EXPERIMENTAL MODELS OF VIRAL ADAPTATION

描述：本研究的目标是开发一种方法来研究 病毒在分子水平上的适应规则可能会告诉我们 如何开发抗病毒疗法。对此有三个具体目标 求婚。(1)检查病毒种群的种群遗传学 时间到了。与这一目标相关的数据将允许三个假设 被称呼为。是替换模式，表示一系列 选择性扫荡？大部分的健康改善都是由于以下几个原因 替换效果很大，而且大多数替换都会有很大的影响 没什么效果吗？当人口达到平衡时， 变异衰减到一个序列？(2)探索 病毒适应过程中的并行和收敛进化。将并行 更改大多发生在主要站点，而不是次要站点 健身福利？相关病毒是否会适应与 同样的变化？(3)检查病毒适应的适应成本 多个特工。适应新的选拔赛需要健身成本吗？ 探员？能否根据对多个代理的响应来预测对 单身特工？适应是否依赖于先前的适应历史？ PI建议使用噬菌体化学药物并使复制种群适应 43.5摄氏度。每3天每6小时采集一次样品，然后每12小时采集一次 七天。将在每个时间点采集96个样本，并进行一组检测 通过预定区域的寡核苷酸筛选进行的替换( 从试点基因组测序工作中选择的集合)。将对健康状况进行分析 (随着细菌感染后每小时噬菌体数量的增加)。这些数据 将用于解决特定目标#1(病毒的群体遗传学 随时间推移的适应) 将进行第一个实验的6个重复(3个在单独的 机构)。这些数据将使PI能够满足特定目标#2( 噬菌体适应过程中收敛进化的含义)。一株分离物 将对每个重复序列进行测序以确定筛选位点。一个 第二阶段的研究涉及对多个代理人进行选择。一个 一系列试剂，如酒精、盐等将被用作 有选择性的药物。选择将在许多不同的媒体上进行， 视需要而定。噬菌体将进化成对大量 代理，包括单独代理和组合代理。这些数据将允许PI 解决具体目标#3(适应多种环境的适应成本 代理)。

DESCRIPTION: The goal of this study is to develop an approach to study the rules of viral adaptation at the molecular level that may inform us about how to develop anti-viral therapies. There are 3 specific aims to this proposal. (1) To examine the population genetics of viral populations over time. The data generated related to this aim will allow three hypotheses to be addressed. Is the pattern of substitution indicative of a series of selective sweeps? Are most of the fitness improvements due to a few substitutions with major effect and most of the substitutions will have very little effect? As the population reaches equilibrium will the level of variation decay to one sequence? (2) To explore the implications of parallel and convergent evolution during viral adaptation. Will parallel changes occur most of the time at sites with major as opposed to minor fitness benefits? Will related viruses adapt to the same selection with the same changes? (3) To examine the fitness cost of viral adaptation to multiple agents. Is there a fitness cost to adapting to a new selective agent? Can responses to multiple agents be predicted from responses to single agents? Is adaptation dependent on the prior history of adaptation? The PI proposes to use phage chemostats and adapt replicate populations to 43.5C. Samples will be taken each 6 hours for 3 days, then each 12 hours for 7 days. 96 samples will be taken each time point and assayed for a set of substitutions by oligonucleotide screening of predetermined regions (the set chosen from a pilot genome sequencing efforts). Fitness will be assayed (as the increase in phage per hour after infection of bacteria). These data will be used to address specific aim #1 (population genetics of viral adaptations over time) Six replicates of the first experiment will be undertaken (3 at a separate institution). These data will allow the PI to address specific aim #2 (the implications of convergent evolution during phage adaptation). One isolate from each replicate will be sequenced to determine screening sites. A second phase of research involves selecting against multiple agents. A series of agents, such as alcohol's, salts, etc. will be used as the selective agents. Selection will take place on a number of different media, as needed. Phage will be evolved that are resistant to a large number of agents, both separately and in combination. These data will allow the PI to address specific aim #3 (the fitness costs of adaptation to multiple agents).