NSF Postdoctoral Fellowship in Biology FY 2021: Using DNA-barcode lineage tracking to study ecological and evolutionary dynamics in the cucumber pathogen Erwinia tracheiphila

2021 财年 NSF 生物学博士后奖学金：利用 DNA 条形码谱系追踪研究黄瓜病原体 Erwinia tracheiphila 的生态和进化动态

• 批准号: 2109800
• 负责人: Milo Johnson
• 金额: $ 13.8万
• 依托单位: Johnson, Milo
• 依托单位国家: 美国
• 项目类别: Fellowship Award
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-06-01 至 2024-05-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2109800&HistoricalAwards=false
• 关键词: NSF; Postdoctoral; Fellowship; Biology; FY

This action funds an NSF Postdoctoral Research Fellowship in Biology for FY 2021, Integrative Research Investigating the Rules of Life Governing Interactions Between Genomes, Environment and Phenotypes. The fellowship supports research and training of the Fellow that will contribute to the area of Rules of Life in innovative ways. This research aims to use new genetic tools to understand the “evolutionary natural history” of an economically important cucumber and squash pathogen, Erwinia tracheiphila. E. tracheiphila infects plants through wounds on leaves or flowers, divides in the xylem of the plant, and is transmitted between plants by striped cucumber beetles. It is an ideal system for studying how plant pathogens adapt to different plant host and insect vector environments. Through a series of infection experiments, the Fellow will observe the process of E. tracheiphila evolution and measure the effects of mutations in squash, cucumber, and beetle environments. This research will further our understanding of this agriculturally important pathogen’s biology and will serve as a first step towards building a new model system for understanding the evolution of pathogens more generally. The Fellow will also participate in the Promoting Inclusivity in Computing (PINC) program at San Francisco State University during this work as part of an effort to broaden participation in computational biology research. This experience will also provide valuable training in education and scientific mentorship.Specifically, this research will use existing E. tracheiphila strain collections and DNA-barcode tracking technologies to study how E. tracheiphila evolves in high resolution. The Fellow will conduct lineage-tracking evolution experiments and barcode-based fitness assays to measure the fitness effects of both naturally occurring and engineered (using transposon mutagenesis) mutations in in-vivo plant and insect environments with and without competitors (other E. tracheiphila strains) and predators (phage). This work will provide a comprehensive dataset on how the fitness effects of mutations depend on the intersection of the environment, the genetic background, and ecological interactions. To maximize the broader impacts of this project, the barcoded E. tracheiphila strain libraries will be made available to other scientists, along with an open-source interactive browser that researchers can use to explore the data and test their own hypotheses. Working with scientists at UC Berkeley and Lawrence Berkeley National Labs, the Fellow will gain training - in functional bacterial genetics, plant-microbial interactions, experimental design, and mentorship - that will be essential for a successful career as a scientist or research professor.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

该行动资助 2021 财年 NSF 生物学博士后研究奖学金，研究基因组、环境和表型之间相互作用的生命规则的综合研究。该奖学金支持研究员的研究和培训，以创新的方式为生活规则领域做出贡献。这项研究旨在利用新的遗传工具来了解一种经济上重要的黄瓜和南瓜病原体欧文氏菌的“进化自然史”。 E. tracheiphila 通过叶子或花上的伤口感染植物，在植物的木质部分裂，并通过条纹黄瓜甲虫在植物之间传播。它是研究植物病原体如何适应不同植物宿主和昆虫媒介环境的理想系统。通过一系列感染实验，研究员将观察 E. tracheiphila 的进化过程，并测量南瓜、黄瓜和甲虫环境中突变的影响。这项研究将进一步加深我们对这种农业上重要的病原体生物学的理解，并将作为建立新模型系统以更广泛地了解病原体进化的第一步。在此工作期间，该研究员还将参与旧金山州立大学的促进计算包容性 (PINC) 计划，作为扩大计算生物学研究参与范围的一部分。这些经验还将提供宝贵的教育和科学指导培训。具体来说，这项研究将使用现有的 E. tracheiphila 菌株库和 DNA 条形码跟踪技术来研究 E. tracheiphila 如何以高分辨率进化。该研究员将进行谱系追踪进化实验和基于条形码的适应性测定，以测量在有或没有竞争者（其他E. tracheiphila菌株）和捕食者（噬菌体）的体内植物和昆虫环境中自然发生和工程（使用转座子诱变）突变的适应性效果。这项工作将提供一个全面的数据集，说明突变的适应度效应如何取决于环境、遗传背景和生态相互作用的交集。为了最大限度地发挥该项目的更广泛影响，带条形码的 E. tracheiphila 菌株库将提供给其他科学家，以及一个开源交互式浏览器，研究人员可以使用它来探索数据并测试他们自己的假设。该研究员将与加州大学伯克利分校和劳伦斯伯克利国家实验室的科学家合作，获得功能性细菌遗传学、植物-微生物相互作用、实验设计和指导方面的培训，这对于科学家或研究教授的成功职业生涯至关重要。该奖项反映了 NSF 的法定使命，并通过使用基金会的智力价值和更广泛的影响审查标准进行评估，被认为值得支持。