NSF Postdoctoral Fellowship in Biology FY 2016

该行动为2015财年的NSF国家植物基因组计划生物学博士后研究奖学金提供资金。该研究金支持研究员在东道实验室的研究和培训计划，研究员还提出了扩大生物学参与的计划。大卫米切尔的研究和培训计划的标题是“全基因组范围的光强度对玉米RNA结构组的影响”。该奖学金的主办机构是宾夕法尼亚州立大学，赞助科学家是菲利普·C·贝维拉夸和莎拉M.由于玉米是一种重要的粮食和燃料作物，已作出努力，通过增加种植密度来提高玉米产量。密集种植增加了冠层覆盖，阻挡了阳光到达下部叶片，从而刺激了避阴反应，限制了作物产量。本研究所获得的信息有助于玉米基因工程在高密度下提高产量。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。通过这个项目，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的新专业知识。此外，每年有六周的时间，代表性不足的高中生将在实验室研究项目中得到指导。这项研究将使Structure-seq适应玉米，以进行高通量、全基因组的体内研究，研究基因表达、RNA二级结构和RNA-蛋白质相互作用对弱光胁迫的响应。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，这项研究将更好地使Structure-seq能够区分RNA-RNA与RNA-蛋白质相互作用。它将检查使用体内交联通过光活化核苷类似物，以提供直接接近这些相互作用的信息。此外，它将修改Structure-seq RNA结构预测算法，以纳入来自邻近信息，序列互补性和已知蛋白质结合基序的约束。本研究生成的数据将在处理后上传至适当的社区数据库，包括用于RNA结构数据的NCBI序列读数档案（SRA）（http：//www.ncbi.nlm.nih.gov/sra）和用于RNA-seq数据的GEO（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).