Table 1. Research Scenarios on Microbial Processes: Relationship to Science Milestones and Facilities

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Table 1. Research Scenarios on Microbial Processes:
Relationship to Science Milestones and Technologies

Progression of GTL Science Milestones and Technologies	Conceptual Science Roadmaps for Microbial Energy and Environmental Processes
Convert Sunlight to Hydrogen and High-Hydrogen Fuels	Convert Cellulose to Fuels	Reduce Toxic Metals in Subsurface Environments
Milestone 1: Determine the Genome Structure and Potential of Microbes and Microbial Communities Production and Characterization of Proteins and Molecular Tags Characterization and Imaging of Molecular Machines	Analysis of hydrogenase families across microbial species: Screen nature for new variants Range of hydrogenase properties Suite of heterologous expression hosts Characterization of partners, energetics, structures, post-translational modifications Wide range of mutations, variations created and screened Functional and structural analysis of machines	Wide range of microbes surveyed for cellulases, ligninases, and other glucosyl hydrolases Partners and structural information established Structure and imaging of interactions important to efficient function	Survey of subsurface species and genomic potential Comparative genomics and superannotation Generation of knockouts, mutations, transmembrane structures to understand function
Milestone 2: Develop a Systems-Level Understanding of Microbial and Community Function and Regulation Whole Proteome Analysis Analysis and Modeling of Cellular Systems	Oxygen sensitivity of hydrogenases Electron-transfer reactions and limitations Reverse-reaction mitigation Partitioning of electrons between hydrogenases and competing pathways Light capture Biophotoelectric antenna	Proteome analysis of expression and regulation Fundamental mechanisms of cellulose deconstruction Transport of sugars Measurement of electron transport chains' redox state, control of electron fluxes Carbon partitioning in cells: Carbon, NAD, NADPH, ATP, ADP	Cellular response to environmental stimuli Proteomics, transcriptomics, and metabolomics to elucidate regulation and responses Intra- and intercellular communications Cells in structures such as biofilms Growth processes, toxicity responses, energy transfer, metabolic responses Microbe-mineral interactions
Milestone 3: Develop the Knowledgebase, Computational Methods, and Capabilities to Advance Understanding of Complex Biological Systems and Predict Their Behavior GTL Integrated Computational Environment for Biology	Pathway models-energetics, electropotential, docking, proton fluxes, cofactors Computational tools for rational design Suites of hosts, pathway cassettes Modeling and measurement of pathways, fluxes, regulation	Design of organisms capable of utilizing all sugars Optimization of sugar transport, regulation Redesign of cellulose structure pH- and temperature-tolerant microbes Principles for enzyme redesign	Modeling capable of visualizing realistic biochemical pathways in cells Interactions of membrane proteins with contaminants and solid-phase electron acceptors Design of experiments in cultured and natural systems
Missions Outputs Systems Engineering	In vivo systems Processes captured in nanostructures, biomimetic systems System design: Light harvesting, conversion to hydrogen or fuel, robustness to oxygen, regulation Transgenic approaches	Improved cellulases and production methods to reduce costs, improve stability Modularized processing to reduce transportation of feedstock Sensors for biomarkers and chemical intermediates	Assessment of long-term cellular and system behavior Remediation strategies Sensors for coupled biochemical and geochemical measurements in situ

Progression of GTL Science Milestones and Technologies

Conceptual Science Roadmaps for Microbial Energy and Environmental Processes

Convert Sunlight to Hydrogen and High-Hydrogen Fuels

Convert Cellulose to Fuels

Reduce Toxic Metals in Subsurface Environments

Milestone 1: Determine the Genome Structure and Potential of Microbes and Microbial Communities

Production and Characterization of Proteins and Molecular Tags

Characterization and Imaging of Molecular Machines

Analysis of hydrogenase families across microbial species: Screen nature for new variants

Range of hydrogenase properties

Suite of heterologous expression hosts

Characterization of partners, energetics, structures, post-translational modifications

Wide range of mutations, variations created and screened

Functional and structural analysis of machines

Wide range of microbes surveyed for cellulases, ligninases, and other glucosyl hydrolases

Partners and structural information established

Structure and imaging of interactions important to efficient function

Survey of subsurface species and genomic potential

Comparative genomics and superannotation

Generation of knockouts, mutations, transmembrane structures to understand function

Milestone 2: Develop a Systems-Level Understanding of Microbial and Community Function and Regulation

Whole Proteome Analysis

Analysis and Modeling of Cellular Systems

Oxygen sensitivity of hydrogenases

Electron-transfer reactions and limitations

Reverse-reaction mitigation

Partitioning of electrons between hydrogenases and competing pathways

Light capture

Biophotoelectric antenna

Proteome analysis of expression and regulation

Fundamental mechanisms of cellulose deconstruction

Transport of sugars

Measurement of electron transport chains' redox state, control of electron fluxes

Carbon partitioning in cells: Carbon, NAD, NADPH, ATP, ADP

Cellular response to environmental stimuli

Proteomics, transcriptomics, and metabolomics to elucidate regulation and responses

Intra- and intercellular communications

Cells in structures such as biofilms

Growth processes, toxicity responses, energy transfer, metabolic responses

Microbe-mineral interactions

Milestone 3: Develop the Knowledgebase, Computational Methods, and Capabilities to Advance Understanding of Complex Biological Systems and Predict Their Behavior

GTL Integrated Computational Environment for Biology

Pathway models-energetics, electropotential, docking, proton fluxes, cofactors

Computational tools for rational design

Suites of hosts, pathway cassettes

Modeling and measurement of pathways, fluxes, regulation

Design of organisms capable of utilizing all sugars

Optimization of sugar transport, regulation

Redesign of cellulose structure

pH- and temperature-tolerant microbes

Principles for enzyme redesign

Modeling capable of visualizing realistic biochemical pathways in cells

Interactions of membrane proteins with contaminants and solid-phase electron acceptors

Design of experiments in cultured and natural systems

Missions Outputs

Systems Engineering

In vivo systems

Processes captured in nanostructures, biomimetic systems

System design: Light harvesting, conversion to hydrogen or fuel, robustness to oxygen, regulation

Transgenic approaches

Improved cellulases and production methods to reduce costs, improve stability

Modularized processing to reduce transportation of feedstock

Sensors for biomarkers and chemical intermediates

Assessment of long-term cellular and system behavior

Remediation strategies

Sensors for coupled biochemical and geochemical measurements in situ

U.S. Department of Energy Office of Science

Genomics:GTL

Table 1. Research Scenarios on Microbial Processes:
Relationship to Science Milestones and Technologies

	Human Genome Project Information Genomics:GTL DOE Microbial Genomics home

U.S. Department of Energy Office of Science

Genomics:GTL

Table 1. Research Scenarios on Microbial Processes: Relationship to Science Milestones and Technologies

Table 1. Research Scenarios on Microbial Processes:
Relationship to Science Milestones and Technologies