Developing Foundations for Nanopore DNA Sequencing Course-based Undergraduate Research Experiences at Minority-Serving Institutions

为少数民族服务机构基于纳米孔 DNA 测序课程的本科生研究经验奠定基础

• 批准号: 2216349
• 负责人: Jason Williams
• 金额: $ 17.96万
• 依托单位: Cold Spring Harbor Laboratory
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-06-15 至 2024-05-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2216349&HistoricalAwards=false
• 关键词: Developing; Foundations; Nanopore; DNA; Sequencing

This project aims to serve the national interest by making it easier for educators to integrate advanced DNA sequencing technologies and related laboratory and data science skills into their teaching. DNA sequencing allows us to read the instructions contained in DNA — the so-called “molecule of life”. DNA sequencing has impacted every area of biology, enabling researchers to understand more about how life works. This technology is used for research that boosts agriculture, monitors biodiversity, creates energy solutions, and improves human health. Previously, DNA sequencing was expensive and time consuming, but technological improvements have lowered the cost and the time involved. Preparing the next generation of researchers to use this advanced technology is essential, but few undergraduate biology educators are equipped to do this. Reasons for this include complex protocols, lack of lesson materials, insufficient computer skills, and educator perceptions of earlier, less accurate versions of this technology. In this project, the Cold Spring Harbor Laboratory DNA Learning Center will work with three partner institutions to reduce these barriers to using advanced DNA sequencing technology in the classroom. Together with New York City College of Technology, Spelman College, and University of Puerto Rico, Río Piedras, the project team will co-develop protocols and teaching tools that integrate advanced DNA sequencing into hands-on training for biology undergraduates. Faculty from these institutions and other partners include 2- and 4-year, Hispanic-serving, and Historically Black institutions, maximizing the potential that the solutions developed can be successfully implemented in a variety of college settings. Independent evaluation of the project will lay a foundation for future dissemination at a national level and will support efforts to create a highly skilled and diverse US STEM workforce.The first project objective intends to develop a biochemistry and bioinformatics workflow to design a kit of reagents and classroom-friendly protocols that minimize cost, are easy-to-use, and are customized to support course-based student research projects. Existing NSF-funded computing solutions (e.g., CyVerse, JetStream, XSEDE) will support prototype bioinformatics workflows, and sample datasets. The project team will develop demonstration DNA sequencing projects (e.g., genome assembly, biodiversity studies, and metagenomics) that explore compelling research questions and that can be integrated into undergraduate coursework. Each project will organize faculty from partner institutions into mentoring networks to promote the development of a “community of practice.” This approach will support the application of evidence-based curriculum guidelines as faculty iteratively develop lessons, devise solutions to implementation challenges, and pilot materials with students. Expert researchers and educators will provide advice on achieving both the scientific and pedagogical goals of the project. Project evaluation will advance our understanding of the barriers to faculty adoption of DNA sequencing technology in course-based research experiences using published assessment tools. The data collected will be applied to fill gaps in knowledge about barriers to student research at minority-serving institutions. Lessons learned will be shared at the institutional level, through virtual networks for genomics and computational biology education, and at national conferences. The NSF IUSE: EHR Program supports research and development projects to improve the effectiveness of STEM education for all students. Through the Level 1 Institutional and Community Transformation track, the program supports efforts to transform and improve STEM education across institutions of higher education and disciplinary communities. This project is also supported by the NSF IUSE:HSI program, which has the goals of enhancing the quality of undergraduate STEM education, and increasing the recruitment, retention, and graduation rates of students pursuing associate’s or baccalaureate degrees in STEM.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

该项目旨在通过使教育工作者更容易将先进的DNA测序技术和相关的实验室和数据科学技能整合到他们的教学中来服务于国家利益。DNA测序使我们能够读取DNA中包含的指令-所谓的“生命分子”。DNA测序影响了生物学的各个领域，使研究人员能够更多地了解生命是如何运作的。这项技术用于促进农业，监测生物多样性，创造能源解决方案和改善人类健康的研究。以前，DNA测序是昂贵和耗时的，但技术的改进降低了成本和所需的时间。培养下一代研究人员使用这种先进技术是必不可少的，但很少有本科生物学教育工作者有能力做到这一点。其原因包括复杂的协议，缺乏教材，计算机技能不足，以及教育工作者对这种技术的早期，不太准确的版本的看法。在该项目中，冷泉港实验室DNA学习中心将与三个合作机构合作，减少在课堂上使用先进DNA测序技术的障碍。该项目团队将与纽约市理工学院、斯佩尔曼学院和里奥皮德拉斯的波多黎各大学一起共同开发协议和教学工具，将先进的DNA测序整合到生物本科生的实践培训中。来自这些机构和其他合作伙伴的教师包括2年和4年，西班牙裔服务，历史上的黑人机构，最大限度地提高了开发的解决方案可以在各种大学环境中成功实施的潜力。对该项目的独立评估将为未来在国家层面的传播奠定基础，并将支持创建高技能和多样化的美国STEM劳动力的努力。第一个项目目标旨在开发生物化学和生物信息学工作流程，以设计试剂盒和课堂友好的协议，最大限度地降低成本，易于使用，并定制以支持基于课程的学生研究项目。现有的NSF资助的计算解决方案（例如，CyVerse、JetStream、XSEDE）将支持原型生物信息学工作流程和样本数据集。项目团队将开发示范DNA测序项目（例如，基因组组装，生物多样性研究和宏基因组学），探索引人注目的研究问题，并可以整合到本科课程。每个项目都将把伙伴机构的教员组织到辅导网络中，以促进“实践社区”的发展。这种方法将支持循证课程指南的应用，因为教师反复开发课程，设计实施挑战的解决方案，并与学生一起试用材料。专家研究人员和教育工作者将为实现该项目的科学和教学目标提供咨询意见。项目评估将促进我们对教师在基于课程的研究经验中采用DNA测序技术的障碍的理解。收集的数据将用于填补少数群体服务机构学生研究障碍方面的知识空白。将通过基因组学和计算生物学教育虚拟网络，在机构一级和在国家会议上分享经验教训。NSF IUSE：EHR计划支持研究和开发项目，以提高所有学生STEM教育的有效性。通过1级机构和社区转型轨道，该计划支持努力改造和改善高等教育机构和学科社区的STEM教育。该项目还得到了NSF IUSE：HSI项目的支持，该项目的目标是提高本科STEM教育的质量，并提高攻读STEM副学士或学士学位学生的录取率、保留率和毕业率。该奖项反映了NSF的法定使命，并通过使用基金会的智力价值和更广泛的影响审查标准进行评估，被认为值得支持。