U.S. Department of Energy’s Office of Science

1. U.S. Department of Energy’sOffice of Science Update on the Biological Systems Science Division Roland F. HirschActing DirectorBiological Systems Science DivisionOffice of Biological & Environmental Research

2. Bioenergy Research Centers: Early Highlights BioEnergy Science Center, led by Oak Ridge National Laboratory • Bio-prospecting in Yellowstone hot pools for new, more effective cellulases operating at high temperatures (metagenomic analysis using DOE Joint Genome Institute) • New high-throughput pipeline up and running, beginning to screen thousands of genetic variants of switchgrass and poplar for amenability to deconstruction (using standard pretreatment/enzymatic hydrolysis method combined with genomics-based analysis) Great Lakes Bioenergy Research Center, led by U. Wisconsin • Exploiting 454 sequencing capabilities at JGI to identify transcription factors in model-plant cell wall biosynthesis • Playing a leading role in the research and public education effort on biofuels andsustainability Joint BioEnergy Institute, led by the Berkeley Lab • Novel ionic liquids pretreatment method in laboratory experiments has shortened enzymatic hydrolysis times by factor of 30 • Has created first hydrocarbons using re-engineered E.coli – initial steps toward microbially produced “green” gasoline, diesel, jet fuel

3. Inter-agency Coordination of Biomass Research • BER has made substantial contributions to a major federal interagency effort on biofuels spearheaded by the Biomass Research and Development Board, a high-level interagency group created by Congress in 2000, chaired by the Secretaries of Agriculture and Energy • BER contributed to the Board’s soon-to-be published National Biofuels Action Plan • BER program managers are serving on active Interagency Working Groups (IWGs) on feedstocks, biomass conversion, biofuels sustainability, and biofuels environment, health, and safety • The IWGs are producing draft reports, including “Increasing Feedstock Production for Biofuels: Economic Drivers, Environmental Implications and the Role of Research,” and “Biomass Conversion” • IWGs are helping to inventory, coordinate, and develop strategy for federally sponsored research efforts on biofuels across agencies

4. Plant Feedstock Genomics for Bioenergy—a DOE-USDA Joint Research Program • Supports fundamental research on plants for improvement of biomass characteristics, productivity, and sustainability • Competitive notice DE-PS-02-08ER08-03 resulted in 10 new awards • DOE contributes $8.8 million over next 3 years • New projects include development of genomic markers, elucidation of regulatory networks for plant cell wall synthesis, investigating genome structure, understanding regulation of nutrient acquisition • Systems include switchgrass, poplar, rice, Brachypodium, foxtail millet, sunflower http://genomicsgtl.energy.gov/research/DOEUSDA/index.shtml

5. Joint Genome Institute Strategic Planning • The JGI held a two day strategic planning retreat in Pacifica, California August 28–29. • The broad topic areas were microbes, plants, synthetic biology/new technologies, computation, and organization. • The need for continued high throughput sequencing, particularly of non-pathogenic microbes, metagenomes, and plants was underscored. • The idea of synthetic biology as a new JGI direction was discussed intensively; the idea that emerged at the end was for a focused pilot of several years duration to concentrate on a clear DOE mission (e.g. carbon capture) and an evaluation in a couple of years to assess community utility. • A new MOU for the JGI’s 6 partners (Berkeley Lab, Lawrence Livermore National Laboratory, Los Alamos National Laboratory, Pacific Northwest National Laboratory, Oak Ridge National Laboratory, Hudson-Alpha Institute) has been drawn up and is being discussed by the partners.   • A draft of the strategic plan is being developed from the retreat with the intent being to present it (still as a draft) to BERAC in February 2009.

6. X-Ray Tomography Highlight • X-ray tomography has determined the structure of organelles in yeast cells during different stages of the cell cycle, providing for the first time 3D images that show how the cells change during the cycle. • The research is reported in the June issue of the Journal of Structural Biology, with selected images shown on the cover. • The authors show that use of the soft X-rays at the Advanced Light Source enables imaging of cellular components without having to expose the cells to potentially damaging staining reagents. • The research was led by Dr Carolyn A. Larabell of the Lawrence Berkeley National Laboratory and the University of California-San Francisco.

7. Optical Imaging Highlight • Dr. Haw Yang’s review article, “Progress in Single-Molecule Tracking Spectroscopy” was highlighted on the cover of the May 27, 2008 issue of Chemical Physics Letters. • Dr. Yang is pioneering the development of experimental approaches that will track single molecule movement in cells, correlating the location of a molecule with its biological and chemical actions, and producing insights about how specific systems function in cells. • This technology will be used to reveal the detailed behavior of the Cellulosome, the molecular complex that plays a fundamental role in the degradation of cellulose, as it interacts with cellulosic plant material.  

8. Genomics Review Paper • The August 14, 2008 issue of Nature features a five-page invited review article “Genomics of Cellulosic Biofuels” by Eddy Rubin, Director of the Joint Genome Institute. • The article describes the enormous promise for development of new routes to cellulosic biofuels from genomic sequencing of plants (sources of biomass precursors of liquid fuels) and microbes (sources of enzymes and pathways to convert biomass to liquid fuels). • Rubin concludes that “Genomic information gathered from across the biosphere, including potential energy crops and microorganisms able to break down biomass, will be vital for improving the prospects of significant cellulose biofuel production.”

9. Review of Human Subjects Protection Program at Sandia • HHS Office of Human Research Protections (OHRP), the federal oversight organization for the protection of human research subjects, conducted a QA consultation at SNL on July 16-17, 2008. • SNL volunteered to be the first DOE site to participate in a QA consultation, a service offered by OHRP to help institutions ensure their human subjects protection programs are in compliance with federal regulations. • OHRP found that SNL had: • the appropriate infrastructure and excellent procedures; • a dedicated and a knowledgeable Human Subjects Administrator; • significant management support; and • a committed Institutional Review Board (IRB). • Next OHRP QA consultation: Oak Ridge – September 18-19, 2008.

10. Recognition of BSSD Scientists: Fred Hawthorne • M. Frederick Hawthorne, Director of the International Institute of Nano and Molecular Medicine at the University of Missouri, Columbia will receive the Priestley Medal of the American Chemical Society for 2009. • Hawthorne was supported by BER medical science program for many years while on the faculty of the University of California at Los Angeles. He is a world-renowned expert on boron chemistry. • The Priestley Medal is the highest honor bestowed by the American Chemical Society.

11. Recognition of BSSD Scientists;George Church • George Church of the Harvard Medical School has a long association with BER from the early days of the Human Genome Project to the current Genomics:GTL program. • The August 2008 issue of Wired features a long profile of him, with the focus on his Personal Genome Project. • The article notes his key role at the 1984 Alta Meeting, convened by DOE to assess the potential for understanding the effects of radiation exposure through the application of genetics.