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.

Undergraduates Developing Resources for Lost Crops of Africa

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Title of Abstract: Undergraduates Developing Resources for Lost Crops of Africa

Name of Author: Christopher Cullis
Author Company or Institution: Case Western Reserve University
Author Title: Professor
PULSE Fellow: No
Applicable Courses: Agricultural Sciences, Biotechnology, Genetics, Plant Biology & Botany
Course Levels: Upper Division Course(s)
Approaches: Material Development
Keywords: critical thinking, data development, research

Goals and intended outcomes of the project or effort, in the context of the Vision and Change report and recommendations: To engage students in a course that can provide research resources for faculty and graduate students in the developing world. These resources could not be generated in a similar timeframe without the activities carried out in this course. Therefore the students materially contribute to the development of a new crop by providing original data for analysis without their having to arrive at a pre-determined ‘correct’ solution. Since the students interact with the faculty and graduate students in Southern Africa the course also provides the students with an experience of international civic engagement and global responsibility. Outcomes The course has been popular with the students, they have become engaged with the material and some have been recruited into related research projects. New data has been developed that is being applied to improving the crops and students from previous years continue to enquire about the progress years later. Student interest has been assessed through permit requests for the course which been oversubscribed each time it is offered. The data generated by the students has contributed to three published papers and is the basis of two manuscripts in preparation and three additional independent research projects. The data is being used to develop molecular markers for various phenotypic characters that the students can measure, for example internode length, flowering time and the number of flowers per inflorescence. They get to understand the relationship between the various ways of categorizing biological material. The new Chemical biology major that has just been developed by the Chemistry Department has organized a follow-on laboratory on Proteomics that will consider using the same experimental material to permit the students to extend their research activities. Students career paths have been altered through taking this course since some initially intent on going to Medical School have switched to research careers.

Describe the methods and strategies that you are using: The method is to include authentic research experiences into the curriculum. This has primarily been done in upper level courses but the experience gained there is being transferred to the introductory courses. These research-based courses allow more students to get authentic research experiences than are available through individual laboratory experiences. The students are also introduced to collaborative research activities since the whole class is working on the same problem, while sharing and interpreting the complete data set. The strategy of developing laboratory course material in the upper level courses and then developing a subset of those experiments to be included in the core courses has previously proved successful, for example, half of the lab exercises in the first lab course of the biology core arose from exercises developed in an earlier iteration of this upper level course.

Describe the evaluation methods that you used (or intended to use) to determine whether the project or effort achieved the desired goals and outcomes: The evaluation of the project has been through student outcome assessment, adoption of similar methodologies in other courses and wider adoption. The student evaluations show the course is well received and the application to a real world problem is highly valued. The exposure to primary data and the challenges in interpretation develop new analytical skills that can be transferred to other courses. The manipulative skills could be applied to career options.

Impacts of project or effort on students, fellow faculty, department or institution. If no time to have an impact, anticipated impacts: The students particularly appreciated the exposure to original data and critical thinking skills. The significant analysis part in each experiment which a scientist should develop in order to improve the ability to carry out research, guided or independent, shows up in the way the students have to reason out for anything that happens in the experiment. The students had to perform the experimental methods that previously they had only been able to learn theoretically. The approach has been adopted in other upper level courses as well as infiltrating the introductory courses and labs. Dissemination within the Institution has had a thought impact but less tangible adoption instances.

Describe any unexpected challenges you encountered and your methods for dealing with them: The problem with a research-based course is that the material has to be updated each year. If the students have to develop new data then the approach has to be modifiable. Therefore choosing a problem that can be sustained over multiple years is essential. The choice of the domestication and marker-based improvement of marama allowed such a progression. Once the basic genomic information has been developed then the students can carry out specific mapping projects that will feed back directly into the improvement program. New export controls have to be factored into projects that deal external entities.

Describe your completed dissemination activities and your plans for continuing dissemination: Dissemination of the project has been at both the local and national levels. The project has been described to various organizations on campus (for example at the University Center for Innovation of Teaching and Education). It has also featured on the web-site of the World-wide Learning Environment through which the first iteration was supported. Results will continue to be published with attribution to the undergraduates who were involved in generating the data. Additionally a full description of the course and associated resources will be published to encourage more participants of the adoption of similar strategies to bring the resources of talented undergraduates to bear on important global problems.

Acknowledgements: Financial support from the McGregor Fund award to the College of Arts and Sciences, Case Western Reserve University. International Collaborators Professor Karl Kunert, University of Pretoria Dr. J. Vorster, University of Pretoria Dr. C. van der Vyver, University of Stellenbosh Dr. P. Chimwamarombe, University of Namibia Mutsa Takwunda, University of Namibia Emanuel Nepolo, University of Namibia

Classroom Research Experience for Community College Students

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Title of Abstract: Classroom Research Experience for Community College Students

Name of Author: Gita Bangera
Author Company or Institution: Bellevue College
Author Title: Assistant Dean
PULSE Fellow: No
Applicable Courses: 1483, Agricultural Sciences, Biochemistry and Molecular Biology, Bioinformatics, Biotechnology, Cell Biology, Ecology and Environmental Biology, General Biology, Genetics, Plant Biology & Botany, Virology
Course Levels: Across the Curriculum, Faculty Development, Introductory Course(s), Upper Division Course(s)
Approaches: Assessment, Changes in Classroom Approach (flipped classroom, clickers, POGIL, etc.), Material Development, Mixed Approach
Keywords: Undergraduate-Research Research-as-pedagogy Student-centered Genomics Bioinformatics

Name, Title, and Institution of Author(s): K. Harrington, Tacoma Community College A. Gargas, Symbiology LLC R. Jeffers, Bellevue College C. Vermilyea, Bellevue College L. Thomashow, USDA-ARS D. Weller, USDA-ARS

Goals and intended outcomes of the project or effort, in the context of the Vision and Change report and recommendations: The Vision and Change report recommends introducing research early and throughout the biology curriculum and demonstrating the passion of scientists for their fields. ComGen - Authentic Research Experiences Expansion project (NSF # 1225857) aims to take the field tested ComGen approach of using authentic research as pedagogy to community colleges (CCs) in the Pacific Northwest. The project is a continuation of a successful strategy of providing CC students with authentic research experiences early in their academic careers. We had originally developed a “mini-graduate school” course with previous funding (NSF# 0717470) where students generate, analyze and communicate new genomic data and critically analyze original scientific literature; we then modified and adapted critical components of this course to fit into a standard Majors’ Cell and Molecular Biology introductory course and piloted it successfully (McCook A. 2011 333: 1572-1573. Wei CA & T Woodin. 2011. CBE - Life Sciences Education 10: 123-131.). Our current project focuses on the dissemination of this course within the Pacific Northwest region and on developing related curricula for other courses within the Life Sciences spectrum. Our student impact outcomes include improved critical thinking skills, increasing students’ knowledge of the process of science and confidence in visualizing themselves as scientists, and increased retention of students in STEM fields. Our overarching goal is to promote widespread adoption of a sustainable, student-focused and institutionalized culture of research pedagogy among regional CCs. To achieve this goal we want to: 1. Create transformative changes in STEM education by integrating easily adoptable authentic research experiences into community college curricula; 2. Build faculty and institutional capacity for providing authentic research experiences to community college students; and 3. Build a sustainable research network to help enrich and expand impact.

Describe the methods and strategies that you are using: We are training faculty from the region’s CCs in using the pedagogical and assessment tools developed from previous NSF funding with workshops customized to their individual needs. We are also developing new tools with input from the faculty participants; providing ongoing support for the faculty for implementation of the curriculum and providing venues for interaction between CC and research faculty for development of a Community of Practice. Our key goal is to develop faculty capacity to follow the “Hands on/Hands off” pedagogical approach: the experience is “hands on” for students and “hands off” for faculty i.e. faculty are encouraged to provide the minimum amount of scaffolding and allow students to take charge of the learning process.

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 have used nationally accepted instruments such as the CURE survey (Lopatto D, et al. 2008. Undergraduate research: Genomics education partnership. Science 322: 684-685.) and our own internally developed assessment tools to document the impact on students and other outcomes. These include an instrument for assessing students’ grasp of the technical details of the research and a survey of the faculty receiving students after their ComGen experience. We are continuing to develop and optimize our assessment instruments with input from the participating faculty.

Impacts of project or effort on students, fellow faculty, department or institution. If no time to have an impact, anticipated impacts: We are currently analyzing the data from our first year of the project but we have shown impact on students’ ability to: perform the technical components of the research, develop tolerance for obstacles in research and visualize themselves as scientists in our pilot work in the previous grant. We have found that even faculty with multiple decades of teaching experience have adopted this approach and found it to be empowering both for themselves and the students. Faculty who have incorporated this teaching method into their curricula insist that they have no interest in returning to the traditional modes of teaching and have started incorporating tools from this process into their other courses as well.

Describe any unexpected challenges you encountered and your methods for dealing with them: So far we have not run into any unexpected challenges in this process. The challenges that we have faced are the usual issues of trying to coordinate the training time for faculty.

Describe your completed dissemination activities and your plans for continuing dissemination: We have so far trained faculty from seven institutions and of these four are already implementing the ComGen pedagogy model. We plan to expand our dissemination efforts to include at least 15 CCs in the Pacific Northwest. We have recruited faculty at the NorthWest Biology Instructors Organization meeting and by direct contact through the network of Department Chairs. As one of 40 Vision and Change Leadership fellows as part of the Partnership for Undergraduate Life Science Education (PULSE), the Principal Investigator will also use the North West PULSE conference (NSF EAGER 1345033) to recruit more faculty not just from the CCs but other (especially minority serving institutions) as well.

Acknowledgements: Thanks to useful input from Jason Fuller, Allen Farrand, Stephen Clark, Pamela Pape-Lindstrom and Stacey Gregersen.