Genes2Shape_From genes to shape: Towards development of a computable flower

Genes2Shape_从基因到形状：迈向可计算花的发展

• 批准号: 355241834
• 负责人: Professor Dr. Henrik Jönsson, Ph.D.
• 金额: --
• 依托单位: Max-Planck-Institut für molekulare Pflanzenphysiologie (MPI-MP)
• 依托单位国家: 德国
• 项目类别: Research Grants
• 财政年份: 2018
• 资助国家: 德国
• 起止时间: 2017-12-31 至 2021-12-31
• 项目状态: 已结题
• 来源: https://gepris.dfg.de/gepris/projekt/355241834?language=en
• 关键词: Genes2Shape_From; genes; shape; Towards; development

This project is aimed at understanding how molecular regulation integrates with mechanics to control overall plant shape, an unresolved problem with wide implications for both fundamental and applied biology. We will address this issue in the Arabidopsis flower, which, besides their obvious importance as reproductive structures, are amongst the best characterised systems in plant developmental biology.From a mechanistic point of view, it is widely accepted that regulatory molecular networks interfere with the properties of the structural cellular elements (cell wall, cytoskeleton) to induce particular growth patterns. How this occurs and how this is coordinated in space is not known. To obtain a mechanistic understanding of such a complex process, information from multiple scales, from molecular networks to physical properties and geometry have to be combined into a single picture. An integrated tool to do so is currently not available.Building on our complementary experience in interdisciplinary research on plant development, we will therefore develop a tool, called the Computable Flower that permits (i) integration of data on geometry, gene expression and biomechanics and (ii) the user to explore, interpret and generate hypotheses based on data supported by mechanistic modelling approaches. The tool therefore provides an integrated description in the form of a 3D dynamic template of the growing flower bud. The Computable Flower will be populated with existing or novel quantitative datasets coming from experimental and computational techniques concerning:(i) the spatial distribution of regulatory molecules such as transcription factors and hormones.(ii) the spatial expression patterns of genes involved in cell wall synthesis and remodelling which operate downstream from these regulatory networks.(iii) the spatial organisation and properties of structural elements, including cell wall stiffness, cytoskeleton and cellulose microfibril organisation.(iv) changes in geometry.In the process we will develop computational models to generate hypotheses regarding biochemical, physical and geometrical properties with simulation outcomes quantitatively compared with experimental data. Predictions coming from the modelling will guide experiments using domain-specific perturbation of genes that influence microtubule and wall status. These transgenic lines will then be subjected to detailed quantitative growth studies to test the validity of the model or to refine it. The above measured datasets and simulation outcomes will be disseminated via an interactive graphical web interface of the Computable Flower, transforming the way data is provided to the community by integrating multiple data types and allowing users to browse the data and build their experiments and models on the latest information and insights. Importantly, the tools generated to create the computable flower will be easily adaptable to a wide range of plant and animal systems.

该项目旨在了解分子调控如何与力学相结合，以控制整体植物形状，这是一个尚未解决的问题，对基础生物学和应用生物学都有广泛的影响。我们将在拟南芥花中解决这个问题，除了它们作为生殖结构的明显重要性之外，它们是植物发育生物学中最具特征的系统之一。从机制的角度来看，人们普遍认为调控分子网络干扰结构细胞元件（细胞壁，细胞骨架）的特性以诱导特定的生长模式。这是如何发生的，以及如何在空间中协调，都是未知的。为了从机理上理解这样一个复杂的过程，必须将来自多个尺度的信息，从分子网络到物理性质和几何形状，组合成一个单一的图像。基于我们在植物发育跨学科研究方面的互补经验，我们将开发一种名为Computable Flower的工具，该工具允许（i）整合几何学，基因表达和生物力学数据，（ii）用户根据机械建模方法支持的数据探索，解释和生成假设。因此，该工具以生长中的花蕾的3D动态模板的形式提供了综合描述。Computable Flower将使用来自实验和计算技术的现有或新的定量数据集进行填充，这些数据集涉及：（i）调控分子（如转录因子和激素）的空间分布。(ii)参与细胞壁合成和重塑的基因的空间表达模式，这些基因在这些调控网络的下游起作用。(iii)结构元素的空间组织和性质，包括细胞壁硬度，细胞骨架和纤维素微纤维组织。(iv)在这个过程中，我们将开发计算模型，以生成关于生化，物理和几何特性的假设，并将模拟结果与实验数据进行定量比较。来自建模的预测将指导使用影响微管和壁状态的基因的域特异性扰动的实验。这些转基因株系随后将接受详细的定量生长研究，以测试模型的有效性或对其进行改进。上述测量数据集和模拟结果将通过Computable Flower的交互式图形网络界面发布，通过集成多种数据类型，转变向社区提供数据的方式，并允许用户浏览数据，并在最新的信息和见解。重要的是，创建可计算花的工具将很容易适应广泛的植物和动物系统。