LAB CONTRIBUTIONS: GROWTH & LONGEVITY OF BACTERIA ENCAPSULATED IN HYDROGELS

We used the paper "Hydrogel-based biocontainment of bacteria for continuous sensing and computation" by Tang et al. (2021) to synthesize the hydrogels. This helped us gain insights into the methods for creating bacteria coated in hydrogels and determine the appropriate quantities for our experiments.

In addition, we studied how long bacteria can survive in hydrogel coatings. To do this, we placed the hydrogels in petri dishes and surrounded them with moist tissues to provide adequate moisture to the hydrogel beads. The plates were then incubated at 37 degrees Celsius. We observed the change in color of the bacteria over a period of five days. In a separate experiment, we used green fluorescent protein (GFP) to verify our previous findings. We created hydrogel balls containing GFP as illustrated in Figure 2 and placed them in the incubator under the same conditions. We checked the growth of the bacteria over another five-day period, and under blue light, we obtained the following results:

Our findings demonstrate that bacteria enclosed in a hydrogel have the ability to grow for a maximum of five days. Although we couldn't further investigate the longevity of bacterial survival due to restrictions in time and resources, this newfound knowledge provides significant insights for other iGEM teams. They can now comprehend the potential duration of bacterial growth in hydrogel environments and reproduce these bacteria using the project-specific protocol that we have developed.

Figure 2

REFERENCES

[1] T.-C. Tang et al., “Hydrogel-based biocontainment of bacteria for continuous sensing and computation,” Nature Chemical Biology, vol. 17, no. 6, pp. 724–731, 2021. doi:10.1038/s41589-021-00779-6

Software Contribution 1: The RSModifer

Problem

As shown in the linear sequence above, there are three BsaI restriction sites present. However, if you need to cleave this sequence only at two of these sites, it becomes a problem especially when the third site is in a gene part vital to get the desired sequence, there is going to be a third undesired cut. This was one of the problems we faced while developing our DNA circuit.

General Solution

Generally, different combinations of bases could code for one amino acid as shown below:

Applying the concept of amino acids to solve the problem mentioned above, bases of some amino acids in the recognition sites are substituted with other bases that code for the same amino acid. In this way, the recognition site is eliminated while also preserving the behavior of the part that contained the unwanted recognition site. Changing these bases manually can be quite a hassle especially if there are multiple of these unwanted recognition sites. There are also certain rules that must be followed considering that three bases code for an amino acid. These rules make the manual changing of bases a complex task.

Our Solution

In our efforts to contribute to Synthetic Biology and to the work of future iGEM teams who may face similar challenges when developing their DNA circuits, we developed a web application (RSModifier) that eliminates the unwanted recognition sites automatically, while also preserving the behavior of the part.

Follow this link to have a feel of the software designed

RSModifier User Menu