共查询到20条相似文献，搜索用时 31 毫秒
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Strohman R 《Science (New York, N.Y.)》2002,296(5568):701-703
Human disease phenotypes are controlled not only by genes but by lawful self-organizing networks that display system-wide dynamics. These networks range from metabolic pathways to signaling pathways that regulate hormone action. When perturbed, networks alter their output of matter and energy which, depending on the environmental context, can produce either a pathological or a normal phenotype. Study of the dynamics of these networks by approaches such as metabolic control analysis may provide new insights into the pathogenesis and treatment of complex diseases. 相似文献
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【背景】 长链非编码RNA（long non-coding RNA,lncRNA）是一类长度>200 nt且不具有编码能力的转录本,能够在真核生物的转录水平和转录后水平通过顺式（cis）、反式（trans）或竞争性内源RNA（competing endogenous RNA,ceRNA）机制调控基因的表达,已被证明在生物体的生长和发育等生物学过程中发挥重要的调控作用。【目的】 结合测序得到的东方蜜蜂微孢子虫（Nosema ceranae）纯化孢子的small RNA（sRNA）组学数据和前期获得的lncRNA组学数据对lncRNA的调控方式进行深入细致的分析和探讨,揭示lncRNA在东方蜜蜂微孢子虫孢子中的潜在功能。【方法】 利用small RNA-seq（sRNA-seq）技术对东方蜜蜂微孢子虫纯化孢子进行测序,通过相关的生物信息学软件对测序数据进行质控。根据lncRNA与mRNA的位置关系预测lncRNA的上下游基因;使用Blast软件比对GO和KEGG数据库,对上下游基因进行功能和代谢通路注释;利用Target Finder软件预测lncRNA-miRNA及lncRNA-miRNA-mRNA调控网络,进而通过Cytoscape v3.7.2软件对调控网络进行可视化;利用RT-PCR对调控网络中的部分lncRNA、miRNA和mRNA的表达进行验证。【结果】 东方蜜蜂微孢子虫纯化孢子样品的sRNA-seq分别得到16 597 883、15 451 791和12 248 316条raw reads,经质控分别得到15 608 370、14 249 255和11 440 684条clean reads,各样品的Q30≥98.58%。共预测出lncRNA的上下游基因310个,它们可注释到代谢进程、细胞进程、催化活性、结合和细胞等相关的35个功能条目;此外还可注释到56条代谢通路,涉及嘌呤代谢、碳代谢和丙酮酸代谢等物质代谢通路,以及甲烷代谢、氧化磷酸化和糖酵解/糖异生等能量代谢通路。上述结果表明相应的lncRNA可能通过cis作用调节上下游基因的表达,从而参与调控东方蜜蜂微孢子虫孢子中的物质和能量代谢以及细胞生命活动。进一步构建lncRNA-miRNA调控网络,分析结果显示MSTRG.3636.1、MSTRG.4498.1和MSTRG.4883.1可靶向结合4个miRNA（nce-miR-7729、nce-miR-7502、nce-miR-8639和nce-miR-8565）,说明此3个lncRNA可作为ceRNA在东方蜜蜂微孢子虫孢子中发挥潜在作用。LncRNA-miRNA-mRNA调控网络分析结果显示,三者之间形成较为复杂的调控网络关系,miRNA处于调控网络的中心并联系lncRNA和mRNA,nce-miR-7502和nce-miR-8639结合的mRNA最多,达到28个;与MSTRG.3636.1、MSTRG.4498.1和MSTRG.4883.1存在靶向关系的miRNA结合多个mRNA,表明上述3个lncRNA可能通过ceRNA机制发挥作用,从而影响东方蜜蜂微孢子虫孢子中的新陈代谢和生命活动。【结论】 lncRNA可能通过cis作用调控上下游基因的表达,以及作为ceRNA通过吸附miRNA间接影响靶基因的表达,从而参与调节东方蜜蜂微孢子虫孢子中的物质和能量代谢等基本生命活动。 相似文献
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Ma'ayan A Jenkins SL Neves S Hasseldine A Grace E Dubin-Thaler B Eungdamrong NJ Weng G Ram PT Rice JJ Kershenbaum A Stolovitzky GA Blitzer RD Iyengar R 《Science (New York, N.Y.)》2005,309(5737):1078-1083
We developed a model of 545 components (nodes) and 1259 interactions representing signaling pathways and cellular machines in the hippocampal CA1 neuron. Using graph theory methods, we analyzed ligand-induced signal flow through the system. Specification of input and output nodes allowed us to identify functional modules. Networking resulted in the emergence of regulatory motifs, such as positive and negative feedback and feedforward loops, that process information. Key regulators of plasticity were highly connected nodes required for the formation of regulatory motifs, indicating the potential importance of such motifs in determining cellular choices between homeostasis and plasticity. 相似文献
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sigL基因编码的产物σ54是许多重要代谢途径的转录因子。为研究sigL基因在苏云金芽胞杆菌中的功能,试验分别测定苏云金芽胞杆菌HD-73菌株和sigL基因缺失突变菌株在基本培养基中对不同碳氮源的利用。结果表明,出发菌株和sigL突变体都不能利用果糖、蔗糖、纤维二糖、柠檬酸作为唯一碳源;sigL突变菌株不能利用肌氨酸、亮氨酸、异亮氨酸、丝氨酸和缬氨酸为唯一氮源,说明sigL缺失可能阻碍这些氨基酸参与的代谢途径。β-半乳糖苷酶活性分析表明,调控肌氨酸代谢途径的soxR基因转录活性在sigL突变体中降低,说明sigL是通过调控编码肌氨酸氧化酶的基因簇(sox)而影响菌体对肌氨酸的利用。 相似文献
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Bakal C Linding R Llense F Heffern E Martin-Blanco E Pawson T Perrimon N 《Science (New York, N.Y.)》2008,322(5900):453-456
Cellular signaling networks have evolved to enable swift and accurate responses, even in the face of genetic or environmental perturbation. Thus, genetic screens may not identify all the genes that regulate different biological processes. Moreover, although classical screening approaches have succeeded in providing parts lists of the essential components of signaling networks, they typically do not provide much insight into the hierarchical and functional relations that exist among these components. We describe a high-throughput screen in which we used RNA interference to systematically inhibit two genes simultaneously in 17,724 combinations to identify regulators of Drosophila JUN NH(2)-terminal kinase (JNK). Using both genetic and phosphoproteomics data, we then implemented an integrative network algorithm to construct a JNK phosphorylation network, which provides structural and mechanistic insights into the systems architecture of JNK signaling. 相似文献
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种子是植物繁育的最主要器官,种子是否正常发育直接影响植株的发育进程,也影响农作物产量和品质。种子发育调控的遗传和分子机制很复杂。目前已有大量直接或间接调控种子发育的基因和影响因子被鉴别,但这些基因之间的互作,不同调控途径如何形成网络协同调控种子发育,还有哪些新基因的参与,仍亟待进一步研究。通过梳理参与调控种子发育的基因、影响因子及其互作模式和调控模式,讨论了如何利用人类需要的等位突变提高农作物产量和品质,以期为植物种子发育调控、粮食产量和品质遗传改良提供理论支撑。 相似文献
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Network motifs: simple building blocks of complex networks 总被引：4，自引：0，他引：4
Milo R Shen-Orr S Itzkovitz S Kashtan N Chklovskii D Alon U 《Science (New York, N.Y.)》2002,298(5594):824-827
Complex networks are studied across many fields of science. To uncover their structural design principles, we defined "network motifs," patterns of interconnections occurring in complex networks at numbers that are significantly higher than those in randomized networks. We found such motifs in networks from biochemistry, neurobiology, ecology, and engineering. The motifs shared by ecological food webs were distinct from the motifs shared by the genetic networks of Escherichia coli and Saccharomyces cerevisiae or from those found in the World Wide Web. Similar motifs were found in networks that perform information processing, even though they describe elements as different as biomolecules within a cell and synaptic connections between neurons in Caenorhabditis elegans. Motifs may thus define universal classes of networks. This approach may uncover the basic building blocks of most networks. 相似文献
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Pokholok DK Zeitlinger J Hannett NM Reynolds DB Young RA 《Science (New York, N.Y.)》2006,313(5786):533-536
Cellular signal transduction pathways modify gene expression programs in response to changes in the environment, but the mechanisms by which these pathways regulate populations of genes under their control are not entirely understood. We present evidence that most mitogen-activated protein kinases and protein kinase A subunits become physically associated with the genes that they regulate in the yeast (Saccharomyces cerevisiae) genome. The ability to detect this interaction of signaling kinases with target genes can be used to more precisely and comprehensively map the regulatory circuitry that eukaryotic cells use to respond to their environment. 相似文献
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The Wnt-Wingless (Wg) pathway is one of a core set of evolutionarily conserved signaling pathways that regulates many aspects of metazoan development. Aberrant Wnt signaling has been linked to human disease. In the present study, we used a genomewide RNA interference (RNAi) screen in Drosophila cells to screen for regulators of the Wnt pathway. We identified 238 potential regulators, which include known pathway components, genes with functions not previously linked to this pathway, and genes with no previously assigned functions. Reciprocal-Best-Blast analyses reveal that 50% of the genes identified in the screen have human orthologs, of which approximately 18% are associated with human disease. Functional assays of selected genes from the cell-based screen in Drosophila, mammalian cells, and zebrafish embryos demonstrated that these genes have evolutionarily conserved functions in Wnt signaling. High-throughput RNAi screens in cultured cells, followed by functional analyses in model organisms, prove to be a rapid means of identifying regulators of signaling pathways implicated in development and disease. 相似文献
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Specificity and stability in topology of protein networks 总被引：4，自引：0，他引：4
Molecular networks guide the biochemistry of a living cell on multiple levels: Its metabolic and signaling pathways are shaped by the network of interacting proteins, whose production, in turn, is controlled by the genetic regulatory network. To address topological properties of these two networks, we quantified correlations between connectivities of interacting nodes and compared them to a null model of a network, in which all links were randomly rewired. We found that for both interaction and regulatory networks, links between highly connected proteins are systematically suppressed, whereas those between a highly connected and low-connected pairs of proteins are favored. This effect decreases the likelihood of cross talk between different functional modules of the cell and increases the overall robustness of a network by localizing effects of deleterious perturbations. 相似文献
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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.该方法能定量地分析代谢网络拓扑结构的相似度.通过对相似度数据分析,揭示了代谢网络的物种特异性;发现了同一进化阶段物种的代谢网络相似度远高于不同进化阶段物种之间的相似度,为代谢网络进化研究提供了数学基础. 相似文献
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接头分子在Toll样受体(Toll like receptors,TLRs)识别病原相关分子模式或损伤相关分子模式、发动和调节先天与后天免疫反应的信号传导网络中发挥着重要的生物学作用,与Toll样受体相结合后,其下游激酶和转录因子传导信号,激活细胞内核转录因子调控作用元件。TLRs接头分子的共同特征是含有TIR结构域,不同TLRs家族成员可依赖于一个或多个接头分子传导信号。对目前已确认的MyD88、MAL/TIRAP、TRIF、TRAM和SARM 5种接头分子在TLRs信号传导途径中的调控作用进行综述,以期为研究接头分子在TLRs信号传导中的作用机制提供参考。 相似文献
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Otero R Lukas M Kelly RE Xu W Laegsgaard E Stensgaard I Kantorovich LN Besenbacher F 《Science (New York, N.Y.)》2008,319(5861):312-315
Nonsymmetrical organic molecules adsorbed on solid surfaces may assemble into random networks, thereby providing model systems for organic glasses that can be directly observed by scanning tunneling microscopy (STM). We investigated the structure of a disordered cytosine network on a gold(111) surface created by thermal quenching, to temperatures below 150 K, of the two-dimensional fluid present on the surface at room temperature. Comparison of STM images to density functional theory calculations allowed us to identify three elementary structural motifs (zigzag filaments and five- and six-membered rings) that underlie the whole supramolecular random network. The identification of elementary structural motifs may provide a new framework for understanding medium-range order in amorphous and glassy systems. 相似文献
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光敏色素互作因子(PIFs)对植物生长发育的调控 总被引：1，自引：0，他引：1
光敏色素相互作用因子(PIFs)属于拟南芥bHLH转录因子家族的第15亚族,是光信号响应过程中的关键负调控因子。光激活的光敏色素通过促进PIFs蛋白降解,直接或间接抑制它们与DNA的结合,从而实现光对植物生长发育的调控。研究发现PIFs在调控种子萌发、幼苗形态建成、避荫反应、昼夜节律以及各种植物激素响应过程中起着重要作用。此外,PIFs作为细胞信号传导的"枢纽"具有更为广泛的作用,能够整合不同信号,精细调控整个转录网络。 相似文献