Advancing Science with DNA Sequence Response to BERAC Review Overview of JGI BERAC Recommendations...
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Advancing Science with DNA Sequence
Response to BERAC Review
• Overview of JGI
• BERAC Recommendations– Managing multi-lab environment– Operation of user facility– LSP program
• JGI Energy Portfolio
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Advancing Science with DNA Sequence
JGI Mission
“User facility providing DNA sequencing & analysis in support of DOE missions in alternative energy, carbon cycling & bioremediation.”
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www.jgi.doe.gov
Advancing Science with DNA Sequence
Cost-effective Sequencing at JGI
$0.00$0.20$0.40$0.60$0.80$1.00$1.20$1.40$1.60$1.80Center 1Center 2Center 3JGICenter 4Center 5Center 6
NIH data provided by Jane Peterson, NHGRI
$0.00
$0.20
$0.40
$0.60
$0.80
$1.00
$1.20
$1.40
$1.60
$1.80
Center 1 Center 2 Center 3 JGI Center 4 Center 5 Center 6
Cntr1 Cntr4Cntr3Cntr2 Cntr5 Cntr6JGI
FY06 capacity: 30 billion basepairs
Advancing Science with DNA Sequence
Success of JGI User Programs
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2003 2004 2005 2006
Microbial Genome Program
ProposedProposed
AcceptedAccepted
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2005 2006 2007
Community Sequencing Program
ProposedProposed
AcceptedAccepted
Advancing Science with DNA Sequence
Primary JGI User Distribution Primary JGI User Distribution
KEY: RED=Academic; Blue=National Laboratory; Black=Industry KEY: RED=Academic; Blue=National Laboratory; Black=Industry
Advancing Science with DNA Sequence
1st Annual JGI User Meeting
JGI User Meeting, April 2006250 Users and potential usersSequence-based science talksTours of JGI facilityPoster sessionsUser Committee formed
Advancing Science with DNA Sequence
JGI Director
PGF LBNLLANL ORNL LLNL SHGCPNNL
The JGI Partnership
Managing in a multi-lab environment: Dual workforce at PGF
Succession planning at PGF
Coordination of partner tasks
Advancing Science with DNA Sequence
BERAC RecommendationsOperations and Management-1
• Management of LBL/LLNL workforce
– Coordination of safety training & tracking• EH&S MOU complete, waiting signatures• LBL has 1º responsibility for EH&S
– Cyber-security MOU• Committee configured, meets this month
Advancing Science with DNA Sequence
BERAC RecommendationsOperations and Management-2
• Succession planning for key JGI positions
– Hired production sequencing lead
– Senior managers identified “seconds”
– Seconds contribute to weekly mgmt meetings
Advancing Science with DNA Sequence
BERAC RecommendationsOperations and Management-3
Coordination of JGI partner lab tasks:
• Weekly genome management conference call• Monthly partners conference call• “Finishing in the future” meeting• Eukaryotic Genome Program summit
Advancing Science with DNA Sequence
BERAC RecommendationsUser Facility
Proposals
Sequencing
Annotation
UserAgreement
DNALibraries
Asssembly
Sequencingscales easily
Efficiency of the user facility:
Peer review
Project management
Assembly & annotation throughput
Advancing Science with DNA Sequence
BEERAC RecommendationsUser Facility-1
• Managing the User Facility:
– Peer review• MGP and CSP programs/review groups merged• Broadened geographical representation• Electronic proposal submission & review• Letter-of-intent process• User committee input on peer review committees
Advancing Science with DNA Sequence
BEERAC RecommendationsUser Facility-2
• Managing the User Facility:
– Formal project management• Appointed project management lead• Hired 2 new project managers• Launched Global Project Tracking System• End-of-project survey in draft form
Advancing Science with DNA Sequence
BERAC RecommendationsUser Facility-3
• Managing the User Facility:
– Improve large genome analysis throughput• JAZZ assembly program overhauled• 2 programmers hired into assembly group• 3 people hired into annotation group
Advancing Science with DNA Sequence
Lab Science Program
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• LSP created by new JGI MOU – Facilitate access to JGI for Natl. Lab
investigators– Fulfill programmatic sequencing
needs of DOE– Shape JGI products and services to
meet needs of the Natl. Labs
• BERAC concerns– Scientific vision for LSP– Implementation
Advancing Science with DNA Sequence
BERAC RecommendationsLSP Program
• LSP lead– Appointed Jerry Tuskan, ORNL, Jan ‘06– Focus on bioenergy– LSP lead now reports to JGI Director
• Implementation– Lab points-of-contact identified– Small-scale sequencing program
• 14 proposals received, 10 approved to date
– Large-scale sequencing program• Plant Genomes for Energy white paper• Fungal Genomes for Energy white paper
Advancing Science with DNA Sequence
Petroleum – 98%
2%
Bioenergy & the JGI
Corn based ethanolSoy-based biodiesel
NSF/USDA/DOEfunded project
LSP project
Transportation Fuels
Advancing Science with DNA Sequence
JGI and Bioenergy
FermentationSaccharification Sugars
Improved Feedstocks
Improved cellulose & lignin degradation
Ethanol producing organisms
Cellulose
•Termite hindgut microbiota•White Rot Fungus•Clostridium thermocellum •Saccharophagus degradans •Acidothermus cellulolyticus
•Saccharomyces cerevisiae•Zymomonas mobilis•Thermoanaerobacter ethanolicus•Pichia stipitis
Cellulosic Materials•Poplar•Maize/Corn Stover•Switchgrass •Brachypodium•Sorghum
Advancing Science with DNA Sequence
Auxin Regulation of Poplar Shape
Enhanced radial growth of Enhanced radial growth of IAA16.3 transgenic treesIAA16.3 transgenic trees
Enhanced radial growth of Enhanced radial growth of IAA16.3 transgenic treesIAA16.3 transgenic trees
IAA16.3IAA16.3
ControlControl
90-day-old Populus cuttings
stem cross sectional area (cm)
transgenic
control
7.1
4.4
Advancing Science with DNA Sequence
GlcGlc
H2O22 -glucosidase
P
GlcGlc-1-P
PCellobiosephosphorylase
12 Exoglucanases
Cellulose
Cellobiose
15 Endoglucanases
New Cellulase Genes from Termite Gut