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Genomic Science Program

Abstracts and Summaries

Research Summary
Genomic Science Contractors–
Grantees Meeting XIV
USDA‐DOE Plant Feedstock Genomics for
Bioenergy Meeting
March 2016

Abstract Book PDF

The Genomic Science program within DOE’s Office of Biological and Environmental Research supports fundamental research to achieve a predictive, systems-level understanding of plants, microbes, and biological communities through the integration of fundamental science and technology development.

Major research areas include the DOE Systems Biology Knowledgebase, Bioenergy Research Centers, microbial and plant Biofuels studies, Biosystems Design projects to enable next-generation biofuels, characterization and genomic-based analyses of Microbes and Microbial Communities, and Biological Systems Research on the Role of Microbial Communities in Carbon Cycling. The Genomic Science program also supports Small Business Innovation Research relevant to DOE energy and environmental missions.

Genomic Science Contractors– Grantees Meeting XIV and USDA‐DOE Plant Feedstock Genomics for Bioenergy Meeting, March 6-9, 2016, Abstract Book PDF provided by Oak Ridge Associated Universities (ORAU).

Individual Abstract PDFs

A | B | C | D | E | F | G | H | J | K | L | M | N | O | P | R | S | T | U | V | W | X | Y | Z
A
Principal Investigator Abstract Title
Adams, Paul Assays for spatial structure and transdomain dynamics in environmental communities [93 KB]
Adams, Paul Atypical Iron Sulfur Cluster Biosynthesis in Sulfate Reducing Bacteria [62 KB]
Adams, Paul Enabling ENIGMA collaborative research in the DOE Systems Biology Knowledgebase [93 KB]
Adams, Paul Extrachromosomal Plasmid DNA Project [96 KB]
Adams, Paul The Metal Resistome Of An Environmental Bacterium [94 KB]
Adams, Paul Microbial responses to toxic metals in the Oak Ridge Reservation environment [94 KB]
Adams, Paul The Phenotypic Landscape Of Bacteria [69 KB]
Adams, Paul Population filtering in sediment biofilms from dynamic, source planktonic communities [116 KB]
Adams, Paul Predictions of Microbial Coexistence on Limited Resources [89 KB]
Adams, Paul The Properties of and Microbial Interactions with Natural Organic Matter Extracted from Oak Ridge FRC [96 KB]
Adams, Paul Single-Base Change by Laboratory-Driven Evolution Eliminates Biofilm Formation in Desulfovibrio vulgaris Hildenborough [94 KB]
Adams, Paul Structural Study of Hydroxycinnamoyl-CoA:shikimate Hydroxycinnamoyl Transferase [118 KB]
Adams, Paul Temporal Variation in Groundwater Microbial Community Structure: Implications for Groundwater Monitoring [114 KB]
Allen, Andrew A Systems-Level Investigation of Low-Light Acclimation in the Marine Diatom Phaeodactylum tricornutum. [110 KB]
Allen, Andrew Cellular Impact of Inactivation of the Nitrate Reductase Gene in the Marine Diatom, Phaeodactylum tricornutum [25 KB]
Allen, Andrew Influence of DNA Delivery on Mechanism of CRISPR-Cas Genome Editing in Marine Diatoms [13 KB]
Allen, Andrew Mechanisms of Carbon Partitioning into Chrysolaminarin, the Storage Polysaccharide of Diatoms [107 KB]
Amador-Noguez, Daniel Metabolic effects and toxicity mechanisms of lignocellulose-derived inhibitors [104 KB]
Arkin, Adam HT-CRISPRi studies of gene regulation and function in E. Coli [99 KB]
Arkin, Adam KBase: An Integrated Systems Biology Knowledgebase for Predictive Biological and Environmental Research [1.66 MB]
Auer, Manfred Ultrastructure of plant cells by electron microscopy: towards increased biofuel production [83 KB]

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B
Principal Investigator Abstract Title
Baker, Scott Accelerating the engineering of improved lipid accumulation in Yarrowia lipolytica [15 KB]
Banfield, Jill Multi-‘Omic’ Analyses of the Dynamics, Mechanisms, and Pathways for Carbon Turnover in Grassland Soil [95 KB]
Beller, Harry Fatty acid-related research at JBEI: methyl ketones and branched fatty acids in E. coli [138 KB]
Benning, Christoph Ectopic expression of WRI1 affects fatty acid homeostasis in Brachypodium distachyon vegetative tissues [53 KB]
Betenbaugh, Michael Phototroph-heterotroph symbiosis for biofuels applications [100 KB]
Betenbaugh, Michael Systems Biology of Autotrophic-Heterotrophic Symbiosis for Biofuel Production [46 KB]
Blumwald, Eduardo Expanding the breeder’s toolbox for perennial grasses: Sequencing the genome of Brachypodium sylvaticum to establish a tractable perennial grass model system and the identification of transgenes conferring tolerance to abiotic stress. [105 KB]
Blumwald, Eduardo Transgene Containment in Perennial Grasses: Ablation of Transgenic Pollen in Brachypodium sylvaticum and Panicum virgatum. [13.2 KB]
Brem, Rachel Functional genomics of lipid accumulation in the oleaginous yeast Rhodosporidium toruloides using randomly bar-coded TDNA-Seq [103 KB]
Brutnell, Thomas High Fidelity Detection of QTL for Biomass Production from Rapid Imaging of a C4 Grass Crop in the Field [113 KB]
Brutnell, Thomas High Throughput Phenotyping and Quantitative Genetics for Biomass Production in a C4 Grass Model [80 KB]
Brutnell, Thomas Natural Variation of Abiotic Stress Tolerance for Biomass Production in a C4 Model Grass [81 KB]
Brutnell, Thomas Quantitative trait loci analysis of leaf carbon isotopic composition in the C4 grass Setaria [ KB]
Brutnell, Thomas Rapid optical profilometry and computer vision of leaf epidermal structure applied to genetic and environmental control of stomatal patterning in model C4 species [116 KB]
Buckley, Daniel DNA-SIP enabled community genomics of cellulose degraders in an agricultural soil [18 KB]
Buckley, Daniel Soil microbial food web mapping with high resolution stable isotope probing [17 KB]
Buckley, Daniel Tillage history drives changes in the dynamics of microbial respiration, assimilation and growth in soil upon addition of dissolved organic carbon (as 13C-xylose) [45 KB]

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C
Principal Investigator Abstract Title
Casler, Michael Genomic Selection and Genome-wide Association Analyses for Bioenergy Traits in Switchgrass [44 KB]
Chanton, Jeffrey An alternate H2 sink in Anaerobic Environments Explains Non-Stoichiometric Greenhouse Gas Production Ratios in Boreal Peatlands and Thawing Permafrost. [10 KB]
Chen, Jay Plant-Microbe Interfaces: Transient expression assays, stable transgenics, and a genome editing system for studying Populus-microbe interactions [103 KB]
Chiang, Vincent Intron-retained splice variants of the VND6 and SND1 transcription factors are dominant negatives that cross-regulate VND6 and SND1 members in Populus trichocarpa. [296 KB]
Church, George Design, Synthesis and Testing of a 57-Codon Genome [46 KB]
Church, George Engineering bacterial translational machinery for incorporation of D-amino acids [23 KB]
Church, George A General Strategy for Sensing Small Molecules in Eukaryotes [46 KB]
Church, George Moving Recombineering Beyond Escherichia Coli [126 KB]
Cole, James RDP: Data and Tools for Microbial Community Analysis [92 KB]
Coleman, Heather Inducible Extreme Expression of Cellulases in Poplar [84 KB]
Coon, Joshua Collaborative Proteomics- Description of the 1 Hour Yeast Proteome and its use in GLBRC [65 KB]
Coruzzi, Gloria EvoNet: A Phylogenomic and Systems Biology approach to identify genes underlying plant survival in marginal, low-Nitrogen soils [405 KB]
Cushman, John Crassulacean Acid Metabolism (CAM) Informatics Tools [111 KB]
Cushman, John Engineering Crassulacean Acid Metabolism (CAM) to Improve Water-use Efficiency of Bioenergy Feedstocks [120 KB]
Cushman, John Engineering Tissue Succulence to Improve Water-use Efficiency of Bioenergy Feedstocks [115 KB]
Cushman, John The Kalanchoe genome -- An important model for systems biology and synthetic biology of crassulacean acid metabolism [15 KB]
Cushman, John High Quality De Novo Genome Sequencing of the Common Ice Plant (Mesembryanthemum crystallinum L.) - a Functional Genomics Resource for Crassulacean Acid Metabolism (CAM) Biodesign [119 KB]

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D
Principal Investigator Abstract Title
Davison, Brian Developing Semi-Synthetic Composite Materials for Investigating Cellulose and Matrix Polymer Interactions During Pretreatment [85 KB]
Davison, Brian Investigating Biopolymer Structural Evolution During Different Biomass Pretreatments by In Situ SANS Studies [2.54 MB]
Davison, Brian Tension Wood Provides Insight Into Structural Changes in Biomass Resulting from Chemical Pretreatment [208 KB]
Davison, Brian Why Is Lignin so Effective at Stopping Enzymes from Hydrolyzing Cellulose and How Does Heat-Treatment Change Lignin Characteristics? [65 KB]
Dudareva, Natalia Model-Guided Metabolic Engineering of Increased 2-Phenylethanol Production in Plants [58 KB]
Dueber, John Towards Repurposing the Yeast Peroxisome for Compartmentalizing Heterologous Metabolic Pathways [71 KB]
Dunbar, John Influence of N availability on interactions between Ascomycete fungi and Actinomycete bacteria during litter decomposition [76 KB]
Dunlop, Mary Engineering Robust Hosts for Microbial Biofuel Production [108 KB]

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E
Principal Investigator Abstract Title
Ecker, Joseph Next-Generation Protein Interactomes for Plant Systems Biology and Biomass Feedstocks Research [100 KB]
Evans, Sarah Connecting nitrogen transformations mediated by the rhizosphere microbiome to perennial cropping system productivity in marginal lands [271 KB]

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F
Principal Investigator Abstract Title
Firestone, Mary An Overview of the Switchgrass Associated Microbes Belowground with Mutualistic Fungi and Soil Mesofauna as Potential Models for Sustainable Cultivation [100 KB]
Firestone, Mary Determining key physiological and metabolic traits of soil microorganisms that regulate C assimilation and transformation [107 KB]
Firestone, Mary Dissecting the role(s) of host genotype and phytobiome composition and function in the successful establishment of switchgrass (Panicum virgatum L) on marginal soils. [148 KB]
Firestone, Mary EcoFun-MAP: an Ecological Function Oriented Metagenomic Analysis Pipeline [104 KB]
Firestone, Mary The interconnected rhizosphere: Roots stimulate high microbial network complexity and alter the expression of enzymes related to organic matter decomposition in soil [102 KB]
Fleming, Ronan The COBRA Toolbox: a comprehensive and powerful modelling resource [107 KB]
Fleming, Ronan Comparison of atom mapping algorithms for metabolic reactions [98 KB]
Fleming, Ronan Finding steady states in genome-scale biochemical reaction networkss [140 KB]
Fleming, Ronan High-quality Genome-scale Metabolic Reconstructions for Multi-scale Microbial Communities [102 KB]
Fleming, Ronan Quadruple-precision solution of genome-scale models of Metabolism and macromolecular Expression [93 KB]
Fleming, Ronan Uniform sampling of metabolic networks [109 KB]
Fox, Brian Genome-Enabled Assembly of Carbohydrate-Active Enzymes for the Deconstruction of Biomass [63 KB]

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G
Principal Investigator Abstract Title
Gardner, Jeffrey Functional Characterization and Regulatory Modeling of Lignocellulose Deconstruction in the Saprophytic Bacterium Cellvibrio japonicus [108 KB]
Garrity, George Semantic Index of Phenotypic and Genotypic Data [46 KB]
Gasch, Audrey Leveraging natural variation in Saccharomyces cerevisiae to elucidate the toxicity mechanisms of lignocellulosic hydrolysate and advanced biofuels. [67 KB]
Ghirardi, Maria The Algal Ferredoxin Interactome [175 KB]
Ghirardi, Maria Design Principles Controlling Hydrogen Metabolism in Phototrophic Organisms [325 KB]
Gibson, Bradford Dynamic Remodeling of Protein Acetylation in Fuel-Producing E. coli with Different Carbon Sources [135 KB]
Gill, Ryan Biochemical Production from Lignocellulose by CRISPR EnAbled Trackable genome Engineering (CREATE) [42 KB]
Gill, Ryan Bioverse: a comprehensive platform for designing biological materials [374 KB]
Gill, Ryan CRISPR EnAbled Trackable Genome Engineering: A Technology for High Throughput Genetic Prototyping of Large DNA constructs. [95 KB]
Gill, Ryan Experimental and Computational Tools for Sequence to Activity Mapping [151 KB]
Gill, Ryan A Strategy for Genome-scale Design, Redesign, and Optimization for Ethylene Production in E. coli [115 KB]
Gill, Ryan The LASER Database: Building a Learning Platform for Metabolic Engineers [334 KB]
Gilna, Paul A New Low-Cost Paradigm for Biological Conversion of Cellulosic Biomass: Evaluation of Economic Potential [78 KB]
Gilna, Paul Absolute Quantitation of Intracellular Metabolite Concentrations in C. thermocellum and T. saccharolyticum [86 KB]
Gilna, Paul Caldicellulosiruptor Pan-Genomics: Perspectives on Newly Sequenced Species, and Genus- Wide Diversity of Cellulose Binding Proteins (tapirins) [106 KB]
Gilna, Paul CELF Pretreatment Enhances Conversion of Biomass to Renewable Fuels [78 KB]
Gilna, Paul Comparison of Multiple Generations of TOP Line Transgenic Switchgrass with Reduced Recalcitrance for Enhanced Bioconversion to Fuels [83 KB]
Gilna, Paul Consolidated Bioprocessing of Cellulose to Isobutanol in Clostridium thermocellum [89 KB]
Gilna, Paul Field Experiments of Seven Switchgrass TOP Lines [92 KB]
Gilna, Paul From Gene to Network, Switchgrass TOP Line RNA-seq Data Analysis Pipeline at BESC [85 KB]
Gilna, Paul GWAS Studies in Populus Reveal Evolution of Two Biosynthetic Enzymes into Transcriptional Regulators Modulating Phosphoenolpyruvate Input and Chorismate Output from the Shikimate Pathway [99 KB]
Gilna, Paul Hemicellulose Biosynthesis is Becoming Crystal Clear [78 KB]
Gilna, Paul Integrated 'Omics Reveals the Details of Metabolic Adaptation of Clostridium thermocellum ATCC-27405 Grown on Switchgrass [105 KB]
Gilna, Paul Modification of GAUT12 Expression Affects Recalcitrance in the Woody Feedstock Populus deltoides [100 KB]
Gilna, Paul Modified Expression of HD-ZIP III and NAC Transcription Factors Impact Biomass Formation and Sugar Release Efficiency in Populus [94 KB]
Gilna, Paul Multiple Levers to Solve Recalcitrance for Lignocellulosic Solubilization [88 KB]
Gilna, Paul Pleiotropic and Epistatic Network-Based Discovery: Integrated SNP Correlation, Co-Expression and Genome-Wide Association Networks for Populus trichocarpa [87 KB]
Gilna, Paul Sebacina for Switchgrass: Application and Benefits [78 KB]
Gilna, Paul The Secretome of Caldicellulosiruptor bescii: Biomass Deconstruction without Conventional Pretreatment [109 KB]
Gilna, Paul Understanding the Hyperactive Multi-Component Cellulase: CelA [79 KB]
Gilna, Paul Using Glycome Profiling on Plant Biomass for Functional Characterization of Cell Wall Hydrolytic Enzymes [74 KB]
Greenberg, E. Peter Plant-Microbe Interfaces: Probing the Molecular Mechanisms of Plant-Bacterial Interactions [95 KB]

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H
Principal Investigator Abstract Title
Hartwell, James Progress towards defining a minimal parts list for the biodesign of Crassulacean acid metabolism (CAM): identification, characterization and ground-truthing of candidate CAM genes using the model species Kalanchoë fedtschenkoi and K. laxiflora [114 KB]
Hazen, Samuel Uncovering genetic mechanisms for biological conversion efficiency in Brachypodium distachyon [124 KB]
Hegg, Eric Alkaline Pretreatment Effectively Reduces Recalcitrance of Zip-Lignin Poplar [170 KB]
Hildebrand, Mark The Effect of Authentic Sinusoidal Light Variation on Growth and Productivity of Microalgae [55 KB]
Hillson, Nathan Integrated BioCAD Toolchain Enables Search for Experimentally Validated Components [83 KB]
Hittinger, Chris The Yeast Biodesign Library: leveraging DNA synthesis to assess and harness genes from diverse organisms [76 KB]
Hofmockel, Kirsten Linking microbes to soil metabolism [90 KB]
Hungate, Bruce Multiple-Element Isotope Probes, NanoSIMS, and the Functional Genomics of Microbial Carbon Cycling in Soils in Response to Chronic Climatic Change [90 KB]

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J
Principal Investigator Abstract Title
Jackson, Randall Functional Metagenomic Comparison of Soil Microbiomes Associated with Six Cellulosic Biofuel Feedstock Production Systems [241 KB]
Jacobson, Daniel Plan-Microbe Interfaces: Pleiotropic and Epistatic Network-Based Discovery of Plant Functions Involved in Microbial Interactions: Integrated SNP Correlation, Co-expression and Genome-Wide Association Networks for Populus trichocarpa [127 KB]
Jansson, Janet Advanced Computational and Modeling Analyses Provide Novel Insights into Interactions in Model Complex Microbial Consortia [17 KB]
Jansson, Janet Autotroph-Heterotroph Communities Increase Interactions and Metabolite Exchange as They Undergo Ecological Succession [18 KB]
Jansson, Janet Cross-Talk Through Microbial Interaction Coordinates Microbial Community Properties [180 KB]
Jansson, Janet Deciphering Microbial Community Interactions Using Model Complex Microbial Consortia [18 KB]
Jansson, Janet Extensive Interdependencies and Unexpected Roles for B Vitamins in Microbial Communities [222 KB]
Jansson, Janet Nitrogen Dynamics Control Carbon Partitioning in Model Complex Microbial Consortia [790 KB]
Jansson, Janet Spatial Interactions of Autotrophs and Heterotrophs Elucidated Using Advanced Quantitative Imaging Techniques [40 KB]
Jansson, Janet Spatially-Resolved Carbon and Energy Transformations in a Vertically Laminated, Phototrophic Mat [173 KB]
Jiao, Yongqin Characterization of a Metal-induced Sensory Transduction System in Caulobacter crescentus [111 KB]
Juenger, Thomas Climate adaptation and sustainability in switchgrass: exploring plant-microbe-soil interactions across continental scale environmental gradients [194 KB]

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K
Principal Investigator Abstract Title
Kuske, Cheryl Phylogenetic signal in soil fungal and bacterial communities in response to experimental nitrogen addition [76 KB]
Kuske, Cheryl Responses of bacterial and fungal communities under nitrogen amendment differ by microhabitat in arid ecosystems [84 KB]

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L
Principal Investigator Abstract Title
Labbé, Jessy Plant-Microbe Interfaces: Fungal and plant small secreted effector proteins play a key role in the development of the Populus-Laccaria ectomycorrhizal symbiosis [101 KB]
Landick, Robert Global Catalog of the Transcriptional Response to Lignocellulosic Biomass-derived Inhibitors in Escherichia coli Identifies Promoters for Synthetic Engineering of Biofuel Microbes [113 KB]
Lee, Taek Soon EIsoprenoid Biofuels Research at JBEI [91 KB]
Lemaux, Peggy EPICON: Epigenetic Control of Drought Response in Sorghum [97 KB]
Liao, James Predicting Gene Targets for Optimizing Lipid Production in Acetic Acid Pathway of Yarrowia lipolytica by Ensemble Modeling [382 KB]
Liao, James Robust Non-Oxidative Glycolysis in Escherichia coli [81 KB]
Lidstrom, Mary New Insights into Methane-Oxidizing Communities in Lake Sediments through Microcosm Manipulation and Systems Biology Studies [31 KB]
Löffler, Frank Denitrification revisited: Contributions of chemodenitrifiers and fungi to soil denitrification [95 KB]
Löffler, Frank Impact of Agricultural Practices on Nitrogen Cycle Genes and Nitrous Oxide Emissions from Midwestern Soils [117 KB]
Loque, Dominique A robust gene stacking method utilizing yeast assembly for plant synthetic biology [79 KB]
Loque, Dominique Exploiting The Substrate Promiscuity of Hydroxycinnamoyl-CoA:shikimate Hydroxycinnamoyl Transferase to Reduce Lignin [157 KB]

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M
Principal Investigator Abstract Title
Magnuson, Jon Fungal Biotechnology: How can we improve enzyme production? [12 KB]
Maranas, Costas Development of a genome-scale Escherichia coli kinetic metabolic model satisfying flux data for multiple mutant strains [296 KB]
Maranas, Costas Development of a Knowledgebase (MetRxn) of Metabolites, Reactions and Atom Mappings to Accelerate Discovery and Redesign [187 KB]
Maranas, Costas Ensemble cell-wide kinetic modeling of anaerobic organisms to support fuels and chemicals production [274 KB]
Martin, Hector Systematic Metabolic Flux Modeling Techniques and Applications at the Joint BioEnergy Institute [105 KB]
McKinlay, James Enhanced Cross-Feeding in a Bacterial Coculture Undermines a Mutualistic Relationship [101 KB]
Merchant, Sabeeha A day in the life of Chlamydomonas [54 KB]
Methe, Barbara The Application of Ecosystem Modeling at Subsurface Sites to Study Carbon, Nutrient and Metal Cycling in Microbial Communities [25 KB]
Moon, Tae Seok Conversion of lignin-derived aromatic compounds into lipids by engineered Rhodococcus opacus strains [124 KB]
Morgan, John Kinetic modeling of the phenylpropanoid pathway in Arabidopsis [165 KB]
Morrell-Falvey, Jennifer Plant-Microbe Interfaces: Microbial transformation of Populus secondary metabolites by microbiome isolates [101 KB]
Mortimer, Jenny Engineering Mannan Biosynthesis in Plants [58 KB]
Mortimer, Jenny The glycosylation of plant sphingolipids affects cellulose crystallization, plant defense signaling and nitrogen fixation ability [60 KB]
Mukhopadhyay, Aindrila A Cas9-Based Toolkit to Program Expression Context in Saccharomyces cerevisiae [110 KB]

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N
Principal Investigator Abstract Title
Nielsen, Jens Put on a diet: Lipid accumulation inhibits TOR signaling in Saccharomyces cerevisiae [78 KB]
Nielsen, Jens Transcriptional regulation and lipid accumulation in Yarrowia lipolytica [11 KB]
Noirot, Philippe Molecular Mechanisms that Underlie the Beneficial Effects of a Plant-Fungus-Bacterial Community Interaction [297 KB]
Noirot, Philippe Predicting Pseudomonads’ ecological roles in the rhizosphere using machine learning and ‘omics’ computational modeling [350 KB]
Noirot, Philippe Soil Bacteria Transport Systems: Ligand and Regulatory Specificity [552 KB]
Northen, Trent Linking Microbial Community Structure, Activity and Carbon Cycling in Biological Soil Crust [76 KB]
Northen, Trent Rapid Determination of Enzyme Activities for Lignocellulose Deconstruction and Analysis of Biofuel Molecules Using Nanostructure-Initiator Mass Spectrometry [105 KB]

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O
Principal Investigator Abstract Title
O'Malley, Michelle Engineering Anaerobic Gut Fungi for Lignocellulose Breakdown [85 KB]
O'Malley, Michelle Engineering Synthetic Systems Inspired by Anaerobic Gut Fungi [79 KB]
Orphan, Victoria Disentangling the Activity of Anaerobic Methane-Oxidizing Archaea from Their Syntrophic Sulfate-Reducing Bacterial Partner [111 KB]

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P
Principal Investigator Abstract Title
Pakrasi, Himadri SYNECHOCOCCUS ELONGATUS UTEX 2973: METABOLIC MODELS AND FLUXOMIC ANALYSIS [109 KB]
Pakrasi, Himadri SYNECHOCOCCUS ELONGATUS UTEX 2973, A NEW CYANOBACTERIAL STRAIN THAT EXHIBITS RAPID AUTOTROPHIC GROWTH [161 KB]
Payne, Samuel A proteomic survey of diverse gut microbes [301 KB]
Pelletier, Dale Plant-Microbe Interfaces: Constructed communities of Populus and bacterial isolates to study microbiome function [104 KB]
Pett-Ridge, Jennifer In silico analyses of interactions between systems objectives for engineering of biological communities [157 KB]
Pett-Ridge, Jennifer Into the deep: variability in soil microbial communities and carbon turnover along a tropical forest soil depth profile [161 KB]
Pett-Ridge, Jennifer Linking microbial identity and function in phototrophic mats and biofilms [502 KB]
Pett-Ridge, Jennifer Multi-omics Approach Unveil Microbial Transformations of Lignocellulose in the Gut of the Wood-Feeding Beetle Odontotaenius disjunctus [286 KB]
Pett-Ridge, Jennifer NanoSIMS Isotope Imaging and Genome-enabled Metabolic Modeling to Investigate Algal-Bacterial Interactions in Biofuel-Producing Communities [455 KB]
Pett-Ridge, Jennifer Taxonomic composition of simplified bacterial communities conferring growth and biomass enhancements to biofuel-producing algae [178 KB]
Pett-Ridge, Jennifer A Trait Based Dynamic Energy Budget Approach to Explore Emergent Microalgal Community Structure [13 KB]
Petzold, Christopher Development of Robust, Reproducible, High-Throughput Proteomic Assays for Cellulosic Biofuel Applications [91 KB]
Pfleger, Brian RNase III as a Tool to Mainpulate Transcript Stability: Identifying in vivo Targets in Escherichia coli [10.6 KB]
Polz, Martin Bacterial Succession Patterns in Algal Degradation: Identifying the Most Efficient Algal Degrading Communities [87 KB]
Polz, Martin The Ecology of Algal Polysaccharide Utilization: Novel Verrucomicrobia Isolates Efficiently Degrade Fucoidan [95 KB]

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R
Principal Investigator Abstract Title
Rabinowitz, Joshua Condition-Dependent Regulation of Protein Turnover Rate in Yeast [208 KB]
Rabinowitz, Joshua Limited Forward Thermodynamic Driving Force in Glycolysis of Slow-Growing Bacteria [211 KB]
Ralph, John Plants for Improved Biomass Deconstruction: Native Zip-lignins across the Plant Kingdom [96 KB]
Rao, Christopher Characterization of the Alginate Lyases and Laminarinases from Vibrio sp. [89 KB]
Rao, Christopher Regulation of sugar consumption in Escherichia coli by amino acids [215 KB]
Reed, Jennifer Computational Analysis of Microbial Metabolism for Fuel and Chemical Production [101 KB]
Retterer, Scott Plant Microbe Interfaces: Emerging Analytical Techniques for Controlling and Monitoring Structural Changes in Developing Multi-Kingdom Systems [92 KB]
Rhee, Seung Comparative metabolic network analysis of Setaria italica and Setaria viridis [94 KB]
Ronald, Pamela Use of KitBase to Facilitate Forward and Reverse Genetics Research in Rice [87 KB]

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S
Principal Investigator Abstract Title
Sale, Kenneth The Biodegradation of Lignin: harnessing the power of enzymes [103 KB]
Sato, Trey Natural Genetic Variations Influence Ionic Liquid Tolerance by Saccharomyces cerevisiae [110 KB]
Sattely, Elizabeth Defining the Minimal Set of Microbial Genes Required for Valorization of Lignin Biomass [111 KB]
Schachtman, Daniel Systems Analysis of the Physiological and Molecular Mechanisms of Sorghum Nitrogen Use Efficiency, Water Use Efficiency and Interactions with the Soil Microbiome [431 KB]
Schadt, Chris Plant-Microbe Interfaces: The Populus Microbiome Atlas Project - Dissecting the microbiome landscape of trees from soil to canopy. [106 KB]
Scheller, Henrik Development of Plants with Multiple Traits for High Yield of Fermentable Sugars [97 KB]
Schilling, Jonathan Spatial Connectomics to Identify Agents Relevant to Lignocellulose Deconstruction in Fungi [15 KB]
Scown, Corinne Advances in Ionic Liquid Pretreatment Technologies: Impact on the Economics of Cellulosic Biofuel Production [216 KB]
Segre, Daniel Designing a Microbial Community for Production of Biofuel from Lignocellulose [388 KB]
Singer, Steven A Strategy to Understand and Improve Microbial Lignin Bioconversion through Solubilization and Separation of the Constituents of the Biopolymer [86 KB]
Singh, Anup Droplet Microfluidic Platform for High Throughput Screening and Synthetic Biology Applications [108 KB]
Singh, Seema One-pot integrated process for the production of ethanol from lignocellulosic biomass [108 KB]
Stahl, David Nitrous Oxide Source Identification from a Fertilized Bioenergy Crop Soil [251 KB]
Stephanopoulos, Gregory Intracellular Metabolite Pool Size Quantification in Oleaginous Yeast Yarrowia lipolytica using Acetate as Carbon Source [9 KB]
Stephanopoulos, Gregory Rewiring metabolism for maximum lipid production in oleaginous yeast Yarrowia lipolyticae [86 KB]
Sullivan, Matthew M-tools and iVirus: Software tools and a cyberinfrastructure for metaomic analyses [133 KB]

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T
Principal Investigator Abstract Title
Thompson, Janelle Systems biology towards a continuous platform for biofuels production [69 KB]
Tiedje, James Rhizosphere metagenomics and metatranscriptomics of biofuel crops [117 KB]
Tringe, Susannah Wetland Microbial Community Response to Restoration [13 KB]
Tyson, Gene Gene- and genome-centric metagenomic analysis of complex microbial communities along a permafrost thaw gradient [125 KB]

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U
Principal Investigator Abstract Title
Ussery, David Plant-Microbe Interfaces: High-Throughput Comparative Genomics for Populus-associated Microbes [91 KB]

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V
Principal Investigator Abstract Title
Vilgalys, Rytas Plant-Microbe Interfaces: Linking diversity and function in fungal communities associated with Populus trichocarpa [106 KB]

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W
Principal Investigator Abstract Title
Wilkerson, Curtis Identification of Grass Stem Specific Promoters for Improvement of Biofuel Crops by Metabolic Engineering [98 KB]
Wolfe, Alan Magnesium controls carbon flux to biomass or fermentation products. [274 KB]
Wolfe, Amy Risk and escape policies, procedures, and practices: Issues and implications for biosystems design (synthetic biology) R&D [93 KB]

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X
Principal Investigator Abstract Title
Xie, Xiaoliang Lipid Production in Single Oleaginous Yeast Cells Using In Vivo Label-Free Imaging [90 KB]

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Y
Principal Investigator Abstract Title
Yeates, Todd Detecting Cysteine Modifications in methanogen Methanosarcina mazei Gö1 [83 KB]
Yeates, Todd Iron storage in ferritin versus a lysosome-related compartment in the green alga Chlamydomonas reinhardtii [84 KB]
Young, Jamey Isotopically nonstationary 13C flux analysis of isobutyraldehyde production in Synechococcus elongatus [179 KB]

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Z
Principal Investigator Abstract Title
Zak, Donald Anthropogenic N deposition slows decay by favoring bacterial metabolism: Insights from metagenomic analyses [86 KB]
Zengler, Karsten A Metabolic and GeneExpression Model Reveals New Insight Into the Acetogen Clostridium ljungdahlii [115 KB]
Zengler, Karsten Omics-Driven Analysis of Clostridium ljundhalii Disentangles the Complexity of Energy Conservation Pathways at the Molecular Level [83 KB]
Zhang, Yaoping Interannual Climate Variability Affects the Microbial Response to and Fermentability of Lignocellulosic Biofuel Crops [105 KB]
Zhou, Jizhong Metagenomics-Enabled Predictive Understanding of Microbial Communities to Climate Warming: Results from Long Term Soil Incubations and Modeling Simulations [129 KB]
Zhou, Jizhong Metagenomics recovers 100s of population genomes from Alaskan permafrost and Oklahoma prairie soils and provides insights into their roles in microbial community response to warming. [305 KB]
Zhou, Jizhong Successional Dynamics of Grassland Microbial Communities in Response to Warming, Precipitation Alternation, and Clipping [103 KB]

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Featuring

Technologies for Characterizing Molecular and Cellular Systems Relevant to Bioenergy and Environment [9/17]


Carbon Cycling Projects Awarded [10/16]


Plant Feedstock Genomics for Bioenergy Abstracts [9/16]


Bioenergy Research Centers
Key Advances Update: 2014-2016 [06/16]


BER Biological Systems Science Division Strategic Plan [10/15]

BER BSSD funds the Genomic Science Program


Research

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