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.

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

Proteomic analysis of isolated Chlamydomonas centrioles reveals orthologs of ciliary-disease genes

We combined Gal4-UAS and the FLP recombinase-FRT and fluorescent reporters to generate cell clones that provide spatial, temporal and genetic information about the origins of individual cells in Drosophila melanogaster. We named this combination the Gal4 technique for real-time and clonal expression (G-TRACE). The approach should allow for screening and the identification of real-time and lineage-traced expression patterns on a genomic scale.

/pdf/g-trace-rapid-gal4-based-cell-lineage-analysis-in-drosophila-3nnrmq7iwf.pdf

G-TRACE: rapid Gal4-based cell lineage analysis in Drosophila

Undergraduate research experiences help retain students in science majors and prepare our workforce for increasingly competitive jobs. Course-based approaches to research and inquiry allow educators to reach larger numbers of students and provide an entry into further research experiences.

Inquiry-based and research-based laboratory pedagogies in undergraduate science.

Light has been exploited for information by organisms through the evolution of photoreceptors and, ultimately, eyes in animals. Only a handful of eye types exist because the physics of light constrains photodetection. In the past few years, genetic tools have revealed several parallel pathways through which light guides behavior and have provided insights into the convergent evolution of eyes. The gene encoding opsin (the primary phototransduction protein) and some developmental genes had very early origins and were recruited repeatedly during eye evolution. Eye lens proteins arose separately and make up a diverse group, many of which were co-opted from other functions. A major challenge now is understanding how newly discovered pathways for processing light evolved and how they collaborate with eyes to harvest information from light.

https://science.sciencemag.org/content/sci/313/5795/1914.full.pdf

Casting a genetic light on the evolution of eyes.

The excitement of scientific research and discovery cannot be fully conveyed by didactic lectures alone. Several recent initiatives and proposals, therefore, have supported a more participatory, discovery-based instruction for undergraduate science education [1,2]. In functional genomics, we have found an ideal platform to simultaneously benefit students and contribute to scientific discovery. The sequencing of eukaryotic genomes has facilitated the identification of complete sets of genes in humans and model genetic organisms. This has allowed many forms of high-throughput analyses of transcriptional profiles, protein interactions, structural motifs, and even genome-wide knock-downs in cell lines or in selected organisms. However, one of the best tools to provide functional information about gene action— obtaining in vivo evidence about the phenotype resulting from heritable loss of function—is difficult and less amenable to high-throughput research. We were able to achieve a large-scale in vivo analysis with a significant number of undergraduate students at UCLA, called the UCLA Undergraduate Consortium for Functional Genomics. This work, a practical manifestation of policy positions proposing discoverybased education, is described in summary form here (and in Box 1) and in detail online at http://www.bruinfly.ucla.edu. This effort combines professional-quality research with a strategy for research-based undergraduate education.

/pdf/discovery-based-science-education-functional-genomic-v2gt11lrbf.pdf

Grant Alkin

Papers

Discovery-Based Science Education: Functional Genomic Dissection in Drosophila by Undergraduate Researchers