BIOLOGICAL BARRIERSTO CELLULOSIC ETHANOL -- BIOLOGICAL BARRIERS TO CELLULOSIC ETHANOL -- TABLE OF CONTENTS -- PREFACE -- INTRODUCTION -- JOINT WORKSHOP CHALLENGES BIOFUEL SCIENCE ANDTECHNOLOGY COMMUNITIES -- AMERICA'S ENERGY CHALLENGES -- The Promise of Biofuels -- A GROWING MANDATE FOR BIOFUELS: POLICY,LEGISLATIVE, AND OTHER DRIVERS -- BENEFITS OF BIOFUELS -- National Energy Security Benefits -- Economic Benefits -- Environmental Benefits -- Climate Change -- Other Environmental Benefits -- FEASIBILITY OF BIOFUELS -- Land Availability -- A BILLION-TON ANNUAL SUPPLY OF BIOMASS: SUMMARY OFPOTENTIAL FOREST AND AGRICULTURAL RESOURCES -- Agricultural Sustainability of Biomass Production -- Today - Fuel Ethanol Production from Corn Grain (Starch Ethanol) -- Tomorrow - Biorefinery Concept to Produce Fuel Ethanol from CellulosicBiomass -- Ethical, Legal, and Social Issues (ELSI) -- EERE OBP PLATFORM FOR INTEGRATED BIOREFINERIES -- ETHICAL, LEGAL, AND SOCIAL ISSUES FOR WIDESPREADDEVELOPMENT OF CELLULOSIC BIOFUELS -- DOE OFFICE OF SCIENCE PROGRAMS -- BIOMASS TO BIOFUELS WORKSHOP: CREATING A COMMONRESEARCH AGENDA TO OVERCOME TECHNOLOGY BARRIERS -- CITED REFERENCES -- BACKGROUND READING -- TECHNICAL STRATEGY: DEVELOPMENTOF A VIABLE CELLULOSIC BIOMASSTO BIOFUEL INDUSTRY -- RESEARCH PHASE (WITHIN 5 YEARS) -- Feedstock Use and Optimization -- Deconstruction -- Fermentation and Recovery -- TECHNOLOGY DEPLOYMENT PHASE (WITHIN 10 YEARS) -- Feedstocks -- Deconstruction -- Fermentation and Recovery -- SYSTEMS INTEGRATION PHASE (WITHIN 15 YEARS) -- Integration and Consolidation -- SYSTEMS BIOLOGY TO OVERCOME BARRIERS TOCELLULOSIC ETHANOL -- LIGNOCELLULOSIC BIOMASS CHARACTERISTICS -- Makeup, Structure, and Processability -- IMAGE ANALYSIS OF BIOENERGY PLANT CELL SURFACES AT THEOBP BIOMASS SURFACE CHARACTERIZATION LAB (BSCL) -- STRUCTURE AND ASSEMBLY OF CELL WALLS.

OPTIMIZING LIGNIN COMPOSITION FOR MORE EFFICIENTBIOETHANOL PRODUCTION -- FACTORS IN RECALCITRANCE OF LIGNOCELLULOSEPROCESSING TO SUGARS -- Plant Architecture -- Cell-Wall Architecture -- Molecular Structure -- OPTIMIZING HEMICELLULOSE ACETYLATION IN CELL WALLS -- Hemicellulose Acetylation Degradation Products Are Toxic to Microbes -- OPTIMIZATION OF PLANT CELL WALLS -- Understanding Cell-Wall Structure and Function -- Control of Lignin Synthesis and Structure -- IMPROVED METHODS, TOOLS, AND TECHNOLOGIES -- Technical Milestones -- Within 5 years -- Within 10 years -- Within 15 years -- CITED REFERENCES -- FEEDSTOCKS FOR BIOFUELS -- THE ARGUMENT FOR PERENNIAL BIOMASS CROPS -- CREATION OF A NEW GENERATION OF LIGNOCELLULOSICENERGY CROPS -- Maximizing Biomass Productivity -- Domestication of Energy Crops -- ENHANCING POPLAR TRAITS FOR ENERGY APPLICATIONS -- MARKER-ASSISTED BREEDING -- Enhancing the Yield of Biomass Crops -- Enhancing Abiotic Stress Tolerance of Biomass Species -- Understanding and Eliminating Undesirable Biomass Crop Characteristics -- Technical Milestones -- Within 5 years -- Within 10 years -- Within 15 years -- ENSURING SUSTAINABILITY AND ENVIRONMENTAL QUALITY -- Technical Milestones -- Within 5 years -- Within 10 years -- Within 15 years -- MODEL SYSTEMS FOR ENERGY CROPS -- TRANSLATIONAL RESEARCH: THE PATH FROM DISCOVERY TOAPPLICATIONS -- Technical Milestones -- Within 5 years -- Within 10 years -- Within 15 years -- THE ROLE OF GTL CAPABILITIES FOR SYSTEMS BIOLOGY -- Protein Production Capabilities -- Molecular Machines Capabilities -- Proteomic Capabilities -- Cellular System Capabilities -- DOE Joint Genome Institute -- Other Needed Capabilities -- Transformation Services -- Chemical Phenotyping Services -- Synthetic Carbohydrate Chemistry -- DECODING THE DNA OF SOYBEAN-A SOURCE OF BIODIESEL.

OTHER BIOFUEL OPPORTUNITIES: DEVELOPMENT OF HIGHPRODUCTIVITYBIODIESEL CROPS -- OIL PALM: AN IMPORTANT BIOFUEL PLANT -- CITED REFERENCES -- FOR FURTHER READING -- DECONSTRUCTING FEEDSTOCKS TO SUGARS -- DETERMINING FUNDAMENTAL PHYSICAL AND CHEMICAL FACTORSIN THE RECALCITRANCE OF LIGNOCELLULOSIC BIOMASS TOPROCESSING -- Research Goals -- Measurement of Biomass Properties -- Models for Direct Enzymatic Interactions, Action -- Technical Milestones -- Within 5 years -- Within 10 years -- Within 15 years -- The Role of GTL and OBP Facilities and Capabilities -- Protein Production -- Molecular Machine and Cellular System Analysis -- DOE Joint Genome Institute -- Crosscutting Tools, Technologies, and Science -- DEVELOPING BETTER ENZYMATIC SYSTEMS FOR BIOLOGICALPRETREATMENT: LIGNINASES AND HEMICELLULASES -- Research Goals -- Hemicelluloses and Hemicellulases -- Lignin and Ligninases -- WHITE ROT FUNGUS: GENOME OF KNOWN LIGNINDEGRADER SEQUENCED -- LIGNIFICATION: RANDOM VS TEMPLATE DIRECTED -- CITED REFERENCES -- Technical Milestones -- Within 5 years -- Within 10 years -- Within 15 years -- Crosscutting Tools, Technologies, and Science -- UNDERSTANDING THE MOLECULAR MACHINERY UNDERPINNINGCELLULOSE SACCHARIFLCATION: CELLULASES ANDCELLULOSOMES -- Research Goals -- Discovering and Improving Free Cellulases -- Understanding and Utilizing Cellulosomes -- NEW CELLULASE ENZYMES DRAMATICALLY REDUCE COSTS OFPLANT BIOMASS BREAKDOWN: R&D 100 AWARD -- Further Advances Needed to Improve Efficiency and Economics -- Technical Milestones -- Within 5 years -- Within 10 years -- Within 15 years -- Crosscutting Tools, Technologies, and Science -- The Role of GTL and OBP Facilities and Capabilities -- Protein Production -- Molecular Machine -- Proteomics -- Cellular System -- DOE Joint Genome Institute -- Metagenomics -- THE CELLULOSOME: THE "SWISS ARMY KNIFE"OF MOLECULAR MACHINES.

HARVESTING THE BIOCHEMICAL POTENTIAL OF MICROORGANISMSTHROUGH METAGENOMICS -- Research Goals -- Technical Milestones -- Within 5 years -- Within 10 years -- Within 15 years -- The Role of GTL and OBP Facilities and Capabilities -- SEQUENCING A SOIL-CELLULOSE DEGRADER -- EXAMPLE OF METAGENOMIC ANALYSIS: UNDERSTANDING THEDYNAMICS OF MICROBIAL COLONIZATION OF DECAYINGBIOMASS -- CHARACTERIZING CELL WALLS USINGHIGH-THROUGHPUT METHODS -- Technical Milestones -- Within 5 years -- Within 10 years -- Within 15 years -- The Role of GTL and OBP Facilities and Capabilities -- Crosscutting Tools, Technologies, and Science -- BREAKTHROUGH, HIGH-PAYOFF OPPORTUNITY: SIMPLIFYING THEBIOCONVERSION PROCESS BY UNDERSTANDING CELL-WALLDECONSTRUCTION ENZYMES EXPRESSED IN PLANTS -- Scientific Challenges and Opportunities -- Research Goals -- Fundamental Science -- Applied Science -- REFERENCES -- CELLULOSOME REFERENCES -- Cellulosome Reviews -- Designer Cellulosomes -- SUGAR FERMENTATION TO ETHANOL -- STARCH: A RECENT HISTORY OF BIOCONVERSION SUCCESS -- OPTIMIZING MICROBIAL STRAINS FOR ETHANOL PRODUCTION:PUSHING THE LIMITS OF BIOLOGY -- Science Challenges and Strategy -- Metabolic Engineering -- Recombinant Approach -- Evolutionary Engineering -- PROTEOMIC AND GENOMIC STUDIES OF INDUSTRIAL YEASTSTRAINS AND THEIR ETHANOL- PROCESS TRAITS: RAPIDLYFINDING THE GENETIC AND FUNCTIONAL BASES -- Technical Milestones -- Within 5 years -- Within 10 years -- Within 15 years -- The Role of GTL Capabilities -- Protein Production -- Molecular Machines -- Proteomics -- Cellular Systems -- DOE Joint Genome Institute -- ADVANCED MICROORGANISMS FOR PROCESS SIMPLIFICATION -- Science Challenges and Strategies for Process Simplification -- A. Elimination of Detoxification -- B. Simultaneous Saccharillcation and Cofermentation -- C. Consolidated Bioprocessing.

D. Other Simplification Opportunities -- Technical Milestones -- Within 5 years -- Within 10 years -- Within 15 years -- The Role of GTL Capabilities -- Protein Production -- Molecular Machine Analysis -- Proteomics -- Cellular Systems -- DOE Joint Genome Institute -- UTILIZATION OF THE FERMENTATION BY-PRODUCT CO2 -- ENABLING MICROBIOLOGICAL TOOLS AND TECHNOLOGIESTHAT MUST BE DEVELOPED -- BREAKTHROUGH, HIGH-PAYOFF OPPORTUNITIES -- Microbial Communities for Robust Energy Production -- Research Directions -- Scientific Challenges and Opportunities -- GIL Facilities and Capabilities -- Model-Driven Design of Cellular Biocatalytic Systems Using Systems Biology -- Research Directions -- Enumeration of Cellular Components, Interactions, and Related Phenotypes. -- Knowledgebase to Develop Dynamics and Kinetics Modeling Techniques. -- Network Reconstruction. -- Development of In Silico Analysis Tools. -- Design of Cellular Systems. -- Scientific Challenges and Opportunities -- The Role of GTL Capabilities -- Protein Production -- Molecular Machines -- Proteomics -- Cellular Systems -- Outcomes and Impacts -- Direct Bioproduction of Energy-Rich Fuels -- Research Directions -- Scientific Challenges and Opportunities -- The Role of GTL Capabilities -- Protein Production -- Molecular Machines -- Proteomics -- Cellular Systems -- DOE Joint Genome Institute -- Other Needs -- Outcomes and Impacts -- Translation to Applications -- Optimal Strains: Fermentative Production of 40% Ethanol from BiomassSugars -- Scientific Challenges and Opportunities -- Research Directions -- An Alternative Route for Biomass to Ethanol: Microbial Conversion ofSyngas -- Background -- Challenges -- Syngas Status in Industry -- CITED REFERENCES -- CROSSCUTTING 21ST CENTURY SCIENCE,TECHNOLOGY, AND INFRASTRUCTURE FOR ANEW GENERATION OF BIOFUEL RESEARCH -- OPPORTUNITIES AND CHALLENGES.

ANALYTICAL TOOLS TO MEET THE CHALLENGES OFBIOFUEL RESEARCH.