Post on 15-Oct-2020
Office of Science
Office of Biological and Environmental Research
Joseph Graber, Ph.D. Program Manager, Genomic Science Program Team Lead DOE Office of Biological and Environmental Research
Overview for NAS Industrialization of Biology Committee
February 27th, 2014
DOE: Biological and Environmental Research
Department of Energy • Office of Science • Biological and Environmental Research 2 BER Overview
Biological and Environmental Research
Understanding complex biological, climatic, and environmental systems across vast spatial and temporal scales
The Scientific Challenges:
Understand how genomic information is translated with confidence to redesign microbes, plants or ecosystems for improved carbon storage, contaminant remediation and sustainable biofuel production
Understand the roles of Earth’s biogeochemical systems (atmosphere, land, oceans, sea ice, subsurface) in determining climate so we can predict climate decades or centuries into the future, information needed to plan for future energy and resource needs.
Department of Energy • Office of Science • Biological and Environmental Research 3 BER Overview
Biological and Environmental Research Approach • Understanding complex biological and environmental systems across
many spatial and temporal scales:
– From the sub-micron to the global
– From individual molecules to ecosystems
– From nanoseconds to millennia
• Integrating science by tightly coupling theory, observations, experiments, models, and simulations
• Supporting interdisciplinary research to address critical national needs
• Engaging national laboratories, universities, and the private sector to generate the best possible science
Department of Energy • Office of Science • Biological and Environmental Research 4 BER Overview
Biological and Environmental Research (BER)
Foundational Science - integrating observations and experimental capabilities with modeling for predictive understanding
Understand the effects of greenhouse gas emissions on Earth’s climate and biosphere
• World-leading capabilities in climate modeling
• Representation of clouds in climate models
• Direct/indirect effects of aerosols on climate
• Interactions of carbon cycle and climate
• Predictive understanding of terrestrial ecosystems, focus on sensitive systems, e.g., Arctic and tropics
Explore frontiers of genome-enabled biology
• Sustainable bioenergy resources
• Function & organization of plant and microbial systems
• Mechanisms and regulation of carbon storage in plant biomass and microbial communities
• Biosystems design
• Systems biology via data integration and analysis within a systems biology knowledgebase
Department of Energy • Office of Science • Biological and Environmental Research 5 BER Overview
Office of Science
Patricia Dehmer (A)
Advanced
Scientific
Computing
Research
Fusion
Energy
High
Energy
Physics
Basic
Energy
Sciences
Climate and
Environmental
Sciences
Gary Geernaert
Director
Biological
Systems
Science
Todd Anderson
Director
Biological and
Environmental
Research
Sharlene Weatherwax, AD
Nuclear
Physics
Background - BER
Department of Energy • Office of Science • Biological and Environmental Research 6 BER Overview
DOE Genomic Science Program
The major objectives of the Genomic Science program are to:
• Determine the molecular components, regulatory elements,
and integrated networks needed to understand genome-
scale functional properties
• Develop “-omics” experimental capabilities and enabling
technologies needed to achieve dynamic, systems-level
understanding of organism and/or community function
• Develop the computational capabilities, and modeling
capacity, and integrated knowledgebase to advance
predictive understanding and manipulation of biological
systems
DOE mission driven fundamental research
aimed at identifying the foundational systems
biology properties of microbes, plants, and
complex communities.
Department of Energy • Office of Science • Biological and Environmental Research 7 BER Overview
Genomic Science Program
Department of Energy • Office of Science • Biological and Environmental Research 8 BER Overview
BioEnergy Science Center (Oak Ridge National Lab)
• Overcoming biomass “recalcitrance” as route to cost-effective cellulosic biofuels
• “Consolidated Bioprocessing” – one-microbe / community to go from plants to fuel
Great Lakes Bioenergy Research Center (U Wisconsin, Michigan State)
• Re-engineering plants to produce more starches and oils
• Using HTP technologies to optimize chem/bio process for biomass deconstruction
• Sustainability of biofuels
Joint BioEnergy Institute (Lawrence Berkeley National Lab)
• New pretreatment process using room temperature ionic liquids
• Beyond cellulosic ethanol: re-engineering E.coli and yeast to produce hydrocarbons – goal of “green” gasoline, diesel, jet fuel
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The DOE Bioenergy Research Centers
New paradigm for research—single focus, multi-disciplinary, team-based Transformational science Rigorous DOE management and progress review against milestones
Department of Energy • Office of Science • Biological and Environmental Research 9 BER Overview
www.genomicscience.energy.gov/
biosystemsdesign/
Biosystems Design for Biofuels Production
DOE Research Areas:
• Microbial Systems Design: Iterative
network and functional measurements,
computational modeling, and genome-
scale engineering to design new
microbial systems for the production of
advanced biofuels
• Plants Systems Design: Integrative
systems biology and large-scale
genome engineering approaches to
deconstruct cell walls and convert them
into advanced biofuels
Department of Energy • Office of Science • Biological and Environmental Research 10 BER Overview
www.kbase.us
DOE Systems Biology Knowledgebase (KBase) Building a Community Resource for Predictive Biology
KBase offers a unified environment for users to view, query, and download data for microbes, plants, and microbial communities. Users can apply a series of powerful demonstration workflows, including genome annotation, metabolic modeling, and phenotype analysis.
Integration across microbes, communities, and plants will enable the
construction of models ranging from the genotypes of complex microbial and plant communities to their phenotypes, enabling researchers to optimize solutions for bioenergy or the environment.
Systems biology data, models, and information
currently integrated for genomes of 5534 unique prokaryotes, 161 archaea, and 175 eukaryotes.
Efforts continue to integrate microbial and plant genomic, proteomic, and transcriptomic data sets from DOE research
Department of Energy • Office of Science • Biological and Environmental Research 11 BER Overview
Biological and Environmental Research (BER)
Scientific User Facilities
Environmental Molecular Sciences Laboratory (EMSL) - providing integrated experimental & computational resources for discovery and technological innovation
Joint Genome Institute (JGI) - meeting the DNA sequencing needs of the bioenergy, carbon cycle, and biogeochemical science communities
Atmospheric aerosols
Nanosized battery
Modeling contaminants
Fungal ligninase
Poplar
Atmospheric Radiation Measurement (ARM) Climate Research Facility - providing continuous field measurements and data products to improve cloud and aerosol science in climate models
Department of Energy • Office of Science • Biological and Environmental Research 12 BER Overview
• Genome Scale Engineering Tools
HTP gene editing/recoding technologies
Improved integration of large synthetic DNA
constructs
Tools for incorporation of synthetic amino acids etc.
• DNA Synthesis and Assembly
Technologies for cost effective, high efficiency
synthesis and assembly of large DNA constructs
• Biosystems Analysis & Tuning:
Tools for high resolution, high throughput
measurement, analysis, and interpretation of the
metabolic and regulatory networks
Improved “wiring diagrams” of manipulated
organisms
Iterative approaches for subsequent “tuning” of
modified pathways
Biosystems Design: Needs in Methods & Technologies
Department of Energy • Office of Science • Biological and Environmental Research 13 BER Overview
• Advanced Biological Design Principles
Understanding foundational principles governing living
systems to improve directed bioengineering, defining the
“solution space” available to designers and suggesting
new approaches.
• Expansion of Genetically Tractable Organisms/Chassis
Extension of synthetic biology tools to a more diverse set
of organisms would provide a broader array of functional
capabilities and growth characteristics
Expanded tools and techniques for plant systems
• Development of Minimal Cell and in vitro Systems
Minimal cell systems (i.e., highly streamlined platform
organisms) or cell free in vitro systems; fully defined
pathways and functional components
• Biocontainment Mechanisms
Tools and methods for assessment of risks associated
with synthetic constructs and incorporation of redundant
safeguards at successive levels of design, build, test,
extend, and manufacture.
Biosystems Design: Needs in Platform Development
Department of Energy • Office of Science • Biological and Environmental Research 14 BER Overview
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• Computational Tools & BioCAD Systems
Expanded tools to accommodate a wider
suite of biological parts and platform
organisms
Facilitate in silico design of synthetic parts
and systems
Develop efficient workflows for
construction and experimental validation
of large numbers of genetic design
variants
• Information Standards and Databases
Development of shared minimum
information standards and bioinformatic
databases to facilitate the sharing of data
that is of known quality, fully transferrable,
and properly curated
Biosystems Design: Computational Tools & Bioinformatics
Department of Energy • Office of Science • Biological and Environmental Research 15 BER Overview
For more information:
DOE-BER: www.science.energy.gove/BER/
Genomic Science Program website: www.genomicscience.energy.gov
Joseph Graber: joseph.graber@science.doe.gov
Pablo Rabinowicz: pablo.rabinowicz@science.doe.gov
Todd Anderson, Director, Biological Systems Science Division
todd.anderson@science.doe.gov
Office of Science
Office of Biological and Environmental Research
Thank you!
Joseph Graber
Joseph.Graber@science.doe.gov
http://science.energy.gov/ber