Corn genome model speeds biofuel, food staple development

Examiner.com
Rita Tatum, South Bend Science Examiner
November 2, 2011

Hoosier corn feeds millions worldwide and offers significant potential as an automotive biofuel, produced in South Bend’s New Energy Corp. corn ethanol plant. Relying on genome modeling, corn crops may be genetically fine-tuned to produce both improved food corn and stronger nonfood fibers for advanced biofuel production rapidly.

Lawrence Berkeley National Laboratory announced today that the first genome-scale model for predicting functions of genes and gene networks has been developed by an international team of researchers from the U.S. Department of Energy’s Joint BioEnergy Institute (JBEI), a multi-institutional partnership led by the Berkeley Lab. Called RiceNet, the model may speed development of improved strains of corn and rice to act as advanced biofuels. Scientists are hopeful the new model also will help boost crop production and improve the quality of two important food staples.

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Cell signalling classification system gives researchers new tool

Science Centric 3 July 2010 09:00 GMT

Using ever-growing genome data, scientists with the Department of Energy's (DOE) Oak Ridge National Laboratory and the University of Tennessee are tracing the evolution of the bacterial regulatory system that controls cellular motility, potentially giving researchers a method for predicting important cellular functions that will impact both medical and biotechnology research.

A new study from the Joint Institute for Computational Sciences, a research venture between ORNL and UT, has demonstrated how knowledge of biological systems can be derived by computational interrogation of genomic sequences. The results have implications for areas ranging from medicine to bioenergy.

'We now have hundreds of millions of DNA sequences from all sorts of organisms deposited in databases. However, our abilities to translate raw genomic data into useful knowledge are still very limited,' said Igor Zhulin, joint faculty professor and principal investigator.

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China completes cassava genome sequencing for energy use research

iStockAnalyst.com
Monday, January 18, 2010 12:51 AM

HAIKOU, Jan. 18, 2010 (Xinhua News Agency) -- China has completed the genome sequencing of three varieties of cassava, the roots of which are used to produce ethanol, scientists said Monday.

The genome sequencing can shed light on the cassava plant as a source of biomass energy. It also lays the foundation for enhancing cassava's ability to grow on barren soil and resistance against drought, said Peng Ming, head of the Biology Institute of the Chinese Academy of Tropical Agricultural Sciences.

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Establishing Standard Definitions For Genome Sequences

ScienceDaily.com

ScienceDaily (Oct. 8, 2009) — In 1996, researchers from major genome sequencing centers around the world convened on the island of Bermuda and defined a finished genome as a gapless sequence with a nucleotide error rate of one or less in 10,000 bases. This effectively set the quality target for the human genome effort and was quickly applied to other genome projects. If a genome sequence didn't meet this stringent criterion, it was simply considered a "draft."

More than a decade later, researchers are finding that with the advent of the latest sequencing technologies the terms "draft" and "finished" are no longer sufficient to describe the varying levels of genome sequence quality being produced. The quality issue is of particular concern for any researcher who wants to use the sequence, in order to know its integrity and reliability. This is of even greater concern for reference genome sequences, such as those genome projects conducted in support of the U.S. Department of Energy (DOE) missions of bioenergy and environmental clean-up, because they provide the foundational knowledge of the gene content and how these organisms interact with the environment.

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Integrated microbial genomes expert review goes primetime

ScienceBlog
May 19, 2009

WALNUT CREEK, CA - After a genome is sequenced and automatically annotated, researchers often manually review the predicted genes and their functions in order to improve accuracy and coverage across the vast genetic code of the particular target organism or community of organisms. These annotations drive the publication of high-profile science relevant to advancing bioenergy research and our understanding of biogeochemistry --the biological, chemical, physical, and geological processes that regulate our environment.

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.

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Michigan State to Create Genomic Clearinghouse for Biofuel Crops

GrainNet.com
Date Posted: August 13, 2008

East Lansing, MI— Michigan State University scientists, armed with a half-million-dollar federal grant, are creating an easily accessible, Web-based genomic database of information on crops that can be used to make ethanol.

"Ultimately this will allow us to create better biofuel crops," said C. Robin Buell, associate professor of plant biology and project leader.

"Right now, about half of the biofuel crops don't have genomic databases, and the ones that do are in many different places and are annotated differently, which makes it difficult to compare and use the information."

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