体效应的树种存活模型。结果表明: 约58%的树种存活对邻体组成有敏感的响应, 共存树种间的功能性状差异影响着50%的树种存活动态。不同树种对邻体组成的响应差异与其耐阴性相关, 耐阴能力较弱的树种更倾向于表现出对邻体的敏感性。低比叶面积、高叶干物质含量、木材密度和最大胸径意味着较强的耐阴能力, 与光资源利用策略有关的生态位分化可能是邻域尺度上物种共存的原因。本研究为量化邻体间的相互作用和解释局域群落的物种共存提供了新的视角。     

Towards precise reconstruction of gene regulatory networks by data integration

Background: More and more high-throughput datasets are available from multiple levels of measuring gene regulations. The reverse engineering of gene regulatory networks from these data offers a valuable research paradigm to decipher regulatory mechanisms. So far, numerous methods have been developed for reconstructing gene regulatory networks. Results: In this paper, we provide a review of bioinformatics methods for inferring gene regulatory network from omics data. To achieve the precision reconstruction of gene regulatory networks, an intuitive alternative is to integrate these available resources in a rational framework. We also provide computational perspectives in the endeavors of inferring gene regulatory networks from heterogeneous data. We highlight the importance of multi-omics data integration with prior knowledge in gene regulatory network inferences. Conclusions: We provide computational perspectives of inferring gene regulatory networks from multiple omics data and present theoretical analyses of existing challenges and possible solutions. We emphasize on prior knowledge and data integration in network inferences owing to their abilities of identifying regulatory causality.     

Structure versus time in the evolutionary diversification of avian carotenoid metabolic networks

Historical associations of genes and proteins are thought to delineate pathways available to subsequent evolution; however, the effects of past functional involvements on contemporary evolution are rarely quantified. Here, we examined the extent to which the structure of a carotenoid enzymatic network persists in avian evolution. Specifically, we tested whether the evolution of carotenoid networks was most concordant with phylogenetically structured expansion from core reactions of common ancestors or with subsampling of biochemical pathway modules from an ancestral network. We compared structural and historical associations in 467 carotenoid networks of extant and ancestral species and uncovered the overwhelming effect of pre‐existing metabolic network structure on carotenoid diversification over the last 50 million years of avian evolution. Over evolutionary time, birds repeatedly subsampled and recombined conserved biochemical modules, which likely maintained the overall structure of the carotenoid metabolic network during avian evolution. These findings explain the recurrent convergence of evolutionary distant species in carotenoid metabolism and weak phylogenetic signal in avian carotenoid evolution. Remarkable retention of an ancient metabolic structure throughout extensive and prolonged ecological diversification in avian carotenoid metabolism illustrates a fundamental requirement of organismal evolution – historical continuity of a deterministic network that links past and present functional associations of its components.     

基因传感器在环境微生物功能基因检测中的应用

分子生物学的快速发展和人们对核酸的深入研究,给基因传感器的研制和发展奠定了坚实的基础.基因传感器是分子生物学与微电子学、电化学、光学等相结合的产物,将在生命科学与信息科学之间架起一座桥梁,成为DNA信息分析检测最有效的手段之一.在近年研究文献的基础上,评述了基因传感器的工作原理、分类及近年来国内外利用其进行环境微生物功能基因检测等方面的研究现状,并提出堆肥微生物功能基因检测将是基因传感器的一个重要发展方向.