The finding “was a happy accident,” says Lora Hooper, an immunologist at the University of Texas Southwestern Medical Center in Dallas. She and her colleagues were studying NFIL3, a protein that guides the development of certain immune cells and turns on the activity of others. The gene for this protein is mutated in some human patients with inflammatory bowel disease, and mice lacking the gene for NFIL3, the team found, had more so-called TH17 cells in their intestines.

These cells are a type of immune cell known as a T cell. They get their name from a signal they produce, called interleukin 17, which tells other T cells to increase the immune response. In normal numbers, TH17 cells, which live in the intestines, help the body fight bacterial and fungal infections. But when there are too many, the immune defense begins to cause illness rather than prevent it. Boosting NFIL3 levels in T cells growing in lab cultures resulted in fewer of them turning into TH17 cells, the researchers found, suggesting that the protein’s job is to prevent T cells from going into that area of specialization. The absence of the protein, the team concluded, leads to runaway TH17 activity.

At this point, the researchers had no reason to suspect a connection to our body’s internal timekeeping system””also known as our circadian clock””which responds to daily cycles of light and dark. But as they continued to explore the connection between NFIL3 and TH17 cells, they found that some of the proteins produced by the body’s “clock genes” attach to the NFIL3 genes. What’s more, cultured cells and mice whose clock genes were experimentally tampered with produced fewer TH17 cells. The researchers surmise that a key protein in the clock network binds to the NFIL3 gene to keep the production of TH17 cells synchronized with periods of light and darkness. And the team found that normal mice produce less NFIL3, and thus more TH17 cells, during the day than at night.

In a final experiment, the researchers gave the mice jet lag. “We didn’t fly them anywhere,” Hooper jokes. Instead, the team shifted the rodents’ light/dark cycles by 6 hours every 4 days. “It would be like flying from the U.S. to Europe, India, and Japan and spending 4 days in each country,” she explains. Mice with altered light cycles had nearly twice as many TH17 cells in their spleens and intestines, compared with mice having a normal day, the team reports online today in Science. The jet-lagged mice also mounted a stronger inflammatory response to irritation by an experimental chemical””a test used to gauge immune-system sensitivity that hints the animals may be more prone to inflammatory disease.