Ciliate Genomics Consortium: Teaching-Research Integration

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Title of Abstract: Ciliate Genomics Consortium: Teaching-Research Integration

Name of Author: Emily Wiley
Author Company or Institution: Claremont McKenna, Pitzer, and Scripps Colleges
Author Title: Associate Professor
PULSE Fellow: No
Applicable Courses: Biochemistry and Molecular Biology, Bioinformatics, Cell Biology, General Biology, Plant Biology & Botany
Course Levels: Faculty Development, Introductory Course(s), Upper Division Course(s)
Approaches: Changes in Classroom Approach (flipped classroom, clickers, POGIL, etc.), Material Development
Keywords: class-based research learning community collaborative research molecular biology functional genomics

Goals and intended outcomes of the project or effort, in the context of the Vision and Change report and recommendations: To improve biological literacy and student-centered education, V&C action items include integrating science process, and introducing research experiences, into all undergraduate biology courses. Developing a model for integrating undergraduate research, with a particular eye to making class-based authentic experiences more sustainable for faculty, was a central goal. The Ciliate Genomics Consortium (CGC) was aimed to 1) improve feasibility/sustainability of undergraduate research in the classroom through melding faculty research goals with student research efforts in a professional learning community model; 2) increase student (early) participation in authentic research by integrating opportunities into a variety of commonly-taught biology courses at different levels and types of institutions; 3) enrich classroom undergraduate research experiences through immediate web publication of students' original findings to an appropriate 'user' group; and 4) expand science leadership opportunities for students.

Describe the methods and strategies that you are using: A learning consortium of faculty and students based on functional annotation of Tetrahymena genes was developed. Scalable research modules for integration into existing courses serve to engage students in making new and highly valued contributions to the larger community of ciliate biologists. Student discoveries are directly disseminated to this community through a database for unpublished results that is hyperlinked to the official genome database, a highly visible and well-utilized community resource. Faculty at any institution can engage their students, in class, in explorations of genes in families related to the faculty member's research program, and results are used to progress their research agenda. Opportunities for collaboration between consortium faculty across institutions and disciplines that create new research possibilities, are provided through workshops run as part of, or separate from, regular scientific meetings. Resulting collaborations allow students to feed into larger projects of interest to multiple faculty members.

Describe the evaluation methods that you used (or intended to use) to determine whether the project or effort achieved the desired goals and outcomes: Changes in student attitudes and motivation to engage science that correlate with using consortium research modules and other consortium activities, such as dissemination of student discoveries and inclusion in a broader learning community, were assessed. Pre/post attitudinal and confidence surveys were administered; voluntary student time spent on the project outside of class was tracked, as were student efforts to seek additional research opportunities in the following year. Comparisons were made with control groups that did not participate in the consortium. Student learning gains from engaging research in class guided by the modules was assessed using the CURE and SALG instruments. To assess sustainability for faculty, the number of course repeats using the research modules was tracked, and the number of faculty publications using student-generated data, and the number of new collaborations between consortium faculty were used as measures of impact to faculty research programs. Impact on the larger ciliate research community was measured by tracking numbers of new gene function annotation entries resulting from the class-based research made on the Tetrahymena Genome Database (TGD) Wiki, or through the database for unpublished results linked to TGD.

Impacts of project or effort on students, fellow faculty, department or institution. If no time to have an impact, anticipated impacts: Nine faculty at 11 different schools (private colleges, universities, and state universities) have integrated the research modules into 12 courses (cell bio, molecular, and intro) taught multiple times, plus bridge programs - over 500 students have contributed toward understanding function of ~300 Tetrahymena genes. Repeated use of modules in courses was 95%. Some courses were designed around this experience (a research course for sophomores, and others) and modules were successfully established in intro biology courses at Claremont and Missouri State U. Through CGC, 10 faculty and 6 students have received technical cross-training through workshops; 52 students have presented their research at conferences (including intro bio students); 23 are authors on peer-reviewed publications. Learning and behavioral outcomes from the research modules include significant gains in students' understanding of research process, how scientists approach real world problems, data analysis, readiness for more demanding research, and gains in student confidence in experimental design and execution, data presentation, scientific writing, oral presentation of results, and scientific record-keeping. Tracking and self-reports showed 25% increase in upper division students, and 6-fold increase in first year students, who pursued additional research within one year after module experience. Adding web publication opportunity produced large gains in motivation to 'do science', measured by tracking voluntary student hours spent on the research project outside of class time, and beyond the end of the course. Faculty research programs benefitted from the class-based research, shown by number of publications (6) with student authors from classes (20) and 5 new multi-year faculty collaborations.

Describe any unexpected challenges you encountered and your methods for dealing with them: Challenge #1: Time/effort to adopt and implement the research modules in a given classroom. Faculty can bring UG students to workshop training sessions - students serve as TAs at the home institution, aiding module implementation and reducing faculty time/effort required. Challenge #2: Faculty reluctance to adopt modules using unfamiliar experimental systems. Instead of only recruiting faculty into work with Tetrahymena, we are also disseminating our UG research model - one that is highly transferable to teacher-researchers in other model system communities with genome annotation needs. Our student results database now has a highly adaptable interface for use by any community. Disseminating the model reduces need for specific training workshops for work with Tetrahymena.

Describe your completed dissemination activities and your plans for continuing dissemination: The Ciliate Genomics Consortium opportunities and outcomes were disseminated through multiple presentations at both scientific and education conferences, through workshops during a primary biannual conference for ciliate biologists, and independent consortium workshops. A CGC website provides one avenue for new people to join the consortium ( At least three publications on consortium activities and outcomes are in preparation. Enhanced efforts to disseminate the consortium model to other model system communities are being planned, and a proposal to NSF to support these and future faculty/student training workshops was submitted.

Acknowledgements: This project was supported by an NSF CAREER award to E. Wiley (MCB-0545560) and HHMI funding to Washington University. The project was developed through the combined efforts of the The Ciliate Genomics Consortium Steering Committee members: Douglas Chalker, Washington University; Joshua Smith, Missouri State University; Nicholas Stover, Bradley University; and Emily Wiley, Claremont McKenna, Pitzer, and Scripps Colleges.