David Lopatto

A Broadly Implementable Research Course in Phage Discovery and Genomics for First-Year Undergraduate Students

ABSTRACT Engaging large numbers of undergraduates in authentic scientific discovery is desirable but difficult to achieve. We have developed a general model in which faculty and teaching assistants from diverse academic institutions are trained to teach a research course for first-year undergraduate students focused on bacteriophage discovery and genomics. The course is situated within a broader scientific context aimed at understanding viral diversity, such that faculty and students are collaborators with established researchers in the field. The Howard Hughes Medical Institute (HHMI) Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES) course has been widely implemented and has been taken by over 4,800 students at 73 institutions. We show here that this alliance-sourced model not only substantially advances the field of phage genomics but also stimulates students’ interest in science, positively influences academic achievement, and enhances persistence in science, technology, engineering, and mathematics (STEM) disciplines. Broad application of this model by integrating other research areas with large numbers of early-career undergraduate students has the potential to be transformative in science education and research training. IMPORTANCE Engagement of undergraduate students in scientific research at early stages in their careers presents an opportunity to excite students about science, technology, engineering, and mathematics (STEM) disciplines and promote continued interests in these areas. Many excellent course-based undergraduate research experiences have been developed, but scaling these to a broader impact with larger numbers of students is challenging. The Howard Hughes Medical Institute (HHMI) Science Education Alliance Phage Hunting Advancing Genomics and Evolutionary Science (SEA-PHAGES) program takes advantage of the huge size and diversity of the bacteriophage population to engage students in discovery of new viruses, genome annotation, and comparative genomics, with strong impacts on bacteriophage research, increased persistence in STEM fields, and student self-identification with learning gains, motivation, attitude, and career aspirations. Engagement of undergraduate students in scientific research at early stages in their careers presents an opportunity to excite students about science, technology, engineering, and mathematics (STEM) disciplines and promote continued interests in these areas. Many excellent course-based undergraduate research experiences have been developed, but scaling these to a broader impact with larger numbers of students is challenging. The Howard Hughes Medical Institute (HHMI) Science Education Alliance Phage Hunting Advancing Genomics and Evolutionary Science (SEA-PHAGES) program takes advantage of the huge size and diversity of the bacteriophage population to engage students in discovery of new viruses, genome annotation, and comparative genomics, with strong impacts on bacteriophage research, increased persistence in STEM fields, and student self-identification with learning gains, motivation, attitude, and career aspirations.

The Genomics Education Partnership: Successful Integration of Research into Laboratory Classes at a Diverse Group of Undergraduate Institutions

Genomics is not only essential for students to understand biology but also provides unprecedented opportunities for undergraduate research. The goal of the Genomics Education Partnership (GEP), a collaboration between a growing number of colleges and universities around the country and the Department of Biology and Genome Center of Washington University in St. Louis, is to provide such research opportunities. Using a versatile curriculum that has been adapted to many different class settings, GEP undergraduates undertake projects to bring draft-quality genomic sequence up to high quality and/or participate in the annotation of these sequences. GEP undergraduates have improved more than 2 million bases of draft genomic sequence from several species of Drosophila and have produced hundreds of gene models using evidence-based manual annotation. Students appreciate their ability to make a contribution to ongoing research, and report increased independence and a more active learning approach after participation in GEP projects. They show knowledge gains on pre- and postcourse quizzes about genes and genomes and in bioinformatic analysis. Participating faculty also report professional gains, increased access to genomics-related technology, and an overall positive experience. We have found that using a genomics research project as the core of a laboratory course is rewarding for both faculty and students.

Genomics Education Partnership

The Genomics Education Partnership offers an inclusive model for undergraduate research experiences, with students pooling their work to contribute to international databases.

Classroom-Based Science Research at the Introductory Level: Changes in Career Choices and Attitude

Our study, focused on classroom-based research at the introductory level and using the Phage Genomics course as the model, shows evidence that first-year students doing research learn the process of science as well as how scientists practice science. A preliminary but notable outcome of our work, which is based on a small sample, is the change in student interest in considering different career choices such as graduate education and science in general. This is particularly notable, as previous research has described research internships as clarifying or confirming rather than changing undergraduates’ decisions to pursue graduate education. We hypothesize that our results differ from previous studies of the impact of engaging in research because the students in our study are still in the early stages of their undergraduate careers. Our work builds upon the classroom-based research movement and should be viewed as encouraging to the Vision and Change in Undergraduate Biology Education movement advocated by the American Association for the Advancement of Science, the National Science Foundation, and other undergraduate education stakeholders.

A Course-Based Research Experience: How Benefits Change with Increased Investment in Instructional Time

While course-based research in genomics can generate both knowledge gains and a greater appreciation for how science is done, a significant investment of course time is required to enable students to show gains commensurate to a summer research experience. Nonetheless, this is a very cost-effective way to reach larger numbers of students.

“Deconstructing” Scientific Research: A Practical and Scalable Pedagogical Tool to Provide Evidence-Based Science Instruction

Focused analysis of current research projects provides an effective platform for teaching early-stage undergraduates the logic of scientific inquiry.

A Central Support System Can Facilitate Implementation and Sustainability of a Classroom-Based Undergraduate Research Experience (CURE) in Genomics

There have been numerous calls to engage students in science as science is done. A survey of 90-plus faculty members explores barriers and incentives when developing a research-based genomics course. The results indicate that a central core supporting a national experiment can help overcome local obstacles.

Scaling Up: Adapting a Phage-Hunting Course to Increase Participation of First-Year Students in Research

To offer a research experience to all students taking introductory biology, the authors modified the traditional two-semester Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES) course by streamlining the first semester Phage Discovery lab and integrating research from the second SEA-PHAGES semester into other courses in the biology curriculum.

Cautiousness, Stereotypy, and Variability in Older and Younger Adults

Older adults and college students were tested with two procedures that measure stereotypy and response variability In Experiment 1 subjects guided a marker through a 6 by 6 matrix by pressing two computer keys. Points were awarded on either a continuous or variable ratio 3 schedule of reinforcement. Points were exchanged for money Continuous reinforcement produced significantly higher stereotypy than intermittent reinforcement did in both age groups. A difference was found in stereotypy between age groups during the variable ratio schedule. This difference may have been caused by the greater task anxiety of the older adults. In Experiment 2 subjects were tested using the matrix procedure with the consequence that response variability was differentially reinforced. Four levels of variability were tested in the two age groups. Both older and younger subjects learned to vary response patterns to obtain points. The results are discussed in the context of cautiousness as an age-related explanation for behavior.

Benefits of Intertwining Teaching and Research

In the Education Forum “Changing the Culture of Science Education at Research universities” (14 January, p. [152][1]), W. A. Anderson et al. argue that research and teaching can be combined in ways that increase their effectiveness. The Education Forum describes seven initiatives to elevate the status of teaching. We would like to add to their list. Rather than detach the content of science from its method, researchers should engage students in authentic research to learn the scientific habits of mind that researchers use to discover and understand knowledge. Unifying teaching and research facilitates synergy, enhances student learning, attracts students to the STEM professions, and boosts professional satisfaction. ![Figure][2] CREDIT: LUXXTEK/[ISTOCKPHOTO.COM][3] Unfortunately, teaching and research have too often been explicitly segregated. An excellent researcher teaching an unrelated curriculum using ineffective pedagogies is unlikely to be judged an effective teacher. Teaching research goes beyond designated methodology courses; it includes inquiry-based and research-like pedagogies throughout the curriculum, including introductory courses. Researchers can increase the quality of teaching and learning by modeling what they do and how they think about it in the classroom. Inquiry-based approaches make good teaching, especially when accompanied by strategies that develop effective teamwork and peer review among a group of diverse students. Engaging students in scholarly work develops strong analytical thinking skills that are essential for effective personal and civic lives as well as professional ones. The solution to the demand for talented STEM workers must include recognizing reciprocity between research and teaching. [1]: /lookup/doi/10.1126/science.1198280 [2]: pending:yes [3]: http://ISTOCKPHOTO.COM