To meet the challenges of the genomic era, undergraduate students need to learn how to operate the new sequencing technologies and analyze the resultant data. This project is developing a series of multi-disciplinary courses in ecosystem genomics that teach next generation DNA sequencing technology to undergraduate students, enabling them to analyze the resultant data and interpret the effects of genomic changes on ecosystem health and function. These courses include genomic theory, hands on experience in next generation sequencing technology, statistical analysis of genomes, and bioinformatics. Students work on real research projects where the organisms sequenced are new to science, and their work becomes part of annotating the tree of life.
The sequencing data becomes available to the public through standard channels as new specimens are selected for sequencing each year of the course. The curricular materials and online protocols are available for adaptation and implementation at both two- and four-year institutions. Evaluative activities examine the interdisciplinary learning gains for students and their perceived enthusiasm for science and research.
Microbes, metagenomes and marine mammals: Enabling the next generation of undergraduates to enter the genomic era. The revolution in DNA sequencing technology continues to dramatically change biological and medical sciences. The training and recruitment of the next generation of researchers who are able to use these new technologies is economically and scientifically vital. We developed a cross-disciplinary class that provided students with practical experience in using a next generation sequencing instrument (Figures). Students performed every step through sequencing to the analysis and annotation of the DNA. Intellectual Impact: The students have sequenced and investigated DNA from 30 microbes, 60 metagenomes, and a marine mammal, the California sea lion, Zalophus californianus (www.sealiongenome.org), increasing our understanding of the genomic landscape of kelp forests. Most important, the students obtained research experience and acquired competence in skills for their future education and careers. A perceived increase in students’ ability to conduct independent scientific research was measured. Outputs to-date include involving 130 students in research, ~30 student presentations, and nine papers co-authored by undergraduates and high school students .Many are now employed in the DNA sequencing industry or have obtained graduate positions. We have been involved in education forums: 1) CSUPERB genomic education workshop, 2) HHMI Bioinformatics workshop, 3) Regional Association of Biology Laboratory Educators, 4) TUES workshop and 5) the Vision and Change in Undergraduate Biology to help develop undergraduate training further. Broader Impacts: I have several videos describing the class (e.g. http://bcove.me/781ky7ra) and have provided course assistance to many universities, including the University of Puerto Rico. Students from my lab are involved in the SDSU Open Days where they describe and display antibiotic resistance and genomic technology to the general public (~ 700 people visit). We have taught metagenomics and DNA sequencing in several countries and have had students visit my lab to learn sequencing, which is providing capacity to these countries. Students (n = 25) from our labs have visited Brazil and Chile, therefore obtaining international experience. We are equipping students for the rapid expansion of DNA sequencing that is currently occurring in the life sciences.
