As part of a semesterlong course which aims to investigate the health of California sea lions and their environment, a group of undergraduate students at San Diego State University are experiencing firsthand the sequencing technology that is revolutionizing life science research. Led by SDSU Professor Elizabeth Dinsdale, the university students are learning how to prepare DNA samples and operate the Genome Sequencer FLX System, a highthroughput sequencing platform from 454 Life Sciences, a Roche Company. Along with their wetlab lessons on molecular biology and sequencing techniques, the students have a much larger goal in mind: to sequence the complete genome of the California sea lion (Zalophus californianus) as well as its marine habitat.
Given the enormity of this task, the SDSU students have joined forces with an international collaboration, led by Dinsdale, which includes scientists from Hubbs-SeaWorld Research Institute, Universidad Autónoma de Baja California, and Centro de Investigación Científica y de Educación Superior de Ensenada. These multinational and multidisciplinary 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 Professor Dinsdale's lab, which uses the Genome Sequencer FLX System to investigate the interactions between the large and small organisms within an ecosystem. Professor 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, Professor Dinsdale and her students will explore how microbes and California sea lions interact and influence kelp forest dynamics and health.
"I am interested in studying the environment in its entirety and this sequencing technology has enabled me to understand how the small things affect environmental health," explained Dinsdale. "By involving the students, we have the capacity to sequence multiple components of the kelp forest and understand how they interact."
In the first four weeks the course, 21 students from the Ecology, Biology, and Computer Sciences departments have generated more than 3 million high quality sequencing reads or over 1 billion bases of DNA using the 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 SDSU will focus on postsequencing analysis of the data generated by Dinsdale's students. Professor Rob Edwards, a project collaborator and preeminent genome and metagenome bioinformatician, will lead the group of students from raw sequence data to biological result. "This is the first time that students will sequence a genome as large as a sea lion in one semester, and then spend the next semester analyzing their data," said Edwards. "This project is a unique opportunity to integrate biology and computer sciences."
"Sequencing has become a fundamental research tool, with applications in both human and environmental microbiology. Educating the next generation of scientists on emerging genomic technologies is critical," said Christopher McLeod, President and CEO of 454 Life Sciences, a Roche Company. "We have designed our newest platform, the GS Junior System, to make highthroughput sequencing accessible to individual researchers and to professors who can incorporate the technology into science curriculums. We are eager to see how the upandcoming crop of scientists will apply sequencing in the future."
Given the enormity of this task, the SDSU students have joined forces with an international collaboration, led by Dinsdale, which includes scientists from Hubbs-SeaWorld Research Institute, Universidad Autónoma de Baja California, and Centro de Investigación Científica y de Educación Superior de Ensenada. These multinational and multidisciplinary 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 Professor Dinsdale's lab, which uses the Genome Sequencer FLX System to investigate the interactions between the large and small organisms within an ecosystem. Professor 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, Professor Dinsdale and her students will explore how microbes and California sea lions interact and influence kelp forest dynamics and health.
"I am interested in studying the environment in its entirety and this sequencing technology has enabled me to understand how the small things affect environmental health," explained Dinsdale. "By involving the students, we have the capacity to sequence multiple components of the kelp forest and understand how they interact."
In the first four weeks the course, 21 students from the Ecology, Biology, and Computer Sciences departments have generated more than 3 million high quality sequencing reads or over 1 billion bases of DNA using the 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 SDSU will focus on postsequencing analysis of the data generated by Dinsdale's students. Professor Rob Edwards, a project collaborator and preeminent genome and metagenome bioinformatician, will lead the group of students from raw sequence data to biological result. "This is the first time that students will sequence a genome as large as a sea lion in one semester, and then spend the next semester analyzing their data," said Edwards. "This project is a unique opportunity to integrate biology and computer sciences."
"Sequencing has become a fundamental research tool, with applications in both human and environmental microbiology. Educating the next generation of scientists on emerging genomic technologies is critical," said Christopher McLeod, President and CEO of 454 Life Sciences, a Roche Company. "We have designed our newest platform, the GS Junior System, to make highthroughput sequencing accessible to individual researchers and to professors who can incorporate the technology into science curriculums. We are eager to see how the upandcoming crop of scientists will apply sequencing in the future."
