Students Learning Genomics With Joint Genome Institute Scientists

MERCED, CA— Professors Miriam Barlow and Mónica Medina of UC Merced's School of Natural Sciences are coordinating a cutting-edge theoretical and experimental course in genomics with researchers from the United States Department of Energy Joint Genome Institute (JGI).

"For undergraduate students, working directly with top biomedical research scientists is a rare and valuable opportunity, and the collaborative approach in our genomics course is groundbreaking," said Dean of Natural Sciences Maria Pallavicini. "It's the kind of opportunity UC Merced was built to offer."

This semester, 14 students are studying with 20 JGI researchers led by Pilar Francino, Ph.D., the head of JGI's evolutionary genomics program.

"We had a great response from everybody," said Francino. "Actually, for some topics we had to choose among several potential lecturers who were interested in teaching."

The scientists take turns visiting the UC Merced campus to teach procedures involved in genome projects. They do this by working with students on several small projects that illustrate different aspects of genome science, like DNA preparation, library construction, sequencing, genome assembly, gene prediction and annotation.

Other scientists will participate from Oak Ridge National Laboratory and Pacific Northwest National Laboratory to teach the students.

The small projects for teaching the course all originated with UC Merced researchers.

  • Medina's contribution is a project sequencing DNA from microbes in coral reefs, with the aim of finding out why coral reefs are becoming sick.
  • Barlow's project involves sequencing plasmids - circular DNA found in bacteria - that contain multiple copies of resistance genes to try to understand if and how plasmids remove resistance genes.
  • Graduate student Shinichi Sunagawa defined a project sequencing genes expressed in sea anemones to study the cell biology of symbiosis.
  • Professor Andrés Aguilar's project aims to determine how species of rockfish have formed by sequencing expressed genes in that group of fish.
  • Finally, Professor Benoît Dayrat contributed a project involving sequencing the mitochondrial genomes of gastropods to determine how they are related to each other.

"This course involves hands-on training familiarizing our students with the protocols in use at the Joint Genome Institute," said Medina, who was with the JGI before accepting a faculty appointment at UC Merced in 2005.

She said JGI director Eddy Rubin approached her about a year ago with a desire to pursue a joint project with UC Merced.

"When I proposed the idea of doing the course as a joint effort between the two institutions, he encouraged his staff to participate," Medina said. "Besides contributing people's time and expertise, he has approved a significant amount of sequencing for student projects that we could not afford otherwise."

The students in the course will analyze and interpret these sequencing projects under the direction of their UC Merced professors and scientists from the JGI.

"The course is intended to train students so that they're competitive for jobs at JGI," Barlow said. "It's a great opportunity. Students will be involved in analyzing data and producing publication-quality results, giving them experience in writing scientific manuscripts at this early stage in their careers."

Barlow also said that UC Merced plans to continue to offer the course in the future with continuing support from JGI.

The DOE Joint Genome Institute, supported by the DOE Office of Science, unites the expertise of five national laboratories, Lawrence Berkeley, Lawrence Livermore, Los Alamos, Oak Ridge, and Pacific Northwest, along with the Stanford Human Genome Center to advance genomics in support of the DOE mission related to clean energy generation and environmental characterization and clean-up. DOE JGI's Walnut Creek, Calif. Production Genomics Facility provides integrated high-throughput sequencing and computational analysis that enable systems-based scientific approaches to these challenges.

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