Linear models of viral propagation

Posted on 17 May 2016 @ 11:17pm by Lieutenant Commander Temerant Bast & Commander Jayla Kij & Lieutenant Commander Adam Casey

1,724 words; about a 9 minute read

Mission: Outbreak
Location: Medical Lab Two
Timeline: MD8 || 1130 Hours

Bast looked over at the cot on which Jayla was sleeping. After having been on her feet for over forty hours, and finally injecting herself with the Risan virus, they had moved the cot she usually kept in her office into Medical Lab Two, where Bast and Casey had set up shop. Their main task was to take over the investigation into the properties of this virus, while keeping an eye on her.

The orderlies had also brought cots for Casey's young daughters, as the ship's new Chief Science Officer was reluctant to leave them in the main Sickbay treatment ward. As Adam placed a cold flannel on Amy's forehead, he held her hand gently. "It'll be okay princess." He whispered. Maria, though tired, was doing a lot better thankfully. "So what do we have so far?" Adam asked Bast.

The Trill Chief of Operations powered up the main monitor in the room, and displayed whatever data they had on the virus. "We've managed to isolate the virus in blood samples from every species on board, except Trill. For some reason, we seem to be immune to it. We have, however, detected antibodies for the virus in Trill samples from Doctor Kij, who has had the most exposure to it. She has just injected herself with a vial filled with dead viruses, to stimulate her antibody production, so that we can isolate the T-cells producing the thing,and use it to cure the rest of the crew."

Adam could hardly believe his ears. "She injected herself with a deadly virus? And you let her? Are you both insane? There are so many things that could... Are you... I can't even begin to say how stupid that was!" Adam exclaimed.

Bast spun on his heels, and shot Jayla's sleeping form a dirty look. "See? I'm not the only one who thinks this was a stupid idea!"

He turned slowly back toward Casey. "Sorry," he said. "We argued about this for some time, but in the end she didn't leave me any choice." He shrugged. "Kij... It's a design flaw. I knew one of her previous hosts, and she was just as bad."

"How am I supposed to get sleep if you two keep jabbering on like a couple of women?" said Jayla, not moving on her cot.

"Shut up, you're the one who put us in this position," replied Bast. He turned back to Casey. "It's been two hours since she injected herself, and I'm not really seeing any increase in her antibody titers."

Jayla was about to angrily retort that she was trying to save lives when his next statement registered. "What do you mean, no increase?" she said irritably, pulling herself off the cot and crossing to look at the monitor in front of which he was sitting. "There must be something!"

"Jayla, are you completely insane? You told me this bloody thing is fatal. My daughter could die, and you inject yourself? If we can't find a cure, then what?" Adam demanded angrily. "Did you think of the consequences? Yeah, I get it, you wanted to save lives, but by threatening yours?"

"It was dead virus!" Jayla retorted irritably. "There is little risk involved. I don't understand what you two are so upset about."

Bast shot her a dirty look. Part of him wanted to point out that there were a lot of unknowns about this virus - they knew nothing about its origins, its mode of replication, even its genetic sequence remained something of a mystery. They knew the Dominion to be a master at genetic engineering; it wasn't beyind the realm of possibility that this could be a Dominion virus, with all the possibilities that presented. A prion-viral hybrid, for example, could still have deadly consequences even with a dead virus.

But it was pointless to rehash this conversation now, the deed was done. "Moving on," he said. "It's been two hours since you injected yourself, and there's been no increase in your antibody titers. Why?"

Without answering, Jayla took a blood sample and quickly ran it through the computer. NEGATIVE flashed across the screen. "What?" hissed Jayla. "What do you mean, negative? It should at least detect the dead virus. Why is it negative?"

"Maybe because it's dead?" Adam asked, still annoyed with Jayla. "A dead virus and a live virus don't tend to have the same chemical makeup. Kind of the point, of course."

Bast took the empty vial from the hypospray, and placed it under the scanner. He activated the electron microscope, and tried to isolate a remaining virus specimen. "Does this look right to you?" he said, bringing up the image on the main monitor.

Jayla cursed. "It looks like it's folded in on itself," she said, pulling up an image of the live virus and putting them side-by-side on the monitor. "See here? It looks like it's just crumpled in."

"So basically you injected yourself for nothing. And if you even think of trying to inject yourself with a live sample, I'll kill you." He warned.

"Don't be crazy," muttered Jayla, though the thought had crossed her mind. "Besides, I've just had a better idea. What if we unfold it?"

Bast frowned. He was familar with the concept of protein folding, but beyond that, he was far out of his comfort zone. His previous host, Wilem, had been a scientist, but physics and biology were vastly different. "What do you mean?" he asked.

"It's actually a simple process," she said. "A bit tedious, and very exact, but simple enough. It looks like, if we just fold this part up," she said, pointing to a bit at the top, "and this piece out," a small section on the left this time, "it should be in the correct shape and fool our systems into believing the virus is on our bodies again. It'll take some time, but we should be able to do it in time to save most of the crew. Computer," she said, gazing at the monitor. "Do we have the equipment for protein folding on board?"

=/\=Affirmative. The equipment and materials necessary are in the lab.=/\=

Jayla looked around. "Well, then," she said. "I know the theory, but I've never actually done it. Casey, have you?"

Adam frowned as he thought carefully for a moment. "There are a number of ways to do it, but I think the best would be Circular dichroism. We can use it to measure the equilibrium unfolding of the proteins, and we can use Dual polarisation interferometry to measure the folding." He said. "After all, when used to characterise protein folding, it measures the conformation by determining the overall size of a monolayer of the protein and its density in real time at sub-Angstrom resolution." Adam explained.

Jayla blinked. She hadn't really studied the subject in depth, so she just took his word for it. "All right," she said. "Just tell us what to do."

================
MD9 - 0347
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Several hours later, they had enough viruses unfolded to inject into a subject. Jayla automatically picked up the hypospray and prepared to inject herself, but was interrupted by both men.

Adam saw Jayla's action, and grabbed her arm, before wrestling the hypospray out of her hand. "ARE YOU EFFING STUPID!" He demanded loudly. "DO YOU WANT TO DIE? IS THAT IT? DO YOU HAVE SOME KIND OF BLOODY DEATH WISH?"

Bast took the hypo from Casey's hand, and scanned the content. "There are enough viruses in here to inoculate every Trill on board. And you were going to inject yourself with this." He looked her in the eye. "Doctor Kij, I'm afraid you're no longer thinking clearly. Get a hold of yourself, or you will be relieved of duty." Rank be damned, he wasn't even sure of the procedure to relieve the ship's Chief Medical Officer of duty when both the Captain and the Chief physician herself were incapacitated. But he hoped the threat would be enough to rattle her back to her senses.

Jayla blinked at them and shook her head. Bast was right; she wasn't thinking clearly. "I think I need more sleep," she said. "Still, I could be growing antibodies while I sleep. Dial back the dosage and inject me?"

Adam went to the bio replicator he had in the lab, and used it to synthesise a vial. He placed it into a hypospray and injected it into her. "I just injected you with Ambizine. You need to sleep." He told her. "No one is injecting you with anything else. You try something that stupid again, I'll have you relieved of duty." He said.

Jayla sighed resignedly. "All right, all right," she said, heading to her cot. "But, someone has to grow the antibodies."

"You leave that to Bast and me. Get some sleep." Adam told her, walking with her to her cot. "I'll let you know if we find anything."

Bast watched as Kij settled into the cot, to get some much-needed sleep for a couple of hours, and turned his attention back to the vial. The last few hours had been particularly challenging, since he was by no means an expert on biological sciences, beyond basic immunology principles he'd learned at the Trill Science Academy - and none of his previous hosts had been, either. He'd basically just had a crash course on the basics of virology. But from what he had understood, the dead virus changed its shape, which led to the epitope, the molecule to which an antibody would attach itself, being geometrically inaccessible to the antibody. So the thing was ignored by the immune system. By applying protein folding principles, they had restored the dead virus to its original shape, thereby rendering the site accessible again.

Then again, he was a bit worried that by restoring its shape, the virus could become active again, so what he was now holding in his hand was potentially as deadly as a vial of live viruses.

He glanced Kij, lying on her cot and trying to get some sleep, and over to the other side of the room, where Casey's two young daughters also rested, one of whom had tested positive for the virus.

And without hesitation, he injected himself with the vial.

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