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

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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.