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Throughout the year, Shedd scientists analyze genetic material to identify the microbes that, along with the animals, call the aquarium home. They rely on a piece of equipment called a robotic extraction and purification device. Now this high-tech instrument is on loan to the Illinois Department of Public Health, streamlining the test for the novel coronavirus.

A plastic dish is held over a dolphin's blowhole as it exhales.

Frank Oliaro manages Shedd’s on-site molecular and microbial ecology laboratory. It’s here that he and his team analyze water samples, skin swabs, filtered air samples and blowhole exhalations from the whales and dolphins to genetically identify the fluctuating populations of bacteria, viruses and other microscopic denizens of the aquarium environment—most of them beneficial and even essential to maintaining the good health of the animals at Shedd. The lab, which is part of the A. Watson Armour III Center for Aquatic Animal Health and Welfare, is the only such research facility among U.S. aquariums.

One of the most powerful tools in the lab is the KingFisher Flex, a robotic device that extracts and purifies DNA and RNA from biological samples. “Manually, I could probably do 20 genetic samples in about four hours,” Frank said, “but with the KingFisher, I can process 96 samples in the same time.”

The state-of-the-art instrument, one of only a handful in Illinois, gets heavy use for weeks at a time. “Recently we did a bunch of samples to study the influence of probiotics on the belugas and water samples in the Abbott Oceanarium during a water change,” Frank said. “We finished extracting all those—1,000 samples over a month or so—just before the aquarium closed to help stop the spread of the coronavirus.

“We were thrilled to make the KingFisher available to do more important things for the time being.”

A search leads to Shedd

At the end of March, Frank got a call from a sales representative at Thermo Fisher, the manufacturer of the KingFisher. “We have a few instruments from the company, and we have good relationships with the reps,” Frank said.

Dr. Bill Van Bonn, vice president for animal health and welfare, picked up the story. “The KingFisher is one of the instruments included in an FDA-approved protocol for screening for the coronavirus.” But at the same time that the KingFishers are in high demand, they are also in short supply. Dr. Bill continued, “The Illinois Department of Public Health approached Thermo Fisher to find out where these instruments were in the state. Thermo Fisher said there weren’t very many, but there’s one at Shedd Aquarium.

“The state then asked Thermo Fisher to contact us to see if we’d let them borrow it. Thermo Fisher called Frank, Frank called me, and the unanimous answer from Shedd Aquarium was, ‘Of course.’ ”

A loan agreement was drafted quickly, and Thermo Fisher technicians picked up the instrument, along with necessary testing supplies, and delivered it to a local Department of Public Health facility. “As far as I know,” Frank said, “it’s been running ever since.”

The machine is being used to extract RNA from nasal swab samples. “You can take that pure extract and, with other instruments, run a specific test to screen for the coronavirus,” Frank said. “The KingFisher does the first step of the protocol. The advantage is it allows you to process the samples much faster than by doing it all by hand.”

A round, plastic-covered Kingfisher machine.

The KingFisher Flex is a robotic device that extracts and purifies DNA and RNA from biological samples.

How it works

Dr. Bill described the 75-pound benchtop instrument as “sort of round, like a mega food processor.” But Frank said the rotating tray reminds him of the open drawer of a CD changer as he loads it with five sterile plastic blocks, called plates. (The instrument can hold up to eight plates.) Each plate has 96 tubular divisions that are filled with a specific solution, called a reagent, that causes a chemical reaction in the multistep process of extracting and purifying the genetic material.

The first, called the bind plate, holds a solution with the genetic samples as well as tiny magnetic beads and a reagent that makes the genetic material stick to the beads. The most time-consuming part of the procedure is manually preparing the samples for the bind plate—literally shaking the samples to break open the cells and expose the genetic material—and using a multichannel pipette to hand-fill each 96-well plate with a reagent.

“Once you have loaded and preprocessed the sample,” Frank said, “you hit ‘start,’ and the KingFisher does the rest.” The instrument can process samples of DNA, RNA, or both. Many viruses, including the coronavirus, can be identified by their RNA.

A robotic arm over the tray holds 96 magnetic rods that are lowered into the bind plate to attract the magnetic beads holding the genetic material. “You can see the beads stuck on the magnets when they come out,” Frank said. Then the arm dips the rods into three successive wash plates, which are moved into position by the tray. In each wash plate, the rods move up and down, agitating the solution, not unlike a washing machine. “That cleans off contaminants and cellular materials, like proteins, that you want to get rid of to just keep the RNA,” the lab manager continued.

In the final step, the rods move the beads into a plate containing a reagent that causes the RNA to release from the beads. “The magnetic rods pull the beads out of the plate, leaving pure RNA behind,” Frank said. “It only takes about an hour to finish.”

Lab manager Frank Olario, wearing safety googles, rubber gloves and a lab coat, lifts a petri dish out of a large centrifuge in Shedd's microbiome lab.

Manager Frank Oliaro at work in the molecular and microbial ecology laboratory.

Unexpected uses

The molecular and microbial ecology lab, formerly known as the microbiome lab, was made possible by a grant from The Grainger Foundation. Frank has been lab manager since its opening in 2016. The $55,000 KingFisher was not part of the original budget, but careful stewardship enabled the team to plan for the future. Frank said, “We thought it would be a great thing to have as we ramp up and do larger studies. It’s not a common piece of equipment we see in many labs.”

“The KingFisher is demonstrating its value all the time,” said Dr. Bill. “We’re using it for so much more than the original Aquarium Microbiome Project envisioned it would be used for, including the Blanding’s turtle head-start program and the western pond turtle shell disease investigation.”

Frank is also collaborating with researchers in Shedd’s Daniel P. Haerther Center for Conservation and Research. “We’re working on a study on the diet of endangered Bahamian iguanas on the islands where they are heavily visited and fed by tourists,” he said. “We’re extracting DNA from the lizards’ scat samples to identify the plant species they eat.”

“Some of these projects are things we never thought about initially,” said Dr. Bill, “but they are really logical uses of the instrument, and it has proven its value. But who knew it would get used for a public health emergency?

“It’s one of the surprising things about what happens at Shedd Aquarium. We’re contributing in so many ways beyond guests being able to come and enjoy seeing the animals.”

The Shedd Aquarium Microbiome Project is made possible by generous gifts from aquarium supporters including the Institute of Museum and Library Services, National Science Foundation, Arthur and Elaine V. Johnson Foundation and Helen Brach Foundation.

Karen Furnweger, web editor