Course-based undergraduate research experiences (CUREs) are widely regarded as one of the most effective approaches to teaching undergraduate STEM topics. This project explored how cutting-edge biotechnology - specifically Oxford Nanopore sequencing - could be leveraged and scaled to enable large numbers of educators to expose students to research experiences and workforce-relevant skills.

DNA sequencing - reading the instructions contained in the so-called molecule of life - 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. A handheld Oxford Nanopore MinION device generates up to 50 billion DNA bases - the equivalent of 16 human genomes - in 72 hours for less than $2,000. Nanopore startup costs are 30-50 times lower than other high-throughput sequencing platforms putting them within reach of most undergraduate classrooms. Nanopore's mobility, ability to generate long reads (>1 million bases), and increasing accuracy have resulted in its adoption for de novo genome assembly, detection of DNA modifications, RNA sequencing, and metagenomics. Consequently, faculty can focus on a single common platform to support a variety of student research questions.

Through the collaborative efforts of Cold Spring Harbor Laboratory's DNA Learning Center, Spelman College, New York City College of Technology, and the University of Puerto Rico - Rio Piedras, the project developed biochemistry protocols, pedagogical resources, and faculty training initiatives that now enable educators across the U.S. to implement CUREs using real-world genomics tools.

Key Accomplishments and Intellectual Merit

This project built the largest network of undergraduate faculty using Nanopore sequencing in their classrooms, demonstrating that Nanopore sequencing makes it practical and affordable for undergraduates across a range of institutional contexts to use the same tools and methods to analyze DNA sequence as researchers at advanced multi-million-dollar genome centers.

The project achieved all its proposed goals by developing and refining low-cost, classroom-friendly protocols for DNA barcoding, 16S microbiome analysis, and whole-genome sequencing. These resources - including annotated protocols and video tutorials - were published in the faculty co-authored Nanopore for Educators eBook (available at nanopore4edu.org). Demonstration projects at partner institutions applied these methods in diverse contexts, from sequencing endangered plants and phages to analyzing microbiomes in wastewater.

Over 174 educators from 29 U.S. states, Puerto Rico, Northern Marianas Islands, and Guam participated in workshops and mentoring networks, significantly increasing their confidence in implementing sequencing-based CUREs. External evaluation confirmed gains in faculty skills and adoption and further refined an adapted "Diffusion of Innovations" framework as a useful tool for assessing faculty readiness to implement DNA sequencing in CUREs.

The project also supported the launch of a public-private partnership with Oxford Nanopore Technologies, helping establish the "Education Beta" program. This program provides discounted reagents to educators, thereby expanding classroom access to sequencing tools. Collectively, these accomplishments have built a sustainable network and a scalable model for integrating genomics into undergraduate biology education.

Broader Impacts

This project increased access to cutting-edge genomics by equipping educators - including those at under-resourced institutions - with the tools, training, and support needed to implement real-world sequencing in their classrooms. By engaging students in hands-on, course-based research, the project fostered scientific identity, critical thinking, and data literacy. These skills support both workforce development in biotechnology and informed public engagement with issues such as DNA privacy, public health, and bioethics.

The open-access Nanopore for Educators eBook and the national faculty network promote sustainable change, enabling long-term integration of genomics across diverse educational contexts. All activities, workshops, and resources remain freely available to undergraduate faculty at any U.S. institution. The core deliverables - especially the eBook, mentoring network, and evaluation insights - offer a scalable and sustainable pathway for expanding course-based research to institutions nationwide.

Last Modified: 06/27/2025
Modified by: Jose L Agosto Rivera