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Note Part 1–> At Lab section: week 6 Week 6 Lab: Gibson assembly
Based on the exploration of the Bacterial Demos repository, genetic circuits were analyzed and simulated with the use of the Asimov Kernel platform.
The Bacterial Demos repository was explored to understand how synthetic genetic circuits function. Different constructs were simulated using the built-in simulator, which displays protein expression over time. These simulations allow visualization of regulatory interactions such as repression and feedback, and how they influence gene expression dynamics.
Figure 1. Demostration of Bacterial Demo’s runtime and identification of the components.
The platform provides an interface to design genetic constructs by combining modular biological parts.
The logic of a basic construct follows the structure:
Promoter → Gene → Terminator
Each component plays a specific role in gene expression. The parts used for this example are shown in Table 1.
Table 1. Construct components
| Type | Function | Use |
|---|---|---|
| pTet | promoter | Initiates transcription; regulated by TetR |
| A1 RBS | Ribosome binding site | Enables translation of the gene |
| TetR | Coding sequence | Encodes a repressor protein |
| L3S2P24 | Bacterial Terminator | Stops transcription |
(Brophy et al., 2014; Letrari et al., 2026)
As it was shown, this construct consists of a promoter (pTet), a ribosome binding site (RBS), the TetR coding sequence, and a terminator. The promoter initiates transcription, while the RBS enables translation of the TetR protein. The TetR protein represses the pTet promoter, forming a negative feedback loop. This regulatory interaction stabilizes gene expression and prevents overproduction of the protein.
Small tutorial:
