Microbes, metagenomes and marine mammals: enabling the next generation of scientist to enter the genomic era

BMC Genomics

Correspondence

Sowmya Chinta¹  Noriko Cassman¹  Kristen Aguinaldo¹  John Matthew Haggerty¹  Julia Christine Busch²  Robert Morey³  Robert Alan Edwards³  Elizabeth Ann Dinsdale³  Clotilde Teiling⁴  Karin Fredrikson⁵  Timothy T Harkins⁶  Meredith Houle Vaughn⁷ 

[1] Biology Department, San Diego State University, 5500 Campanile Dr., 92182, San Diego, CA, USA;Biology Department, San Diego State University, 5500 Campanile Dr., 92182, San Diego, CA, USA;Scripps Institute of Oceanography, University of California, 9500 Gilman Drive, 92023, San Diego, La Jolla, USA;Computer Sciences Department, San Diego State University, 5500 Campanile Dr., 92182, San Diego, CA, USA;Roche 454 Lifesciences, 15 Commercial Street, 06405, Branford, CT, USA;Roche 454 Lifesciences, 15 Commercial Street, 06405, Branford, CT, USA;Immun Array 800, East Leigh Street, Suite 15, 23219, Richmond, VA, USA;Roche 454 Lifesciences, 15 Commercial Street, 06405, Branford, CT, USA;Life Technologies, Advanced Application Development, 01915, Beverly, MA, USA;School of Teacher Education, San Diego State University, 5500 Campanile Dr., 92182, San Diego, CA, USA;

关键词: Undergraduate education;    DNA sequencing;    Sea lion;    Metagenome;   

DOI  :  10.1186/1471-2164-14-600

 received in 2013-01-07, accepted in 2013-08-28,  发布年份 2013

来源: Springer

【 摘 要 】

BackgroundThe revolution in DNA sequencing technology continues unabated, and is affecting 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 influencing research and development efforts to advance genome biology. Here we present a cross-disciplinary course that provides undergraduate students with practical experience in running a next generation sequencing instrument through to the analysis and annotation of the generated DNA sequences.ResultsMany 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. The students conducted the work flow from DNA extraction, library preparation, running the sequencing instrument, to the extraction and analysis of the data. They sequenced microbes, 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.ConclusionsStudents learned important skills for their future education and career opportunities, and a perceived increase in students’ ability to conduct independent scientific research was measured. DNA sequencing is rapidly expanding in the life sciences. 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.

【 授权许可】

Unknown   
© Edwards et al.; licensee BioMed Central Ltd. 2013. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.