He's just so wonderful to her. John was so supportive of her, of her dreams," Flores said. "They would talk on the cell phone for hours, and they would just be so connected."
The discovery of the body ended a massive search by state and federal authorities that had expanded to a Connecticut waste-processing facility in Hartford, in addition to the Yale lab, in the hopes of finding clues to her mysterious disappearance.
Using cadaver-sniffing dogs in round-the-clock shifts, FBI agents and state troopers dressed in hazardous-material suits began searching the facility in Hartford Saturday night.
Police scanned blueprints of the lab and brought in blood-sniffing dogs, paying particular attention to the building's basement.
Yale had also offered a $10,000 reward for information leading to Le's whereabouts.
After the body was found, Yale president Richard Levin wrote in a letter to the university's staff and students:
"It is my tragic duty to report that the body of a female was found in the basement of the Amistad Building late this afternoon. The identity of the woman has not yet been established," Levin's letter said. "Law enforcement officials remain on the scene; this is an active investigation, and we hope it is resolved quickly."
Adding to the intrigue surrounding the case was an article Le wrote for a campus magazine earlier this year about how to stay safe on the Ivy League campus.
The article, titled "Crime and Safety in New Haven," was published in February in the magazine produced by Yale's medical school and compares higher instances of robbery in New Haven to other cities with Ivy League universities.
"In short, New Haven is a city and all cities have their perils," Le wrote. "But with a little street smarts, one can avoid becoming yet another statistic."
Le, who is 4 feet 11 and weighs 90 pounds, had left many of her belongings in the lab when she disappeared.
"She left her pocketbook, her cell phone, everything in the lab," Le's co-worker Debbie Apuzzo said.
Le's Facebook page showed her posing in wedding dresses and smiling with fiance Widawsky, a Columbia University graduate student in physics, whom she described as her best friend.
"He's an amazing kid, just a wonderful, wonderful boy, and he must be heartbroken," Widawsky's friend Linda Matychack said. "I just can't imagine."
Le's family issued a statement Tuesday through a family friend, the Rev. Dennis Smith, thanking the local and state police and FBI for their hard work and sensitivity. He also mentioned staff members and students of Yale University. "Our loss would have been immeasurably more difficult to cope with without your support." ABC News' Emily Friedman contributed to this report