EAGER: Exploratory Research in Accordion-Style Genome Dynamics

智力优点在所有生物体中，动态的遗传变化都可能发生，其中染色体片段相对于周围区域的拷贝增加或减少。 基因组的这种扩张和收缩，被称为"手风琴式动力学"，可以在适应和进化中发挥关键作用。虽然这个过程有许多重要的生物学意义，但很难研究。识别特定遗传改变的困难源于染色体变化的瞬时性和随机性以及群体中不同细胞中发生的事件的可变性。本计画将利用土壤细菌不动杆菌ADP-1的特性，进行实验研究。这种细菌中天然转化和重组的高效率使得有可能设计和工程化菌株，其中群体的大多数细胞具有在高拷贝串联阵列中彼此相邻排列的染色体的相同区段的多个拷贝。然后，这些工程菌株可以作为实验室模型来研究适应和进化中拷贝数变化的分子细节。首先，特定的基因将从基因组中删除。接下来，其他基因将被正确定位，以便如果基因组扩展到串联阵列中，它们可以取代缺失的基因。在重组的细菌群体中，大量具有相同的染色体"扩展"版本的细胞增加了进化过程的机会，以优化新的遗传和酶活性。重组的细菌群体还放大了在实验期间可以检测到的信号，使得可以更容易地观察到特定的遗传变化。这项研究将涉及测试特定的基因集，以证明基因组扩展如预测的那样发生。在建立串联阵列之后，将有可能改变细菌的生长条件，以允许以高度灵敏和可再现的方式监测和测试遗传进化。开发一个系统，经历定向遗传扩增的优势还包括促进细菌生产的重要化合物的生物技术和产生新的酶与有用的activity.Broader ImpactsThe染色体重排的操作和分析将有助于在科学界的努力，以利用大规模的DNA序列数据。此外，格鲁吉亚大学正在进行的项目将与该项目相吻合，以帮助扩大参与和增加多样性。这些计划包括NSF支持的原核生物学本科生研究经验（REU）网站计划。对土壤细菌不动杆菌ADP1的研究也被整合到本科实验室课程中，该课程使用真实的研究项目，让学生参与主动学习和科学参与。 高中生、本科生和研究生将参与该项目，他们将接受遗传学、生物化学和生物信息学的多学科培训。

Intellectual MeritIn all organisms dynamic genetic changes can occur in which segments of the chromosome increase or decrease in copy relative to surrounding regions. Such expansion and contraction of the genome, termed "accordion-style dynamics," can play a critical role in adaptation and evolution. Although the process has many important biological implications, it is difficult to study. The difficulty in identifying specific genetic alteration stems from the transient and stochastic nature of the chromosomal changes and the variability of the events that occur in different cells of the population. This project will exploit special features of a soil bacterium, Acinetobacter baylyi ADP1, to facilitate experimental investigation. The high efficiency of natural transformation and recombination in this bacterium make it possible to design and engineer strains in which most cells of the population have multiple copies of the same segment of the chromosome arranged adjacent to each other in a high copy tandem array. These engineered strains can then serve as laboratory models to investigate the molecular details of the contribution of copy number change in adaptation and evolution. First, specific genes will be deleted from the genome. Next, other genes will be properly positioned such that they can substitute for the missing genes if the genome expands to place them in tandem arrays. In the restructured bacterial population, the large number of cells that have the same "expanded" version of the chromosome increase the opportunity for evolutionary processes to optimize new genetic and enzymatic activities. The restructured bacterial population also amplifies the signals that can be detected during experimentation such that the specific genetic changes can be much more readily observed. This research will involve testing specific gene sets to demonstrate that genomic expansion occurs as predicted. Having established the tandem arrays, it will be possible to vary the growth conditions for the bacteria to allow genetic evolution to be monitored and tested in a highly sensitive and reproducible manner. The advantages of developing a system that undergoes directed genetic expansion also include facilitating the bacterial production of important compounds for biotechnology and generating new enzymes with useful activities.Broader ImpactsThe manipulation and analysis of chromosomal rearrangements will contribute to efforts in the scientific community to take advantage of large scale DNA sequence data. In addition, ongoing programs at the University of Georgia will dovetail with this project to help broaden participation and increase diversity. Such programs include an NSF-supported Research Experiences for Undergraduate (REU) site program in prokaryotic biology. Research on the soil bacterium Acinetobacter baylyi ADP1 is also being integrated into an undergraduate lab course that uses authentic research projects to involve students in active learning and scientific engagement. High school students, undergraduates, and graduate students will participate in this project, and they will receive multidisciplinary training in genetics, biochemistry, and bioinformatics.