Results
Solid Matrix
Our idea of a 3D-printer made it necessary to immobilize our cells inside a three dimensional matrix. We figured that the matrix needed to have the following properties:
- Clear substance with good transmission of light to enable us to actuate the immobilized cells precisely with light.
- Possibility to distribute the cells evenly within the matrix.
- Environment that ensures the survival of the bacteria.
The idea to immobilize our bacteria in something like a solid growth medium (like agar-plates) was a step in the right direction, but standard LB-agar was not the solution. In the end, we chose GELRITE as a gelling agent, “a highly-purified, natural anionic heteropolysaccharide that forms rigid, brittle, agar-like gels” (source: gelrite spec sheet, see labbook/methods).
Clear substance with good transmission of light:
The matrix should be prepared with minimal media such as M9 instead of LB, because LB shows a strong absorption in the lower range of visible light (hence its yellow color). Minimal media are clear, which is a great advantage.
The cell density in the matrix is also an important factor, because with increasing cell number the gel becomes blurry due to refraction of light (see diagrams).
Distribution of cells and cell survival:
To make sure that the cells are distributed evenly within the matrix, the bacteria need to be added to the medium before gelling occurs. The gelling temperature of GELRITE depends on both the amount of GELRITE powder and the salt concentration of the used liquid. A 0.5 % GELRITE gel prepared with M9 medium solidifies at around 46 °C. This means that the cells that shall be immobilized must survive such temperatures for a few minutes. This is why we made some experiments with the heat resistant E. coli strain BH28 (kindly provided by Jeanette Winter). Fluorescence microscopy showed that the cells can survive the gelling process and produce GFP or RFP upon induction. The temperature seems to be the most critical factor regarding cell survival, as minimal media, with which the gel is prepared, provide enough nutrients for the bacteria.
Cloning of constructs
Cloning of AND-Gate and reporter constructs were successful and plasmids have been verified via sequencing after every cloning step. Those sequences were entered into the registry. The cloning scheme for our AND-Gate and reporter constructs can be seen on our Design page.
High Fidelity PCR was performed on BBa_K322127 in order to amplify the ~3.9 kbp region of PcyA (Phycocyanobilin:ferredoxin oxidoreductase) gen and cph8 genes, as well as the OmpC promotor region. This PCR-product forms new part BBa_K568000.
A correct clone of our final optogenetical AND-Gate BBa_K568001 construct was successfully sequenced with VR primer into first 1000 bp of T7ptag region. Testing of this construct according to our Design notes in CP919 cells with GFP reporter part BBa_I746907 was not possible within timescale.
Size of our cloned reporter plasmid BBa_K568003, containing T7 promoter with RBS and lacZ is correct (T7promoter_RBS_lacZ approx. 3kbp pSB1AK8 approx. 3.4 kbp). One clone was verified via sequencing. This part was further characterized performing Miller Assays in BL21(DE3) cells. See "characterization of parts" or Registry entry for detailed information.
Characterisation of parts
Red Light Sensor
To prove the proper function of the red light sensor, we did several Miller Assays, trying to induce gene expression upon
Blue Light Sensor
Reporter Plasmid
"
Results
Solid Matrix
Our idea of a 3D-printer made it necessary to immobilize our cells inside a three dimensional matrix. We figured that the matrix needed to have the following properties:
The idea to immobilize our bacteria in something like a solid growth medium (like agar-plates) was a step in the right direction, but standard LB-agar was not the solution. In the end, we chose GELRITE as a gelling agent, “a highly-purified, natural anionic heteropolysaccharide that forms rigid, brittle, agar-like gels” (source: gelrite spec sheet, see labbook/methods).
Clear substance with good transmission of light:
The matrix should be prepared with minimal media such as M9 instead of LB, because LB shows a strong absorption in the lower range of visible light (hence its yellow color). Minimal media are clear, which is a great advantage. The cell density in the matrix is also an important factor, because with increasing cell number the gel becomes blurry due to refraction of light (see diagrams).
Distribution of cells and cell survival:
To make sure that the cells are distributed evenly within the matrix, the bacteria need to be added to the medium before gelling occurs. The gelling temperature of GELRITE depends on both the amount of GELRITE powder and the salt concentration of the used liquid. A 0.5 % GELRITE gel prepared with M9 medium solidifies at around 46 °C. This means that the cells that shall be immobilized must survive such temperatures for a few minutes. This is why we made some experiments with the heat resistant E. coli strain BH28 (kindly provided by Jeanette Winter). Fluorescence microscopy showed that the cells can survive the gelling process and produce GFP or RFP upon induction. The temperature seems to be the most critical factor regarding cell survival, as minimal media, with which the gel is prepared, provide enough nutrients for the bacteria.
Cloning of constructs
Cloning of AND-Gate and reporter constructs were successful and plasmids have been verified via sequencing after every cloning step. Those sequences were entered into the registry. The cloning scheme for our AND-Gate and reporter constructs can be seen on our Design page.
High Fidelity PCR was performed on BBa_K322127 in order to amplify the ~3.9 kbp region of PcyA (Phycocyanobilin:ferredoxin oxidoreductase) gen and cph8 genes, as well as the OmpC promotor region. This PCR-product forms new part BBa_K568000.
A correct clone of our final optogenetical AND-Gate BBa_K568001 construct was successfully sequenced with VR primer into first 1000 bp of T7ptag region. Testing of this construct according to our Design notes in CP919 cells with GFP reporter part BBa_I746907 was not possible within timescale.
Size of our cloned reporter plasmid BBa_K568003, containing T7 promoter with RBS and lacZ is correct (T7promoter_RBS_lacZ approx. 3kbp pSB1AK8 approx. 3.4 kbp). One clone was verified via sequencing. This part was further characterized performing Miller Assays in BL21(DE3) cells. See "characterization of parts" or Registry entry for detailed information.
Characterisation of parts
Red Light Sensor
To prove the proper function of the red light sensor, we did several Miller Assays, trying to induce gene expression upon
Blue Light Sensor
Reporter Plasmid