Difference between revisions of "Part:BBa K4586012"
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| + | After the ligation step, we did culture of the ligated product to specifically select the optimum colonies to screen it using Colony PCR to make sure that our parts were correctly ligated in the plasmid. | ||
| + | The cell culture plate of transformed pCDNA vector containing insert parts is shown in the following figure. | ||
| + | This plasmid contains | ||
| + | 1-Syn-notch (CD8 alpha-his tag-Anti CD19-mouse notch core-ZF21.16\VP64)) | ||
| + | 2-Booster gene 1 (SDC4, STEAP3) | ||
| + | 3-Booster gene 2 (NAdB) | ||
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==References== | ==References== | ||
Latest revision as of 14:08, 12 October 2023
NadB
Part Description
NadB is the first enzyme in the NAD biosynthesis pathway that is useful in the production of ATP by increasing the metabolism rate of gene-modified cells through the FAD-dependent oxidation of L-aspartate to iminoaspartate, which has an essential role in exosome synthesis.
Usage
This part is implemented in our system to improve the efficacy of our therapeutic agent by increasing the default level of exosome synthesis within our engineered MSCs. This enzyme can therefore speed up the metabolism of gene-modified cells and, in our project, also accelerate exosome biogenesis as shown in figure 1.
Figure 1: This figure illustrates the design of our biological circuit coding for booster genes(SDC4,STEAP3 and NadB) and their role in increasing the synthetic capacity of MSCs to secrete exosomes that carry our therapeutic agent represented in Cas12k/gBAFF-R
Literature Characterization
The study created a reporter construct by joining the C-terminus of CD63, one of the most used exosome markers, to nanoluc (nluc), a tiny and potent bioluminescence reporter10. After progressive centrifugation to eliminate masking signals12, luminescence in the cell-culture supernatant was measured. This reporter gene was co-transfected with plasmids expressing potential candidates for exosome production augmentation.
The study found STEAP3 syndecan-4 (SDC4), and (NadB) as potential synthetic exosome production boosters. Combined expression of these genes significantly increased exosome production, and a tricistronic plasmid vector ( known as exosome production booster), which guarantees that transfected cells receive all boosted genes at a fixed ratio ,produced a 15-fold to 40-fold increase (depending on cell conditions) in the luminescence signal in the supernatant.
Characterization By Mutational Landscape
In order to optimize the function of our parts, we've used the concept of Directed Evolution through applying different mutations and measuring the effects of these mutations on their evolutionary epistatic fitness. As displayed in the chart below, the mutation (H196R) shows the highest epistatic fitness, while the lowest score was associated with the mutation (C308H).
Figure . An illustration of the effects of different mutations on the Epistatic Fitness of NADB.
charactrization by mathematical modelinge
Presence of NadB part will aid in increasing the level of engineered exosomes so it plays an effective role to increase the efficacy of the therapeutic agent.
We compared both condition of exosomes production when using booster genes and without it
(1)No booster genes with conditioned release
This Represents the relation between the activation of the internal domain of the Syn-Notch (represented as red line) and production of exosomes with specific cargo (represented as blue line) as the production of the engineered exosomes is initiated once the internal domain is activated.
(2)Booster gene with conditioned release
This Represents the relation between the activation of the internal domain of the Syn-Notch (represented as red line) and production of exosomes with specific cargo (represented as blue line) as the production of the engineered exosomes is initiated once the internal domain is activated.
Experimental Characterization
In order to amplify this DNA part, we used PCR amplification to reach the desired concentration to complete our experiments using specific forward and reverse primers, running the parts on gel electrophoresis as this part presents in lane (P3) including NAdB, and then measuring the specific concentration of the running part using Real-Time PCR as shown in the following figure.
We performed the double digestion method for this part in the prefix and suffix with its specific restriction enzyme and applied this part to gel electrophoresis as shown in the following figure lane (P3).
After the ligation step, we did culture of the ligated product to specifically select the optimum colonies to screen it using Colony PCR to make sure that our parts were correctly ligated in the plasmid. The cell culture plate of transformed pCDNA vector containing insert parts is shown in the following figure. This plasmid contains 1-Syn-notch (CD8 alpha-his tag-Anti CD19-mouse notch core-ZF21.16\VP64)) 2-Booster gene 1 (SDC4, STEAP3) 3-Booster gene 2 (NAdB)
References
Kojima, R., Bojar, D., Rizzi, G., Hamri, G. C. E., El-Baba, M. D., Saxena, P., ... & Fussenegger, M. (2018). Designer exosomes produced by implanted cells intracerebrally deliver therapeutic cargo for Parkinson’s disease treatment. Nature communications, 9(1), 1305. Sequence and Features
- 10COMPATIBLE WITH RFC[10]
- 12COMPATIBLE WITH RFC[12]
- 21COMPATIBLE WITH RFC[21]
- 23COMPATIBLE WITH RFC[23]
- 25INCOMPATIBLE WITH RFC[25]Illegal AgeI site found at 406
Illegal AgeI site found at 1026 - 1000COMPATIBLE WITH RFC[1000]