RCN-UBE: A New Faculty Development Approach to Expand Authentic Course-based Research Opportunities Focused on Microbial Bioinformatics and Functional Genomics

该 RCN-UBE 项目旨在通过向美国各地 2 年制和 4 年制学院和大学的教员提供培训研讨会、更新的基于网络的基因组重新注释平台和协作支持网络，极大地将真实基因组学、生物信息学和功能基因组学研究纳入本科课程。基因组信息的指数级增长已经改变了生物学，但该信息的价值取决于对基因功能（注释）的准确预测和实验评估，测试这些预测。该网络将使教师能够让学生参与概念、技能和实验思维，这不仅提高学生的科学素养和解决问题的能力，而且还使他们能够通过对微生物基因组中大量基因进行更深入的第二遍注释和对预测基因功能的实验测试来为科学和社会做出贡献。网络培训研讨会将基于地理节点模型，其中附近的参与者组商定共同的会议地点和时间，然后一名或多名培训师前往该地点举办周末研讨会。每个研讨会将重点关注（a）基因注释（基因组学和生物信息学）和功能预测或（b）基因功能的实验测试（功能基因组学）。基因注释培训将分为几个模块，例如序列相似性搜索和蛋白质定位预测，并将涉及适当的免费生物信息学工具。使用免费的网络平台对细菌和古细菌基因组进行重新注释 (GENI-ACT)，用户可以轻松地为多个课程中的大量学生构建、分配和管理基因注释。每个基因注释的虚拟实验室笔记本允许单独或协作地收集和分析数据。该平台功能包括学生将自己的生物信息学分析与研究文献中的数据以及他们自己的功能基因组学工作相结合，以得出结论并将数据提供给更大的研究社区和公众。功能基因组学研讨会将重点讨论如何在实验室课程背景下将众所周知的（例如，转座子诱变、PCR）和更专业的实验室策略（例如，定点诱变、蛋白质过度表达）结合起来，以测试基因的预测功能。将鼓励参与者与培训师和其他参与者就非模型菌株和他们感兴趣的基因的适当策略进行集思广益。将鼓励参与者使用免费提供的网络教学/研究支持结构（GENI-SCIENCE）在附近机构内部和之间建立合作。网络利用社交媒体工具提供了进一步的思想和支持的交流。该项目由生物科学理事会 (BIO) 生物基础设施司和教育和人力资源理事会 (EHR) 本科教育司联合资助，作为他们努力解决本科生物教育愿景和变革：行动呼吁 (http://visionandchange.org/finalreport/) 中提出的挑战的一部分。该项目还得到 BIO 理事会分子和细胞生物科学部 (MCB) 的共同资助。

This RCN-UBE project aims to greatly expand the incorporation of authentic genomics, bioinformatics, and functional genomics research into the undergraduate curriculum by providing training workshops, an updated Web-based genome re-annotation platform and a collaborative support network to faculty members at 2- and 4-year colleges and universities across the U.S. Biology has been transformed by the exponential increase in genomic information, but the value of that information hinges upon accurate predictions of gene function (annotation) and experimental evaluation that tests those predictions. The network will empower faculty to engage students in the concepts, skills, and experimental thinking that not only increases student scientific literacy and problem-solving abilities but also allows them to contribute to science and society right now through the deeper second-pass annotation of large numbers of genes in microbial genomes and experimental testing of predicted gene function.Network training workshops will be based on a geographic node model wherein groups of nearby participants agree on a common meeting site and time, and then one or more trainers travel to that site to run a weekend workshop. Each workshop will focus on either (a) gene annotation (genomics and bioinformatics) and functional prediction or (b) experimental testing of gene function (functional genomics). Training in gene annotation will be broken down into several modules such as sequence similarity searches and prediction of protein localization, and will involve appropriate freely available bioinformatics tools. The use of a freely available Web platform for re-annotation of genomes from Bacteria and Archaea (GENI-ACT) allows for users to easily construct, assign, and manage gene annotations across a large number of students in multiple courses. Virtual lab notebooks for each gene annotation allow individual or collaborative work in collecting and analyzing data. The platform capability includes students combining their own bioinformatics analyses with data from the research literature and their own functional genomics efforts to reach conclusions and make the data available for the larger research community and public. Workshops on functional genomics will focus on how to bring together well-known (e.g., transposon mutagenesis, PCR) and more specialized lab strategies (e.g., site-directed mutagenesis, protein overexpression) within the context of laboratory courses to test the predicted function of genes. Participants will be encouraged to brainstorm with trainers and other participants on appropriate strategies for non-model bacterial strains and genes of interest to them. Participants will be encouraged to form collaborations within and between nearby institutions using a freely available Web teaching/research support structure (GENI-SCIENCE). Further cross-fertilization of ideas and support are provided by the network using social media tools. This project is being jointly funded by the Directorate for Biological Sciences (BIO), Division of Biological Infrastructure, and the Directorate for Education and Human Resources (EHR), Division of Undergraduate Education as part of their efforts to address the challenges posed in Vision and Change in Undergraduate Biology Education: A Call to Action (http://visionandchange.org/finalreport/). This project is also co-funded by the Division Molecular and Cellular Biosciences (MCB) in the BIO directorate.