Genes2Shape_From genes to shape: Towards development of a computable flower

这个项目旨在了解分子调控如何与力学相结合来控制整体植物形状，这是一个对基础生物学和应用生物学都具有广泛影响的悬而未决的问题。我们将在拟南芥花中解决这个问题，它除了作为生殖结构具有明显的重要性外，也是植物发育生物学中最具特征的系统之一。从机械学的角度来看，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)的性质，以诱导特定的生长模式。这是如何发生的，以及这是如何在太空中协调的，目前尚不清楚。为了从机制上理解这样一个复杂的过程，从分子网络到物理性质和几何图形的多个尺度的信息必须结合到一幅图中。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可计算花卉的工具，它允许(I)整合几何、基因表达和生物力学的数据，以及(Ii)用户基于机械建模方法支持的数据来探索、解释和生成假说。因此，该工具以正在生长的花蕾的3D动态模板的形式提供了完整的描述。可计算的花朵将被来自实验和计算技术的现有或新的定量数据集填充：(I)转录因子和激素等调控分子的空间分布；(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运行；(Iii)结构元素的空间组织和属性，包括细胞壁硬度、细胞骨架和纤维素微纤维组织。(Iv)几何结构的变化。在这个过程中，我们将开发计算模型来生成关于生化、物理和几何性质的假设，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管壁状态的基因的特定领域扰动的实验。这些转基因品系随后将接受详细的定量生长研究，以测试该模型的有效性或对其进行改进。上述测量的数据集和模拟结果将通过可计算花卉的交互式图形网络界面发布，通过整合多种数据类型改变向社区提供数据的方式，并允许用户浏览数据并根据最新的信息和见解建立他们的实验和模型。重要的是，创造可计算花朵的工具将很容易适应广泛的植物和动物系统。

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.