Sharlene C. Weatherwax, Ph.D. Director Biological Systems Science Division

1. BERAC MeetingBiological Systems Science Division Update Sharlene C. Weatherwax, Ph.D. Director Biological Systems Science Division Biological & Environmental Research Office of Science February 18, 2009

2. Science Focus Areas (SFAs) include: GTL Fundamental Science GTL Biofuels Low Dose Radiochemistry and Instrumentation ELSI December 2008--SFA program plans received January 2009—SFA lab POCs have received BER feedback and guidance for revisions February 2009--most SFA program plans are approved May 2009--full Science Research plans are due Summer 2009--merit review panel planned Lab Science Focus Area Program Plans

3. 09-03 Joint USDA-DOE Plant Feedstock Genomics Genomics-based research that will lead to the improved use of biomass and plant feedstocks for the production of fuels such as ethanol or renewable chemical feedstocks Fundamental research on plants that will improve biomass characteristics, biomass yield, or sustainability 09-08 Integrated Radiochemistry Research Projects of Excellence Integrated involvement of graduate-student and postdoctoral trainees in the fundamental research that seeks improvements in radiolabeling and radiotracer development chemistry Enhancement of training opportunities 08-21Low Dose Radiation Research - Integrated Program Projects 08-20 Low Dose Radiation Research -Basic Biology and Modeling NSF 08-588 Interagency Opportunities in Metabolic Engineering Current Solicitations

4. The National Synchrotron Light Source II (NSLS II) is being built at Brookhaven National Laboratory. It is scheduled to be completed in 2015. BER and NIH co-sponsored a workshop held in September 2008 in Washington, DC. Participants included researchers in cell biology, diagnostic medicine, microbiology and geomicrobiology and plant biology, and experts in synchrotron applications and imaging techniques. An informal report on the meeting is available on the web at: http://www.science.doe.gov/ober/BSSD/struct_bio.html The report notes several areas for which imaging and spectroscopy technologies planned for the NSLS II could have a significant impact in biological science. Workshop on Biological Imaging and Spectroscopy at the NSLS II

5. Combining techniques in x-ray crystallography and optical spectroscopy to study enzyme function Objective • Develop new synchrotron technologies for studying systems important to cellular function Approach • Protein Crystallography Resource scientists at Brookhaven National Laboratory designed and installed an optical spectrometer system at a crystallographic beam line at the National Synchrotron Light Source • Biologists at Georgia State University, Georgia Tech and the University of Miami provided the experimental question: How do flavoproteins activate oxygen to help convert food into energy? Impact • A new experimental technology is available for applying unique light source capabilities to biology • Increased value of the DOE National User Facilities to the research community • New insights into a large group of enzymes which catalyze many cellular functions Allen Orville, Brookhaven National Laboratory, et al., Biochemistry, 2009, 48(4), 720–728 “Crystallographic, Spectroscopic, and Computational Analysis of a Flavin C4a-Oxygen Adduct in Choline Oxidase

6. Workshop on Low Dose EpidemiologyDecember 10 – 11, 2008 • Objective: • to discuss existing studies of low dose/dose-rate epidemiology, and future needs DATA Extrapolations to low dose Topics: • What have we learned from past studies? (A-bomb survivors, nuclear workers, DOE workers, Techa River, radiologists, CT scans, shipyard workers, etc.) • Which studies are most valuable for setting US worker and public exposure standards? • Which studies should be updated for added value? Conclusions: • Low dose radiobiology data suggests a critical need to reexamine low dose human epidemiological studies • Many worker studies can be usefully expanded and updated to the present, and meta analysis performed

7. [11C]Formaldhyde + Radiochemistry, Imaging and Instrumentation: New Synthetic Methods for Imaging Compounds Hooker et al, Brookhaven National Laboratory

8. Annual investigator meeting held February 8-11, 2009 in North Bethesda, Maryland Bioenergy Research Centers University researchers National laboratory scientists Joint USDA-DOE Plant Feedstock Genomics for Bioenergy awardees Program managers from DOE, NIH, NSF, USDA, EPA Over 500 registrants! Carbon Cycling and Biosequestration workshop report available at http://genomicsgtl.energy.gov/carboncycle/ Knowledgebase workshop report available soon! Planned workshop on Advanced Characterization and Imaging of Biological Systems Genomics: GTL

9. Scientific Discovery through Advanced Computing (SciDAC) and GTL Science Objective To predict an organism’s phenotype from its genomic sequence. Approach • Identify all possible metabolic pathways from substrate to product • Create topological and flux analyses of these metabolic networks and test predictions • Developed a computational framework, OptKnock, to re-engineer and optimize pathways to overproduce desired molecules, such as ethanol Result New computational tools available for redesigning metabolic networks Costas Maranas, Penn State University Biotechnology and Bioengineering, 100, 1039, 2008; BMC Systems Biology, 2, 24, 2008; BMC Bioinformatics, 9, 43, 2008

10. First year on-site progress reviews GLBRC—September 23-24, 2008 JBEI—September 29-30, 2008 BESC—October 14-15, 2008 External review team plus DOE staff safety officer evaluated: science and management progress against stated milestones Review findings Reviewers were enthusiastic about each BRC’s successful execution of the first year start up phase All centers have demonstrated significant research accomplishments Reviewers all expressed confidence in leadership of each BRC director Specific recommendations communicated to BRC directors DOE Bioenergy Research Centers

11. High Throughput Feedstock Characterization Pipeline Established at DOE BioEnergy Science Center (BESC) Objectives • Detection of feedstock chemical, structural, and genetic features to provide targets for development of improved biomass varieties.   Photo Approach • High throughput pipeline analyzes feedstock recalcitrance.  • Link to follow-up pipelines: • feedstock characterization • multi-sample HTP pretreatment • plant transformation screening • Integrate information into a LIMS (Laboratory Information Management System).  Results • Analysis of a thousand poplar tree (Populus) samples has led to the new knowledge of links between genes and genetic markers that will help develop feedstocks with less recalcitrance.

12. Emim acetate pre-treatment of switchgrass Swollen cell wall after 10 minutes of Pretreatment Before Pretreatment 3 hours of IL pre-treatment After addition of water lignin separates New Ionic Liquid Pretreatment Methods Developed at the Joint BioEnergy Institute Objective • Rapidly dissolve lignocellulosic material and reduce toxic byproducts that increase the cost of downstream processes. Approach • Investigate ionic liquids (room temperature molten salts) during pretreatment. • Ionic liquids free cellulose and hemicellulose from lignin in a short period of time at mild temperatures • Ionic liquids decrystallize cellulose Results • Up to 5-fold improvement in efficiency of enzymatic breakdown of biomass to fermentable sugars

13. Leaf Cutter Ants Analyzed for Novel Deconstruction Microbes and Enzymes at DOE Great Lakes Bioenergy Research Center Objective • Explore natural sources of novel enzymes and microbes both as candidates for biorefineries and for insight into biochemical options for deconstruction Jarrod Scott & Bert Hölldobler Results • Microbial community dominated by enterics--more similar to human gut than cow or termite guts • Dominant fungus doesn’t degrade cellulose • Hundreds of good cellulose degraders isolated Approach • Set up operating Leaf Cutter Ant colony in GLBRC • Screen for microbial diversity and enzyme activities, and sequence metagenome

14. Held December 4-5, 2008 in Walnut Creek, CA Fourteen reviewers evaluated science, operations, informatics, management, and safety Organization: Briefings Meetings with representatives from JGI partners, JGI staff, users, JGI management Poster session Facility tour Review findings and recommendations to be issued soon JGI Strategic Planning underway DOE Joint Genome InstituteScience and Operations Review

15. Soybean genome Major biodiesel crop 13 million shotgun reads representing >7 fold genome coverage Interagency development of genomic resources Sorghum genome 2nd grass genome 730 Mb Drought resistant biofuels crop January 29, 2009 edition of Nature DOE Joint Genome InstituteRecent Scientific Highlights

16. Offer extended to an IPA for a biologist position Interview process underway for Program Specialist Current position available for a plant biologist—closes March 16 Division Retreat scheduled for April 15 BSSD--Personnel Updates