Team:Shanghaitech/project
Huge Gap between the public & synthetic biology
Public participation is a powerful booster for science advancement. The game, FoldIT, had encouraged thousands of people contribute to the structural biology research using their three-dimensional pattern matching and spatial-temporal reasoning ability. Folding@Home, another protein folding program based on public participation, had accumulated the computing efficiency that overrun all other super-computers during 2007-2012.
We image a future of synthetic biology like this, when people in different field can contribute their intelligence to advance synthetic biology. However, it is not easy for non-biologists to start working on gene blocks since it requires a complex understanding of molecular cloning, sufficient biosafety training as well as an actual lab. In this project, we tried to build a public platform for synthetic biology with two attempts.
First, we simplified the “block” concept to the public.Instead of using gene blocks, we consider a group of functionally defined bacteria as a “block”. Quorum sensing (QS) system in synthetic biology is great examples to show that bacteria cells can communicate to achieve different functions. Thus, we use QS system as the executioners to achieve synthetic aim in our project.
Secondly, we built an interactive platform that combines software control with an automatic liquid handling system. With this platform, most people, even elementary school students, can design their synthetic biology experiment online and have the robot perform their experiments.
Pack the difficulties in the box: how can our project narrow the gap
We aim to build a platform named MagicBlock, consisting of an interactive software interface, bacteria and robots. Designers can use the software interface to design gene circuits of a bio-product. Several MagicBlocks, the bacteria, are cultured according to the gene circuits retrieved from the cloud server and these blocks are interacted by liquid handling robot for supernatant transfer.
What’s Lux-like Quorum Sensing system?
In Gram Negative bacteria, Acyl Homoserine Lactones (AHLs) are used to communicate among their community. A family of AHL-synthetases keep synthesize AHLs in a relative low level. When the bacteria population increases and the synthesized AHLs reach a critical concentration, AHLs bind and induce the dimerization of LuxR-like receiver proteins, which in turn allow the protein to bind specific promoters to initiate gene expression. We've used this feature of communicating between bacteria to connect our MagicBlocks together.
"Primary Bio-Blocks" are Bio-Blocks containing single quorum sensing system.
We've named simple Bio-Blocks containing only one quorumsensing system "Primary Bio-Blocks". These simple bio-blocks are mainly used as input/output (I/O) units, response to physical or chemicalstimulations, send input signals to the whole MagicBlock system, or express highlevel of a reporter protein as the output.
We generated a collection of these bacteria sensors andreporters. Since they are sharing the similar design, one can easily switchbetween these bio-blocks to change the function for different purpose.
To validate thefunction of these primary bio-blocks, experimental tests have been combinedwith mathematic modeling to better characterize each QS system.
More about Primary BioBlock"Advanced Bio-Blocks" are Bio-Blocks containing more than one quorum sensing systems.
"Advanced Bio-Blocks" refer to bio-blocks containing more than one quorum sensing systems. Applying multiple quorum sensing systems is not a straightforward thing. We've examined the cross-talk between AHLs and their receiver proteins. Las quorum sensing system from Pseudomonas aeruginosa and Rpa system from Rhodopseudomonas palustris demonstrated great orthogonal function in our experiments, thus we used them to construct the advanced bio-blocks.
Mainly used as the intermediate layers carrying out logic processing, the Advanced Bio-Blocks often produce one kind of AHLs in response to another. However, it is hard to measure the actual level of each AHL. We have generated an indirect method to determine the efficiency of Advanced Bio-Blocks by mathematic modeling.
More about Advanced BioBlockDynamical model of a typical Bio-Block
After expression experiments, we have collected enough data to describe the kinetics properties of a BioBlock. We've modeled the response and re-generation of AHLs in typical intermediate bioblocks and determine parameters for liquid handling robot we used to transfer liquid supernatant between bacteria.
Automated devices helps to realize bio-block concept.
Figure: How the whole system works?
Automated devices are used to transfer culture supernatant and connect different MagicBlocks together. Users could design genetic circuits through our software with easy to use user interface, then their design will automatically be translated as machine code controlling the robotic liquid handling system, transferring supernatant between bacteria cultures and connecting bio-blocks.
Hardware
Common liquid handling robots are far too expensive for a project aiming at public engagement. We've built a Low-cost Robotic Liquid handling system to assemble our MagicBlocks. For a cost of only $150, our improvise liquid handling robot had been proved competent to complete the task of assembling Bio-Blocks.
More about our HardwareSoftware
Our controlling software is one of the essential parts to allow people to design a synthetic gene circuit. We've created an user-friendly software for this purpose. Anyone could use it to assemble MagicBlocks with the function of their desire, but no need for any wet-lab training.
More about our SoftwareHuman Practice in our project
In the Human Practice part, we found the problem, designed a product, tested it and received evaluation.
After interviewing people at different ages and with different occupations, we encountered many people with fascinating ideas, yet have little biological knowledge or lab experience. Hence we invented MagicBlock, an integrated platform for users to design and modify their bio-product simply by programming. The public were invited to the workshops, where they were guided to use MagicBlock to design their own bio-products and created various thought-provoking designs. We got feedback and improved theMagicBlock accordingly. In the end, it is rewarding to find out that ourMagicBlock can really inspire people’s creativity and help them to realize it.
We’ve also got experts’ opinions by interviewing, seeking advice on building the MagicBlockas well as the related mathematic modeling.
Learn more Human PracticeReference:
- Miller, M. B., & Bassler, B. L. (2001). Quorum sensing in bacteria. Annual Reviews in Microbiology, 55(1), 165-199.
- Dong, S. H., Frane, N. D., Christensen, Q. H., Greenberg, E. P., Nagarajan, R., & Nair, S. K. (2017). Molecular basis for the substrate specificity of quorum signal synthases. Proceedings of the National Academy of Sciences, 114(34), 9092-9097.
- Yusufaly, T., & Boedicker, J. Q. (2017). Mapping quorum sensing onto neural networks to understand collective decision making in heterogeneous microbial communities. arXiv preprint arXiv:1703.01353.
- Zhdanov, V. P. (2017). Mathematical aspects of the regulation of gene transcription by promoters. Mathematical biosciences, 283, 84-90.
- Gomez, M. M., & Arcak, M. (2017). A tug-of-war mechanism for pattern formation in a genetic network. ACS Synthetic Biology.
- Tamsir, A., Tabor, J. J., & Voigt, C. A. (2011). Robust multicellular computing using genetically encoded NOR gates and chemical/wires/'. Nature, 469(7329), 212-215.
- Minogue, T. D., Trebra, M. W. V., Bernhard, F., & Bodman, S. B. V. (2002). The autoregulatory role of EsaR, a quorum‐sensing regulator in Pantoea stewartii ssp. stewartii: evidence for a repressor function. Molecular microbiology, 44(6), 1625-1635.
- Halleran, A., & Murray, R. M. (2017). Cell-free and in vivo characterization of Lux, Las, and Rpa quorum activation systems in E. coli. bioRxiv, 159988.
