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IBC 2011, vol. 3, article no. 10, pp. 1-10 | doi: 10.4051/ibc.2011.3.3.0010
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Reports on negative result (Synthetic biology, Biological computation/Database, Biomathematics/Mathematical Biology and Medicine )
Bacterial Hash Function Using DNA-Based XOR Logic Reveals Unexpected Behavior of the LuxR Promoter
Brianna Pearson1+, Kin H. Lau1+, Alicia Allen2, James Barron1,3, Robert Cool2, Kelly Davis4, Will DeLoache1, Erin Feeney1, Andrew Gordon2, John Igo5, Aaron Lewis5, Kristi Muscalino4, Madeline Parra4, Pallavi Penumetcha1, Victoria G. Rinker1,6, Karlesha Roland1,7, Xiao Zhu2, Jeffrey L. Poet5,8, Todd T. Eckdahl2,8, Laurie J. Heyer4,8 and A Malcolm Campbell1,8,*
1
Department of Biology, Davidson College, Davidson, NC 28035
2
Department of Biology, Missouri Western State University, St. Joseph, MO 64507
3
Department of Biology, Hampton University, Hampton, VA 23668
4
Department of Mathematics, Davidson College, Davidson, NC 28035
5
Department of Computer Science, Math and Physics, Missouri Western State University, St. Joseph, MO 64507
6
Woodlawn School, Davidson, NC 28036
7
Department of Mathematics, Spelman College, Atlanta, GA 30314
8
Genome Consortium for Active Teaching (GCAT)
*Corresponding author
+These authors contributed equally to this work
received: July 08, 2011 ; accepted: July 15, 2011 ; published : July 18, 2011
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Synopsis

Introduction: Hash functions are computer algorithms that protect information and secure transactions. In response to the NIST’s "International Call for Hash Function”, we developed a biological hash function using the computing capabilities of bacteria. We designed a DNA-based XOR logic gate that allows bacterial colonies arranged in a series on an agar plate to perform hash function calculations.
Results and Discussion: In order to provide each colony with adequate time to process inputs and perform XOR logic, we designed and successfully demonstrated a system for time-delayed bacterial growth. Our system is based on the diffusion of ß-lactamase, resulting in destruction of ampicillin. Our DNA-based XOR logic gate design is based on the opposition of two promoters. Our results showed that Plux and POmpC functioned as expected individually, but Plux did not behave as expected in the XOR construct. Our data showed that, contrary to literature reports, the Plux promoter is bidirectional. In the absence of the 3OC6 inducer, the LuxR activator can bind to the Plux promoter and induce backwards transcription.
Conclusion and Prospects: Our system of time delayed bacterial growth allows for the successive processing of a bacterial hash function, and is expected to have utility in other synthetic biology applications. While testing our DNA-based XOR logic gate, we uncovered a novel function of Plux. In the absence of autoinducer 3OC6, LuxR binds to Plux and activates backwards transcription. This result advances basic research and has important implications for the widespread use of the Plux promoter.

Keywords : hash function, time-delayed bacterial growth, DNA-based XOR logic gate, Plux, LuxR, PompC, bidirectional promoter, bacterial computer, synthetic biology
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:: Comments
::C1::Pearson et al. designed an interesting assay system to evaluate hash function in E. coli. However, the assay system did not work because the Plux promotor behaves aberrantly. They suspected two possibilities for this aberrant behavior. One possibility may result from the fact that the Plux promotor used in that study is shorter than that of previous studies. Another one is cytoplasmic differences between V. fischeri and E. coli. If the latter is the case, it is very interesting because disruptions of gene regulation have been reported in Drosophila species hybrids. Therefore, it is possible that there are "regulatory incompatibilities" at least in the LuxR quorum sensing system between V. fischeri and E. coli.
Posted by: sj-BLSA ( 2011-09-19 )
Declaration of Competing Interests :
co-author
::C2::The previous comment makes a good point about different species having different proteins which could be the reason for the "new" function we detected. However, the longer vs. shorter promoter is interesting. Since the DNA is not truncated in nature, our version is shorter than others and shorter than the native promoter could be. But the cells do not have to look at all of the DNA we provide them. Even the longer promoter used by others contains our shorter version. It may be that we cut out a functional piece, but it may be that the shorter version is also a biological unit in situ.

The promoter we used is already widely used by synthetic biologists. So even if our construct deleted a functional unit, many other biologists are using the same part and may be affected by the same unexpected behavior we documented.

Thank you for your comment. It is nice to have a dialog about our research, even if we never get to have it in person.
Posted by: macampbell@********** ( 2011-09-20 )
::C3::As a biological scientist it is not easy to understand how bacterial computer works for hash function and what is the strongest point of this system for development of hash function from this paper. Easier explanation and examples in the introduction may be recommended..
Posted by: sjcha-BLSA ( 2011-09-20 )
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- Chris Anderson
- Sven Panke
Edited by
- Keun Woo Lee
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- Brianna Pearson
- Kin H. Lau
- A Malcolm Campbell
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- A Malcolm Campbell
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