Introductory Lab Involves Students in Genomics Research

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Title of Abstract: Introductory Lab Involves Students in Genomics Research

Name of Author: Clare O'Connor
Author Company or Institution: Boston College
Author Title: Associate Professor
PULSE Fellow: No
Applicable Courses: Biochemistry and Molecular Biology, Biotechnology, Cell Biology, Genetics
Course Levels: Introductory Course(s), Upper Division Course(s)
Approaches: Changes in Classroom Approach (flipped classroom, clickers, POGIL, etc.), Material Development
Keywords: metabolism genomics yeast laboratory research

Name, Title, and Institution of Author(s): Laura E. Hake, Boston College Douglas M. Warner, Boston College

Goals and intended outcomes of the project or effort, in the context of the Vision and Change report and recommendations: The explosion of genomic sequence information, particularly for microbial organisms, presents unique opportunities to engage large numbers of undergraduate students in authentic research projects. The Boston College Biology Dept. replaced two traditional 1-credit labs that accompanied introductory lecture classes in molecular cell biology and genetics with a 3-credit laboratory class that meets twice weekly for 3 hour sessions and immerses sophomore students in a semester-long research project in comparative functional genomics. Each semester for the past two years, 12 sections of 15 students have participated in the course project. Students have analyzed the conservation of several enzymes involved in methionine biosynthesis, between the budding yeast, Saccharomyces cerevisiae, and the fission yeast, Schizosaccharomyces pombe. The two species diverged from a common ancestor ~1 billion years ago. With the methionine pathway for context, course materials were designed to incorporate the core concepts of evolution, structure/function, information transfer, pathways and energy transformations and systems biology that were articulated in Vision and Change. The course activities and assignments were designed to increase Vision and Change core student competencies associated with the application of the scientific process, the use of quantitative reasoning and the communication of scientific results and ideas. In the course, students learn to design experiments, collect and interpret experimental data, find information in databases, read and analyze primary literature articles, and present and discuss scientific data, both orally and in written form.

Describe the methods and strategies that you are using: The course uses deletion constructs and overexpression plasmids generated by the Saccharomyces genome project for student investigations. Students work in teams of three to design experiments addressing the functional conservation of proteins involved in methionine synthesis. During the first part of the semester, students identify mutant strains by their nutritional requirements and the polymerase chain reaction. Students next use restriction endonucleases to identify plasmids that are engineered to express enzymes in yeast. Each group receives three plasmids: one plasmid carries the S. cerevisiae enzyme, a second carries the S. pombe homolog that they have identified with bioinformatics tools, and the third is a negative control. Once the strains and plasmids are identified, students transform the yeast deletion strains with the overexpression plasmids, and they determine if the plasmid genes complement the mutations in the yeast strains. A positive complementation result provides a functional test of evolutionary conservation. Finally, students analyze expression of plasmid-encoded proteins using western blots. Throughout the semester, students post their experimental results to a data sharing wiki. There are 12 sections to the course, so students are able to see if their results, either positive or negative, are reproducible.

Describe the evaluation methods that you used (or intended to use) to determine whether the project or effort achieved the desired goals and outcomes: A variety of evaluation methods are used to assess student learning and project goals. Notebook assignments and pre-lab quizzes are used for each laboratory session. Students submit a series of lab reports, culminating in a final research paper. Student teams make oral presentations throughout the semester and present a poster at the end of the semester. Student learning outcomes have been measured by pre- and post-course concept tests and surveys, as well as a variety of assignments and presentations throughout the semester. Our evaluation team also developed protocols for focus groups and classroom observations. The TA training program was assessed by pre- and post-training surveys, as well as a confidence and anxiety index that was administered at the beginning and end of the training workshop, and again at the end of the semester.

Impacts of project or effort on students, fellow faculty, department or institution. If no time to have an impact, anticipated impacts: Student learning gains were measured with pre- and post-course concept tests and student confidence surveys. The average student score on the concept tests increased from 8/20 at the beginning of the semester to 15/20 at the end of the semester. Comparison of pre- and post-course confidence data from two semesters, using a 5-point Likert scale, showed statistically significant gains in measures associated with experimental design (+0.23|0.30), technical proficiency (+0.21|0.79), written and oral communication (+0.10|0.73), database usage (+1.48/1.58) and ability to use and understand primary literature (+0.12|0.37). Products of the project include a lab manual, data sharing site and a website. We have also developed a TA training program that incorporates the principles of scientific teaching. Evaluation shows that this workshop decreases TA anxiety and increases their confidence with respect to teaching.

Describe any unexpected challenges you encountered and your methods for dealing with them: The project has encountered very few institutional barriers to change. The biology department has supported the course since its inception. The biggest barriers to change involve students and graduate teaching assistants. Students are accustomed to traditional labs in which experiments are chosen to demonstrate a principle, and the outcomes are known. BI204 takes them out of their normal comfort zone. Some students become upset when an experiment doesn't 'work' or the next experiment in a sequence isn't yet defined. By the end of the semester, however, most students have adapted to the open-ended nature of scientific investigation and appreciate participating in a semester-long project. The teaching assistants present a challenge in their diversity, which can impact student learning. We have addressed this challenge by implementing a training workshop and by preparing and posting narrated tutorials on the class website - essentially 'flipping the classroom.'

Describe your completed dissemination activities and your plans for continuing dissemination: Our course was deliberately designed with flexibility in mind. Our course was designed with S. cerevisiae as the model organism, because of both the resources available from the S. cerevisiae genome project, as well as its pivotal position as a single-cell eukaryote that could reproduce clonally as a haploid (prokaryote-like) or as a diploid (eukaryote-like). Educators should be able to adapt the activities in the project to metabolic pathways and organisms of their own particular interest. To date, we have used professional meetings as our primary venue for dissemination. We have presented posters at the annual meetings of the American Society for Cell Biology (ASCB), the Society for the Advancement of Biology Undergraduate Education (SABER) and the American Society for Microbiology - Conference for Undergraduate Educators (ASM-CUE) meetings. As a result of these meetings, we have shared our materials with faculty at several institutions, who have adapted the materials to suit their particular courses. This past spring, Michael Wolyniak at Hampden Sydney College has used our materials and strains in his genetics course, together with our evaluation instruments. His results with the course materials are similar to ours, suggesting that the course can be readily adapted to a range of undergraduate settings. Alison Thomas at Anglia Ruskin University, Cambridge, England, will be using several of our labs in her department's genetics practicals during the upcoming term. Our project is also part of a research coordination network on course-based undergraduate research, CUREnet. We plan to continue these dissemination efforts, which have been successful to date. Several manuscripts are being prepared for publication in journals that focus on undergraduate science education.

Acknowledgements: This project was supported by the Division of Undergraduate Education and the Molecular and Cellular Biosciences Division at the National Science Foundation (NSF 114028). We would also like to acknowledge dozens of graduate teaching assistants who taught the various lab sections and who contributed valuable feedback on the course and ways to improve it. Finally, we would like to thank that hundreds of undergraduate students for their enthusiasm, hard work and valuable comments.