Computational biology of plant development: Towards a deductive science

植物发育的计算生物学：走向演绎科学

• 批准号: RGPIN-2019-06279
• 负责人: Prusinkiewicz, Przemyslaw
• 金额: $ 2.48万
• 依托单位: University of Calgary
• 依托单位国家: 加拿大
• 项目类别: Discovery Grants Program - Individual
• 财政年份: 2020
• 资助国家: 加拿大
• 起止时间: 2020-01-01 至 2021-12-31
• 项目状态: 已结题
• 来源: https://www.nserc-crsng.gc.ca/ase-oro/Details-Detailles_eng.asp?id=715038
• 关键词: Computational; biology; plant; development; Towards

Computational Biology of Plant Development: Towards a Deductive Science Since the early 2000s, a mechanistic understanding of plant development has begun to emerge through a combination of molecular genetics, advances in microscopy, and computational models. Surprisingly, the development of diverse structures may result from related mechanisms expressed in different contexts. For instance, the development of leaves leading to their various shapes, and their positioning on the supporting stem, are manifestations of a common molecular mechanism involving the interaction between the plant hormone auxin and its transporters, the PIN proteins. The universality of this and other mechanisms (e.g., competition between plant organs for space) suggests that the essence of diverse developmental processes in plants can be reduced to, and deduced from, a small number of fundamental principles. The quest for such principles is the overarching objective of my proposed research. I plan to proceed by devising mathematically well-founded methods for representing and simulating the development of heterogeneous plant structures. As a starting point, I will use the models of leaves with embedded veins that were previously developed in my lab. The resulting methods will be applied to address the patterning of flower heads: the flower-like inflorescences (flower clusters) characteristic of plants in the aster family, such as gerbera, sunflower and daisy. The conspicuous regularity and mathematical properties of the spiral patterns found in these heads have attracted interdisciplinary interest over centuries, yet the patterning mechanism has remained unknown. Based on unique data obtained in collaboration with biologist colleagues and computational models being devised in my lab, I believe that we can solve this long-standing problem. The solution will provide a point of departure to explain a related phenomenon, the development of the vascular structure of flower heads. The results will be generalized to a wider spectrum of biological structures. Taken together, this work will constitute a step towards characterizing diverse processes and structures in plants in terms of broadly applicable, general principles. The proposed research has an inherently interdisciplinary character, applying methods of computer science and mathematics to problems originating in biology, and involves collaborations with plant scientists. Computational models based on experimental data will be devised and used to explore causal relations in the self-organizing developmental processes under study. The geometric aspects of the emerging structures link this research program to computer graphics.

植物发育的计算生物学：走向演绎科学 自 2000 年代初以来，通过分子遗传学、显微镜技术的进步和计算模型的结合，人们开始对植物发育的机制有了认识。令人惊讶的是，不同结构的发展可能是由不同背景下表达的相关机制引起的。例如，叶子的发育导致各种形状，以及它们在支撑茎上的定位，都是涉及植物激素生长素及其转运蛋白 PIN 蛋白之间相互作用的常见分子机制的表现。这种机制和其他机制（例如植物器官之间对空间的竞争）的普遍性表明，植物不同发育过程的本质可以简化为少数基本原理，并从中推断出来。寻求这些原则是我提出的研究的总体目标。 我计划继续设计有基础的数学方法来表示和模拟异质植物结构的发育。作为起点，我将使用之前在我的实验室开发的带有嵌入式静脉的叶子模型。由此产生的方法将应用于解决花头的图案：紫苑科植物（如非洲菊、向日葵和雏菊）的花状花序（花簇）特征。几个世纪以来，在这些头部中发现的螺旋图案的显着规律性和数学特性引起了跨学科的兴趣，但图案机制仍然未知。 基于与生物学家同事合作获得的独特数据以及我实验室设计的计算模型，我相信我们可以解决这个长期存在的问题。 该解决方案将为解释相关现象（花头维管结构的发育）提供一个出发点。结果将推广到更广泛的生物结构。总而言之，这项工作将朝着根据广泛适用的一般原则来表征植物中的不同过程和结构迈出一步。 拟议的研究具有本质上的跨学科特征，将计算机科学和数学方法应用于源于生物学的问题，并涉及与植物科学家的合作。 将设计并使用基于实验数据的计算模型来探索所研究的自组织发展过程中的因果关系。新兴结构的几何方面将本研究项目与计算机图形学联系起来。