From Bacterial Chemotaxis to the Prediction of Complex Networks: The Oxford Integrative Systems Biology Centre

从细菌趋化性到复杂网络的预测：牛津综合系统生物学中心

• 批准号: BB/D020190/1
• 负责人: Judith Armitage
• 金额: $ 1138.29万
• 依托单位: University of Oxford
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2007
• 资助国家: 英国
• 起止时间: 2007 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FD020190%2F1
• 关键词: Bacterial; Chemotaxis; Prediction; Complex; Networks

Life arises not just from individual molecules, but from their dynamic interactions. A great deal of time and money has been spent globally on sequencing genomes, followed by high-throughput methods for transcriptomic, proteomic and metabolomic measurement. Cells, however, are complex systems of networks and pathways. A long term goal of molecular biology must be to take a sequenced genome and be able to model the intracellular activities of a cell, and ultimately a complex organism. The availability of accurate and robust models has the potential to enable major advances in a range of activities ranging through pharmaceuticals and health care to food production and bioremediation. Approaches can be top down, bottom up or through accurate definition of limited inputs and outputs whilst ignoring the intervening detail. The goal is an accurate model of the dynamic activities of a cell under a specific set of growth conditions, when many proteins may be present but not active, only interacting with target proteins or DNA when activated to do so (the so-called 'sensome' or 'interactome'). None of the techniques available to date can reliably say which proteins are active when or which interact with which. Even recent developments in, for example, fast through-put guided yeast two hybrid systems tell you what can interact, not what does interact in vivo and when. We believe the best way forward is to initially focus on a limited number of tractable and important biological systems, for example, the bacterial histidine protein kinase (HPK) dependent chemosensory pathway or a defined section of the yeast cell cycle pathway, and to develop a reliable, predictive model for those systems. With, for example the bacterial chemosensory pathway, models can be tested through to species with complex pathways and these then extended to the total complement of HPK pathways in selected bacterial species. The long term goal is to carry these approaches to more complex pathways in higher organisms, and eventually to extend the models to sensory systems in general, with each model tested biologically as the programme develops. These studies will lead not only to an understanding of the complex interactive networks of signalling pathways, but also to the identification of signature motifs, possibly providing new targets for antimicrobials.

生命不仅来自单个分子，而且来自它们的动态相互作用。在全球范围内，大量的时间和金钱已经花费在基因组测序上，随后是用于转录组学、蛋白质组学和代谢组学测量的高通量方法。然而，细胞是复杂的网络和通路系统。分子生物学的一个长期目标必须是获得测序的基因组，并能够模拟细胞的细胞内活动，最终模拟复杂的生物体。准确和可靠的模型有可能使从制药和保健到食品生产和生物修复等一系列活动取得重大进展。方法可以是自上而下，自下而上或通过精确定义有限的输入和输出，而忽略干预的细节。目标是在一组特定的生长条件下细胞动态活动的精确模型，当许多蛋白质可能存在但不活跃时，仅在激活时与靶蛋白或DNA相互作用（所谓的“感觉体”或“相互作用体”）。迄今为止，没有一种技术能够可靠地说出哪些蛋白质在什么时候是活性的，或者哪些蛋白质与哪些蛋白质相互作用。即使是最近的发展，例如，快速通量引导酵母双杂交系统告诉你什么可以相互作用，而不是什么在体内和何时相互作用。我们认为，最好的前进道路是最初专注于有限数量的易处理和重要的生物系统，例如，细菌组氨酸蛋白激酶（HPK）依赖的化学传感途径或酵母细胞周期途径的定义部分，并为这些系统开发一个可靠的预测模型。例如，对于细菌化学感受途径，可以通过具有复杂途径的物种来测试模型，然后将这些模型扩展到选定细菌物种中的HPK途径的总补体。长期目标是将这些方法用于高等生物中更复杂的途径，并最终将模型扩展到一般的感觉系统，随着程序的发展，每个模型都进行生物测试。这些研究不仅有助于理解信号通路复杂的相互作用网络，还有助于识别特征基序，可能为抗菌剂提供新的靶点。

项目成果

Revisiting date and party hubs: novel approaches to role assignment in protein interaction networks.

• DOI: 10.1371/journal.pcbi.1000817
• 发表时间: 2010-06-17
• 期刊: PLoS computational biology
• 影响因子: 4.3
• 作者: Agarwal S;Deane CM;Porter MA;Jones NS
• 通讯作者: Jones NS

Predicting and validating protein interactions using network structure.

• DOI: 10.1371/journal.pcbi.1000118
• 发表时间: 2008-07-25
• 期刊: PLoS computational biology
• 影响因子: 4.3
• 作者: Chen PY;Deane CM;Reinert G
• 通讯作者: Reinert G

Mechanism of bacterial signal transduction revealed by molecular dynamics of Tsr dimers and trimers of dimers in lipid vesicles.

• DOI: 10.1371/journal.pcbi.1002685
• 发表时间: 2012
• 期刊: PLoS computational biology
• 影响因子: 4.3
• 作者: Hall BA;Armitage JP;Sansom MS
• 通讯作者: Sansom MS

Feedback control architecture and the bacterial chemotaxis network.

• DOI: 10.1371/journal.pcbi.1001130
• 发表时间: 2011-05
• 期刊: PLoS computational biology
• 影响因子: 4.3
• 作者: Hamadeh A;Roberts MA;August E;McSharry PE;Maini PK;Armitage JP;Papachristodoulou A
• 通讯作者: Papachristodoulou A

A two-dimensional model of the colonic crypt accounting for the role of the basement membrane and pericryptal fibroblast sheath.

结肠隐窝的二维模型，涉及基底膜和周围成纤维细胞鞘的作用。

• DOI: 10.1371/journal.pcbi.1002515
• 发表时间: 2012
• 期刊: PLoS computational biology
• 影响因子: 4.3
• 作者: Dunn SJ;Appleton PL;Nelson SA;Näthke IS;Gavaghan DJ;Osborne JM
• 通讯作者: Osborne JM