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Under One Roof Growing Omics at UIUC

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By Meredith W. Salisbury

We got together three cell biologists, three physicists, and three chemists,” says Neil Kelleher, an expert in ultra-high field FT-ICR mass spectrometry. No, this isn’t the beginning of a joke — it’s the beginning of his new proteomics-based research program at the Institute for Genomic Biology.

Kelleher is one of eight research theme leaders — roughly the equivalent of a PI — at the still-being-built IGB, based at the University of Illinois at Urbana-Champaign. He sees moving his proteomics team from its departmental home to the multidisciplinary institute as a way to fast-track his move to cell biology. “I’m trying to evolve out of being called a mass spectrometrist. … The interdisciplinary dream [is] hard to realize with the departmental silos,” he says. “It will transform our ability to move into cell biology more quickly and to do more meaningful work at a faster rate.”

It’s just that sort of vision that IGB was designed to foster, if you ask the institute’s director, Harris Lewin. Silos were banished at the outset: UIUC faculty members were invited to submit proposals to become members of the new institute, but one requirement was that each proposal “had to involve faculty from more than one department and preferably more than one college,” Lewin says. Illini scientists responded to the concept: IGB received 20 proposals and accepted eight of them.

Each research proposal had to fall into one of the institute’s three program areas: systems biology, genome technology, and cellular and metabolic engineering. It was an early mandate, says Lewin, that technology would play a critical aspect of the institute. The university “has a history of very strong core facilities,” so not only would scientists have good tools from the start, but any cores built at the institute would have to hold up to high expectations, he adds.

Standing Alone

On a practical note, IGB will benefit tremendously from an administrative decision to treat the institute like a separate college, according to Lewin. Financially, that means IGB gets to keep all except a small fraction of indirect costs from any grants it receives. It also gives IGB a “campus-wide reach” — which is why the institute’s first 50 faculty appointments hail from 30 different departments across eight colleges and other university divisions. “Any of these institutes or centers that try to develop within a college are always going to be constrained,” Lewin says.

But this freedom also means IGB has to work harder to prove itself. Faculty appointed there can’t take R01 and other individual grants with them; all grants awarded to the IGB must involve at least two investigators from more than one department. In the time before the new building opens, researchers selected from the competition have kept themselves busy applying for IGB-eligible funding. Don Ort’s genomic ecology program was the first success, winning a three-year DOE grant providing $1 million annually. “That’s the kind of scale — at least $1 million and up” — that will be needed to sustain the institute, says Lewin. Since then, the neural and behavioral genomics theme scored with a $5 million grant from NSF, and Lewin says other grants “in the $6 million to $10 million range” are pending.

As the money has flowed, so too have new faces at the university. When the institute was formed, “the provost gave me the power to hire about 30 new faculty,” Lewin says, of which about a third have been hired so far. A cluster of bioinformatics experts have been signed on, and Lewin’s team is currently bringing in stem cell biologists. The two other groups he hopes to bring on board are scientists involved in evolutionary and developmental biology as well as in genome technology.

Those new faculty don’t get to leapfrog directly into the institute, though. Most will be placed in traditional departments, often filling the holes left by faculty who have already moved to the IGB. In time, Lewin expects the junior faculty to cycle their way in. “They will be the future of the institute,” he says — noting that these hires also serve an important role in keeping good relations with university departments, which otherwise might have objected to the brain drain caused by IGB.

It also prevents the envy that comes along with any shiny new building. IGB will be housed in new $75 million facility set to open in the middle of this year. Some institute researchers are currently working in interim space, but most will stay in their home lab until the new building opens. IGB will be characterized by spacious, wide-open labs — “there are no walls inside the lab,” Lewin says, to help facilitate sharing and collaboration — and each research area will get 10,000 square feet.

Research at the Ready

On the science front, IGB’s first forays will come from the eight proposals selected from the first research competition. Those areas, known at IGB as research themes, include proteomics; genomic ecology; neural and behavioral genomics; host-microbe systems; biocomplexity; novel antibiotics from microbial genomes; molecular bioengineering; and regenerative biology and tissue engineering.

That mix — about a third each of biomedical, agricultural, and environmental — “gives us a very different profile than most of the major genome centers in the country,” Lewin says. Those research themes are also expected to evolve over time. There is no tenure at the IGB, and projects will be evaluated at five-year intervals, Lewin says, so there will be opportunity to strip out programs and add in new ones.

One of the earliest research themes selected was Don Ort’s “genomic ecology for global change” project. “We’re really interested in the concept that we can explore questions at the level of the genome and the proteome to answer questions that reach all the way to the level of ecosystems,” Ort says. His team is comprised of bioinformaticists, biochemists, systems biologists, system ecologists, and genome scientists. Their first project will involve a model ecosystem using corn and soybean, both of which have well-defined genomes, making it easier to study genomic variation.

Lewin says the members of each research theme had to define the technology they’d need in their research. In Ort’s case, that means lots of microarrays to study gene expression changes over time — Affymetrix makes a soybean chip, and Illini researchers have also made a cDNA slide that will come in handy — as well as GC, LC, and GC-TOF mass spec for the corresponding metabolomics component of his research. Research themes like Ort’s — that is, those based more on biology than on technology — will become testbeds for the themes driven more by tech development, says Lewin. One case is Kelleher’s precision proteomics group, which aims to “combine the best of mass spec and fluorescence technologies to interrogate cell biology and disease at the molecular level,” Kelleher says. “The core of the theme is to develop next-generation technologies,” which will be tested out in other IGB labs. “What I bring to the table is ultra-high field mass spec and a big software development team,” he adds.

Case in point: Gene Robinson’s neural and behavioral genomics lab, which relies heavily on the honeybee model organism as well as mouse, Drosophila, and songbirds. Robinson, who is using new technologies and bioinformatics to get a better handle on neural and behavioral components — particularly across species — will “be attempting to identify core elements of plasticity,” he says. In addition to the battery of bioinformatics tools his team will use, early experiments will involve microarrays, and Robinson is looking forward to taking advantage of Kelleher’s proteomics know-how to peel another layer of information out of the honeybee.

All of this remains, of course, to be tested. That will happen as the institute gears up and the new building officially opens in several months. In the meantime, though, hopes are high and feedback, says Lewin, has been positive. “The word is spreading about what we’re doing here.”



InfoSpot

Name: Institute for Genomic Biology

Host: University of Illinois at Urbana-Champaign

Director: Harris Lewin

Began: Funding approved in 2003; doors to new facility set to open in late summer 2006

Staff: 430 at capacity; currently has 50 faculty members, 50 affiliate faculty, plus students and postdocs

Funding stats: The institute already commands $15 million and has $36 million pending, says Director Harris Lewin. Leading agencies so far are NSF, DOE, USDA, and NIH.

Key research areas: proteomics; genomic ecology; neural/behavioral genomics; host-microbe systems; biocomplexity; antibiotics from microbial genomes; molecular bioengineering; regenerative biology and tissue engineering.

Core facilities: When completed, the institute will have a plant growth facility; microfabrication facility for MEMS devices; microscopy center; vivarium; bioinformatics group; and metabolomics facility. A proteomics facility, which currently exists outside of the institute, may be brought in-house.

 

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