U.S. Department of Energy Office of Biological and Environmental Research

BER Research Highlights


New Method to Compare Organism Functionality
Published: April 16, 2012
Posted: May 24, 2012

Systems biology approaches to bioenergy and environmental research are enabled by reliable models of processes in living cells. Advances in genome sequencing and computational modeling have led to the development of over 100 genome-scale network reconstructions (constraint-based models). Rapid increases in this number are expected, so methods that use algorithms to compare functional characteristics between organisms will be increasingly important. Scientists at the University of Wisconsin have reported a novel approach that embeds two constraint-based models into an optimization model. This combination identifies those genes and reaction pathways that contribute most to differences in metabolic functionality. The authors identified several differences in metabolism in two cyanobacteria that have potential for biofuel production, Synechococcus and Cyanothece. For example, they demonstrated the necessity for a particular protein (plastocyanin) for photosynthesis in Cyanothece, but not in Synechococcus. The new approach also aids the curation of constraint-base models by identifying pathways that are coded by the organism, but that are missing from the model.

Reference: Hamilton, J. J., and J. L. Reed. 2012. "Identification of Functional Differences in Metabolic Networks Using Comparative Genomics and Constraint-Based Models," PLoS ONE 7(4), e34670. DOI:10.1371/journal.pone.0034670. (Reference link)

Contact: John Houghton, SC-23.2, (301) 903-8288
Topic Areas:

  • Research Area: Genomic Analysis and Systems Biology
  • Research Area: Microbes and Communities
  • Research Area: Sustainable Biofuels and Bioproducts
  • Research Area: Computational Biology, Bioinformatics, Modeling

Division: SC-23.2 Biological Systems Science Division, BER

 

BER supports basic research and scientific user facilities to advance DOE missions in energy and environment. More about BER

Recent Highlights

Aug 24, 2019
New Approach for Studying How Microbes Influence Their Environment
A diverse group of scientists suggests a common framework and targeting of known microbial processes [more...]

Aug 08, 2019
Nutrient-Hungry Peatland Microbes Reduce Carbon Loss Under Warmer Conditions
Enzyme production in peatlands reduces carbon lost to respiration under future high temperatures. [more...]

Aug 05, 2019
Amazon Forest Response to CO2 Fertilization Dependent on Plant Phosphorus Acquisition
AmazonFACE Model Intercomparison. The Science Plant growth is dependent on the availabi [more...]

Jul 29, 2019
A Slippery Slope: Soil Carbon Destabilization
Carbon gain or loss depends on the balance between competing biological, chemical, and physical reac [more...]

Jul 15, 2019
Field Evaluation of Gas Analyzers for Measuring Ecosystem Fluxes
How gas analyzer type and correction method impact measured fluxes. The Science A side- [more...]

List all highlights (possible long download time)