Undergraduate students at San Diego State University are using a high-throughput sequencing platform from 454 Life Sciences to investigate the health of sea lions and their environment.
Led by Elizabeth Dinsdale, a university professor, the students are learning how to prepare DNA samples and operate the Genome Sequencer FLX System.
The students intend to sequence the complete genome of the California sea lion (Zalophus californianus) as well as its marine habitat.
For this task, the students have joined forces with an international collaboration, led by Dinsdale, which includes scientists from Hubbs-Seaworld Research Institute, Universidad Autonoma de Baja California and Centro de Investigacion Cientifica y de Educacion Superior de Ensenada.
The collaborators will work together to describe the genetic adaptations that allow California sea lions to thrive in the complex coastal marine habitats of the eastern Pacific Ocean.
In order to better understand the marine ecosystems in which the sea lions live, the students will also sequence microbial metagenomes from the kelp forest.
The engagement of students in this sequencing work will add directly to the research efforts of Dinsdale's laboratory, which uses the Genome Sequencer FLX System to investigate the interactions between the large and small organisms within an ecosystem.
Dinsdale has previously demonstrated that metagenomes provide a profile of the metabolic potential of microbial communities and can identify perturbations in the ecosystem.
In the kelp forest project, Dinsdale and her students will explore how microbes and California sea lions interact and influence kelp forest dynamics and health.
In the first four weeks of the course, 21 students from the Ecology, Biology and Computer Sciences departments have generated more than three million sequencing reads or more than a billion bases of DNA using 454 Life Sciences' Genome Sequencer FLX System.
The sequences include the first parts of the sea lion genome, the whole genome of a previously unsequenced bacterium and three microbial metagenomes from the kelp forest.
Next semester, a subsequent course at the university will focus on the post-sequencing analysis of the data generated by Dinsdale's students.
Prof Rob Edwards, a project collaborator and pre-eminent genome and metagenome bioinformatician, will lead the group of students from raw sequence data to biological result.
'We have designed our newest platform, the GS Junior System, to make high-throughput sequencing accessible to individual researchers and to professors who can incorporate the technology into science curriculums,' said Christopher McLeod, president and chief executive officer of 454 Life Sciences, a Roche company.
