Part:BBa_K1598005
pYear-RBS-TPH1-6xHis-Terminator
This is a composite part consisting of the PyeaR promoter, an RBS, the TPH1 expressing gene and a double terminator. The subparts in the biobricks BBa_K381001 and BBa_K1598002 have been tested by iGEM UCL 2015.
Contents
Usage and Biology
Clinical depression is likely caused by a chronic low grade-response to inflammation [1]. Although the pathway from inflammation to depression is complex and not fully understood it has been shown that the immune response is often accompanied by symptoms such as oxidative and nitrosative stress in the gut. [2]. Therefore, we have used the PyeaR promoter, which is sensitive to nitric oxide in the cell, upstream of human TPH1. The rate-limiting step of synthesis of serotonin is catalyzed by tryptophan hydroxylase, TPH, which converts tryptophan, an essential amino acid, into 5-hydroxytryptophan (5-HTP) [8]. It was shown that microbial colonization of the gut is essential for maintaining normal levels of tryptophan hydroxylase and serotonin in the blood [9]. We have created a synthetic device that produces functional human tryptophan hydroxylase to restore healthy serotonin levels in affected patients. Thus, we have created a composite system, which senses and responds to mood.
Sequence and Features
- 10COMPATIBLE WITH RFC[10]
- 12COMPATIBLE WITH RFC[12]
- 21COMPATIBLE WITH RFC[21]
- 23COMPATIBLE WITH RFC[23]
- 25COMPATIBLE WITH RFC[25]
- 1000COMPATIBLE WITH RFC[1000]
Testing
Introduction
To demonstrate a functional prototype of our project, we decided to show our system working under real-world conditions simulated in the lab using a Gut-on-a-Chip design similar to the one made at Harvard University[1].
The idea is to model the rate at which our genetically engineered bacterial culture (E. Coli Nissle) grows and colonizes the gut, and to characterize its expression of 5-HTP, a serotonin precursor that acts as an anti-depressant. With the assistance of Dr. Chiang, from UCL’s Microfluidics Lab, we designed using SolidWorks a 3D version of the chip model described in the attachment.
We improved the original Gut-on-a-Chip designed at Harvard University by making it a more realistic mimic of reality and more financially feasible.The new design doesn't require a porous membrane, and is inspired by a bulging bioreactor. In addition to replicating the peristaltic motion of the longitudinal muscles in the intestines like Harvard's design, this model will also replicate the motions created by circular muscles.
Mammalian Cell Culture
Results
Column: Cell Count (Cells per ul)
| 50000 | 25000 | 12500 | 6250 | 3125 | 1563 |
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| 781 | 391 | 195 | 98 | 49 | Negative Control |
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Protocol for Determining Adherence Time:
- Repeat steps 1 to 12 as described in the protocol above.
- Seed 6000 cells into 3 wells respectively of 4 96 well plates.
- Repeat steps 14 to 24 for one plate at intervals of 1 hour.
Adherence Results
1 hour
2 hours
3 hours
4 hours
We cultured bacterial cells on mammalian cells in the chip to simulate the gut environment and measured the bacterial cell density
Bacterial Optimum Cell Seeding Density Determination
To determine the optimum concentration of bacteria that can live in the chip, without negatively affecting the mammalian cells already growing in it, and to thus find a safe concentration of bacteria that should be administered
The graph above was used to determine the cell density for each dilution. Upon looking at each well under the microscope after 16hours, it was noted that the mammalian cells only survived when the bacterial cell seeding density was 1.29E+08 CFU/mL. Thus, we determined our optimum bacterial cell seeding density and ideal probiotic dosage to adminster.
Bacterial and Mammalian Cell Interactions in Microfluidics Chip
We grew our genetically engineered E Coli. Nissle with the mammalian cells in the chip to study the rate at which our probiotic grows and colonizes the gut. We also studied the interactions between the 2 cells, and established that they symbiotically co-exist at constant cell densities after over 16hours in real-world conditions.
As illustrated by the graph above, mammalian cell density rapidly declines from approximately 1400 cells/mm^2 to 700 cells/mm^2 in the 1st 2 hours, when our bacteria are introduced into the device at t=0. The CFU/mL of bacteria also falls significantly from 1.29E+08 to 2E+07. This is because the microenvironments of both types of cells has significantly changed due to the introduction of bacteria, and they’re now competing for nutrients.
After 2 hours, both bacterial and mammalian cell densities begin to recover as they get used to the new conditions and begin comfortably coexisting. In around 6 hours, the mammalian cell density reaches it peak of 700 cells/mm^2 and stays constant at the same level for over 16 hours. The same occurs with the bacterial cell density as it reaches its maximum of approximately 9.5E+08 CFU/mL, and stationary phase at around 11 hours. Hence, our microfluidics device has shown that both cell types have found an equilibrium and can happily co-exist in balance in simulated real world gut conditions.
Since mammalian cells are more delicate than bacteria, we can extrapolate that our probiotic will not have any negative impact on the gut’s natural microbiome. This also helps us address an issue raised at the UK iGEM Meet-Up. There was a concern that the introduction of our probiotic may significantly alter the balance of the natural gut microbiome, and have several side-effects. However, as established through our experiment, our probiotic prototype’s bacterial cell density growth plateau’s after a while, leaving the other cells healthy, although there is an initial drop in cell density. In conclusion, our probiotic prototype takes around 11hours to colonize the gut, and we also determined an optimum bacterial cell density for probiotic dosage.
Characterisation of PyeaR Promoter: PyeaR
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