Microbes, Metagenomes and Marine Mammals: Enabling the Next

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Title of Abstract: Microbes, Metagenomes and Marine Mammals: Enabling the Next

Name of Author: elizabeth dinsdale
Author Company or Institution: San Diego State University
Author Title: Dr
PULSE Fellow: No
Applicable Courses: Bioinformatics, Microbiology, Virology
Course Levels: Upper Division Course(s)
Approaches: Mixed Approach
Keywords: DNA sequencing, practical research experience

Name, Title, and Institution of Author(s): Robert A. Edwards, San Diego State University Meredith Houle Vaughn, San Diego State University

Goals and intended outcomes of the project or effort, in the context of the Vision and Change report and recommendations: The revolution in DNA sequencing technology continues unabated, and is impacting all aspects of the biological and medical sciences. The training and recruitment of the next generation of researchers who are able to use and exploit the new technology is severely lacking and potentially negatively impacting research and development efforts to advance genomics. Here we present a cross-disciplinary course which has three goals: 1) Inspiring student learning by allowing students to use the latest technology and generate new data; 2) Engaging students by integrating teaching and research; 3) Enabling students to integrate genomics in areas of biology and ecology. Many labs across world are installing next generation sequencing technology and we show that the undergraduate students produce quality sequence data and were excited to participate in cutting edge research.

Describe the methods and strategies that you are using: A practical course in DNA sequencing and annotating novel genomes from start to finish with a next-generation sequencer was offered to upper division undergraduates and graduate students as a lecture and laboratory course and was open to students across biology and computer sciences.

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 first evaluation of the course was to assess the quality of the DNA sequencing data that the students produced. They sequenced 40 microbes, 60 metagenomes, and a marine mammal, the Californian sea lion, Zalophus californianus. The students met sequencing quality controls, had no detectable contamination in the targeted DNA sequences, provided publication quality data, and became part of an international collaboration to investigate carcinomas in carnivores. Evaluation of the course where conducted using pre and post formative and summative tests that assess student learning, in scientific conduct, genomic analysis, biology and computer science. Overall, the students perceived ability to conduct scientific research increased from 3.3 to 3.8 (t = -6.08; p = 0.001). The students show an increased confidence in conducting projects where 1) no one knows the outcome, 2) they have input into the process, 3) they need to work as a whole class and 4) they have responsibility for part of the process. The students increased in their ability to interpret primary literature, present data and keep a lab book. Skills required in becoming a successful scientist. In addition, students’ overall self-confidence in their ability to conduct genomic sequencing and analysis increased from 3.0 to 3.9 (t = -3.21; p = 0.01). All students would recommend the course to other students and had extremely positive comments about the course, and recognized that it would provide benefits for their future careers.

Impacts of project or effort on students, fellow faculty, department or institution. If no time to have an impact, anticipated impacts: Outputs to date include involving 130 students in research, 5 publications, 33 student presentation, and 5 papers in review all of which include student co-authors. We have been involved in four education forums, 1) CSUPERB genomic education workshop, 2) HHMI Bioinformatics workshop, 3) RABLE San Diego meeting to help develop laboratory training and 4) NSF TUES- Course Curriculum, Laboratory Improvement Conference. Developing and teaching this course have trained undergraduate students the newest technology, developed their scientific processing skills, helped many students obtain employment, and developed sequencing capabilities in Brazil and Chile.

Describe any unexpected challenges you encountered and your methods for dealing with them: Logistics to conduct the hands-on sequencing course was difficult because there is a high potential for contamination of the environmental DNA with the linker DNA, following the samples through the process and manipulation of large datasets. These logistical problems were overcome by teaching the course across multiple rooms and in a rotation fashion, so that every student gets to complete all the processes. Last a web site was set up to follow the samples and manipulate the data.

Describe your completed dissemination activities and your plans for continuing dissemination: The course is in its fourth year and other Faculty are providing samples and support to run the course. The Faculty receives publication quality data and the students get the practice at sequencing and annotation. Teaching undergraduates to use the latest technology to sequence genomic DNA ensures they are ready to meet the challenges of the genomic era and allows them to participate in annotating the tree of life. We are helping other universities set up similar courses and have visited Earlham College and the University of Puerto Rico. We are developing a faculty workshop to enable faculty to conduct and teach next generation sequencing and annotation.

Acknowledgements: We acknowledge Roche 454 Lifesciences for providing the backing to conduct the course. The course and EAD was supported by a NSF for Transforming Undergraduate Education in Science: 1044453 from the Division of Undergraduate Training grant. RAE is supported by NSF grants DBI: 0850356 from the Division of Biological Infrastructure and DEB: 1046413 from the Division of Environmental Biology.