A Minimal Cell Model to Determine Genomic Structure

本项目的目标是开发一个动态的最小细胞的数学模型，作为一种工具，以确定组织原则，将静态的线性序列信息的基因组的动态非线性功能的细胞。 该模型将分两个阶段开发。 首先，将从单个E的现有数学模型创建原型最小细胞模型。coli细胞。 该模型基于代表相关化学物质组的参数，并已被证明可以准确预测细胞大小、形状、生长速率和组成。 在开发的第二阶段，将在原型最小细胞模型中添加关于途径网络的详尽细节，以便单独和明确地描述化学物种和化学反应。 在此期间的项目，与染色体复制，核糖核苷酸和脱氧核糖核苷酸合成，运输，转录相关的网络的细节将被添加。 该项目还将通过实验确定基因表达与该基因在三维包装染色体中的位置之间的关系，以便将此信息纳入基因表达的数学描述中。 同步化的细胞群体将被用于研究在E.大肠杆菌分裂周期

The objective of this project is to develop a dynamic mathematical model of a minimal cell as a tool to identify the organizing rinciples which relate the static linear sequence information of the genome to the dynamic non-linear functioning of the cell. This model will be developed in two stages. First, a prototype minimal cell model will be created from an existing mathematical model of a single E. coli cell. This model is based on parameters which represent groups of related chemical species and has been shown to accurately predict cell size, shape, growth rate, and composition. In the second stage of development, exhaustive detail on networks of pathways will be added to the prototype minimal cell model so that chemical species and chemical reactions are described individually and explicitly. During this period of the project, details on the networks associated with chromosome replication, ribonucleotide and deoxyribonucleotide synthesis, transport, transcription will be added. This project is to also experimentally determine the relationship between a gene's expression and the position of that gene in the three-dimensional packed chromosome so that this information can be included in mathematical descriptions of gene expression. Synchronized cell populations will be used to study the relationship between position and expression during different phases of the E. coli division cycle.