Sandia LabNews

DOE announces 'Genome to Life' grants

Sandia to lead one of five ‘Genomes to Life’ programs

Sandia will lead one of five major research awards — and participate in two others — announced this week by the Department of Energy for what it terms "post-genomic" research.

Secretary of Energy Spencer Abraham announced the new projects, entitled "Genomes to Life," in Washington Tuesday. They will total $103 million over the next five years. Research will be conducted at six national laboratories, including Sandia; 16 universities and research hospitals; and four private research institutes. The work is headed by DOE’s Office of Science.

Said Abraham, "One could hardly imagine when the Energy Department began the human genome project in the ’80s that the resulting information and technologies could yield such diverse benefits."

He said the new research program is expected to provide "biotechnology solutions to help produce clean energy, clean up the environment, and contribute to the President’s policy on climate change."

The Sandia-led effort is headed by Grant Heffelfinger (1802) and involves $19.1 million over three years to understand the sequestration of carbon in a seaborne bacteria called Synechococcus. The grant — subtitled "From Molecular Machines to Hierarchical Modeling" — brings together a formidable collection of research institutions, including Sandia, Oak Ridge National Laboratory, Lawrence Berkeley National Laboratory, Los Alamos National Laboratory, National Center for Genome Resources in Santa Fe, N.M., the University of California at San Diego, the University of Tennessee at Knoxville, the University of Michigan at Ann Arbor, The Molecular Science Institute in Berkeley, Calif., the University of California at Santa Barbara, and the University of Illinois at Urbana-Champaign.

Of the total for this project, $2.35 million comes to Sandia, with internal distribution of approximately $1 million going to Computation, Computers, and Mathematics Center 9200; $650,000 to Exploratory Systems and Development Center 8100, with the remaining $500,000 to Materials and Process Sciences Center 1800. Other research monies will be distributed among the ten partners.

The reason that Sandia — not particularly known for biological expertise — was awarded its leadership role, says Grant, is that "the Genomes to Life program is jointly sponsored by the Office of Science’s Office of Biological and Environmental Research and the Office of Advanced Scientific Computing Research.

"The Genomes to Life project has four goals," he says: "to understand the molecular machines of life, regulatory networks, and how microbial communities work together. The final goal is to develop computational capabilities to address the first three.

"So our proposal, though it has a biological title, is based on our world-class computing and experiment-analysis expertise — abilities we’ve proven time and time again. So it makes sense for Sandia to lead what I think of as the Genomes to Life program’s lead effort in goal 4."

By the end of the project, Grant’s intent is to have "developed and prototyped a set of computational capabilities to enable the advancement of life science research for DOE’s missions, particularly in sequestration of carbon by Synechococcus.

Other projects in which Sandia is formally involved are led by:

  • Oak Ridge, which received $23.4 million over three years to develop a research program for identification and characterization of protein complexes, and
  • Lawrence Berkeley National Laboratory, which received $36.6 million over five years for rapid deduction of stress response pathways in metal/radionuclide reducing bacteria.

The awards are, without exception, for multi-institutional, multidisciplinary projects that involve both biological and computational sciences. Their purpose is to go beyond the workings of small groups of genes and instead focus on entire networks of genes and even entire biological systems. Single-celled organisms are first; later, more complex creatures — including humans — will be studied.

The human genome and those of other organisms — microbes, plants, worms, and mice — are expected to provide new perspectives on the inner workings of biological systems.

The program will use advanced computation, genomic information, and other resources to "take advantage of solutions that nature has already devised to help solve problems in energy production, environmental cleanup, and carbon cycling," according to a DOE news release. "Through a systems approach to biology at the interface of the biological, physical, and computational sciences, the program seeks to understand entire living organisms and their interactions with the environment."

One goal of the Genomes to Life program is to understand molecular machines and their controls so well that they can be used and even redesigned to address national needs. (The concept is widespread that nature creates arrays of molecular machines with precise and efficient functions that include motion, molecular detection, chemical synthesis and degradation, and light emission and detection.)

The program is also expected to lead to an understanding of the complex regulatory networks that control the assembly and coordinate the operations of these machines.

Another goal is to better understand the complex workings of microbial communities that could help solve energy and environmental challenges. These organisms normally do their work as part of communities made up of many different microbes. Eight types of microbes will be studied in these research projects because of their potential for bioremediation of metals and radionuclides, degradation of organic pollutants, production of hydrogen or sequestration of carbon, or because of their importance in ocean carbon cycling. All of these individual microbes have had their genetic sequence determined under DOE’s Microbial Genome program.

The project’s 10-year goal is to advance systems biology, computation, and technology to increase sources of biological-based energy; help understand the earth’s carbon cycle, design ways to enhance carbon capture, and lead to cost-effective ways to clean up the environment.

Because these projects require sophisticated computational tools, new computational techniques to predict the functions and behaviors of complex biological systems are expected to be developed.

More information on the Genomes to Life program is available at