Team:The Tech Museum/Project

To generate random color diversity in bacteria, we designed and had assembled libraries of tri-color plasmids (thanks to the generous sponsorship of DNA2.0). The base arrangement of plasmid functional elements was modeled on the three-color expression plasmid pZS2-123 designed by Cox et al. (2010). Our plasmids contain three different reporter proteins that are each controlled by combinatorially-inserted promoter-rbs pairs of varying strengths. Nine previously described promoter-rbs pairs that span a range of expression levels were selected from the literature (Kosuri et al. 2013; see notebook for specific sequences). When paired with the 3 reporters, the output of this assembly strategy is a plasmid pool with 729 unique combinations. Theoretically, each unique plasmid should drive a specific ratio of the three different colored reporter proteins to produce a defined hue.

In total, 4 plasmid pools were generated. Two reporter protein versions of the library were made: one with fluorescent proteins (PaprikaRFP, KringleYFP, CindyLouCFP) and one with chromogenic proteins (red, yellow, blue). Additionally, each of these was also made with both a low and high copy ORI. We tested and optimize all four of these plasmid pools in our visitor-accessible museum wetlab setup. After optimization of e. coli transformation and plating conditions, we determined that the low copy fluorescent plasmid pool was ideal, so it was used for all subsequent exhibit prototyping and data collection with museum visitors.

Requirements:

meteor
gphoto2 homebrew
barcode scanner (currently only working in linux)
opencfu no-gui homebrew

Usage:

install requirements, buy camera & usb scanner
clone repo
update server/lib/settings.js to disable opencfu, barcode scanner, and gphoto calls as neededset $METEOR_ENV as desired
start meteor (it will need to be restarted after initializing npm meteor package)
read the instruction manual;

Bacteria Photobooth /Scanning station

Supplies:
UV light box
Camera
Tripod
Cloth/box

Results:
Using our iGEM project, our team of museum visitors helped us analyzed a total of 2674 colonies of bacteria on 61 different petri dishes. Together, we found a total of 324 unique colors! The aggregate data for bacteria color frequency and distribution looked like this:

Safety:
We did not use any dangerous organisms or reagents.

References:
Cox, R. S., Dunlop, M. J., & Elowitz, M. B. (2010). A synthetic three-color scaffold for monitoring genetic regulation and noise. Journal of Biological Engineering, 4(1), 10. doi:10.1186/1754-1611-4-10

Geissmann, Q. (2013). OpenCFU, a new free and open-source software to count cell colonies and other circular objects. PloS One, 8(2), e54072. doi:10.1371/journal.pone.0054072

Kosuri, S., Goodman, D. B., Cambray, G., Mutalik, V. K., Gao, Y., Arkin, A. P., … Church, G. M. (2013). Composability of regulatory sequences controlling transcription and translation in Escherichia coli. Proceedings of the National Academy of Sciences of the United States of America, 110(34), 14024–9. doi:10.1073/pnas.1301301110