Dosing Automations

When pairing the Pioreactor with dosing pumps, there are new capabilities and experiments you can run. The Pioreactor is preprogrammed with the following dosing automations. In the below automations, values highlighted like so are configurable.

Sleep

Requires: None

The sleep automation is the simplest automation: doing nothing. The automation will still "wake up" every duration minutes, but does nothing.

Chemostat

Requires:

  • 2 peristaltic pumps:
    •  one media pump
    •  one waste pump
  • 2 liquid containers with luer attachments
    •  one labelled "waste"
    •  one labelled "media"

The chemostat automation is the second simplest dosing automation. Every duration minutes, the media and waste pumps run and exchange volume (mL) of liquid inside the Pioreactor. Initially, the culture is growing and consuming nutrients and energy. Eventually, a nutrient will become scarce and will stall growing. Upon a pump refresh, this growth-limiting nutrient becomes abundant once again, and the culture can grow, up until consuming all of it again and stalling growth. Thus, the bioreactor enters into a nutrient near-equilibrium (hence the term "chemostat", for "chemical-static"). However, more long-term, because the culture is under an evolutionary pressure to grow, adaptions will occur that will improve the acquisition or utilization of the growth-limiting nutrient.

PID Turbidostat

Requires:

  • 2 peristaltic pumps:
    •  one media pump
    •  one waste pump
  • 2 liquid containers with luer attachments
    •  one labelled "waste"
    •  one labelled "media"

First, what is a turbidostat? A turbidostat ("turbidity-static") tries to keep the turbidity (also called optical density, or OD), constant over time. This is usually accomplished by taking frequent measurements of the turbidity, and performing a set media/waste pump cycle when the optical density exceeds some target OD. The Pioreactor improves upon this simple procedure by introducing a dynamic controller that will control how much volume to exchange upon each cycle. This means that there needs to be no manual tuning after starting the automation. (Traditional turbidostats need to be tuned to adapt to the growth of the culture: either the volume exchanged or the frequency of exchanges). A max volume parameter needs to be set, and the PID Turbidostat automation will choose some value between 0 and max volume, and run a cycle every duration minutes.

PID Morbidostat

Requires:

  • 3 peristaltic pumps:
    • one media pump
    • one waste pump
    • one alt-media pump
  • 3 liquid containers with luer attachments
    • one labelled "waste"
    • one labelled "media"
    • one labelled "alt media"

By introducing another pump (labelled "alt media"), another dimension of experiments opens up. We can exploit the short-time scale of adaption in microbes to evolve the culture from thriving in the original media to thriving in the alternative media, or some point inbetween the two. Think of it as slowly shifting the environment between the two media stocks so that the microbes are under constant evolutionary pressure. This is where the name morbidostat is from: "morbid-static". There are many use cases of this, outlined in our documentation on directed evolution.

In the Pioreactor software, the transition between environments is controlled by observing the growth rate, and artificially keeping it suppressed (set to be target growth rate) by dynamically adjusting the ratio between the original media and the alternative media when a pump cycle is run. A pump cycle is run every duration minutes. Another parameter is the target OD, which should be low to keep the culture in a state of nutrient abundance (so that the primary evolutionary pressure is the alternative media adaptation).

Continuous Cycle

Requires:

  • 1 peristaltic pump
  • The Pioreactor inline sensor insert
  • Another vessel, like a bioreactor or fermenter

This algorithm is different than the others as there is no reservoirs of fresh media, or a waste container. Instead, a pump cycles liquid between the larger vessel (ex: a larger bioreactor, or fermenter) and the Pioreactor. In this configuration, the Pioreactor is more like an inline sensor than a bioreactor.

 

How to change the dosing automation?

In order to change the dosing automation, the dosing events must first be started. You can see this on the Pioreactor's Manage modal:

Start the job if not already started

Next, in the Settings tab, under the heading Dosing automation, click on Change dosing automation:

From this model, you can start a new dosing algorithm with given settings.

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