Theoretical and Experimental Studies of the Population and Evolutionary Dynamics of Bacteria and Bacteriophage.

摘要 细菌和古生菌的病毒，噬菌体，被吹捧为地球上最丰富的生物，和一种 人们对它们的分子生物学、结构和复制机制有很多了解。尽管如此， 关于种群生物学，仍然有一些基本的问题没有得到回答或没有完全得到回答， 这些病毒的生态作用和进化。在这次调查中，我们将解决并回答以下问题 这些基本问题中的三个：1--什么是生态、遗传和进化条件 维持裂解(毒力)噬菌体并调节细菌种群密度？2-下 什么条件会有利于温和的而不是纯粹的裂解模式的噬菌体复制和 传播？3-在什么条件下，裂解噬菌体和温带噬菌体的选择有利于进化 和维持CRISPR-Cas介导的适应性免疫，而不是包膜或其他成分 抵抗机制？为了解决这些问题，我们将使用数学和计算机模拟 模型，其属性将用数值分析，参数估计在 将用于种群动态和进化实验的实验系统。我们 将检验从我们对这些模型的分析中产生的预测(假设) 细菌和噬菌体保持在液体、表面和半固体培养中。根据这些研究的结果 在实验中，我们将修改我们的模型，使其更加逼真。这些实验将在 大肠埃希菌、铜绿假单胞菌、丁香假单胞菌和金黄色葡萄球菌 裂解和/或温带噬菌体。除了它们对学术生态的重要性外，人口和 进化生物学，这项基础科学研究的结果很可能具有实用价值。这 调查将提供一个经验支持的理论，可以用来促进设计和 利用噬菌体治疗人类和家庭细菌感染方案的评价 并控制农作物中的病原菌暴发。 好了！

ABSTRACT The viruses of bacteria and archaea, phage, are touted to be the most abundant organisms on Earth, and a great deal is known about their molecular biology, structure, and mechanisms of replication. Nevertheless there remain fundamental unanswered or incompletely answered questions about the population biology, ecological role, and evolution of these viruses. In this investigation we will address and provide answers to three of these fundamental questions: 1- What are the ecological, genetic and evolutionary conditions for lytic (virulent) phage to be maintained in and regulate the densities of bacterial populations? 2- Under what conditions will selection favor a temperate rather than a purely lytic mode of phage replication and transmission? 3- Under what conditions will selection by lytic and temperate phage favor the evolution and maintenance of CRISPR-Cas mediated adaptive immunity, rather than envelope or other constitutive resistance mechanisms? To address these questions, we will use mathematical and computer simulation models, the properties of which will be analyzed numerically with parameters estimated in the experimental systems that will be employed for population dynamic and evolutionary experiments. We will test the predictions (hypotheses) generated from our analysis of these models in populations of bacteria and phage maintained in liquid, surface, and semisolid culture. Based on the results of these experiments, we will modify our models to make them more realistic. The experiments will be done with Escherichia coli, Pseudomonas aeruginosa, Pseudomonas syringae, and Staphylococcus aureus and their lytic and/or temperate phage. In addition to their importance to academic ecology, population and evolutionary biology, the results of this basic science study may well have practical utility. This investigation will provide an empirically supported theory that could be used to facilitate the design and evaluation of programs to use phage for the treatment of bacterial infections in humans and domestic animals, and to control outbreaks of pathogenic bacteria in crops. !