Fig 1.
(a) The platform comprises a control computer (left), main reactor (centre), and peristaltic pump board (right). It is open source and can be constructed for approximately $300 using only PCBs and off-the-shelf components. Scale bar indicates 1 cm, giving the main reactor dimensions of 11.5 × 5.3 × 5.3 cm. (b) Schematic of subsystems and interconnections. A lab computer or network connects to the control computer, which runs the platform's operating system and can interface with up to eight reactor/pump pairs in parallel. Each reactor has a 12- to 25-mL working volume and contains a range of measurement and actuation tools for precise in situ manipulation of biological systems. These include a UV LED, a 650-nm laser (for OD measurement), seven-colour LEDs in the visible range (for optogenetics and fluorescence measurement), and a spectrometer. An infrared thermometer and heat plate are used to regulate temperature, and the culture is agitated using magnetic stirring. Each reactor has a modular pump board with four direction- and speed-controllable peristaltic pumps. For a detailed descriptions of each hardware subsystem, see S1A–S1D Data. LED, light-emitting diode; OD, optical density; PC, personal computer; PCB, printed circuit board.
Fig 2.
Hardware subsystems, software, and automation.
(a) The main reactor with sides removed and subsystems labelled. The vertical PCB on the left hosts driving circuitry for many subsystems, as well as power regulation and filtering. (b) Emission spectra of the visible optical outputs in the device (UV LED peak is at 280 nm). (c) Images of optical outputs, with laser set to 50% and LEDs to 5% intensity. LEDs are focused and perpendicular to the spectrometer to maximise faint fluorescence signals. (d) Measurement filter bands of the platform's spectrometer. (e) Magnetic stirring provides a powerful vortex when set to a high rate. (f) Software architecture, which packages multiplexed low-level commands (digital communications following I2C standard) into an easy-to-use web interface accessed from a connected PC or network. (g) A typical 60-second experimental automation cycle. Initially stirring is disabled so liquid can settle, reducing noise in measurements and providing a flat surface for removal of waste media. (h) Media temperature (‘Temp’) controlled to follow a predefined path over 5 hours. Heat input is provided by the heat plate; cooling is passive. (i) The OD of Escherichia coli in exponential growth phase, maintained within approximately 2% of its set-point. (j) OD can be set to follow a dithered waveform (with cells rapidly diluted to a lower OD value whenever the upper limit is reached) to accurately measure growth [27]. Following a change in temperature set-point from 25°C to 37°C growth accelerates significantly. FP, fluorescent protein; LED, light-emitting diode; OD, optical density; OS, operating system; PC, personal computer; PCB, printed circuit board.
Fig 3.
(a) Growth curves of E. coli (four replicates). (b) Dependence of E. coli growth rate on temperature (‘Temp’); error bars represent standard deviation of growth rates measured over 5 hours at each temperature. (c) Measured growth rate following activation of UV source at specified power level at t = 1 hour. The population is able to adapt to low UV intensities and eventually returns to its initial growth rate (S1N Data). (d) Biofilm OD versus time for cells before and after adaptation in Chemostat mode for 120 hours, calculated as described in S1O Data. OD, optical density; WT, wild type.
Fig 4.
(a,b) Optogenetic CcaS-CcaR system coupled to GFP expression [33], stimulated with slow- and fast-varying inputs (green/red light activate/deactivate gene expression, respectively). (c) Fluorescence expression (left axis) controlled by varying optogenetic excitation intensity (right axis) in OL. (d) Fluorescence expression regulated in CL to follow a predetermined profile, using a PI controller. a.u., arbitrary units; CL, closed loop; GFP, green fluorescent protein; OL, open loop; PI, proportional-integral.
Fig 5.
(a) Two-plasmid system for inducible expression of GFP and RFP. (b) Fluorescence of GFP (left axis) and RFP (right axis) following induction at times T1 and T2 with indicated inducer combinations. (c) GFP fluorescence measured during short time period near T1. A small increase is observed in the two samples to which aTc is added due to the fluorescence of the inducer compound itself. a.u., arbitrary units; GFP, green fluorescent protein; RFP, red fluorescent protein.