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Image: Caldicellulosiruptor bescii on Birchwood Xylan Image: Camelina Image: 3D Neutron Image of Wheat Seedling Image: Acidobacterium Image: Amino Acid Identity and Order Dictated By DNA Genetic Code Image: Atmospheric Processes Image: Bacterial Communication Image: Barley Image: BESC Imaging of Plant Cell Walls at Multiple Scales (b) Image: BESC Research on Biomass-Deconstructing Microbes Image: Bioenergy Crop Genomics Image: Bioenergy Crop Research at BESC Image: Bioenergy Crop Research at JBEI Image: Bioenergy Crop Research at the Joint BioEnergy Institute Image: BioEnergy Science Center Imaging of Plant Cell Walls at Multiple Scales (a) Image: Building Novel Biological Systems for Useful Purposes Image: Caduceus with DNA Helix Image: CAM Kinase II Image: Carbon Transformation and Transport in Soil Image: Categories of Global Omics Measurements Image: Cellular Systems for Diverse National Needs (Populus) Image: Cellular Systems for Diverse National Needs (Shewanella) Image: Cellulose Structure and Hydrolysis Challenges Image: Cellulose Synthase Complexes Image: Cellulose: Processed by Microbes into Ethanol-Convertible Sugars Image: Cellulosic Biomass Feedstock: Corn Stover Image: Cellulosic Biomass Feedstock: Poplar Image: Cellulosic Biomass Feedstock: Switchgrass Image: Chromosome 1 Image: Chromosome 1 Image: Chromosome 10 Image: Chromosome 10 Image: Chromosome 11 Image: Chromosome 11 Image: Chromosome 12 Image: Chromosome 12 Image: Chromosome 13 Image: Chromosome 13 Image: Chromosome 14 Image: Chromosome 14 Image: Chromosome 15 Image: Chromosome 15 Image: Chromosome 16 Image: Chromosome 16 Image: Chromosome 17 Image: Chromosome 17 Image: Chromosome 18 Image: Chromosome 18 Image: Chromosome 19 Image: Chromosome 19 Image: Chromosome 2 Image: Chromosome 2 Image: Chromosome 20 Image: Chromosome 20 Image: Chromosome 21 Image: Chromosome 21 Image: Chromosome 22 Image: Chromosome 22 Image: Chromosome 3 Image: Chromosome 3 Image: Chromosome 4 Image: Chromosome 4 Image: Chromosome 5 Image: Chromosome 5 Image: Chromosome 6 Image: Chromosome 6 Image: Chromosome 7 Image: Chromosome 7 Image: Chromosome 8 Image: Chromosome 8 Image: Chromosome 9 Image: Chromosome 9 Image: Chromosome Paints Image: Chromosome Poster Image: Chromosome X Image: Chromosome X Image: Chromosome Y Image: Chromosome Y Image: Climate Model Output Image: Climate System Image: Community of Cells Image: Components of the Global Carbon Cycle (Cover Image) Image: Confocal microscope image of bacteria on the surface of poplar roots Image: Confocal microscope image of bacteria on the surface of poplar roots Image: Construction of an Overlapping Clone Library Image: Contemporary View of Lignin Substructures Image: Converting Cellulose to Sugars Image: Coupling of the Carbon and Nitrogen Cycles Image: Crystalline Cellulose Image: Design-Build-Test-Learn Cycle Image: Dissolving Cell-Wall Compounds with Ionic Liquids Image: DNA Image: DNA Details Image: DNA in a Bottle Image: DNA Replication Prior to Cell Division Image: DNA Strands Image: DNA Structure Image: DNA with Features Image: DNA with Features (version 2) Image: DNA: The Molecule of Life Image: DNA: The Molecule of Life (with text) Image: Dynein Complex Image: Effects of DNA Sequence Variation Image: Expressing the Genome in Bacterial Cells Image: Expressing the Genome in Plant Cells Image: FISH Mapping on DNA Fibers Image: Fragment of a Cellulose Molecule Image: From Biomass to Advanced Biofuels and Bioproducts Image: From Chromosomes to Proteins Image: From DNA to Humans Image: From Genome Data to Full Cell Simulation Image: From the Cell to Protein Machines Image: Gene Chips Reveal Susceptibilities Image: Gene Regulatory Network Image: Gene Regulatory Network (GRN) Version 2 Image: Genome Sequence Trace Image: Genomic Geography Image: Genomic Geography: Chromosome 19 Image: Genomic Science Program Image: Genomic Science Program Image: GLBRC Research on Bioenergy Crop Sustainability Image: Global Soil Regions Image: Great Lakes Bioenergy Research Center Sustainable Biofuel Landscapes Image: Growth-Rate Modification Image: Health or Disease? 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Caldicellulosiruptor bescii on Birchwood Xylan

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Presenting the possibility of eliminating the pretreatment step from cellulosic biofuel production, a hot springs bacterium known as Caldicellulosiruptor bescii has shown that it can efficiently degrade crystalline cellulose, xylan (a hemicellulose), and various types of non-pretreated biomass including hardwoods such as poplar, high-lignin grasses such as switchgrass, and low-lignin grasses such as Bermuda grass. With an optimal growth temperature of 75 celsius, C. bescii was able to break down 65% of switchgrass biomass without pretreatment. This bacterium is the most heat-tolerant biomass degrader known (withstanding temperatures up to 90 celsius), and it primarily produces hydrogen as an end product when grown on plant biomass.

Credit or Source: Image courtesy of Mike Adams, University of Georgia

Citation(s):

US DOE. 2010. Bioenergy Research Centers: An Overview of the Science, DOE/SC-0127, US Department of Energy. (p. 19) (website)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/.

Camelina

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Camelina, an oilseed feedstock crop that can be grown on marginal farmland with relatively low fertilizer inputs and no irrigation.

Credit or Source: Jean-Nicolas Enjalbert, Colorado State University

Citation(s):

US DOE, USDA. 2014. Plant Feedstock Genomics for Bioenergy Joint Awards 2006–2014, U.S. Departments of Agriculture and Energy. (p. 2) (PDF)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/.

3D Neutron Image of Wheat Seedling

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Three-dimensional neutron image of a wheat seedling with roots colonized by gadolinium-labeled Pantoea sp. YR343 approximately 5 days after inoculation. Root colonization is observed as a rough textural pattern (orange) along the root surface. Researchers can rotate the image on screen for more in-depth analysis.

Credit or Source: Oak Ridge National Laboratory

Citation(s):

US DOE. 2014. New In Situ Imaging and Measurement Technologies for Biological Systems, US Department of Energy Office of Science. (PDF)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/.

Acidobacterium

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These uncultured cells were labeled with a fluorescent molecule used to identify members of the Acidobacterium division of bacteria, which has only three known cultured members.

Credit or Source: Los Alamos National Laboratory

Citation(s):

Genomes to Life Program Roadmap, April 2001, DOE/SC-0036, U.S. Department of Energy Office of Science. (website)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/.

Amino Acid Identity and Order Dictated By DNA Genetic Code

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All living organisms are composed largely of proteins. Proteins are large, complex molecules made up of long chains of subunits called amino acids. Twenty different kinds of amino acids are usually found in proteins. Within the gene, each specific sequence of three DNA bases (codons) directs the cells protein-synthesizing machinery to add specific amino acids. For example, the base sequence ATG codes for the amino acid methionine. Since 3 bases code for 1 amino acid, the protein coded by an average-sized gene (3000 bp) will contain 1000 amino acids. The genetic code is thus a series of codons that specify which amino acids are required to make up specific proteins.

Credit or Source: Office of Biological and Environmental Research of the U.S. Department of Energy Office of Science. science.energy.gov/ber/

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/ and genomics.energy.gov/.

Atmospheric Processes

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Representative subset of the atmospheric processes related to aerosol lifecycles, cloud lifecycles, and aerosol-cloud-precipitation interactions that must be understood to improve future climate predictions.

Credit or Source: U.S. DOE. 2010. Atmospheric System Research (ASR) Science and Program Plan (asr.science.energy.gov/).

Citation(s):

US DOE. Climate Placemat: Energy-Climate Nexus, US Department of Energy Office of Science. (p. 1)

Prepared by the Biological and Enviornmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/ and genomics.energy.gov/

Bacterial Communication

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Bacteria, such as these Shewanella putrefaciens cells growing on iron oxide particles, use chemical signals to coordinate biofilm formation and other community-level behaviors.

Credit or Source: DOE Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory. See EMSL’s Flickr gallery at www.flickr.com/photos/emsl/

Citation(s):

U.S. DOE 2012. Biosystems Design: Report from the July 2011 Workshop, DOE/SC-0141, U.S. Department of Energy Office of Science. (p. 12) (PDF)

Barley

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Cultivated barley is the fourth most abundant crop in the world and a model for plant genetics research.

Credit or Source: freefotouk, Flickr CC BY 2.0

Citation(s):

U.S. Department of Energy, Biological and Environmental Research (BER) (Highlights)

Provided by U.S. Department of Energy, Biological and Environmental Research (BER)

BESC Imaging of Plant Cell Walls at Multiple Scales (b)

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BESC researchers are integrating technologies for imaging plant tissues and cell walls from millimeter to nanometer scales. Part of a cross-section of a switchgrass stem at micrometer scale. Autofluorescent signals from compounds in the stem show less lignin and more sunlight-absorbing chlorophyll in the green outer layer on the right. Deeper blue areas toward the stem’s center show more highly lignified xylem tissue used for water and nutrient transport. (b) Atomic force micrograph showing nanometer-scale detail of the interwoven mesh of rope-like, lignocellulosic microfibril bundles in a switchgrass cell wall.

Credit or Source: BESC researcher Shi-You Ding, National Renewable Energy Laboratory

Citation(s):

US DOE. 2009. Bioenergy Research Centers: An Overview of the Science, DOE/SC-0116, US Department of Energy. (p. 19)

BESC Research on Biomass-Deconstructing Microbes

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Isolated from decaying grass compost, Clostridium cellulolyticum degrades cellulosic biomass using multienzyme complexes called cellulosomes. This scanning electron micrograph shows C. cellulolyticum cells growing on switchgrass biomass.

Credit or Source: Photo by Thomas Hass and Shi-You Ding, National Renewable Energy Laboratory

Citation(s):

US DOE. 2010. Bioenergy Research Centers: An Overview of the Science, DOE/SC-0127, US Department of Energy. (p. 15) (website)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/.

Bioenergy Crop Genomics

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Use genomic insights to develop grasses and trees as bioenergy crops with improved cell-wall degradability, crop sustainability, and biomass and biofuel yield.

Credit or Source: DOE Great Lakes Bioenergy Research Center

Citation(s):

US DOE. May 2010. Biological Systems Science Division: A Division of the U.S. Department of Energy Office of Biological and Environmental Research, US Department of Energy Office of Science. (p. 2a) (website)

US DOE. 2009. Bioenergy Research Centers: An Overview of the Science, DOE/SC-0116, US Department of Energy.

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/ and genomics.energy.gov/

Bioenergy Crop Research at BESC

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Transformed Populus shoots grow in a greenhouse. These plants are altered in targeted cell-wall pathway genes.

Credit or Source: Image courtesy of Oak Ridge National Laboratory

Citation(s):

US DOE. 2010. Bioenergy Research Centers: An Overview of the Science, DOE/SC-0127, US Department of Energy. (p. 15) (website)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/.

Bioenergy Crop Research at JBEI

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JBEI’s director of Grass Genetics, Pam Ronald, in the Miscanthus plot at the University of California, Davis.

Credit or Source: Photo courtesy of Dan Putnam, UC, Davis

Citation(s):

US DOE. 2010. Bioenergy Research Centers: An Overview of the Science, DOE/SC-0127, US Department of Energy. (p. 9) (website)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/.

Bioenergy Crop Research at the Joint BioEnergy Institute

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Lignocellulose in the cell walls of potential bioenergy crops like switchgrass (pictured) or other plant material has the potential to provide biofuels that yield the same energy as gasoline and can be easily distributed through the existing pipeline and gas station infrastructure, provided it can be efficiently broken down into its constituent sugars.

Credit or Source: Roy Kaltschmidt, Lawrence Berkeley National Laboratory

Citation(s):

US DOE. 2009. Bioenergy Research Centers: An Overview of the Science, DOE/SC-0116, US Department of Energy. (p. 14)

BioEnergy Science Center Imaging of Plant Cell Walls at Multiple Scales (a)

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BESC researchers are integrating technologies for imaging plant tissues and cell walls from millimeter to nanometer scales. (a) Part of a cross-section of a switchgrass stem at micrometer scale. Autofluorescent signals from compounds in the stem show less lignin and more sunlight-absorbing chlorophyll in the green outer layer on the right. Deeper blue areas toward the stem’s center show more highly lignified xylem tissue used for water and nutrient transport. Atomic force micrograph showing nanometer-scale detail of the interwoven mesh of rope-like, lignocellulosic microfibril bundles in a switchgrass cell wall.

Credit or Source: BESC researcher Shi-You Ding, National Renewable Energy Laboratory

Citation(s):

US DOE. 2009. Bioenergy Research Centers: An Overview of the Science, DOE/SC-0116, US Department of Energy. (p. 19)

Building Novel Biological Systems for Useful Purposes

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Synthetic biologists design and build novel organisms to generate products not made by natural systems. This process may involve constructing entirely new biological systems from a set of standard parts—genes, proteins, and metabolic pathways—or redesigning existing biological systems. The tools of synthetic biology also can be used to study the interior of living cells at the molecular level, providing critical new information and insight into the machinery of life and the natural world. Synthetic biology holds promise for advances in many areas, including the development of renewable, carbon-neutral energy sources; nonpolluting biological routes for the production of chemicals; safer and more effective pharmaceuticals; and better environmental remediation technologies. At JBEI, researchers are using synthetic biology to develop new platform hosts for producing enzymes and fuels and to create biomolecular parts and devices for constructing new fuel-generating organisms and improved plants. Among other advances, such goals will be achieved through the improved capabilities of fermentative organisms to tolerate processing conditions and inhibit unwanted by-products. Capabilities also will be engineered into fuel-producing organisms to convert 5-carbon sugars into fuel and make use of lignin monomers. Following the strategy that biological systems can be revamped more effectively or built from scratch if standardized parts are employed, investigators are assembling a catalog of well-characterized biosynthetic components to help in designing, testing, optimizing, and implementing integrated large-scale biosynthetic units. These tools and principles, used by JBEI Chief Executive Officer Jay Keasling to develop a relatively inexpensive microbial-based alternative for producing the antimalarial drug artemisinin, will aid in developing the next generation of biofuels.

Credit or Source: Image courtesy of Manfred Auer, Lawrence Berkeley National Laboratory

Citation(s):

US DOE. 2010. Bioenergy Research Centers: An Overview of the Science, DOE/SC-0127, US Department of Energy. (p. 10) (website)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/.

Caduceus with DNA Helix

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All diseases have a genetic component, whether inherited or resulting from the body's response to environmental stresses like viruses or toxins. The successes of the Human Genome Project (HGP) have even enabled researchers to pinpoint errors in genes--the smallest units of heredity--that cause or contribute to disease. The ultimate goal is to use this information to develop new ways to treat, cure, or even prevent the thousands of diseases that afflict humankind.

Credit or Source: Office of Biological and Environmental Research of the U.S. Department of Energy Office of Science. science.energy.gov/ber/

Citation(s):

Human Genome Program, U.S. Department of Energy, Genomics and Its Impact on Science and Society: A 2008 Primer, 2008. (Original version 1992, revised 2001 and 2008.) (website)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/ and genomics.energy.gov/.

CAM Kinase II

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Details on the binding and dynamics of CAM kinase II and its activator calmodulin were revealed using a combination of mutagenesis, crystallography, NMR, neutron scattering, and computational technologies at Los Alamos National Laboratory.

Credit or Source: Los Alamos National Laboratory

Citation(s):

Genomes to Life Program Roadmap, April 2001, DOE/SC-0036, U.S. Department of Energy Office of Science. (website)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/.

Carbon Transformation and Transport in Soil

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The dynamics of carbon transformations and transport in soil are complex and can result in sequestration of carbon in the soil as organic matter or in groundwater as dissolved carbonates, increased emissions of CO2 to the atmosphere, or export of carbon I various forms into aquatic systems. [Source: The U.S. Climate Change Science Program: Vision for the Program and Highlights of the Scientific Strategic Plan, 2003.

Credit or Source: Office of Biological and Environmental Research of the U.S. Department of Energy Office of Science. science.energy.gov/ber/

Citation(s):

US DOE. 2005. Genomics:GTL Roadmap, DOE/SC-0090, U.S. Department of Energy Office of Science. (p. 235) (website)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/.

Categories of Global Omics Measurements

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High-throughput sequencing also allows microbial communities to be investigated en masse, thus giving rise to metagenomic analyses. DOE has played a critical and pioneering role in these studies, which are far beyond what, until only recently, was deemed possible. The newest generation of technologies enables the sequencing of a significant fraction of genomes in a simple microbial community. However, more-complex communities and rare genomes within a community still are not amenable to systematic characterization. In addition, capturing metagenomic profiles at multiple time points during environmental transitions is critical for adequately monitoring the genomic changes associated with an environmental perturbation. As the wealth of omics data grows, better tools are needed for data management, analysis, and integration. Although improvements in sequencing and analytical technologies can reveal the presence of low abundance organisms, these capabilities need to be extended to the single-cell level.

Credit or Source: Office of Biological and Environmental Research of the U.S. Department of Energy Office of Science. science.energy.gov/ber/

Citation(s):

US DOE. 2009. New Frontiers in Characterizing Biological Systems: Report from the May 2009 Workshop, DOE/SC-0121, US Department of Energy Office of Science. (website)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/

Cellular Systems for Diverse National Needs (Populus)

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Different cell types make up the various plant tissues in Populus trichocarpa (a poplar species), a model system for bioenergy and carbon cycling. Guided by the biological information encoded within genome sequences, we can begin to identify, understand, re-engineer, and harness specific cellular systems for energy production, environmental remediation, and other national needs.

Credit or Source: Poplar image by DOE BioEnergy Science Center, DOE Oak Ridge National Laboratory

Citation(s):

US DOE. 2009. New Frontiers in Characterizing Biological Systems: Report from the May 2009 Workshop, DOE/SC-0121, US Department of Energy Office of Science. (website)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/

Cellular Systems for Diverse National Needs (Shewanella)

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Shewanella oneidensis cells can reduce uranium and metals in contaminated environments. Guided by the biological information encoded within genome sequences, we can begin to identify, understand, re-engineer, and harness specific cellular systems for energy production, environmental remediation, and other national needs.

Credit or Source: Shewanella oneidensis image by Rizlan Bencheikh and Bruce Arey, Environmental Molecular Sciences Laboratory, DOE Pacific Northwest National Laboratory.

Citation(s):

US DOE. 2009. New Frontiers in Characterizing Biological Systems: Report from the May 2009 Workshop, DOE/SC-0121, US Department of Energy Office of Science. (website)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/

Cellulose Structure and Hydrolysis Challenges

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Within the plant cell wall, chains of cellulose molecules associate with other polymers to form linear structures of high tensile strength known as microfibrils. Layers upon layers of microfibrils make up the cell wall. Each microfibril is about 10 to 20 nm in diameter and may consist of up to 40 cellulose chains. A microfibril's crystalline and paracrystalline (amorphous) cellulose core is surrounded by hemicellulose, a branched polymer composed of a mix of primarily pentose sugars (xylose, arabinose), and some hexoses (mannose, galactose, glucose). In addition to cross-linking individual microfibrils, hemicellulose also forms covalent associations with lignin, a rigid aromatic polymer. Lignin is not pictured since its structure and organization within the cell wall are poorly understood. Pretreatment of biomass with enzymes or acids is necessary to remove the surrounding matrix of hemicellulose and lignin from the cellulose core prior to hydrolysis. The crystallinity of cellulose presents another challenge to efficient hydrolysis. The high degree of hydrogen bonding that occurs among the sugar subunits within and between cellulose chains forms a 3D lattice-like structure. The highly ordered, water-insoluble nature of crystalline cellulose makes access and hydrolysis of the cellulose chains difficult for the aqueous solutions of enzymes. Paracrystalline cellulose lacks this high degree of hydrogen bonding, thus giving it a structure that is less ordered. Each cellulose molecule is a linear polymer of thousands of glucose residues. Cellobiose, which consists of a pair of glucose residues (one right side up and one upside down) is the repeating unit of cellulose. [Microfibril portion of this figure adapted from J. K. C. Rose and A. B. Bennett, Cooperative Disassembly of the Cellulose-Xyloglucan Network of Plant Cell Walls: Parallels Between Cell Expansion and Fruit Ripening, Trends Plant Sci. 4, 176-83 (1999).]

Credit or Source: Office of Biological and Environmental Research of the U.S. Department of Energy Office of Science. science.energy.gov/ber/

Citation(s):

US DOE. 2005. Genomics:GTL Roadmap, DOE/SC-0090, U.S. Department of Energy Office of Science. (p. 204) (website)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/.

Cellulose Synthase Complexes

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Cellulose synthesis: Many enzymes involved in cell-wall synthesis or modification are thought to be located in complexes. Within the plasma membrane are rosettes composed of the enzyme cellulose synthase; these protein complexes move through the membrane during the synthesis of glucan chains (36 per rosette) that aggregate to form cellulose microfibrils. Cellulose synthase complexes interact with the cytoskeleton in a poorly characterized way, impacting cellulose fibril orientation and perhaps length. Understanding the function of these complexes and their interactions with sugar-producing metabolic pathways will be important for eventually controlling cell-wall composition. A number of cellulose synthase genes have been cloned for a variety of plants.

[Some images taken from "Genomics:GTL Transforming Cellulosic Biomass," U.S. Department of Energy Office of Science and Office of Energy Efficiency and Renewable Energy, June 2006, genomicscience.energy.gov/biofuels/ and U.S. DOE. 2006. "Breaking the Biological Barriers to Cellulosic Ethanol: A Joint Research Agenda," DOE/SC/EE-0095, U.S. Department of Energy Office of Science and Office of Energy Efficiency and Renewable Energy, genomicscience.energy.gov/biofuels/.]

Credit or Source: Office of Biological and Environmental Research of the U.S. Department of Energy Office of Science. science.energy.gov/ber/

Citation(s):

US DOE. May 2007. Biofuels Primer Placemat: From Biomass to Cellulosic Ethanol and Understanding Biomass: Plant Cell Walls, US Department of Energy Office of Science. (website)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/ and genomics.energy.gov/.

Cellulose: Processed by Microbes into Ethanol-Convertible Sugars

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Cellulose, the main structural component of plant cell walls, is a linear polymer consisting of thousands of glucose residues arranged in a rigid, crystalline structure. Layers upon layers of cellulose-containing microfibrils give plant cell walls their remarkable strength. Each microfibril consists of a crystalline cellulose core encased within a complex outer layer of amorphous polysaccharides known as hemicellulose. The crystallinity of cellulose and its association with hemicellulose and other structural polymers such as lignin are two key challenges that prevent the efficient breakdown of cellulose into glucose molecules that can be converted to ethanol. Adding to the difficulty is the diverse mix of simple sugar molecules generated from the hydrolysis of cellulose and hemicellulose. Fermentative microorganisms prefer to use six-carbon sugars (e.g., glucose) as substrates for producing ethanol; however, hemicellulose is composed of a variety of five-carbon sugars that are not efficiently converted into ethanol by microorganisms.

Credit or Source: Genome Management Information System, Oak Ridge National Laboratory [Microfibril structure adapted from J. K. C. Rose and A. B. Bennett, Cooperative Disassembly of the Cellulose-Xyloglucan Network of Plant Cell Walls: Parallels Between Cell Expansion and Fruit Ripening, Trends Plant Sci. 4, 176–83 (1999).]

Citation(s):

US DOE. 2005. Genomics:GTL Roadmap, DOE/SC-0090, U.S. Department of Energy Office of Science. (p. 27) (website)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/.

Cellulosic Biomass Feedstock: Corn Stover

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Plant Residues and Energy Crops: Biotechnology offers the promise of dramatically increasing ethanol production using cellulose, the most abundant biological material on earth, and other polysaccharides (hemicellulose). Residue including postharvest corn plants (stover) and timber residues could be used, as well as such specialized high-biomass "energy" crops as domesticated poplar trees and switchgrass. Biochemical conversion of cellulosic biomass to ethanol for transportation fuel currently involves three basic steps: (1) Pretreatments to increase the accessibility of cellulose to enzymes and solubilize hemicellulose sugars; (2) Hydrolysis with special enzyme preparations to break down cellulose to sugars; and (3) Fermentation to ethanol. Making cellulosic biomass conversion to ethanol more economical and practical will require a science base for molecular redesign of numerous enzymes, biochemical pathways, and full cellular systems.

[Some images taken from "Genomics:GTL Transforming Cellulosic Biomass," U.S. Department of Energy Office of Science and Office of Energy Efficiency and Renewable Energy, June 2006, genomicscience.energy.gov/biofuels/ and U.S. DOE. 2006. "Breaking the Biological Barriers to Cellulosic Ethanol: A Joint Research Agenda," DOE/SC/EE-0095, U.S. Department of Energy Office of Science and Office of Energy Efficiency and Renewable Energy, genomicscience.energy.gov/biofuels/.]

Credit or Source: Office of Biological and Environmental Research of the U.S. Department of Energy Office of Science. science.energy.gov/ber/

Citation(s):

US DOE. May 2007. Biofuels Primer Placemat: From Biomass to Cellulosic Ethanol and Understanding Biomass: Plant Cell Walls, US Department of Energy Office of Science. (website)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/ and genomics.energy.gov/.

Cellulosic Biomass Feedstock: Poplar

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Plant Residues and Energy Crops: Biotechnology offers the promise of dramatically increasing ethanol production using cellulose, the most abundant biological material on earth, and other polysaccharides (hemicellulose). Residue including postharvest corn plants (stover) and timber residues could be used, as well as such specialized high-biomass "energy" crops as domesticated poplar trees and switchgrass. Biochemical conversion of cellulosic biomass to ethanol for transportation fuel currently involves three basic steps: (1) Pretreatments to increase the accessibility of cellulose to enzymes and solubilize hemicellulose sugars; (2) Hydrolysis with special enzyme preparations to break down cellulose to sugars; and (3) Fermentation to ethanol. Making cellulosic biomass conversion to ethanol more economical and practical will require a science base for molecular redesign of numerous enzymes, biochemical pathways, and full cellular systems.

[Some images taken from "Genomics:GTL Transforming Cellulosic Biomass," U.S. Department of Energy Office of Science and Office of Energy Efficiency and Renewable Energy, June 2006, genomicscience.energy.gov/biofuels/ and U.S. DOE. 2006. "Breaking the Biological Barriers to Cellulosic Ethanol: A Joint Research Agenda," DOE/SC/EE-0095, U.S. Department of Energy Office of Science and Office of Energy Efficiency and Renewable Energy, genomicscience.energy.gov/biofuels/.]

Credit or Source: Office of Biological and Environmental Research of the U.S. Department of Energy Office of Science. science.energy.gov/ber/

Citation(s):

US DOE. May 2007. Biofuels Primer Placemat: From Biomass to Cellulosic Ethanol and Understanding Biomass: Plant Cell Walls, US Department of Energy Office of Science. (website)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/ and genomics.energy.gov/.

Cellulosic Biomass Feedstock: Switchgrass

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Plant Residues and Energy Crops: Biotechnology offers the promise of dramatically increasing ethanol production using cellulose, the most abundant biological material on earth, and other polysaccharides (hemicellulose). Residue including postharvest corn plants (stover) and timber residues could be used, as well as such specialized high-biomass "energy" crops as domesticated poplar trees and switchgrass. Biochemical conversion of cellulosic biomass to ethanol for transportation fuel currently involves three basic steps: (1) Pretreatments to increase the accessibility of cellulose to enzymes and solubilize hemicellulose sugars; (2) Hydrolysis with special enzyme preparations to break down cellulose to sugars; and (3) Fermentation to ethanol. Making cellulosic biomass conversion to ethanol more economical and practical will require a science base for molecular redesign of numerous enzymes, biochemical pathways, and full cellular systems.

[Some images taken from "Genomics:GTL Transforming Cellulosic Biomass," U.S. Department of Energy Office of Science and Office of Energy Efficiency and Renewable Energy, June 2006, genomicscience.energy.gov/biofuels/ and U.S. DOE. 2006. "Breaking the Biological Barriers to Cellulosic Ethanol: A Joint Research Agenda," DOE/SC/EE-0095, U.S. Department of Energy Office of Science and Office of Energy Efficiency and Renewable Energy, genomicscience.energy.gov/biofuels/.]

Credit or Source: Office of Biological and Environmental Research of the U.S. Department of Energy Office of Science. science.energy.gov/ber/

Citation(s):

US DOE. May 2007. Biofuels Primer Placemat: From Biomass to Cellulosic Ethanol and Understanding Biomass: Plant Cell Walls, US Department of Energy Office of Science. (website)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/ and genomics.energy.gov/.

Chromosome 1

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Credit or Source: Genome Management Information System, Oak Ridge National Laboratory

Citation(s):

Human Chromosomes from "Human Genome Landmarks: Selected Genes, Traits, and Disorders" Poster, 2002. (Gene Gateway)

Chromosome 1

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Credit or Source: Genome Management Information System, Oak Ridge National Laboratory

Citation(s):

Human Chromosomes from "Human Genome Landmarks: Selected Genes, Traits, and Disorders" Poster, 2002. (Gene Gateway)

Chromosome 10

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Credit or Source: Genome Management Information System, Oak Ridge National Laboratory

Citation(s):

Human Chromosomes from "Human Genome Landmarks: Selected Genes, Traits, and Disorders" Poster, 2002. (Gene Gateway)

Chromosome 10

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Credit or Source: Genome Management Information System, Oak Ridge National Laboratory

Citation(s):

Human Chromosomes from "Human Genome Landmarks: Selected Genes, Traits, and Disorders" Poster, 2002. (Gene Gateway)

Chromosome 11

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Credit or Source: Genome Management Information System, Oak Ridge National Laboratory

Citation(s):

Human Chromosomes from "Human Genome Landmarks: Selected Genes, Traits, and Disorders" Poster, 2002. (Gene Gateway)

Chromosome 11

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Credit or Source: Genome Management Information System, Oak Ridge National Laboratory

Citation(s):

Human Chromosomes from "Human Genome Landmarks: Selected Genes, Traits, and Disorders" Poster, 2002. (Gene Gateway)

Chromosome 12

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Credit or Source: Genome Management Information System, Oak Ridge National Laboratory

Citation(s):

Human Chromosomes from "Human Genome Landmarks: Selected Genes, Traits, and Disorders" Poster, 2002. (Gene Gateway)

Chromosome 12

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Credit or Source: Genome Management Information System, Oak Ridge National Laboratory

Citation(s):

Human Chromosomes from "Human Genome Landmarks: Selected Genes, Traits, and Disorders" Poster, 2002. (Gene Gateway)

Chromosome 13

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Credit or Source: Genome Management Information System, Oak Ridge National Laboratory

Citation(s):

Human Chromosomes from "Human Genome Landmarks: Selected Genes, Traits, and Disorders" Poster, 2002. (Gene Gateway)

Chromosome 13

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Credit or Source: Genome Management Information System, Oak Ridge National Laboratory

Citation(s):

Human Chromosomes from "Human Genome Landmarks: Selected Genes, Traits, and Disorders" Poster, 2002. (Gene Gateway)

Chromosome 14

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Credit or Source: Genome Management Information System, Oak Ridge National Laboratory

Citation(s):

Human Chromosomes from "Human Genome Landmarks: Selected Genes, Traits, and Disorders" Poster, 2002. (Gene Gateway)

Chromosome 14

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Credit or Source: Genome Management Information System, Oak Ridge National Laboratory

Citation(s):

Human Chromosomes from "Human Genome Landmarks: Selected Genes, Traits, and Disorders" Poster, 2002. (Gene Gateway)

Chromosome 15

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Credit or Source: Genome Management Information System, Oak Ridge National Laboratory

Citation(s):

Human Chromosomes from "Human Genome Landmarks: Selected Genes, Traits, and Disorders" Poster, 2002. (Gene Gateway)

Chromosome 15

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Credit or Source: Genome Management Information System, Oak Ridge National Laboratory

Citation(s):

Human Chromosomes from "Human Genome Landmarks: Selected Genes, Traits, and Disorders" Poster, 2002. (Gene Gateway)

Chromosome 16

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Credit or Source: Genome Management Information System, Oak Ridge National Laboratory

Citation(s):

Human Chromosomes from "Human Genome Landmarks: Selected Genes, Traits, and Disorders" Poster, 2002. (Gene Gateway)

Chromosome 16

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Credit or Source: Genome Management Information System, Oak Ridge National Laboratory

Citation(s):

Human Chromosomes from "Human Genome Landmarks: Selected Genes, Traits, and Disorders" Poster, 2002. (Gene Gateway)

Chromosome 17

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Credit or Source: Genome Management Information System, Oak Ridge National Laboratory

Citation(s):

Human Chromosomes from "Human Genome Landmarks: Selected Genes, Traits, and Disorders" Poster, 2002. (Gene Gateway)

Chromosome 17

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Credit or Source: Genome Management Information System, Oak Ridge National Laboratory

Citation(s):

Human Chromosomes from "Human Genome Landmarks: Selected Genes, Traits, and Disorders" Poster, 2002. (Gene Gateway)

Chromosome 18

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Credit or Source: Genome Management Information System, Oak Ridge National Laboratory

Citation(s):

Human Chromosomes from "Human Genome Landmarks: Selected Genes, Traits, and Disorders" Poster, 2002. (Gene Gateway)

Chromosome 18

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Credit or Source: Genome Management Information System, Oak Ridge National Laboratory

Citation(s):

Human Chromosomes from "Human Genome Landmarks: Selected Genes, Traits, and Disorders" Poster, 2002. (Gene Gateway)

Chromosome 19

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Credit or Source: Genome Management Information System, Oak Ridge National Laboratory

Citation(s):

Human Chromosomes from "Human Genome Landmarks: Selected Genes, Traits, and Disorders" Poster, 2002. (Gene Gateway)

Chromosome 19

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Credit or Source: Genome Management Information System, Oak Ridge National Laboratory

Citation(s):

Human Chromosomes from "Human Genome Landmarks: Selected Genes, Traits, and Disorders" Poster, 2002. (Gene Gateway)

Chromosome 2

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Credit or Source: Genome Management Information System, Oak Ridge National Laboratory

Citation(s):

Human Chromosomes from "Human Genome Landmarks: Selected Genes, Traits, and Disorders" Poster, 2002. (Gene Gateway)

Chromosome 2

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Credit or Source: Genome Management Information System, Oak Ridge National Laboratory

Citation(s):

Human Chromosomes from "Human Genome Landmarks: Selected Genes, Traits, and Disorders" Poster, 2002. (Gene Gateway)

Chromosome 20

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Credit or Source: Genome Management Information System, Oak Ridge National Laboratory

Citation(s):

Human Chromosomes from "Human Genome Landmarks: Selected Genes, Traits, and Disorders" Poster, 2002. (Gene Gateway)

Chromosome 20

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Credit or Source: Genome Management Information System, Oak Ridge National Laboratory

Citation(s):

Human Chromosomes from "Human Genome Landmarks: Selected Genes, Traits, and Disorders" Poster, 2002. (Gene Gateway)

Chromosome 21

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Credit or Source: Genome Management Information System, Oak Ridge National Laboratory

Citation(s):

Human Chromosomes from "Human Genome Landmarks: Selected Genes, Traits, and Disorders" Poster, 2002. (Gene Gateway)

Chromosome 21

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Credit or Source: Genome Management Information System, Oak Ridge National Laboratory

Citation(s):

Human Chromosomes from "Human Genome Landmarks: Selected Genes, Traits, and Disorders" Poster, 2002. (Gene Gateway)

Chromosome 22

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Credit or Source: Genome Management Information System, Oak Ridge National Laboratory

Citation(s):

Human Chromosomes from "Human Genome Landmarks: Selected Genes, Traits, and Disorders" Poster, 2002. (Gene Gateway)

Chromosome 22

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Credit or Source: Genome Management Information System, Oak Ridge National Laboratory

Citation(s):

Human Chromosomes from "Human Genome Landmarks: Selected Genes, Traits, and Disorders" Poster, 2002. (Gene Gateway)

Chromosome 3

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Credit or Source: Genome Management Information System, Oak Ridge National Laboratory

Citation(s):

Human Chromosomes from "Human Genome Landmarks: Selected Genes, Traits, and Disorders" Poster, 2002. (Gene Gateway)

Chromosome 3

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Credit or Source: Genome Management Information System, Oak Ridge National Laboratory

Citation(s):

Human Chromosomes from "Human Genome Landmarks: Selected Genes, Traits, and Disorders" Poster, 2002. (Gene Gateway)

Chromosome 4

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Credit or Source: Genome Management Information System, Oak Ridge National Laboratory

Citation(s):

Human Chromosomes from "Human Genome Landmarks: Selected Genes, Traits, and Disorders" Poster, 2002. (Gene Gateway)

Chromosome 4

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Credit or Source: Genome Management Information System, Oak Ridge National Laboratory

Citation(s):

Human Chromosomes from "Human Genome Landmarks: Selected Genes, Traits, and Disorders" Poster, 2002. (Gene Gateway)

Chromosome 5

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Credit or Source: Genome Management Information System, Oak Ridge National Laboratory

Citation(s):

Human Chromosomes from "Human Genome Landmarks: Selected Genes, Traits, and Disorders" Poster, 2002. (Gene Gateway)

Chromosome 5

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Credit or Source: Genome Management Information System, Oak Ridge National Laboratory

Citation(s):

Human Chromosomes from "Human Genome Landmarks: Selected Genes, Traits, and Disorders" Poster, 2002. (Gene Gateway)

Chromosome 6

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Credit or Source: Genome Management Information System, Oak Ridge National Laboratory

Citation(s):

Human Chromosomes from "Human Genome Landmarks: Selected Genes, Traits, and Disorders" Poster, 2002. (Gene Gateway)

Chromosome 6

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Credit or Source: Genome Management Information System, Oak Ridge National Laboratory

Citation(s):

Human Chromosomes from "Human Genome Landmarks: Selected Genes, Traits, and Disorders" Poster, 2002. (Gene Gateway)

Chromosome 7

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Credit or Source: Genome Management Information System, Oak Ridge National Laboratory

Citation(s):

Human Chromosomes from "Human Genome Landmarks: Selected Genes, Traits, and Disorders" Poster, 2002. (Gene Gateway)

Chromosome 7

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Credit or Source: Genome Management Information System, Oak Ridge National Laboratory

Citation(s):

Human Chromosomes from "Human Genome Landmarks: Selected Genes, Traits, and Disorders" Poster, 2002. (Gene Gateway)

Chromosome 8

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Credit or Source: Genome Management Information System, Oak Ridge National Laboratory

Citation(s):

Human Chromosomes from "Human Genome Landmarks: Selected Genes, Traits, and Disorders" Poster, 2002. (Gene Gateway)

Chromosome 8

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Credit or Source: Genome Management Information System, Oak Ridge National Laboratory

Citation(s):

Human Chromosomes from "Human Genome Landmarks: Selected Genes, Traits, and Disorders" Poster, 2002. (Gene Gateway)

Chromosome 9

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Credit or Source: Genome Management Information System, Oak Ridge National Laboratory

Citation(s):

Human Chromosomes from "Human Genome Landmarks: Selected Genes, Traits, and Disorders" Poster, 2002. (Gene Gateway)

Chromosome 9

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Credit or Source: Genome Management Information System, Oak Ridge National Laboratory

Citation(s):

Human Chromosomes from "Human Genome Landmarks: Selected Genes, Traits, and Disorders" Poster, 2002. (Gene Gateway)

Chromosome Paints

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Human chromosomes "painted" by flourescent dyes to detect abnormal exchange of genetic material frequently present in cancer. Chromosome paints also serve as valuable resources for other clinical and research applications.

Credit or Source: Lawrence Livermore National Laboratory

Citation(s):

Human Genome Program, U.S. Department of Energy, Human Genome Program Report, 1997. (website)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/.

Chromosome Poster

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Human Genome Landmarks: Selected Genes, Traits, and Disorders

Credit or Source: Office of Biological and Environmental Research of the U.S. Department of Energy Office of Science. science.energy.gov/ber/

Citation(s):

Human Chromosomes from "Human Genome Landmarks: Selected Genes, Traits, and Disorders" Poster, 2002. (Gene Gateway)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/.

Chromosome X

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Credit or Source: Genome Management Information System, Oak Ridge National Laboratory

Citation(s):

Human Chromosomes from "Human Genome Landmarks: Selected Genes, Traits, and Disorders" Poster, 2002. (Gene Gateway)

Chromosome X

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Credit or Source: Genome Management Information System, Oak Ridge National Laboratory

Citation(s):

Human Chromosomes from "Human Genome Landmarks: Selected Genes, Traits, and Disorders" Poster, 2002. (Gene Gateway)

Chromosome Y

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Credit or Source: Genome Management Information System, Oak Ridge National Laboratory

Citation(s):

Human Chromosomes from "Human Genome Landmarks: Selected Genes, Traits, and Disorders" Poster, 2002. (Gene Gateway)

Chromosome Y

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Credit or Source: Genome Management Information System, Oak Ridge National Laboratory

Citation(s):

Human Chromosomes from "Human Genome Landmarks: Selected Genes, Traits, and Disorders" Poster, 2002. (Gene Gateway)

Climate Model Output

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Credit or Source: Oak Ridge National Laboratory

Citation(s):

US DOE. Climate Placemat: Energy-Climate Nexus, US Department of Energy Office of Science. (p. 1)

Prepared by the Biological and Enviornmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/ and genomics.energy.gov/

Climate System

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Credit or Source: Biological and Environmental Research Information System

Citation(s):

US DOE. Climate Placemat: Energy-Climate Nexus, US Department of Energy Office of Science. (p. 2)

Prepared by the Biological and Enviornmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/ and genomics.energy.gov/

Community of Cells

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Although microbes are single-cell organisms, they typically live in communities composed of more than one kind of microbe -- often many different kinds. Considering that life is found in virtually every environmental niche from arctic tundra to parched deserts to boiling sea vents on the deepest ocean floor, the global genetic "catalog" encoding all of life's amazingly diverse capabilities must be astonishing, yet very few details are known.

Credit or Source: Office of Biological and Environmental Research of the U.S. Department of Energy Office of Science. science.energy.gov/ber/

Citation(s):

Genomes to Life Program Roadmap, April 2001, DOE/SC-0036, U.S. Department of Energy Office of Science. (website)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/ and genomics.energy.gov/.

Components of the Global Carbon Cycle (Cover Image)

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This is a very simplified representation of the contemporary global carbon cycle from the report cover. See the companion figure, Components of the Global Carbon Cycle (alternate), for details about this natural flux between the terrestrial biosphere and the atmosphere and between the marine biosphere and the atmosphere.

Credit or Source: Office of Biological and Environmental Research of the U.S. Department of Energy Office of Science. science.energy.gov/ber/

Citation(s):

U.S. DOE. 2008. Carbon Cycling and Biosequestration: Report from the March 2008 Workshop, DOE/SC-108, U.S. Department of Energy Office of Science. (website)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/ and genomics.energy.gov/

Confocal microscope image of bacteria on the surface of poplar roots

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Viable Pseudomonas sp. GM17 are stained green (with Syto9), and dead cells are stained red (with propidium iodide). The root surface is visualized by autofluorescence.

Credit or Source: J. L. Morrell-Falvey, Oak Ridge National Laboratory

Citation(s):

U.S. DOE. 2014. Research for Sustainable Bioenergy: Linking Genomic and Ecosystem Sciences, Workshop Report, DOE/SC-0167. U.S. Department of Energy Office of Science. genomicscience.energy.gov/sustainability/. (p. 12) (PDF)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/.

Confocal microscope image of bacteria on the surface of poplar roots

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Pantoea sp. YR343 expressing GFP (green fluorescent protein); the plant root is detected by autofluorescence in the red channel.

Credit or Source: J. L. Morrell-Falvey, Oak Ridge National Laboratory

Citation(s):

U.S. DOE. 2014. Research for Sustainable Bioenergy: Linking Genomic and Ecosystem Sciences, Workshop Report, DOE/SC-0167. U.S. Department of Energy Office of Science. genomicscience.energy.gov/sustainability/. (p. 12) (PDF)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/.

Construction of an Overlapping Clone Library

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A collection of clones of chromosomal DNA, called a library, has no obvious order indicating the original positions of the cloned pieces on the uncut chromosome. To establish that two particular clones are adjacent to each other in the genome, libraries of clones containing partly overlapping regions must be constructed. These clone libraries are ordered by dividing the inserts into smaller fragments and determining which clones share common DNA sequences.

Credit or Source: Office of Biological and Environmental Research of the U.S. Department of Energy Office of Science. science.energy.gov/ber/

Citation(s):

Human Genome Program, U.S. Department of Energy, Genomics and Its Impact on Science and Society: A 2008 Primer, 2008. (Original version 1992, revised 2001 and 2008.) (website)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/ and genomics.energy.gov/.

Contemporary View of Lignin Substructures

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Lignification: Random vs Template Directed. In terms of energy content, lignins are thought to be the most abundant of all biopolymers. They are composed of p-hydroxyphenylpropanoid units interconnected through 8-O-4, 8-5, 8-8, 8-1, 5-5, and 4-O-5 linkages. Corresponding substructures in the polymer include alkyl aryl ethers, phenylcoumarans, resinols, tetrahydrofuran-spiro-cyclohexadienones, biphenyls, dibenzodioxocins, and diaryl ethers (see Fig. A). The primary precursors themselves—the three monolignols p-coumaryl, coniferyl, and sinapyl alcohols—differ only according to their aromatic methoxy substitution patterns. These monolignols are oxidized enzymatically through single-electron transfer to generate the respective phenoxy radicals. The actual coupling of a monolignol radical with the growing end of a lignin chain, however, may not fall under direct enzymatic control. Accordingly, many investigators have assumed that lignin primary structures must be random or combinatorial as far as sequences of interunit linkages are concerned. More recently, this theory has been reinforced by reports that certain kinds of non-native monolignols can be incorporated into macromolecular lignin structures. Lignins and lignin derivatives exhibit two fundamental characteristics that traditionally have been viewed as evidence in favor of randomness in their configurations: They are both noncrystalline and optically inactive.1 Nevertheless, a number of observations are thought by some to point in the opposite direction. The individual molecular components in (nonpolyionic) lignin preparations tend to associate very strongly with one another in a well-defined way. These processes are thought to be governed by vital structural motifs derived from corresponding features disposed nonrandomly along the native biopolymer chain. Moreover, dimeric pinoresinol moieties are linked predominantly to the macromolecular lignin chain through at least one of their aromatic C-5 positions.We do not know whether such features can be explained through combinatorial mechanisms under simple chemical control or if higher-level control mechanisms are required. One hypothesis proposes a way to replicate specific sequences of interunit linkages through a direct template polymerization mechanism. According to this model, an antiparallel double-stranded lignin template, maintained in a dynamic state at the leading edge of each lignifying domain, determines the configuration of the daughter chain being assembled on the proximal strand’s exposed face. Furthermore, replication fidelity could be controlled by strong nonbonded orbital interactions between matching pairs of aromatic rings in the parent and the growing daughter chains. The overall process seems to be consistent with the lack of both crystallinity and optical activity in macromolecular lignin domains.Finally, required sequence information may be encoded in polypeptide chains that embody arrays of adjacent lignol-binding sites analogous to those found in dirigent positioning proteins.2 Cited References: 1. J. Ralph et al. 2004. Lignins: Natural Polymers from Oxidative Coupling of 4-Hydroxyphenylpropanoids, Phytochemistry Rev. 3, 29–60. 2. S. Sarkanen. 1998. Template Polymerization in Lignin Biosynthesis, pp. 194–208 in Lignin and Lignan Biosynthesis 697, ed. N. G. Lewis and S. Sarkanen, American Chemical Society, Washington, D.C. Theory proposed by G. Brunow and coworkers in 1998 (reproduced with permission).

Credit or Source: Biological and Environmental Research Information System, Oak Ridge National Laboratory. Sponsored by the U.S. Department of Energy Biological and Environmental Research Program.

Citation(s):

U.S. DOE. 2006. Breaking the Biological Barriers to Cellulosic Ethanol: A Joint Research Agenda, DOE/SC/EE-0095, U.S. Department of Energy Office of Science and Office of Energy Efficiency and Renewable Energy. (p. 94) (website)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/.

Converting Cellulose to Sugars

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Cellulases include a mix of enzymes that break down cellulose into simple sugars that can be fermented by microorganisms to ethanol. Three general classes of cellulases—endoglucanases, exoglucanases, and cellobiases—work together in a coordinated fashion to hydrolyze cellulose. Endoglucanases internally cleave a cellulose chain, and exoglucanases bind the cleaved ends of the cellulose chain and feed the chain into its active site where it is broken down into double glucose molecules called cellobiose. Cellobiases split cellobiose to yield two glucose molecules. The cellulase pictured is an exoglucanase whose binding domain on the right extracts a cellulose chain. At the active site in the larger catalytic domain on the left, the cellulose chain is hydrolyzed to yield cellobiose subunits. [Image from M. Himmel et al., Cellulase Animation, run time 11 min., National Renewable Energy Laboratory (2000).] Citation : Genomics:GTL Roadmap, U.S. Department of Energy Office of Science, August 2005, genomicscience.energy.gov/roadmap/

Credit or Source: M. Himmel, National Renewable Energy Laboratory "Genomics:GTL Roadmap," U.S. Department of Energy Office of Science, August 2005, genomicscience.energy.gov/roadmap/

Citation(s):

US DOE. 2005. Genomics:GTL Roadmap, DOE/SC-0090, U.S. Department of Energy Office of Science. (p. 100) (website)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/.

Coupling of the Carbon and Nitrogen Cycles

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Credit or Source: Office of Biological and Environmental Research of the U.S. Department of Energy Office of Science. science.energy.gov/ber/

Citation(s):

U.S. DOE. 2008. Carbon Cycling and Biosequestration: Report from the March 2008 Workshop, DOE/SC-108, U.S. Department of Energy Office of Science. (p. 65) (website)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/ and genomics.energy.gov/.

Crystalline Cellulose

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The glucan chains contain thousands of glucose residues.

[Some images taken from "Genomics:GTL Transforming Cellulosic Biomass," U.S. Department of Energy Office of Science and Office of Energy Efficiency and Renewable Energy, June 2006, genomicscience.energy.gov/biofuels/ and U.S. DOE. 2006. "Breaking the Biological Barriers to Cellulosic Ethanol: A Joint Research Agenda," DOE/SC/EE-0095, U.S. Department of Energy Office of Science and Office of Energy Efficiency and Renewable Energy, genomicscience.energy.gov/biofuels/.]

Credit or Source: Office of Biological and Environmental Research of the U.S. Department of Energy Office of Science. science.energy.gov/ber/

Citation(s):

US DOE. May 2007. Biofuels Primer Placemat: From Biomass to Cellulosic Ethanol and Understanding Biomass: Plant Cell Walls, US Department of Energy Office of Science. (website)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/ and genomics.energy.gov/.

Design-Build-Test-Learn Cycle

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An iterative design strategy is based on the cyclic process of developing an initial design or prototype, testing that prototype, analyzing its performance against specific metrics, learning what worked and what did not work, designing a new protoype based on what was learned, and completing the cycle again. The goal is to improve design or prototype quality and functionality.

Credit or Source: Office of Biological and Environmental Research of the U.S. Department of Energy Office of Science. science.energy.gov/ber/

Citation(s):

U.S. DOE. 2015. Lignocellulosic Biomass for Advanced Biofuels and Bioproducts: Workshop Report, DOE/SC-0170. U.S. Department of Energy Office of Science. (p. 37) (website)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/.

Dissolving Cell-Wall Compounds with Ionic Liquids

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These confocal fluorescence images show switchgrass cell walls (A) before pretreatment with the EmimAc ionic liquid and (B) 10 minutes after treatment, in which the cell walls have swollen in size, a prelude to complete solubilization of cellulose, hemicellulose, and lignin.

Credit or Source: Image courtesy of Seema Singh, Sandia National Laboratories

Citation(s):

US DOE. 2010. Bioenergy Research Centers: An Overview of the Science, DOE/SC-0127, US Department of Energy. (p. 12) (website)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/.

DNA

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Credit or Source: Office of Biological and Environmental Research of the U.S. Department of Energy Office of Science. science.energy.gov/ber/

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/ and genomics.energy.gov/.

DNA Details

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Apart from reproductive gametes, each cell of the human body contains 23 pairs of chromosomes, each a packet of compressed and entwined DNA. Every strand of the DNA is a huge natural polymer of repeating nucleotide units, each of which comprises a phosphate group, a sugar (deoxyribose), and a base (either adenine, thymine, cytosine, or guanine). Every strand thus embodies a code of four characters (A's, T's, C's, and G's), the recipe for the machinery of human life. In its normal state, DNA takes the form of a highly regular double-stranded helix, the strands of which are linked by hydrogen bonds between adenine and thymine (A,T) and between cytosine and guanine (C, G). Each such linkage is said to constitute a base pair; some three billion base pairs constitute the human genome. It is the specificity of these base-pair linkages that underlies the mechanism of DNA replication illustrated here. Each strand of the double helix serves as a template for the synthesis of a new strand, the nucleotide sequence of which is strictly determined. Replication thus produces twin daughter helices, each an exact replica of its sole parent.

Credit or Source: Office of Biological and Environmental Research of the U.S. Department of Energy Office of Science. science.energy.gov/ber/

Citation(s):

Human Genome Program, U.S. Department of Energy, To Know Ourselves, 1996. (website)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/ and genomics.energy.gov/.

DNA in a Bottle

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DNA underlies every aspect of human health, both in function and dysfunction. Obtaining a detailed picture of how genes and other DNA sequences function together and interact with environmental factors ultimately will lead to the discovery of pathways involved in normal processes and in disease pathogenesis. Such knowledge will have a profound impact on the way disorders are diagnosed, treated, and prevented and will bring about revolutionary changes in clinical and public health practice.

Credit or Source: Office of Biological and Environmental Research of the U.S. Department of Energy Office of Science. science.energy.gov/ber/

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/ and genomics.energy.gov/.

DNA Replication Prior to Cell Division

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Each time a cell divides into two daughter cells, its full genome is duplicated; for humans and other complex organisms, this duplication occurs in the nucleus. During cell division the DNA molecule unwinds and the weak bonds between the base pairs break, allowing the strands to separate. Each strand directs the synthesis of a complementary new strand, with free nucleotides matching up with their complementary bases on each of the separated strands. Strict base-pairing rules are adhered to adenine will pair only with thymine (an A-T pair) and cytosine with guanine (a C-G pair). Each daughter cell receives one old and one new DNA strand. The cells adherence to these base-pairing rules ensures that the new strand is an exact copy of the old one. This minimizes the incidence of errors (mutations) that may greatly affect the resulting organism or its offspring.

Credit or Source: Office of Biological and Environmental Research of the U.S. Department of Energy Office of Science. science.energy.gov/ber/

Citation(s):

Human Genome Program, U.S. Department of Energy, Genomics and Its Impact on Science and Society: A 2008 Primer, 2008. (Original version 1992, revised 2001 and 2008.) (website)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/ and genomics.energy.gov/.

DNA Strands

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Cells are the fundamental working units of every living system. All the instructions needed to direct their activities are contained within the chemical DNA (deoxyribonucleic acid). DNA from all organisms is made up of the same chemical and physical components. The DNA sequence is the particular side-by-side arrangement of bases along the DNA strand (e.g., ATTCCGGA). This order spells out the exact instructions required to create a particular organism with its own unique traits. The genome is an organisms complete set of DNA. Genomes vary widely in size: the smallest known genome for a free-living organism (a bacterium) contains about 600,000 DNA base pairs, while human and mouse genomes have some 3 billion. Except for mature red blood cells, all human cells contain a complete genome. DNA in the human genome is arranged into 24 distinct chromosomes--physically separate molecules that range in length from about 50 million to 250 million base pairs. A few types of major chromosomal abnormalities, including missing or extra copies or gross breaks and rejoinings (translocations), can be detected by microscopic examination. Most changes in DNA, however, are more subtle and require a closer analysis of the DNA molecule to find perhaps single-base differences. Each chromosome contains many genes, the basic physical and functional units of heredity. Genes are specific sequences of bases that encode instructions on how to make proteins. Genes comprise only about 2% of the human genome; the remainder consists of noncoding regions, whose functions may include providing chromosomal structural integrity and regulating where, when, and in what quantity proteins are made. The human genome is estimated to contain 25,000 genes.

Credit or Source: Office of Biological and Environmental Research of the U.S. Department of Energy Office of Science. science.energy.gov/ber/

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/ and genomics.energy.gov/.

DNA Structure

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The four nitrogenous bases of DNA are arranged along the sugar- phosphate backbone in a particular order (the DNA sequence), encoding all genetic instructions for an organism. Adenine (A) pairs with thymine (T), while cytosine (C) pairs with guanine (G). The two DNA strands are held together by weak bonds between the bases. A gene is a segment of a DNA molecule (ranging from fewer than 1 thousand bases to several million), located in a particular position on a specific chromosome, whose base sequence contains the information necessary for protein synthesis.

Credit or Source: Office of Biological and Environmental Research of the U.S. Department of Energy Office of Science. science.energy.gov/ber/

Citation(s):

Human Genome Program, U.S. Department of Energy, Genomics and Its Impact on Science and Society: A 2008 Primer, 2008. (Original version 1992, revised 2001 and 2008.) (website)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/ and genomics.energy.gov/.

DNA with Features

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Cells are the fundamental working units of every living system. All the instructions needed to direct their activities are contained within the chemical DNA (deoxyribonucleic acid). DNA from all organisms is made up of the same chemical and physical components. The DNA sequence is the particular side-by-side arrangement of bases along the DNA strand (e.g., ATTCCGGA). This order spells out the exact instructions required to create a particular organism with its own unique traits. The genome is an organisms complete set of DNA. Genomes vary widely in size: the smallest known genome for a free-living organism (a bacterium) contains about 600,000 DNA base pairs, while human and mouse genomes have some 3 billion. Except for mature red blood cells, all human cells contain a complete genome. DNA in the human genome is arranged into 24 distinct chromosomes--physically separate molecules that range in length from about 50 million to 250 million base pairs. A few types of major chromosomal abnormalities, including missing or extra copies or gross breaks and rejoinings (translocations), can be detected by microscopic examination. Most changes in DNA, however, are more subtle and require a closer analysis of the DNA molecule to find perhaps single-base differences. Each chromosome contains many genes, the basic physical and functional units of heredity. Genes are specific sequences of bases that encode instructions on how to make proteins. Genes comprise only about 2% of the human genome; the remainder consists of noncoding regions, whose functions may include providing chromosomal structural integrity and regulating where, when, and in what quantity proteins are made. The human genome is estimated to contain 25,000 genes.

Credit or Source: Office of Biological and Environmental Research of the U.S. Department of Energy Office of Science. science.energy.gov/ber/

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/ and genomics.energy.gov/.

DNA with Features (version 2)

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Cells are the fundamental working units of every living system. All the instructions needed to direct their activities are contained within the chemical DNA (deoxyribonucleic acid). DNA from all organisms is made up of the same chemical and physical components. The DNA sequence is the particular side-by-side arrangement of bases along the DNA strand (e.g., ATTCCGGA). This order spells out the exact instructions required to create a particular organism with its own unique traits. The genome is an organisms complete set of DNA. Genomes vary widely in size: the smallest known genome for a free-living organism (a bacterium) contains about 600,000 DNA base pairs, while human and mouse genomes have some 3 billion. Except for mature red blood cells, all human cells contain a complete genome. DNA in the human genome is arranged into 24 distinct chromosomes--physically separate molecules that range in length from about 50 million to 250 million base pairs. A few types of major chromosomal abnormalities, including missing or extra copies or gross breaks and rejoinings (translocations), can be detected by microscopic examination. Most changes in DNA, however, are more subtle and require a closer analysis of the DNA molecule to find perhaps single-base differences. Each chromosome contains many genes, the basic physical and functional units of heredity. Genes are specific sequences of bases that encode instructions on how to make proteins. Genes comprise only about 2% of the human genome; the remainder consists of noncoding regions, whose functions may include providing chromosomal structural integrity and regulating where, when, and in what quantity proteins are made. The human genome is estimated to contain 25,000 genes.

Credit or Source: Office of Biological and Environmental Research of the U.S. Department of Energy Office of Science. science.energy.gov/ber/

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/ and genomics.energy.gov/.

DNA: The Molecule of Life

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Cells are the fundamental working units of every living system. All the instructions needed to direct their activities are contained within the chemical DNA (deoxyribonucleic acid). DNA from all organisms is made up of the same chemical and physical components. The DNA sequence is the particular side-by-side arrangement of bases along the DNA strand (e.g., ATTCCGGA). This order spells out the exact instructions required to create a particular organism with its own unique traits. The genome is an organisms complete set of DNA. Genomes vary widely in size: the smallest known genome for a free-living organism (a bacterium) contains about 600,000 DNA base pairs, while human and mouse genomes have some 3 billion. Except for mature red blood cells, all human cells contain a complete genome. DNA in the human genome is arranged into 24 distinct chromosomes--physically separate molecules that range in length from about 50 million to 250 million base pairs. A few types of major chromosomal abnormalities, including missing or extra copies or gross breaks and rejoinings (translocations), can be detected by microscopic examination. Most changes in DNA, however, are more subtle and require a closer analysis of the DNA molecule to find perhaps single-base differences. Each chromosome contains many genes, the basic physical and functional units of heredity. Genes are specific sequences of bases that encode instructions on how to make proteins. Genes comprise only about 2% of the human genome; the remainder consists of noncoding regions, whose functions may include providing chromosomal structural integrity and regulating where, when, and in what quantity proteins are made. The human genome is estimated to contain 25,000 genes. Although genes get a lot of attention, its the proteins that perform most life functions and even make up the majority of cellular structures. Proteins are large, complex molecules made up of smaller subunits called amino acids. Chemical properties that distinguish the 20 different amino acids cause the protein chains to fold up into specific three-dimensional structures that define their particular functions in the cell.

Credit or Source: Office of Biological and Environmental Research of the U.S. Department of Energy Office of Science. science.energy.gov/ber/

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/ and genomics.energy.gov/.

DNA: The Molecule of Life (with text)

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Cells are the fundamental working units of every living system. All the instructions needed to direct their activities are contained within the chemical DNA (deoxyribonucleic acid). DNA from all organisms is made up of the same chemical and physical components. The DNA sequence is the particular side-by-side arrangement of bases along the DNA strand (e.g., ATTCCGGA). This order spells out the exact instructions required to create a particular organism with its own unique traits. The genome is an organisms complete set of DNA. Genomes vary widely in size: the smallest known genome for a free-living organism (a bacterium) contains about 600,000 DNA base pairs, while human and mouse genomes have some 3 billion. Except for mature red blood cells, all human cells contain a complete genome. DNA in the human genome is arranged into 24 distinct chromosomes--physically separate molecules that range in length from about 50 million to 250 million base pairs. A few types of major chromosomal abnormalities, including missing or extra copies or gross breaks and rejoinings (translocations), can be detected by microscopic examination. Most changes in DNA, however, are more subtle and require a closer analysis of the DNA molecule to find perhaps single-base differences. Each chromosome contains many genes, the basic physical and functional units of heredity. Genes are specific sequences of bases that encode instructions on how to make proteins. Genes comprise only about 2% of the human genome; the remainder consists of noncoding regions, whose functions may include providing chromosomal structural integrity and regulating where, when, and in what quantity proteins are made. The human genome is estimated to contain 25,000 genes. Although genes get a lot of attention, its the proteins that perform most life functions and even make up the majority of cellular structures. Proteins are large, complex molecules made up of smaller subunits called amino acids. Chemical properties that distinguish the 20 different amino acids cause the protein chains to fold up into specific three-dimensional structures that define their particular functions in the cell.

Credit or Source: Office of Biological and Environmental Research of the U.S. Department of Energy Office of Science. science.energy.gov/ber/

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/ and genomics.energy.gov/.

Dynein Complex

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The dynein motor, a cellular complex believed to be composed of 12 distinct protein parts, performs fundamental transportation tasks critical to the cell; defects in its structure can prove fatal. This machine converts chemical energy stored in an ATP molecule into mechanical energy that moves material though the cell along slender filaments called microtubules. One of the dynein motor's most important functions occurs during cell division, when it helps move chromosomes into proper position.

Credit or Source: Office of Biological and Environmental Research of the U.S. Department of Energy Office of Science. science.energy.gov/ber/

Citation(s):

Genomes to Life Program Roadmap, April 2001, DOE/SC-0036, U.S. Department of Energy Office of Science. (website)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/ and genomics.energy.gov/.

Effects of DNA Sequence Variation

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Each DNA molecule contains many genes--the basic physical and functional units of heredity. A gene is a specific sequence of nucleotide bases, whose sequences carry the information required for constructing proteins, which provide the structural components of cells and tissues as well as enzymes for essential biochemical reactions. The human genome is estimated to comprise more than 25,000 genes. All living organisms are composed largely of proteins--which are coded for by genes. Proteins are large, complex molecules made up of long chains of subunits called amino acids. Twenty different kinds of amino acids are usually found in proteins. Within the gene, each specific sequence of three DNA bases (codons) directs the cells protein-synthesizing machinery to add specific amino acids. For example, the base sequence ATG codes for the amino acid methionine. Since 3 bases code for 1 amino acid, the protein coded by an average-sized gene (3000 bp) will contain 1000 amino acids. The DNA code is thus a series of codons that specify which amino acids are required to make up specific proteins. Some variations in a person's genetic code will have no effect on the protein that is produced, others can lead to disease or an increased susceptibility to a disease.

Credit or Source: Office of Biological and Environmental Research of the U.S. Department of Energy Office of Science. science.energy.gov/ber/

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/ and genomics.energy.gov/.

Expressing the Genome in Bacterial Cells

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Bacteria are prokaryotes—single-celled organisms that lack a nucleus. Because no nuclear membrane separates a bacterium’s genome from ribosomes and other cellular contents, protein synthesis can start before an mRNA transcript is complete. Bacterial genes do not have introns (noncoding regions of DNA). Thus editing mRNA transcripts, which involves removing introns prior to protein synthesis, is not needed.

Credit or Source: Biological and Environmental Research Information System, Oak Ridge National Laboratory

Citation(s):

US DOE. Genomics Placemat: Genomics for Energy and Environmental Science, US Department of Energy Office of Science. (p. 1) (website)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/ and genomics.energy.gov/.

Expressing the Genome in Plant Cells

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Plants are eukaryotes—organisms with cells that contain a membrane-bound nucleus. A eukaryote’s DNA is in the nucleus where mRNA is transcribed. The genes in plants and other eukaryotic organisms, such as humans and animals, contain noncoding regions called introns. In the nucleus, introns are removed from mRNA transcripts, and the remaining coding regions (called exons) are spliced back together. Once edited, the mRNA is transported outside the nucleus for translation into proteins by ribosomes.

Credit or Source: Biological and Environmental Research Information System, Oak Ridge National Laboratory

Citation(s):

US DOE. Genomics Placemat: Genomics for Energy and Environmental Science, US Department of Energy Office of Science. (p. 1) (website)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/ and genomics.energy.gov/.

FISH Mapping on DNA Fibers

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The fluorescence microscope reveals several individual cloned DNA fibers from yeast artificial chromosomes (YACs, in blue) after molecular combing to attach and stretch the DNA molecules across a glass microscope slide. Also shown are the locations of two P1 clones, labeled green and red, mapped onto the YAC fibers using FISH. Digital imaging technology can be used to assemble physical maps of chromosomes with a resolution of about 3 to 5 kilobases.

Credit or Source: University of California, San Francisco

Citation(s):

Human Genome Program, U.S. Department of Energy, Human Genome Program Report, 1997. (website)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/.

Fragment of a Cellulose Molecule

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Alternating glucose residues are in an inverted orientation so the cellobiose (a disaccharide) is the repeating structural unit. Enzymes such as cellulases synthesized by fungi and bacteria work together to degrade cellulose and other structural polysaccharides in biomass. Optimizing these complex systems will require a more detailed understanding of their regulation and activity.

[Some images taken from "Genomics:GTL Transforming Cellulosic Biomass," U.S. Department of Energy Office of Science and Office of Energy Efficiency and Renewable Energy, June 2006, genomicscience.energy.gov/biofuels/ and U.S. DOE. 2006. "Breaking the Biological Barriers to Cellulosic Ethanol: A Joint Research Agenda," DOE/SC/EE-0095, U.S. Department of Energy Office of Science and Office of Energy Efficiency and Renewable Energy, genomicscience.energy.gov/biofuels/.]

Credit or Source: Office of Biological and Environmental Research of the U.S. Department of Energy Office of Science. science.energy.gov/ber/

Citation(s):

US DOE. May 2007. Biofuels Primer Placemat: From Biomass to Cellulosic Ethanol and Understanding Biomass: Plant Cell Walls, US Department of Energy Office of Science. (website)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/ and genomics.energy.gov/.

From Biomass to Advanced Biofuels and Bioproducts

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Credit or Source: Office of Biological and Environmental Research of the U.S. Department of Energy Office of Science. science.energy.gov/ber/

Citation(s):

U.S. DOE. 2018. U.S. Department of Energy Bioenergy Research Centers, DOE/SC–0191. U.S. Department of Energy Office of Science (genomicscience.energy.gov/centers/brcbrochure.pdf). (PDF)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/.

From Chromosomes to Proteins

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Detailed chromosome descriptions, together with other biological resources, software, and instrumentation generated in the first seven years of the DOE Human Genome Program (HGP), are enabling researchers to begin focusing on their most challenging goal: Determining the sequence of DNA subunits (the bases A, T, C, G) found in the 24 different human chromosomes. Differences in DNA sequence underlie much of life's diversity. The image depicts the progress of human genome research, beginning with a microscopic view of a duplicated chromosome (left). Genome researchers begin with a very small chromosomal fragment (asterisk), using enzymes to cut it into the smaller pieces (red bars) required for DNA sequencing. Automated technology determines the DNA sequence of all or part of each fragment (graph with color-coded peaks). Another HGP goal is to identify the estimated 25,000 genes, which account for only about 5 percent of human DNA. Computer analysis of DNA sequences is one way investigators identify gene features in DNA sequences (solid line with tick marks). In a living cell, individual gene segments from DNA molecules are assembled into short-lived intermediary molecules (short red line), and the information is translated by the cell's machinery into three-dimensional proteins (black globular structure at right). All organisms are made up largely of proteins that provide the structural components and specialized enzymes required by cells and tissues. Public resources and technologies arising from the HGP and other genome efforts worldwide are laying the foundation for future explorations into the functions of each protein encoded by the genes. This research, which also will investigate how proteins work together in systems and pathways and react to external cues, will extend far into the future.

Credit or Source: Office of Biological and Environmental Research of the U.S. Department of Energy Office of Science. science.energy.gov/ber/

Citation(s):

Human Genome Program, U.S. Department of Energy, Human Genome Program Report, 1997. (website)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/ and genomics.energy.gov/.

From DNA to Humans

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Each DNA molecule contains many genes--the basic physical and functional units of heredity. A gene is a specific sequence of nucleotide bases, whose sequences carry the information required for constructing proteins, which provide the structural components of cells and tissues as well as enzymes for essential biochemical reactions. The human genome is estimated to comprise more than 25,000 genes. All living organisms are composed largely of proteins--which are coded for by genes. Proteins are large, complex molecules made up of long chains of subunits called amino acids. Twenty different kinds of amino acids are usually found in proteins. Within the gene, each specific sequence of three DNA bases (codons) directs the cells protein-synthesizing machinery to add specific amino acids. For example, the base sequence ATG codes for the amino acid methionine. Since 3 bases code for 1 amino acid, the protein coded by an average-sized gene (3000 bp) will contain 1000 amino acids. The DNA code is thus a series of codons that specify which amino acids are required to make up specific proteins.

Credit or Source: Office of Biological and Environmental Research of the U.S. Department of Energy Office of Science. science.energy.gov/ber/

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/ and genomics.energy.gov/.

From Genome Data to Full Cell Simulation

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This concept diagram schematically illustrates a path from basic genome data to a more detailed understanding of complex molecular and cellular systems. New computational analysis, modeling, and simulation capabilities are needed to meet this goal. The points on the plot are very approximate, depending on the specifics of problem abstraction and computational representation. Research is under way to create mathematics, algorithms, and computer architectures for understanding each level of biological complexity.

Credit or Source: Biological and Environmental Research Information System, Oak Ridge National Laboratory. GTL Roadmap, p. 89 (genomicsgtl.energy.gov/roadmap/). Sponsored by the U.S. Department of Energy Biological and Environmental Research Program.

Citation(s):

U.S. DOE. 2006. Breaking the Biological Barriers to Cellulosic Ethanol: A Joint Research Agenda, DOE/SC/EE-0095, U.S. Department of Energy Office of Science and Office of Energy Efficiency and Renewable Energy. (p. 169) (website)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/.

From the Cell to Protein Machines

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Cells are the fundamental working units of every living system. All the instructions needed to direct their activities are contained within the chemical DNA (deoxyribonucleic acid). DNA from all organisms is made up of the same chemical and physical components. The DNA sequence is the particular side-by-side arrangement of bases along the DNA strand (e.g., ATTCCGGA). This order spells out the exact instructions required to create a particular organism with its own unique traits. The genome is an organisms complete set of DNA. Genomes vary widely in size: the smallest known genome for a free-living organism (a bacterium) contains about 600,000 DNA base pairs, while human and mouse genomes have some 3 billion. Except for mature red blood cells, all human cells contain a complete genome. DNA in the human genome is arranged into 24 distinct chromosomes--physically separate molecules that range in length from about 50 million to 250 million base pairs. A few types of major chromosomal abnormalities, including missing or extra copies or gross breaks and rejoinings (translocations), can be detected by microscopic examination. Most changes in DNA, however, are more subtle and require a closer analysis of the DNA molecule to find perhaps single-base differences. Each chromosome contains many genes, the basic physical and functional units of heredity. Genes are specific sequences of bases that encode instructions on how to make proteins. Genes comprise only about 2% of the human genome; the remainder consists of noncoding regions, whose functions may include providing chromosomal structural integrity and regulating where, when, and in what quantity proteins are made. The human genome is estimated to contain 25,000 genes. Although genes get a lot of attention, its the proteins that perform most life functions and even make up the majority of cellular structures. Proteins are large, complex molecules made up of smaller subunits called amino acids. Chemical properties that distinguish the 20 different amino acids cause the protein chains to fold up into specific three-dimensional structures that define their particular functions in the cell.

Credit or Source: Office of Biological and Environmental Research of the U.S. Department of Energy Office of Science. science.energy.gov/ber/

Citation(s):

Human Genome Program, U.S. Department of Energy, Genomics and Its Impact on Science and Society: A 2008 Primer, 2008. (Original version 1992, revised 2001 and 2008.) (website)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/ and genomics.energy.gov/.

Gene Chips Reveal Susceptibilities

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Credit or Source: Mitch Doktycz, Life Sciences Division, Oak Ridge National Laboratory; U.S. Department of Energy Human Genome Program, www.ornl.gov/hgmis

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/.

Gene Regulatory Network

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GRNs are remarkably diverse in their structure, but several basic properties are illustrated in this figure. In this example, two different signals impinge on a single target gene where the cis-regulatory elements provide for an integrated output in response to the two inputs. Signal molecule A triggers the conversion of inactive transcription factor A (green oval) into an active form that binds directly to the target gene's cis-regulatory sequence. The process for signal B is more complex. Signal B triggers the separation of inactive B (red oval) from an inhibitory factor (yellow rectangle). B is then free to form an active complex that binds to the active A transcription factor on the cis-regulatory sequence. The net output is expression of the target gene at a level determined by the action of factors A and B. In this way, cis-regulatory DNA sequences, together with the proteins that assemble on them, integrate information from multiple signaling inputs to produce an appropriately regulated readout. A more realistic network might contain multiple target genes regulated by signal A alone, others by signal B alone, and still others by the pair of A and B.

Credit or Source: Office of Biological and Environmental Research of the U.S. Department of Energy Office of Science. science.energy.gov/ber/

Citation(s):

Genomes to Life Program Roadmap, April 2001, DOE/SC-0036, U.S. Department of Energy Office of Science. (website)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/ and genomics.energy.gov/.

Gene Regulatory Network (GRN) Version 2

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Gross anatomy of a minimal gene regulatory network (GRN) embedded in a regulatory network. A regulatory network can be viewed as a cellular input-output device. At minimum, a gene regulatory network typically contains the following components: (1) an input signal reception and transduction system that mediates intra and extracellular cues (left box; often, more than one signal impinges on a given target gene); (2) a "core component" complex composed of transacting regulatory proteins and cognate cis-acting DNA sequences (circle; functionally similar components may be associated with multiple target genes, resulting in similar gene-expression patterns); and (3) primary molecular outputs from target genes, which are RNA and protein (box to right of circle). The net effects are changes in cell phenotype and function (right box). Direct and indirect feedbacks typically are important. More realistic networks often feature multiple tiers of regulation, with first-tier gene products regulating expression of another group of genes, and so on. Beyond GRN boundaries are signaling responses and feedbacks, such as those that drive bacterial chemotaxis, which do not involve regulation of gene expression but instead act directly on proteins and protein machine assemblies (dashed arrows). Some regulatory networks have no embedded GRN component.

Credit or Source: Office of Biological and Environmental Research of the U.S. Department of Energy Office of Science. science.energy.gov/ber/

Citation(s):

Genomes to Life Program Roadmap, April 2001, DOE/SC-0036, U.S. Department of Energy Office of Science. (website)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/ and genomics.energy.gov/.

Genome Sequence Trace

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Human Genome Program, U.S. Department of Energy

Credit or Source: Office of Biological and Environmental Research of the U.S. Department of Energy Office of Science. science.energy.gov/ber/

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/ and genomics.energy.gov/.

Genomic Geography

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In the cell nucleus, RNA is produced by transcription, in much the same way that DNA replicates itself. RNA, however, substitutes the sugar ribose for deoxyribose and the base uracil for thymine, and is usually single-stranded. One form of RNA, messenger RNA or mRNA, conveys the DNA recipe for protein synthesis to the cell cytoplasm. There, bound temporarily to a cytoplasmic particle known as a ribosome, each three-base codon of the mRNA links to a specific form of transfer RNA (tRNA) containing the complementary three-base sequence. This tRNA, in turn, transfers a single amino acid to a growing protein chain. Each codon thus unambiguously directs the addition of one amino acid to the protein. On the other hand, the same amino acid can be added by different codons; in this illustration, the mRNA sequences GCA and GCC are both specifying the addition of the amino acid alanine (Ala).

Credit or Source: Office of Biological and Environmental Research of the U.S. Department of Energy Office of Science. science.energy.gov/ber/

Citation(s):

Human Genome Program, U.S. Department of Energy, To Know Ourselves, 1996. (website)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/ and genomics.energy.gov/.

Genomic Geography: Chromosome 19

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The human genome can be mapped in a number of ways. The familiar and reproducible banding pattern of the chromosomes constitutes one kind of physical map, and in many cases, the positions of genes or other heritable markers have been localized to one band or another. More useful are genetic linkage maps, on which the relative positions of markers have been established by studying how frequently the markers are separated during a natural process of chromosomal shuffling called genetic recombination. The cryptically coded ordered markers near the top of this figure are physically mapped to specific regions of chromosome 19; some of them also constitute a low-resolution genetic linkage map. (Hundreds of genes and other markers have been mapped on chromosome 19; only a few are indicated here.) A higher-resolution physical map might describe, as shown here, the cutting sites (the short vertical lines) for certain DNA-cleaving enzymes. The overlapping fragments that allow such a map to be constructed are then the resources for obtaining the ultimate physical map, the base-pair sequence for the human genome. At the bottom of this figure is an example of output from an automatic sequencing machine.

Credit or Source: Office of Biological and Environmental Research of the U.S. Department of Energy Office of Science. science.energy.gov/ber/

Citation(s):

Human Genome Program, U.S. Department of Energy, Human Genome Program Report, 1997. (website)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/ and genomics.energy.gov/.

Genomic Science Program

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Artwork with black background (logo). See also artwork with transparent background.

Credit or Source: Office of Biological and Environmental Research of the U.S. Department of Energy Office of Science. science.energy.gov/ber/

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/.

Genomic Science Program

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Artwork with transparent background (logo). See also artwork with black background.

Credit or Source: Office of Biological and Environmental Research of the U.S. Department of Energy Office of Science. science.energy.gov/ber/

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/.

GLBRC Research on Bioenergy Crop Sustainability

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To improve the sustainability of crops and agricultural residues used for energy production, GLBRC researchers are studying the symbiotic associations of crop roots with arbuscular mycorrhizal (AM) fungi. Interactions with AM fungi benefit host plants by improving the uptake of nutrients, especially phosphorus, nitrogen, and potassium from the soil. Establishing these symbiotic associations in crops grown under suboptimal conditions has the potential to increase biomass production while limiting use of fertilizers and pesticides.

Credit or Source: Photo courtesy of the Great Lakes Bioenergy Research Center

Citation(s):

US DOE. 2010. Bioenergy Research Centers: An Overview of the Science, DOE/SC-0127, US Department of Energy. (p. 22) (website)

Global Soil Regions

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Credit or Source: U.S. Department of Agriculture, Natural Resources Conservation Service www.nrcs.usda.gov/wps/portal/nrcs/site/national/home/

Citation(s):

U.S. DOE. 2008. Carbon Cycling and Biosequestration: Report from the March 2008 Workshop, DOE/SC-108, U.S. Department of Energy Office of Science. (p. 66) (website)

Biological and Environmental Research Information System, Oak Ridge National Laboratory, Oak Ridge, TN genomicscience.energy.gov/ and genomics.energy.gov/

Great Lakes Bioenergy Research Center Sustainable Biofuel Landscapes

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At Michigan State University’s W. K. Kellogg Biological Station, GLBRC researchers are evaluating the performance of a variety of novel bioenergy crop production systems for crop yield and quality, impacts on microbial-plant interactions, biogeochemical and biodiversity responses, and water use.

Credit or Source: Kurt Stepnitz, Michigan State University

Citation(s):

US DOE. 2009. Bioenergy Research Centers: An Overview of the Science, DOE/SC-0116, US Department of Energy. (p. 11)

Growth-Rate Modification

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The Arabidopsis plant on the right has been modified by altering the expression of regulatory genes controlling growth.

Credit or Source: Mendel Biotechnology

Citation(s):

U.S. DOE. 2006. Breaking the Biological Barriers to Cellulosic Ethanol: A Joint Research Agenda, DOE/SC/EE-0095, U.S. Department of Energy Office of Science and Office of Energy Efficiency and Renewable Energy. (p. 65) (website)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/.

Health or Disease?

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Each DNA molecule contains many genes--the basic physical and functional units of heredity. A gene is a specific sequence of nucleotide bases, whose sequences carry the information required for constructing proteins, which provide the structural components of cells and tissues as well as enzymes for essential biochemical reactions. The human genome is estimated to comprise more than 25,000 genes. All living organisms are composed largely of proteins--which are coded for by genes. Proteins are large, complex molecules made up of long chains of subunits called amino acids. Twenty different kinds of amino acids are usually found in proteins. Within the gene, each specific sequence of three DNA bases (codons) directs the cells protein-synthesizing machinery to add specific amino acids. For example, the base sequence ATG codes for the amino acid methionine. Since 3 bases code for 1 amino acid, the protein coded by an average-sized gene (3000 bp) will contain 1000 amino acids. The DNA code is thus a series of codons that specify which amino acids are required to make up specific proteins. Some variations in a person's genetic code will have no effect on the protein that is produced, others can lead to disease or an increased susceptibility to a disease.

Credit or Source: Office of Biological and Environmental Research of the U.S. Department of Energy Office of Science. science.energy.gov/ber/

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/ and genomics.energy.gov/.

HGP Impacting Many Disciplines

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The large, multidisciplinary Human Genome Project (HGP)  the effort to find all human genes and characterize a reference genomepromises to revolutionize the future so profoundly that the 21st has been dubbed the "biology century." Almost everyone will be affected by applications of information and technologies derived from the HGP era of the late 20th century. Entirely new approaches will be implemented in biological research and the practice of medicine and agriculture. Genetic data will provide the foundation for research in many biological subdisciplines, leading to an unprecedented understanding of the inner workings of whole biological systems. The benefits of genomic research are, or soon will be, realized in such areas as forensics and identification science, ecology and environmental science, toxic-waste cleanup, creation of new bioenergy sources and more efficient industrial processes, and in understanding the mysteries of evolution, anthropology, and human migration. Among the fields that HGP research will impact are engineering, computer science, mathematics, counseling, sociology, ethics, religion, law, agriculture, education, pharmaceuticals, instrumentation, nuclear medicine, forensics, bioremediation, biofuels, and journalism. Cross-disciplinary students with solid backgrounds in science and in one or more other fields such as journalism, law, and computer science will be needed to tackle the issues and applications arising from the HGP.

Credit or Source: Office of Biological and Environmental Research of the U.S. Department of Energy Office of Science. science.energy.gov/ber/

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/ and genomics.energy.gov/.

HGP Impacting Many Disciplines (alternate)

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The large, multidisciplinary Human Genome Project (HGP)  the effort to find all human genes and characterize a reference genomepromises to revolutionize the future so profoundly that the 21st has been dubbed the "biology century." Almost everyone will be affected by applications of information and technologies derived from the HGP era of the late 20th century. Entirely new approaches will be implemented in biological research and the practice of medicine and agriculture. Genetic data will provide the foundation for research in many biological subdisciplines, leading to an unprecedented understanding of the inner workings of whole biological systems. The benefits of genomic research are, or soon will be, realized in such areas as forensics and identification science, ecology and environmental science, toxic-waste cleanup, creation of new bioenergy sources and more efficient industrial processes, and in understanding the mysteries of evolution, anthropology, and human migration. Among the fields that HGP research will impact are engineering, computer science, mathematics, counseling, sociology, ethics, religion, law, agriculture, education, pharmaceuticals, instrumentation, nuclear medicine, forensics, bioremediation, biofuels, and journalism. Cross-disciplinary students with solid backgrounds in science and in one or more other fields such as journalism, law, and computer science will be needed to tackle the issues and applications arising from the HGP.

Credit or Source: Office of Biological and Environmental Research of the U.S. Department of Energy Office of Science. science.energy.gov/ber/

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/ and genomics.energy.gov/.

HGP: Impacting Many Disciplines (vertical)

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The large, multidisciplinary Human Genome Project (HGP)  the effort to find all human genes and characterize a reference genomepromises to revolutionize the future so profoundly that the 21st has been dubbed the "biology century." Almost everyone will be affected by applications of information and technologies derived from the HGP era of the late 20th century. Entirely new approaches will be implemented in biological research and the practice of medicine and agriculture. Genetic data will provide the foundation for research in many biological subdisciplines, leading to an unprecedented understanding of the inner workings of whole biological systems. The benefits of genomic research are, or soon will be, realized in such areas as forensics and identification science, ecology and environmental science, toxic-waste cleanup, creation of new bioenergy sources and more efficient industrial processes, and in understanding the mysteries of evolution, anthropology, and human migration. Among the fields that HGP research will impact are engineering, computer science, mathematics, counseling, sociology, ethics, religion, law, agriculture, education, pharmaceuticals, instrumentation, nuclear medicine, forensics, bioremediation, biofuels, and journalism. Cross-disciplinary students with solid backgrounds in science and in one or more other fields such as journalism, law, and computer science will be needed to tackle the issues and applications arising from the HGP.

Credit or Source: Office of Biological and Environmental Research of the U.S. Department of Energy Office of Science. science.energy.gov/ber/

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/ and genomics.energy.gov/.

Hydrolysis

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Goal: Break down cellulose into its component sugars using enzyme preparations. Enzymes such as cellulases synthesized by fungi and bacteria work together to degrade cellulose and other structural polysaccharides in biomass. Optimizing these complex systems will require a more detailed understanding of their regulation and activity.

[Some images taken from "Genomics:GTL Transforming Cellulosic Biomass," U.S. Department of Energy Office of Science and Office of Energy Efficiency and Renewable Energy, June 2006, genomicscience.energy.gov/biofuels/ and U.S. DOE. 2006. "Breaking the Biological Barriers to Cellulosic Ethanol: A Joint Research Agenda," DOE/SC/EE-0095, U.S. Department of Energy Office of Science and Office of Energy Efficiency and Renewable Energy, genomicscience.energy.gov/biofuels/.]

Credit or Source: Office of Biological and Environmental Research of the U.S. Department of Energy Office of Science. science.energy.gov/ber/

Citation(s):

US DOE. May 2007. Biofuels Primer Placemat: From Biomass to Cellulosic Ethanol and Understanding Biomass: Plant Cell Walls, US Department of Energy Office of Science. (website)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/ and genomics.energy.gov/.

Imaging Carbon Allocation in Plants with Radionuclides

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Panel A shows radiolabeled sugar distribution throughout a poplar sapling. High sugar levels are red, and low levels are blue. Panel B shows greater sugar accumulation in the roots after the sapling's leaf is exposed to a hormone signaling attack.

Credit or Source: R. Ferrieri and M. Thorpe, Brookhaven National Laboratory

Citation(s):

US DOE. May 2010. Biological Systems Science Division: A Division of the U.S. Department of Energy Office of Biological and Environmental Research, US Department of Energy Office of Science. (p. 3a) (website)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/ and genomics.energy.gov/

Integrated Climate Science

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Credit or Source: Globe image courtesy of the National Center for Atmospheric Research

Citation(s):

US DOE. Climate Placemat: Energy-Climate Nexus, US Department of Energy Office of Science. (p. 1)

Prepared by the Biological and Enviornmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/ and genomics.energy.gov/

JGI Sequencing

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Dramatic Increase in Genome Sequencing Throughput. Over the past decade, new technologies have enabled an exponential increase in the generation, analysis, and comparison of sequencing datasets at the U.S. Department of Energy’s Joint Genome Institute (JGI) and other sequencing centers. Today, JGI generates petabytes of high-quality sequence and analysis data. [Image courtesy JGI]

Credit or Source: Office of Biological and Environmental Research of the U.S. Department of Energy Office of Science. science.energy.gov/ber/

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/.

Life in a Biofilm

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Life in a Biofilm. Most microbes live attached to solid surfaces (biotic or abiotic) within highly organized and functionally interactive communities called biofilms. These biofilms can be composed of populations that developed from a single species or a community derived from multiple species. All exhibit collective and interdependent behavior, with different genes rapidly brought into play as conditions dictate (see figure). Among the many advantages of biofilm living are nutrient availability with metabolic cooperation, acquisition of new genetic traits, and protection from the environment. Researchers are only beginning to realize the prevalence and significance of biofilms. These communities probably play major roles in such complex natural processes as the cycling of nitrogen and sulfur and the degradation of environmental pollutants and organic matter, activities that require a range of metabolic capabilities. Recent metagenomic and metaproteomic studies focused on biofilm members in an acid mine drainage environment. [Reference: M. E. Davey and G. A. O’Toole, “Microbial Biofilms: From Ecology to Molecular Genetics,” Microbiol. Mol. Biol. 64(4), 847–67 (2000).] Strength in Numbers. Microbes in biofilms live an interdependent, community-based existence (see accompanying text above). In this overhead view of an idealized biofilm, four microcolonies in the center of the figure represent organisms that both generate and consume hydrogen. Two participate in syntrophism, in which hydrogen producers use organic acids generated by fermenting organisms that gain their carbon and energy by using various sugars. In addition to potential metabolic interactions, signaling molecules may aid in inter- and intraspecies communication. These genetic factors and environmental influences contribute to the biofilms’ spatial organization. [Figure and caption adapted from Davey and O’Toole, 2000.] Quorum Sensing. Microbes communicate with each other by sending and detecting a wide variety of chemical signals (autoinducers). These molecules trigger group behaviors, including the formation and persistence of biofilms, symbiosis, and other processes. Many of these activities are density dependent, that is, when a threshold concentration of chemicals is detected (reflecting a certain number of cells), microbes respond with a change in gene expression. This process, called quorum sensing, facilitates coordination of gene expression by the entire community, in essence enabling it to behave like a multicellular organism. Quorum sensing allows microbial communities to adapt rapidly to environmental changes and reap benefits that would be unattainable as individuals. Quorum sensing first was described in the bioluminescent marine bacterium Vibrio fischeri. This microbe lives in symbiotic association with several marine animal hosts, who use the light it produces to attract prey, avoid predators, or find a mate. In exchange, V. fischeri obtains a nutrient-rich home environment. V. fischeri emits light only inside a specialized light organ of the host, where the concentration of these organisms becomes dense; it does not give off light when free living in the ocean. Light production depends on producing, accumulating, and responding to a minimum-threshold concentration of an autoinducer (acylated homoserine lactone). Only under the nutrient-rich conditions of the light organ can V. fischeri grow to such high populations. Also, trapping the diffusible autoinducer molecule in the light organ with the bacterial cells allows it to accumulate to a concentration sufficient for V. fisheri to detect it. Recent studies have revealed diverse chemical languages that enable bacterial communication both within and between species (the latter called cross talk). The extracellular matrix surrounding mature biofilms (composed of glycans and other components) plays a crucial role in transmitting these chemical signals into and between cells. Biotechnological researchers are developing molecules structurally related to autoinducers to exploit quorum-sensing capabilities and possibly improve industrial production of natural products. References J. W. Hastings and K. H. Nealson, “Bacterial Bioluminescence,” Annu. Rev. Microbiol. 31, 549–95 (1977). S. Schauder and B. L. Bassler, “The Language of Bacteria,” Genes Devel. 15, 1468–80 (2001).]

Credit or Source: Adapted from a drawing by M. E. Davey and G. A. O'Toole. Source: Genome Management Information System, Oak Ridge National Laboratory

Citation(s):

US DOE. 2005. Genomics:GTL Roadmap, DOE/SC-0090, U.S. Department of Energy Office of Science. (p. 18) (website)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/.

Metabolic Network Model for Escherichia coli

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Metabolic maps provide a framework for studying the consequences of genotype changes and the relationships between genotypes and phenotypes. This metabolic network model for Escherichia coli incorporated data on 436 metabolic intermediates undergoing 720 possible enzyme-catalyzed reactions. In this diagram, the circles contain abbreviated names of the metabolic intermediates, and the arrows represent enzymes. The very heavy lines indicate links with high metabolic fluxes. Analyses were correct 90% of the time in predicting the ability of 36 mutants with single-gene deletions to grow on different media. [adapted from J.S. Edwards and B.O. Palsson, Proc. Nat. Acad. Sci. 97, 5528­33 (2000)]

Credit or Source: Office of Biological and Environmental Research of the U.S. Department of Energy Office of Science. science.energy.gov/ber/

Citation(s):

Genomes to Life Program Roadmap, April 2001, DOE/SC-0036, U.S. Department of Energy Office of Science. (website)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/ and genomics.energy.gov/.

Metabolically Engineered Bacteria Produce Biodiesel

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To accelerate development of next-generation biofuels, researchers supported by the Department of Energy Office of Biological and Environmental Research are studying the biochemical pathways encoded in microbial genomes. Using this genomic information, researchers are developing new microbial systems that can produce biodiesel and other chemical replacements for petroleum products.

Credit or Source: Jonathan Remis, Joint BioEnergy Institute, Lawrence Berkeley National Laboratory

Citation(s):

US DOE. Genomics Placemat: Genomics for Energy and Environmental Science, US Department of Energy Office of Science. (p. 2) (website)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/ and genomics.energy.gov/.

Microarray

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Credit or Source: Office of Biological and Environmental Research of the U.S. Department of Energy Office of Science. science.energy.gov/ber/

Citation(s):

Genomes to Life Program Roadmap, April 2001, DOE/SC-0036, U.S. Department of Energy Office of Science. (website)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/ and genomics.energy.gov/.

Microbial Communities and Soil Carbon Cycling and Storage

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This conceptual diagram provides a framework for integrating genomic, transcriptomic, proteomic, and metabalomic information with biogeochemical process data to better understand the relationship between microbial communities and soil carbon cycling and storage. Arrows represent the flow of information (in red) or carbon (in blue) among components. Advanced understanding of the microbe-carbon relationship requires a comprehensive molecular characterization of intact soil microbial communities, including descriptions of actively expressed genes (transcriptome) and genomic potential. This effort could be guided by stable-isotopic targeting of soil microbes important in mediating specific carbon transformations in soil. Synthesis of this descriptive molecular data and environmental drivers will help create models of the mechanistic basis of gross community carbon processing and enable prediction and simulation of microbial community carbon processing under changing environmental conditions. More information regarding Key Research Questions noted on the figure can be found in the report on p. 39.

Credit or Source: Office of Biological and Environmental Research of the U.S. Department of Energy Office of Science. science.energy.gov/ber/

Citation(s):

U.S. DOE. 2008. Carbon Cycling and Biosequestration: Report from the March 2008 Workshop, DOE/SC-108, U.S. Department of Energy Office of Science. (p. 37) (website)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/ and genomics.energy.gov/.

Microbial Processes in Thawing Permafrost Soils

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By analyzing the DNA and proteins of microbial communities in Alaskan permafrost (permanently frozen soil), scientists can gain new insights into the biological mechanisms controlling some of the world’s greatest reservoirs of terrestrial carbon.

Credit or Source: Biological and Environmental Research Information System, Oak Ridge National Laboratory. Photograph from the DOE Atmospheric Radiation Measurement Climate Research Facility image library (http://www.flickr.com/photos/armgov/).

Citation(s):

US DOE. Genomics Placemat: Genomics for Energy and Environmental Science, US Department of Energy Office of Science. (p. 1) (website)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/ and genomics.energy.gov/.

Microfibril Structure

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Cellulose microfibrils are composed of linear chains of glucose molecules containing ß-1,4-linkages that hydrogen bond to form the microfibrils.

[Some images taken from "Genomics:GTL Transforming Cellulosic Biomass," U.S. Department of Energy Office of Science and Office of Energy Efficiency and Renewable Energy, June 2006, genomicscience.energy.gov/biofuels/ and U.S. DOE. 2006. "Breaking the Biological Barriers to Cellulosic Ethanol: A Joint Research Agenda," DOE/SC/EE-0095, U.S. Department of Energy Office of Science and Office of Energy Efficiency and Renewable Energy, genomicscience.energy.gov/biofuels/.]

Credit or Source: Office of Biological and Environmental Research of the U.S. Department of Energy Office of Science. science.energy.gov/ber/

Citation(s):

US DOE. May 2007. Biofuels Primer Placemat: From Biomass to Cellulosic Ethanol and Understanding Biomass: Plant Cell Walls, US Department of Energy Office of Science. (website)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/ and genomics.energy.gov/.

Miscanthus Growth over a Single Growing Season in Illinois

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Illinois. Miscanthus has been explored extensively as a potential energy crop in Europe and now is being tested in the United States. The scale is in feet. These experiments demonstrate results that are feasible in development of energy crops.

Credit or Source: S. Long, University of Illinois

Citation(s):

U.S. DOE. 2006. Breaking the Biological Barriers to Cellulosic Ethanol: A Joint Research Agenda, DOE/SC/EE-0095, U.S. Department of Energy Office of Science and Office of Energy Efficiency and Renewable Energy. (p. 7) (website)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/.

Molecular Machines of Life

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Proteasome: Breaking down unneeded proteins is accomplished by the orderly action of several multiprotein complexes. At the heart of this process is a multiprotein complex called the proteasome. Dynein Complex: An entirely different class of molecular machines functions as motors, converting chemical energy into mechanical motion, both linear and rotary. The dynein motor, a cellular complex believed to be composed of 12 distinct protein parts, performs fundamental transportation tasks critical to the cell; defects in its structure can prove fatal.

Credit or Source: Office of Biological and Environmental Research of the U.S. Department of Energy Office of Science. science.energy.gov/ber/

Citation(s):

Genomes to Life Program Roadmap, April 2001, DOE/SC-0036, U.S. Department of Energy Office of Science. (website)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/ and genomics.energy.gov/.

Molecular structure of a transfer ribonucleic acid (tRNA).

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Single-stranded ribonucleic acid (RNA) can fold up and twist to form 3-D structures like this transfer RNA (tRNA). During protein synthesis, tRNA binds and delivers an amino acid to the ribosome, which adds the amino acid to the growing protein chain.

Credit or Source: Protein Data Bank (www.rcsb.org) PDB ID 4TNA visualized using iMol

Citation(s):

US DOE. Genomics Placemat: Genomics for Energy and Environmental Science, US Department of Energy Office of Science. (p. 2) (website)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/ and genomics.energy.gov/.

Molecular Structures

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Nitrogenase complex with the Fe protein bound to the MoFe protein.

Credit or Source: Lawrence Berkeley National Laboratory

Citation(s):

US DOE. 2013. DOE User Facilities Advanced Technologies for Biology: Synchrotron and Neutron Beam Facilities Accelerating Biological Research, US Department of Energy Office of Science. (p. 8)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/.

Mouse and Human Genetic Similarities

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This figure demonstrated the genetic similarity (homology) of the superficially dissimilar mouse and human species. The similarity is such that human chromosomes can be cut (schematically at least) into about 150 pieces (only about 100 are large enough to appear here), then reassembled into a reasonable approximation of the mouse genome. The colors and corresponding numbers on the mouse chromosomes indicate the human chromosomes containing homologous segments.

Credit or Source: Lawrence Livermore National Laboratory

Citation(s):

Human Genome Program, U.S. Department of Energy, Human Genome Program Report, 1997. (website)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/.

Mouse and Human Genetic Similarities (Vertical Orientation)

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This figure demonstrated the genetic similarity (homology) of the superficially dissimilar mouse and human species. The similarity is such that human chromosomes can be cut (schematically at least) into about 150 pieces (only about 100 are large enough to appear here), then reassembled into a reasonable approximation of the mouse genome. The colors and corresponding numbers on the mouse chromosomes indicate the human chromosomes containing homologous segments.

Credit or Source: Lawrence Livermore National Laboratory

Citation(s):

Human Genome Program, U.S. Department of Energy, Human Genome Program Report, 1997. (website)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/.

Multinetwork Analysis of a Carbon- and Nitrogen-Responsive Metabolic Regulatory Network

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An Arabidopsis multinetwork (Gutiérrez et al. 2007) was used to generate a regulatory network consisting of metabolic genes (blue hexagons) regulated by carbon, light, and nitrogen treatments. This predicted metabolic regulatory network, containing genes involved in energy metabolism and amino acid biosynthesis, is connected by several transcription factors (green diamonds) that may act as network hubs to coordinate regulation of carbon and nitrogen metabolic genes. The processes associated with nonmetabolic genes, also potentially regulated by these transcription factors, are listed in colored ovals; numbers of genes within each category are shown in parentheses. Importantly, these genes include some of unknown function, which can now be associated with nitrogen regulatory networks. [Source: Gifford, M. L., R. A. Gutiérrez, and G. M. Coruzzi. 2006. "Modeling the Virtual Plant: A Systems Approach to Nitrogen-Regulatory Gene Networks," Essay 12.2, Chapter 12: Assimilation of mineral nutrients. 6e.plantphys.net. In A Companion to Plant Physiology, Fourth Edition by Lincoln Taiz and Eduardo Zeiger. Sinauer Associates, Inc., Publishers, Sunderland, Mass. (See also www.virtualplant.bio.nyu.edu and Gutiérrez, R. A., et al. 2007.)]

Credit or Source: Office of Biological and Environmental Research of the U.S. Department of Energy Office of Science. science.energy.gov/ber/

Citation(s):

U.S. DOE. 2008. Carbon Cycling and Biosequestration: Report from the March 2008 Workshop, DOE/SC-108, U.S. Department of Energy Office of Science. (p. 57) (website)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/ and genomics.energy.gov/.

Multiscalar Energy-Land-Water Interactions

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Energy sustainability is multiscalar, involving energy-land-water interactions at scales ranging from cellular to global. Interactions within and among scales largely will define the resiliency of different energy sustainability strategies; thus, questions must be scale aware and answers appropriately scalable.

Credit or Source: Office of Biological and Environmental Research of the U.S. Department of Energy Office of Science. science.energy.gov/ber/

Citation(s):

BERAC. 2017. Grand Challenges for Biological and Environmental Research: Progress and Future Vision; A Report from the Biological and Environmental Research Advisory Committee, DOE/SC–0190, BERAC Subcommittee on Grand Research Challenges for Biological and Environmental Research (science.energy.gov/~/media/ber/berac/pdf/Reports/ BERAC-2017-Grand-Challenges-Report.pdf). (p. 58) (PDF)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/.

Multiscale Explorations for Systems Understanding

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Achieving a predictive understanding of fundamental life processes requires investigations that span multiple levels, from the information encoded in individual plant and microbial genomes to the functioning of cells as communities in an ecosystem. Important to this challenge is understanding the complex interactions between each level of biological organization and the environment.

Credit or Source: Office of Biological and Environmental Research of the U.S. Department of Energy Office of Science. science.energy.gov/ber/

Citation(s):

U.S. DOE. 2019. DOE Genomic Science Program: Systems Biology for Energy and the Environment, US Department of Energy Office of Science. (PDF)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/.

New Cellulase Enzymes Dramatically Reduce Costs of Plant Biomass Breakdown: R&D 100 Award

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Further Advances Needed to Improve Efficiency and Economics. Cellulase enzymes are used to break down the cellulose of plant cell walls into simple sugars that can be transformed (fermented) by microbes to fuels, primarily ethanol, as well as to chemicals, plastics, fibers, detergents, pharmaceuticals, and many other products.Like starch and sugar, cellulose is a carbohydrate (compound of carbon, hydrogen, and oxygen) made up of simple sugars (glucose) linked together in long chains called polysaccharides. These polymers form the structural portion of plant cell walls, and unraveling them is the key to economical ethanol fermentation. Technical barriers to large-scale use of cellulose technology include the low specific enzyme activity and high enzyme-production costs, as well as a general lack of understanding about enzyme biochemistry and mechanistic fundamentals. In 2004, the DOE National Renewable Energy Laboratory (NREL), working with two of the largest industrial enzyme producers (Genencor International and Novozymes Biotech), achieved a dramatic reduction in cellulase enzyme costs. Cellulases belong to a group of enzymes known as glycosyl hydrolases, which break (hydrolyze) bonds linking a carbohydrate to another molecule. The new technology involves a cocktail of three types of cellulases—endoglucanases, exoglucanases, and beta-glucosidases. These enzymes work together to attack cellulose chains, pulling them away from the crystalline structure and breaking off cellobiose molecules (two linked glucose residues), splitting them into individual glucose molecules, and making them available for further processing. This breakthrough work resulted in 20- to 30-fold cost reduction and earned NREL and collaborators an R&D 100 Award. Further cost reductions are required, however, to support an economical and robust cellulose biorefinery industry. For example, costs of amylase enzymes for converting corn grain starch to ethanol are about 1 to 2 cents per gallon of ethanol produced, but the most optimistic cost estimates for cellulase preparations now are about tenfold higher than that. Routes to improving enzyme efficiencies include the development of enzymes with more heat tolerance and higher specific activities, better matching of enzymes and plant cell-wall polymers, and development of high-solid enzymatic hydrolysis to lower capital costs. A comprehensive understanding of the structure and function of these enzymatic protein machines, how their production and activity are controlled, and changes they promote on plant cell-wall surfaces will be critical for success.

Credit or Source: Cellulase image from M. Himmel et al., Cellulase Animation, run time 11 min., National Renewable Energy Laboratory (2000).

Citation(s):

U.S. DOE. 2006. Breaking the Biological Barriers to Cellulosic Ethanol: A Joint Research Agenda, DOE/SC/EE-0095, U.S. Department of Energy Office of Science and Office of Energy Efficiency and Renewable Energy. (p. 27) (website)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/.

Nitrogen Cycle

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Credit or Source: Office of Biological and Environmental Research of the U.S. Department of Energy Office of Science. science.energy.gov/ber/

Citation(s):

U.S. DOE. 2008. Carbon Cycling and Biosequestration: Report from the March 2008 Workshop, DOE/SC-108, U.S. Department of Energy Office of Science. (p. 41) (website)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/ and genomics.energy.gov/.

Oceanic Food Web

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Microscopic plants and other photosynthetic organisms that drift with ocean currents lie at the heart of the marine carbon cycle. Sunlit surface waters teem with phytoplankton that convert inorganic carbon dissolved in surface waters to organic carbon, which forms the basis of the marine food web, and account for about half of all primary production on Earth (Field et al. 1998; Falkowski, Barber, and Smetacek 1998). In contrast to terrestrial carbon-turnover times that may take months to years, carbon cycles rapidly in oceans, with the entire phytoplankton population in some environments replacing itself weekly (Falkowski 2002). Phytoplankton are grazed upon by marine heterotrophs known as zooplankton. These grazer species range from microscopic protozoa and copepods to worms, krill, crabs, jellyfish, and the larvae of fish and other organisms. Comprising most of the animal mass in the ocean, zooplankton serve as the crucial link between primary producers and the rest of the marine food web. Viruses, which act as predators in oceanic food chains by infecting and lysing marine bacteria, also play an important but still poorly understood role in marine carbon turnover. The overall efficiency with which organic carbon is exported to the deep ocean depends on the type of photoautotrophic cells that create the organic material and the efficiency with which heterotrophic organisms respire it.

Carbon Flow and Fate

Carbon fixed in phytoplankton eventually enters the water column as either particulate or dissolved organic carbon through direct exudation, consumption by grazing zooplankton, viral lysis, or cell death. Subsequently, most of this carbon material is degraded by heterotrophic bacteria, resulting in particulate solubilization and conversion of organic carbon back to CO2. Some of the organic matter, however, sinks intact to the underlying twilight zone (the ocean's barely lit middle layer) and beyond, where lower temperatures, lack of oxygen, and other factors significantly slow degradation. CO2 fixed during photosynthesis by phytoplankton in the upper ocean can be transferred to the depths via three major processes: passive sinking of particles, physical mixing of particulates and dissolved organic matter through currents, and active transport by zooplankton migrating to deeper waters. Detrital particles and organic matter associated with mineral structures from phytoplankton, for example, may resist rapid microbial degradation and sift down as flakes, also called marine snow, becoming platforms for microbes to live on. As this particulate organic matter falls deeper, it can cluster with other small particles, such as zooplankton fecal pellets, molts, and larvacean houses, to form larger, heavier aggregates held together by a polysaccharide matrix. The carbon in these particles can be isolated from exchange with the atmosphere for centuries to millennia before upwelling currents return it and other nutrients from the deep ocean to warm surface waters. Some carbon is lost at each step of the way, however, as the organisms involved consume or degrade the organic carbon and remineralize it to CO2 through respiration. However, if climate change and ocean acidification significantly alter marine ecosystems' functions, the efficiency of this biologically mediated ocean carbon export may change, leading to an indirect effect on the net annual uptake of carbon.

References:

Falkowski, P. G. 2002. "The Ocean's Invisible Forest: Marine Phytoplankton Play a Critical Role in Regulating the Earth's Climate. Could They Also be Used to Combat Global Warming?" Scientific American 287(2), 54-61.

Falkowski, P. G., R. T. Barber, and V. Smetacek. 1998. "Biogeochemical Controls and Feedbacks on Ocean Primary Production," Science 281(5374), 200-06.

Field, C. B., et al. 1998. "Primary Production of the Biosphere: Integrating Terrestrial and Oceanic Components," Science 281(5374), 237-40.

Credit or Source: Office of Biological and Environmental Research of the U.S. Department of Energy Office of Science. science.energy.gov/ber/

Citation(s):

U.S. DOE. 2008. Carbon Cycling and Biosequestration: Report from the March 2008 Workshop, DOE/SC-108, U.S. Department of Energy Office of Science. (p. 81) (website)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/ and genomics.energy.gov/.

Overview of Plant Cell Walls

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Plants can have two types of cell walls, primary and secondary. Primary cell walls contain cellulose consisting of hydrogen-bonded chains of thousands of glucose molecules, (Containing β-1,4-linkages) in addition to hemicellulose and other materials all woven into a network. Certain types of cells, such as those in vascular tissues, develop secondary walls inside the primary wall after the cell has stopped growing. These cell-wall structures also contain lignin, which provides rigidity and resistance to compression. The area formed by two adjacent plant cells, the middle lamella, typically is enriched with pectin. Figure adapted from L. Taiz and E. Zeiger, Plant Physiology (1991).

[Some images taken from "Genomics:GTL Transforming Cellulosic Biomass," U.S. Department of Energy Office of Science and Office of Energy Efficiency and Renewable Energy, June 2006, genomicscience.energy.gov/biofuels/ and U.S. DOE. 2006. "Breaking the Biological Barriers to Cellulosic Ethanol: A Joint Research Agenda," DOE/SC/EE-0095, U.S. Department of Energy Office of Science and Office of Energy Efficiency and Renewable Energy, genomicscience.energy.gov/biofuels/.]

Credit or Source: Office of Biological and Environmental Research of the U.S. Department of Energy Office of Science. science.energy.gov/ber/

Citation(s):

US DOE. May 2007. Biofuels Primer Placemat: From Biomass to Cellulosic Ethanol and Understanding Biomass: Plant Cell Walls, US Department of Energy Office of Science. (website)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/ and genomics.energy.gov/.

Pathway Kinetics

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The pathway kinetics model depicts the mechanisms of the "decision circuit" that commits a bacterial virus [lambda] to one of two alternate pathways in its life cycle. The lytic path sets the stage for immediate replication of the virus and destruction of its Escherichia coli host cell, while the lysogenic path selects for the incorporation of viral DNA into the host genome, allowing the virus to remain in a dormant state. In the diagram, bold horizontal lines indicate stretches of double-stranded DNA, arrows over genes show the transcription direction, and dashed boxes enclose operator sites that comprise a promoter control complex. The core of the decision circuit is the four-promoter, five-gene regulatory network; initiation of pathway actions involve other coupled genes not shown. Many pathogenic organisms use a similar mechanism of concentration-independent probabilistic pathway selection to switch surface features and evade host responses. In the model above, pathway selection at different virus concentrations, predicted using a kinetic model of the genetic regulatory circuit, is consistent with experimental observations. Developing this model required nearly 40 empirical rate constants and the use of a supercomputer.

Credit or Source: Adapted from A. Arkin, J. Ross, and H. H. McAdams, Genetics 149, 1633-48 (1998). Credit or Source: Office of Biological and Environmental Research of the U.S. Department of Energy Office of Science. science.energy.gov/ber/

Citation(s):

Genomes to Life Program Roadmap, April 2001, DOE/SC-0036, U.S. Department of Energy Office of Science. (website)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/ and genomics.energy.gov/.

Photosynthesis Production of Hydrogen from Water

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An overview of steps involved in using light energy to produce carbohydrates or hydrogen is depicted in this figure and described below. 1. Light Absorption by Photosystem II (PSII) Initiates the Photosynthetic Pathway. PSII is a large molecular complex that contains several proteins and light-absorbing pigment molecules. The primary pigment molecules are chlorophylls and carotenoids, but cyanobacteria also have other pigments called phycobilins that absorb light at different wavelengths. The pigments are bound to proteins to form antenna complexes that absorb photons and transfer the resultant excitation energy to the reaction center of PSII, where energized electrons move to a small electron-carrier molecule. This molecule shuttles the excited electrons to the next complex in the photosynthetic electron-transport chain. To replace electrons lost in the transfer, the reaction center strips low-energy electrons from two water molecules, releasing four protons and an oxygen (O2) molecule into the thylakoid space. 2. Electron Transport Through the Cytochrome Complex Generates a Proton Gradient. The electron carrier from PSII passes through the thylakoid membrane and transfers its electrons to the cytochrome complex, which consists of several subunits including cytochrome f and cytochrome b6. A series of redox reactions within the complex ultimately transfer the electrons to a second electron carrier that acts as a shuttle to photosystem I (PSI). As electrons are transported through the complex, protons (H+) outside the thylakoid are carried to the inner thylakoid space. The increase in proton concentration inside the thylakoid space creates a proton gradient across the thylakoid membrane. 3. Light Absorption by PSI Excites Electrons and Facilitates Electron Transfer to an Electron Acceptor Outside the Thylakoid Membrane. PSI is another large protein-pigment complex that contains lightabsorbing antenna molecules and a reaction center. Light absorbed by the PSI reaction center energizes an electron that is transferred to ferredoxin (Fd), a molecule that carries electrons to other reaction pathways outside the thylakoid. The reaction center replaces the electron transferred to ferredoxin by accepting an electron from the electron-carrier molecule that moves between the cytochrome complex and PSI. 4. Under Certain Conditions, Ferredoxin can Carry Electrons to Hydrogenase. Normally, ferredoxin shuttles electrons to an enzyme that reduces NADP+ to NADPH, an important source of electrons needed to convert CO2 to carbohydrates in the carbon-fixing reactions. Under anaerobic conditions, hydrogenase can accept electrons from reduced ferredoxin molecules and use them to reduce protons to molecular hydrogen (H2). 5.Dissipation of Proton Gradient is Used to Synthesize Adenosine Triphosphate (ATP). ATP synthase couples the dissipation of the proton gradient generated in step 2 to the synthesis of ATP. Translocation of protons from a region of high concentration (thylakoid space) to a region of low concentration (outside thylakoid) releases energy that can be used to drive the synthesis of ATP from adenosine diphosphate (ADP) and phosphate (P). ATP is a high-energy molecule used to convert CO2 to carbohydrates in the carbon-fixing reactions.

Credit or Source: Office of Biological and Environmental Research of the U.S. Department of Energy Office of Science. science.energy.gov/ber/

Citation(s):

US DOE. 2005. Genomics:GTL Roadmap, DOE/SC-0090, U.S. Department of Energy Office of Science. (p. 211) (website)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/.

Pine Feedstocks

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Field trial of pine feedstocks population used in genome-wide selection project.

Credit or Source: Matias Kirst, University of Florida, Gainesville

Citation(s):

US DOE, USDA. 2014. Plant Feedstock Genomics for Bioenergy Joint Awards 2006–2014, U.S. Departments of Agriculture and Energy. (p. 3) (PDF)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/.

Poplar Trees

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Poplar Tree Offers Potential for Greater Carbon Storage An international team including the DOE Joint Genome Institute recently sequenced the genome of the black cottonwood or poplar tree (Populus). This research could be used to improve tree breeding and forest management practices that would enable significant quantities of carbon to be sequestered by this and, eventually, other trees. In addition, a significant fraction of carbon associated with a stand of trees is in soil organic-matter pools rather than in aboveground biomass or living roots. The poplar genome sequence information might be used to develop ways to enhance both the production and translocation of organic compounds from leaves and shoots to roots and soil, where it might lead to longterm storage of carbon. In addition to carbon storage, poplar produces products and services of considerable value to humans and many ecosystems. Moreover, poplar trees are highly productive in many environments and have a wide ecological range or distribution.

Credit or Source: Oak Ridge National Laboratory

Citation(s):

US DOE. 2005. Genomics:GTL Roadmap, DOE/SC-0090, U.S. Department of Energy Office of Science. (p. 237) (website)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/.

Pretreatment

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[Some images taken from "Genomics:GTL Transforming Cellulosic Biomass," U.S. Department of Energy Office of Science and Office of Energy Efficiency and Renewable Energy, June 2006, genomicscience.energy.gov/biofuels/ and U.S. DOE. 2006. "Breaking the Biological Barriers to Cellulosic Ethanol: A Joint Research Agenda," DOE/SC/EE-0095, U.S. Department of Energy Office of Science and Office of Energy Efficiency and Renewable Energy, genomicscience.energy.gov/biofuels/.]

Credit or Source: Figure adapted from N. Mosier et al. 2005. “Features of Promising Technologies for Pretreatment of Lignocellulosic Biomass,” Bioresource Technology 96(3), 673-86, by the Biological and Environmental Research Information System on behalf of the Office of Biological and Environmental Research of the U.S. Department of Energy Office of Science. science.energy.gov/ber/

Citation(s):

US DOE. May 2007. Biofuels Primer Placemat: From Biomass to Cellulosic Ethanol and Understanding Biomass: Plant Cell Walls, US Department of Energy Office of Science. (website)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/ and genomics.energy.gov/.

Probing Microbial Communities

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Microbial communities and ecosystems must be probed at the environmental, community, cellular, subcellular, and molecular levels. The environmental structure of a community will be examined to define members and their locations, community dynamics, and structure-function links. Cells will be explored to detect and track both extra- and intercellular states and to determine the dynamics of molecules involved in intercellular communications. Probing must be done at the subcellular level to detect, localize, and track individual molecules. Preferably, measurements will be made in living systems over extended time scales and at the highest resolution. A number of techniques are emerging to address these demanding requirements; a brief listing is on the right side of the figure.

Credit or Source: Biological and Environmental Research Information System, Oak Ridge National Laboratory. Sponsored by the U.S. Department of Energy Biological and Environmental Research Program.

Citation(s):

U.S. DOE. 2006. Breaking the Biological Barriers to Cellulosic Ethanol: A Joint Research Agenda, DOE/SC/EE-0095, U.S. Department of Energy Office of Science and Office of Energy Efficiency and Renewable Energy. (p. 165) (website)

US DOE. 2005. Genomics:GTL Roadmap, DOE/SC-0090, U.S. Department of Energy Office of Science. (p. 176) (website)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/.

Processes of the Terrestrial Carbon Cycle

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Credit or Source: Office of Biological and Environmental Research of the U.S. Department of Energy Office of Science. science.energy.gov/ber/

Citation(s):

U.S. DOE. 2014. DOE Genomic Science Program: Mission-Driven Systems Biology. 2014 Strategic Plan. U.S. Department of Energy Office of Science. (p. 11) (website)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/.

Proteasome

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Breaking down unneeded proteins is accomplished by the orderly action of several multiprotein complexes. At the heart of this process is a multiprotein complex called the proteasome. These machines of destruction consist of a tunnel-like core with a cap at either or both ends. The core is formed by four stacked rings surrounding a central channel that acts as a degradation chamber. The caps recognize and bind to proteins targeted by the cell for destruction, then use chemical energy to unfold the proteins and inject them into the central core, where they are broken into pieces. This is a fundamental kind of machine that has been highly conserved during evolution. Some form of it is found in organisms ranging from simple bacteria to humans.

Credit or Source: Office of Biological and Environmental Research of the U.S. Department of Energy Office of Science. science.energy.gov/ber/

Citation(s):

Genomes to Life Program Roadmap, April 2001, DOE/SC-0036, U.S. Department of Energy Office of Science. (website)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/ and genomics.energy.gov/.

Protein Complex

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Proteins rarely solo. More often, they work by assembling into larger multiprotein complexes, some of which have the characteristics of rather complicated protein "machines." These machines, in turn, execute such major functions as protein synthesis and degradation, cell-to-cell signaling, and a host of other operations. The properties of each kind of protein, which cause it to assemble with others into machines and to execute very specific and critical reactions in the cell, are the direct consequence of the protein's amino acid sequence that dictates its final structure.

Credit or Source: Office of Biological and Environmental Research of the U.S. Department of Energy Office of Science. science.energy.gov/ber/

Citation(s):

Genomes to Life Program Roadmap, April 2001, DOE/SC-0036, U.S. Department of Energy Office of Science. (website)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/ and genomics.energy.gov/.

Protein Machines

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Genomes are "brought to life" by being read out or "expressed" according to a complex set of directions embedded in the DNA sequence. The products of expression are proteins that do essentially all the work of the cell: they build cellular structures, digest nutrients, execute other metabolic functions, and mediate much of the information flow within a cell and among cellular communities. To accomplish these tasks, proteins typically work together with other proteins or nucleic acids as multicomponent "molecular machines" -- structures that fit together and function in highly specific, lock-and-key ways.

Credit or Source: Office of Biological and Environmental Research of the U.S. Department of Energy Office of Science. science.energy.gov/ber/

Citation(s):

Genomes to Life Program Roadmap, April 2001, DOE/SC-0036, U.S. Department of Energy Office of Science. (website)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/ and genomics.energy.gov/.

RAD Complex

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MolScript v1.4 (C) 1993 Per Kraulis (Raster3D support E A Merritt 1993)The role of the Rad checkpoint complex was inferred from the 3-D structure predicted by comparative modeling at Lawrence Livermore National Laboratory. The Rad complex delays cell division to allow time for DNA repair to take place.

Credit or Source: Lawrence Livermore National Laboratory

Citation(s):

Genomes to Life Program Roadmap, April 2001, DOE/SC-0036, U.S. Department of Energy Office of Science. (website)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/.

Reduced Carbon Dioxide Emissions by Ethanol from Biomass

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When compared with gasoline, ethanol from cellulosic biomass could dramatically reduce emissions of the greenhouse gas carbon dioxide (CO2). Although burning gasoline and other fossil fuels increases atmospheric CO2 concentrations, the photosynthetic production of new biomass takes up most of the carbon dioxide released when bioethanol is burned.

Credit or Source: Adapted from ORNL Review https://www.ornl.gov/content/ornl-review-v33n2

Citation(s):

US DOE. June 2007. Biofuels: Bringing Biological Solutions to Energy Challenges, US Department of Energy Office of Science. (PDF)

U.S. DOE. 2006. Breaking the Biological Barriers to Cellulosic Ethanol: A Joint Research Agenda, DOE/SC/EE-0095, U.S. Department of Energy Office of Science and Office of Energy Efficiency and Renewable Energy. (p. 7) (website)

Prepared by the Biological and Enviornmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/

Rhizosphere Consortia

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As the roots of Avena fatua push through soil to acquire nutrients and water, they also provide carbon to a complex microbial community inhabiting the soil environment adjacent to the plant roots.

Credit or Source: E. Nuccio, Lawrence Livermore National Laboratory

Citation(s):

U.S. DOE. 2014. Research for Sustainable Bioenergy: Linking Genomic and Ecosystem Sciences, Workshop Report, DOE/SC-0167. U.S. Department of Energy Office of Science. genomicscience.energy.gov/sustainability/. (p. 15) (PDF)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/.

RuBisCO Carbon-Fixation Enzyme

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RuBisCO has an active site (binding pocket) that binds ribulose-1,5-bisphosphate (RuBP) and catalyzes the reaction between RuBP and CO2 or O2. In the figure, the two large RuBisCO subunits (blue and cyan) sandwich an RuBP molecule (orange) in the active site. The site is gated by the C-terminus (yellow), lysine 128 (purple), and loop 6 (green), which undergo periodic conformational changes that open or close the site. Reactants enter and products escape while it is in an open state, and carbon- fixation reactions occur during the closed state. Simulations of this gating mechanism allow predictions of the gating rate, which can be linked to RuBisCO performance characteristics.

GTL research teams led by Sandia National Laboratories and Oak Ridge National Laboratory are developing new experimental and computational tools to investigate carbon-sequestration behavior in marine cyanobacteria, in particular, Synechococcus and Synechocystis. These abundant marine microbes are known to play an important role in the global carbon cycle. Whole-cell imaging using a newly developed 3D hyperspectral microscope enabled researchers to detect the distribution of photosynthetic pigments in individual Synechocystis cells. The GTL team also improved the quality and information content in DNA microarray technology by combining hyperspectral imaging technology and patented multivariate statistical analysis. The new system collects a full fluorescence emission spectrum at each pixel, as compared to the single bands of a spectrum collected by current scanners. All relevant wavelengths of light thus are measured at each point across a surface rather than simply at predefined bands of wavelengths. This approach enables the identification, modeling, and correction of gene expressions for unknown and unanticipated emissions; increases throughput by accommodating many spectrally overlapped labels in a single scan; and improves sensitivity, accuracy, dynamic range, and reliability. The scanner is being modified to allow 3D imaging of many fluorescently tagged molecules in cells and tissues. New massively parallel modeling and simulation tools also developed by the team have yielded structural insight into the specificity of RuBisCO, an enzyme central to photosynthetic carbon fixation. The team also developed the computational capability to track spatial and temporal variations in protein species concentrations in realistic cellular geometries for important cyanobacterial subcellular processes. These tools include the Large-Scale Atomic/Molecular Massively Parallel Simulator (LAMMPS, https://lammps.sandia.gov/), a molecular simulation tool; and ChemCell, a whole-cell modeling tool that captures those and other results into a spatially realistic metabolic pathway simulation. LAAMPS enables investigations of the protein-sequence effect on different RuBisCO specificities and reaction rates in various species. Using this tool, researchers discovered that mutations in RuBisCO’s amino acid sequence substantially altered the free-energy barrier for gating the binding pocket. This result provided a molecular-level explanation for the experimentally observed species variations in RuBisCO performance (see illustration). LAMMPS was released as open-source software in September 2004 and was downloaded over 4000 times to June 2005. Via 3D simulations of diffusion and reaction in realistic geometries, ChemCell captured the carbon-fixation process carried out by RuBisCO in the carboxysome, a subcellular organelle. [Grant Heffelfinger, Sandia National Laboratories.]

Reference: M. B. Sinclair et al., “Design, Construction, Characterization, and Application of a Hyperspectral Microarray Scanner,” Appl. Optics 43, 2079–88 (2004).

Credit or Source: Paul Crozier, Sandia National Labs

Citation(s):

US DOE. 2005. Genomics:GTL Roadmap, DOE/SC-0090, U.S. Department of Energy Office of Science. (p. 66) (website)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/.

Scale of Decimal Units

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Scale of decimal units covered in Genomics:GTL Roadmap

Credit or Source: Office of Biological and Environmental Research of the U.S. Department of Energy Office of Science. science.energy.gov/ber/

Citation(s):

US DOE. 2005. Genomics:GTL Roadmap, DOE/SC-0090, U.S. Department of Energy Office of Science. (website)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/ and genomics.energy.gov/.

Scales and Processes of the Global Carbon Cycle

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The global carbon cycle is determined by the interactions of climate, the environment, and Earth’s living systems at many levels, from molecular to global. Relating processes, phenomena, and properties across spatial and temporal scales is critical for deriving a predictive mechanistic understanding of the global carbon cycle to support more precise projections of climate change and its impacts. Each domain of climate, ecosystem, and molecular biology research has a limited reach in scales, constrained by the complexity of these systems and limitations in empirical and modeling capabilities. While comprehensive linkage of genomes to global phenomena is intractable, many insightful connections at intermediate scales are viable with integrated application of new systems biology approaches and powerful analytical and modeling techniques at the physiological and ecosystem levels. Biological responses (blue) are to the right of the systems ovals, and climate and environmental factors (green) are to the left of the systems ovals.

Credit or Source: Office of Biological and Environmental Research of the U.S. Department of Energy Office of Science. Globe portion of figure courtesy of Gary Strand, National Center for Atmospheric Research, with funding from the National Science Foundation and the Department of Energy. science.energy.gov/ber/

Citation(s):

U.S. DOE. 2009. U.S. Department of Energy Office of Science Systems Biology Knowledgebase for a New Era in Biology: A Genomics:GTL Report from the May 2008 Workshop, DOE/SC-113, U.S. Department of Energy Office of Science. (p. 11) (website)

U.S. DOE. 2008. Carbon Cycling and Biosequestration: Report from the March 2008 Workshop, DOE/SC-108, U.S. Department of Energy Office of Science. (p. 16) (website)

U.S. DOE. 2015. Office of Biological and Environmental Research Molecular Science Challenges; Workshop Report, DOE/SC-0172, U.S. Department of Energy Office of Science. (website)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/.

Scanning Electron Microscopy: (a) Enzyme Hydrolysis Only

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(a) A corn stover particle shows a smooth surface with a few micron-sized pores after enzyme hydrolysis converted 11% of cellulose to glucose in 3 h. (b) This corn stover particle has many more pores. It was pretreated in water at 190°C for 15 min and hydrolyzed by enzymes at 50°C for 3 h, resulting in 40% cellulose conversion to glucose. The results illustrate that pretreatment changes lignocellulosic-structure susceptibility to attack by enzymes. Higher resolution in future imaging techniques will facilitate a deeper understanding of underlying molecular mechanisms.

Credit or Source: Images and conditions from unpublished work of M. Zeng, N. Mosier, C. Huang, D. Sherman, and M. Ladisch, 2006.

Citation(s):

U.S. DOE. 2006. Breaking the Biological Barriers to Cellulosic Ethanol: A Joint Research Agenda, DOE/SC/EE-0095, U.S. Department of Energy Office of Science and Office of Energy Efficiency and Renewable Energy. (p. 88) (website)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/.

Scanning Electron Microscopy: (b) Enzyme Hydrolysis Following Pretreatment

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(a) A corn stover particle shows a smooth surface with a few micron-sized pores after enzyme hydrolysis converted 11% of cellulose to glucose in 3 h. (b) This corn stover particle has many more pores. It was pretreated in water at 190°C for 15 min and hydrolyzed by enzymes at 50°C for 3 h, resulting in 40% cellulose conversion to glucose. The results illustrate that pretreatment changes lignocellulosic-structure susceptibility to attack by enzymes. Higher resolution in future imaging techniques will facilitate a deeper understanding of underlying molecular mechanisms.

Credit or Source: Images and conditions from unpublished work of M. Zeng, N. Mosier, C. Huang, D. Sherman, and M. Ladisch, 2006.

Citation(s):

U.S. DOE. 2006. Breaking the Biological Barriers to Cellulosic Ethanol: A Joint Research Agenda, DOE/SC/EE-0095, U.S. Department of Energy Office of Science and Office of Energy Efficiency and Renewable Energy. (p. 88) (website)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/.

SNPs: Single Nucleotide Polymorphisms

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Slight variations in our DNA sequences can have a major impact on whether or not we develop a disease and on our particular responses to such environmental insults as bacteria, viruses, and toxins. They also impact our reactions to drugs and other therapies. One of the most common types of sequence variation is the single nucleotide polymorphism (SNP). SNPs are sites in the human genome where individuals differ in their DNA sequence, often by a single base. For example, one person might have the base A (adenine) where another might have C (cytosine), and so on. Researchers in public and private sectors are generating maps of these sites, which can occur in genes as well as in noncoding regions. Scientists believe such SNP maps will help them identify the multiple genes associated with such complex diseases as cancer, diabetes, vascular disease, and some forms of mental illness. SNP maps provide valuable targets for biomedical and pharmaceutical research.

Credit or Source: Office of Biological and Environmental Research of the U.S. Department of Energy Office of Science. science.energy.gov/ber/

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/ and genomics.energy.gov/.

Social Issues

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The human genome provides researchers insight into individual and family medical histories and may help predict future risks. This raises a number of issues including: Who owns genetic information? Who should have access to an individual's genetic information? Do genes control behavior? How should genetic information be used in reproductive decisions? How does personal genetic information affect self-identity and society's perceptions? and many more. Because all these new issues are arising, the U.S. Department of Energy (DOE) and the National Institutes of Health (NIH) have devoted 3% to 5% of their annual Human Genome Project (HGP) budgets toward studying the ethical, legal, and social issues (ELSI) surrounding availability of genetic information. This represents the world's largest bioethics program, which has become a model for ELSI programs around the world.

Credit or Source: Office of Biological and Environmental Research of the U.S. Department of Energy Office of Science. science.energy.gov/ber/

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/ and genomics.energy.gov/.

Some Metabolic Pathways that Impact Glucose Fermentation to Ethanol

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This pathway map demonstrates the complexity of even a simple, widely utilized, and relatively well understood process such as glucose fermentation to ethanol. Glucose and ethanol are identified.

Credit or Source: E. Gasteiger et al., “Expasy: The Proteomics Server for In-Depth Protein Knowledge and Analysis,” Nucleic Acids Res. 31, 3784–88 (2003). Screenshot source: web.expasy.org/pathways/

Citation(s):

U.S. DOE. 2006. Breaking the Biological Barriers to Cellulosic Ethanol: A Joint Research Agenda, DOE/SC/EE-0095, U.S. Department of Energy Office of Science and Office of Energy Efficiency and Renewable Energy. (p. 128) (website)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/.

Sorghum

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Credit or Source: Lawrence Berkeley National Laboratory

Citation(s):

US DOE, USDA. 2014. Plant Feedstock Genomics for Bioenergy Joint Awards 2006–2014, U.S. Departments of Agriculture and Energy. (PDF)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/.

Switchgrass Bales from a 5-Year-Old Field in Northeast South Dakota in 2005

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Each 1200-lb. bale represents 48 gallons of ethanol at a conversion rate of 80 gallons per ton. The cultivar used in this field has a yield potential of 5 to 6 tons per acre (corresponding to 400 to 500 gallons per acre) because it was bred for use as a pasture grass. In experimental plots, 10 tons per acre have been achieved. Proccessing goals target 100 gallons per ton of biomass, which would increase potential ethanol yield to 1000 gallons per acre.

Credit or Source: K. Vogel, University of Nebraska.

Citation(s):

U.S. DOE. 2006. Breaking the Biological Barriers to Cellulosic Ethanol: A Joint Research Agenda, DOE/SC/EE-0095, U.S. Department of Energy Office of Science and Office of Energy Efficiency and Renewable Energy. (p. 58) (website)

Switchgrass Harvest

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Switchgrass fertilization experiments at harvest time in Tennessee.

Credit or Source: T. O. West, Pacific Northwest National Laboratory

Citation(s):

U.S. DOE. 2014. Research for Sustainable Bioenergy: Linking Genomic and Ecosystem Sciences, Workshop Report, DOE/SC-0167. U.S. Department of Energy Office of Science. genomicscience.energy.gov/sustainability/. (p. 10) (PDF)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/.

Switchgrass--Fluorescence Microscopy

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Fluorescence signals primarily come from chlorophyll, lignin, carotenes, and xanthophylls in plants, each with a different wavelength (color); ligninfluorescence is blue-greenish. Cell lignification is determined by using different filter sets.

Credit or Source: National Renewable Energy Laboratory and the DOE BioEnergy Science Center.

Citation(s):

US DOE. 2009. Bioenergy Research Centers: An Overview of the Science, DOE/SC-0116, US Department of Energy. (p. 19)

U.S. DOE. 2009. U.S. Department of Energy Office of Science Systems Biology Knowledgebase for a New Era in Biology: A Genomics:GTL Report from the May 2008 Workshop, DOE/SC-113, U.S. Department of Energy Office of Science. (p. 87) (website)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/.

Telomere Staining

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Human Genome Program, U.S. Department of Energy, Human Genome Program Report, 1997.

Credit or Source: Robert Moyzis, University of California, Irvine, CA; U.S. Department of Energy Human Genome Program

Terrestrial Ecosystem Parameters Important to Earth System Models

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As extensions of general circulation models, ESMs include biogeochemical processes, vegetation changes, and human influences to more completely simulate the multitude of factors influencing climate in all its complexity. Accurately predicting future CO2 feedbacks and concentrations is a key objective driving development of ESMs. Central to meeting this goal is a detailed understanding of the global carbon cycle, including how its sources and sinks behave and respond to climatic and atmospheric change.

Credit or Source: Office of Biological and Environmental Research of the U.S. Department of Energy Office of Science. science.energy.gov/ber/

Citation(s):

U.S. DOE. 2008. Carbon Cycling and Biosequestration: Report from the March 2008 Workshop, DOE/SC-108, U.S. Department of Energy Office of Science. (p. 19) (website)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/ and genomics.energy.gov/.

Terrestrial Photosynthetic Carbon Cycle

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Credit or Source: Image adapted from and used courtesy of N. Scott and M. Ernst, Woods Hole Research Center, whrc.org

Citation(s):

U.S. DOE. 2008. Carbon Cycling and Biosequestration: Report from the March 2008 Workshop, DOE/SC-108, U.S. Department of Energy Office of Science. (p. 28) (website)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/ and genomics.energy.gov/.

Thawing Permafrost

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Thawing permafrost cracks and crumbles, activating microbial metabolism of undegraded organic material once trapped in frozen soil sublayers.

Credit or Source: Dentren at en.wikipedia Wikipedia

Citation(s):

US DOE. 2011. Biological Systems Research on the Role of Microbial Communities in Carbon Cycling, , US Department of Energy Office of Science. (p. 2) (PDF)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/.

The Genetic Code

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Universal among all life forms, the genetic code is the language used to write the mRNA instructions for building proteins. Each three-letter codon in the mRNA specifies a particular amino acid. Since there are 20 different amino acids and 64 different codons, an amino acid can be represented by more than one codon. The methionine codon (AUG) is the start codon initiating protein synthesis. Three stop codons signify the end of a protein sequence.

Credit or Source: Biological and Environmental Research Information System, Oak Ridge National Laboratory

Citation(s):

US DOE. Genomics Placemat: Genomics for Energy and Environmental Science, US Department of Energy Office of Science. (p. 1) (website)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/ and genomics.energy.gov/.

The Termite Gut: Nature's Microbial Bioreactor for Digesting Wood and Making Biofuels

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The microbial community within a termite's gut is one of nature's most efficient bioreactors-typically converting 95% of cellulose into simple sugars within 24 hours. More than 200 species of microbes make up this community, and they produce a bounty of wood-busting enzymes that could be put to work in biorefineries making ethanol from several forms of cellulosic biomass. This diverse array of microbial capabilities that could jumpstart a new biofuel industry is the result of a codependent strategy for survival. Without wood-eating microbes, a termite would not be able to extract nutrients and energy from wood, and without the termite to grind wood into tiny pieces and provide an oxygen-free habitat within its gut, the microbes would not be able to survive. In addition to efficiently degrading cellulose into sugars, some termite-gut microbes are biochemically capable of generating other potential fuels such as hydrogen or methane. Hydrogen produced by one group of microbes is consumed by other gut microbes that create energy-producing by-products the termite can use. Investigating the termite-gut community reveals a vast collection of biological pathways that may one day be put to use for multiple energy applications. A collaboration of researchers from the Department of Energy's Joint Genome Institute (DOE JGI), the California Institute of Technology, Diversa, and INBIO (National Biodiversity Institute of Costa Rica) has sequenced and analyzed microbial DNA extracted from the guts of hundreds of termites harvested from a nest in a Costa Rican rainforest. Preliminary results already have identified several novel enzymes capable of degrading cellulose into sugars, and the San Diego-based biotechnology company Diversa has used insights from this discovery to create a high-performance enzyme cocktail for processing plant biomass into biofuels. DOE JGI researchers continue to investigate other microbial communities in the guts of insects that consume different plant materials. The goal is to understand and reconstruct a diverse range of metabolic processes that could be scaled up for industrial biofuel production.

[Some images taken from "Genomics:GTL Transforming Cellulosic Biomass," U.S. Department of Energy Office of Science and Office of Energy Efficiency and Renewable Energy, June 2006, genomicscience.energy.gov/biofuels/ and U.S. DOE. 2006. "Breaking the Biological Barriers to Cellulosic Ethanol: A Joint Research Agenda," DOE/SC/EE-0095, U.S. Department of Energy Office of Science and Office of Energy Efficiency and Renewable Energy, genomicscience.energy.gov/biofuels/.]

Credit or Source: Office of Biological and Environmental Research of the U.S. Department of Energy Office of Science. science.energy.gov/ber/

Citation(s):

US DOE. June 2007. Biofuels: Bringing Biological Solutions to Energy Challenges, US Department of Energy Office of Science. (PDF)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/ and genomics.energy.gov/.

Thylakoids in Green Algae and Cyanobacteria

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Photosynthetic Production of Hydrogen from Water Although microorganisms are capable of carrying out different types of photosynthesis, that found in plants, algae, and cyanobacteria is best understood. Photosynthesis in these organisms is a complex series of reactions that use light energy to drive electron transfer from water to carbon dioxide to yield carbohydrates. Instead of using electrons harvested from water to synthesize carbohydrates from CO2, under certain conditions green algae and cyanobacteria can use them to reduce protons and produce hydrogen gas (H2). Molecular complexes involved in mediating electron flow from water to carbon-fixing or hydrogen-production reactions make up the photosynthetic electron-transport chain found in the thylakoid membranes of cyanobacteria and green algae. In eukaryotic green algae, thylakoid membranes are housed within a cellular organelle known as the chloroplast; in prokaryotic cyanobacteria, thylakoids are found in the cytoplasm as an intracellular membrane system (see Fig. A).

Credit or Source: Office of Biological and Environmental Research of the U.S. Department of Energy Office of Science. science.energy.gov/ber/

Citation(s):

US DOE. 2005. Genomics:GTL Roadmap, DOE/SC-0090, U.S. Department of Energy Office of Science. (p. 210) (website)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/.

Understanding Biomass: Plant Cell Walls

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Explains plant cell wall structure and some of the issues preventing their efficient conversion to ethanol.

[Some images taken from "Genomics:GTL Transforming Cellulosic Biomass," U.S. Department of Energy Office of Science and Office of Energy Efficiency and Renewable Energy, June 2006, genomicscience.energy.gov/biofuels/ and U.S. DOE. 2006. "Breaking the Biological Barriers to Cellulosic Ethanol: A Joint Research Agenda," DOE/SC/EE-0095, U.S. Department of Energy Office of Science and Office of Energy Efficiency and Renewable Energy, genomicscience.energy.gov/biofuels/.]

Credit or Source: Office of Biological and Environmental Research of the U.S. Department of Energy Office of Science. science.energy.gov/ber/

Citation(s):

US DOE. May 2007. Biofuels Primer Placemat: From Biomass to Cellulosic Ethanol and Understanding Biomass: Plant Cell Walls, US Department of Energy Office of Science. (website)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/ and genomics.energy.gov/.

Using Mice to Understand Human Gene Function

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Credit or Source: Office of Biological and Environmental Research of the U.S. Department of Energy Office of Science. science.energy.gov/ber/

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/ and genomics.energy.gov/.

Validation of Gene Expression in Vascular Tissues (a)

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To confirm the expression of identified genes in vascular tissues, probes that specifically bind the mRNA of a small number of the identifed genes were applied to switchgrass tissue. The darker regions indicate the vascular bundles where the probes bound the abundant mRNA from the active expression of targeted genes in these regions.

Credit or Source: Image courtesy of Elison Blancaflor, The Samuel Roberts Noble Foundation

Citation(s):

US DOE. 2010. Bioenergy Research Centers: An Overview of the Science, DOE/SC-0127, US Department of Energy. (p. 19) (website)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/.

View of Simplified Microbial Anatomy

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Pili Extend as Nanowires to Transfer Electrons. Investigators noted that Geobacter species specifically produced fine, hair-like structures known as pili on one side of the cell during growth on Fe(III) oxide.

Credit or Source: Office of Biological and Environmental Research of the U.S. Department of Energy Office of Science. science.energy.gov/ber/

Citation(s):

US DOE. 2005. Genomics:GTL Roadmap, DOE/SC-0090, U.S. Department of Energy Office of Science. (p. 74) (website)

Prepared by the Biological and Environmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/.

Walker Branch Watershed

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Credit or Source: Oak Ridge National Laboratory

Citation(s):

US DOE. Climate Placemat: Energy-Climate Nexus, US Department of Energy Office of Science. (p. 2)

Prepared by the Biological and Enviornmental Research Information System, Oak Ridge National Laboratory, genomicscience.energy.gov/ and genomics.energy.gov/