Genomic Core Facility
Instrumentation and throughput
Our current facility operates an Applied Biosystems 3730XL DNA Analyzer and a LI-COR 4200 IR system that can generate 1100 bp read lengths. Because the LI-COR system is economically inefficient relative to the 3730XL, we reserve its use for special or small-scale projects. There are no other capillary or slab-based sequencing machines within 75 miles of Woods Hole.
Excluding quality control and maintenance runs, we successfully processed ~310,000 reads during 2003 on our existing 3730XL sequencing system. Except for fifteen days of maintenance plus an additional two weeks of scheduled vacations in late December, our 3730XL operated near capacity on a continuous basis, seven days/week. The ability to load a dozen or more 96 or 384-well plates allows the instrument to run unattended for at least 48 hours, or with minimal interactions for longer periods of time. Approximately 50% of our usage in 2003 corresponds to NIH-supported genome projects (Giardia lamblia and the carpenter ant symbiont Blochmannia) while the balance was consumed by our NASA-supported metagenomic studies, an NSF genome project (Nosema locustae) and LEXEN-related cDNA projects.
The remaining machine time (approximately 28,800 reads) was fully utilized by other investigators in the Woods Hole scientific community, including NIEHS-supported work in the laboratories of John Stegeman and Mark Hahn.
Our total usage represented a fifty percent increase over the previous year (2002), which relied upon 3700 technology installed in January 2002. By comparison, the relatively low throughput of five LI-COR systems (purchased before the availability of capillary instruments) constrained our sequencing output to 52,000 reads prior to 2001.
Role in WHCOHH
The Genomics Facility Core is housed in the W. M. Keck Ecological and Evolutionary Genetics Facility at the MBL and directed by Mitchell Sogin. The Genomics Facility Core has budgeted funds for a minimum of 54,000 sequencing reads in 2004. Individual investigators have the option to provide resources for additional DNA sequencing reads and we anticipate significant escalations in future years.
The Genomics Facility Core provides more than simple sequencing services. The faculty of the Bay Paul Center, which manages the W. M. Keck Ecological and Evolutionary Genetics Facility, is committed to providing support and advice to WHCOHH investigators.
Three interlocking programs define the scope of research in the Bay Paul Center. They are:
- the Program in Global Infectious Diseases
- the Program in Molecular Evolution, and the
- Program in Molecular Microbial Diversity.
Strategies and databases developed in the Josephine Bay Paul Center are applicable to questions being addressed by the WHCOHH investigators. The Genomics Facility Core makes available, as they are developed, technology advances that can reduce the costs of microbial population structure studies based upon DNA sequencing techniques.
DNA sequencing in the Josephine Bay Paul Center for Comparative Molecular Biology and Evolution
Over the past decade, scientists in the Woods Hole community have adapted molecular biology and high-throughput DNA sequencing technologies to address important questions about parasitology, microbial diversity, genome evolution, molecular evolution, and ecology. These research initiatives capitalized on early investments in DNA sequencing in the Josephine Bay Paul Center for Comparative Molecular Biology and Evolution (JBPC) at the Marine Biological Laboratory (MBL) in Woods Hole.
Our DNA sequencing and associated robotic technology has supported genome projects for parasitic protists, Serial Analysis of Gene Expression (SAGE) projects for Giardia lamblia, Emiliania huxleyi and several Trypanosoma species, NASA-sponsored metagenomic and large-scale molecular microbial population structure studies, and NSF-sponsored LEXEN and Microbial Observatory Programs at Plum Island and Costa Rica.
There is a clear trend towards higher levels of DNA sequencing activity in the Woods Hole scientific community.