Contact: Dr. Mary Lipton
Our ability to study changes in biological systems and describe their variability from large volumes of proteomics data enable new insights into diverse organisms and complex biological systems, such as microbial communities present in the soil and ocean. For example, proteomics data have augmented the genomic annotation of Shewanella oneidensis by validating the expression of hypothetical and small proteins missed by the original genome annotation as, well as identifying mobile elements and pseudogenes. See highlight.
Using 0.7 Terabytes (~150 DVDs) of data obtained from numerous proteomics studies of S. oneidensis MR-1, an important microbe for bioremediation, PNNL researchers and collaborators generated the first comprehensive map of post-translational modifications in a bacterial genome. The massive volume of data, which was provided by PNNL's High-Throughput Proteomics Production Facility, was the result of steady growth in throughput and data production over recent years. It included samples from 17 cell culture conditions and comprised the largest LC-MS/MS dataset ever reported for a bacterium.
Statistical analysis of quantitative proteomic data, aided by normalization approaches developed for this purpose, has led to the elucidation of genes important to iron respiration in G. sulfurreducens and differential growth patterns in light and dark in Peligibacter ubique.
Characterization of the proteins in the photosynthetic membrane of R. sphaeroides through protein localization studies has revealed new proteins important to photosynthesis and hydrogen production. Initial applications of our proteomics capability to microbial communities has revealed new strain heterogeneity in organisms in the Sargasso Sea, as well as novel biological functions present in the ground water communities of bioremediation sites.
Bioenergy Research Center. PNNL is a partner in the Great Lakes Bioenergy Research Center(GLBRC), a DOE Genomics:GTL Center that is exploring scientifically diverse approaches to converting sunlight and various plant feedstocks—agricultural residues, wood chips, and grasses—into biofuels.
In addition to its broad range of scientific research projects, the GLBRC is collaborating with agricultural researchers and producers to help develop the most economically viable and environmentally sustainable practices for bioenergy production. PNNL enables the GLBRC to complete high-throughput analysis of bioenergy proteins and organisms and analyze the entire life cycle of bioenergy practices.
Integrated Field-Scale Subsurface Research Challenge: Rifle Site, Environmental Remediation Sciences Program. PNNL is leading a field study at a uranium mill tailings site in Rifle, Colorado, to identify new approaches and strategies to help resolve questions about the movement of subsurface and contaminants.
The Rifle Field Study involves a diverse team of researchers who are examining the stimulation of subsurface microorganisms aimed at reducing and immobilizing uranium in the subsurface.
Researchers have found that bioremediation of uranium is possible, but optimal control and manipulation of the process is still unknown.