Circuit Kit: Overview

In order to raise awareness, and motivate continued innovation in the field of synthetic biology, our iGEM team took the initiative to design a simple hardware demonstration platform, with which mentors can allow students to interact with a physical model of our project! The platform uses a microcontroller and a collection of simple circuits and components which communicate with a Matlab GUI to demonstrate how the various portions of our BioBricks interact to accomplish our goal.

Microcontrollers 101:

Typically, microcontrollers are general purpose microprocessors which have additional parts that allow them to read, and control external devices. We often use the terms microcontroller and microprocessor interchangeably.

Why use microcontrollers to help spread synthetic biology awareness? Microcontrollers are a good starting point for teaching students about general input/output systems, which are the primary design focus of synthetic biology: creating biological systems that transform environmental inputs into useful outputs. A basic microcontroller typically includes a microprocessor, digital inputs/outputs, analog inputs/outputs, and some type of communication interface (e.g. serial, wi-fi, bluetooth, etc).

Although our kit utilizes an off-the-shelf microcontroller (AtMega328P-PU based Arduino), we additionally designed a simplified version. This allows other collaborators and students to potentially replicate, or modify the project and eventually fabricate their own simplified microcontrollers for use in DIY synthetic biology education. In many senses, the BioBricks being developed through the iGEM foundation essentially function like minute microcontroller systems. It is thus important to identify this similarity, and provide students and future researchers with an opportunity to explore it.

Simplified Microcontroller:

Below is a list of components used in our simplified microcontroller, and an image of the schematic designating the physical connections between the components and the AtMega328P-PU. These connections can initially be wired using a breadboard, which allows students to gain a simplified understanding of what connections are being made in off-the-shelf microcontrollers. If they choose, students can use the provided schematic files to order a pcb of their own from any of a variety of pcb manufacturers.

• A single promoter is composed of 3 promoter regions, represented by identically-colored resistors.
• Note the orientation of the components when inserting each region.
• The top resistor should connect slots 1 & 2. The middle resistor should connect slots 2 & 3. The bottom resistor should connect slots 3 & 4.

• Right click the provided folder, and select "Add to Path -> Selected Folders and Sub-Folders"

• Note that the software will first sweep through the entire range of all possible fluorescence input levels, and plot the measured fluorescence values.
• Allow the program to run to completion, populating the output tables.

• This will move the output tables, and calculated values to the workspace.

• Observe the plot_data.m function if you wish to plot your own data

• Remove the Spinach sequence,
• Remove the tRNA stabilizer (one or both components),
• Remove the RBS sequence, and replace with one of the 3-pin headers with blue wire (short),
• Remove the FAP sequence, and replace with one of the 3-pin headers with blue wire (short),
• Remove the START/END sequence,
• Remove either DFHBI or MG by toggling the switches off (illuminated when 'ON'),
• …or any combination of the previous.

The goal was to create a model of our biosensor that clearly represents its main components and makes clear how the biosensor works. We also planned to enable the students to simulate changes in the “environment” and to observe the outcome of these changes. To achieve this goal, we built an affordable, microcontroller-based, hardware platform and also developed an associated, open-source, simulation software.

The combined hardware/software platform allows the students to directly manipulate electronic components, which are formal equivalents of the BioBricks used in our sensor, and to observe the effect of changing these components on the current or voltage output, which is the equivalent of the fluorescence intensity in our lab experiments. In using the kit, the students get a feel for how different promoters are compared using the biosensor; they can rank "virtual promoters" in the order of their strength. Students who use the kit gain hands-on experience and understand how all the parts of the biosensor work together to measure the mRNA and protein levels, without working in the wet lab. The figure on the right is a photograph of the hardware platform on which the correspondence between the biological components of the biosensor and the electronic components of the kit are identified.

The software used in the platform is based on the model derived for the analysis of the fluorescence data obtained with the biosensor. We have also created a GUI that allows the students to modify the parameters used in the model and to visualize on a computer display the current/voltage output (which is the equivalent of the fluorescence output in our experiments).

To obtain feedback for how high school students use the circuit kit, the team has given several presentations about synthetic biology and our project to high school students enrolled in the Summer Academy of Math and Science and in AP Biology at Carnegie Mellon University. We have also sought and obtained feedback on the kit from a Physics teacher from a local Public School in Pittsburgh. This feedback and input gained in these presentations is used to refine the kit.