Wednesday, June 10, 2020

Quest: Extremophile


Dr Sam Wilder had to hand it to Dr Soo Kwan-Bae. Her choice of Weissella kimchii had been inspired.

Dr Bae had chosen a bacteria that thrived in acid environments. She picked a bacteria that cheerfully multiplied at cold temperatures, temperatures that were easy to maintain as long as you could pump water out of the ground or were near a flowing spring. She had chosen an organism that tolerated strong brine. And then she had enhanced the bacteria by injecting DNA that made it resistant to a common antibiotic.

Dr Bae's chosen vehicle for the vaccine was an extremophile. It SPRINTED under conditions that caused other, competing bacteria to wither and die. Every biological process is a race. There will be winners and there will be losers. Dr Bae's choice made it relatively easy for those who followed her to design a race course where the bacteria with the Ebola DNA embedded within it would always win.

Dr Sam did not delegate the task of culturing the two strains of bacteria to any of her staff. They were at a critical time in ramping up ammonia production. Besides, this was a job that she had done twenty-thousand times before. It was not bravado to say that she was the one most qualified to bring the Ebola vaccination culture back to life.

Dr Sam decided to keep things simple. She painted blue stripes around seven, one quart mason jars and green stripes around another seven. Why seven? Because her canning kettle held seven jars.

Dr Sam threw the required ratio of sliced cabbage, garlic cloves, vinegar and sea salt into a blender and pureed the mix. She repeated until she had enough nutrient mix to put approximately 200ml into each mason jar. Then she purged the air-space with nitrogen and screwed the lids onto the jars.

The jars wanted to float in the canner. She weighted them down and performed a soft-sterilization on the contents. Given that the contents were extremely inhospitable to anaerobic contaminants, she didn’t see any benefit to pressure autoclaving them.

Dr Sam moved the “blue” jars to the booth with the HEPA downdraft ventilation. The HEPA filter removed all particulates down to, and below, the size of bacteria. Dr Sam spritzed the outsides of the jars with 70% alcohol

Dr Sam fiddled around and recorded her notes while the jars cooled. When the first batch was down to 90F, she went to the next step.

Dr Sam pulled a full 1.0ml out of the “blue” sample test tube and diluted it with 7 parts sterile water. Then, after giving the “seed solution” in the small syringe time to diffuse, she cracked open each jar, in turn, and injected precisely 1.0ml.

Closing the lid she swirled the solution to evenly mix the seed solution with the nutrients. She handled the jars, one-at-a-time, from start to finish to ensure the time the lids were open and the nutrients exposed to "the wild" for a very minimal time...even though the HEPA booth was (theoretically) sterile.

She had precisely 1.0ml of seed solution left after inoculating the last culture bottle. She re-diluted it and then used a single drop to seed the top of a Petri dish.

Then she repeated the process with the “green” culture.

Dr Sam would view the Petri dish beneath UV light to determine if she needed to blast the culture with antibiotic to “weed out” the wild strains of Weissella kimchii. In a perfect world, Dr Sam would have done the Petrie dish first and lifted the colonies of bacteria that glowed blue(or green) with a fine hypodermic needle or a tiny loop of wire made from a guitar string.

But Dr Sam no longer lived in a perfect world. She lived in a world where the four horsemen were on the march...and she needed a bullet to stop the one named Pestilence.

Dr Sam had hunted high-and-low for a place where the temperature was a steady 55F. In the end, she could do no better than to bury an old beer cooler in the damp ground near the steam engine. The thudding engine shook the ground and stirred the contents of the jars.

Like Sally, Sam decided the safest place to store the vials of culture were on her person.

Even though events were accelerating toward some, unknown conclusion, Dr Sam could only wait, and watch. The cultures would either take off, or die. The resulting broth would either be filled with the appropriate “blue” and “green” strains, or they would be swamped by “wild” bacteria.

Dr Sam was not in the habit of praying. But that was in the process of changing.

She had seen what Ebola did to humans. It had much in common with a snake bite. You see, snake venom is actually their saliva. It is an adaptation that starts to digest the victim before it has been swallowed. That is what Ebola did. It digested the victim, chopping apart the proteins that comprised the cell walls as efficiently as if it were in the stomach of an apex carnivore.

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1 comment:

  1. Interesting set of options, and she is doing the best she can.

    ReplyDelete