Light Control
we did co-transformation for the red light and green light system separately. the bacteria after co-transformation were irradiated by red or green light in our device, and we use sfGFP as reporter gene. By monitoring relative intensity of fluorescence, we could prove the system’s feasibility. Following is the result observed by multiple plate reader.
（The device we used for testing--designed by TEAM_XJTLU）
In addition, to realize the second generation of cipher machine, we need to ensure that the light-induced system could be coupled with the oscillation system. That is to say, the response time of the light-induced system must be shorter than half period of the oscillation. Thus, we measured the system’s response time. Following is the results:
Conclusion: After a series of experiment, we are able to prove the feasibility of the light-induced system. While there is a possibility of leak, the differences between the two groups can be measured by devices. Also, after our measurement of the response time about 3 hours, it falls within the oscillation’s regulating range, which is consistent with our modeling results. So far, we can prove that the concept of the second generation of cipher machine is correct.
Oscillation
In order to realize the single-period oscillation, we design a circuit based on negative feedback mechanism (fig1), which is composed of gene luxI，aiiA and sfGFP.
To prove the effect of this circuit, we implanted it in E.coli MG1655 and raised them in test tubes. Meanwhile, we monitored the change of GFP fluorescence intensity. Although we could observe oscillation, amplitude rose higher and higher. After analysis, we think this happened due to the increased bacteria population and thus, the resulting increased AHL accumulated in the medium.
To get a stable oscillation, we designed a microfluidics device based on our project. In practice, we add bacteria solution to microfluidics chips, so each chamber is distributed with bacteria. Then, we add fresh medium with an appropriate velocity continuously, to provide adequate nutrition and take away the excessive bacteria due to proliferation and the accumulated AHL. By now, we ensure the system’s stability. We use fluorescence microscope to take pictures every 5 minutes and observe the stable oscillation. (Shown in the figures below:)
Logic gate
For proving our feasibility of AND gate, we used lactose promoter and arabinose promoter as the inputs of AND gate, and used GFP as the reporter gene. We designed a series of experiments to verify its precision and did research about its response time and response concentration.
First, we did four parallel experiments: the bacteria solutions were added by IPTG of 10^-3mol/L, arabinose of 10^-4mol/L, both of them, and neither of them. Following is the result.
Seeing from the figure, solutions with no inducers or only one inducer can produce little GFP fluorescence which verify the precision and feasibility of the AND gate. But, GFP fluorescence is high when only adding arabinose. This may because the leak of Plac. We will optimize our experiment by adding a weaker RBS between Plac and T7ptag.
Next, we designed experiments to verify the response concentration. Through these experiments, we can also conclude under which concentration can the AND gate have the best effect. We designed a series of gradient about how many inducers should be added. The concentration of IPTG and arabinose varied from 10^-3, 10^-5, 10^-6, 10^-7, to 0. Following is the result.
Seeing from the figure, with the increase of the inducers’ concentration, the value of fluorescence also increases. The figure has met our expectation. However, there has a peak when adding IPTG of 10^-7mol/L and arabinose of 10^-6mol/L, and we think this is because inaccuracy caused by measurement.
At last, we measured the response time. We used an inverted fluorescence microscope to take pictures every 10 minutes after adding inducers. Therefore, we could get the curve about the change of fluorescence intensity according to time. Until now, we still do not have the results.
