Synthetic biology will realize its potential as an engineering discipline when we can reproduce, exchange, compare, and build upon each other’s work. We have to be able to talk to do that. Standards make it so we can talk to each other effectively.
We’re already using standards for genetic designs, DNA assembly, and part performance. Now we are prototyping a new draft standard for experimental parameters in bench-scale (e.g., 96-well plate or shake flask) experiments, the Minimum Information Standard for Engineered Organism Experiments (MIEO).
How well a cell performs its designed function depends on experimental conditions. Even the simplest experiment has many different experimental factors in play, and it can be hard to track them all. MIEO is being created to solve that problem.
MIEO includes three categories of factors: media composition and properties; container geometry and shaking; and other factors including time, environment, inoculum, selective agents, and inducers.
We demonstrated the utility of MIEO by evaluating the effect of 22 experimental factors on the growth and productivity of Escherichia coli engineered to produce the small-molecule lycopene and the fluorescent protein RFP, and in surprising ways: the highest titer was achieved by reducing the shaking speed while increasing the well volume. Container factors are particularly tricky, because often labs have incubator setups that are expensive and difficult to change.
We usually tell each other about our experimental conditions using free-form text in a Methods section. We decide ad hoc about what’s most important, and we don’t tell you about details we assume, or assume don’t matter. A better way to talk would be with a structured conversation, where we’re sure to tell you the whole story, with all the key details. Our draft standard MIEO modular checklist is a way to be certain this conversation happens, and that both parties hear the same thing.
Standards development works best when it is a community-driven, bottom-up effort. So, we’re sharing a draft of MIEO for anyone to check out and edit and remark upon at http://jimb.stanford.edu/mieo/.
Let’s build this standard into a knowledgebase and a resource for the community!