US Department of Energy Joint Genome Project selects two proposals submitted by Danforth Center

November 10, 2011

ST. LOUIS, MO -- The U.S. Department of Energy (DOE) Joint Genome Institute (JGI) has selected two projects from a highly competitive pool of applications, submitted by Danforth Plant Science Center Principal Investigators, Dr. Thomas Brutnell and Dr. Todd Mockler as part of its 2012 Community Sequencing Program (CSP).

The 2012 CSP call invited researchers to submit proposals for projects that advance capabilities in fields such as plant-microbe interactions, microbes involved in carbon capture and greenhouse gas emission, and metagenomics--the characterization of complex collections of microbes from particular environmental niches. This data will enhance research projects that aim to improve biofuel feedstock production, focusing on the potential of microorganisms to improve feedstock growth and prevent devastating diseases that hinder yields.

The project proposed by Drs. Brutnell and Mockler will develop sequence-based community tools for Setaria viridis-a model genetic system for bioenergy grasses. Brutnell and Mockler and colleagues Jeff Bennetzen (University of GA), Katrien Devos (University of GA), Elizabeth Kellogg (University of Missouri-St. Louis) and Andrew Doust (Oklahoma State University) will use high- throughput sequencing technology to rapidly advance genetic resources in Setaria viridis (also known as green bristlegrass). Setaria is rapidly emerging as a model system for bioenergy grasses as it is closely related to the primary bioenergy feedstock crops such as switchgrass, Miscanthus and sugarcane, but is a much more manageable genetic system. This project will include providing sequence blueprints for more than 50 diverse varieties of Setaria as well as providing the data to facilitate the development of mutagenized populations and lines that can be used to map genetic variation. The development of these genetic resources will enable scientists to identify genes that contribute to a number of traits that are essential to develop efficient biomass production including increased stress tolerance, water and nitrogen use efficiency and biomass production.

The second project of which Dr. Mockler is a co-PI with Dr. Samuel Hazen at the University of Massachusetts; will create a library of grass transcription factors for the energy crop model system Brachypodium distachyon. Brachypodium serves as a model for potential energy crops such as switchgrass, sorghum, and Miscanthus, as well as for the cereal crops that constitute a large part of the world's diet. Transcription factors are proteins that regulate gene expression, and the Brachypodium transcription factors targeted in this project are implicated in grass cell wall biosynthesis and the regulation of growth and biomass accumulation by light. Hazen, Mockler, and collaborator Dr. Steve Kay at the University of California San Diego will use this project as the cornerstone of a new high-throughout platform for analyzing protein-DNA interactions for the purpose of understanding important traits in grass species.

These grants will provide a huge boost to the development of these two model grasses and will greatly accelerate the ability of scientists to translate basic scientific discoveries into application.

"The Enterprise Rent-A-Car Institute for Renewable Fuels has a strong foundation in developing algal and seed oil biofuels. These new grants will expand the Institute's portfolio to include development of model systems for lignocellulosic feedstocks," said Brutnell. "I am particularly excited about the prospects of the Danforth Center becoming a leader in molecular tool development for these model grasses."

A total of 41 proposals were approved from the 152 submitted, culled from the 188 letters of intent originally received. The projects were then reviewed and approved by an outside panel before being vetted by the DOE.

The total allocation for the coming year's CSP portfolio will exceed 30 trillion bases (terabases or Tb), a 100-fold increase compared with just two years ago, when just a third of a terabase was allocated to more than 70 projects. This amounts to the equivalent of at least 10,000 human genomes in data.

"These selections truly take advantage of the DOE JGI's massive-scale sequencing and data analysis capabilities," said Eddy Rubin, DOE JGI Director. "The projects span the globe and the unexplored branches of the tree of life, and promise to yield a better understanding of the interplay between climate, ecosystem and organism."
-end-
For the complete list of CSP 2012 sequencing projects please visit, http://www.jgi.doe.gov/sequencing/cspseqplans2012.html.

About the Joint Genome Institute

Supported by the Office of Biological and Environmental Research in the DOE Office of Science, the DOE JGI's Community Sequencing Program enables scientists from universities and national laboratories around the world to probe the hidden world of microbes and plants for innovative solutions to the nation's major challenges in energy, climate, and environment.

About The Donald Danforth Plant Science Center

Founded in 1998, the Donald Danforth Plant Science Center is a not-for-profit research institute with a mission to improve the human condition through plant science. Research at the Danforth Center will feed the hungry and improve human health, preserve and renew the environment, and enhance the St. Louis region and Missouri as a world center for plant science. The Center's work is funded through competitive grants and contract revenue from many sources, including the National Institutes of Health, U.S. Department of Energy, National Science Foundation, U.S. Department of Agriculture, U.S. Agency for International Development and the Bill & Melinda Gates Foundation.

The Donald Danforth Plant Science Center invites you to visit its new website, http://www.danforthcenter.org, featuring interactive information on the Center's scientists, news and research, including the Enterprise Rent-A-Car Institute for Renewable Fuels, the Center for Advanced Biofuel Research, and the National Alliance for Advanced Biofuels and Bioproducts. Public education outreach, RSS feeds and the brand-new "Roots & Shoots" blog help keep visitors up to date with Center's current operations and areas of research. Follow us on Twitter at @DanforthCenter.

Donald Danforth Plant Science Center

Related Transcription Factors Articles from Brightsurf:

Circular RNA regulates neuronal differentiation by scaffolding an inhibitory transcription complex
In a screening for a functional impact to the neuronal differentiation process, Danish researchers identified a specific circular RNA, circZNF827, which surprisingly 'taps the brake' on neurogenesis.

Transcription factors may inadvertently lock in DNA mistakes
A team of Duke researchers has found that transcription factors have a tendency to bind strongly to ''mismatched'' sections of DNA, i.e. sections of the genome that were not copied correctly.

New role assigned to a human protein in transcription and genome stability
DNA-RNA hybrids, or R loops, are structures that generate genomic instability, a common feature of tumor cells.

CeMM study reveals how a master regulator of gene transcription operates
Using TPD technology, CeMM researchers set out to understand set out to understand the primary role of a key regulator of transcription, the human Mediator complex.

Researchers find new role for dopamine in gene transcription and cell proliferation
A joint group of researchers at the George Washington University and the University of Pittsburgh have found that dopamine and the dopamine D2 receptor modulate expression via the Wnt/β-catenin signaling pathway.

SMAD2 and SMAD3, two almost identical transcription factors but with distinct roles
Both transcription factors regulate the expression of genes involved in embryo development, among other functions, although they exert very different roles.

Study explores role of mediator protein complex in transcription and gene expression
A new study led by Ryerson University called 'The Med31 Conserved Component of the Divergent Mediator Complex in Tetrahymena thermophila Participates in Developmental Regulation' advances existing knowledge about transcription and gene expression.

New members found in a transcription factor complex that maintains beta cells
A protein complex in the nucleus of beta cells contains different proteins that work together to regulate genes important for the development and maintenance of functional beta cells.

Testifying while black: A linguistic analysis of disparities in court transcription
A new study has found that court reporters transcribe speakers of African American English significantly below their required level of accuracy.

Transcription factor network gets to heart of wood formation
Research on high-level switches that control wood formation has applications in timber, paper and biofuels, as well as making forests healthier.

Read More: Transcription Factors News and Transcription Factors Current Events
Brightsurf.com is a participant in the Amazon Services LLC Associates Program, an affiliate advertising program designed to provide a means for sites to earn advertising fees by advertising and linking to Amazon.com.