Review of the Department of Energy's Genomics: GTL Program (2006) / Chapter Skim
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1 Role of Genomics in Advancing Science
1 Role of Genomics in Advancing Science
Pages 9-24
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From page 9... ...
The program has been funding microbial genomics projects relevant to DOE mission goals since 2002. DOE plans to expand the program and build infrastructure for it.
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From page 10... ...
With the completion of the draft human genome sequence in 2003, the basis for rapidly understanding much of the genome information through comparative genomics was in place. The sequencing of the human genome has provided detailed genetic information about specific genes and pathways in humans and has opened vast possi
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From page 11... ...
The time required to obtain a gene sequence is also falling rapidly. In 1989, Andre Goffeau set up a consortium to sequence the 12.5-million-base-pair genome of the budding yeast Saccharomyces cerevisiae.
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From page 12... ...
The idea is that vast data stores -- when properly collected, annotated, and stored in accessible databases -- are available for intense data mining by members of the scientific community who have specific hypothesis-driven questions. The various genome projects are considered discovery science, and this has proved to be a powerful scientific tool.
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From page 13... ...
Therefore, DOE provided $5.3 million to initiate the HGP at its national laboratories. The National Institutes of Health joined DOE in the HGP in 1988 because it recognized that genomic tools could be important in understanding human genetic disorders.
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From page 14... ...
JGI's massive sequencing capabilities have served the DOE microbial genome program by sequencing the entire genomes of many microorganisms. In addition, JGI began the Community Sequencing Program, which solicits genome sequencing proposals for organisms that are relevant to DOE missions, and other organisms important to other community dynamics.
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From page 15... ...
Charged with securing the nation's energy supply, DOE's Office of Energy Efficiency and Renewable Energy (EERE) has a Biomass Program and a Hydrogen, Fuel Cells, and Infrastructure Technologies Program, both of which substantially involved the National Renewable Energy Laboratory.
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From page 16... ...
. Using Systems Biology to Find Solutions for Carbon Sequestration, Environmental Remediation, and Energy Security Although scientists often gain insight into microorganisms or microbial processes one at a time, such studies, even when pieced together, do not provide a global picture of how a biological system works.
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From page 17... ...
The emerging field of synthetic biology will provide fundamental insights into cellular systems, improve our understanding of natural phenomena, and promote the development of a new engineering discipline focusing on the design and development of complex cell behaviors with predictable and reliable properties. Using the two complementary approaches to study microorganisms and microbial communities to understand their structure and function, predict their behavior accurately, and manipulate them for desired functions is the key theme of DOE's Genomics: GTL program.
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From page 18... ...
reverse engineer and re-design a `simple' natural bacterium" (MIT Synthetic Biology Working Group, 2005)
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ROLE OF GENOMICS IN ADVANCING SCIENCE 19 TABLE 1-1 Major Events Leading to the Release of the 2005 Genomics: GTL Roadmap Year Event 1999 November 24 Martha Krebs, director of DOE Office of Science, charges BERAC to define the department's potential scientific roles after the HGP is completed 2000 August BERAC publishes Bringing the Genome to Life in response to Krebs's 1999 charge October 29-November 1 Genomes to Life roadmapping workshop 2001 January 25-26 Genomes to Life roadmapping workshop June 23 Genomes to Life workshop on role of biotechnology in mitigating greenhouse-gas concentrations August 7-8 First Genomes to Life computational biology workshop September 6-7 Visions for computational biology and systems biology workshop for Genomes to Life program December 10-11 Genomes to Life: Technology assessment for mass spectrometry workshop 2002 January 22-23 Computing infrastructure and networking workshop for Genomes to Life March 6-7 Computer science for Genomes to Life workshop March 18-19 Mathematics for Genomes to Life workshop April 16-18 Imaging workshop for Genomes to Life program April 16-19 Computing-strategies workshop June 19-20 Genomes to Life systems biology facilities planning workshop I July 23 DOE awards $103 million for post genomics research. August 16-17 Genomes to Life systems biology facilities planning workshop II October 14-15 Genomes to Life systems biology facilities planning workshop III December 3-4 Genomes to Life draft facilities strategy and plan submitted to BERAC by Life Sciences Division of Biological and Environmental Research program 2003 April 1-2 GTL facility for whole-proteome analysis workshop April 23 DOE awards $9 million for energy-related genomics research May 12-14 Bioinformatics in GTL facility for whole-proteome analysis May 29-30 GTL facility for production and characterization of proteins and molecular tags workshop continued
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From page 20... ...
Large amounts of data would need to be collected to characterize proteins, molecular machines, gene regulatory networks, and entire microbial communities in natural environments at the molecular level. Computational methods and capabilities would need to be developed to integrate the data and to gain a predictive understanding of these complex biological systems.
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From page 21... ...
Other energy-related plans of the Genomics: GTL bioenergy program include efforts to redirect microbial photosynthesis to generate hydrogen fuel in a process that uses energy derived from sunlight to convert water into hydrogen and oxygen and research into the remarkable ability of some soil microorganisms to produce electricity from simple organic compounds. Bioremediation DOE is charged with remediating thousands of our nation's most contaminat ed landscapes, many of which are the legacy of a diverse network of defense facilities.
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From page 22... ...
Much of the research funded by the program aims to lay the foundation for future study by solving key issues in genome-directed science. For example, · Several research projects aim to develop computational models to under stand complex microbial systems, and other researchers are developing data warehouses and computational tools to organize and relate genomic information for bench scientists.
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From page 23... ...
Facility instrumentation will include mass spectroscopy to characterize molecular machines and imaging capabilities to localize them in cells. Computational capabilities will allow for modeling and simulation of molecular interactions to understand how these complex structures arise.
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From page 24... ...
Instrumentation would include cultivation technologies for microbial communities under highly controlled environmental conditions and imaging instrumentation to resolve the molecular makeup of cells spatially and temporally. Computational capabilities would focus on data analysis and modeling, including simulating complex microbial communities.
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