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， 如何开发抗病毒疗法。 有三个具体目标， 提议 (1)为了研究病毒种群的群体遗传学， 时间 与这一目标相关的数据将允许三个假设， 被解决。 这种替代模式是否表明了一系列 选择性扫描 大部分的健身改善是由于一些 大部分的替代品会有很大的影响， 小影响？ 当人口达到平衡时， 变异衰减为一个序列 (2)为了探索 病毒适应过程中的平行和趋同进化。 将平行 大多数情况下，变化发生在主要而不是次要的站点 健身福利？ 相关的病毒是否会适应相同的选择 同样的变化？ (3)为了研究病毒适应的适应性成本， 多个特工 适应一个新的选择是否有健身成本 探员？ 对多种药物的反应是否可以通过对 单一代理人？ 适应是否依赖于先前的适应史？ PI建议使用噬菌体恒化器并调整复制种群， 43.5C. 将在3天内每6小时采集一次样本，然后每12小时采集一次样本 7天。 每个时间点将采集96份样本，并对一组样本进行分析 通过对预定区域的寡核苷酸筛选（ 从试验性基因组测序工作中选择的集合）。 健康将被检测 (as细菌感染后每小时噬菌体的增加）。 这些数据 将用于解决具体目标#1（病毒的群体遗传学） （随着时间的推移） 第一个实验将重复进行六次（单独进行3次） 机构）。 这些数据将使PI能够解决具体目标#2（ 噬菌体适应过程中的趋同进化的影响）。 一种分离物 将对每个重复样品进行测序以确定筛选位点。 一 研究的第二阶段涉及对多个代理进行选择。 一 一系列的代理人，如酒精，盐等将被用作 选择剂。 选择将在许多不同的媒体上进行， 根据需要 噬菌体将进化成抵抗大量的 代理人，无论是单独或组合。 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） 代理商）。

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).