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{shortcode-8c0dd475ea3269f67b1a4d37d27db5cc232a1fc2}hen Harvard Medical School professor Dragana Rogulja wanted to learn how sleep deprivation affects the human body, she began by studying specimens from another species entirely: Drosophila melanogaster, the common fruit fly.
Rogulja, who studies what happens to the brain during sleep, found that sleep deprivation leads to damage in fly intestines, a phenomenon she also discovered in mice. She eventually hopes to extend her research to understand why humans and other animals need to sleep.
But Rogulja’s lab — and thousands of others worldwide — could soon find themselves without access to the database that underpins their research. Called FlyBase, the free online repository includes a complete map of the Drosophila melanogaster genome, updated continuously, and lets researchers instantly access more than 87,000 papers on Drosophila, stretching back to the 17th century. If it’s an academic cliche that science stands on the shoulders of giants, there is perhaps no clearer embodiment of the adage than FlyBase.
Throughout its more than 30-year existence, FlyBase has relied on federal grants worth millions of dollars annually, the latest of which was cut in May by the Trump administration. The grant, awarded by the National Institutes of Health and worth $2 million a year, was a casualty of the White House’s multibillion dollar freeze on Harvard’s federal funding.
Since then, the scientists who maintain the database have not been able to replace the funding — and FlyBase is paying the price. Eight Harvard employees who help maintain the database were laid off in August, after the Faculty of Arts and Sciences denied a request from the researchers for more bridge funding to maintain the program.
When FlyBase lost its grant in the spring, the FAS provided Harvard Medical School professor Norbert Perrimon, the project’s principal investigator, funding to continue running the database.
But that bridge funding will run out in October. And after Perrimon asked this summer for more funding from an FAS initiative designed to fund research by FAS affiliates whose grants were canceled, the school denied his request on Aug. 8.
The denial means that four full-time and four part-time Harvard employees have been laid off. Two have already departed, one will leave sometime in the middle of this month, and another five will leave by mid-October.
The departures jeopardize the future of the critical database, which is used worldwide to study issues ranging from cancer to the science of gene expression, and show the limits of Harvard’s capacity to continue funding research once covered by federal grants.
A federal judge struck down the freeze on Harvard’s funding last week. But it’s not clear when — or if — the money will start to flow again. And the Trump administration has already vowed to appeal the ruling.
FlyBase, Perrimon said on Sunday, has not seen any funding returned.
The layoffs at FlyBase were first reported by The Transmitter, a neuroscience news site, in August.
The database is maintained by research teams at four institutions: Harvard, Indiana University Bloomington, the University of Cambridge, and the University of New Mexico. Those groups were all supported by the canceled Harvard grant.
Flies are similar to humans in most fundamental ways, meaning discoveries made about the insects are often directly relevant for human biology, said Rogulja, who used the database for her research. As a top catalogue of fruit fly genes and genomes, FlyBase is essential for experiments using the small but scientifically rich creatures.
Scientists researching fruit flies can use FlyBase to access past research on how changes to the flies’ genetic material affect the flies themselves. The database also allows researchers to contact labs that have developed different fly lines, populations of flies that have been genetically edited to express certain characteristics.
“We didn’t go a single day without using FlyBase. We used it to look up the names of genes, expression patterns of genes, what have you, every day for the five years that I was there working on my PhD,” said Susan E. St. Pierre, a researcher at Massachusetts General Hospital who used the repository to complete research for her doctorate degree from Harvard.
The FAS did not provide an explicit justification for denying the request for additional bridge funding, Perrimon said. FAS spokesperson James M. Chisholm wrote in a statement that the Research Continuity Funding program, to which Perrimon applied for funding in July, only supports “FAS senior or tenure-track faculty” whose research was impacted by funding cuts. Perrimon is an affiliate of the FAS’s Molecular and Cellular Biology department, but his primary appointment is at HMS.
“The FAS and MCB are actively working to identify and secure additional funding to safeguard FlyBase’s operations,” Chisholm wrote. “Given the importance of FlyBase to the broader U.S. and international scientific research community, we are hopeful other institutions and other stakeholders at Harvard will support those efforts.”
In the meantime, the four teams began scrambling to find alternative sources of funding.
Only the Cambridge and Indiana teams have been successful. At Cambridge, donations have come in from European fly researchers, the university, and the Wellcome Trust, a charitable foundation that supports scientific research aimed at improving health outcomes. The funding will allow the team to continue its work for one to two years.
The Indiana team, meanwhile, received funding for a year from Thom Kaufman, an Indiana University professor, and NIH supplemental funding awarded to the Bloomington Drosophila Stock Center. The Indiana team also raised about $75,000, according to Perrimon.
The Harvard and New Mexico FlyBase researchers have not been as lucky.
The New Mexico team was forced to lay off its curator. And at Harvard, efforts to convince philanthropies and other private funders to back the project have so far borne little fruit. In late August, the FlyBase team sent an email asking scientists nationwide who are involved in fly experiments for donations, and the FlyBase website was updated to include a message in neon green soliciting financial support from fly labs in the United States and United Kingdom.
Over the summer, Perrimon also began reaching out to potential supporters after hearing that the FAS denied his request for funding. But most private foundations, he said, are not interested in funding the project.
“Who knows, maybe the miracle is going to happen,” Perrimon added. “But so far, we don’t know.”
Scientists who study flies have also asked Harvard directly to reconsider its decision to deny FlyBase additional funding. Two days after the team solicited donations from fly researchers, 19 current and former leaders of the Drosophila Board — a group of scientists dedicated to fly research — penned a letter to Harvard President Alan M. Garber ’76 and Rachelle Gaudet, the Molecular and Cellular Biology department chair, asking that Harvard provide bridge funding for the next year.
Gaudet responded a few days later, writing that the University is exploring internal and external avenues of near-term support and is also working with Perrimon on a long-term solution.
“While we are navigating a fluid situation, given FlyBase’s visibility and global impact, I am cautiously optimistic that a sustainable path forward can be found,” Gaudet wrote in the email. She did not list more specific steps that either the University or department is taking.
Since FlyBase was established in the early 1990s, its freely available online repository has become essential to research on genomics, neuroscience, and immunology.
“You can’t do fly experiments without FlyBase. You can’t find the reagents that you need. You can’t find the fly lines that you need. You can’t find the researcher who created the line that you can then write to and get some of the flies. All of that happens through FlyBase,” St. Pierre, the MGH researcher, said.
Because users can access the website without paying, FlyBase needs other income sources to run, said Mark A. Peifer, a biologist at the University of North Carolina who helped draft the letter to Garber and Gaudet.
“It’s all free, but it didn’t come down on stone tablets,” he said.
—Staff writer William C. Mao can be reached at william.mao@thecrimson.com. Follow him on X @williamcmao.
—Staff writer Veronica H. Paulus can be reached at veronica.paulus@thecrimson.com. Follow her on X @VeronicaHPaulus.
—Staff writer Anna Shao can be reached at anna.shao@thecrimson.com.
