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![Page 1: TinkerCell Tutorial: The Bacterial Photography System Thanks and appreciation to Deepak Chandra from U of W, who developed TinkerCell and modified it to.](https://reader036.fdocuments.us/reader036/viewer/2022062517/56649f2c5503460f94c47703/html5/thumbnails/1.jpg)
TinkerCell Tutorial:The Bacterial Photography System
Thanks and appreciation to Deepak Chandra from U of W, who developed TinkerCell and modified it
to teach the bacterial photography system. The system itself was made by the 2006 Univ.
Texas iGEM team.
![Page 2: TinkerCell Tutorial: The Bacterial Photography System Thanks and appreciation to Deepak Chandra from U of W, who developed TinkerCell and modified it to.](https://reader036.fdocuments.us/reader036/viewer/2022062517/56649f2c5503460f94c47703/html5/thumbnails/2.jpg)
Start a new canvas Select “New canvas” from the File menu or use the “New” icon at the left of the top toolbar
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Assemble Reporter From the “Parts” tab, select and place an “Inducible Promoter”, “RBS”, and “Coding” icon on the canvas.
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Align and Name Drag items on the canvas next to one another to align them. Rename the promoter “PompC” and the coding sequence “LacZ”.
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Add a transcription factor From the “Molecules” tab, add a transcription factor to the canvas and rename it OmpRp
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Visual appeal: add a 'P' Select OmpRp, then from the “Edit” menu, choose “Add Decorator”. From the “Decorator” tab, select “phosphorylation”.
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Regulate transcription From the “Regulation” tab, choose “Regulation”, then click OmpRp and PompC. Choose “Transcriptional Activation” from the pop-up.
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Add light receptor From the “Molecules” tab, place a “Receptor” on the canvas and rename it Cph8.
![Page 9: TinkerCell Tutorial: The Bacterial Photography System Thanks and appreciation to Deepak Chandra from U of W, who developed TinkerCell and modified it to.](https://reader036.fdocuments.us/reader036/viewer/2022062517/56649f2c5503460f94c47703/html5/thumbnails/9.jpg)
Regulate OmpRpwith Cph8
From the “Regulation” tab, choose “Regulation, then click on Cph8 and OmpRp, then select “Allosteric Inhibition” from the popup menu.
![Page 10: TinkerCell Tutorial: The Bacterial Photography System Thanks and appreciation to Deepak Chandra from U of W, who developed TinkerCell and modified it to.](https://reader036.fdocuments.us/reader036/viewer/2022062517/56649f2c5503460f94c47703/html5/thumbnails/10.jpg)
Add the BetaGal proteinFrom the “Molecules” tab, place an “Enzyme” on the canvas. Name it “BetaGal”.
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Produce BetaGal proteinFrom the “Reactions” tab, choose “1 to 1” then click on the lacZ orf and the beta-gal protein, and choose “Protein Production” from the popup menu.
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Add the colorful moleculeFrom the “Molecules” tab, place two “small molecules” on the canvas. Name the first “SGal” and the second “COLOR”.
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Supply SGalDouble-click on SGal, select the “Initial Values” tab, and change its initial concentration from 1 uM to 15.
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Add the color reactionFrom the “Reaction” tab, choose “2 to 1”, then click on BetaGal, SGal, and COLOR.
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Add a chassisFrom the “Compartments” tab, choose “Cell”. Place and resize it on the canvas to include all components (but leave Cph8 in the membrane).
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Add lightFrom the “Molecules” tab, place a small molecule outside the cell and rename it “Light”.
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Regulate Cph8 with lightFrom the “Regulation” tab, choose “Regulation” and click on Light and Cph8 and choose “Activation” from the popup menu.
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Turn on the lightFrom the “Inputs” tab, choose “Step input” and click on the Light molecule.
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Change the timingDouble click on the “step” that’s on the canvas then click the numerical icon. Change “Step_time” to 50.
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Start Simulating!Your circuit should be complete. Now you can start modeling the outputs. Use the “play” arrow to run simulations with different inputs for each element.