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