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US Department of Energy Taps Genomatica For Environmental Microbial Modeling Project


Genomatica, a systems biology startup based in San Diego, Calif., signed on the US government as its first customer last week.

Two grants from the Department of Energy’s Offices of Advanced Scientific Computing Research and Biological and Environmental Research, totaling over $2 million in funding over the next three years, will support development of the company’s in silico technology for generating models of metabolism and metabolic regulation.

The grants are among the first of the DOE’s Genomes to Life project, announced earlier this year, which aims to put genomic sequence knowledge to practical use for environmental research.

The awards to Genomatica will support further development of the company’s constraints-based modeling technology to build models for two microorganisms of interest for bioremediation: Geobacter sulfurreducens, a bacterium that is able to reduce heavy metals in soil, and Shewanella oneidensis, a unicellular algae that is able to metabolize a diverse range of organic molecules.

Genomatica is collaborating with researchers from Penn State University, the University of Massachusetts, and Oak Ridge National Laboratory on the project.

Company founder and acting CEO Bernhard Palsson, a professor in the department of bioengineering at the University of California, San Diego, said that the award will help Genomatica in its efforts to develop the “second generation” of its modeling technology.

Palsson said that unlike kinetic-theory driven approaches that mathematically model individual operons and are very difficult to scale up to the whole genome, Genomatica''s constraints-based procedure is based on the principle that “we can''t decide what cells actually do,” said Palsson. “Cells will never be modeled mathematically to the same level of exactness as chemical or physical systems are.” Instead, he said, the method assigns a range of known constraints that cells operate under and predicts behaviors based on that range.

The technique has been validated against experimental data and has a current hit rate of 70-80 percent for Escherichia coli, yeast, and several other organisms. Palsson said the failures seen so far are due to the lack of biological regulation data in the model, data the group will now have access to through the DOE grant.

In the company’s work on Geobacter, for example, Derek Lovely''s lab at the University of Massachusetts is producing the bacteria, making knockouts, and characterizing it, while Genomatica will synthesize this experimental data into its model.

Genomatica has already developed models of human pathogens such as Haemophilus influenza and Helicobacter pylori. The company also plans to build models of human cells, an application that Palsson said has particular applications in cancer research.

While the company has not yet announced any additional customers, Palsson said it is pursuing work in both the public and the private domain. Genomatica intends to partner with companies interested in developing targets using its models of pathogens, he said.

— BT


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