NSF Postdoctoral Fellowship in Biology FY 2016

本行动资助2015财年美国国家科学基金会国家植物基因组计划生物学博士后研究奖学金。该奖学金支持奖学金获得者在主办实验室的研究和培训计划，该奖学金获得者还提出了扩大生物学参与的计划。David Mitchell的研究和培训计划的标题是“光强度对玉米RNA结构影响的全基因组研究”。该奖学金的主办机构是宾夕法尼亚州立大学，赞助科学家是Philip C. Bevilacqua博士和Sarah M. Assmann博士。由于玉米是重要的粮食和燃料作物，人们通过增加种植密度来提高玉米产量。密集的种植增加了树冠覆盖，阻挡了阳光照射到下层叶子，从而刺激了遮荫躲避反应，从而限制了作物产量。本研究所得信息可用于玉米基因工程，提高高密度种植条件下的产量。在这项研究中使用和开发的强大工具将彻底改变RNA结构和功能的研究方式。通过该项目，研究人员将获得植物生物学技术以及计算和生物信息学分析方面的新专业知识。此外，每年有六周的时间，未被充分代表的高中生将在实验室研究项目中得到指导。本研究将采用Structure-seq技术对玉米进行高通量、全基因组的体内基因表达、RNA二级结构和RNA-蛋白相互作用在弱光胁迫下的响应研究。通过应用新的结构探测化学试剂，使Structure-seq能够探测所有四种RNA碱基，本研究将更好地使Structure-seq能够区分RNA-RNA和RNA-蛋白相互作用。它将检查通过光激活核苷类似物的体内交联的使用，以提供这些相互作用的直接接近信息。此外，它将修改structure -seq RNA结构预测算法，以纳入邻近信息，序列互补性和已知蛋白质结合基序的约束。本研究产生的数据将在处理后上传到相应的社区数据库，包括NCBI序列读取档案（SRA）的RNA结构数据（http://www.ncbi.nlm.nih.gov/sra）和GEO的RNA-seq数据（www.ncbi.nlm.nih.gov/geo）。

This action funds an NSF National Plant Genome Initiative Postdoctoral Research Fellowship in Biology for FY 2015. The fellowship supports a research and training plan in a host laboratory for the Fellow who also presents a plan to broaden participation in biology. The title of the research and training plan for this fellowship to David Mitchell is "A Genome-wide Investigation of Light Intensity Effects on the Maize RNA Structurome". The host institution for the fellowship is the Pennsylvania State University and the sponsoring scientists are Dr. Philip C. Bevilacqua and Dr. Sarah M. Assmann.As maize is a vital food and fuel crop, efforts have been made to increase maize yields by increasing planting density. Dense planting increases the canopy cover and blocks sunlight from reaching the lower leaves, thus stimulating shade avoidance responses which limits crop yield. Information obtained from this research can contribute to genetic engineering of maize to improve yield under high planting densities. Powerful tools used and developed in this research will revolutionize how RNA structure and function are studied. Through this project, the researcher will gain novel expertise in plant biology techniques and in computational and bioinformatics analysis. Furthermore, for six weeks annually underrepresented high school students will be mentored in laboratory research projects.This research will adapt Structure-seq to maize to perform high-throughput, genome-wide in vivo investigation of gene expression, RNA secondary structures, and RNA-protein interactions in response to low-light stress. By applying new structure-probing chemical reagents that allow Structure-seq to probe all four RNA bases, this research will better enable Structure-seq to distinguish RNA-RNA from RNA-protein interactions. It will examine the use of in vivo crosslinking via photoactivatable nucleoside analogues to provide direct proximity information on these interactions. Furthermore, it will modify the Structure-seq RNA structure prediction algorithm to incorporate constraints from proximity information, sequence complementarity, and known protein binding motifs. Data generated from this research will be uploaded upon processing to the appropriate community databases, including the NCBI Sequence Reads archive (SRA) for RNA structure data (http://www.ncbi.nlm.nih.gov/sra) and GEO for RNA-seq data (www.ncbi.nlm.nih.gov/geo).