Sharlene C. Weatherwax, Ph.D.Director

Biological Systems Science DivisionBiological & Environmental Research

Office of ScienceFebruary 18, 2009

BERAC MeetingBERAC Meeting

Biological Systems Science Division Biological Systems Science Division UpdateUpdate

Lab Science Focus Area Program Plans

• 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

Current Solicitations

• 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

• 08-21 Low Dose Radiation Research - Integrated Program Projects• 08-20 Low Dose Radiation Research -Basic Biology and Modeling

• NSF 08-588 Interagency Opportunities in Metabolic Engineering

Workshop on Biological Imaging and Spectroscopy at the NSLS II

• 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.

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

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?

Objective• Develop new synchrotron

technologies for studying systems important to cellular function

Combining techniques in x-ray crystallography and optical spectroscopy to study enzyme function

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

Workshop on Low Dose EpidemiologyDecember 10 – 11, 2008

Objective: to discuss existing studies of low dose/dose-rate epidemiology, and future needs

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

DATA

Extrapolations to low dose

Objectives•To broaden the use of radiotracers by developing a fundamental synthetic “tool-kit” including precursors such as high specific activity [11C]-formaldehyde. •To apply these new methods to the synthesis of radiotracers that will quantify the dynamics of organic compounds and nanoparticles in biological systems.

Approach•Develop synthesis methods which are simple and can be readily reproduced in other labs • Apply these new methods to the synthesis of macromolecules, such as proteins and nanoparticles.

Impact• The widespread availability of [11C]formaldehyde and other synthetic precursors will increase the number of compounds that can be labeling with carbon-11 for use in biological imaging related to energy, environment, and health

[11C]Formaldhyde

11CH3

IN

CH3

CH3 CH3

O

+ NCH3

CH3 CH3

O

11CH3

11CH H

O

Radiochemistry, Imaging and Instrumentation: New Synthetic Methods for Imaging Compounds

Hooker et al, Brookhaven National Laboratory

Genomics: GTL

• 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

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

Objective

To predict an organism’s phenotype from its genomic sequence.

Scientific Discovery through Advanced Computing (SciDAC) and GTL Science

add rxn's

combination ofmechanisms

enable uptake

add transportrxn's

make rxn'sreversible

compartment

Biotechnology and Bioengineering, 100, 1039, 2008; BMC Systems

Biology, 2, 24, 2008; BMC Bioinformatics, 9, 43, 2008

Result

New computational tools available for redesigning

metabolic networks

Costas Maranas, Penn State University

DOE Bioenergy Research Centers

• 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

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.

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). 

Photo

Objectives•Detection of feedstock chemical, structural, and genetic features to provide targets for development of improved biomass varieties.  

High Throughput Feedstock Characterization Pipeline Established at DOE BioEnergy Science Center (BESC)

Results•Up to 5-fold improvement in efficiency of enzymatic breakdown of biomass to fermentable sugars

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

Objective•Rapidly dissolve lignocellulosic material and reduce toxic byproducts that increase the cost of downstream processes.

New Ionic Liquid Pretreatment Methods Developed at the Joint BioEnergy Institute

Emim acetate pre-treatment of switchgrass

Emim acetate pre-treatment of switchgrass

Before Pretreatment

Swollen cell wall after 10 minutes of Pretreatment

3 hours of IL pre-treatment

After addition of water lignin separates

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

Objective•Explore natural sources of novel enzymes and microbes both as candidates for biorefineries and for insight into biochemical options for deconstruction

Leaf Cutter Ants Analyzed for Novel Deconstruction Microbes and Enzymes at DOE

Great Lakes Bioenergy Research Center

Jarrod Scott & Bert Hölldobler

DOE Joint Genome InstituteScience and Operations Review

• 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 InstituteRecent Scientific Highlights

• 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

BSSD--Personnel Updates

• 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