Merks Roeland M H, Guravage Michael, Inzé Dirk, Beemster Gerrit T S
Centrum Wiskunde & Informatica, 1098 XG Amsterdam, The Netherlands.
Plant Physiol. 2011 Feb;155(2):656-66. doi: 10.1104/pp.110.167619. Epub 2010 Dec 9.
Plant organs, including leaves and roots, develop by means of a multilevel cross talk between gene regulation, patterned cell division and cell expansion, and tissue mechanics. The multilevel regulatory mechanisms complicate classic molecular genetics or functional genomics approaches to biological development, because these methodologies implicitly assume a direct relation between genes and traits at the level of the whole plant or organ. Instead, understanding gene function requires insight into the roles of gene products in regulatory networks, the conditions of gene expression, etc. This interplay is impossible to understand intuitively. Mathematical and computer modeling allows researchers to design new hypotheses and produce experimentally testable insights. However, the required mathematics and programming experience makes modeling poorly accessible to experimental biologists. Problem-solving environments provide biologically intuitive in silico objects ("cells", "regulation networks") required for setting up a simulation and present those to the user in terms of familiar, biological terminology. Here, we introduce the cell-based computer modeling framework VirtualLeaf for plant tissue morphogenesis. The current version defines a set of biologically intuitive C++ objects, including cells, cell walls, and diffusing and reacting chemicals, that provide useful abstractions for building biological simulations of developmental processes. We present a step-by-step introduction to building models with VirtualLeaf, providing basic example models of leaf venation and meristem development. VirtualLeaf-based models provide a means for plant researchers to analyze the function of developmental genes in the context of the biophysics of growth and patterning. VirtualLeaf is an ongoing open-source software project (http://virtualleaf.googlecode.com) that runs on Windows, Mac, and Linux.
植物器官，包括叶子和根，是通过基因调控、模式化细胞分裂与细胞扩张以及组织力学之间的多层次相互作用来发育的。这些多层次的调控机制使经典分子遗传学或功能基因组学研究生物发育的方法变得复杂，因为这些方法隐含地假定了在整个植物或器官层面上基因与性状之间存在直接关系。相反，要理解基因功能需要深入了解基因产物在调控网络中的作用、基因表达的条件等。这种相互作用很难凭直觉理解。数学和计算机建模使研究人员能够设计新的假设并得出可通过实验验证的见解。然而，所需的数学和编程经验让实验生物学家难以进行建模。问题解决环境提供了建立模拟所需的具有生物学直观性的虚拟对象（“细胞”、“调控网络”），并以熟悉的生物学术语呈现给用户。在此，我们介绍用于植物组织形态发生的基于细胞的计算机建模框架VirtualLeaf。当前版本定义了一组具有生物学直观性的C++对象，包括细胞、细胞壁以及扩散和反应的化学物质，这些对象为构建发育过程的生物学模拟提供了有用的抽象概念。我们逐步介绍如何使用VirtualLeaf构建模型，并提供叶脉和分生组织发育的基本示例模型。基于VirtualLeaf的模型为植物研究人员提供了一种手段，使其能够在生长和模式形成的生物物理学背景下分析发育基因的功能。VirtualLeaf是一个正在进行的开源软件项目（http://virtualleaf.googlecode.com），可在Windows、Mac和Linux上运行。
