Coding

Part:BBa_K1632010:Design

Designed by: Riku Shinohara   Group: iGEM15_Tokyo_Tech   (2015-08-18)
Revision as of 13:38, 15 September 2015 by JunKawamura (Talk | contribs) (→‎Materials and Methods)

fimB (wild-type)


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]


Design Notes

sequence confirmed

Materials and Methods

1. Construction
All the samples were DH5α strain with antibiotic resistance to ampicillin and kanamycin.

A. PBAD/araC_FimB (6A1) +fim switch[default ON](wild-type)_rbs_gfp (3K3)
B. PBAD/araC_FimB (6A1) +fim switch[default OFF](wild-type)_rbs_gfp (3K3)
C. rbs_M256IcysE (6A1) + fim switch[default ON](wild-type)_rbs_gfp (3K3) …positive control 1
D. rbs_M256IcysE (6A1) + fim switch[default OFF](wild-type)_rbs_gfp (3K3) …negative control 1
E. PBAD/araC_FimB (6A1) + J23119_rbs_gfp(3K3) …positive control 2
F. PBAD/araC_FimB (6A1)+rbs_gfp(3K3) …negative control 2

Fig. 1. Plasmids



2. Assay protocol
1. Prepare overnight cultures for the each sample in 3 mL of LB medium containing ampicillin (50 microg / mL), kanamycin (30 microg / mL)　and glucose (final concentration of mass of glucose is 0.5 percent) at 37 ℃ for 12h.
2. Make a 1:100 dilution in 3 mL of fresh LB containing Amp, Kan and glucose (final concentration of mass of glucose is 0.5 percent).
3.Grow the cells at 37 ℃ until the observed OD590 reaches 0.4 (Fresh Culture)
4. After incubation, take 1 mL of the samples, and centrifuge at 5000x g, 1 min, 25 ℃
5. Remove the supernatant by using P1000 pipette
6. Suspend the pellet in 1 mL of LB containing Amp and Kan, and centrifuge at 5000x g, 1 min, 25 ℃
7. Remove the supernatant by using P1000 pipette
8. Suspend the pellet in 1 mL of LB containing Amp and Kan, and centrifuge at 5000x g, 1 min, 25 ℃
9. Remove the supernatant by using P1000 pipette
10. Add 1 mL of LB containing Amp and Kan, and suspend.
11. Add 30 microL of suspension in the following medium.
① 3 mL of LB containing Amp, Kan, glucose (final concentration of mass of glucose is 0.5 percent) and 30 microL of sterile water
 ② 3 mL of LB containing Amp, Kan and 30 microL of 2 mM arabinose (final concentration of arabinose is 20 microM)
 ③ 3 mL of LB containing Amp, Kan and 30 microL of 20 mM arabinose (final concentration of arabinose is 200 microM)
 ④ 3 mL of LB containing Amp, Kan and 30 microL of 500 mM arabinose (final concentration of arabinose is 5 mM)
 12. Grow the samples at 37 ℃ for 6.5 hours.
13. Measure OD590 of all the samples every hour.
14. Start preparing the flow cytometer 1 h before the end of incubation.
15. After the incubation, take the samples, and centrifuge at 9000x g, 1min, 4℃.
16. Remove the supernatant by using P1000 pipette
17. Add 1 mL of filtered PBS (phosphate-buffered saline) and suspend. (The ideal of OD is 0.3)
18. Dispense all of each suspension into a disposable tube through a cell strainer.
19. Use flow cytometer to measure the fluorescence of GFP. (We used BD FACSCaliburTM Flow Cytometer of Becton, Dickenson and Company.)

Source

PCR from MG1655

References

Timothy S. Ham et al. (2006) A Tightly Regulated Inducible Expression System Utilizing the fim Inversion Recombination Switch. Biotechnol Bioeng 94(1):1-4
Hung M. et al. (2014) Modulating the frequency and bias of stochastic switching to control phenotypic variation. Nat Commun 5:4574. doi:10.1038/ncomms5574