BioBuilding: Synthetic Biology for Teachers: Lab 3

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TinkerCell
USB key with program for loading on student laptops. Alternatively, program can be downloaded from Tinkercell homepage though a slow internet connection will make this a slow download.

I. TinkerCell description
The ultimate goal for this activity is to simulate the operation of the bacterial photography system using the CAD tool. The tool we've chosen (Tinkercell) is one of many but is useful in this teaching context since the program is visually appealing to use, can be an informative "drawing" tool in other contexts when you'll be teaching gene expression, and does not require extensive computer programming skills to be useful. The drawbacks with this program are that it can be unstable (i.e. crash unexpectedly), and that it will need to be loaded on to the school laptops rather than used via the web. We would be very interested in hearing your experience with this program in your classroom and hope you will offer feedback and suggestions through the BioBuilder website.

II. Electronics System description
As you know, the bacterial photography system is constructed from two devices. The devices are connected through the two-component signaling pathway. We can construct an analogous system from electrical components. The devices are connected through an operational amplifier and a resistor of varying impedance. We can thus use these two devices to build a circuit that will operate similarly to our bacterial photography system: the photodiode will sense light and generate an electrical signal that will be detected by the LED which produces a color. Depending on your goals, it might be sufficient to build the circuit with the largest resistor in place for the OpAmp, since this circuit should behave identically to the bacterial photography system (i.e. the LED on in the dark and off when the flashlight is shining on the photodiode). If you'd like to explore the issue of "gain" in the signaling system, then the resistor associated with the OpAmp can be swapped out for smaller ones, and the system can be observed to behave less digitally since the gain will be proportional to the resistance.
 * 1) A Sensor: an input detection device which, in response to dark, produces a signal.
 * 2) An Actuator: an output generating device which takes an input signal from the first device and produces a detectable output.
 * 1) A photodiode: a sensor device that allows current to pass through it in response to incoming light
 * 2) An LED: an actuator that responds to a current input by emitting colored light. We also include a resistor in this box so we don't burn out the LED.

III. U-do-it Bacterial Photograph
Since the bacterial photography system requires expensive indicator media and a specialized light source in an incubator, we do not have an easy way for you to try this part of the work in your classroom. We're working on it! But in the meantime if you'd like to send a transparency for us to develop for you in our lab, please contact us through the BioBuilder site and we'll work out a way to collaborate! Students might like to see their school logo or favorite actor in a bacterial photograph. As you think about an image to develop, remember that the goal is to have each cell growing distinctly in the light or dark. Light can bounce around edges and may blur the resulting image if the black and white are highly intermingled. In general, it’s better to have a dark background and a light image rather than the other way around. Once you've chosen an image to develop, generate a computer file with this image and print it to a transparency. To darken the dark parts of your photo, you might want to print it on two transparencies and we'll use them both to mask the Petri dish and we can send you a digital photo of your result.

Feedback
We're always looking to hear back from you if you've thought about this unit, tried it, or stumbled across it and want to know more. Please email us through BioBuilder, info AT biobuilder DOT org.

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 * BioBuilding: Synthetic Biology for Teachers
 * BioBuilding: Synthetic Biology for Teachers: Lab 1
 * BioBuilding: Synthetic Biology for Teachers: Lab 2
 * BioBuilding: Synthetic Biology for Teachers: Lab 3
 * BioBuilding: Synthetic Biology for Teachers: Lab 4
 * BioBuilding: Synthetic Biology for Teachers: Essay
 * BioBuilding: Synthetic Biology for Teachers: Design Assignment
 * BioBuilding: Synthetic Biology for Teachers: Glossary
 * BioBuilding: Synthetic Biology for Teachers: Teacher's resource room
 * BioBuilding: Synthetic Biology for Students
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