The JGI Community SequencingProgram (CSP) is contributing to an ambi-tious international effort to decode thegenome of Eucalyptus, one of the world’smost valuable fiber and paper-producingtrees—with the goal to maximize its poten-tial in the burgeoning bioenergy marketand for capturing excess atmosphericcarbon.

The scientific effort to characterize theEucalyptus genome, uniting some two

dozen institutions worldwide, is led byAlexander Myburg of the University ofPretoria (South Africa), with co-leads DarioGrattapaglia, of EMBRAPA and CatholicUniversity of Brasília (Brazil), and JerryTuskan of Oak Ridge NationalLaboratory—JGI’s Laboratory ScienceProgram lead. The 600-million-nucleotidetree genome was selected as one of JGI’sCSP FY2008 major allocations.

inside this issue2. JGI Faces3. Meet the JGI PMO3. ERT Takes Cribbing4. Awards & New Hires5. LANL Hosts FACE5. MegaBace Bye-Bye6. Dino Jamboree7. Rock Star Educator8. JGI Long-Term Lease8. DSMZ Jumpstarts GEBA9. New Tracking System10. Poplar Watch11. Undergrad Workshop11. Stan Man Wins12. Pennacchio Honored12. Kennedy Triathlete

PRIMERthe

Eucalyptus Tapped for Next TreeGenome Project Through CSP

Fall 2007 Volume 4 Issue 2

BY BRUCE BALFOUR

On August 30 and 31, leaders fromthe three new DOE Bioenergy ResearchCenters met for the first time at JGI inWalnut Creek.

Arriving from the Great LakesBioenergy Research Center (GLBRC),the BioEnergy Science Center (BESC),and the Joint BioEnergy Institute (JBEI),they came to hear about JGI’s expert-ise, talk about their research plans,look for collaboration opportunities, andoffer a preview of the sequencingcapacity they’ll need over the next fewyears.

An integral part of the $375 millioninitiative launched by Energy SecretaryBodman in June, each BRC combinesthe efforts of national labs, universities,and private industry working with nation-al user facilities such as JGI, makingthe collaborations in these centers

unusually complex for DOE-funded proj-ects. DOE program manager PatrickGlynn characterized the relationshipbetween the vertically integrated BRCsas “competition/collaboration” wherethey’re all working toward the samegoals to increase the rate of discovery.Participants welcomed this approach.

“As scientists in this field, we havesuccessfully competed and collaboratedfor years, so I don’t foresee any prob-lems,” said Wolf Frommer, Stanford pro-fessor and Vice President ofFeedstocks at JBEI.

JGI Director Eddy Rubin kicked offthe session with encouraging wordsabout JGI’s history of increasing speed,efficiency, and sequencing capacitywhile continually lowering costs. He pre-dicted an even more dramatic trajectoryfor sequencing-by-synthesis technolo-gies currently being vetted.

In response to a

The genome analysis of a tiny greenalga has uncovered hundreds of genesthat are uniquely associated with car-bon dioxide capture and generation ofbiomass. Among the

NEW BIOENERGY RESEARCH CENTERSMEET AT JGI

Chlamy Genome CatalogsCarbon Capture Role asAncient Cousin of Plantsand Animals

(cont. on page 14)

(cont. on page 13)

Chlamy in synchronized swim

(cont. on page 15)

Fall 2007 Vol. 4, Issue 2

2 / THE PRIMER

NICK EVERSON

Finance & Materials Manager

Nick comes to us via LLNL, where hewas the lead resource manager for theBiosciences and Biotechnology Division. Priorto LLNL, he also worked at Intel Corporationin Santa Clara as a financial analyst and inthe US Navy as a submarine electrician. Nick

has a BS in BusinessAdministration fromUC Berkeley’s HaasSchool of Business,and is returning toHaas this fall to pur-sue his MBA in theEvening & WeekendMBA program. Nicklives with his wife,Janet, and two chil-

dren, Declan and Annabelle, in Hayward andenjoys golfing, basketball, and spending qual-ity time with his family.

YAKOV GOLDER

Informatics Department Head

Yakov joined JGI in April 2007 andoversees the Genome Data Systems, IMG,Genome Assembly, Genome Annotation,Comparative Genomics, ProductionInformatics, Infrastructure, and SystemsAdministration. Yakov received his B.S. inComputer Science from the City College ofNew York (CUNY) and M.S. in ComputerScience from New York Institute ofTechnology. He has more than 20 years oftechnical leadership experience at estab-lished corporations and startups in thedelivery of complex, high-performance soft-ware applications, including social net-working, workflow management, invest-ment management, customer relationshipmanagement (CRM), and health care. Priorto JGI, Yakov served as Vice President ofTechnology at CNET Networks, where heoversaw the engineering organization inthe online community division. There he

was responsible for the high-performancephoto-sharing web sitewww.webshots.com, which boasted over1B page views monthly. Prior to CNET,Yakov worked at eBay where he wasresponsible for two critical areas of eBay’scomplex web infrastructure: applicationdata persistence and messaging. Yakov’ssignificant experience in designing andbuilding enterprise class software sys-tems. for both the private and public sec-tor, builds upon previous involvement indevelopment of both software as a serviceweb sites and more traditional softwareproduct development in the engineering,industrial automation and online communi-ties markets. Yakov also brings a wealth ofknowledge to JGI in the application ofestablished and emerging developmentpatterns & practices, a solid grasp ofapplying agile methods, and experience inbuilding and coaching high-performance

project teams. Yakovis married to formerLBNL scientist ElinaGolder-Novoselskyand lives in WalnutCreek. He enjoystraveling, good food(Elina does the gour-met cooking), tabletennis and chess.

CHERYL R. KUSKE

LANL JGI Center Director & Group Leader

Cheryl received her BS and MSdegrees from North Carolina StateUniversity in horticulture & plant pathology,respectively. Through her MS thesis and 3years working in the agrichemicals indus-try, she studied soilborne fungal and nem-atode pathogens of plants. She obtainedher PhD degree in plant pathology andmolecular biology from UC Davis in 1989,where she studied non-cultured bacterialplant pathogens now known as phytoplas-

mas. She receivedDirector’s Fundedand AlexanderHollaenderPostdoctoralresearch fellowshipsat LANL, and con-ducted her postdoc-toral research onbiochemical and

molecular characterization of enzymesinvolved in heavy metal accumulation andresistance in plants. Cheryl’s researchover the past 14 years has focused ondevelopment and use of molecular meth-ods to study soil, water and aerosol micro-bial communities. Her research programhas been dual track with applications toDOE missions and to biothreat security.Cheryl received LANL’s DistinguishedPatent Award in 2004 for development ofbacterial biosensors, and the LANLFellow’s Prize for Research for her contri-butions to environmental microbiology andbiosecurity in 2006. She joined the JGI inJune of 2007 as the LANL JGI CenterDirector. Cheryl and her husband Larryhave 2 children, age 8 and 10. The familyenjoys outdoor activities, including skiing,whitewater sports, hiking and bicycling.

CHRIS WATCHMAKER

Principal Human Resources Generalist

Chris joins JGIafter spending thepast three and one-half years at LBNLin the OperationsHR area. Prior tocoming to the Lab,Chris worked inHuman Resourcesat AppliedBiosystems. He has

over twenty years of HR experience inbiotech, the staffing

JGI FACES

Nick Everson

Yakov Golder

(cont. on page 15)

Cheryl Kuske

Chris Watchmaker

Once all the documentation is inplace, the PM works with the PI toapprove and ship samples for sequenc-ing by the JGI. Once samples arereceived, the PM’s focus shifts to theproduction line. PMs help navigate a

projectthrough thevariousphases ofproductionsequencingby providingthe function-al groupleads withinformationabout theproject,helping the

PI resolve problems, and tracking theproject in a global project tracking data-base.

Project managers face several chal-lenges in helping a PI achieve theresearch goals set forth in a proposal.The most common problem is obtainingappropriate starting material. Often, col-laborating labs have difficulty obtaining

sufficientDNA, or DNAof sufficient-ly high quali-ty, for thedesiredamount ofsequencing.In suchcases, thePMO directsthe scien-

tists to proto-cols that have

worked for other groups, or in somecases puts them in touch with JGI scien-tists who offer advice.

The JGI Project Management Office(PMO) was established to better handlethe organization, tracking, and flow ofsequencing projects through the JGIsequencing pipeline. Led by David Bruce,the PMO consists of a team of threeother project managers: Lynne Goodwin,Kerrie Barry, and Christa Pennacchio,each of whom specializes in plant,microbial, or environmental projects.Also working closely with the PMO arescientist Susannah Tringe and produc-tion manager Tijana Glavina del Rio.

The JGI Global Project TrackingSystem (GPTS) database is the projectmanager’s primary resource for trackingand communicating project progressthrough the sequencing process. ThePMO is involved in a project from themoment a proposal is approved to theclose-out of the research.

A project manager (PM) is assignedto oversee the progression of each proj-ect throughout the pipeline steps, andto facilitate communication between theJGI functional groups and the PI toensure the research goals set forth bythe proposal are being met in a timelyfashion.

Fall 2007 Vol. 4, Issue 2

THE PRIMER / 3

ERT Hosts CribbingWorkshop

In September, the JGI EmergencyResponse Team (ERT) learned a tech-nique called “cribbing” that will allowthem to safely extricate victims trappedunder heavy debris. This techniqueenables a small team to lift as muchas 12 tons! First, the debris must bestabilized so it will not shift and poten-tially increase injuries to the victim.Once the debris has been stabilized,the cribbing team removes all smallpieces of debris. Any remaining heavyor large debris will then be lifted off ofthe victim by using a fulcrum and leverto raise the heavy object off of the vic-tim a few inches while the team buildsup the box cribs under each corner.This procedure is repeated until the vic-tim is free of the debris and can bepulled to safety.

To learn this and other techniquesthat you can use in an emergency situa-tion, consider sitting in on some of theERT classes, or even joining the team. Formore information, please contact WendySchackwitz (WSSchackwitz@lbl.gov).

Meet the JGI Project Management Office

Kerrie Berry

Christa Pennacchio

From left to right: Nancy Hammon,Catherine Adam, Mike Houston (localCommunity Emergency Response Team(CERT) member), Sam Pitluck, and KristenTaylor demonstrate cribbing technique inthe lot beside the JGI warehouse.

David Bruce and Lynne Goodwin

Fall 2007 Vol. 4, Issue 2

4 / THE PRIMER

Mansi ChovatiaResearch AssociateSequencing/Cloning TechnologyVictor KuninBioinformaticist Project ScientistMicrobial EcologyNikos KyrpidesComputational Biologist Staff ScientistGenome BiologyNatalia IvanovaComputational Biologist ScientistGenome BiologyKostas MavrommatisBioinformaticist Research ScientistGenome Biology

OPA AWARD:

IMG/M Team: Natalia Ivanova andNikos KyrpidesDeveloping the IMG/M system andmetagenomic data analysis andcontributing to advancing JGI’s lead-ership in the field of metagenomicsin support of the DOE mission foralternative energy production, globalcarbon cycling, and bioremediation. Rolling QC Team: Harris Shapiro,Jasmyn Pangilinan and Joel Martin Contributions towards the successof the JGI’s Rolling QC Project.Individual Award: Rob EganAccomplishment in successfullyrestoring the data management sys-tem in a remarkably short period oftime.

SPOT Awards:

Property Inventory Team: Ron McKeever& Mark JacinthoOutstanding performance in successfullycompleting the LBNL Wall-to-WallInventory in an efficient and customer-service focused manner.Rolling QC Team:Alex Copeland, RobEgan, Jeff Froula, Ed Kirton, MichaelZhangExceptional team effort leading to thesuccess of the Rolling QC project, there-by improving the accuracy and efficiencyof the JGI’s sequencing work.

Crystal WrightResearch AssociatePrograms/Genetic AnalysisNatasha ZvenigorodskyResearch AssociatePrograms/Sequencing TechnologyKanwar SinghSr. Research AssociatePrograms/Sequencing TechnologyMarcel HuntemannSoftware Developer 1Programs/PhylogenomicsJohn SchiappacasseFinancial Analyst 3OperationsNick EversonFinance & Materials ManagerOperationsAndrew AllisonResearch TechnicianSequencingLaura SandorResearch TechnicianSequencing

Bejaine BayotResearch TechnicianSequencingPeter WilliamsComputer ScientistInformaticsIgor ShabalovSoftware Developer 4InformaticsCristina AlbersHR Assistant IIIHuman ResourcesMathew DunfordSystems Administrator 3Systems AdministrationMatthias HessComputational Bio PD FellowGenetic AnalysisChrista PennacchioSr. Scientific Engr. Assoc.CSPMargie LozanoAdministrative Assistant IIIOperationsAnna EngelbrektsonResearch AssocMicrobial BiologyAnthony KoskyGroup LeadWeb EngineeringEric GreenwadeComputer ScientistGenome Data SystemsSimon MinovitskySoftware Developer 3Genome Annotation Portal Group

JGI P

ROM

OTIO

NSAW

ARDS

JGI N

EW E

MPL

OYEE

S

AWARDS & NEW HIRES

The winner of this year’s LawrenceBerkeley National Laboratory"Runaround" t-shirt design contest isParag Vaishampayan, JGI post-doc.Vaishampayan said his design wasinspired by the bioenergy programs at

the Lab and JGI. The Runaround tookplace Friday, Oct. 19. T-shirts were begiven to all participants and volunteers.The results can be found at:http://www.lbl.gov/today/2007/Oct/22-Mon/10-22-07.html

JGI Post-Doc Wins T-Shirt Contest for 30th Anniversary LBNL Runaround

Winner ParagVaishampayan

Fall 2007 Vol. 4, Issue 2

THE PRIMER / 5

BY CHERYL KUSKE

The Department of Energy Office ofScience has been studying the respons-es of terrestrial ecoystems to elevatedcarbon dioxide and ozone using free-aircarbon dioxide enrichment (FACE) andopen top chamber (OTC) experimentalfield sites. After 10-12 years of opera-tion, the six FACE and OTC site experi-ments will be coming to completion,offering an excellent opportunity todetermine the effects of long-term ele-vated CO2 on below-ground plant param-eters and soil microbial communities.We now have a unique opportunity toconduct disruptive sampling of the soilsin the sites, which opens the door to avariety of below-ground studies to corre-late to the extensive datasets on plantperformance and other ecologicalparameters. In August, Cheryl Kuskeand David Bruce of the LANL JGI hosteda small workshop at DOE in Germantownwith the goal of developing a science

and implementation plan, based onmetagenomic technology, to assess theclimate change responses of the below-ground microbial communities in the DOEterrestrial ecosystem FACE and OTC sites.

The workshop was attended by sci-entists from the FACE sites, representa-tives from the JGI, and DOE programmanagers. Workshop participants cameto consensus on major research ques-tions that could be addressed usinggenomics, especially those that wouldspan all six ecosystems under investiga-tion, and discussed several approachesto using genomic and metagenomictechnologies that could be applied tothese research questions. We began tooutline a four-tier research and sequenc-ing strategy that will become the basisof a written roadmap and strategic plan.This initiative would use JGI’s substantialsequencing capability to address a sig-nificant DOE mission in terrestrial ecosys-tem climate change response. Thisresearch area requires a comparative

genomics approach to define responseslinked to the climate change parametersin the very complex soil system. In addi-tion to providing information on below-ground microbial responses to long-termclimate change, this initiative will poten-tially push current sequencing technolo-gies and enable research, technology,and analytical advances that could beapplicable to other ecosystems.

LANL HOSTS FACE METAGENOMICS WORKSHOP

ORNL Open Top Chamber (OTC) field site

BY CHRIS DAUM

On August 2, the JGI ProductionGenomics Facility witnessed the endof a sequencing era. Thirty-sixMegaBACE 4500 sequencers wereloaded with plates and processedtheir final sequencing runs. For thelast eight years, three generationsof MegaBACE DNA sequence analy-sis platforms have been an indis-pensable component of the JGI pro-duction sequencing line. Duringtheir long run, 480,000 sampleplates were loaded, generatingmore than 62 billion high-qualitybases. The MegaBACE platform has

been phased out to allow for theintegration of next-generation tech-nologies.

With the inception of the capil-lary-based MegaBACE 1000 plat-form in late 1999, significantadvances were made over theindustry standard slab gel instru-ments of the time, particularly inthe areas of automation, workflow,and operation. The 84 MB1000instruments in use at the JGI wenton to play a crucial role in theHuman Genome Project.

With the launch of the updatedMegaBACE 4000 platform in late2001, a new standard for high-

throughput sequencing was set,with its 384-capillary array systemaccelerating the sequencing analy-sis process. The JGI adopted thisupdated platform in early 2002 andused 21 MB4000 instruments as aprincipal sequencing platform untilDecember 2004. With the advent ofthe MegaBACE 4500 platform inearly 2003, the paradigm of high-throughput DNA sequencing waspoised to shift forward once again.Development work and onsite test-ing of the new MegaBACE platformbegan at the JGI in February 2003in collaboration with GE HealthCare(formerly

MegaBACEs Go Bye-Bye

(cont. on page 16)

Fall 2007 Vol. 4, Issue 2

6 / THE PRIMER

BY IRENE WAGNER-DÖBLER, HELMHOLTZ-CENTRE

FOR INFECTION RESEARCH, BRAUNSCHWEIG,

GERMANY; IWD@GBF.DE

Dinoroseobacter shibae is a member ofthe Roseobacter group, a phylogenetic line-age within the Alphaproteobacteria, which isabundant in the ocean. It was isolated fromtoxic dinoflagellate cells, eukaryotic unicellularphotosynthetic algae that are responsible for“red tides” resulting in paralytic shellfish poi-soning. Dinoroseobacter shibae itself is ableto conduct a special type of bacterial photo-synthesis, called aerobic anoxygenic photo-synthesis, and has a complex quorum-sens-ing system that presumably helps the organ-ism to control its interaction with the host.

After JGI and its collaborators hadsequenced the genome, an annotationJamboree was held in Braunschweig,Germany, from September 10-14, to unravelthe genetic adaptations of D. shibae to itshabitat as they are reflected in the genome.The hosting institute, Helmholtz-Center forInfection Research (HZI), provided the neces-

sary facilities: Aroom for workingwith 30 high-speed Internetconnections, ameeting room fordaily seminars,and unlimited fuel

for the scientists(coffee and cookies). The 28 participantsincluded professors of microbiology and PhDstudents from the universities ofBraunschweig, Göttingen and Oldenburg,and microbiologists from the GermanCulture Collection (DSMZ).

Thanks to a grant from the Volks-wagenFoundation, JGI Genome Biology Programhead Nikos Kyrpides was able to participateand provide two talks about IMG(http://img.jgi.doe.gov/), a kick-off presenta-tion on the first day, and a general talk forthe whole HZI at the end of the Jamboree.

He demonstrated IMG’s latest features, pro-vided access to specialized software,answered questions, and contributed signifi-cantly to the success of the Jamboree.

Five days of full-time work on thegenome was a special experience for all.

Some hadnever mined agenome beforein such a way,and were excit-ed about theeasy accessIMG provides,and about theoverwhelmingamount of infor-

mation presented. The fundamentals ofbiochemistry and physiology, known only toexperienced professors, proved to be ofinvaluable importance. The interdisciplinarynature of the gathering was also important:Pathways identified by biochemists weregiven possible adaptive significance byecologists. All enjoyed the possibility tointeract closely and directly, across the key-board or over coffee—not to forget goodfriendly talks in the evening over beer,which helped bring the group together. TheJamboree provided the outline of possiblekey stories for the genome paper. Theseare now being completed by the contribut-ing scientists, together with the manualannotation of the genome, with the aim ofhaving the manuscript ready by December.

Dinoroseobacter shibae Jamboree in Germany

Prorocentrum lima, atoxic dinoflagellate, fromwhich Dinoroseobactershibae was isolated.

Irene Wagner-Döbler

LATEST JGI ANNOTATION JAMBOREES

Daphnia, Bloomington, IN, July 7-9, 2007Volvox, JGI, Aug 6-10, 2007http://conferences.cgb.indiana.edu/daphnia2007/index.htmlAureococcus, Southampton, NY, Oct 3-5, 2007www.aureococcus.orgEukaryote Annotation report: 15 new eukaryotes were annotated in FY07,6 genomes were updated 7 currently in annotation18 Genome Portals were publicly released

Pichia stipitis

Ostreococcus lucimarinus

Nematostella vectensis

Chlamydomonas reinhardtii

Physcomitrella patens

Laccaria bicolor

Branchiostoma floridae

Monosiga brevicollis

Trichoderma reesei, finished

Naegleria gruberi

Thalassiosira pseudonana, finished

Phaeodactylum tricornutum, finished

Sporobolomyces roseus

Nectria haematococca MPVI, finished

Phycomyces blakesleeanus

Daphnia pulex

Postia placenta

Volvox carteri

Lottia gigantea

Mycosphaerella fijiensis

Micromonas pusilla CCMP1545

Capitella sp. I

Aureococcus anophageferrens

Helobdella robusta

Trichoplax adhaerens

Trichoderma virens

Phytophthora capsici

Micromonas pusilla NOUM17, finished

Micromonas pusilla CCMP1545, improved

Emiliania huxleyi

Selaginella moellendorfii

Sorghum bicolor

Batrachochytrium dendrobatidis JAM81

Chlorella sp. NC64A

Ostreococcus RCC809

Trichoderma atroviride

Anno

tate

d

Publ

ic

Publ

ishe

d

– done during FY07

– prior to FY07

– October 2007

– in progress

Annotated Eukaryotes FY2007

Fall 2007 Vol. 4, Issue 2

THE PRIMER / 7

BY RANDY MONROE

My summer at JGI began before theschool year ended, working with PhilHugenholtz’s Microbial Ecology team com-prised of Phil, Falk Warnecke, SuzanYilmaz, Julita Madejska, Hector GarciaMartin, and Victor Kunin.

It was, and still is, a fantastic opportu-nity to be involved with cutting-edge sci-ence that allows the integration of labora-tory skill sets for the middle-school level.This unique opportunity began a year ago,with the idea of learning about our localmetagenomic resource with a goal todesign and introduce a program for theFoothill students. I was presented with thetask of finding a relatively little knowngroup of bacteria called OP11.

Approximately 10 years ago, Phil dis-covered some novel thermophilic (a typeof extremophile that likes temperaturesabove 45C) bacteria in YellowstoneNational Park, in a hot spring calledObsidian Pool near the Mud Pots in thesoutheastern side of the park. He namedone group of these thermophiles OP11.Since its discovery, OP11 and many relat-ed organisms have grown into an entirelypreviously unknown major bacterial line-age. This lineage has never been culturedand reproduced in the laboratory, nor hasit ever been seen under a microscope, butDNA analysis has shown it to be quiteabundant in a variety of locations, includ-ing the extreme environments of hotsprings and hydrothermal vents, in theteeth of people with periodontal disease,and in several other habitats lacking oxy-gen (anaerobic).

My challenge was to find the critterand get a picture of it! After some initialtraining in DNA extraction, PCR, and elec-

trophoresis gels, I was to go toYellowstone and obtain some fresh sam-ples. I coordinated the journey with one ofPhil’s long-time colleagues, veteranYellowstone sampler John Spear from theColorado School of Mines who studiedunder microbe guru Norman Pace, now atUniversity of Colorado, Boulder.

In Yellowstone, we sampled atObsidian Pool (78C), OP Prime Pool (56C),and the new mud vent we deemed OPMud Vent (85C), Sperm Pool (56C),Octopus Pool (88C and 50C edge), NorrisGeyser Basin, and Mammoth, and hadthose samples shipped to JGI.

Upon returning to JGI, Phil wanted toorganize a local sampling expedition. Iarranged a day trip for Phil, Falk, Suzan andI to visit the East Bay Municipal Utility

District’s Wastewater Facility near the SanFrancisco-Oakland Bay Bridge and obtainsome samples from two anaerobicdigesters. We then headed to East BayRegional Park in Hayward to the saltponds, and to the South Bay city of Alviso toDon Edwards National Wildlife Refuge toobtain some truly remarkable smellinganaerobic organisms.

Back in the lab, I am ultimately goingto perform Fluorescence In SituHybridization (FISH) to view and photo-graph one of these remarkable organismsand learn more from those images.

How does all of this tie together? Well,in 1978 my stepfather, Jim Christy, discov-ered Pluto’s moon Charon, naming it aftermy mother, Charlene. In January 2006, wewere invited to NASA’s Cape Canaveral forthe launch of the New Horizons probeheaded to Pluto and the Kuiper Belt on aLockheed Martin Atlas V rocket. As aneducator on the New Horizons Team, Ialso had the opportunity to work atLockheed Martin last summer in missiledefense studying Infrared Technologies. IRtechnologies are an important tool instudying hydrothermal vent systems. It ispossible that life began on primordialEarth in such vents. If other locations,such as Europa, a moon of Jupiter, havevent systems, there may also be life there,too. It is quite possible that OP11 is livingelsewhere in the solar system. Wouldn’t itbe grand to find it?

Randy Monroe is a 6th grade earth sci-ence teacher at Foothill Middle School inWalnut Creek, CA. In addition to his workas an educator, Randy Monroe is the frontman for premier Van Halen tribute band,Hot for Teacher: http://www.hftrocks.com/.His summer experience was sponsored byLawrence Livermore National Laboratory’sEdward Teller Education Center (ETEC):http://etec.ucdavis.edu. In addition, Randyreceived support from the IndustryInitiatives for Science and Math Education(IISME): http://www.iisme.org/

Rock Star Educator SpendsSummer at JGI

Randy Monroe samples the South Bay salt flats

Randy Monroe (right) with his mentor JGIMicrobial Ecology Program Head PhilHugenholtz

Fall 2007 Vol. 4, Issue 2

8 / THE PRIMER

JGI has secured a five-year exten-sion on its lease with an option for anadditional five years. The University ofCalifornia Regents have signed off on adeal with landlord Hall Equities Groupthat will ensure JGI’s long-term pres-ence in the community of Walnut Creek,situated halfway between its parentfacilities, Lawrence Berkeley andLawrence Livermore NationalLaboratories. The new lease enablesDOE JGI to expand the current facility onits Walnut Creek campus to include avacant 18,000-square-foot building, whichwill be renovated and opened in early in2008. This addition will serve to con-solidate administrative and informaticsstaff and feature a new education out-

reach laboratory, bringing JGI’s totalfootprint to 80,000 square feet.

“We are delighted to be able to extendour stay here in Walnut Creek,” said JGIDirector Eddy Rubin. “We have grownconsiderably over the last ten years aswe have transitioned from determiningthe DNA code for the human genome toa national user facility for the DNAsequencing of many different importantorganisms. Our goal is to sustain ourleadership in providing the informationthat will advance the nation’s interestsin developing renewable sources ofclean energy, tracking the fate of car-bon in our atmosphere, and restoringour environment.”

“Walnut Creek is proud to be home

to one of the world’s leading DNAsequencing centers in JGI,” said SusanRainey, Mayor of the City of WalnutCreek, California. “In our very own back-yard, we can lay claim to having aworld-class scientific resource—onefirst involved in sequencing the humangenome, then the first tree genome, andnow characterizing other plants andmicrobes that will play a major role inimproving our energy future. In addition,JGI researchers are serving to inspirethe next generation of scientists andengineers through the thousands oflocal high school students who havetoured the facility over the years. Welook forward to building on this produc-tive community partnership for at leastthe next decade.”

JGI Secures Long-Term Lease on PGF

Early this year, JGI launched theGenomic Encyclopedia of Bacteria andArchaea (GEBA) project, aimed at system-atically filling in the gaps in sequencingalong the bacterial and archaeal branchesof the tree of life. To test the feasibility ofthe GEBA approach, JGI has since under-taken a pilot project in collaboration withthe German Collection of Microorganismsand Cell Cultures, DSMZ, to sequence100 bacterial and archaeal genomesbased on the phylogenetic positions oforganisms.

DSMZ (http://www.dsmz.de/) is anon-profit research institution with the mis-sion to do “science for service and servicefor science.” DSMZ is one of Europe’sleading suppliers of cultures and biologicalmaterials to customers and collaboratorsworldwide. The organism selectionprocess for the pilot project is based on acombination of objective analysis of therRNA tree of life and consultation with ascientific advisory board. All genomesequence data will be released to thecommunity through the JGI Web site and

Genbank. In recent months, the relation-ship between JGI and DSMZ has taken offwell beyond expectations.

“The start of this collaboration waseasy because of the long-term linksbetween some of the key players involved,including myself and Erko Stackebrandt atDSMZ, and Jonathan Eisen, PhilHugenholtz and Nikos Kyrpides at JGI,”

said Hans-Peter Klenk,Head of theDepartmentofMicrobiologyat DSMZ. “Weknew from thevery beginningthat there is aserious mutu-

al interest in this project and that we cantrust our partners to make this project asuccess.”

Genomic DNA is now routinely beingshipped from Germany to Walnut Creek.Four microbes from the initial batch have

been finished in draft form, 20 more are inproduction, and 53 in the queue. “Theexchange of DNA and information is verypromising and bodes well for the timelycompletion of the pilot, with the benefitsextending well beyond,” said Klenk.

“The GEBA project perfectly fits to ourvision for the future of microbial taxonomyand the collection of type strains in gener-al. With the continued decrease in costsfor genome sequencing and analysis, wepredict that in only a few years, novel typestrains will be accessed into strain collec-tions only after their genome sequencehas been revealed and analyzed.”

In addition, JGI is acquiring samplesfrom sources closer to home, from theAmerican Type Culture Collection (ATCC).ATCC (http://www.atcc.org/) is a private,nonprofit resource dedicated to the collec-tion, preservation and distribution ofauthentic cultures of living microorgan-isms, viruses, DNA probes, plants, andhuman and animal cells.

Klenk said that the worldwide scientificcommunity will benefit (cont. on next page)

DSMZ Connection Jumpstarts GEBA

DSMZ bacterial collectionin Germany (Courtesy picture-alliance/dpa)

Fall 2007 Vol. 4, Issue 2

THE PRIMER / 9

BY PAT KALE

Members of the JGI InformaticsDepartment, led by Yakov Golder, are hardat work creating a better way for JGI man-agers, staff and collaborators to monitorthe progress of genomic projects as theymake their way through the PGF and part-ner institutions. From the time a proposalis submitted through any of the JGI propos-al-based programs, until the time that thefinal data set is submitted to NCBI, a sys-tem of software applications and databas-es will track the progress of all work per-formed on a collaborator’s behalf. The goalis to make the JGI as transparent to collab-orators as possible.

The Global Project Tracking System(GPTS) will form the backbone of this ambi-tious software system. It will provide thedatabase, software interfaces, and statustracking coordination that will enable theproduction informatics department staff tobuild useful applications. This software willenable JGI staff and collaborators toinquire about the status of any genome,and answer such questions as: Has the

collaborator submitted the informationrequired by the JGI before DNA is shipped?Has the Project Management Office (PMO)completed the user agreement? Hassequencing commenced? Has the tracedata been submitted to NCBI? DavidPletcher, who leads the ProductionInformatics group, is in charge of GPTSphase 1.

The goal of GPTS phase 1 is to deliverthe basic functionality of its predecessorsystem in a form that has been redesignedfor better performance and improved scala-bility. The PMO can expect to have forms tomanage proposals, user agreements, PMOprojects, contacts, accounts, and samples.In addition, search, summary reports, anddata export to Excel spreadsheets will beprovided. Two related software develop-ment efforts are in progress in David’sgroup. The sample tube entry form, creat-ed by Duncan Scott, will replace the wholegenome tracking spreadsheet currentlymaintained by Eileen Dalin. The plate track-ing tools, created by Khela Baskett, willimprove the ability of the productionsequencing staff to schedule and trackplates. GPTS phase 1 was rolled out at the

end of September 2007.Since the release, data cleanup and

application fine-tuning efforts are underwayto correct any incomplete or bad data,check and update contact and cost-accounting information, apply new conven-tions for controlled vocabularies, fix minorbugs, and train additional users.

In parallel with GPTS phase 1, severalother software development efforts are inthe works. They will feed data into GPTS,and report data from GPTS to the PMOand collaborators. The CollaboratorStatus Reporter, which provides collabo-rators with at-a-glance status information,will be released with GPTS phase 1. TheRequired Information application willautomate the process of submitting,reviewing and accepting sample informa-tion prior to the shipment of DNA. Lookfor this application to be completedbefore the end of the year. Follow-on proj-ects include a contact management sys-tem, a LIMS for the Cloning Technologygroup, and a Web portal for the PMO.These projects are the responsibility ofthe Web Team (Joni Fazo, Rene Perrier,Annette Greiner), led by Pat Kale.

NEW TRACKING SYSTEM ROLLED OUT

from the GEBA pilot project by gaining accessto a much better balanced database formicrobial genomes.

“The phylogenetically diverse genomesanalyzed within the GEBA pilot project willprovide urgently needed anchors for theimproved annotation of data coming out ofthe many ongoing metagenome projects. Inaddition, DSMZ will provide easy andaffordable access to biological material,cultures as well as DNA, of all GEBA pilotproject strains to the world-wide scientific

community—without any strings attached.“Moreover, participation in the GEBA pilot

project provides an excellent opportunity totrain our staff and the next generation ofgenomicists.”

“Hans-Peter is one of the pioneers ofmicrobial genomics, said GEBA godfatherJonathan Eisen. “He was the first author onthe second archaeal genome to be publishedand he has been a leader in microbial evolu-tion studies for some 20 years. It is an honorto work with him on such an important topic.”

“I view the entire project as a triumphof cutting-edge science from two govern-ment institutions with perfect complemen-tarity, forming an international partnershipfor the benefit of the entire community,”said Nikos Kyrpides, JGI Genome BiologyProgram head.

JGI, DSMZ and others involved are pur-suing possible options for funding a continu-ation of GEBA beyond the pilot phase tosequence hundreds, and perhaps even thou-sands, of microbial genomes.

DSMZ Connectioncont. from page 8

Fall 2007 Vol. 4, Issue 2

10 / THE PRIMER

BY JERRY TUSKAN

Populus trichocarpa is a species thathas indeterminate growth, which meansthat as long as the conditions are right,it will keep putting out new leaves andelongating its stem. That’s an unusualtrait. Most plants grow in a determinantmanner—they have a set number of celldivisions and that’s it. In the case ofperennial plants, the extent of determi-nant growth is determined by the condi-

tions of the previous year. The plantretains a metabolic signal of how muchto grow the subsequent year. In thecase of perennials, which can’t affordto invest too many resources in adrought year or a cold-interrupted grow-ing season, it’s a way of predicting whatthe next year is going to be like.

Poplars, on the other hand, will keepgrowing until water, nitrogen, and/ornutrients become limited, or daylightshortens, and to some degree, coldweather sets in. However, because itdoes not have as many cold receptors,if you keep giving it nitrogen and water,it will grow right into the early frost peri-od in the fall.

For bioenergy applications, we areseeking to harness these traits, becausethe more of the growing season that aplant can capture, the more biomassthey put on. One of the objectives is tomaximize how long the leaves are dis-played to the sun. Some researchersare selecting for photoperiod responsebecause plants can perceive when thedays start getting shorter and in responsethey start setting buds. Typically, moresouthern sources of plant material setbud later, requiring a much shorter dayto cause them to set bud. So, in short-rotation biomass farms, we can use thattrait to maximize the amount of biomass.

The other change occurring thistime of year is the secondary thickeningof the cell walls within the xylem. Witheach primary cell division, cell wall forms.In trees, a secondary cell wall is formedthat becomes the woody part of itsarchitecture, i.e., the stem. There arethree layers of cells (S1, S2, S3)required to construct mature xylemcells. Lignification is the final step inthe maturation process. In September,as the growing season begins to

decline, and because of the poplar’sindeterminant habit, most of the cellsformed late in the season will not actu-ally mature that season. Secondarythickening and secondary cell wall for-mation is arrested and lignification con-tinues next season.

Because of the relationship betweenindeterminant growth and lignification, ifyou take a core from a poplar tree youwon’t see annual rings like a redwoodor a pine.

As a tree ceases to grow late in theseason, there is a spike of lignification.This process has implications for bioen-ergy. Lignin is not convertible to sugarbecause it’s polyphenolic and impedesthe invasion of microbes and their cellwall degrading enzymes. Among our goalsis to minimize the lignin, to the extentpossible, and still have the plant cellsand tissue remain healthy. So, elucidat-ing the process of cell wall formationduring dormancy, and what triggers thatmaturation process and the depositionof lignin, will help us tailor plants for ourenergy crop domestication project.

Over the next five years, we hope totease apart some of this complexity tobetter our understanding of the molec-ular mechanisms behind cell wall for-mation, lignification, and indeterminantgrowth.

JGI Poplar Virtual Yard (Meter)Stick: 192 inches (16 feet) asof Oct 10, 2007, representing a3.5x growth spurt in less than13 months since the ceremonialplanting.

Jerry Tuskan, Oak Ridge NationalLaboratory, is the JGI Laboratory ScienceProgram Lead

Poplar Watch

Jerry Tuskan and his poplar friend

Fall 2007 Vol. 4, Issue 2

THE PRIMER / 11

On October 18 and 19, JGI’sUndergraduate Research Program con-vened the first Workshop in MicrobialGenome Annotation. Nineteen educatorsfrom 14 institutions participated, repre-senting a diverse cross-section ofresearch universities, state and liberalarts colleges. The goal of the workshopwas to provide the tools and ideas foradvancing genomics and bioinformaticsacross undergraduate curricula.

Cheryl Kerfeld, JGI’s EducationProgram head, presented a survey of cur-rent bioinformatics tools and strategiesfor integrating annotation across the lifesciences curriculum, including algorithmsfor gene calling, pathway annotation, andcharacterization of hypothetical proteinfunction.

The participants subdivided into work-

ing groups based on their teaching inter-ests—biochemistry, microbiology, molecu-lar genetics, and those planning to devel-op bioinformatics courses—to explorecurriculum options that they will imple-ment at their respective institutions in thewinter-spring term of 2008.

The educators were sent back to theirinstitutions with homework—to engagetheir classes in collectively annotating(assigning biological function to thesequence of) the microbe Ammonifexdegensii—a heat-loving bug of geothermalorigin. Folker Meyer and his team atArgonne National Laboratory are working

closely with Kerfeld in developing the plat-form of bioinformatics tools that the stu-dents will use to complete their assign-ment.

“We had an extraordinarily productiveshort time together,” said Kerfeld. “I amoptimistic that when we reconvene at JGInext June, they’ll all be primed to discusstheir results and be in a position to begindrafting a paper.”

Kerfeld said that the participants willcomplete a survey conducted by the OakRidge Institute for Science and Education(ORISE), which will serve as starting mate-rial for an evaluation

JGI Hosts Undergraduate Educators forMicrobial Genome Annotation Workshop

Front to back, left to right; Front row: Cheryl Bailey, University of Nebraska-Lincoln; KelynneReed, Austin College; Sharyn Freyermuth, University of Missouri; Ferda Soyer, Izmir Instituteof Technology (Turkey); Zhaohui Xu, Bowling Green State University. Second row: KathleenScott, University of South Florida; Sabine Heinhorst, University of Southern Mississippi;Cheryl Kerfeld, JGI; Tuajuanda Jordan, HHMI; Jay Lennon, Michigan State University. Back row:Daniela Bartels, ANL; Brad Goodner, Hiram college; Erin Sanders-Lorenz, UCLA; ChristopherKvaal, Saint Cloud State University; Mitrick Johns, Northern Illinois University; Folker Meyer,ANL; Jayna Ditty, University of St. Thomas; Tobias Paczian, ANL. Stuart Gordon, Hiram College,not pictured.

(cont. on page 14)

JGI’s StanmanTops NorCal Greg Stanley, the Joint GenomeInstitute’s facilities manager, wonthe NorCal Top Comp AssociationChampionship in late Septemberwith his 409 c.i. Chevy smallblock-powered dragster. The eventtook place at Famoso Racewaynear Bakersfield.

Fall 2007 Vol. 4, Issue 2

12 / THE PRIMER

BY MEGAN KENNEDY

My triathlon went much better than antic-ipated. I finished in 3:03:38—much betterthan my 3:20 estimate. All worries of sealsand sharks were gone in the chaos of amass swim start. After the pack spread out,I had a good swim. The spectators saw apod of dolphins swim by—a good sign that

there weren't anysharks in the area.One of the mostimpressive andinspiring parts of therace was watchingthe founder of theChallenged Athletes

Foundation usecrutches in thesoft sand to get

into the water, then crutch his way out andaround the swims' half way point and go

back into the water.I had a strong

bike ride and was sofocused on not draft-ing that I hardly hadany time to enjoy thebeautiful scenery. I'll

have to go backand bike it at amore leisurely

pace. The run was the toughest part, havingpushed myself during the swim and bikeportions. The cheering from my teammates,coaches, and family kept me going.

Thank you for the donations to theLeukemia and Lymphoma Society. 1.4 mil-lion dollars were raised by Pacific GroveTeam in Training triathletes. To date, 800million dollars have been raised for bloodcancer research!

Thank you!Megan

PS: For those who asked how to signup for races, check out active.com and ony-ourmarkevents.com. Active also provideslinks to local sports teams.

There's still time to help the Leukemia& Lymphoma Society fight cancer and sup-port patients. http://www.active.com/donate/tntgsf/mckennedy

Megan Kennedy, JGI SequencingDepartment staffer, writes about theTriathlon at Pacific Grove onSeptember 8, which entailed a 0.9-mile swim through kelp beds, 24.8-mile bike ride and a 6.2-mile run.

Megan exceeded her contributiongoal, collecting $3,550 on behalf ofthe Leukemia and LymphomaSociety.

Megan Kennedy bikes

Megan Kennedy runs

Len Pennacchio—JGI Genetic AnalysisProgram Head and Senior Staff Scientist inthe Genomics Division at Lawrence BerkeleyNational Laboratory—is the recipient of ThePresidential Early Career Award for Scientistsand Engineers (PECASE) for his significantcontributions to the generation and interpre-tation of the human genome sequence.Specifically, he is being honored for his sys-tematically assigning gene regulatory func-tion to the human genome through the cou-pling of vertebrate comparative genomicsand large-scale studies in mice, using aworld-class and unique mouse resource thathe established.

“Len is extraordinarily capable at gettingthings done,” said JGI Director Eddy Rubin.“I think that we’ll be seeing more great

accomplishments coming from Len’s contri-butions.”

The Presidential Early Career Award forScientists and Engineers was created tohonor and support the extraordinary achieve-ments of young professionals at the outsetof their independent research careers in thefields of science and technology. ThePresidential Award embodies the high priorityplaced by the government on maintaining thescientific leadership position of the UnitedStates by producing outstanding scientistsand engineers who will broadly advance sci-ence and the missions important to the par-ticipating federal agencies.

Pennacchio and the other 2006 PECASErecipients were honored in an award ceremo-ny in Washington, DC at the Presidential Hall

of the Dwight D. Eisenhower Executive OfficeBuilding on November 1, 2007. Each awardrecipient receives a plaque, a citation fromthe President, and $50,000 per year for fiveyears to support their research.

Pennacchio (left) receiving thePECASE plaque from DOE DeputyUndersecretary Clay Sell in theWashington DC ceremony on Nov 1

JGI Triathlete–Mission Accomplished!

Len Pennacchio Receives Presidential Award

The project will be also be supportedby ArborGen, LLC, a South Carolina-basedforestry biotechnology company. ArborGenwill provide access to their collection ofEucalyptus sequences and will work toenable transformation of the model E. grandis clone that will be the sourceof the genomic sequence.

“Sequencing the Eucalyptus genomewill help us overcome many of the majorobstacles toward achieving a sustainableenergy future,” said Myburg. “Embeddedin this information is the molecular circuitmap for superior growth and adaptation inwoody plants that can be optimized forbiomass production. Its unique evolution-ary history, keystone ecological status, andadaptation to marginal environments makeEucalyptus the focus of choice for expand-ing our knowledge of the evolution andadaptive biology of all perennial plants.”

The genus Eucalyptus, comprised ofover 700 different species, includes someof the fastest growing woody plants in theworld and, at approximately 18 millionhectares in 90 countries, it is one of themost widely planted genus’ of plantationforest trees in the world.

“The Eucalyptus genome will provide awindow into the tree’s metabolic pathways,shedding light on such traits as cold toler-ance, osmotic potential, membrane integri-ty, and other agronomic features,” said co-lead Tuskan. “As the genus is amenableto genetic transformation, it can serve asa validation platform for candidate geneexpression studies—helping us to expandEucalyptus’ range and exploit its potentialas a bioenergy plantation crop.”

“This monumental project will enableimproved breeding strategies for cellulosicethanol feedstocks and contribute to envi-ronmentally sound improvements in pro-ductivity for the global forestry industry,”said project collaborator Maud Hinchee,Chief Technical Officer of ArborGen. “This

Fall 2007 Vol. 4, Issue 2

THE PRIMER / 13

Maximizing Eucalyptus

effort will help us advance our goals of pro-ducing renewable high-value biomass froma smaller environmental footprint.”

A considerable amount of carbon isalready tied up in Eucalyptus biomass.Coupled with the emerging economicincentives for carbon sequestration,Eucalyptus is a prime candidate forincreased efforts to remove carbon fromthe atmosphere. “In countries such asBrazil, Eucalyptus is used as a source ofrenewable energy for high-quality steel pro-duction in a way that reduces the net pro-duction of greenhouse gases. Eucalyptusis capable of sequestering carbon at rateof 10 tons of carbon/hectare/year andhas a positive net carbon balance evenwhen it is used to generate energy fromcharcoal or for pulp and paper production.Furthermore, plantation forestry ofEucalyptus plays a crucial role in reducingthe pressure on tropical forests and asso-ciated biodiversity,” said project co-leadGrattapaglia.

Eucalyptuscont. from page 1

Genome-Wide ExperimentalDetermination of Barriers to HorizontalGene Transferhttp://www.scienceonline.org/cgi/content/abstract/1147112Science Express Reports 18 October 2007[DOI: 10.1126/science.1147112] Rotem Sorek, Yiwen Zhu , Christopher J.Creevey , M. Pilar Francino , Peer Bork ,Edward M. RubinA JGI survey identified genes that kill the bac-teria employed in the sequencing processand throw a microbial wrench in the works. Italso offers a possible strategy for the discov-ery of new antibiotics.

Sea Anemone Genome RevealsAncestral Eumetazoan GeneRepertoire and Genomic Organizationhttp://www.sciencemag.org/cgi/content/abstract/317/5834/86Science 6 July 2007: Vol. 317. no. 5834, pp.86 – 94, DOI: 10.1126/science.1139158Nicholas H. Putnam, Mansi Srivastava, UffeHellsten, Bill Dirks, Jarrod Chapman, AsafSalamov, Astrid Terry, Harris Shapiro, ErikaLindquist, Vladimir V. Kapitonov, Jerzy Jurka,Grigory Genikhovich, Igor V. Grigoriev, SusanM. Lucas, Robert E. Steele, John R. Finnerty,Ulrich Technau, Mark Q. Martindale, Daniel S.Rokhsar Sea anemones are seemingly primitive ani-mals that, along with corals, jellyfish, andhydras, constitute the oldest eumetazoanphylum, the Cnidaria. Here, we report a com-parative analysis of the draft genome of anemerging cnidarian model, the starlet seaanemone Nematostella vectensis. The seaanemone genome is complex, with a generepertoire, exon-intron structure, and large-scale gene linkage more similar to verte-brates than to flies or nematodes, implyingthat the genome of the eumetazoan ancestorwas similarly complex.

Genome sequencing reveals complexsecondary metabolome in the marineactinomycete Salinispora tropicahttp://www.pnas.org/cgi/content/abstract/104/25/10376PNAS | June 19, 2007 | vol. 104 | no. 25 |10376-10381Daniel W. Udwary, Lisa Zeigler, Ratnakar N.Asolkar, Vasanth Singan, Alla Lapidus, WilliamFenical, Paul R. Jensen, and Bradley S. MooreOur analysis shows that S. tropica dedicatesa large percentage of its genome (approx9.9%) to natural product assembly, which isgreater than previous Streptomyces genomesequences as well as other natural product-producing actinomycetes.

Recent Notable JGI-Enabled Publications

Fall 2007 Vol. 4, Issue 2

14 / THE PRIMER

question from DOE Office of Biologicaland Environmental Research’s Dan Drellabout whether it would be useful for theBRCs to do any in-house sequencing,Jay Keasling noted that JBEI has noplans to buy sequencers or to try andduplicate the expertise available at JGI.

Each of the three BRC directorsgave an overview of their plans for thenext five years. Jay Keasling discussedthe organization of JBEI and initial feed-stock targets of Arabidopsis and rice.Martin Keller described the BESC struc-ture and their goal to overcome bio-mass recalcitrance for improving bio-mass processing. Tim Donohue ofGLBRC talked about plans for conver-sion of biomass into energy productswhile also studying economic and envi-ronmental sustainability of the biomass-to-biofuel pipeline.

During the lunch break, JGISequencing Department Head Susan

Lucas led a group through a tour of thesequencing line, ending up at the 454and Illumina sequencers for a detaileddiscussion of new techniques.

To highlight the array of expertise

available at JGI, Jim Bristow spoke afterlunch about project management; PaulRichardson discussed microbialsequencing and IMG; Susannah Tringeexplained eDNA, metagenomics, and

Bioenergy Centerscont. from page 1

of the workshop. The Howard HughesMedical Institute (HHMI) senior programofficer for science education, TuajuandaJordan, participated in the workshop asan observer.

“This workshop really serves as amodel for stretching our resources tobring together scientists and educators,”said Jordan. “This is a trend we are see-ing, something that HHMI is doing aswell. The tools developed by Argonne arehelping to bring these communitiestogether. This is the prevailing model forscience education in this country—and Ithink it’s terrific.”

“What this means to a faculty mem-ber trying to innovate science education: Idon't have to go it alone,” said CherylBailey, Ph.D., Assistant Professor,

Department of Biochemistry, UniversityNebraska-Lincoln. “We can see how thisworks across many institutions to helpthose in the future incorporate this typeof learning at their institution. The backingby JGI gives us the credibility to makechanges in our science courses; the work-shop was a true collaborative effort withinput and feedback working on all levelsof the project. It is truly a wonderful wayto innovate science education and servesto both develop faculty members and thestudents they engage.”

The American Society for Microbiology(ASM) has a long-standing commitment toundergraduate education. In theirCommittee on Undergraduate Education’sstrategic plan, released earlier this year,

they cited their interest in supporting andassessing pilot projects, including theJGI’s, to involve undergraduate students ingenomic research and those initiativesthat leverage undergraduate teaching fel-lowships and undergraduate genomicresearch programs to attract underrepre-sented populations.

Said ASM Education DepartmentDirector, Amy Chang, “I am encouraged bythe reports of JGI’s first microbial annota-tion workshop for undergraduate educa-tors. Their objective is consistent with ourinterests in building a network of educa-tors and providing access to the pertinenttools to create opportunities those stu-dents interested in pursuing careers inmicrobial genomics and bioinformatics.”

Undergraduate Educatorscont. from page 11

IMG/M. Tringe also pointed out that therate-limiting step in sequencingmetagenomes is in getting good-qualitygenomic DNA samples. Jerry Tuskantalked about his eucalyptus project andthe JGI plant program. The last talk ofthe first day was by Len Pennachio, whoexplained resequencing and comparedthe relative advantages of the Sanger,454, and Illumina processes.

“JGI’s activities are on a criticalpath for all of the Centers,” said Glynn.

“This is our number one priority,”said JGI Deputy Director Jim Bristow.“JGI can commit to getting the Center’shighest priority projects done. Whatrules at the end of the day, is gettinghigh quality DNA through the door.”

The participants acknowledged thatthis was an important first step in aprocess to identify, refine, and prioritizebioenergy-relevant sequencing targetsthat JGI will seek to accommodate inthe production queue in the comingyears.

Fall 2007 Vol. 4, Issue 2

THE PRIMER / 15

15,000-plus genes revealed in the studyare those that encode the structure andfunction of the specialized organelle thathouses the photosynthetic apparatus,the chloroplast, which is responsible forconverting light to chemical energy. Thegenome also provides a glimpse backthrough time to the last common ances-tor of plants and animals. The project,led by JGI; the University of California,Los Angeles; and the CarnegieInstitution, and including contributionsfrom over 100 international collabora-tors, is featured in the Oct. 12 edition ofthe journal Science (Science 318, 245(2007); DOI: 10.1126/sci-ence.1143609).

The single-celled algaChlamydomonas reinhardtii, while lessthan a thousandth of an inch in diame-ter, or about one-fiftieth the size of agrain of salt, is packed with manyancient and informative surprises.Affectionately known to its largeresearch community as “Chlamy,” thealga is a powerful model system for thestudy of photosynthesis and cell motility.The genes that encode the alga’s “flagel-la,” which propel it much like a humansperm tail, were also cataloged in this

study. Defects in these genes are associ-ated with a growing list of human dis-eases.

“The Chlamy genome is like a greentime capsule that affords a view into thecomplex core machinery that gave rise totoday’s energy-capturing and oxygen-pro-ducing chloroplasts,” said DanielRokhsar, DOE JGI Computational BiologyProgram head, who co-led the effort withDOE JGI Computational Scientist SimonProchnik, Arthur Grossman of theCarnegie Institution and StanfordUniversity, and Sabeeha Merchant ofUCLA.

“DOE JGI’s particular interest inChlamy centers on its keen ability to effi-ciently capture and convert sunlight intoenergy, and its role in managing the glob-al pool of carbon,” said Rokhsar. Thesequence analysis presents a compre-hensive set of genes—the molecular andbiochemical instructions—required forthese capabilities. Rokhsar said that withthese data now publicly available, newstrategies for biology-based solar energycapture, carbon assimilation, and detoxi-fication of soils by employing algae toremove heavy metal contaminants willbegin to surface. The analysis will also

shed light on the capabilities of relatedalgae that can produce biodiesel andbiocrude as alternatives to fossil fuels.

The results will also help researchersfigure out the construction of chloroplas-ts, which house the machinery insideplant and algal cells that serve as “solarpanels,” absorbing sunlight and couplingcarbon dioxide and water to produce thestarting materials—sugars—that fuel allother metabolic processes. These path-ways, described in the DNA sequence,represent opportunities for improving effi-ciencies for this conversion process andultimately biofuels production.

Other DOE JGI authors on the ChlamyScience paper include Astrid Terry, AsafSalamov, Erika Lindquist, Harris Shapiro,Susan Lucas; Jane Grimwood andJeremy Schmutz at the Stanford HumanGenome Center; and theChlamydomonas Annotation Team led byIgor Grigoriev and including PeterBrokstein, Inna Dubchak, DavidGoodstein, Leila Hornick, Wayne Huang,Jinal Jhaveri, Yigong Lou, Diego Martinez,Abby Ngau, Bobby Otillar, AlexanderPoliakov, Aaron Porter, LukaszSzajkowski, Gregory Werner, and KeminZhou.

Chlamy Genomecont. from page 1

CHRISTA PENNACCHIO

Senior Project Manager

Christa is a new member of theJGI Project Management Office, sup-porting ESTs and new technologies.Prior to that, she worked as aBiomedical Scientist at LLNL, initiallymapping and characterizing chromo-some 19 genes as part of the HumanGenome Project, and most recently

managing the I.M.A.G.E. Consortium,a collaborative gene discovery effortthat has produced over 10M publiclyavailable cDNA clones. Christareceived her BS in Biology from SaintMary’s College. She lives in Oaklandwith her husband Len and son Alex,and enjoys gardening, cooking/eatingand reading.

industry, public accounting and HR consult-ing. Chris has a BA in English from UCDavis and a MA in Higher EducationAdministration/Labor & Industrial Relationsfrom Michigan State University. Chris liveshere in Walnut Creek with his wife, Cindy,and two sons, Robert and Michael. Heenjoys sports (including coaching youthteams), cooking and spending time withfamily. By the way, Chris is an avid baseballand Cal football fan.

JGI Facescont. from page 2

Fall 2007 Vol. 4, Issue 2

16 / THE PRIMER

CONTACT

David Gilbert, Editordegilbert@lbl.gov(925) 296-5643

CSO 14229

Amersham). During this assessmentperiod, the MB4500 system wentthrough several modifications, reagentreformulations, and software changes.By July 2003, three official releaseversions of the MB4500s wereinstalled for proof-of-principlesequencing validation tests. The deci-sion was made to upgrade all

MB4000s to the new MB4500 plat-form and, by early 2005, the JGI wasoperating 36 of these instruments fulltime, with their new solid-state lasersystem offering longer read lengths.

On September 6, the machines

MegaBACE 4500 poses with Chris Daum

were wheeled out of Building 100,wrapped in plastic, fork-lifted ontotrucks and transported to LBNL’s 904warehouse where the excess processhas begun. The former MegaBACE lab-oratory will be retrofitted to accommo-date new sequencing technology instru-ments and procedures that are current-ly being developed and integrated intothe JGI Production SequencingPipeline. The first of these will be theRoche (454) Genome Sequencer plat-form.

Anyone interested in obtaining apiece of history and using theMegaBACE 4500, contact LBNLProperty Management’s Cindy Lytle,(510) 486-6569, CJLytle@lbl.gov orDave McFann (510) 486-6769,DJMcFann@lbl.gov.

DOE offers a unique donation pro-gram called the Energy-RelatedLaboratory Equipment (ERLE) GrantProgram, where any nonprofit, educa-tional institution of higher learning—such as a university, college, juniorcollege, technical institute, museum,or hospital—is eligible to apply. Theapplicant must be located in the USand interested in establishing orupgrading energy-oriented educationalprograms in the life sciences, physicaland environmental sciences, or inengineering. For additional information:http://erle.osti.gov/erle/.

MegaBACEscont. from page 5

March 26-28, 2008JGI User Meeting

Hold the Date

CommunitySequencingProgram

Sequencing Plansfor 2008JGI’s current list of major alloca-tions for the CommunitySequencing Program can be seenon our website at:

http://www.jgi.doe.gov/sequencing/cspseqplans2008.html

Letters of Intent dueJanuary 21, 2008

Forms and information for electronic submission will be posted soon on the JGI website.

CSP Bioenergy Call