NSF/MCB-BSF: Rare genes and alleles in halophilic archaeal populations and communities

研究将解决以下问题：（1）微生物（细菌和古细菌）如何分化并适应新环境？(2)稀有基因在适应过程中的作用是什么？细菌和古细菌种群的进化和适应，“自私”或寄生基因在这些种群中的传播，特别是谱系内变异的维持，其中不同的微生物细胞包含略有不同的基因互补，以多种方式影响植物，动物和人类生活。这个跨学科项目将理论探索与环境样本研究和栖息在盐水环境中的古细菌的实验室实验相结合。该项目将在理论和计算生物学以及涉及基因组测序、遗传工程和实验室测试的遗传研究方面对参与者进行培训。这项研究将涉及高中学生和教师，本科生和研究生以及博士后研究员，他们将参与国际合作，以开发和测试关于罕见基因长期生存的假设。本研究将执行以下任务：（1）通过理论、建模和计算机模拟实验确定哪些群体动态可以导致泛基因组非核心部分的等位基因持续存在。找到允许种群内劳动分工出现和分子寄生虫在种群内生存的条件。 特别是，探索人口瓶颈，基因流动和重组内和之间的种群和物种的稀有基因随着时间的推移持续的影响。(2)确定哪些群落动态可以导致等位基因的共存和物种多样化。研究将集中在低或不均匀的人口内基因转移率的影响，可能是由于限制性修饰（RM）的不相容性或通过成簇的规律间隔的短回文重复序列（CRISPR）系统的靶向，我们将探索何时在人口内出现的劳动分工预计将导致多样化。(3)鉴定在盐生菌属中具有有限分布的基因。和Halorubrum spp.从基因组和元基因组序列中分析种群和物种，通过基于生物信息学的方法表征这些基因，并选择合适的候选基因进行遗传实验。(4)进行实验以确定自私遗传元件、RM和CRISPR-Cas系统对后代中重组和基因频率的影响。(5)在Hfx中进行生长竞争实验。volcanii（加上或减去一个感兴趣的基因）来衡量基因的适应性成本，这些基因有助于产生共同的共享利益和自私的遗传元素。这个美国/以色列合作项目得到了美国国家科学基金会分子和细胞生物科学部以及国际科学和工程办公室和以色列两国科学基金会的支持。

The research will address the following questions: (1) How do microorganisms (bacteria and archaea) diverge and become adapted to new environments? (2) What is the role of rare genes in the adaptation process? Evolution and adaptation of bacterial and archaeal populations, the spread of "selfish" or parasitic genes in those populations, and especially the maintenance of within-lineage variation, in which different microbial cells contain slightly different complements of genes, impacts plant, animal and human life in many ways. This interdisciplinary project combines theoretical explorations with the study of environmental samples and laboratory experimentation on archaea that inhabit saline environments. The project will train its participants in theoretical and computational biology and genetic research that involves genome sequencing, genetic engineering and laboratory tests. The research will involve high-school students and teachers, undergraduate and graduate students, and postdoctoral fellows in an international collaboration to develop and test hypotheses on the long-term survival of rare genes. The research will execute the following tasks: (1) Through theory, modeling, and in silico experiments determine which population dynamics can lead to persistence of alleles in the non-core portion of the pan-genome. Find conditions that allow for the emergence of a within population division of labor, and for the within population survival of molecular parasites. In particular, explore the impact of population bottlenecks, gene flow and recombination within and between populations and species on the persistence of rare genes over time. (2) Determine which community dynamics can lead to the coexistence of alleles and to species diversification. Research will focus on the effect of low or uneven rates of within population gene transfer, possibly due to incompatibility of restriction modification (RM) or targeting by clustered regularly spaced short palindromic repeats (CRISPR) systems and we will explore when a division of labor that arose within a population is expected to lead to diversification. (3) Identify genes having limited distribution in Haloferax spp. and Halorubrum spp. populations and species from genome and meta-genome sequences, characterize these genes through bioinformatics based approaches, and select suitable candidates for genetic experimentation. (4) Perform experiments to determine the effect of selfish genetic elements, RM and CRISPR-Cas systems on recombination and gene frequencies in the off-spring. (5) Perform growth competition experiment in Hfx. volcanii (plus versus minus a gene of interest) to measure fitness cost of genes contributing to the production of a common shared good and for selfish genetic elements.This collaborative US/Israel project is supported by the Division of Molecular and Cellular Biosciences and the Office of International Science and Engineering at the US National Science Foundation and the Israeli Binational Science Foundation.