Bioenergy/GTL & Structural Biology
DOE GTL Scientific Focus Area (SFA) "Ecosystems and Networks Integrated with Genes and Molecular Assemblies (ENIGMA)"
ENIGMA seeks to advance the increasingly high resolution mapping from molecules to microbes and leverage the discovery of mechanisms composing the subcellular, cellular, and intercellular networks of metabolite, protein, RNA and DNA molecules that drive macroscopic biogeochemical processes, integrating these into the larger framework of interacting microbial communities and ecosystems to address DOE goals.
By developing and applying high resolution and high throughput platforms of both ‘top down’ systems approaches (i.e. metagenomics, proteomics, metabolomics, etc) and ‘bottom up’ structural approaches (i.e. EM and SAXS), we are rapidly advancing environmental microbes to model-organism status. Aided by critical consortium and field studies, the single-organism molecular data extend across increasingly complex microbial communities to determine how these networks transform environmental signals to behaviors and to link laboratory results to the measurements from field studies. The SFA enables these unique multiscale studies through the development of an increasingly sophisticated computational framework for storage, analysis, visualization and modeling of these data. The framework is designed to predict the key factors enabling microorganisms to survive, compete, and cooperate in DOE relevant environments while performing processes impacting remediation, carbon sequestration and bioenergy production. We develop new frameworks for collecting and quantitatively analyzing multi-scale information—from molecules to organisms, from cells to communities, and from communities to ecosystems in order to meet the challenges and opportunities of the DOE GTL mission. Research in the ENIGMA Scientific Focus Area is funded by the U.S. Department of Energy Office of Biological and Environmental Research Division.
Laboratory Research Manager: Paul Adams (PBD)
Technical Co-Manager: Adam Arkin (PBD)
Leadership: Adam Arkin (PBD), Nitin Baliga (Institute of Systems Biology), Mark Biggin (GD), Adam Deutschbauer (PBD), Terry Hazen (ESD), Greg Hura (LSD), Trent Northen (LSD), John Tainer (LSD) and Joe Jizhong Zhou (University of Oaklahoma).
Website: ENIGMA SFA
Molecular Assemblies and Genes in Communities (MAGIC)
MAGIC provides robust GTL technologies and comprehensive characterizations to efficiently couple gene sequences and genomic analyses with protein interactions: thereby elucidating functional relationships and pathways within organisms and between ecosystem community members.
Principal Investigator: John Tainer
Website: MAGIC
Genemap MS
This project is developing high-throughput methods for validating genome annotation using mass spectrometry based proteomic surveys, metabolomics, and new technologies for detecting biochemical activities on arrayed metabolite substrates.
Principal Investigator: Trent Northen
Website: Microbial Communities
Private EBI project "Precision Atlases of Plant Cell Walls"
The success of lignocellulosic biofuels as a renewable transportation fuel energy source depends on overcoming the recalcitrance of plant cell walls through genetic engineering. Cell walls have evolved to withstand chemical, enzymatic and microbial attack. Any efforts for plant cell wall re-engineering requires a realistic cell wall model. We employ electron tomography of high-pressure frozen, cryo-sectioned or freeze-substituted samples in order to obtain detailed 3D architectural information. Together with compositional data obtained by Raman microspectroscopy, such 3D architecture, allows us to create a model of the cell wall and elucidate its building properties. This effort is a collaboration between the Auer, Downing and Parvin laboratories.
Leader: Manfred Auer
Website: Energy Biosciences Institute (EBI)
