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

UnPAK(大学生表型拟南芥基因敲除)项目使用拟南芥植物来研究DNA序列的差异如何以及何时导致与生存、生长和繁殖相关的特征的差异。它将在索尔克研究所产生的突变的综合集合中检测突变的影响，然后将结果汇编到一个全面的数据库中。为了研究遗传和环境效应的相互作用，UnPAK的实验在多个种植设施和实验室内和跨多个生长设施和实验室重复进行，其中一部分实验故意操纵土壤因素、水分和温度，以了解这些重要的生态因素如何与遗传相互作用。UnPAK将调查足够多的突变系，以覆盖拟南芥基因组的三分之一(约9000个基因)。所有数据将被上传到arabidopsisunpak.org的公共数据库中，这个观察到的特征数据库与现有的基因组数据库相链接。UnPAK产生的证据将使检验关于基因组特征和重要植物特征之间关系的中心假设成为可能。例如，这些数据可以用来测试突变的影响是通过基因属性，如过去的选择分子签名、基因功能、基因家族大小，还是通过自然种群中的变异模式来预测的。unPAK的中心是本科生研究人员在实验室和课堂上的参与，在遗传学、生态学、进化论和生物信息学方面对本科生进行综合教育和培训。该网络覆盖了不同的高等教育机构，在3年内有100多名本科生学徒参与了13个实验室的工作。该计划将支持20多个基于课程的本科生研究经验(CURE)，覆盖600多名学生。任何关于特定基因对水果生产、生存或生活史的影响的发现，都将对作物物种的潜在应用产生重大的、更广泛的影响。作为该项目的最后一部分，unPAK研究网络本身正在进行研究。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。

The unPAK (undergraduates Phenotyping Arabidopsis Knockouts) project 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 will be uploaded into a public database at arabidopsisunpak.org, and this database of observed traits is linked 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.