Wednesday, November 25, 2015

Gyrases, More Gyrases, and Diesel Fuel

Today I Learned:
1) As bacteria switch from exponential phase (when they grow like mad) to stationary phase (when they're in population equilibrium and don't grow much), they severely curtail the amount of gyrases and other DNA-relaxing enzymes. Makes sense -- they're not replicating or transcribing a ton, so they're not introducing as much strain into their genomes/plasmids.

2) Speaking of gyrases and topoisomerases, there's experimental evidence that, at least on plasmids, the amount of gyrases and topoisomerases in bacterial cells is not even close to enough to actually keep plasmids relaxed. Once expression starts, the plasmid pretty quickly gets supercoiled, which may be part of what drives burstiness in bacterial transcription. Do bacterial genes on plasmids burst more than bacterial genes on chromosomes? Could you reduce burstiness by expressing a ton of gyrase?

3) ...a few things about diesel fuel. Diesel fuel is a by-product of gasoline production, and is chemically fairly similar to jet fuel. It is more efficient than gasoline, and currently burns cleaner. I'm not entirely sure why we use predominantly gasoline, but I think it's because a) diesel is fairly hard to burn, so simple sparking doesn't work on diesel, and b) because diesel used to be super dirty and produced a lot of pollutants.

Also, diesel is surprisingly similar to vegetable oil and can basically be run straght on vegetable oil (peanut oil works particularly nicely). The problem vegetable oil has is that it's very viscous compared to real diesel, which gunks up the engine. There are a few ways around this. One is to rig up a system that heats the vegetable oil a lot before introducing it into the engine. This works, but can be kind of a pain. Some people also just pour engine oil into their tanks to help lubricate stuff. That sounds risky to me. The most elegant option IMHO is to chemically take out the impurities that make it viscous. Specifically, there are enough surfactants in vegetable oil that allow water-soluble contaminants to stay in the oil, and you can remove those surfactants with some chemistry involving methanol and some other stuff I didn't catch in the conversation where I learned this. With the surfactants gone, the water-soluble contaminants just fall right out of solution, and you have clean oil for your diesel engine!

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