A Synthetic-Biology Approach to Study Scaling Properties of Self-Organized Patterns

该工作以基因工程电路为模型系统，旨在研究自组织模式的标度特性。它侧重于在动物发育过程中或在个体之间，器官相对于整个身体的独特性质、比例不变性或保持恒定的相对大小。该项目代表了合成生物学的变革性应用，以解决生物学中悬而未决的基本问题。所提出的计算和实验框架为探索自组织图案形成的基础设计原则以及新出现的缩放特性提供了明确的背景。除了提供新的生物学见解外，拟议的工程化系统还可以作为未来工程努力的基础，例如制造新的生物材料。此外，由拟议工作产生的实验技术和计算基础设施将适用于分析自然和合成生物网络。计算和实验系统和工具都将提供给广泛的研究界。同样重要的是，该项目的研究将为具有生物、工程、数学和物理科学背景的预科学生、本科生和研究生提供接触生物工程和合成生物学的跨学科研究的机会。从拟议的研究中获得的建模示例和实验，以及从文献中提取的其他示例，将用于培训这些学生。此外，课程和课程开发将促进系统和合成生物学知识在杜克大学内外的传播。最后，为了支持短期和长期的教育目标，建议的努力包括开发一本针对高水平本科生和研究生的系统与合成生物学教科书。技术描述：该项目旨在结合数学建模和合成基因电路的实验分析来探索自组织模式标度特性背后的基本机制。比例不变性是指在动物发育过程中或个体之间，一个器官相对于整个身体的相对大小保持不变。已经提出了许多机制来解释生物模式形成中的尺度不变性。然而，无论它们特定的分子相互作用如何，这些机制中的绝大多数都需要形态根梯度作为空间线索，这要么是预先定义的，要么是作为构图过程的一部分产生的。在初步工作中，使用由合成基因电路编程的大肠杆菌，研究人员证明了在没有明显形态原梯度的情况下，在健壮的、自组织的基因表达模式中，环大小与菌落大小的完美尺度不变性的产生。这一观察提出了一个基本的、尚未解决的问题：在没有空间形态梯度的情况下，如何在自组织模式中发生尺度不变性？为了解决这个问题，研究人员建议开发和优化一个实验平台，以检查工程菌中自组织图案形成的缩放特性。该平台将喷墨打印技术和合成基因电路结合在一起，在基于机械的数学模型的指导下，探索形态生成素在图案形成过程中作为时间线索的作用。该奖项由MCB的系统和合成生物学计划以及CBET的生物技术、生化和生物工程计划共同资助。

Using engineered gene circuits as a model system, the proposed work aims to examine the scaling properties of self-organized patterns. It focuses on a unique property, scale invariance, or maintenance of constant relative size of an organ with respect to the whole body during animal development or between individuals. The project represents a transformative application of synthetic biology to address unresolved, fundamental questions in biology. The proposed computational and experimental framework provides a well-defined context for exploring design principles that underlie generation of self-organized pattern formation as well as the emergent scaling properties. In addition to offering new biological insights, the proposed engineered systems can serve as the foundation for future engineering endeavors, such as fabrication of novel biomaterials. Furthermore, experimental techniques and computational infrastructure arising from the proposed work will be applicable for analyzing both natural and synthetic biological networks. Both computational and experimental systems and tools will be made available to the broad research community. Equally important, the research in this project will provide opportunities for pre-college students, undergraduates, and graduate students with backgrounds in biology, engineering, mathematics, and physical sciences to become exposed to interdisciplinary research in bioengineering and synthetic biology. Modeling examples and experiments derived from the proposed research, along with other examples drawn from the literature, will be used to train these students. In addition, the course and curriculum development will facilitate dissemination of knowledge in Systems and Synthetic Biology both at and beyond Duke University. Finally, to support both short-term and long-term education goals, the proposed efforts include development of a textbook on systems and synthetic biology that targets upper-level undergraduate students and starting graduate students.Technical description: The project aims to use a combination of mathematical modeling and experimental analysis of synthetic gene circuits to explore the fundamental mechanisms underlying scaling properties of self-organized patterns. Scale invariance refers to maintenance of constant relative size of an organ with respect to the whole body during animal development or between individuals. A number of mechanisms have been proposed to explain scale invariance in biological pattern formation. Regardless of their specific molecular interactions, however, the vast majority of these mechanisms require morphogen gradients as the spatial cue, which are either predefined or generated as part of the patterning process. In preliminary work, using Escherichia coli programmed by a synthetic gene circuit, the investigator has demonstrated the generation of perfect scale invariance of ring size versus colony size in robust, self-organized ring patterns of gene expression in the absence of an apparent morphogen gradient. This observation raises a fundamental, unresolved question: How does scale invariance occur in self-organized patterns in the absence of a spatial morphogen gradient? To address this question, the investigator proposes to develop and optimize an experimental platform to examine scaling properties of self-organized pattern formation in engineered bacteria. This platform couples inkjet printing technology and synthetic gene circuitry to explore the role of morphogen as a temporal cue in the pattern formation process, guided by mechanistically based mathematical models.This award is funded jointly by the Systems and Synthetic Biology Program in MCB and the Biotechnology, Biochemical and Biomass Engineering Program in CBET.