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JGI Funds Partners Developing Enabling Technologies for Energy-related, Environmental Genomics

NEW YORK (GenomeWeb News) – The US Department of Energy's Joint Genome Institute has funded six new initiatives to develop technologies that will help JGI and its users conduct their research efforts into microbiology, metagenomics, and plant genomics.

JGI said yesterday that it plans to provide these new projects, which are supported under the Emerging Technologies Opportunity Program (ETOP), with a total of around $3.5 million over the next two years.

JGI's mission is to maintain a genome science user facility that provides large-scale genomic technologies for researchers studying energy-related and environmental questions. The institute expects its service offerings, tools, and facilities to continue to advance in part through this program, which enlists partners to develop specialized tools that complement its capabilities.

"A core philosophy of the DOE JGI is that our suite of technical and analytical capabilities needs to evolve continuously so that the scientific achievements of our users can be maximized," Jim Bristow, JGI's deputy director of science programs, said in a statement.

"While state-of-the art massive-scale sequencing remains a critical component of the DOE JGI, other large-scale capabilities, particularly those that will help link sequence to function, will be provided to JGI users in the future," Bristow added.

Among those receiving funding under the program, Stanford University Professor of Bioengineering Stephen Quake was chosen as a new ETOP partner to study single-cell approaches to metagenomics, with the goal of making it easier to isolate single cells from complex environmental samples.

Jay Shendure, an associate professor of genome sciences at the University of Washington, will be funded to develop an accurate gene synthesis technology with tag-directed retrieval of sequence-verified DNA molecules, which could "streamline the DNA synthesis pipeline and increase the output" of synthesized DNA, JGI said.

Massachusetts Institute of Technology Principal Investigator Roman Stocker and University of Vienna Professor Michael Wagner will develop a high-throughput microbial cell sorting technology that combines labeling with heavy water, microspectroscopy, microfluidics, and flow cytometry. They expect that their technology could speed up the functional characterization of genes from metagenomic sequencing projects, a high priority area for JGI.

Rod Wing, director of the Arizona Genomics Institute, received an ETOP award to develop technology to generate high-quality DNA from plants and other organisms, large insert libraries, and maps for improving physical map and sequence-level assemblies. These tools could make it easier for JGI and its partners to isolate large volumes of DNA from plants while maintaining high-quality sequences.

A group of three investigators were selected to develop a pipeline for high-throughput recovery of near-complete and complete microbial genomes from complex metagenomic datasets.

Jill Banfield, a faculty professor at University of California, Berkeley and Lawrence Berkeley National Laboratory, Chongle Pan, a staff scientist at Oak Ridge National Laboratory, and Brian Thomas, a programmer and analyst at UC Berkeley, think that this technology could be used to better isolate and characterize entire microbial genomes from the fragmentary sequences that are typical in environmental samples.

Jon Magnuson, a biochemist at Pacific Northwest National Laboratory, will work on developing and implementing high-throughput methods for fungal culturing and isolating nucleic acids, tools that could make JGI's sequencing efforts "considerably easier," the institute said.

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