By Meredith Wadman

Candace Kerr was working late on 23 August when a postdoc sent her the link to a CNN story in an e-mail entitled: "Bad news for stem cell researchers." Kerr, a stem-cell scientist at Johns Hopkins University in Baltimore, Maryland, says that as her eyes flew down the screen, she thought: "This can't be real. This can't be right." Earlier that day, in Washington DC, a district-court judge had put a temporary stop (pdf) on government funding for research involving human embryonic stem cells, pending resolution of a suit that is seeking to make the hold permanent (see 'The legalese behind the funding freeze').

"I was devastated," Kerr says. "It was a huge blow to the research I have spent so much time working on."

She summoned enough presence of mind to e-mail her lab technician, asking her to freeze 20 plates of human embryonic stem cells first thing in the morning. They were part of an experiment funded by the National Institutes of Health (NIH). Then, recalls Kerr, "I went home and stared at the walls and thought: 'What am I going to do next? What is going to sustain me for my job in the future?'"

Kerr is one of hundreds of researchers whose NIH-supported work has been thrown into legal limbo and financial jeopardy by the ruling. The day after the injunction, NIH director Francis Collins affirmed that all new proposals for research on human embryonic stem cells -- more than 60 in total -- had been pulled from peer review. Funding has also been suspended for existing multi-year projects by university-based researchers, beginning with 22 projects, worth a total of US$54 million, that were set to receive their next chunk of money this month. Even grants such as Kerr's that use stem-cell lines that were eligible for funding during the George W. Bush administration are not exempt: the Department of Justice read the injunction to apply to them too, Collins said.

For Kerr, there is little but bad news in Collins's message. In the short term, it means she can unfreeze her cells -- the government's interpretation of the injunction allows researchers to spend any grant money already in hand. For Kerr, that amounts to about $100,000 left of an existing two-year award for work aiming to identify factors that regulate pluripotency in embryonic stem cells. Once that money runs out next year, however, the ruling will prevent her from applying for more. And it could get worse: On 30 August, scientists working at the NIH campus in Bethesda, Maryland, were told to immediately shut down all experiments involving human embryonic stem cells. Uncertainty around the correct legal interpretation of the injunction means that 2010 money already in the hands of 199 grantees may still be in jeopardy.

"Even if the injunction is reversed in a couple of weeks, the impact will be in months and years," because of the disruption to NIH review cycles, says Linzhao Cheng, like Kerr, a stem-cell scientist at the Institute for Cell Engineering at Johns Hopkins. Cheng estimates that 40% of his lab's funding, provided by two NIH grants, has been stopped by the injunction.

Still, he counts himself lucky, because he has generous support from the state of Maryland to fall back on -- and because just one week before the injunction he received the second year's worth of monies for an NIH grant. For Kerr, an assistant professor striving to win tenure, the situation is much less certain. Although she gets modest Maryland state funding, it is not at all clear how she will be able to keep operating if she cannot apply for NIH grants. Last June, she submitted three proposals for projects, including one that would have used neural support cells derived from embryonic stem cells to attempt to treat spinal-cord injury in rats. All three are among the projects pulled from peer review. And with the injunction preventing her from applying for further funding on her current work, Kerr's plans are in limbo. A protégé of John Gearhart, one of the first scientists to isolate the cells, Kerr has spent the past seven years building expertise in human embryonic stem cells. To try to switch specialities and begin competing with much more experienced investigators in other areas would be "a real crusher", she says.

Well established researchers are feeling just as bleak. "It's like making a sculpture and then seeing it destroyed in front of you," says Ali Brivanlou, who works with stem cells at the Rockefeller University in New York.

Cheng worries most about persuading younger scientists to join a field beset with political uncertainties. "Why take the risk to work on embryonic stem cells that may not be fundable?" he asks.

The sense of shock seemed almost universal among US scientists last week. "This ruling does greater harm to human embryonic-stem-cell researchers than any policy ever enacted," says Sean Morrison, director of the Center for Stem Cell Biology at the University of Michigan in Ann Arbor.

Collins echoed that assessment when he spoke to reporters after the injunction was issued. "This goes beyond politics," he said, pointing out that stem-cell research holds the promise of effective treatments for an array of diseases that urgently need them. "This decision potentially places all of that in jeopardy," he said.