# Presentation: 545353

##  BERAC Meeting Biological Systems Science Division Update

**Director**
**Biological Systems Science Division**
**Biological & Environmental Research**
**Office of Science**
**February 18, 2009**

** ****BERAC Meeting**** ****Biological Systems Science Division Update**

## 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](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 EpidemiologyDecember 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**

**Notes:**
Workshop report will be submitted for peer review in Radiation Research Journal.

## Radiochemistry, Imaging and Instrumentation: 

| 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 |

- 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_[ ](http://genomicsgtl.energy.gov/carboncycle/index.shtml)_ available at _[http://genomicsgtl.energy.gov/carboncycle/](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**

*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

## Photo

- 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).

**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)**

## New Ionic Liquid Pretreatment Methods Developed at the Joint BioEnergy Institute

- 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**

## Leaf Cutter Ants Analyzed for Novel Deconstruction Microbes and Enzymes at DOE Great Lakes Bioenergy Research Center

- 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 InstituteScience 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

## 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

- 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