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Genomic Science Program

Abstracts and Summaries

Research Summary
Genomic Science Contractors–
Grantees Meeting
USDA-DOE Plant Feedstock Genomics for
Bioenergy Meeting
February 2017

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 and USDA-DOE Plant Feedstock Genomics for Bioenergy Meeting, February 6-8, 2017, Abstract Book PDF provided by Oak Ridge Associated Universities (ORAU).

Agenda PDF

Meeting Introduction
Todd Anderson, Director, Biological Systems Science Division, DOE BER

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
Paul Adams High-quality protein production for structural studies: From plant cell wall synthesis to microbial production of bioproducts.
Paul Adams Exposure History Dependence of Microbial Mediated Substrate Transformation Rates in Groundwater
Paul Adams High-throughput testing of carbon source on microbial community assembly and antibiotic production
Paul Adams Identification of Novel Biosynthetic and Catabolic Pathways in Diverse Bacteria Using Highthroughput Genetics
Paul Adams Mechanism for Microbial Population Collapse in a Fluctuating Resource Environment
Paul Adams Mechanisms of Uranium Reduction in Sulfate-Reducing Bacteria
Paul Adams Microbes at the blurred boundary of natural and built environments
Paul Adams Microbial Interactions with Natural Organic Matter Extracted from the Oak Ridge FRC
Paul Adams Multiplex characterization of microbial traits using dual barcoded genome fragment expression library in diverse bacteria
Paul Adams Stress mediates relative importance of deterministic and stochastic assembly in groundwater microbial communities
Paul Adams Systems Biology Guided by Global Isotope Metabolomics
Paul Adams Temporal Variability and Microbial Activity in Groundwater Ecosystems
Paul Adams The role of adaptive evolution in shaping the structure and function of model microbial consortia
Paul Adams Understanding the thermodynamic Foundations of microbial Growth Efficiencies in the Lab and Field
Steven Allison Trait-based approaches for linking metagenomic data with microbial carbon cycling under drought conditions
Ana Paula Alonso Development of Resources and Tools to Improve Oil Content and Quality in Pennycress
Daniel Amador-Noguez Limited thermodynamic driving force in glycolysis of cellulolytic clostridia
Daniel Amador-Noguez Development of metabolomic methods for investigating metabolic regulation of the MEP pathway in Zymomonas mobilis and Escherichia coli
Adam Arkin Pooled Assembly, Genotyping and Scoring of Complex Synthetic Genomic Libraries

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B
Principal Investigator Abstract Title
Scott Baker Nitrogen limitation and lipid production in Yarrowia lipolytica
Peter Balint-Kurti Physiological and Molecular-Genetic Characterization of Basal Resistance in Sorghum
Jillian Banfield Microbial community proteogenomic analyses indicate extensive depth-dependent CO oxidation and C1 metabolism in soil and increased capacity for N2O reduction with increased rainfall
Harry Beller Discovery of a Novel Bacterial Enzyme Enabling First-Time Biochemical Production of Toluene
Michael Betenbaugh Constraint-Based Community Modeling Reveals Condition-Dependent Interactions
Eduardo Blumwald Biocontainment in Perennial Grasses: Transgenic Pollen Ablation in Brachypodium sylvaticum and Panicum virgatum
Eduardo Blumwald Genome Editing of CENH3 in Switchgrass and Brachypodium: A Histone Variant Essential for Centromere Specification
Federica Brandizzi Optimizing MLG Production for Improved Biofuel Crop
Rachel Brem Functional Genomics of Lipid Accumulation in Rhodosporidium toruloides
Eoin Brodie A Trait Based Dynamic Energy Budget Approach to Explore Emergent Microalgal-Bacterial Dynamics and Productivity
Patrick Brown A Sorghum NAC Gene Affects Vascular Development and Biomass Properties
Jack Brown Developing Non-food Grade Brassica Biofuel Feedstock Cultivars with High Yield, Oil Content, and Oil Quality that are Suitable for Low Input Production Dryland Systems.
Amy Brunner Spatiotemporal Transcriptomics of Populus Growth in Response to Daylength and Nutrient Availability
Thomas D Bruns A Simple Pyrocosm for Controlled, Replicated Studies of Post-Fire Soil Microbial Communities
Thomas Bruns Determination of the Roles of Pyrophilous Microbes in the Breakdown and Sequestration of Pyrolyzed Forms of SOM
Thomas Brutnell High throughput phenotyping and quantitative genetics to understand productivity and drought traits in the model C4 grass Setaria
Thomas Brutnell Utilizing Setaria viridis as a Model for Molecular Characterization of Jasmonate- Mediated Growth and Defense Responses
Thomas Brutnell Quantitative Trait Loci for Leaf Carbon Isotopic Signature and Transpiration Efficiency in the C4 grass Setaria
Thomas Brutnell Seteria viridis as a Model System to Accelerate Gene Discovery in Panicoid Grasses
Thomas Brutnell Grasses Suppress Shoot-Borne Roots to Conserve Water During Drought
Thomas Brutnell Development and application of novel phenotyping techniques to understand the genetic control of productivity and drought traits in the model C4 grass Setaria
Daniel Buckley High Resolution DNA Stable Isotope Probing of Soil Indicates Changes in Microbial Community Metabolism Associated in Disturbance Due to Tillage
Daniel Buckley Mapping microbial food web dynamics in soil with high resolution stable isotope probing
C. Robin Buell Exploiting Natural Diversity to Identify Alleles and Mechanisms of Cold Adaptation in Switchgrass

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C
Principal Investigator Abstract Title
William Cannon Multi-scale Modeling of Circadian Rhythms: From Metabolism to Regulation and Back
Clint Chapple Model-Guided Metabolic Engineering of Increased 2-Phenylethanol Production in Plants
Clint Chapple Measurement and modeling of phenylpropanoid metabolic flux in Arabidopsis
Jay Chen Plant-Microbe Interfaces: Populus genomics, genetics and molecular biology
George Church Design, Synthesis, and Testing Toward a 57-Codon Genome
George Church Exploring Species Specificity of Lambda Red Recombination
George Church Non-Standard Amino Acid Incorporation in the New Era of Recoded Genomes
George Church Retron Library Recombineering: Construction and Functional Interrogation of Trackable Genomic Edits
Robert Clubb Quantitative Measurements of Cellulase Display in the Model Gram+ Microbe Bacillus subtilis Define Determinants Required for Enzyme Display and Activity
James Cole RDP: Data and Tools for Microbial Community Analysis
Heather Coleman Expression of a Hyperthermophilic Endoglucanase in Poplar to Improve Ethanol Production
Heather Coleman Extreme Inducible Expression of Cellulases in Poplar
Heather Coleman Modified Cell Wall Composition through Expression of an Expansin-Like Protein in Poplar
Luca Comai A population of copy number variants for poplar functional genomics
Joshua Coon GLBRC Targeted Metabolomics
Gloria Coruzzi EvoNet: A Phylogenomic and Systems Biology approach to identify genes underlying plant survival in marginal, low-Nitrogen soils
Hugo Cuevas Genomic dissection of anthracnose resistant response in sorghum [Sorghum bicolor (L.)]
Cameron Currie Extracellular Products Mediate Bacterial Synergism in Cellulose Degradation
John Cushman Leveraging Agave and Kalanchoe Genomics Resources to Transfer Crassulacean Acid Metabolism (CAM) Modules into C3 Species Using Synthetic Biology Approaches
John Cushman Engineering Crassulacean Acid Metabolism (CAM) to Improve Water-use Efficiency of Bioenergy Feedstocks

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D
Principal Investigator Abstract Title
Gautam Dantas Aromatic tolerance and utilization in adapted Rhodococcus opacus strains for lignin bioconversion
Brian Davison Combining Deuterium-Labeling and Neutron Scattering to GAin Molecular-Level Insights Relevant to Biomass Deconstruction
Brian Davison Conformation of Low-Molecular Weight Lignin in Water: Insights on the Chemical Character of Lignin
Brian Davison Deuteration Effects on Switchgrass Structure and Mechanism: Lignin Deposition Changes in Cell Walls of Deuterated Switchgrass
Brian Davison Real-Time Elucidation of Structure and Morphology of Native and Mutant Poplar During Dilute Acid and Alkali Pretreatments Using Neutron Scattering
Kristen DeAngelis Get Your Model Out of the Clouds! Ground-Truthing Assumptions About how the Earthfs Tiniest Engines Drive the Carbon Cycle
Shi-You Ding Quantification of monolignol ferulate conjugate in Zip-lignin poplar by stimulated Raman scattering microscopy
Timothy Donohue Using Genetic and Bioreactor Engineering to Produce Oleaginous Bacteria
John Dueber Repurposing the Yeast Peroxisome for Compartmentalizing Multi-enzyme Pathways
John Dunbar Ecological Factors Affecting Carbon Flow from Surface Litter
John Dunbar Microbial Community Traits Linked to Carbon Flux Patterns in Soil
John Dyer Genomics and Phenomics to Identify Yield and Drought Tolerance Alleles for Improvement of Camelina as a Biofuel Crop

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E
Principal Investigator Abstract Title
Serge Edme Genetics and Genomics of Pathogen Resistance in Switchgrass
Thomas Eng Genome Wide Identification of Bacterial Membrane Capacity Determinants
Sarah Evans Is there a direct link between free-living nitrogen fixation rates and nitrogen mineralization rates?
Sarah Evans The Effects of Growth Promoting Rhizobacteria and Endophytes on Switchgrass Growth and Root Architecture
Sarah Evans Switchgrass Growth and Transcriptomic Responses to Nitrogen Availability and the Rhizosphere Microbiome
Sarah Evans The Contribution of Alternative Nitrogenases to Nitrogen Fixation in Switchgrass Rhizospheres on Marginal Lands

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F
Principal Investigator Abstract Title
Mary Firestone Bacterial Traits Linking Avena Exudate Chemistry and Rhizosphere Bacterial Community Structure During Root Development
Mary Firestone Monitoring fluxes of atmospherically-reactive gases (CO2, CH4 and N2O) during the conversion of grasslands into a biofuel crop (Panicum virgatum)
Mary Firestone Plant-microbe and microbe-microbe interactions mediate switchgrass sustainability: following rhizosphere microbial communities during switchgrass establishment
Mary Firestone Dissecting the Chemistry of Switchgrass-Microbe Interactions Using Cultivation, Exometabolomics and Mass Spectrometry Imaging
Mary Firestone Faunal Population Dynamics Throughout Switchgrass Developmental Stages
Mary Firestone Directing traffic in the rhizosphere: how phage and fauna shape the flow and fate of root carbon through microbial pathways
Mary Firestone Mapping the pathways of root carbon flow into and through soil microbial food webs
Mary Firestone Roots stimulate expression of decomposition transcripts in the soil microbiome
Ronan Fleming Automatic generation of genome-scale metabolism and expression models for bacteria
Ronan Fleming CHRR: Coordinate hit-and-run with rounding for uniform sampling of metabolic networks
Ronan Fleming Comparative evaluation of atom mapping algorithms for metabolic reactions
Ronan Fleming DistributedFBA.jl: High-level, high-performance flux balance analysis in Julia
Ronan Fleming Software development of The Constraint-Based Reconstruction and Analysis Toolbox
Ronan Fleming Thermodynamically constraining a genome-scale metabolic model with von Bertalanffy .0
Ronan Fleming Cardinality optimisation in constraint-based modelling of metabolism
Brian Fox A Cellulase Family Reunion: Observing and Predicting the Structural Changes Accompanying the Evolution of GH5 Enzyme Specificity
Serita Frey Fungal Responses To Elevated Temperature And Soil Nitrogen Availability
Serita Frey Microbial Growth and Metabolism in Soil . Refining the Interpretation of Carbon Use Efficiency
Deanna Funnell-Harris Resistance to Stalk Pathogens for Bioenergy Sorghum

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G
Principal Investigator Abstract Title
Hector Garcia Martin Quantitative metabolic modeling at the Joint BioEnergy Institute (JBEI)
Jeffrey Gardner Systems analysis in Cellvibrio japonicus resolves predicted redundancy of Β- glucosidases and determines essential physiological functions
Maria Ghirardi The Algal Ferredixin Interactome
Ryan Gill A novel design strategy for industrially relevant, unnatural modular megasynthases
Ryan T. Gill Combinatorial engineering of 3-hydroxypropionate production from hemicellulose hydrolysate
Ryan Gill Developing a predictive method for tunable control over gene expression based on CRISPR interference technology
Ryan Gill Enhanced CRISPR-based trackable protein engineering using modeling
Ryan Gill Extending functional genome annotations using high-throughput CRISPRi
Ryan Gill Rapid and Efficient One-Step Metabolic Pathway Integration in E. coli
Ryan Gill Genome-scale design and engineering approach towards optimizing ethylene production in E. coli
Paul Gilna Characterization of Populus Transgenic Plants Overexpressing PtDUF266A (OXPtDUF266A) and Biofuel Production
Paul Gilna Defined Tetra-Allelic Gene Disruption of the 4-Coumarate:Coenzyme A ligase 1 Gene by CRISPR/Cas9 in Switchgrass Results in Lignin Reduction and S/G Ratio Alteration
Paul Gilna Evaluation of Multiple Levers for Overcoming the Recalcitrance of Cellulosic Biomass
Paul Gilna Explaining and Predicting Biomass Recalcitrance with Rigidity Percolation Theory
Paul Gilna Field Experiments of Nine Switchgrass TOP Lines
Paul Gilna From Gene to Network: Switchgrass TOP Line RNA-seq Data Analysis Pipeline at BESC
Paul Gilna Gene Expression Differences between Clostridium thermocellum Biofilm and Planktonic Cells Lead to Specialized Activities and Growth
Paul Gilna Investigating the Role of Polysaccharide Methylation in the Plant Cell Wall
Paul Gilna Lignin Valorization through Biologial Funneling
Paul Gilna Metabolic Network Modeling of Clostridium thermocellum for Systems Biology and Metabolic Engineering
Paul Gilna Modification of Pectin Biosynthesis Leads to Higher Biomass Yield and Saccharification in Bioenergy Feedstock
Paul Gilna Modifying Carbon, Nitrogen, and Electron Metabolism in Clostridium thermocellum to Enhance Cellulosic Biofuel Yield and Titer
Paul Gilna New Insights on the Lignin Pathway in Grasses
Paul Gilna Pleiotropy Decomposition of 609 Populus trichocarpa Genotypes
Paul Gilna Pyruvate Decarboxylase: Rationally Evolving Thermostable Enzymes for Metabolic Engineering
Paul Gilna Rational Methyltransferase Expression in Escherichia coli for Transformation of New Organisms
Paul Gilna Signaling Between Switchgrass and Fungal
Paul Gilna Switchgrass Fermentation by Thermophilic Microbiomes
Paul Gilna The Effect of Lignin and Hemicellulose Removal on Switchgrass Deconstruction by Clostridium thermocellum
Paul Gilna The Unique Mechanism of the Dominant Multi-Component Cellulase from Caldicellulosiruptor bescii

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H
Principal Investigator Abstract Title
Maria Harrison Genetic dissection of AM symbiosis to improve the sustainability of feedstock production
Caroline Harwood Plant-Microbe Interfaces: Probing the molecular mechanisms of plant-bacterial interactions
Eric Hegg Using N and O Isotopes to Determine the Source of Microbial N2O Production
Mark Hildebrand A Systems Biology and Pond Culture-Based Understanding and Improvement of Metabolic Processes Related to Productivity in Diverse Microalgal Classes for Viable Biofuel Production.
Mark Hildebrand The Effect of Carbon Flux Topology and Synchronized Culture Growth on Microalgal Productivity
Nathan Hillson j5 Software Through the Years: Insights from Aggregate Public Usage Metrics
Kirsten Hofmockel Molecular interactions of the plant-soil-microbe continuum of bioenergy ecosystems
Bruce Hungate Quantitative stable isotope probing with 15N in soil microbial communities
Bruce Hungate Studying Microbial Stress Responses in Soil Ecosystems

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J
Principal Investigator Abstract Title
Daniel Jacobson Plant-Microbe Interfaces: Plant-based genome-wide association viriome/microbiome analysis (GWAVA)
Yongqin Jiao Identification of a U/Zn/Cu responsive global regulatory two-component system in Caulobacter crescentus
Thomas Juenger Climate adaption and sustainability in switchgrass: Exploring plant-microbe-soil interactions across continental scale environmental gradients

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K
Principal Investigator Abstract Title
Shawn Kaeppler Transcriptional Analysis of Flowering Time in Switchgrass
Jay Keasling Engineering Polyketide Synthases to Generate Lightly Branched Biofuels
Cheryl Kuske Comparative Analyses of the Genomes and Secretomes of Ascomycota Fungi Reveal Diverse Functions in Plant Biomass Decomposition
Cheryl Kuske Meta-omic, Enzymatic and Soil Chemical Measures Identify Surface Soil Decomposition Processes as Influenced by N Amendment in a Temperate Pine Forest

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L
Principal Investigator Abstract Title
Robert Landick Optimization of Isobutanol Production by Zymomonas mobilis
Taek Soon Lee Isopentenyl diphosphate (IPP)-bypass mevalonate pathways for C5 alcohol production
Peggy Lemaux EPICON: Epigenetic Control of Drought Response in Sorghum
James Liao Robust non-Oxidative Glycolysis in Escherichia coli
James Liao Predicting multiple gene targets for optimal oil production in acetic acid metabolism of Yarrowia lipolytica by ensemble modeling
Mary Lidstrom Communal Metabolism of Methane and the Rare Earth Element Switch
Frank Loffler Multiomic Insights into the Activity and Dynamics of Soil Nitrifier Communities in Midwestern Agricultural Soils
Dominique Loque Development of Novel Approaches to Optimize Energy Crops
Dominique Loque Expression of S-adenosylmethionine Hydrolase in Tissues Synthesizing Secondary Cell Walls Alters Specific Methylated Cell Wall Fractions and Improves Biomass Digestibility
Dominique Loque Transcript switches for fine-tuning of transgene expression
Chaofu Lu Systems Biology to Improve Camelina Seed and Oil Quality Traits

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M
Principal Investigator Abstract Title
Jon Magnuson Rhodosporidium toruloides for conversion of depolymerized cellulose, hemicellulose, and lignin into bioproducts
Christos T Maravelias Process Systems Engineering for Biofuels and Bio-based Chemicals
Costas Maranas 13C-assisted flux elucidation using genome-scale carbon mapping models
Costas Maranas Application of the MetRxn database to highlight multi-tissue/organisms and expansion to include algorithms for predicting novel reactions and pathways
Costas Maranas Ensemble cell-wide kinetic modeling of anaerobic organisms to support fuels and chemicals production
Costas Maranas k-ecoli457: A genome-scale Escherichia coli kinetic metabolic model satisfying flux data for multiple mutant strains
M. David Marks Advancing Field Pennycress as a New Oilseed Biofuels Feedstock that does not Require New Land Commitments
Jennifer Martiny Analysis of an Abundant Bacterial Genus in a Leaf Litter Community
Xavier Mayali Isotope tracing and phylogenetic composition of simplified bacterial communities conferring growth and biomass enhancements to biofuel-producing microalgae
Lee Ann McCue Chemical Analysis of Carbon and Nitrogen Cycling Through the Extracellular Matrix Produced During the Formation of a Multi-Species Community
Lee Ann McCue High-Resolution Spatial Analysis Reveals How Nitrogen Source Governs Carbon Partitioning Between Members in a Phototrophic Consortium
Lee Ann McCue Metabolite Characterization in Complex Microbial Communities
Lee Ann McCue Modeling Approaches for Understanding Metabolic Coupling in Microbial Communities
Lee Ann McCue Newly Identified Regulatory Roles for Vitamin B12 Suggest Coordination of Community Metabolism
John McKay Germplasm Development for Sustainable Production of Camelina sativa Oil
James McKinlay Factors Governing Mutualism Dynamics in a Hydrogen-Producing Coculture
Christof Meile Potential Mechanisms of Anaerobic Methane Oxidation and Challenges to Slow-Growing Microbial Communities
Sabeeha Merchant Functional analysis of copper and silver storage sites and their role in metal homeostasis in Chlamydomonas
Sabeeha Merchant An O-Glycosylated Archaeal Flagellin
Ray Ming Pyramiding genes and alleles for improving energy cane biomass yield
James Moran Spatially Resolved Rhizosphere Function for Elucidating Key Controls on Below-ground Nutrient Interactions
John Morgan Kinetic modeling of the phenylpropanoid pathway in Arabidopsis
Jennifer Morrell-Falvey Plant-Microbe Interfaces: Comparative genomics and functional characterization of Populus-associated endophytes
Jenny Mortimer Characterization of Plant Golgi-Localized Nucleotide Sugar Transporters
Wellington Muchero Species-specific evolution of membrane.bound receptors mediating hostsymbiont specificity in the genus Salix
John Mullet Utility of a Sorghum bicolor RNA atlas for improving energy sorghum stem composition
John Mullet Genomics of Energy Sorghum's Water Use Efficiency/Drought Resilience

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N
Principal Investigator Abstract Title
Ali Navid System-level analysis of metabolic trade-offs and changes during diurnal cycle of Chlamydomonas reinhardtii
George Newcombe Characterizing the Defense Hierarchy of Populus trichocarpa
Jens Nielsen Leucine Biosynthesis is Involved in Regulating High Lipid Accumulation in Yarrowia lipolytica
Jens Nielsen Lipid Accumulation and its Impact on Amino Acid Metabolism in Saccharomyces cerevisiae
Basil Nikolau Integrated and Dynamic Multispectroscopic In Situ Imaging of Plant Metabolism at the Level of Subcellular Compartments
Philippe Noirot Multi-Omics Analysis of a Mycorrhizal System
Philippe Noirot Functional assignment of ligand specificities for Pseudomonas transport proteins
Philippe Noirot Strain-Specific Transportomic Capacity of Pseudomonas fluorescens Linked to Plant Growth Promotion in Aspen Seedlings under Nutrient Stress
Philippe Noirot Genetic Systems to Enable Biosystems Design in Rhizosphere Pseudomonas
Trent Northen Linking Soil Biology and Chemistry Using Knowledge of Exometabolite Substrate Preferences
Trent Northen Self-Assembled Gold Nanoparticle Film For Nanostructure-Initiator Mass Spectrometry With Passive On-Line Salt Fractionation

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O
Principal Investigator Abstract Title
Michelle O'Malley Engineering Anaerobic Gut Fungi for Lignocellulose Breakdown
Victoria Orphan Anabolic activity in Geobacter biofilms as a function of distance to insoluble electron acceptor
Victoria Orphan Comparative genomics and functional characterization of assimilatory sulfate reduction in methanogenic and methanotrophic archaea

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P
Principal Investigator Abstract Title
Himadri Pakrasi Systems Level Study of a Novel Fast-Growing Cyanobacterial Strain for Next Generation Biofuel Production
Samuel Payne Enabling Metaproteomics Research
Kabir Peay Does mycorrhizal symbiosis determine the climate niche for Populus as a bioenergy feedstock?
Dale Pelletier Plant-Microbe Interfaces: Understanding the Populus microbiome structure in response to host stress
Jennifer Pett-Ridge Hyper-accumulated Mn, co-localized in Chlamydomonas reinhardtii acidocalcisomes with Ca and P, can be mobilized in Mn-deficient situations and protects against oxidative stress
Jennifer Pett-Ridge How Redox Fluctuation Shapes Microbial Community Structure and Mineral- Organic Matter Relationships in a Humid Tropical Forest Soil
Christopher Petzold High-throughput quantitative proteomic profiling of Escherichia coli central carbon metabolism
Brian Pfleger RNase III as a Tool to Manipulate Transcript Stability: Identifying in vivo Targets in Escherichia coli
Martin Polz Identifying the most efficient algal degrading communities: Diversity, composition and mechanisms
Martin Polz The Ecology of Macroalgal Polysaccharide Utilization: Verrucomicrobia Isolates Initiate Fucoidan and Carrageenan Degradation Cascades

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R
Principal Investigator Abstract Title
Joshua Rabinowitz Glycolysis Balances Enzyme Efficiency and Metabolic Adaptivity
Joshua Rabinowitz Systems-Level Analysis of Mechanisms Regulating Yeast Metabolic Flux
John Ralph Suppression of CINNAMOYL-CoA REDUCTASE increases the level of monolignol-ferulates in maize lignins
Srivatsan Raman Designing highly specific protein-based small molecule biosensors
Christopher Rao Characterization of the Alginate Lyases and Laminarinases from Vibrio sp.
Chris Rao Protein Acylomes in Fuel-Producing E. coli. Changes in Posttranslational Modifications with Different Carbon Sources
Christopher Rao Amino Acids Are Preferred Over Glucose and Other Sugars in Escherichia coli by a Novel Mechanism of Carbon Catabolite Repression
Christopher Rao Increasing growth yield and decreasing acetylation in Escherichia coli by optimizing the carbon-to-magnesium ratio in peptide-based media
Jennifer Reed Approaches for Evaluating the Production Potential of High Volume Products in Microbial Systems
Jennifer Reed Application of machine learning and active learning to enhance chemical yields in microbes
Virginia Rich Linking Arctic Lake Sediment Microbial Ecology to Carbon Biogeochemistry
Virginia Rich The IsoGenieDB: An Integrated Solution to Cross-Disciplinary Data Management
Phil Robertson Methods for high-throughput massively parallel soil ecofunctional gene analysis
G. Philip Robertson Associative Nitrogen Fixation across a Nitrogen Input Gradient
G Philip Robertson Partitioning Nitrous Oxide (N2O) Emissions from Ammonia Oxidizing Bacteria (AOB) and Ammonia Oxidizing Archaea (AOA) in Corn and Switchgrass Ecosystems
Pamela Ronald Functional analysis of cell wall related genes in Sorghum bicolor

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S
Principal Investigator Abstract Title
Kenneth Sale Formation of a phenyl-choline ether structure in lignin reduces inhibition of cellulase activity by lignin
Daniel Schachtman Systems Analysis of the Physiological and Molecular Mechanisms of Sorghum Nitrogen Use Efficiency, Water Use Efficiency and Interactions with the Soil Microbiome
Daniel Schachtman Harvesting the Root Microbiome of Grasses toward Sustainable Increases in Crop Production
Daniel Schachtman Metabolomics as a Molecular Tool to Understand the Mechanism of Nitrogen Use Efficiency and Interactions with the Soil Microbiome in Energy Sorghum.
Christopher Schadt Plant-Microbe Interfaces: Dissecting the microbiome of Populus tree species from the soil to the canopy using amplicon sequencing and shotgun metagenomic analyses
Christopher Schadt Plant-Microbe Interfaces: Linking host genotype fitness and soil conditions to microbiome community assembly in the Populus root-soil interface
Henrik Scheller At the Interface: Glycoproteins, Glycolipids, and WAK-mediated Signaling are Required for Plant-Microbial Symbiosis in Medicago truncatula
Jonathan Schilling Spatial Connectomics to Identify Agents Relevant to Lignocellulose Deconstruction in Fungi
Jonathan Schilling Distinct growth patterns and time-dependent secretome alterations by two taxonomically divergent brown rot fungi
Corinne Scown Life Cycle Assessment of Ionic Liquid-based Biofuel Production
Daniel Segre Synthetic microbial ecology for biofuel production from lignocellulose
Ashley Shade A New Synthetic Community System for Studying Microbial Interactions Driven by Exometabolites
Steven Singer A Bacterial Pioneer Leaves a Complex Legacy
Anup Singh Droplet-Based Analog and Digital Microfluidic Platforms for High-Throughput Screening and Synthetic Biology Applications
Seema Singh Ionic Liquid Pretreatment Technology: Challenges and Opportunities
Gary Siuzdak Systems Biology Guided by Global Isotope Metabolomics
Lawrence Smart Genomics-Assisted Breeding for Leaf Rust (Melampsora) Resistance in Shrub Willow (Salix) Bioenergy Crops
Lawrence Smart Differential Expression, Regulatory Divergence, and Sex Dimorphism Pervade the Shrub Willow (Salix spp.) Transcriptome
David Stahl Factors Affecting Nitrous Oxide Production from Ammonia Oxidizers and Possible Mitigation Options
Gregory Stephanopoulos Optimal feed control for maximization of lipid production from dilute acetic acid by an engineered oleaginous yeast Yarrowia lipolytica
Gregory Stephanopoulos rewiring metabolism for maximum lipid production in oleaginous yeast Yarrowia lipolytica
Rhona Stuart Exploring the functional aspects of microalgal interactions with associated microbes, predators and pathogens
Garret Suen Evaluating the Cellulolytic Properties of Novel Fibrobacteres isolates from Mammalian Herbivores
Matthew Sullivan Soil viral ecology along a permafrost thaw gradient

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T
Principal Investigator Abstract Title
Janelle Thompson Systems biology towards a continuous platform for biofuels production: Engineering an environmentally-isolated Bacillus strain for biofuel production and recovery under supercritical CO2.
Janelle Thompson Systems biology towards a continuous platform for biofuels production: Heterologous gene expression and isobutanol synthesis in B. megaterium SR7 and biofuel extraction under supercritical CO2.
Timothy Tschaplinski Plant-Microbe Interfaces: Metabolic consequences of the introduction of a Populus trichocarpa lectin receptor-like kinase into Arabidopsis thaliana, a non-ectomycorrhizal host species

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V
Principal Investigator Abstract Title
Rytas Vilgalys Plant-Microbe Interfaces: Characterizing the diversity and function of the ectomycorrhizome of Populus trichocarpa

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W
Principal Investigator Abstract Title
Peter Weber Quantifying the contribution of viruses and phage to nutrient cycling with NanoSIMS
David Weston Plant-Microbe Interfaces: Model communities of Populus bacterial isolates to study mechanisms of microbiome function
Curtis Wilkerson Exploring RNA-Seq Expression Data With GxSeq

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Y
Principal Investigator Abstract Title
Xiaohan Yang Plant-Microbe Interfaces: Small-RNA (sRNA) and open reading from (sORF) response to endo- and eco-mycorrhizal symbioses in Populous
Todd Yeates Design, Characterization, and Emerging Applications of Highly Symmetric Protein Nanostructures
Jamey Young Mapping photoautotrophic metabolism of engineered cyanobacteria to identify reactions that limit production of renewable chemicals

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Z
Principal Investigator Abstract Title
Karsten Zengler Omics-Driven Analysis of Clostridium ljundhalii Disentangles the Complexity of Energy Conservation in Autotrophic and Heterotrophic Growth Conditions
Karsten Zengler Using a Metabolic and Gene-Expression Model to Predict and Analyze the Phenotypic Response of Acetogen Clostridium ljungdahlii
Yaoping Zhang Comparative Studies of Diverse Feedstocks and Identification of High Levels of Hemicellulose and Degradation Inhibitors That Impact Microbial Biofuel Synthesis
Huimin Zhao Optimization of Alginate Utilization in Engineered Bacteria for Biofuels Production
Jizhong Zhou Long-term priming-induced changes in permafrost soil organic matter decomposition
Jizhong Zhou Time-series metagenomics of experimentally warmed Alaskan tundra and Oklahoma temperate soils enables fine-resolution assessment of belowground C cycling feedbacks to climate change
Jizhong Zhou Successional Dynamics of Grassland Microbial Communities in Response to Warming, Precipitation Alternation, and Clipping

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Featuring

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


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