Assessing a Year-Long, Research Lab in a Core Biology Course

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Title of Abstract: Assessing a Year-Long, Research Lab in a Core Biology Course

Name of Author: Marcy Kelly
Author Company or Institution: Pace University
PULSE Fellow: No
Applicable Courses: Biochemistry and Molecular Biology, Bioinformatics, Biotechnology, Cell Biology, Genetics
Course Levels: Introductory Course(s), Upper Division Course(s)
Approaches: Material Development, Research projects in the teaching laboratory
Keywords: microarray, nextgen RNA sequencing, year-long core biology course, novel research

Name, Title, and Institution of Author(s): David S. Zuzga, LaSalle University

Goals and intended outcomes of the project or effort, in the context of the Vision and Change report and recommendations: It is anticipated that enrollment in this year-long laboratory program will yield the following outcomes for the students: 1. Develop a strong foundation in the following core concepts associated with biological literacy: (a) Structure and function at the cellular and molecular level; (b) Information flow, exchange and storage through genes and proteins; (c) Pathways and transformations of energy and matter involved in cellular communication and responses to the environment 2. Become proficient in the following biological core competencies and disciplinary practices: (a) Realize the steps involved in the process of science including the examination and critique of scientific literature, hypothesis generation, experimental design, data interpretation, trouble-shooting and experimental revision and, the generation of biologically relevant datasets; (b) Development of quantitative reasoning skills to interrogate large datasets; (c) Appreciate the interdisciplinary nature of science by navigating biological data repositories and Bioinformatics to obtain information pertaining to specific genes and gene families; (d) Communicate and collaborate with other scientists in graphic form, written form, and verbally.

Describe the methods and strategies that you are using: The year-long program is completed by all biology majors and is spread over two courses: Genetics (BIO231) and Introduction to Cellular and Molecular Biology (BIO335). During the first semester (BIO231), students examine global changes in gene expression in response to osmotic stress in S. cerevisiae. Students perform an osmotic stress experiment, isolate RNA and prepare samples for analysis by either microarray or nextgen RNA sequencing, apply bioinformatics to examine differential expression in a large data set, and, importantly, interrogate the dataset with Gene Ontology tools to identify candidate genes not previously described as functional regulators of the osmotic stress response. Linking the two semesters, students write proposals for conducting functional studies of candidate genes and engage in peer review sessions to rank proposals and select candidate genes for investigation in the subsequent semester. In BIO335, students develop a cloning strategy for a selected candidate gene and design experiments to characterize the function of the gene products in osmotic stress. Thus, students are provided with an authentic research experience and the opportunity to identify novel roles for genes in the stress response.

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 two outcomes for the year-long laboratory course can be simplified for the means of describing the assessment plan. The first outcome, develop a strong foundation in the core concepts associated with biological literacy, focuses on the acquisition of biological content knowledge by the students participating in the year-long laboratory program. The second outcome, become proficient in biological core competencies and disciplinary practices, focuses on the enhancement of the critical thinking skills of the students participating in the year-long laboratory program. Several quantitative and qualitative assessment tools will be utilized to assess whether or not the students participating in the year-long laboratory program made gains in biological content knowledge and critical thinking skills: (a) Writing assignments required for the BIO231 and BIO335 laboratory courses; (b) Pre- and post- program open ended questions; (c) BIO231 and BIO335 final course grades; (d) Performance on the Department of Biology and Health Sciences-NYC major assessment exam; (e) Participation in the Classroom Undergraduate Research Experience (CURE) survey.

Impacts of project or effort on students, fellow faculty, department or institution. If no time to have an impact, anticipated impacts: The implementation of the laboratory program has yielded significant impacts at the student, faculty, and institutional level. Student Impact: The year-long lab course is integrated into core courses, ensuring that all biology majors will obtain authentic research experiences. At Pace, these courses have an enrollment of approximately 60-80 students per year. It is anticipated that participation in the lab program will enhance students’ potential to conduct scientific research. Projects initiated during the year-long laboratory program may be pursued in faculty mentored, independent research courses. Indeed, four students are continuing their investigations. Faculty and Institutional Impact: A Phase I TUES grant from the NSF was recently awarded to support the expansion of the program to peer institutions. Two participating faculty members (from Pace and La Salle University) recently attended an NSF and HHMI funded GCAT-SEEK workshop to develop RNA sequencing laboratory protocols to broaden the methodological framework of the program. Indeed, the laboratory program itself is modular and scalar - the framework of the program, generation and analysis of a transcriptome database, selection of candidate genes, cloning, and design of an experiment to test the functional role of the candidate gene can be readily adopted by Biology Departments at other institutions. The core courses in which the proposed laboratory program are integrated are ubiquitous offerings in the undergraduate setting, negating the need for partner institutions to develop courses de novo. Moreover, the program can also accommodate a breadth of faculty research questions, providing the opportunity for faculty to integrate their own research into the lab program, thus leveraging faculty expertise in the course. Indeed, the program will be adopted at La Salle University and further efforts will be made to recruit partner institutes in anticipation of a Phase II TUES proposal.

Describe any unexpected challenges you encountered and your methods for dealing with them: Hurricane Sandy struck the New York City metropolitan area in October 2012. The students enrolled in the BIO231 course at that time had isolated their RNA and were getting ready to send it out for analysis. Unfortunately, due to power loss from the storm, all of the student RNA samples were lost. The students were provided with the data sets obtained by the students enrolled in BIO231 the year before. This enabled us to continue with the work as planned without any interruption to our schedule. As we continue to implement this program, the datasets we employ will become increasingly robust and can be interrogated by the students in the advent of challenges - whether they are experimental or otherwise.

Describe your completed dissemination activities and your plans for continuing dissemination: To reach as broad and audience as possible, the program outline and accompanying assessment data will be presented at the major annual meetings of faculty associated with this program and reported in journals with a pedagogical foci. Furthermore, faculty involved in this program have diverse research interests which allows for the program to be introduced at major meetings for societies that include pedagogical sessions. These include the annual meetings of the, the American Society of Microbiology (ASM) and the American Association for Cancer Research. Finally, assessment data and the program structure will be disseminated among faculty with interests in novel pedagogical ideas via ASM’s Biology Scholars Program Listserv and GCAT SEEK’s Listserv. In each of these venues, emphasis will be placed upon 1) the success of the program in enhancing student learning and 2) the adaptability of this program by any institution.

Acknowledgements: We would like to thank and acknowledge GCAT-SEEK for the nextgen sequencing training and analyses and Dr. David Lopatto for allowing us to participate in the CURE survey ( MPK would like to acknowledge the American Society of Microbiology’s Biology Scholars Program (NSF Award # 0715777) for helping her develop the research ideas for this assessment study. Support for the development and assessment of this year long laboratory program is from an NSF Type 1 TUES grant to MPK (NSF Award # 1246000).