Centre for Plant Integrative Biology

植物综合生物学中心

• 批准号: BB/D019613/1
• 负责人: Thomas Hodgman
• 金额: $ 1161.09万
• 依托单位: University of Nottingham
• 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%2FD019613%2F1
• 关键词: Centre; Plant; Integrative; Biology

Life is extremely complex. Even apparently simple organisms like plants contain many tens of thousands of genes which make many tens of thousands of proteins in each of the many millions of cells that make up a living organism. Integrative Systems Biology promises ultimately to make sense of this mind-numbing volume of molecular, cellular and tissue scale information by employing mathematical models to identify key underlying principles which can be tested experimentally. We propose a flagship Centre to pioneer the use of Integrated Systems Biology in Plant and Crop Sciences to create a virtual root model. While the root has largely been neglected in breeding programmes, it is the organ that is critical for seedling establishment and later dictates a plant's growth and development, through water and nutrient uptake and response to abiotic stress. The root is therefore a prime candidate for study using an Integrated Systems Biology approach. The Centre will initially focus on Arabidopsis thaliana (At), since it is the pre-eminent reference species for crops which uniquely has the advanced knowledge base necessary realistically to initiate ISB in plants. However, the work will play a crucial role in the development of sustainable crops by providing an ISB model to probe genetic-environment interactions associated with root growth and function. The reasons why Arabidopsis is exceptionally well suited to establishing the systems-biology approaches for the description of multi-cellular organisms include the following: (i) Arabidopsis is an exceptionally well-characterised species, not only among plants but also among all multi-cellular organisms. (ii) Plants have fewer cell and tissue types than animals, the cells are not independently mobile, allowing their fate more readily to be traced, and their growth and development are regulated by a few hormones. This makes them simpler to study than animals, while having many features in common, one of particular note in the current context being the crucial role of stem cells. (iii) Plant growth is dominated by the so-called root and shoot apical meristems (in which stem cells reside), allowing for a division of labour in which the former will be considered in the current project and the latter by collaborators in the USA. The virtual root will be capable of integration with the virtual shoot being developed in the USA, paving the way for a virtual higher plant. The proposed research programme will involve biologists, computer scientists, engineers, informaticians, mathematicians and statisticians all working together in a single location in a concerted attack on understanding the mechanisms underpinning root growth, studying all the relevant scales (from metabolite and gene to root) and combining the results in models which will allow the computational simulation of the root as a whole, thereby providing insight into the influence of genetic and environmental effects in particular. A carefully-structured programme of research will first consider the three domains which make up the root (the elongation zone, the root apical meristem and the region of lateral root emergence) and will then combine the information and models obtained from each of these in order to describe the whole root; this will require the detailed treatment of 'emergent properties' whereby the whole is more than the sum of the parts. These models will allow new hypotheses about the associated mechanisms to be generated and tested and hence will ultimately suggest ways of improving sustainable practices in agriculture (e.g. reducing chemical inputs by increasing nutrient uptake in the soil) whilst maintaining crop yields. More generally, the programme will also provide a roadmap for how systems-biology approaches can be applied to other multi-cellular species and an extensive programme of outreach will therefore be pursued to promote such undertakings to researchers in relevant areas.

生命是极其复杂的。即使是像植物这样表面上简单的生物体，也含有数万个基因，这些基因在构成生物体的数百万个细胞中的每一个细胞中制造数万种蛋白质。综合系统生物学承诺最终通过采用数学模型来确定可以通过实验测试的关键基本原理，从而理解分子，细胞和组织尺度信息的这种令人麻木的数量。我们建议建立一个旗舰中心，率先在植物和作物科学中使用集成系统生物学来创建虚拟根模型。虽然根部在育种计划中很大程度上被忽视，但它是对于幼苗建立至关重要的器官，并且后来通过水和营养的吸收以及对非生物胁迫的反应决定植物的生长和发育。因此，根是使用集成系统生物学方法进行研究的主要候选者。该中心最初将重点关注拟南芥（At），因为它是农作物的杰出参考物种，独特地拥有在植物中启动ISB所需的先进知识基础。然而，这项工作将通过提供一个ISB模型来探测与根系生长和功能相关的遗传-环境相互作用，在可持续作物的发展中发挥关键作用。拟南芥特别适合建立描述多细胞生物的系统生物学方法的原因包括以下几点：（i）拟南芥是一个非常好的特征物种，不仅在植物中，而且在所有多细胞生物中。(ii)植物的细胞和组织类型比动物少，细胞不能独立地移动的，使它们的命运更容易被追踪，它们的生长和发育受几种激素的调节。这使得它们比动物更容易研究，同时具有许多共同特征，在当前背景下特别值得注意的是干细胞的关键作用。(iii)植物生长由所谓的根和芽顶端分生组织（干细胞存在于其中）主导，允许劳动分工，前者将在当前项目中考虑，后者由美国的合作者考虑。虚拟根将能够与美国正在开发的虚拟芽整合，为虚拟高等植物铺平道路。拟议的研究计划将涉及生物学家、计算机科学家、工程师、信息学家、数学家和统计学家，他们将在一个地点共同努力，共同了解根系生长的机制，研究所有相关的尺度。（从代谢物和基因到根），并将结果结合在模型中，这将允许对根进行整体的计算机模拟，从而提供了对遗传和环境影响的深入了解。一个精心设计的研究方案将首先考虑构成根的三个领域（伸长区、根顶端分生组织和侧根出现的区域），然后将联合收割机从每个领域获得的信息和模型结合起来，以描述整个根;这将需要详细处理“涌现特性”，从而使整体大于部分之和。这些模型将允许产生和测试有关机制的新假设，从而最终提出改善农业可持续做法的方法（例如通过增加土壤中的养分吸收来减少化学投入），同时保持作物产量。更广泛地说，该方案还将提供一个路线图，说明如何将系统生物学方法应用于其他多细胞物种，因此将开展广泛的外联方案，向相关领域的研究人员推广这类工作。

项目成果

Getting to the root of plant biology: impact of the Arabidopsis genome sequence on root research.

• DOI: 10.1111/j.1365-313x.2010.04129.x
• 发表时间: 2010-03
• 期刊: The Plant journal : for cell and molecular biology
• 作者: Benfey PN;Bennett M;Schiefelbein J
• 通讯作者: Schiefelbein J

Combining semi-automated image analysis techniques with machine learning algorithms to accelerate large-scale genetic studies.

• DOI: 10.1093/gigascience/gix084
• 发表时间: 2017-10-01
• 期刊: GigaScience
• 影响因子: 9.2
• 作者: Atkinson JA;Lobet G;Noll M;Meyer PE;Griffiths M;Wells DM
• 通讯作者: Wells DM

Mapping the site of action of the Green Revolution hormone gibberellin.

绘制绿色革命激素赤霉素的作用位点。

• DOI: 10.1073/pnas.1301609110
• 发表时间: 2013
• 期刊: Proceedings of the National Academy of Sciences of the United States of America
• 影响因子: 11.1
• 作者: Band LR

An Updated Protocol for High Throughput Plant Tissue Sectioning.

• DOI: 10.3389/fpls.2017.01721
• 发表时间: 2017
• 期刊: Frontiers in plant science
• 影响因子: 5.6
• 作者: Atkinson JA;Wells DM
• 通讯作者: Wells DM