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Students Learning Genomics With Joint Genome Institute Scientists

March 6, 2007


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.