BioElectronic Interface

The wired system for collecting data. It uses a pH meter as the high-impedance voltmeter to measure the value from the custom created sensor.

Reporters are molecules that allow the detection of a range of processes or molecules in a system. Reporter systems currently used in biology are proteins or enzymes whose expression is typically based on visual assessment. While techniques exist to get quantitative data from these reporters, they often require sophisticated equipment and are prone to large background noise. Furthermore, such optical reporter systems are frequently imposing a burden on the cell as the quantity of reporter molecules and thus energy associated to their expression is considerable. Synthetic biology is a new field that hold great promise to revolutionise biotechnology by applying engineering concepts to biology. However, currently some of the most powerful engineering tools such as Fourier and Laplace transforms are not widely being applied to reporter systems.

The new hardware setup for voltage measurement out of the sensor. The keen eye will recognise XBee modules we use for 802.15.4 wireless communication.

We report the construction of a novel type of reporter mechanism based on programmable in vivo potassium efflux in Escherichia coli. We have successfully assembled the custom genetic circuit driving the expression of the mutated potassium efflux pump KefC and have built liquid phase potassium ion sensors capable of translating the change in extracellular potassium concentration into an electronic digital signal. This creates a bio-electronic interface in synthetic biology facilitating the application of strong analytical techniques to biological signals.

Furthermore, we have built hardware and software tools to enable automatic collection of experimental data. Wireless coordinated sensors were constructed and linked with the potassium sensor, incubator, spectrophotometer and an ambient light sensor. Web-based graphing software was developed to federate the data.

Applications

Rapid prototyping of biosensors

By swapping the promoter regulatory unit on the constructed plasmid is a fast way to change the biosensor target. Many promoters already exist in the synthetic biology parts registry and more are being added and characterised every year. Notably many metal-sensitive promoters have been added in recent years thanks to the numerous biosensor projects by iGEM teams. Furthermore, this approach is more scaleable as these synthetic biology-based biosensors self-replicate with an approximate doubling time of 20 minutes.

Schematic for the application of signal processing techniques with our reporter. We hope to be able to pinpoint a frequency response to a change in conditions e.g. 5C increase in temperature.

Reporter signal processing in biology

The constructed reporter is quantitative by design. Within 3 minutes, an estimated 80% of the intracellular potassium is effluxed. Because the reporter is an active part of the cellular machinery once triggered, we expect that differences in signal profile will arise as a result of changes in intracellular conditions. Using traditional signal analysis techniques such as Fourier Transformation, we hope to identify unique frequency responses that correspond to specific changes in experimental conditions.

Institutions

Imperial College London

This project was started in the Ellis Lab as my undergraduate thesis work. There, I constructed the DNA circuitry, transformed cells, built the tip-based potassium sensors (at the Cass Laboratory) and created the first version (wired) of the data collection mechanism using a pH meter.

IBM Research

The project was then continued at IBM Research. There, we created novel hardware based on off-the-shelf components as well as software to allow automated collection and display of data. The software interface demo is available here. The visualiser code makes use of Dygraph and Google Visualisation code.

Overview