For over a century, humble fruit fries have paved the way for many important scientific breakthroughs.
This small insect helped researchers understand that x-rays can cause genetic mutations. The gene is passed from parents to children via chromosomes. A gene called period helps our body maintain time, and the destruction of its internal clock leads to jet lag, increasing the risk of neurological and metabolic diseases.
These findings, along with nearly 90,000 other studies, are part of an important online database called FlyBase, which researchers use on a daily basis to design new experiments more quickly. These tests could help explore the underlying causes of the disease and develop new treatments. Science is based on previous insights, and a handy repository of past advances serves as a kindling for future discoveries.
The website receives approximately 770,000 pages of viewing monthly from scientists working around the world to develop personalized therapies for rare cancers, model neurodegenerative diseases in humans, and screen drug candidates for conditions such as Alzheimer’s disease.
Now, its important resources are on the brink of layoffs that risk its future and its ability to make research more efficient.
This spring, the Trump administration revoked a grant used to maintain its flybase as part of a wide $2.2 billion funding cut at Harvard University.
“I use a flybase every day, and that’s very essential,” said Celeste Berg, professor of genomic sciences at the University of Washington. “What we know about human genes and how they work comes from model systems like Drosophila.”
Humans share about 60% of our genes with fruit fly, and are also known by the scientific name Drosophila Melanogaster.
Flybase’s current and solid future highlights how interconnected and interdependent research efforts will be, and how the impact of funding for one institution can ripple around the world. Over 4,000 labs use flybases.
Harvard received approximately $2 million a year in federal funds to maintain the flybase, a majority of the website’s total operating budget. However, the University of New Mexico, Indiana University and the University of Cambridge in the UK are partners and beneficiaries in helping Harvard manage fly-based.
“This doesn’t just affect Harvard,” said Brian Calvi, a biology professor at Indiana University who is part of the flybase management team. “The ripple effects are for the international biomedical research community.”
According to Norbert Perimon, a professor of developmental biology at Harvard, Harvard’s Faculty of Arts and Sciences rescued the flybase with interim funds, but its support will halt in October.
Earlier this month, a judge ordered the Trump administration to restore funding for Harvard researchers who lost the grant, but the money has not started flowing to flybase, Perimon said. The administration has pledged to appeal decisions that could halt funding flows.
The White House did not respond to requests for comment. The U.S. Department of Health and Human Services, which oversees the National Institutes of Health, declined to comment.
Transmitter, the Neuroscience News site, first reported on layoffs on Flybase. Harvard Crimson reported on the decision not to continue the interim funding of Harvard’s Faculty of Arts and Sciences.
Calbi said the Flybase grant provided full or partial salaries to eight people at Harvard, three in Indiana, five in Cambridge and one at the University of New Mexico. Both Indiana and Cambridge have been able to secure funds to run some of the programs until next year. The New Mexico position ended in August.
Operating since 1992, Flybase has been supported by the federal government for over 30 years. It curates and summarizes research papers, organizes findings on specific genes, and catalogs information on genetically modified fruit flys to tear how specific genes lead to normal development.
Fruit fly is the most important animal model for biomedical research, as scientists were able to map the brain to the genome. It is also relatively easy to handle.
A professor at Genome Sciences and an avid fly-based user, Berg studies human development and how cells form organs. FlyBase allows you to search and identify genes of interest for your experiment. Next, we test how altering the expression of these genes affects cell placement.
Thousands of fruit fly paper are added and summed up to the fly base each year. Without Flybase, Berg said researchers and clinicians could struggle to catch up and miss important connections about specific genes.
Researchers in undiagnosed disease networks can use Flybase to help identify whether pediatric genetic mutations contribute to rare, unknown diseases. Scientists will identify genetic mutations in these patients and compare those mutations with previous studies of those genes in flies.
FlyBase offers crowdfunding support on its website.
“Given the importance of flybase to the broader US and international scientific research community, James Chisholm, spokesman for the Faculty of Arts at Harvard University, said:
Two Harvard-based staff members have already been fired from their flybase jobs, with six others scheduled for layoffs in late September and early October, Perimon said.
“If we can’t maintain key personnel, it’ll be very difficult to get people back with the knowledge to keep the database running,” Perimon said. “That would be the point of not having a fly-based return.”
Fundraising disruptions threaten plans to move fly-based data to a new long-term home called the Genome Resource Alliance. Fruit fly, along with rats, mice and worms, is one of several common “model organisms” and is used in labs to lay the foundation for understanding human biology.
Since 2017, the National Institutes of Health has spent around $5 million a year consolidating several databases, including the Flybase, Wormbase and Mouse Genome databases, among several others. Each contains information that human health researchers can cross-reference them to more efficiently study genes important to human health.
“If you’re studying human genes and you have to study everything that’s known, you need to go to all of these (the website) and learn the systems,” says Paul Sternberg, a professor of biology at California Institute of Technology, who leads the Alliance’s efforts. “One-stop shopping is required.”
The alliance’s budget expired on June 30th, and Sternberg said it was awaiting a reclamation decision from the NIH itself. He said the disruption in funding at Flybase represents a new, unexpected obstacle to making the findings more convenient and easier.
“We need to do this quickly, but when we’re losing our staff and energy, that’s why we’re at risk,” Sternberg said. “Don’t throw any extra obstacles. That’s all.”
Flybase had planned to merge with the Alliance in 2029. Now, Calvi and others are pushing for faster mergers before Flybase’s financial runways disappear. Any donations that the organization is seeking are intended to help it pay.
“So far, it’s under $100,000,” Calvi said of the organization’s crowdfunding efforts. “We probably need a million.”
