IGEM:Cambridge/2008/Notebook/Bacillus/2008/08/14: Difference between revisions
(Autocreate 2008/08/14 Entry for IGEM:Cambridge/2008/Notebook/Bacillus) |
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== | == Results of transformation== | ||
{|class="wikitable" style="text-align:center" border="1" | |||
|- | |||
! Vector !! Antibiotic !! number of colonies !! Transformation efficiency | |||
|- | |||
| ECE166 || Cm5 || 31 || 62 | |||
|- | |||
| Control || Cm5 || 0 || | |||
|- | |||
| ECE171 || Kan5 || 5 + a lot of small colonies || ? | |||
|- | |||
| Control || Kan5 || 1 + 5 very small || | |||
|- | |||
| ECE153 || Spc50 || about 25 (on a side) || 50 | |||
|- | |||
| Control || Spc50 || 6 + 2 very small || | |||
|} | |||
- Problem with our control, maybe we should check the resistance of competent cells (before transformation) | |||
==BioBrick extraction for testing promoters and RBS in ''B.subtillis''== | |||
The primers for inducible ''B.subtillis'' promoters have been ordered. Meanwhile, we would like to be able to compare the RBS and promoter strengths in ''E.coli'' and ''B.subtillis'', using GFP fluorescence to quantify gene expression. | |||
We attempted to isolate 4 BioBricks: I13522 (GFP under constitutive promoter), E0040 (GFP only), R0040 (a promoter), & B0034 (an ''E.coli'' RBS). | |||
So far, only the former two, extracted from 2007 wells, grew after transformation. Single-colony PCR was used to test the transformants. | |||
Expected VF2-VR fragment sizes: | |||
I13522 - ~2.4 kb | |||
E0040 - 958 bp | |||
R0040 - 292 bp | |||
B0034 - 250 bp | |||
==Transformation of vectors 188, 189, 190== | |||
- Transformation of yesterday did not work! there was nothing on plates, even on the control plate | |||
- Try again, same protocol, 2μL of DNA, control : PUC9 | |||
- Plate on Amp100 for control and Amp100 + Cm5 for vectors | |||
==Double digest of ECE166 (extracted from transformed Bacillus yesterday)== | |||
- Transformation from 07/08 | |||
- 16μL of DNA, 2μL of Buffer EcoRI, 1μL of EcoRI (Biolab) and 1μL of HindIII | |||
- Incubator at 37°C for 35min, heat shock at 80°C for 5min | |||
- Run on a gel with 4μL of DNA | |||
* Result : no bands! not enough DNA! | |||
- Run on a new gel with 16μL of DNA | |||
* Result : " bands, one of about 2000b, and one of about 5000b> The big one seem to be too small... | |||
We are going to check this transformation with fluorescence too! | |||
==Erythromycin plate== | |||
- Erythromycin plate for the transformation 13/08/08 | |||
- IA771 (control, they should survive) | |||
- IA771 + ECE166 (non integration vector, so colonies should survive) | |||
- IA771 + ECE171 (integration vector but in another locus, should survive) | |||
- IA771 + 153 9integration vector, they should die if they are transformed) | |||
==New stocks== | |||
- LB stocks with antibiotic of ECE151, 153, 166 | |||
- LB stock of ECE153 with Spc50 (one from colonies from LB stock from 11/08 and one from 13/08 transformation plates) | |||
==Check fluorescence with microscope== | |||
* ECE166 from the plate from 13/08 | |||
We diluted one colony from this plate into SDW and observed with microscope. | |||
Result : Bacillus is fluorescent! There are some bacteria which are brighter than others, but it is because it is not an integration vector. This transformation worked!!! | |||
* ECE153 | |||
We added xylose, but we did not incubate our sample after that, so it did not work> We will try again tomorrow with a period of incubation> | |||
We will have to | |||
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Results of transformation
- Problem with our control, maybe we should check the resistance of competent cells (before transformation) BioBrick extraction for testing promoters and RBS in B.subtillisThe primers for inducible B.subtillis promoters have been ordered. Meanwhile, we would like to be able to compare the RBS and promoter strengths in E.coli and B.subtillis, using GFP fluorescence to quantify gene expression. We attempted to isolate 4 BioBricks: I13522 (GFP under constitutive promoter), E0040 (GFP only), R0040 (a promoter), & B0034 (an E.coli RBS). So far, only the former two, extracted from 2007 wells, grew after transformation. Single-colony PCR was used to test the transformants. Expected VF2-VR fragment sizes: I13522 - ~2.4 kb E0040 - 958 bp R0040 - 292 bp B0034 - 250 bp Transformation of vectors 188, 189, 190- Transformation of yesterday did not work! there was nothing on plates, even on the control plate - Try again, same protocol, 2μL of DNA, control : PUC9 - Plate on Amp100 for control and Amp100 + Cm5 for vectors Double digest of ECE166 (extracted from transformed Bacillus yesterday)- Transformation from 07/08 - 16μL of DNA, 2μL of Buffer EcoRI, 1μL of EcoRI (Biolab) and 1μL of HindIII - Incubator at 37°C for 35min, heat shock at 80°C for 5min - Run on a gel with 4μL of DNA
- Run on a new gel with 16μL of DNA
We are going to check this transformation with fluorescence too! Erythromycin plate- Erythromycin plate for the transformation 13/08/08 - IA771 (control, they should survive) - IA771 + ECE166 (non integration vector, so colonies should survive) - IA771 + ECE171 (integration vector but in another locus, should survive) - IA771 + 153 9integration vector, they should die if they are transformed) New stocks- LB stocks with antibiotic of ECE151, 153, 166 - LB stock of ECE153 with Spc50 (one from colonies from LB stock from 11/08 and one from 13/08 transformation plates) Check fluorescence with microscope
We diluted one colony from this plate into SDW and observed with microscope. Result : Bacillus is fluorescent! There are some bacteria which are brighter than others, but it is because it is not an integration vector. This transformation worked!!!
We added xylose, but we did not incubate our sample after that, so it did not work> We will try again tomorrow with a period of incubation> We will have to | |||||||||||||||||||||||||||||
