News and Announcements
Twitter the News from DOE Joint Genome Institute
January 2012
Winter 2012 edition of the JGI newsletter The Primer is now available
December 2011
The U.S. Department of Energy Joint Genome Institute (DOE JGI) is offering several five-day workshops on Microbial Genomics and Metagenomics during 2012. Each workshop presents the same agenda and content and includes two days of intensive seminars and three days of hands-on tutorials for the following tools: IMG, IMG/M, IMG-ER, IMG-EDU, VISTA, GREENGENES and ARB. Our goal is to provide you with training in microbial genomic and metagenomic analysis and demonstrate how the cutting-edge science and technology of DOE JGI can enhance your research.Information and Registration
November 2011
Plant Feedstock Genomics for Bioenergy: A Joint Research Funding Opportunity Announcement SC_FOA_0000598. The U.S. Department of Energy's Office of Science, Office of Biological and Environmental
Research (BER), and the U.S. Department of Agriculture (USDA), National Institute of Food
and Agriculture (NIFA), hereby announce their interest in receiving applications for 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. Specifically, applications
are sought for fundamental research on plants that will improve biomass characteristics, biomass
yield, or sustainability. Systems biology approaches to identify genetic indicators enabling plants
to be efficiently bred or manipulated, or research to predict phenotype from underlying genotype
that could lead to improved feedstock characterization and sustainability are also encouraged.
Pre-Application Due Date: December 16, 2011, 4:30 p.m. Eastern Time
(Pre-applications are Required)
Application Due Date: February 24, 2012, 11:59 p.m. Eastern Time
Applications must be submitted through Grants.gov to be considered for
award.
2012 Genomic Science Meeting The Department of Energy Office of Biological and Environmental Research 2012 Genomic Science Annual Contractor-Grantee Meeting will be held February 26-29, 2012 , at the Bethesda North Marriott Hotel and Conference Center. Abstract deadline December 15, 2011. Attendance by invitation only. Information and Registration
October 2011
Registration is now live for the 2012 DOE Joint Genome Institute (JGI) Genomics of Energy & Environmental Meeting 7, March 20-22, 2012, Walnut Creek, California. Information and Registration
Fall 2011 edition of the JGI newsletter The Primer is now available
September 2011
Microbial Genome Analysis Workshop for Undergraduate Educators. On January 19-20, the U.S. Department of Energy (DOE) Joint Genome Institute (JGI) Education Program will be hosting its Sixth Annual Workshop in Microbial Genome Analysis for Undergraduate Educators. To read more about the Undergraduate Research in Microbial Genome Analysis program at the DOE JGI, please visit http://www.jgi.doe.gov/education/genomeannotation.html. The deadline to apply to join the program for the 2012-2013 academic year is November 18. There is a limited amount of NSF funding to support participation.
August 2011
DOE and USDA Fund Ten New Projects for Biomass Genomics Research. See website and press release.
July 2011
BSSD Director Position Announced. The Department of Energy, Office of Science, Office of Biological and Environmental Research, Biological Systems Sciences Division (BSSD), is seeking a motivated and highly qualified individual to serve as the Director. Â For detailed information about the position, check the USAJobs website.
National Laboratories and Universities Team up to Build a Community Systems Biology Knowledgebase.
In July 2011, DOE announced the selection of a collaboration of top scientists from across the Nation to lead development of a computer-based Systems Biology Knowledgebase. Leading the collaboration will be principal investigator Adam Arkin of Lawrence Berkeley National Laboratory (LBNL), with co-principal investigators Rick Stevens of Argonne National Laboratory (ANL), Robert Cottingham of Oak Ridge National Laboratory (ORNL), and Sergei Maslov of Brookhaven National Laboratory. Also participating as investigators in the multi-institutional program are Pamela Ronald of the University of California, Davis; Matthew DeJongh of Hope College in Michigan; Gary Olsen of the University of Illinois at Urbana-Champaign; Doreen Ware of the Cold Spring Harbor Laboratory; and Mark Gerstein of Yale University.
June 2011
Two Program Manager positions for Genomic Sciences within BER's Biological Systems Science Division (BSSD) will be posted soon to the USAJobs website. The positions will be located at DOE headquarters in Germantown, MD. According to new federal rules, and unlike past hiring processes, these announcements will be posted for only 10 days. For the official announcements please regularly check the USAJobs website at http://www.usajobs.gov/.
April 2011
Abstracts available from the Genomic Science Contractor-Grantee Workshop held April 10-13, 2011. Joint meeting with USDA-DOE Plant Feedstock Genomics for Bioenergy.
JGI CSP letter of intent deadline has been extended to Monday, May 2. JGI CSP now accepting letters of intent for large-scale sequence based genomic science projects in alternative fuels, global carbon cycling and biogeochemistry. Submit at http://proposals.jgi-psf.org/.
Spring 2011 edition of the JGI newsletter The Primer is now available
DOE JGI offers several five-day workshops on Microbial Genomics and Metagenomics during 2010-2011. Next workshop September 26-30, 2011
March 2011
JGI’s Community Sequencing Program (CSP) is now accepting letters of intent for large-scale sequence based genomic science projects that address questions of relevance to DOE missions in alternative fuels, global carbon cycling and biogeochemistry. While applications will be accepted that address any aspect of these mission areas, up to50% of capacity for this call will be allocated for projects that address the following areas of special emphasis, and exploit the diversity of JGI capabilities. More information.
December 2010
2011 Genomic Science Meeting The Department of Energys Office of Biological and Environmental Research 2011 Genomic Science Annual Contractor-Grantee Workshop will be held jointly with the USDA-DOE Plant Feedstock Genomics for Bioenergy Awardee meeting. The meeting will take place from April 10th (evening reception) through April 13th (ending early afternoon) 2011, at the Hyatt Regency Crystal City at Reagan National Airport. Please note that the timing of the annual meeting was shifted to avoid snowfall. Attendance by invitation only.
2011 DOE JGI Meeting 6th Annual DOE Joint Genome Institute "Genomics of Energy & Environment" meeting March 22-24, 2011 in Walnut Creek, California. downloadable/printable color flyer For more information and/or to register go to: http://go.usa.gov/1FL
November 2010
Plant Feedstock Genomics for Bioenergy. DOE and USDA announce funding call. The U.S. Department of Energy's Office of Science, Office of Biological and Environmental Research (OBER), and the U.S. Department of Agriculture (USDA), National Institute of Food
and Agriculture (NIFA), hereby announce their interest in receiving applications for genomicsbased
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. Specifically, applications
are sought for fundamental research on plants that will improve biomass characteristics, biomass
yield, or sustainability. Systems biology approaches to identify genetic indicators enabling plants
to be efficiently bred or manipulated, or research to predict phenotype from underlying genotype
that could lead to improved feedstock characterization and sustainability are also encouraged. Potential applicants are required to submit a brief preapplication, referencing DE-FOA-0000417
for receipt by DOE by 4:30 p.m., Eastern Time, December 17, 2010.
October 2010
Carbon Cycling 2010 Awards Biological Systems Research on the Role of Microbial Communities in Carbon Cycling. Summary of projects awarded in summer 2010 under Funding Opportunity Announcement DE-PS02-09ER09-25 Download PDF
The Fall 2010 edition of the DOE Joint Genome Institute newsletter, The Primer, has arrived and can be downloaded here:http://go.usa.gov/aVu. Hard copies are available by request from MMLozano@lbl.gov.
Back issues of The Primer are available for download at this page: http://bit.ly/d0VkZt
Highlights include:
- DOE JGI’s 2011 Community Sequencing Program Portfolio
- Alga for Biodiesel Sequenced
- Fungal Lessons on Breaking Biomass Better
- Microbes That can Take the Heat
- and more!
DOE JGI Workshops The DOE JGI offers several five-day workshops on Microbial Genomics and Metagenomics during 2010-2011.
Each workshop presents the same agenda and content, and will include two days of intensive seminars and three days of hands-on tutorials, including tutorials for the following tools: IMG, IMG/M, IMG-ER, IMG-EDU, VISTA, GREENGENES and ARB .
The goal is to provide you with training in microbial genomic and metagenomic analysis and demonstrate how the advancing science and technology of DOE JGI can enhance your research. Upcoming Workshops: October 18-22, 2010;
Future workshops will be announced on JGI's website as they are scheduled.
Contact: Marsha Fenner
DOE Joint Genome Institute
2800 Mitchell Drive, B400
Walnut Creek, CA 94598
Phone: 925-296-5781
MWFenner@lbl.gov
September 2010
USDA and DOE Fund New Projects for Biomass Genomics Research Departments of Energy and Agriculture jointly selected 9 projects for awards
totaling $9 million for biobased-fuel research. [Sept 2, 2010]
List of Awardees
July 2010
Brochure: "Bioenergy Research Centers: An Overview
of the Science," Revised July 2010 [faster-download
PDF or higher-quality PDF]
The Summer 2010 edition of the DOE Joint Genome Institute newsletter, The Primer, has arrived and can be downloaded here: PDF
Highlights include:
- A report from the recent, "The Sequencing, Finishing, Analysis in the Future" Meeting
- The Volvox genome Science publication
- Amazonian Stinkbird guts (research/researcher) profile
- California Biomass Collaborative’s Seventh Annual Forum report
- Genomics educational flash cards (in exchange for your science highlights!)
- and more!
Hard copies are available by request from
MLozano@lbl.gov
Back issues of
The Primer are available for download at this page:
http://www.jgi.doe.gov/News/primer/. Some older hard copies available as well.
May 2010
Funding Opportunity Announcement DE-FOA-0000368, "Genomic Science and Technology for Energy and the Environment"
The Office of Biological and Environmental Research (BER) hereby announces interest in receiving applications for research that supports the Genomics Science Program and addresses DOE's missions in energy and the environment in the following research areas:
-
a) Microbial Environmental Processes: To develop a systems-level understanding of the functional processes used by microbes and microbial consortia that link the internal metabolic processes of microbial species to their external biogeochemical activities;
-
b) Microbial and Plant Processes for Bioenergy: To develop new approaches that advance our understanding of the systems biology of plant and microbes in producing biofuels including the utilization of lignocellulosic biomass and microbial synthesis of advanced biofuel;
-
c) Characterizing Key Molecular Species, Events, and Multicellular Processes for Genomic Science: To develop innovative technology approaches to characterize biological processes and networks at the subcellular, cellular and multicellular levels.
Preapplications are REQUIRED and due June 28, 2010.
More details are available at
this PDF
and the full announcement is available on grants.gov.
New Dates! 2011 Genomic Science Meeting The Department of Energys Office of Biological and Environmental Research 2011 Genomic Science Annual Contractor-Grantee Workshop will be held jointly with the USDA-DOE Plant Feedstock Genomics for Bioenergy program meeting. The meeting will take place from April 10th (evening reception) through April 13th (ending early afternoon) 2011, at the Hyatt Regency Crystal City at Reagan National Airport. Please note that the timing of the annual meeting was shifted to avoid snowfall. Attendance by invitation only.
The DOE JGI Newsletter: The Spring 2010 edition is now available for download.. Hard copies can be requested from MMLozano@lbl.gov. Featured are highlights from the 5th Annual Genomics of Energy & Environment Meeting. Videos of the talks. Save the date for next year's meeting: March 21-25, 2011.
More DOE JGI news:
5th annual Sequencing, Finishing and Analysis in the Future meeting will be held June 2-4, 2010 in Santa Fe, NM, and will feature keynote speakers Claire Fraser-Liggett, Director, Institute for Genome Sciences, Chad Nusbaum, Co-Director, Broad Institute Genome Sequencing and Analysis Program, and Folker Meyer, Associate Director, Institute for Genomics and Systems Biology, Argonne Natl. Lab. For more information
Animated JGI
The DOE JGI collaborated with Emeryville, Calif.-based Ex’pression College for Digital Arts to create a short video on the DOE JGI’s role in developing sustainable clean energy. View it on YouTube.
Happy Anniversary IMG
The Integrated Microbial Genomes (IMG) system (Nucleic Acids Research, 2010, Vol. 38) serves as a community resource for comparative analysis and annotation of all publicly available genomes from three domains of life in a uniquely integrated context. On this occasion, IMG 3.1 has been released
IMG/M, IMG ER and IMG/M ER have also been updated with the new IMG 3.1 reference genomes.
GenePRIMP Goes Live
To assist in checking the quality of the microbial DNA sequences generated before they are submitted to the public archive GenBank, which is overseen by the National Center for Biotechnology Information, the JGI has been using a quality control tool known as the Gene Prediction IMprovement Pipeline or GenePRIMP, which is described in a paper was published online May 2 in Nature Methods. A video of first author Amrita Pati explaining how GenePRIMP works is available online
Lawrence Berkeley National Laboratory to host a free 2-day workshop introduces educational adaptations of iPlant discovery environments developed to support innovative curricula and exciting student research projects to prepare the scientists of the future.
April 2010
DOE JGI: 2009 Progress Report Now Available The U.S. Department of Energy Joint Genome Institute (DOE JGI) has just released its 2009 Progress Report, highlighting the achievements of the last year and touching on the initiatives ahead to advance the frontiers of DNA sequence-enabled science relevant to DOE's mission areas of bioenergy, carbon cycling and biogeochemistry. The 68-page color document can be downloaded from the JGI website (PDF). Free hard copies can be requested from MMLozano@lbl.gov
"Energy Genomics" Animation Debuts And for those who didn't already see it at the DOE JGI annual Energy & Environment User Meeting last week...we, in collaboration with recent graduates and staff at the Ex'pression College for Digital Arts, have developed a short animation, "Energy Genomic," to describe the role DOE JGI plays in advancing the Department of Energy mission by characterizing plants and microbes for next generation biofuels. The animation can be viewed here
March 2010
CSP 2011: Call for Proposals Letters of intent for the DOE Joint Genome Institute Community Sequencing Program (CSP) 2011 are due March 31, 2010.
Sequencing projects will be chosen based on scientific merit--judged through independent peer review--and relevance to the DOE missions of bioenergy, global carbon cycling, and biogeochemistry.
Areas of emphasis are:
- Large-scale resequencing of organisms with a reference sequence
- Single cell genomes
- Large-scale microbial isolate sequencing
- Eukaryotic whole genome sequencing
- Large-scale metagenome sequencing
Microbial Proposals for small-scale sequencing are accepted for review on a quarterly basis.
Deadline for the next microbial review is April 7, 2010. These will include projects for:
- Bacterial and archaeal isolates
- Bacterial resequencing
For more information about the CSP or to submit, see: http://proposals.jgi-psf.org
February 2010
JGI User Meeting March 24-26, 2010 in Walnut Creek, CA.
Download Poster
Funding Opportunity Announcements Plant Feedstock Genomics for Bioenergy: A Joint Research Funding Opportunity Announcement USDA, DOE Details
Contribute to Defining Knowledgebase Requirements and Specifications A Wiki has been created to provide open access to an interactive resource for viewing, providing comments, and contributing to this community-driven effort to specify the requirements for the DOE Systems Biology Knowledgebase. Go to the Wiki and select “How to Participate” to join this effort. Wiki
Awardee Meeting Genomic Science Awardee meeting was held February 7-10, 2010. Abstracts available
January 2010
Awardee Meeting Genomic Science Awardee meeting will be held February 7-10, 2010. Attendance by invitation only. Poster and Speaker Abstracts now available.
December 2009
Funding Opportunity Announcement DE-FOA-0000223. Plant Feedstock
Genomics for Bioenergy: A Joint Research Funding Opportunity Announcement
USDA, DOE.The U.S. Department of Energy's Office of Science, Office
of Biological and Environmental Research (OBER), and the U.S. Department
of Agriculture (USDA), National Institute of Food and Agriculture (NIFA),
hereby announce their interest in receiving applications for 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.
Specifically, applications are sought for fundamental research on plants
that will improve biomass characteristics, biomass yield, or sustainability.
Systems biology approaches to identify genetic indicators enabling plants
to be efficiently bred or manipulated, or research that yields fundamental
knowledge of the structure, function and organization of plant genomes leading
to improved feedstock characterization and sustainability are also encouraged.
Preapplications required, deadline 4:30 p.m., Eastern Time, January 4, 2010.
[More details at http://science.doe.gov/grants/pdf/DE-FOA-0000223.pdf]
Funding Opportunity Announcements Office of Science Annual
Notices for Fiscal Year 2010 have been posted. These Announcements are published
annually and will remain open until succeeded by another issuance by the
Office of Science usually posted after the beginning of the Fiscal Year
(October 1, 2010). Applications submitted under these Announcements, DE-FOA-0000178
and DE-FOA-0000179, may be awarded with funds and under the Terms and Conditions
provided under the American Recovery and Reinvestment Act of 2009.
November 2009
Awardee Meeting Genomic Science Awardee meeting will be held February 7-10, 2010. Attendance by invitation only. Abstracts due December 11. Details available on website.
Contribute to Defining Knowledgebase Requirements and Specifications
A Wiki has been created to provide open access to an interactive resource for viewing, providing comments, and contributing to this community-driven effort to specify the requirements for the DOE Systems Biology Knowledgebase. Go to the Wiki and select “How to Participate” to join this effort.
October 2009
The Fall 2009 edition of the DOE JGI newsletter, The Primer, has arrived. Features include:
- Gap Resolution software now available for academic use
- New DOE JGI Fungal Program
- Genomic Standards Consortium's 8th meeting notes
- Marine microbial lifestyles
- T. reesei redux
- Upcoming 5th Annual Genomics of Energy & Environment meeting, March 24-26, 2010: http://www.jgi.doe.gov/meetings/usermeeting/
- Follow us on TWITTER: doe_jgi
For those who would like access to an electronic file, it can be downloaded as a
PDF and previous editions are
available here.
Hard copies can be requested from:
MMLozano@lbl.gov
DOE JGI, Others, Propose a New set of Standards to build on Bermuda
Standard. A group of researchers from several sequencing centers,
including the DOE Joint Genome Institute (JGI), the Sanger Institute and
the Human Microbiome Project (HMP) Jumpstart Consortium sequencing institutes,
has proposed a new set of standards that expand upon the so-called Bermuda
standard. In the October 9 issue of the journal Science, they propose four
additional categories between draft and finished status that reflect
varying levels of completeness. See press
release. See Science.
Adopt a GEBA Genome The DOE Joint Genome Institutes Education Program is providing opportunities
for colleges and universities across the country to adopt bacterial genomes,
such as those sequenced as part of the GEBA project, for analysis. This
Adopt a GEBA Genome Education Program makes available a selection of recently
sequenced genomes for use in undergraduate courses. The organisms ideally
provide a unifying thread for concepts across the life sciences curriculum.
For example, students can analyze the six open reading frames for a given
fragment of DNA, compare the results of various gene calling algorithms,
assign function by sequence homology, and use gene ortholog neighborhoods
for comparative genomics and annotate biochemical pathways, while learning
the underlying biological concepts in a variety of science courses. For
more information, and to apply for the November 2, 2009 deadline, see: http://www.jgi.doe.gov/education/genomeannotation.html
August 2009
Funding Opportunity Announcement "Computational Biology and Bioinformatic Methods to Enable a Systems Biology Knowledgebase" (DE-FOA-0000143) BER hereby announces its interest in receiving applications for potential funding of computational biology and bioinformatic methods and analytics to enable the planned Systems Biology Knowledgebase. The goal of systems biology is to understand living systems, a simple microbe or a complex ecosystem, so well that we can develop predictive, computational models of the systems that "behave" the same way as the living system. Such predictive models would enable scientists to accurately predict an organism's or a more complex system's behavior. Preapplications required, deadline November 5, 2009. Formal applications must be received by January 29, 2010 [More details at http://science.doe.gov/grants/pdf/DE-FOA-0000143.pdf]
DOE JGI Releases Integrated Microbial Genomes (IMG) 2.9 IMG serves as a community resource for comparative analysis and annotation of all publicly available genomes from three domains of life in a uniquely integrated context.
In addition to the content update (more than one million new genes) and User Interface extensions (all described in the "What's New" in IMG 2.9).
A notable new feature is the inclusion of protein expression data from a recent Arthrobacter chlorophenolicus study and tools for examining these data.
[8/18/09]
Press Release: GLBRC Receives $8 Million in Recovery Act Funding. The Department of Energy (DOE) Great Lakes Bioenergy Research Center (GLBRC) has received $8.099 million in new funding from the U.S. Department of Energy through the American Recovery and Reinvestment Act to provide crucial support for plant cell wall imaging and sustainability research.
CONTACT: Tim Donohue, 608-262-4663, tdonohue@bact.wisc.edu; John Ralph, 608-890-2429, jralph@wisc.edu; Phil Robertson, 269-671-2267, robertson@kbs.msu.edu [8/6/09] Press Release
July 2009
Microbial Genomics & Metagenomics workshop September 14-18, 2009. The U.S. Department of Energy Joint Genome Institute (DOE JGI) is offering a five-day workshop on Microbial Genomics and Metagenomics September 14-18, 2009 in Walnut Creek, California. The workshop will include two days of intensive seminars and three days of hands-on tutorials. Our goal is to provide you with training in microbial genomic and metagenomic analysis and demonstrate how the cutting-edge science and technology of DOE JGI can enhance your research.
For more information, see:
http://www.jgi.doe.gov/meetings/mgm/
USDA and DOE Jointly Fund 7 New Projects for Biomass Genomics Research.
Departments of Energy and Agriculture jointly selected 7 projects
for awards totaling $6.3 million for biobased-fuel research. See press
release and list
of awardees. [July 22, 2009]
Brochure: "Bioenergy Research Centers: An Overview
of the Science," Revised July 2009 [faster-download
PDF or higher-quality PDF]
Summer 2009 DOE JGI Newsletter The Primer Available Download the PDF;
Back issues;
Additional hard copies: MMLozano@lbl.gov.
For IMG Expert Review (ER) and IMG/M ER users, the latest paper can be accessed here.
Funding Opportunity Announcement Biological Systems Research on the Role of Microbial Communities in Carbon Cycling (DE-PS02-09ER09-25) The Office of Biological and Environmental Research (BER) of the Office of Science (SC), U.S. Department of Energy (DOE), hereby announces its interest in receiving applications for research that supports the Genomics:GTL research program. In this Funding Opportunity Announcement (FOA), applications are solicited for: i.) Systems-level studies on regulatory and metabolic networks of microbes and microbial consortia involved in biogeochemical cycling of carbon, ii.) Development of metatranscriptomic, metaproteomic, and other genome-enabled approaches to understand how shifts in environmental variables impact microbially-mediated carbon cycling processes in terrestrial ecosystems, and iii.) Development of methods and techniques for imaging and analysis of microbially-mediated carbon cycling processes in terrestrial ecosystems. Closing date November 9, 2009. [More details at http://science.doe.gov/grants/pdf/DE-PS02-09ER09-25.pdf]
June 2009
DOE JGI Releases IMG/M 2.8. The Integrated Microbial Genomes system/with Microbiome Samples (IMG/M)
2.8 has now been released and includes reference genomes from IMG 2.8 (released in April 2009, see http://img.jgi.doe.gov) and 111 GEBA genomes (http://img.jgi.doe.gov/geba). New metagenome datasets include:
- 1 Endophytic microbiome from rice;
- 8 Yellowstone hot pool microbial communities;
- 7 Marine planktonic communities from Hawaii Ocean Time-series;
- 1 Bioreactor wastewater terephthalate-degrading community sample
Other new features are described here
Check out IMG/M 2.8
May 2009
DOE JGI Releases Expanded Phytozome.net. An enhanced version of Phytozome.net, a web portal for comparative plant genomics geared to advance biofuel, food, feed, and fiber research, has been released by the U.S. Department of Energy (DOE) Joint Genome Institute (JGI). Phytozome provides a central hub for web access to a rapidly growing number of plant genomes, and includes tools for visualization of plant genomes and associated annotations, sequence analysis, and bulk, as well as targeted, plant data retrieval. [05/09] Details
Integrated Microbial Genomes Expert Review (IMG ER) Goes Primetime:
Provides Expert-Driven QC for Microbial Genome Information. Scientists at the U.S. Department of Energy (DOE) Joint Genome Institute
(JGI) and the Biological Data Management and Technology Center (BDMTC)
at Lawrence Berkeley National Laboratory have launched the Expert Review
(ER) version of the Integrated Microbial Genomes (IMG) system. IMG ER
supports and enhances the review and revision of annotations for both
publicly available genome datasets and those newly released from private
institutions. Details and Press Release [5/18/09]
April 2009
DOE-USDA Biofuels Sustainability Workshop Report Available.
Sustainability of Biofuels: Future Research Opportunities, a report from the October 2008 DOE-USDA workshop is now available. Details
February 2009
GTL Strategic Plan.
The 2008 Genomics:GTL Strategic Plan is now available electronically. [02/09] Details
GTL Abstracts.
Abstracts available from Genomics:GTL Awardee meeting, held Feb 8-11, 2009. Details
January 2009
DOE JGI Completes Sorghum Genome. Walnut Creek,
CAScientists at the U.S. Department of Energy (DOE) Joint Genome Institute
(JGI) and several partner institutions have published the sequence and analysis
of the complete genome of sorghum, a major food and fodder plant with high
potential as a bioenergy crop. The genome data will aid scientists in optimizing
sorghum and other crops not only for food and fodder use, but also for biofuels
production. The comparative analysis of the sorghum genome appears in the
January 29, 2009, edition of the journal Nature. See
Release
DOE JGI Announces 2009 Users Meeting. March 25-27,
2009 in Walnut Creek, California. See Website
for more details.
December 2008
Carbon Cycling and Biosequestration Report from the OBER hosted Carbon Cycling and Biosequestration Workshop, March 2008. This report outlines the workshop's findings and highlights key opportunities for research on biological aspects of the global carbon cycle. Further details and PDFs.
DOE JGI Issues Call for Genome Sequencing Proposals
The U.S. Department of Energy Joint Genome Institute (DOE JGI), through its Community Sequencing Program (CSP), is soliciting proposals related to the DOE missions of bioenergy, global carbon cycling and biogeochemical processes influencing contaminant transport. Targets include bacterial and archaeal isolates, large-scale eukaryotic or bacterial resequencing efforts that exploit next-generation sequencing technologies, eukaryotic reference genomes, and environmental microbial genomes (metagenomes). Letters of intent will be accepted beginning December 15, 2008 and are due January 30, 2009.
For further details, see:
http://www.jgi.doe.gov/CSP/user_guide/ and this PDF.
Soya genome sequenced
Biofuel potential spurs U.S. consortium to map DNA of nutritious bean. December 10, 2008, Nature
November 2008
Awardee Meeting Genomics:GTL Awardee meeting will be held February 8-11, 2009. Attendance by invitation only. Abstracts due December 8.
USDA and DOE Funding Opportunity Announcement
Departments of Energy and Agriculture have jointly issued a research funding
opportunity. Preapplications due Dec. 9, 2008. See details.
October 2008
USDA and DOE Release National Biofuels Action Plan.
[Oct. 7, 2008] See press
release and download document
(PDF 4.9 KB).
August 2008
DOE JGI Director Eddy Rubin Highlights the Genomics of Plant-Based Biofuels in Nature. [Aug. 13, 2008] See
JGI press
release and
article.
Atlantic Monthly Features JGI Termite Research. See article and accompanying video.
July 2008
USDA and DOE Fund 10 New Projects for Biomass Genomics Research. Departments of Energy and Agriculture jointly selected 10 projects for awards totaling $10 million for biobased-fuel research. [July 31, 2008] See
Press
Release and
List of Awardees.
Interagency Opportunities in Metabolic Engineering. (NSF
08-588). This solicitation describes a collaborative effort among the Department
of Agriculture, Department of Commerce, Department of Defense, Department
of Energy, Environmental Protection Agency, National Aeronautics and Space
Administration, National Institute of General Medical Sciences (National
Institutes of Health), and the National Science Foundation. The intent of
this interagency solicitation is to provide an opportunity for an interagency
granting activity in the area of metabolic engineering (ME). The eight participating
agencies or departments are providing research funding and agency in-kind
support such as equipment, laboratory space, personnel time, and materials
in support of this solicitation. Upon conclusion of the review process,
meritorious proposals may be recommended for funding by a participating
agency or department. Each participating agency will make its own awards
and the subsequent grant administration procedures will be in accordance
with the individual policies of the awarding agency or department. Full
proposals are due October 22, 2008.
Announcement.
JGI Announces 2009 Targets Pine Tree, Boat-Boring Bivalve
Bugs, Duck Weed, Oil-Producing Microalgae, Stinkbird Gut, 40 Others Top
DOE Joint Genome Institute 2009 Genome Sequencing Targets. Press
Release.
May 2008
Position
available: Director of the Life and Medical Sciences Division in U.S.
Department of Energy (DOE)-Office of Science, Office of Biological and Environmental
Research (BER). This Division manages the GenomicsGTL Program;
Low Dose Radiation Research and Radiochemistry and Instrumentation programs;
the DOE Bioenergy
Research Centers; and scientific user facilities such as the DOE Joint
Genome Institute.
The Life and Medical
Sciences Division is seeking a motivated and highly qualified individual
to be responsible for basic research impacting energy resources, production,
conversion, efficiency, storage, and the mitigation of the adverse impacts
of energy production and use.
The Office of Science is the single
largest supporter of basic research in the physical sciences in the United
States. We oversee and are the principal Federal funding organization of
the nation's research programs in high-energy physics, nuclear physics,
and fusion energy sciences. The Office of Science is also the Federal government's
largest single provider of funds for the chemical and materials sciences.
We manage fundamental research programs in basic energy science and support
unique and vital parts of the United States research in climate changes,
geophysics, genomics, life sciences, and science foundation.
April 2008
Data Sharing Policy Information and data sharing policy of the Genomics:GTL Program announced. PDF
March 2008
JGI Genomics of Energy & Environment Meeting DOE JGI meeting. March 26-28, 2008. Walnut Creek, CA Website
Pittcon Symposia Features BRCs The Analytical Instrumentation for Biofuels R&D Session at the March 1-7, Pittcon meeting in New Orleans will have presentations from each of the Bioenergy Research Centers.
February 2008
JGI Updates Microbial Metagenomics Data System The Joint Genome Institute of the U.S. Department of Energy has released an upgraded version of its metagenomics data management and analysis system that includes five new metagenome data sets taken from recent studies. Announcement
Abstracts from the Genomics:GTL Contractor-Grantee
Workshop VI, Bethesda, Md., February 10-13, 2008
Brochure: "Bioenergy Research Centers: An Overview of the Science," February 9, 2008 Revised July 2009 [faster-download PDF; higher-quality PDF]
January 2008
Funding Opportunity: Biological Hydrogen Production. DE-PS02-08ER08-12, "Systems Biology, Model Organism Development, and Enzyme Discovery for Biological Hydrogen Production." Preapplications are required, due 2/22/2008. Applications are due 4/9/2008. The Office of Biological and Environmental Research (BER) of the Office of Science (SC), U.S. Department of Energy (DOE), hereby announces its interest in receiving applications for research that supports the Genomics: GTL research program (genomicscience.energy.gov). In this Solicitation, applications are solicited for: i.) systems-level research to improve understanding of microbial regulatory and metabolic networks related to hydrogen production, ii.) development of new model organisms for microbial hydrogen production, and iii.) targeted approaches for the identification and characterization of enzymes and biochemical pathways relevant to biological hydrogen production in genome and metagenome sequences. Announcement.
December 2007
Awardee Meeting Website Genomics:GTL Awardee meeting will be held February 10-13, 2008. Attendance by invitation only. [12/07]
October 2007
Funding Opportunity: Plant Feedstock Genomics for Bioenergy: A Joint
Research Solicitation from USDA and DOE. DE-PS02-08ER08-03. Preapplications
are required and due November 13, 2007; Application Due Date: January 23, 2008.
DOE Office
of Science, Office of Biological and Environmental Research (OBER), and USDA
Cooperative State Research, Education, and Extension Service (CSREES) invite
applications for 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. Specifically, applications are sought for
fundamental research on plants that will improve biomass characteristics, biomass
yield, or sustainability. Systems biology approaches to identify genetic indicators
enabling plants to be efficiently bred or manipulated, or research that yields
fundamental knowledge of the structure, function and organization of plant
genomes leading to improved feedstock characterization and sustainability are
also encouraged.
Funding Opportunity: International Cooperative Biodiversity Groups The
National Institutes of Health, the National Science Foundation, the U.S.
Department of Agriculture, and the U.S. Department of Energy invite
applications
for the establishment or continuation of "International Cooperative Biodiversity
Groups" (ICBG) to address the interdependence of biodiversity exploration
for potential applications in health, agriculture and energy, with investments
in research capacity that support sustainable use of these resources, the knowledge
to conserve them, and equitable partnership frameworks among research and development
organizations in the U.S. and low and middle income countries. The Government
is budgeting $3 – 4 million in FY 08 for the initial
awards. Microbial organisms (inclusive of prokaryotes, virus, fungi, algae
and protists) from terrestrial or marine sources as well as marine invertebrates
are of greatest interest to the participating agencies in this competition. Announcement
DOE Provides $30 Million to Jump Start Bioenergy
Research Centers. The U.S. Department of Energy (DOE) today announced
it has invested nearly $30 million in end-of-fiscal-year (2007) funds
to accelerate the start-up of its three new Bioenergy Research Centers,
bringing total DOE Bioenergy Research Center investment to over $400 million. [10/1/07]
Press Release
New GTL Awards for FY 2007 DOE announced the funding of 44 new projects. [10/1/07]. Details are available here.
September 2007
Awardee Meeting Dates Announced Genomics:GTL Awardee meeting will be held February 10-13, 2008. Attendance by invitation only. [9/07]
August 2007
Nature Collections Energy Supplement.
Supported by the Department of Energy and Office of Science, this supplement outlines the promises and pitfalls of new energy technologies. Free access. [Aug. 2007]
Supplement
Funding Opportunity: Development of Saccharifying Enzymes for Commercial
Use. EERE is requesting applications for the development of hydrolytic
enzymes or enzyme system preparations that can effectively saccharify pretreated
lignocellulosics to produce fermentable sugars under process relevant conditions.
Letter of Intent due Sept. 10, Applications due Oct. 15. [8/24/07]
June 2007
Energy Department Selects Three
Bioenergy Research Centers for $375 Million in
Federal Funding Secretary Samuel W. Bodman announced three new Bioenergy Research
Centers intended to accelerate basic research in the development of cellulosic
ethanol and other biofuels. [6/26/07]
Press Release, more details
DOE Joint Genome Institute Announces 2008 Genome Sequencing Targets. June
8, 2007.
Eucalyptus, foxtail millet, red algae, and novel microbial communities
added to growing bioenergy and carbon cycling portfolio. Press
Release
Energy and Agriculture Departments Provide $8.3 Million in Funding
for Biofuels Research. June 7, 2007. U.S. Energy Secretary Samuel
Bodman and Agriculture Secretary Mike Johanns today announced that the
Department of Energy and the Department of Agriculture have jointly selected
11 projects for awards totaling $8.3 million for biobased fuels research
that will accelerate the development of alternative fuel resources. Press
Release
Plant Feedstock Genomics for
Bioenergy Workshop at the
2008 Plant and Animal Genome Conference, January 15, 2008. Workshop
announcement on PAG
web.
Organizers: Sharlene Weatherwax, U.S. Department of Energy
(sharlene.weatherwax@science.doe.gov)
and
Chavonda Jacobs-Young, USDA/CSREES
(cjacobs@csrees.usda.gov)
"Plant Feedstock Genomics for Bioenergy" workshop will provide an overview of genomics-based research that can lead to the improved use of biomass and plant feedstocks for the production of fuels such as ethanol or renewable chemical feedstocks. Presentations will focus on fundamental research opportunities on plants to improve biomass characteristics, biomass yield, or that will facilitate lignocellulosic degradation. Also, systems biology approaches to identify genetic indicators enabling plants to be efficiently bred or manipulated, or research that yields fundamental knowledge of the structure, function and organization of plant genomes leading to improved feedstock characterization and sustainability.
This will be the USDA-DOE Awardees meeting for 2008. The 2009 meeting will
return to the Genomics:GTL Contractor-Grantee
Workshop.
Future USDA-DOE Awardees Meetings.
The 2008 Plant and Animal Genome Conference Workshop will be the USDA-DOE
Awardees meeting for 2008. The 2009 meeting will return to the Genomics:GTL
Contractor-Grantee Workshop.
March 2007
ASM Microbial Energy Conversion Report. ASM has released
a new report on microbial energy conversion. This report is based on a colloquium,
sponsored by the American Academy of Microbiology, convened March 10-12,
2006, in San Francisco, California. DOE BER contributed support for the
report.
February 2007
Three Bioenergy Research Centers Planned (02/05/07)
- Press Release Press Release:
Department of Energy Requests $24.3 Billion for FY 2008 Budget
GTL Awardee Meeting 2007. Joint Genomics: GTL Awardee Workshop
V and Metabolic Engineering 2007 and USDA-DOE Plant Feedstock Genomics
for Bioenergy Awardee Workshop 2007, North Bethesda, MD,
February
11 to February 14, 2007.
Abstracts now available.
December 2006
Funding Opportunity: Ethical, Legal, and Societal Implications (ELSI)
of Research on Alternative Bioenergy Technologies, Synthetic Genomics,
or Nanotechnologies. Funding
Opportunity Announcement
DE-PS02-07ER07-16. The deadline for preapplications (which are required)
is Thursday February 8, 2007. Formal applications are due on Thursday, April
19,
2007.
The aims of this Notice are to support explorations of the potential societal
implications arising from scientific research in areas of systems microbiology
pertaining to the DOE mission of bioenergy, and, in addition, issues arising
from synthetic genomics applied to bioenergy, and research on nanomaterials
and nanotechnologies relevant to bioenergy. For more information, see the
PDF.
JGI: Community Sequencing Program (CSP)
Opportunity
A letter of intent is due by January 12, 2007.
Proposal deadline is March 2, 2007
For more information, see this
website.
The Community Sequencing Program (CSP) was created to provide the scientific
community at large with access to high-throughput sequencing at the
Department of Energy's Joint Genome Institute (JGI) for projects of
relevance to DOE missions. Sequencing projects will be chosen based
on scientific merit--judged through independent peer review--and relevance
to issues in global carbon cycling, alternative energy production,
and bioremediation. Criteria for participation in this program, the
review process, and interactions between JGI and participants are outlined
on this web site. Through this program, the Department of Energy aims
to advance sequence-based scientific research from a broad range of
disciplines.
The CSP consists of two programs:
- a small-genome program for shotgun sequencing of genomes smaller than
200 Mb and other sequencing projects with a total request of less than
1 Gb.
- a large-genome program for shotgun sequencing of genomes larger than
200 Mb. Large-genome proposals must be supported by experimental evidence
of the organism's genome size, polymorphism rate, and repeat content.
In the absence of this information, applicants are encouraged to submit
a small-genome proposal to obtain this information.
Proposals to the two programs will be reviewed separately, but the application
and review processes are similar.
For information about the site or program please write to csp2008@jgi.doe.gov.
November 2006
Keasling Named Scientist of the Year
Discover magazine has named GTL researcher Jay Keasling, a chemical
engineer with a joint appointment at Berkeley Lab and UC Berkeley, as
its 2006
Scientist of the Year. Keasling was cited for "developing ways to program
DNA as easily as people program computers." In an interview with writer
Carl Zimmer, Keasling describes the synthetic biology techniques by
which he engineered bacteria and yeast to produce a precursor to artemisinin,
a super antimalarial drug. Similar techniques could be used to produce
ethanol from plant cellulose, Keasling said. (Discover)
Program Announcement
to DOE National Laboratories
LAB 07-14. New Genomic Strategies and Technologies for Studying Complex
Microbial Communities and Validating Genomic Annotations. Preproposal due January
18, 2007. See PDF
New Grant Opportunities. Program Notices DE-PS02-07ER07-12 - New Analytical
and Imaging Technologies for Lignocellulosic Material Degradation, and for Multiplexed
Screening for
Plant Phenotypes and DE-PS02-07ER07-13 - Quantitative Microbial Biochemistry
and Metabolic Engineering for Biological Hydrogen Production, have been posted
today in Grants.gov.
-
DE-PS02-07ER07-12 has preapplication REQUIRED and due January 4, 2007
with the formals due March 6, 2007. Notice on Grants.gov or
PDF.
Dr. Sharlene Weatherwax and Dr. John Houghton are the Program contacts.
-
DE-PS02-07ER07-13 has preapplication REQUIRED and due January 4, 2007
with the formals due March 8, 2007. Notice on Grants.gov or PDF.
Dr. Sharlene Weatherwax is the Program contact.
October 2006
DOE EERE Requests Applications to Develop Efficient Ethanol-Producing
Organisms. The U.S. Department of Energy (DOE), Office of Energy
Efficiency and Renewable Energy (EERE) has announced a Funding Opportunity
Announcement (FOA) entitled “Development of Robust, Highly Efficient
Fermentative Organisms for the Conversion of Lignocellulosic Biomass to
Ethanol.” Funding Opportunity Number: DE-PS36-07GO97002 at Grants.gov.
[10/25/2006] Funding
Call
President Bush Discusses Energy at Renewable Energy Conference.
Remarks by the President on Energy. [10/12/06] Press
release
Transcript of Remarks by Agriculture Secretary Mike Johanns [10/11/06]
"DOE Bioenergy Initiative," Presentation by Under Secretary for Science Dr. Raymond L. Orbach at the DOE/USDA Advancing Renewable Energy Conference, St. Louis, MO [10/12/06] PDF
Secretaries Bodman & Johanns Kick Off Renewable Energy Conference
with $17.5 Million for Biofuels Research & Development Grants.
U.S. Department of Agriculture (USDA) Secretary Mike Johanns and U.S. Department
of Energy (DOE) Secretary Samuel Bodman today announced nearly $17.5 million
for 17 biomass research, development and demonstration projects, to help
break our nation's addiction to oil. [10/11/06] Press
release
USDA-DOE Announce New Funding Opportunity for Biomass Genomics
Research. The U.S. Departments of Energy and Agriculture (DOE and
USDA) issued a solicitation for research proposals for new plant feedstock
genomics research projects. Funding Opportunity Number: DE-PS02-07ER07-03.
[10/10/06] more...
September 2006
First tree genome sequence published; consortium led by DOE Joint Genome Institute. Press release
DOE & USDA Advancing Renewable Energy Conference Oct. 10-12, 2006.
August 2006
USDA and DOE Fund Genomics Projects For Bioenergy Fuels Research
(DOE Press Release) Energy Secretary Samuel Bodman and Agriculture Secretary
Mike Johanns today announced that the Department of Agriculture and the Department
of Energy have jointly awarded nine grants totaling $5.7 million for biobased
fuels research that will accelerate the development of alternative fuel resources.
[8/9/06]
more...
News Release: USDA and DOE Name Biomass Research
and Development Technical Advisory Committee Members, August 9, 2006
DOE Issues Call for New Bioenergy Research Centers
July 2006
Biomass to Biofuels Plan Now Available. Breaking the
Biological Barriers to Cellulosic Ethanol: A Joint Research
Agenda is a research roadmap resulting from the December 2005 joint DOE
SC-EERE Biomass to Biofuels Workshop.
DOE JGI Sequences, Releases Genome of Symbiotic Tree Fungus DNA sequence of Laccaria
bicolor, a fungus that forms a beneficial symbiosis
with trees and inhabits one of the most ecologically and
commercially important microbial niches in North American
and Eurasian forests, has been determined by the U.S.
Department of Energy DOE Joint Genome Institute (DOE JGI). [7/24/06]
Press Release
Genome Sequencing of Unculturable Bacteria. Conventional DNA
sequencing of a microbial genome usually entails extracting sufficient DNA from
a culture grown up from a single bacterium. Most microbes from natural environments,
however, do not have established laboratory culture conditions, making it a challenge
to obtain enough DNA for analysis. This situation holds for many strains of the
most prevalent photosynthetic marine microbe, Prochlorococcus, which play major
roles in carbon cycling and fixation. In the June 2006 issue of Nature Biotechnology,
George Church led a GTL-funded team of MIT-Harvard Medical School scientists
in developing a new strategy that allows high-fidelity amplification of DNA from
a single cell. The breakthrough comes from using DNA-digesting enzymes to cut
away undesirable branched DNA structures that tend to form during early rounds
of DNA amplification, leaving only linear DNAs to be amplified tremendously for
subsequent sequencing. This technique enabled researchers to obtain the genomic
sequence from a single Prochlorococcus microbe, and opens a window to
obtain genomic information from individual members in complex microbial communities.
Reference: Kun Zhang et al, (2006) Sequencing genomes from single cells by polymerase
cloning, Nat. Biotech 24 (6) 680-686.
Bug Juice: Harvesting Electricity from Microorganisms. Electricity-producing
bacteria ("electricigens") such as Geobacter and Rhodoferax can effectively
convert diverse organic matter to electricity. These organisms are able
to transfer electrons directly to an electrode instead of using electron-shuttling
intermediates. In an article appearing in the July 2006 issue of Nature
Reviews Microbiology, GTL researcher Derek Lovley (University of
Massachusetts, Amherst) describes the physiology and ecology of these organisms
and discusses how to increase their power output for microbial fuel systems.
Energy-Rich Portfolio of New Genome Sequencing Targets for DOE
JGI. Bioenergy crop plants switchgrass and cassava, other important
agricultural commodities such as cotton, and microbes geared to break
down
plant material to render biofuels, round out the roster of more than 40
projects to be tackled by the U.S. Department of Energy Joint Genome Institute
(DOE JGI) over the next year. More...
GTL Researchers at Pacific Northwest National Laboratory Discover
Conductive Nanowires in Bacteria. Details published in the July
10 advance online Proceedings of the National Academy of Sciences.
More...
June 2006
An Integrated Model of Microbial Stress Response. GTL researchers
at Lawrence Berkeley National Laboratory discover key clues to microbial
stress response and adaptation. Details appear in J. Bact. 188 (11)
4068-4078. [6/06] Details
May 2006
Image Gallery Updated: The Genomics:GTL image gallery has been updated.
April 2006
Call for Bioenergy Sequencing Targets. Recommendations are
being sought for microbial sequencing targets in support of the bioenergy mission
of the Office of Biological and Environmental Research (OBER). Nominations
should be
received by 4:30 p.m. (EDT), August 10, 2006, to be accepted for merit review.
March 2006
DOE Office of Science to Revise Plans for Genomics:GTL Facilities.
The Department of Energys Office of Science announced today that it is revising
its plans for the deployment of new research facilities to support its Genomics:GTL
program. The decision to reshape plans for the new GTL research facilities comes
in response to the Presidents recently announced Advanced Energy Initiative
and a review of the GTL program by the National Research Council of the
National Academies. The January 9, 2006, funding opportunity announcement has
been canceled.
February 2006
Review
of the Department of Energy’s Genomics: GTL Program, National Research
Council of the National Academies (February 2006; PDF, 679 kb)
NOTE: Final draft is posted at link above (May 2006).)
Abstracts for Joint Genomics: GTL Contractor-Grantee Workshop
IV and Metabolic Engineering Working Group Interagency Conference on
Metabolic Engineering. Abstracts for
the joint workshop held February 12 - 15 are now posted. Abstracts were
required from each DOE/BER
funded
project.
January 2006
Ari Patrinos, Associated Director of Science for Biological
and Environmental Research of the Office of Science of the U.S. Department
of Energy, is leaving DOE to become President of Synthetic Genomics, Inc.,
on February 8, 2006. For more information, see
press release.
USDA and DOE to Coordinate Research of Plant and Microbial Genomics:
Soybean DNA to be Decoded. The U.S. Departments of Agriculture
and Energy announced January 16th they will share resources and coordinate
the study of plant and microbial genomics, and the Department of Energy
will tackle the sequencing of the soybean genome as the first project resulting
from the agreement. For more information, see press
release.
DOE Joint Genome Institute Announces First Annual Users Meeting.
The meeting will be held March 29 - April 1, 2006 in Walnut Creek, CA.
See announcement for more information.
[ CANCELED (03/28/06) ] Funding Opportunity Announced: January 9. Genomics:GTL Facility for the Production
and Characterization of Proteins and Molecular Tags. This Funding Opportunity
Announcement requests that the scientific community submit applications
for the development of a scientific user facility for the Production and
Characterization of Proteins and Molecular Tags that involves the design,
construction (construction is used generically here and could include new
construction, renovation of existing space, leasing space or other options
proposed by the applicants), and research and development related to the
design, configuration, and operation of the facility that will serve as
a major scientific user facility for the scientific community including
the Genomics: GTL program.
December 2005
Joint Genomics: GTL Contractor-Grantee Workshop IV and Metabolic
Engineering Working Group Interagency Conference on Metabolic Engineering
Feb 12-15, 2006. The
next Genomes to Life (GTL) program workshop will be held February 12
- February
15 at the Bethesda North Marriott Hotel and Conference Center, located in North
Bethesda, Md. Abstract submission due December 20, 2005. Abstracts
are required from each
DOE/BER
funded project. Details on meeting logistics, including the workshop
agenda, abstract submission, and hotel location and
reservation
information can be found on the workshop website at http://www.orau.gov/gtl2006/.
[Contact: Sharlene Weatherwax at Sharlene.Weatherwax@science.doe.gov]
Chemical and Engineering News Article Features GTL Program.
See "Genomics
and Clean Energy: Developing Biotechnology Area is Attracting More Than
Just Biologists" in the December 12, 2005 (83:50, pp. 39-41) issue.
GTL Researcher Jay Keasling featured in Time
magazine, named one of the World Economic Forum's 2006
Tech Pioneers.
November 2005
GTL Researcher James Cate and Collaborators Provide New Insights into
Ribosome Structure and Operation in the November 4, 2005, Issue of Science.
In the November 4, 2005, issue of Science, GTL researcher James Cate
(Lawrence Berkeley National Laboratory) and collaborators offer new insights
into the operation of the ribosome, the molecular complex that manufactures proteins
in the cell. The team determined two high-resolution ribosome crystal structures,
resulting in the first detailed view of the interface between ribosome subunits
as well as its center for producing proteins. The research is part of the GTL
effort to develop strategies to label complexes to track their operation in cells.
The National Institutes of Health partially supported this work.
October 2005
Energy Department Awards $92 Million for Genomics Research.Press
Release (Oct. 3, 2005).
Genomics:GTL Roadmap Now Available. The Genomics:GTL
Roadmap, a systems microbiology plan for DOE missions, is now available
in PDF form.
June 2005
GTL Researcher Derek Lovley Describes New Discovery in 23 June
Issue of Nature (435: 1098-1101).
An Electrifying Discovery.
In the June 23 issue of Nature (435: 1098-1101), GTL researcher
Derek Lovley of the University of Massachusetts, Amherst, described the discovery
of electron-conducting "nanowires" on the outer cell surface
of the metal-reducing microorganism Geobacter. These projections
(called pili) appear to be conduits by which the microbe transfers electrons
onto iron oxides during the process of dissimilatory iron reduction.
Normally,
the pili that extend from bacteria play a role in attachment or motility.
But Geobacter uses pili to gain energy by transferring electrons
onto the
iron oxide surface, a process that has been harnessed for remediation
of contaminated groundwater. Discovery of this fundamental mechanism
of microbial
metal reduction could lead to better models for subsurface bioremediation
processes. The authors say this finding also suggests that we might
be able to mass-produce protein nanowires based on Geobacter biology.
Time Magazine
Features Venter, DOE Genomics Research (06/20/05)
May 2005
Protein Study Finds Clues to Microbes' Survival Techniques.
In the first comprehensive study of gene expression in a microbial
community from an "extreme" natural environment, scientists from
Lawrence Livermore and Oak Ridge national laboratories, the University
of California, Berkeley, and Xavier University in New Orleans have
identified more than 2,000 proteins produced by five key species in the
community. The findings appeared May 5 on the Science Express Website, an advance
online publication of the journal Science.
April 2005
JGI Study Reveals New Technique for Fingerprinting Environmental Samples.Groundbreaking
research led by the JGI demonstrates for the first time that the signatures
of genes in terrestrial and aquatic samples can accurately diagnose the
health of sampled environments. The study, published in the April 22nd
issue of Science, predicts that large-scale genome sequencing will
accelerate advances in environmental sciences akin to the contributions DNA
sequencing
has made
to the biomedical sciences. [More...]
GTL Featured in Recent Issues of The Scientist and The
Economist. GTL was the subject of a Vision column by Dr. Ari
Patrinos [DOE Office of Biological and Environmental Research (BER)] in the
March 14, 2005, issue of The Scientist.
The column presents a case for being "bullish" on the promise of biotechnology
to deliver solutions to principal DOE energy and environmental security
missions. The use of bacteria to precipitate uranium out of groundwater,
the potential for a synthetic genome to provide organisms with selected characteristics
that address DOE needs, and the use of the DNA sequence of the Populus tree
to create opportunities for enhancing biomass potential were cited as examples
of biotechnologys promise for DOE needs. Additionally, in 2005 in The
World, a companion publication to The Economist,
BER is cited as leading the way to use microbes for generating energy
and cleaning up pollution. Development of a synthetic bacterium from "off-the-shelf" parts
in the laboratories of J. Craig Venter and George Church offers the promise
of synthetic biology to form the basis of important and possibly revolutionary
technology.
JGI Microbial Genome Database Tool Reported in Science.
The March 18, 2005, issue of Science reports on the new Integrated
Microbial Genomes (IMG) site at the DOE Joint Genome Institute (JGI) (p. 1701, “Microbial
Get Together.”) This new DOE clearinghouse (http://img.jgi.doe.gov/cgi-bin/pub/main.cgi)
helps researchers analyze the deluge of DNA data on microorganisms.
The IMG site currently stores nearly 300 draft or completed genome sequences
from archaea, bacteria, and other microbes, along with tools for sifting through
the data. Visitors can get acquainted with all 2526 protein-coding genes carried
by the marine cyanobacterium Synechococcus, for example. Besides accessing
basic information about the gene, its protein, and its function, visitors can
summon
diagrams
illustrating which biochemical pathways are influenced by the gene. Browsing
tools make it easy to pinpoint similar genes in different organisms and compare
them
side by side.
March 2005
Call for DNA Sequencing Targets. Recommendations are being
sought for microbial sequencing targets in support of the science missions
of the Office of Biological and Environmental Research.
Federal Register notice available here.
Nominations should be received by 4:30 p.m. (EDT), July 14, 2005, to be accepted
for merit review.
GTL in The Scientist. "Vision: Biotechnology reenergized,"
an article by Ari Patrinos discussing
how the goals and promise of the Genomes to Life program have energy and environmental
applications,
was featured in the March 14, 2005, issue of The Scientist. Free registration
is required.
February 2005
Third GTL Contractor-Grantee Workshop Held.
The third Genomics:GTL program workshop was held February 6-9. Abstracts available
here.
January 2005
DOE Establishes Institutes for the Advancement of Computational Biology
Research &
Education. In the fall of 2004, DOE established three institutes for
the advancement of computational biology research and education. The institutes
will support the advancement of computational
biology research as an intellectual pursuit and will provide innovative approaches
to educating biologists as computational scientists. The institutes will focus
on advancing computational biology research and education
as counterbalancing and complementary activities to experimental biology.
[More
about the institutes...]
(January 27, 2005)
D. ethenogenes. TIGR scientists decipher genome
of Dehalococcoides
ethenogenes,
a microbe that can be used to clean up groundwater contaminants. Science 307:
105-108. Press
Release.
(January 7, 2005)
December 2004
Call for DNA Sequencing Proposals.
Joint Genome Institute (JGI) Community Sequencing Program (CSP) is calling
for proposals to two programs. Letter of intent due January 28, 2005. Applications
due February 25, 2005.
[more...]
GTL-Related Call for Proposals.
A solicitation to DOE National Laboratories on Poplar Genome-Based Research
for Carbon Sequestration in Terrestrial Ecosystems. See Announcement
LAB 05-10. Preproposals due by January 18, 2005, and formal proposals
by March 8, 2005.
November 2004
GTL Contrator-Grantee
Workshop.The third Genomes to Life (GTL) program
workshop will be held February 6 (no-host evening reception) through February
9 (ending at
noon)
at
the Wardman
Park hotel
in Washington, D.C. Abstract submission due December
10, 2004. Abstracts are required from each DOE/BER funded project. Details
on meeting logistics, including the workshop agenda, abstract submission,
and hotel location and reservations, can be found on the workshop
website at http://www.orau.gov/gtl2005/.
[Contact: Timothy Boyle at 301/903-0353 or timothy.boyle@science.doe.gov]
October 2004
Resesarcher Wins Innovators' Award. GTL researcher Colin
Hill wins MIT’s Technology
Review “World’s
100 Top Young Innovators” award. [More...
]
September 2004
Funding Solicitation. OBER and OASCR are requesting proposals from
large, well-integrated, multidisciplinary research
teams in support of the Genomics:GTL program. See Notice
DE-FG01-04ER04-32 and Announcement
LAB 04-32. Preapplications due by October 25, 2004. Formal
applications due by January 18, 2005. See
Funding for more...
Diatom Genome Revealed, Key to Global Carbon Cycling: The
draft genome sequence for the 34-Mb genome of the saltwater diatom Thallassiosira
pseudonana appears in the October 1, 2004, issue of Science.
[More...]
News Brief. Radiation-resistant bug's survival tied to high
levels of manganese in a Science
Express paper published on October 30, 2004. More...
Consortium Releases First Tree DNA Sequence.An international
consortium including DOE, Genome Canada, and a Swedish team has released the
first complete DNA sequence of a tree, Populus trichocarpa. 9/21/04
[Details...]
July 2004
News Brief. GTL researcher Derek Lovley (University of
Massachusetts) was highlighted in a syndicated Knight-Ridder newspaper
article for his Geobacter work. 7/26/04 [More...]
May 2004
Feedback. The public is invited to provide comments and
suggestions on this Genomics:GTL program by completing this
form.
Bacteria
Found in Hanford Waste. Scientists studying the soil beneath
a leaking Hanford nuclear waste storage tank have discovered more than 100
species of
bacteria living in a toxic, radioactive environment that most would have thought
inhospitable to all forms of life. (Seattle Post-Intelligencer, 5/26/04)
JGI Decodes Wood and
Toxic Waste-Degrading Fungus Genome. The Joint
Genome Institute (JGI) announced the publication of a high-quality
draft genome sequence of the white rot fungus, Phanerochaete chrysosporium.
These are the only known microbes capable of efficiently degrading the
recalcitrant aromatic plant polymer lignin, one of the most abundant
natural materials on earth. They also have demonstrated the ability to
remediate explosive contaminants, pesticides, and toxic waste with similar
chemical structures to lignin. The sequence findings were published in
the June 2004 issue of Nature Biotechnology.
April 2004
DNA Sequence Completed for Corrosive Bacterium Desulfovibrio
vulgaris. A team of scientists led by The Institute
for Genomic Research has sequenced the genome of Desulfovibrio
vulgaris, a bacterium that damages oil and
natural gas pipelines and causes staggering economic losses at industrial
sites worldwide. In their analysis, scientists also found a network of
proteins that have the potential to remediate pollutants such as uranium
and chromium, commonly found at DOE contaminated sites.The study, funded
by DOE, was reported in the May 2004 issue of Nature Biotechnology.
[More...]
Sequencing Targets.Recommendations are sought for sequencing
targets in support of the science missions of the Office of Biological
and Environmental Research (BER). Candidates due by July 1, 2004.
March 2004
Researchers Discover 1.2 Million New Genes in Sargasso Sea
Microbes. Department of Energy-funded researchers at the Institute
for Biological Energy Alternatives (IBEA) have sequenced microbes in the
Sargasso Sea and have discovered at least 1,800 new species and more than
1.2 million new genes. The results will be published in the journal Science.
IBEA researchers’ discoveries include 782 new rhodopsin-like photoreceptor
genes (only a few dozen have been characterized in microorganisms to date).
March 4, 2004
February 2004
JGI
Microbial Sequencing Priorities for FY 2004.
Progress updated monthly.
JGI Launches Community Sequencing Program (CSP). “The
primary goal of the CSP is to provide a world-class sequencing resource
for the expanding
the diversity of disciplines—geology, oceanography, and ecology, among
others—that can benefit from the application of genomics,” says
JGI Director Eddy Rubin. Press Release
Contractor-Grantee Abstracts. Genomics:GTL Contractor-Grantee
Workshop II, Washington, D.C., February 29-March 4, 2004, meeting abstracts
are now available in PDF.
First Genomes Revealed from Environmental
Microbial Communities. Researchers from the Department
of Energy Joint Genome Institute and the University of California, Berkeley,
report the first genomic characterization
of a microbial community. The results announced February 1st online in
the journal Nature reveal how the genetic identities of microorganisms
thriving in toxic conditions, "extremophiles," were recovered
from a natural biofilm growing at an Environmental Protection Agency Superfund
site. Four of the five microbes have to this point defied laboratory
culture and have been studied only in their natural habitat, in this instance
runoff from an abandoned mine, or acid mine drainage.
Jillian Banfield and her colleagues from U.C. Berkeley, who have been
studying this site for the past 8 years, retrieved the sample from
the depths
of one of the nation's worst Superfund sites in Iron Mountain, California,
near the northern town of Redding. [2-2-04]
JGI Press Release
Nature
04 March 2004 428: 37-49
January 2004
Funding Solicitation. OBER is requesting proposals from
the DOE national labs in support of the Microbial Genome Program. See Announcement
04-07. Preapplications due by January 29, 2004. Formal applications
due by April 15, 2004. See Funding
for more...
Funding Solicitation. OBER is requesting applications in
support of the Microbial Genome Program. See Notice 04-07 at http://science.doe.gov/grants/pdf/DE-FG01-04ER04-07.pdf.
Preapplications due by January 29, 2004. Formal applications due by April
15, 2004. See Funding for more...
Genomatica
Awarded Prestigious Frost & Sullivan Technology
Leadership Award for SimPheny™.
Frost & Sullivan, a leading international marketing consulting company,
has named Genomatica, Inc., a leader in silico systems biology companies,
as recipient of the 2003 Technical Insights Award for Technology Leadership.
January 07, 2004 [More...]
December 2003
Online Article. "Complete
Genome Sequence of the Metabolically Versatile Photosynthetic Bacterium
Rhodopseudomonas palustris," Nature Biotechnology,
December 14, 2003, Frank W Larimer, et al . See also Website Rhodopseudomonas
palustris Complete Genome Sequence and Annotation
News Brief. "Energy Department-Funded Scientists Decode
DNA of Bacterium that Cleans Up Uranium Contamination and Generates
Electricity," December
11, 2003 (Press Release and Science Article)
Computing Report. Report on Three Genomes to Life Workshops:
Data Infrastructure, Modeling and Simulation, and Protein Structure
Prediction, Gaithersburg, Maryland; July 22–24, 2003 (PDF
file, 410 kb)
November 2003
News Brief. "Researchers Funded by the DOE "Genomes
to Life" Program Achieve Important Advance in Developing Biological
Strategies to Produce Hydrogen, Sequester Carbon Dioxide and Clean Up the
Environment."
See November 13, 2003, press release. See
also
remarks by Secretary of Energy Spencer Abraham.
October 2003
PNNL Awarded Proteomics Grant. The National Institutes
of Health has awarded Pacific Northwest National Laboratory a large
grant to study proteomics. See the October 7, 2003 press
release.
Funding Solicitations. FY 2004 DOE SBIR/STTR Program
Solicitations are now available and will close on January
6, 2004 (http://sbir.er.doe.gov/sbir).
More information on Funding.
September 2003
Funding Awards. 2003 SBIR Phase II Awards
Announced. Next solicitation will be issued on October 7, 2003
(http://sbir.er.doe.gov/sbir).
More information on Funding.
August 2003
News Brief. Natural and Accelerated
Bioremediation Research (NABIR) Highlighted in the San Francisco
Chronicle,
August 6, 2003
News Brief. Genomes
of Tiny Microbes Yield Clues to Global Climate Change, August
13, 2003
Facility Workshop. GTL and Beyond:
Data Standards Workshop.
September 10-11, 2003,
San Francisco, California
July 2003
News Brief. New
Phase II SBIR Awards Support Genomes to Life Research, July 30, 2003
News Brief. PNNL's
Richard Smith Wins 7th R&D 100 Award for FT-MS Proteome Express
Project,
July 30, 2003
May 2003
Facility Workshop. Characterization
and Imaging of Molecular Machines Facility Workshop, June 17-18,
2003. Atlanta Airport Hilton, Atlanta, Georgia
News Brief. DOE Joint
Genome Institute and Oregon State University Sequence Key Soil Microorganism
in Carbon
and
Nitrogen Cycles
News Brief. Two DOE
SC BER Genome Scientists Win Major Microbiology Awards
Facility Workshop. Protein
Production & Characterization Facility Workshop, Argonne National
Laboratory, May 29-30, 2003
Announcement. Recommendations
for Sequencing Targets Sought. Deadline June 26, 2003
April 2003
Press Release. Energy
Department Awards $9 Million for Energy
Related Genomic Research. April 23, 2003
DOE Jobs. Microbial
Geneticist; Office of
Science, Office of Biological and Environmental Research, Life Sciences
Division. Closes 6/06/2003.
Special Articles. "Realizing
the Potential of the Genome Revolution: The Genomes to Life Program," Marvin
E. Frazier, Gary M. Johnson, David G. Thomassen, Carl E. Oliver,
and Aristides Patrinos, Science 300, 290 (2003)
February 2003
New Publications. Genomes
to Life Contractor - Grantee Workshop I Abstracts, Arlington, Virginia,
February 9-12, 2003
Call for Applications. See Funding for
current call for research applications.
