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: 2215496
• 负责人: James Melton
• 金额: $ 4.99万
• 依托单位: Spelman College
• 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=2215496&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测序技术以及相关的实验室和数据科学技能整合到他们的教学中，从而为国家利益服务。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测序既昂贵又耗时，但技术进步降低了成本和时间。让下一代研究人员做好使用这种先进技术的准备是至关重要的，但很少有本科生物学教育者有能力做到这一点。造成这种情况的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、不太准确的版本的认识。在这个项目中，冷泉港实验室DNA学习中心将与三个伙伴机构合作，减少在课堂上使用先进DNA测序技术的这些障碍。项目团队将与纽约城市理工学院、斯佩尔曼学院和波多黎各大学Río Piedras合作，共同制定协议和教学工具，将先进的DNA测序整合到生物学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年制和4年制，西班牙裔服务和历史上的黑人机构，最大限度地发挥了开发的解决方案在各种大学环境中成功实施的潜力。该项目的独立评估将为未来在全国范围内的推广奠定基础，并将支持创建高技能和多样化的美国STEM劳动力的努力。第一个项目目标是开发一个生物化学和生物信息学工作流程，以设计一套试剂和课堂友好的协议，以最大限度地降低成本，易于使用，并可定制，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（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，并可整合到本科课程中。每个项目都将把来自合作院校的教师组织到指导网络中，以促进“实践社区”的发展。这种方法将支持基于证据的课程指南的应用，因为教师会迭代地开发课程，设计解决实施挑战的方案，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建议。项目评估将促进我们对教师在课程研究经验中使用已发表的评估工具采用DNA测序技术的障碍的理解。收集到的数据将用于填补有关少数族裔院校学生研究障碍的知识空白。通过基因组学和计算生物学教育的虚拟网络，以及在国家会议上，将在机构一级分享经验教训。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。通过一级机构和社区转型轨道，该计划支持高等教育机构和学科社区的STEM教育转型和改善。该项目还得到了NSF IUSE:HSI计划的支持，该计划的目标是提高STEM本科教育的质量，提高攻读STEM副学士学位或学士学位的学生的招聘、保留和毕业率。该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。