Summer of Nanopore Sequencing 2025

• May 14–16: Arecibo C3 STEM Center, Arecibo, PR
• June 2–4: Kennedy-King College, Chicago, IL
• June 9–11: Pima Community College and Arizona-Sonora Desert Museum, Tucson, AZ
• June 23–25: Forsyth Tech Community College, Winston-Salem, NC
• June 30–July 2: Dolan DNA Learning Center, Cold Spring Harbor, NY
• August 6–8: San Jacinto College, Generation Park, Houston, TX

Nanopore sequencing, which analyzes individual DNA molecules in real time, is the “next big thing” in biology education. It promises to put real-time DNA sequencing within reach of any motivated bioscience teacher. We envision a MinION miniature nanopore sequencing device in every biology teaching lab within a decade.

The DNA Learning Center (DNALC) and Oxford Nanopore are working together to adapt nanopore sequencing for use in education—including improved chemistry, workflows, directions, and packaging/pricing attractive to high school and college faculty. The DNALC’s popular DNA Subway is currently being redeveloped for full mobile use, including a new line for nanopore sequence analysis. Workshop participants will be the first to test this streamlined approach for combining MinION sequence data with the DNA Subway pipeline—providing DNA sequencing and analysis any time, any place, by anyone.

The workshop will appeal especially to high school and college faculty who mentor student research or participate in large, distributed projects, such as DNA barcoding (DNALC), SEA-PHAGES (Howard Hughes Medical Institute), and Tiny Earth (University of Wisconsin). At less than $10 per barcode or metabarcode sample and $30 per phage or organelle genome, nanopore sequencing is a speedy and cost-effective alternative to commercial sequencing. Nanopore takes DNA sequencing out of the “black box,” exposing students to every step of the workflow. Workshop participants will have the unique opportunity to immediately sequence and analyze DNA from samples they bring to the workshop. Barcode, metabarcode, and small genome sequencing will be covered.

All workshop participants will receive a $300 stipend. Although we expect that most participants will commute to the workshop, funding for travel, room, and board is available for a limited number of qualified applicants living outside commuting distance.

Applications will be reviewed and acceptances emailed continuously, beginning April 18, 2025.

Supported by grants from the U.S. National Science Foundation Advanced Technological Education Program (#1901984), and Arecibo Center for STEM Education and Research (#2321729). Equipment and supplies provided by Oxford Nanopore.

DNA Barcoding Workshop
Urban Barcode Project (UBP) Educator Training

Participants will be introduced to the DNA barcoding laboratory investigation and bioinformatics infrastructure. Teachers are eligible to attend the training workshop if they teach a high school science class or a science research program in the New York metropolitan area. Teachers who complete this workshop are invited to organize student teams and propose Urban Barcode Project (UBP) projects.

Once trained, teachers register on the barcoding portal on this site to enter student research teams in grades 9 to 12. Teams will develop an original research proposal and receive feedback from UBP staff. Teams with accepted proposals will receive supplies, equipment, and scientific support needed to conduct experiments. Results will be shared at an annual symposium.

Participants in this workshop will learn:

• Introduction to DNA barcoding and biodiversity
• Sample collection and documentation
• DNA extraction
• Polymerase Chain Reaction (PCR)
• Gel electrophoresis
• Program implementation

The Cold Spring Harbor Laboratory DNA Learning Center is an approved Sponsor of Continuing Teacher and Leader Education (CTLE).

Application closed

Using Cell-free Systems to Synthesize and Express Bacteriophage Genomes: Practical Biomanufacturing for Bioscience Educators

Synthetic biology and biomanufacturing are buzzwords of an emerging bioeconomy based on our increasing ability to manipulate living systems. This workshop will equip bioscience educators with the knowledge, skills, and resources to introduce students to a simple workflow to manufacture bacteriophages (phages) with new host specificity, illustrating how biomolecules are adapted to interact with cell-surface receptors.

Discover the cutting-edge cell-free transcription-translation (TXTL) system for in vitro phage biomanufacturing with instructors from the University of Minnesota and Cold Spring Harbor Laboratory. This workshop emerges from a distinguished lineage of bacteriophage research that began at CSHL and provided the first tools to explore the molecular mechanics of living cells. The “Phage Course,” founded at CSHL in 1945 by Max Delbrück and Salvador Luria, trained the first two generations of molecular biologists. Al Hershey and Martha Chase’s “blender experiment,” conducted at CSHL in 1952, provided conclusive evidence that DNA is the molecule of heredity. Delbrück, Luria, Hershey shared the 1969 Nobel Prize for this seminal work.

Bacteriophages are being rediscovered as powerful tools to meet the pharmaceutical challenge of untreatable, multi-drug resistant bacterial infections. In the food industry, bacteriophages prevent formation of biofilms on equipment surfaces, sanitize fresh fruits and vegetables, and extend the shelf life of packaged foods. Using phages to treat bacterial infections in livestock increases resilience and helps eliminate the reservoir of antibiotic-resistant bacteria. Phages also provide a virtually limitless source of bioactive materials that are increasingly exploited in biotechnology, nanotechnology, and bioremediation.

Phages are used in education as examples of simple genetic systems. The SEA-PHAGES Program of the Howard Hughes Medical Institute annotates phage genomes, and is one of the most widely implemented infrastructures for course-based undergraduate research experiences (CUREs). TXTL is a logical next step for students who have been exposed to phage and/or bacterial genetics, providing them an opportunity to explore the use of phages in biomanufacturing.

Workshop participants will conduct hands-on experiments to express reporter genes and whole phage genomes in vitro, using a cell-free extract. Participants will complete an entire workflow to engineer wild-type T7 phage to infect a new E. coli host. This begins with long PCRs to amplify several fragments of the T7 genome, plus PCR mutagenesis of the tail fiber gene. The PCR products are then assembled and packaged as complete T7 genomes using the cell-free TXTL system. Spotting assays compare the host range of wild-type and mutant T7 phages. Participants will then conduct nanopore DNA sequencing, delivering same-day results to investigate point mutations in the tail fiber gene that account for infectivity.

A $400 stipend will be provided. Travel funds are available.

Funded by a grant from the National Science Foundation: Future Manufacturing #2228971.