DNA Barcoding and Metabarcoding for CURES Workshops
Funded by the NSF Improving Undergraduate STEM Education Initiative
The Cold Spring Harbor Laboratory DNA Learning Center (DNALC), in collaboration with New York City College of Technology (City Tech), Bowie State University (BSU), and James Madison University (JMU), is offering two five-day workshops on DNA barcoding or metabarcoding in course-based undergraduate research experiences (CUREs). Applicants to these free workshops should be undergraduate teaching faculty with a sincere desire to involve students in authentic research projects, especially in CUREs for students in introductory courses.
DNA Barcoding Workshop
2021 Virtual Workshop
June 7, 9, 11, 14, 16, 2021, 1:00–4:00 p.m. EDT
- Monday, June 7: Intro and Sample collections
- Wednesday, June 9: Pipetting, Extraction, PCR
- Friday, June 11: Gels and Sequencing
- Monday, June 14: DNA subway (can be swapped with w/Wed if sequences get held up)
- Wednesday, June 16: Implementations, other resources, and exit survey
Just as the unique pattern of bars in a universal product code (UPC) identifies each consumer product, a “DNA barcode” is a unique pattern of DNA sequence that identifies each living thing. DNA barcoding provides a powerful way for biology faculty to lead CUREs, which have been shown to increase student retention and success when provided early in undergraduate programs. Barcoding integrates ideas from molecular biology, genetics, bioinformatics, ecology, and biodiversity—while at the same time providing the flexibility to address a variety of student-driven questions. Barcoding can be mastered in a relatively short time, allowing students to generate new data and reach a satisfying research endpoint within a single course. Furthermore, undergraduate students often have limited patience for bioinformatics, and DNA barcoding provides a wet-lab or field-based “hook” to increase engagement. Bioinformatics analysis of DNA barcodes generated via Sanger sequencing are conducted in the user-friendly DNA Subway Blue Line, an open-access, browser-based pipeline.
DNA Metabarcoding Workshop
2021 Virtual Workshop
June 21, 23, 25 & August 3, 5, 2021
- Week 1, June 21–25:
Monday (1:00–3:00 p.m. EDT), Wednesday, Friday, 1:00–4:00 p.m. EDT
- 6 week recess for participant sample collection, processing, & sequencing
- Week 2, August 3–5:
Tuesday, Thursday, 1:00–4:00 p.m. EDT
Rather than analyzing one DNA barcode at a time, metabarcoding leverages next generation sequencing (NGS) to analyze thousands of DNA barcodes from complex mixtures of DNA—representing microbes (microbiomes) or environmental DNA (eDNA). Moving from DNA barcoding to metabarcoding perfectly embodies the conceptual transition from single gene to massively parallel genome analysis, introducing students to NGS analysis and data science. A single lane of an NGS machine can accommodate hundreds of student metabarcoding samples. Similar to DNA barcoding, metabarcoding draws on techniques from molecular biology, genetics, bioinformatics, ecology, and biodiversity. Bioinformatics analysis of metabarcoding NGS data are conducted in the recently developed DNA Subway Purple Line, a browser-based pipeline incorporating QIIME2, a research-grade metabarcoding platform.
Workshop participants learn all the biochemical and bioinformatics techniques required to implement DNA barcoding or metabarcoding, including the use of the DNALC’s sequence analysis tools. Workshop seminars introduce key concepts (“big ideas”), CURE development, management and evaluation, data science, methods to work with diverse student populations, workforce development, and details about the project. Seminars include insights from project Co-PIs, including DNALC’s experts; faculty leading JMU’s curriculum, which engages 800 students and 20 instructors in DNA barcoding each semester; and City Tech and Bowie State faculty who lead DNA barcoding and metabarcoding with diverse student populations. The competencies required for bioinformatics, genome science, and biological data sciences are also presented.
Faculty who complete the workshops receive travel support, a stipend, and have year-round mentoring and support from project Co-PIs as they implement barcoding CUREs. Those implementing CUREs receive free reagents and DNA sequencing for student research. DNA barcoding workshop participants from the previous year are eligible to attend metabarcoding workshops—any remaining spots will be filled competitively. Select faculty will be invited to mentor other faculty, building a network of educators implementing DNA barcoding CUREs.
Faculty are asked to participate in a series of evaluation activities throughout the project, beginning with workshop evaluation. Faculty who go on to implement CUREs are enrolled in additional evaluation activities centered on their experiences as well as those of their students. Select schools will be asked to participate in additional longitudinal evaluation of students.