Bioreactors have an advantage of being able to closely control an environment for microbes. Often, we wish for a bioreactor to precisely control a single, important variable, and we observe how the microbes respond. We can even push this variable to an extreme value - to an environment that the microbes are not familiar with, with interesting results. Let's explore the "zoo" of ⋆-stat strategies, what they are used for, how to implement them, and how microbes respond.
One of our goals with the Pioreactor is design it such that you don't need to be a biologist, or an electrical engineer, or relevant for this article: a statistician. This article describes our internal algorithm that computes the culture's growth rate, but importantly: you don't need to know this algorithm to use the Pioreactor! We've designed the internal statistical algorithm to be robust enough that you can sit back and watch. This article is for the users who really want to dig deep into how we compute growth rates and the statistics behind it.
This week, we added some updates to the user-interface, a new data-viz, and did our first tests comparing heated and non-heated effects on growth rates.
One important property we wanted Pioreactors to have was low variance between units. That is, one Pioreactor should be interchangeable with another. This property means that differences in experiment results are solely the result of biological culture conditions, and not on the Pioreactor construction or materials. In fact, we take inspiration from cloud computing providers: the customer shouldn't have to worry about which hardware they are running on, and the cloud provider can swap out hardware without the customer noticing.
Did you know that the traditional S-shaped growth curve in microbiology is terribly inaccurate? It's inaccurate for many reasons, but the reason I want to discuss today is that some microbes have multiple growth spurts - like two "S"s ontop of each other. For example, when there are two sources of sugar in the media, the microbes will first consume the more accessible sugar, and then after a pause to reconfigure their metabolism, and then start to consume the second source of sugar. This leads to two growth spurts, and hence two "S"s.
A few months ago, Escarpment Labs released their brewer-focused nutrient formula, Yeast Lightning. I was very excited: the ability to get nutrient rich formula without going through the typical route of a laboratory supplier ($$) was welcome! Previously I was using homemade hydrolyzed bakers yeast, which was a pain to make and not very shelf-stable. I was also hoping that it sufficient for my yeast cultures, but I had no idea what key nutrients may have been missing or lacking.