DNA Barcoding: Scalable Infrastructure for Student Research

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Title of Abstract: DNA Barcoding: Scalable Infrastructure for Student Research

Name of Author: David Micklos
Author Company or Institution: Cold Spring Harbor Laboratory
Author Title: Executive Director
PULSE Fellow: No
Applicable Courses: Biochemistry and Molecular Biology, Bioinformatics, Biotechnology, Ecology and Environmental Biology, Evolutionary Biology, General Biology, Integrative Biology, Plant Biology & Botany
Course Levels: Across the Curriculum, Faculty Development, Introductory Course(s)
Approaches: Material Development
Keywords: DNA barcoding, genetics, conservation biology, DNA sequencing, bioinformatics

Name, Title, and Institution of Author(s): Bruce Nash, Cold Spring Harbor Laboratory Jermel Watkins, Cold Spring Harbor Laboratory Cornel Ghiban, Cold Spring Harbor Laboratory Mohammed Khalfan, Cold Spring Harbor Laboratory Sheldon McKay, Cold Spring Harbor Laboratory Eunsook Jeong, Cold Spring Harbor Laboratory Susan Lauter, Cold Spring Harbor Laboratory Christine Marizzi, Cold Spring Harbor Laboratory Melissa Lee, Cold Spring Harbor Laboratory Antonia Florio, Cold Spring Harbor Laboratory Oscar Pineda-Catalan, American Museum of Natural History

Goals and intended outcomes of the project or effort, in the context of the Vision and Change report and recommendations: Many science educators search for ways to scale student research from local, individual projects to distributed, class-based experiments that involve many students working simultaneously on aspects of the same problem. DNA barcoding fulfills the promise of modern, Internet-enabled biology – allowing students to work with the same data, with the same tools, at the same time as high-level researchers. DNA barcoding projects can stimulate independent student thinking across different levels of biological organization, linking molecular genetics to ecology and evolution – with the potential to contribute new scientific knowledge about biodiversity, conservation biology, and human effects on the environment. DNA barcoding also integrates different methods of scientific investigation – from in vivo observations to in vitro biochemistry to in silica bioinformatics. DNA barcoding provides a practical way to bring open-ended experimentation into lower-level undergraduate courses. Projects can operate at various scales – from working with other students to investigate a local ecosystem, museum collection, or conservation issue to joining an International Barcode of Life ‘campaign’ to explore an entire taxonomic group or global biome. Projects may also take on a forensic slant, when students attempt to identify product fraud (such as mislabeled food items) or to identify the sources of commercial products (such as plants or animals used in traditional medicines). The core lab and phylogenetic analysis can be mastered in a relatively short time, allowing students to reach a satisfying research endpoint within a single academic term. Using DNA barcoding as the common method across a range of projects decreases the need for intensive, expert preparation and mentoring – thus providing a practical means to engage large numbers of students in meaningful research.

Describe the methods and strategies that you are using: Just as the unique pattern of bars in a universal product code (UPC) identifies each consumer product, a short ‘DNA barcode’ (about 600 nucleotides in length) is a unique pattern of DNA sequence that can potentially identify any living thing. We developed an integrated biochemical and bioinformatics (B&B) workflow for DNA barcode analysis. The biochemistry uses non-caustic reagents to isolate DNA from plant, animal, or fungi. The barcode region is amplified by polymerase chain reaction and visualized by agarose gel electrophoresis. The barcode amplicons are mailed to GENEWIZ, which provides inexpensive sequencing – $3.00 per forward and reverse read. Within 48 hours, the finished barcode sequences are automatically uploaded to DNA Subway, the DNALC’s bioinformatics workflow for education. The Blue Line of DNA Subway includes all tools needed to visualize and edit barcode sequences, search GenBank (www.ncbi.nlm.nih.gov/genbank/) for matches, align sequences, and construct phylogenetic trees. The Blue Line includes web applications that heretofore could only be used as stand-alone applications – including an electropherogram viewer/editor and a ‘zoomable’ sequence aligner/barcode viewer. An export feature simplifies barcode sequence submissions to GenBank, automatically providing sequence files, associated metadata, and sequence annotations in the required NCBI format. The barcode experiment, including extensive teacher prep and planning, is available in three formats: the online lab notebook www.dnabarcoding101.org, the lab-text Genome Science: A Practical and Conceptual Introduction to Molecular Genetic Analysis in Eukaryotes (Cold Spring Harbor Laboratory Press, 2012), and a stand-alone kit marketed by Carolina Biological Supply Company.

Describe the evaluation methods that you used (or intended to use) to determine whether the project or effort achieved the desired goals and outcomes: We evaluate the impacts of DNA barcoding research programs on both students and teachers, using mixed methods to provide both breadth and depth of perspectives. In addition to project statistics (participant demographics, completed projects, novel DNA sequences, etc.) we use online surveys and structured interviews. Teachers and students complete pre- and post-experience surveys to gauge changes in knowledge, attitudes and behaviors, and to compare the barcoding research projects with other research experience. Students complete the validated Survey of Undergraduate Research Experience (SURE-III) which allows comparisons with national cohorts. Structures interviews at completion of projects delve further into participant experiences and how programs could be improved.

Impacts of project or effort on students, fellow faculty, department or institution. If no time to have an impact, anticipated impacts: In terms of student impact, the largest gains in self-confidence (78% ‘Large’ or ‘Very large gain’), learning laboratory techniques (78%), working independently (78%), analyzing data (78%), and becoming part of a learning community (77%). Surveys and structured interviews overwhelming show that students appreciated ownership of barcoding projects and the sense of ‘doing real science.’ For most, it is their first experience with open-ended research. When compared with other research experiences DNA barcoding provides more ‘real world’ science (81% of students), more chance for hands-on experience (69%) and to learn science (76%), more opportunity to develop critical thinking (83%) and independent inquiry skills (70%), and more understanding of the scientific process (68%). The experience increases students’ interest in studying science or pursuing a career in science (83%), while still being more fun than other research experiences (84%). DNA barcoding research projects have a broader impact, potentially improving the quality of instruction for many students beyond those who actually did barcoding projects. Participating teachers state they had, or plan to, incorporate into their classroom instruction: DNA barcoding concepts (73%), more independent research (68%), bioinformatics exercises (59%), and wet labs (41%). These changes are in a range of classes – including general biology (55%), AP Biology (41%), biology electives (40%), environmental science (18%), and honors biology (18%). In addition, 59% had or planned to share resources or train colleagues in new biochemical (36%) and bioinformatics (32%) techniques. These results demonstrate that the DNA barcoding infrastructure developed at the DNALC can scale to introduce large numbers of students to authentic research.

Describe any unexpected challenges you encountered and your methods for dealing with them: Formative evaluation of DNA barcoding projects revealed some challenges, which we have addressed. We schedule project cycles to allow sufficient time for recruitment and training so that sample collection occurs during warmer weather. Teacher training is critical to the success of student projects, so we provide at a minimum one-day training sessions in biodiversity, DNA barcoding, and bioinformatics. Individual project settings vary greatly (for example, student grade level, background and familiarity with laboratory techniques, access to equipment at their school) so we now provide an array of support options: Open Labs at the Harlem DNA Lab and Genspace; equipment footlockers; and virtual and real staff. We refined the B&B workflows, including a specimen database and DNA Subway function to submit novel sequences to Genbank.

Describe your completed dissemination activities and your plans for continuing dissemination: We have conducted several DNA barcoding programs to date. These include the New York City-based Urban Barcode Project, DNALC summer camps, and teacher training programs. We have developed two websites: www.dnabarcoding101.org and www.urbanbarcodeproject.org. The websites include vodcasts on barcoding and student projects, protocols, guidelines for proposal preparation, and database management tools for tracking student projects and metadata. We also developed a DNA barcoding kit that is disseminated through Carolina Biological Supply Company. To date we have trained over 1000 teachers, and more than 450 students have participated in the UBP and barcoding summer camps. Students’ projects have examined: 1) wildlife in parks and public spaces; 2) traded products and possible commerce of endangered species; 3) food mislabeling; 4) public health and disease vectors; and 5) exotics and invasive species. Each project culminates in a poster presentation, with the UBP also including a symposium of finalist oral presentations at the American Museum of Natural History. For the UBP alone, more than 1,600 samples and 4,000 single sequence reads have been processed, and 65 novel sequences have been submitted to GenBank with student authors

Acknowledgements: Funding from Alfred P. Sloan Foundation, Pinkerton Foundation, NSF Advanced Technology Education, NSF Transforming Undergraduate Education in Science, and NSF Plant Science Cyberinfrastructure Collaborative. Project collaborators include American Museum of Natural History, Genspace, the Gateway Institute for Precollege Education, and NYC Department of Education.