RUI: Collaborative: unPAK: undergraduates Phenotyping Arabidopsis Knockouts: A distributed genomic approach to examine evolutionarily important traits

RUI：协作：unPAK：本科生拟南芥表型敲除：检查进化重要性状的分布式基因组方法

• 批准号: 1355041
• 负责人: Hilary Callahan
• 金额: $ 22.56万
• 依托单位: Barnard College
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2014
• 资助国家: 美国
• 起止时间: 2014-06-01 至 2018-05-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1355041&HistoricalAwards=false
• 关键词: RUI; Collaborative; unPAK; undergraduates; Phenotyping

The unPAK project (undergraduates Phenotyping Arabidopsis Knockouts) uses the plant Arabidopsis thaliana to examine how and when differences in DNA sequences lead to differences in traits related to survival, growth, and reproduction. It will detect effects, if any, of mutation in a comprehensive collection of mutants generated by the SALK Institute, and will then compile results in a comprehensive database. To examine the interaction of genetic and environmental effects, unPAK's experiments are replicated within and across multiple growth facilities and labs, and a subset of experiments deliberately manipulate soil factors, moisture, and temperature to see how these important ecological factors interact with genetics. unPAK will survey enough mutant lines to reach coverage of a third of the A. thaliana genome (approximately 9,000 genes). All data are uploaded into a public database at arabidopsisunpak.org, and the unPAK project links its database of observed traits to existing genomic databases. Evidence produced by unPAK will enable testing central hypotheses about the relationship between genomic features and important plant characteristics. For example, the data can be used to test whether the effects of mutation are predicted by gene attributes such as molecular signatures of selection in the past, gene function, gene family size, or by patterns of variability in natural populations.unPAK is centered around participation of undergraduate researchers in the lab and the classroom, educating and training undergraduates integratively in genetics, ecology, evolution, and bioinformatics. The network extends across diverse post-secondary institutions, with over 100 undergraduate apprentices participating across 13 laboratories in 3 years. Greater than 20 course-based undergraduate research experiences (CUREs) will be supported by the program, reaching over 600 students. Any discoveries about the influence of particular genes on fruit production, survival, or life history will have significant broader impacts in potential application to crop species. As a final part of the project the unPAK research network itself is being studied. Using mixed-methods approaches from the social sciences, researchers are documenting interactions among network participants to analyze changes in network structure over time, and to investigate factors that influence student participation and outcomes, including students' accrual of human, cultural, and social capital.

unPAK项目（本科生拟南芥敲除表型）使用植物拟南芥来研究DNA序列的差异如何以及何时导致与生存，生长和繁殖相关的性状差异。 它将在SALK研究所产生的一系列突变体中检测突变的影响（如果有的话），然后将结果编入一个综合数据库。为了研究遗传和环境影响的相互作用，unPAK的实验在多个生长设施和实验室内和跨多个生长设施和实验室复制，并且实验的一个子集故意操纵土壤因素，湿度和温度，以了解这些重要的生态因素如何与遗传学相互作用。unPAK将调查足够的突变株系，以覆盖三分之一的A。拟南芥基因组（约9，000个基因）。所有数据都上传到arabidopsisunpak.org的公共数据库中，unPAK项目将其观察到的性状数据库与现有的基因组数据库链接起来。unPAK产生的证据将能够测试关于基因组特征和重要植物特征之间关系的核心假设。例如，这些数据可以用来测试突变的影响是否是由基因属性预测的，如过去选择的分子特征，基因功能，基因家族大小，或自然种群的变异模式。该网络扩展到不同的高等教育机构，在3年内有100多名本科生学徒参加了13个实验室。 超过20个基于课程的本科研究经验（CURES）将由该计划支持，达到600多名学生。任何关于特定基因对水果产量、生存或生活史影响的发现，都将对作物物种的潜在应用产生重大而广泛的影响。作为该项目的最后一部分，正在研究巴和平研究网络本身。使用社会科学的混合方法，研究人员正在记录网络参与者之间的互动，以分析网络结构随时间的变化，并调查影响学生参与和结果的因素，包括学生对人力，文化和社会资本的积累。