While working at Friday Harbor Laboratories, a field station run by the University of Washington, Osamu Shimomura discovered a jellyfish protein that allows scientists to trace the movement of cells and proteins.

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The bomber planes, he thought, had a certain beauty, flashing silver against the blue sky before dropping their explosive cargo on industrial plants near Nagasaki, Japan.

He watched them from a hill next to his own factory, where he was assigned to work on fighter-plane engines about 9 miles from town, and was following them one Thursday morning in August 1945 when they took an unusual route toward the center of the city.

“We were blinded for about 30 seconds,” Osamu Shimomura later remembered, recalling the U.S. atomic bomb blast that destroyed nearly half of Nagasaki. “Then, about 40 seconds after the flash, a loud sound and sudden change of air pressure followed. We were sure there was a huge explosion somewhere, but we didn’t know where.”

Dr. Shimomura, who was then 16, emerged from the attack shaken but physically unscathed – a blessing he later attributed to his grandmother, who had insisted he take a bath after walking home from the factory soaked with grimy, highly radioactive “black rain.” He went on to build an unlikely new life as a chemist, performing experiments that transformed scientists’ understanding of bioluminescence, in which living organisms produce and emit light, sometimes while surrounded by total darkness.

Recalling his first major achievement as a chemist in the mid-1950s, the crystallization of a substance that enables a small Japanese crustacean to glow, he once wrote: “Since the end of the war, my life had been dark, but this gave me hope for my future.”

Less than a decade later, Shimomura had uncovered an unusual protein within a beautiful, brightly glowing jellyfish – a discovery that earned him a one-third share of the Nobel Prize in chemistry and formed the basis of a powerful new scientific tool, enabling biologists to follow the intricate movements of cells and individual proteins.

He was 90 when he died Oct. 19 in Nagasaki, according to the Marine Biological Laboratory in Woods Hole, Massachusetts, which announced the death but did not give a cause. Shimomura had served as a senior scientist at the institute from 1982 until his retirement in 2001, and was also a professor emeritus at the Boston University School of Medicine.

Traveling during the summer to conduct field work, Shimomura studied bioluminescent fireworms in Bermuda, cave worms and limpets in New Zealand, and a plethora of glowing bacteria, twinkling fireflies and neon-colored squid and krill. His central discovery was centered on a North American jellyfish, Aequorea victoria, sometimes called the crystal jelly.

He was working at Princeton University when a colleague, the biologist Frank Johnson, brought the animals to his attention and suggested that Shimomura travel to Friday Harbor, Washington, where the jellyfish seemed to congregate in Puget Sound. The two men went there together in the summer of 1961, traveling across the country with a pair of research assistants – including Shimomura’s wife, Akemi – in a seven-day trip by station wagon.

In an autobiographical essay for the Nobel Prize, Shimomura wrote that they set up shop at Friday Harbor Laboratories, a field station run by the University of Washington, where “a constant stream of floating jellyfish passed along the side of the lab dock every morning and evening, riding with the tidal current.”

With a simple dip net, he and the Princeton team scooped up jellyfish one by one, using a pair of scissors – and later a “jellyfish cutting machine” – to eliminate unnecessary body parts. Skeptical residents asked Shimomura how he was planning to eat the jellyfish, doubtful that they were actually being used for research. But by the end of the summer, he and his team had taken samples from 10,000 of the creatures, enabling him to isolate a pair of luminescent proteins early the following year.

The first and most promising protein, aequorin, was later used as an indicator for calcium. The second – green fluorescent protein, or GFP, which appears fluorescent green under ultraviolet light – remained little known for more than two decades, until Martin Chalfie, a biological sciences professor at Columbia University, decided to use it in his work with a transparent roundworm.

“It didn’t take much to realize that if I put that fluorescent protein inside this transparent animal, I would be able to see the cells that were making it,” Chalfie told the New York Times in 2008. “And that’s what we set out to do.”

After the gene that makes the protein was discovered by Douglas Prasher, of the Woods Hole Oceanographic Institution, Chalfie inserted the gene into E. coli bacteria and then, in 1994, into several roundworm cells – forming a molecular “lantern,” as he called it, that caused those cells to shine green under ultraviolet light.

Another scientist, Roger Tsien, who died in 2016, expanded the palette, finding that mutating the GFP gene could create different colors and brighten the glow.

Shimomura’s jellyfish gene is now used to “tag” different proteins within cells, and different cells within organisms, as researchers track processes ranging from the development of nerve cells in the brain to the spread of cancer across the body. For their work with GFP, Shimomura, Chalfie and Tsien all shared the 2008 Nobel Prize in chemistry.

In a phone interview, Nipam Patel, director of the Marine Biological Laboratory, said the laureates’ work ushered in a revolution in microscopy and biological imaging.

“With GFP, you can see exactly what’s going on inside a living organism. You can see what the neurons are doing, the way neurons are connected together. You can monitor what single proteins are doing inside a cell, or watch individual bacteria inside a colony. That changed the way we do experiments, where we used to depend on dead things and try to guess what was going on when it was alive. Now you can watch the processes as they happen.”

The son of an army captain, Osamu Shimomura was born in Fukuchiyama, in Kyoto Prefecture, on Aug. 27, 1928. He spent part of his childhood in the Chinese region of Manchuria, where his father served in the Japanese occupying forces, and in Sasebo, near Nagasaki, where his grandmother raised him and a younger brother while his parents lived at an army outpost near the Soviet border.

By 1944, as the tide of World War II turned against Japan, Shimomura’s father urged the family to move to the countryside to avoid American bombing raids. Instead, Shimomura’s mother took them to her parents’ home in Isahaya, near Nagasaki, where he and his 10th-grade classmates were assigned to work at a naval aircraft arsenal that was subsequently destroyed by U.S. bombers, killing some of Shimomura’s friends.

An unexceptional student in high school, when he found little time to study amid the war effort, Shimomura tried to enter three separate colleges but was rejected each time. He was eventually admitted to the Nagasaki College of Pharmacy, despite having little interest in becoming a pharmacist. After graduating in 1951, he studied organic chemistry under Yoshimasa Hirata at Nagoya University and performed his successful experiments with the Japanese crustacean, crystallizing a light-emitting compound known as luciferin.

He received a doctorate in organic chemistry in 1960 and joined Princeton later that year, remaining at the school before joining the Marine Biological Laboratory in 1982. He was awarded the Order of Culture from Akihito, the emperor of Japan, in 2008.

Survivors include his wife and longtime research assistant, the former Akemi Okubo; a son, Tsutomu Shimomura, a computer security expert credited with helping the FBI capture hacker Kevin Mitnick in 1995; a daughter, Sachi Shimomura, an English professor at Virginia Commonwealth University; and two grandchildren.

In his essay for the Nobel Prize, Shimomura recalled that his career in organic chemistry was almost entirely the result of chance. While in college, he said, he had attracted the attention of a professor who offered to introduce him to a molecular biologist at Nagoya University. But the biologist wasn’t on campus when they arrived in Nagoya, and instead they met Hirata.

The chemist chatted with Shimomura for a few minutes, then told him, “Come to my lab. You may start at any time.”

“This was surprising, because we had just met,” Shimomura wrote. “I didn’t know much about molecular biology or organic chemistry, so it didn’t matter to me which specialty I would study. I thought Professor Hirata’s words might be the direction given by heaven, and I decided to go to his lab. It seems that this decision determined my future, directing me to the studies of bioluminescence, aequorin and green fluorescent protein.”