CAREER: Emergence of Population Diversity from Stem Cell Decision Making in Asexual Planarians

个体的多样性对于种群的生存和进化是不可或缺的。这个职业项目考察了在多细胞再生有机体中，个体细胞的决策是如何产生多样性的。淡水浮游生物以其基于大量成年多能干细胞(ASCs)的再生能力而闻名。这些ASCs允许它们通过二元分裂进行繁殖，从而创建了一个克隆种群，并提出了一个问题，即该物种如何能够创造足够的多样性来在进化时间尺度上生存下来。PI最近利用统计物理学的工具证明了生殖在很大程度上是随机的，但生殖模式的分子和物理决定因素仍有待研究。这个项目的目的是验证这样的假设，即种群多样性是由个别蠕虫体内的脊椎动物繁殖机制的特殊性和ASCs的表观遗传多样性共同作用的结果。国际学生联合会将把这项建议的研究目标整合到三项教育活动中，重点是“在研究中学习”和学生的长期参与：(1)国际学生联合会正在与Vista Magnet中学建立合作伙伴关系，使六年级学生能够在整个学年与她的实验室一起开展研究项目。(2)继续努力促进高中生参与研究。特别是，她将继续让Torrey Pines高中的学生全年都能在她的实验室从事研究，使他们能够设计和执行自己的科学项目。(3)PI将继续努力在她自己的小组中以及通过她开发的以研究为中心的新的定量生物学实验室课程来促进本科生的研究。该课程将于2016年推出，目前仅面向即将入学的生物新生。在这一提议的背景下，PI将通过在课程中增加更多的物理来扩大学生群体到物理新生，从而在内容和学生群体方面创建一门真正的跨学科研究驱动的生物学和物理交界处的实验室课程。在单细胞生物体的背景下，细胞决策如何导致群体中的特定表型已经受到了许多关注，但关于表观遗传如何影响多细胞生物体中的群体多样性的了解较少。这项研究将利用行星动物和一个独特的实验装置来弥合这一知识差距，在这个装置中，已经记录了数千个个体生殖事件，并形成了PI在种群水平上研究的统计框架。PI的策略是：(1)通过对ASC定位、细胞动力学和单细胞测序的量化，检验ASC在空间方向和/或分子和细胞特征(分裂和死亡率、遗传和表观遗传多样性)方面的差异性分布假设；(2)研究无性繁殖的生物力学，利用牵引力测量和延时成像来了解资源如何在后代中分配；以及(3)基于细胞和组织水平的实验数据建立数学模型，以预测种群水平的表型多样性。该模型将通过rna-seq和统计分析，将其预测与现有的实验数据和特殊设计的创始人个体的繁殖模式进行比较，其中所有细胞已知来自单一的ASC。总之，这些方法将允许PI检验这样一个假设，即个体干细胞的空间表观遗传异质性与随机繁殖机制相结合，决定了种群水平上的种内表型差异，这将通过生殖行为来衡量。这项拟议的工作将为跨代表观遗传在无性多细胞生命进化成功中的作用提供新的线索。在更广泛的层面上，干细胞决策目前受到相当大的关注，因为了解干细胞如何随机地改变状态并对环境线索做出反应是成功的干细胞治疗所必需的。该项目得到了物理学部的生命系统物理学计划和分子和细胞生物科学部的细胞团的联合支持

Diversity of individuals is indispensable for population survival and evolution. This CAREER project examines how diversity can emerge from decision making of individual cells in a multicellular regenerative organism. Freshwater planarians are famous for their regenerative capabilities that are based on a large number of adult pluripotent stem cells (ASCs). These ASCs allow them to reproduce by binary fission, thus creating a clonal population and raising the question of how this species is able to create sufficient diversity to survive on evolutionary time scales. Using tools from statistical physics the PI recently demonstrated that reproduction is largely random, but that reproductive patterns exist whose molecular and physical determinants remain to be investigated. This project aims at testing the hypothesis that population diversity arises from a joint effect of the specifics of planarian reproduction mechanics and epigenetic diversity of ASCs in individual worms. The PI will integrate the research objectives of this proposal into three educational initiatives, which focus on "learning through research" and long-term engagement of students: (1) The PI is establishing a partnership with Vista Magnet Middle school that allows 6th graders to work together with her lab on research projects throughout the school year. (2) The PI will continue her efforts toward participation of high school students in research. In particular, she will continue to enable students from Torrey Pines High School to engage in research in her lab throughout the year, which allows them to design and execute their own science projects. (3) The PI will continue her efforts in promoting undergraduate research, in her own group as well as through a new research-centered, quantitative biology laboratory course that she has developed. The course will launch in 2016 and is currently for incoming biology freshmen only. In the context of this proposal, the PI will widen the student population to physics freshmen by adding more physics to the curriculum, and thus create a truly interdisciplinary research-driven laboratory course at the interface of biology and physics in terms of content and student population.How cellular decision-making causes specific phenotypes in a population has received a lot of attention in the context of single celled organisms, but less is known about how epigenetic inheritance affects population diversity in multicellular organisms. This study will close this knowledge gap using planarians and a unique experimental setup, whereby thousands of individual reproductive events have already been recorded and form the statistical framework for the PI's studies on the population level. The PI's strategy is to (1) test the hypothesis that within individual planarians, ASCs are differentially distributed, in terms of spatial orientation and/or molecular and cellular characteristics (division and death rates, genetic and epigenetic diversity) through quantification of ASC localization, cellular dynamics, and single cell sequencing, (2) investigate the biomechanics of asexual reproduction to understand how resources get distributed among offspring using traction force measurements and time-lapse imaging, and (3) develop a mathematical model based on the cellular and organismal level experimental data to predict population level phenotypic diversity. The model will be tested by comparing its predictions with existing experimental data and the reproductive patterns of specially designed founder individuals in which all cells are known to originate from a single ASC, through RNA-seq and statistical analysis. Together, these approaches will allow the PI to test the hypothesis that spatial epigenetic heterogeneity of stem cells in individuals combined with a stochastic reproduction mechanism determine intraspecies phenotypic differences on the population level, which will be measured in terms of reproductive behaviors. The proposed work will shed new light onto the role of transgenerational epigenetic inheritance for the evolutionary success of asexual multicellular life. On a broader level, stem cell decision-making is currently receiving considerable attention because an understanding of how stem cells switch states stochastically and in response to environmental cues is indispensable for successful stem cell therapies.This project is being jointly supported by the Physics of Living Systems program in the Division of Physics and the Cellular Cluster in the Division of Molecular and Cellular Biosciences