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DOE s New 20-Year Plan Features as Much as $500M in Proteomics Projects


The US Department of Energy’s Office of Science this week released a 20-year roadmap recommending the creation of 28 new high-priority, high-cost major facilities – and at least two of these, possibly totaling up to half a billion dollars, will be proteomics-focused

DOE secretary Spencer Abraham announced the release of the 48-page report, available here, just a few days before Congress is set to vote on an energy bill. The DOE Office of Science has requested $3.3 billion in funding for FY 2004. “Nothing of this scope has ever been attempted by our department or indeed by any other science agency in government,” Abraham said in an address to the National Press Club, in which he discussed the roadmap.

The two facilities with heavy proteomics focuses — a Protein Production and Tags facility (PPTF) and a Whole Proteome Analysis facility (WPAF) — are part of a four-facility plan already dreamed up by the DOE Genomes to Life program, which picked up $103 million in funding for research collaborations last summer (see PM 9-2-02) and has as its goal the application of genomic data and high-throughput technologies to study cellular mechanisms of microbes that might be useful for energy production, environmental cleanup, and other energy-related issues. “The ambition is very large,” said Bob Rosner, chief scientist at the DOE-sponsored Argonne National Laboratory. “Ultimately, the DOE wants to be the agency that funds the work that gets us to the point where we can take a cell and go from the genome and understand how the entire cell functions in detail.”

More specifically, the mandate of the PPTF would be to “use highly automated processes to mass-produce and characterize tens of thousands of proteins per year, create ‘tags’ to identify these proteins and make these products available to researchers nationwide,” the report stated. Once the infrastructure and techniques for doing this large-scale production are in place, the facility and its database of proteins would be made available for outside researchers to use for their own projects. The mandate of the WPAF would be to “provide researchers with the ability investigate how microbes adapt to changes in their environment by turning certain portions of their genome ‘on’ and ‘off,’” according to the report. The facility and techniques would then be made publicly available.

The other two GTL facilities, also given nods in the DOE report, are the Characterization and Imaging of Molecular Machines and the Analysis and Modeling of Cellular Systems facilities. George Michaels, director of bioinformatics and computational biology at the DOE’s Pacific Northwest National Laboratory and head of PNNL’s WPAF proposal, said that the total proposed budget for all four facilities would be about $880 million, with each facility getting roughly $200 million. DOE spokesman Jeff Sherwood would neither confirm nor deny this estimate, saying that it was too early for the DOE to release numbers on possible budgets, but Brian Kay, who is heading up an effort at ANL in collaboration with Los Alamos National Lab to win the PPTF, confirmed that his proposal calls for about $200 million in funds.

PPTF, Characterization and Imaging Facility Prioritized

The DOE grouped the 28 facilities, which Office of Science director Raymond Orbach chose from among 53 recommended by the office’s six divisions, into “near-term,” “mid-term,” and “far-term” categories depending mostly on scientific readiness. The PPTF would be one of the first new DOE facilities to be built should the necessary funding be approved; it is ranked third in the “near-term priority” category. The Characteriz-ation and Imaging facility also made it into the near-term category at number seven, while the Analysis and Modeling and Whole Proteome facilities tied for priority 14 under the mid-term category.

According to Kay, the call for PPTF proposals is likely to come in the next three to six months. “The protein production facility is one of the first things to be built, because the science is ready – we know how to do it,” Rosner said. The science required for the other GTL facilities is not yet as developed, according to Rosner, but “having the protein production facility will definitely push that along faster.”

Although the selection process for host labs of the PPTF and the WPAF will technically be open competitions, the advisory committee report that recommended the facilities noted that “National Labs are an obvious set of candidates” as sites for the facilities. From the confidence with which ANL’s Rosner and Kay and PNNL’s Michaels discussed their proposals, the appointment of ANL to host the PPTF and of PNNL to host the WPAF seem to be nearly certain. Rosner was not shy about explaining why he thought ANL was such an obvious choice. “National labs are the places where the federal government has put in the resources so that facilities of this scale can function, and where the infrastructure isn’t something that’s here today and gone tomorrow, which is the problem with universities often,” Rosner said. Rosner also noted that ANL’s access to the Advanced Photon Source for structural biology work and a recently funded ANL-based biosafety level 3 laboratory as part of a University of Chicago-based Regional Center of Excellence in Biodefense grant (see PM 9-12-03, 8-1-03) made it a particularly suitable choice. “There’s a nice fit between the folks who are studying the disease-causing organisms, the folks that will be able to produce the proteins on a large scale, and the folks that will be able to do characterization – it’s almost one-stop shopping,” he said.

Kay revealed that ANL already has a detailed proposal in the works for a high-throughput production platform that would “rely heavily on robotics and microfluidics” – in particular, he said, Beckman Coulter’s liquid handling robots. “We envision that microfluidics will play a crucial role to allow miniaturization of the assay, have rapid throughput, and have low overhead in terms of using up the protein that has been made,” he said.

The process would have several stages: the amplification of ORFs with PCR and cloning into vectors; the expression of proteins either in E. coli, in the vector’s host, in vitro, or even through de novo chemical synthesis; purification with column chromatography, QA/QC of the products using anything from SDS PAGE to mass spec; and finally either storage of the proteins, or use of the proteins for additional characterization analysis or the generation of affinity reagents. The final product either way would be a curated online database based at ANL.

Kay hopes that the facility would also be given the means to recruit the best scientists from around the country to work at the facility. “This is like building a baseball franchise – you don’t just take the locals,” he said.

Michaels is similarly confident about PNNL’s positioning in the competition for the WPAF. But sincel he doesn’t expect the call for these proposals to come until “sometime in the 2005 timeframe,” he did not give plans for the facility that were quite so specific as Kay’s. “We probably have the largest collection of high field mass specs here that provide the highest level of sensitivity for doing peptide protein analysis than anywhere else,” Michaels said. Michaels also noted PNNL’s supercomputing capabilities – the lab has the fastest DOE computer used for unclassified work – as well as its recent $10.2 million NCRR grant to establish a PNNL-based national proteomics research resource center (see PM 10-17-03), its ongoing project to develop global proteome databases for microorganisms, and its work on the HUPO Plasma Proteome Project, as available infrastructure that should help the lab in its bid. As for what PNNL still needs to acquire, Michaels said that many techniques such as highly accurate quantitation are still needed to be developed before the WPAF could open its doors, and that this development would require a lot of new resources. “Before we get through the quantitation stage it’s going to require some significant investments in developing the processes and techniques for turning mass spec into a highly quantitative science for proteins,” he said.

Of course, all of this is hypothetical until Congress provides the money. “It will be up to Congress and the Administration to determine how much to spend on science and on new scientific facilities and to balance them against other tional priorities,” Abraham said.



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