Difference between revisions of "Part:BBa K1632003:Experience"
(→‎Invertion assay with FimB)
 
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====Invertion assay with FimB====
 
====Invertion assay with FimB====
  
−
<b>1. Construction</b><br>
+
=====1. Construction=====
  
−
All the samples were DH5α strain with antibiotic resistance to ampicillin and kanamycin.<br>
+
All the samples were DH5alpha strain with antibiotic resistance to ampicillin and kanamycin.<br>
  
−
(1) PBAD/araC_fimB (pSB6A1) + ''fim'' switch[default ON](Tokyo_Tech/J23119)_rbs_gfp (pSB3K3) <br>
+
(1) PBAD/araC_''fimB''(wild-type) (pSB6A1) + ''fim'' switch[default ON](Tokyo_Tech/J23119)_''gfp'' (pSB3K3) <br>
−
(2) PBAD/araC_fimB (pSB6A1) + ''fim'' switch[default OFF](Tokyo_Tech/J23119)_rbs_gfp (pSB3K3) <br>
+
(2) PBAD/araC_''fimB''(wild-type) (pSB6A1) + ''fim'' switch[default OFF](Tokyo_Tech/J23119)_''gfp'' (pSB3K3) <br>
−
(3) pSB6A1 + ''fim'' switch[default ON](Tokyo_Tech/J23119)_rbs_gfp (pSB3K3) …positive control 1<br>
+
(3) pSB6A1 + ''fim'' switch[default ON](Tokyo_Tech/J23119)_''gfp'' (pSB3K3) …positive control 1<br>
−
(4) pSB6A1 + ''fim'' switch[default OFF](Tokyo_Tech/J23119)_rbs_gfp (pSB3K3) …negative control 1<br>
+
(4) pSB6A1 + ''fim'' switch[default OFF](Tokyo_Tech/J23119)_''gfp'' (pSB3K3) …negative control 1<br>
−
(5) PBAD/araC_fimB (pSB6A1) + J23119_rbs_gfp(pSB3K3) …positive control 2 <br>
+
(5) PBAD/araC_''fimB''(wild-type) (pSB6A1) + J23119_''gfp''(pSB3K3) …positive control 2 <br>
−
(6) PBAD/araC_fimB (pSB6A1) + rbs_gfp(pSB3K3) …negative control 2 <br>
+
(6) PBAD/araC_''fimB''(wild-type) (pSB6A1) + rbs_''gfp''(pSB3K3) …negative control 2 <br>
  
−
<b>2. Assay protocol</b><br>
+
=====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 %) at 37 ℃ for 12h.<br>
+
1. Prepare overnight cultures for each sample in 3 mL of LB medium containing ampicillin (50 microg / mL), kanamycin (30 microg / mL) and glucose (final concentration is 0.5 %) at 37 ℃ for 12h.<br>
−
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 %).<br>
+
2. Make a 1:100 dilution in 3 mL of fresh LB containing Amp, Kan and glucose (final concentration is 0.5 %).<br>
−
3.Grow the cells at 37 ℃, shaking at 180 rpm until the observed OD590 reaches 0.4 (Fresh Culture).<br>
+
3. Incubate the cells at 37 ℃, shaking at 180 rpm until the observed OD590 reaches 0.4 (Fresh Culture).<br>
−
4. After incubation, take 1 mL of the samples, and centrifuge at 5000x g, 1 min, 25 ℃ <br>
+
4. After the incubation, take 1 mL of the samples, and centrifuge at 5000x g, 1 min, 25 ℃ <br>
 
5. Remove the supernatant.<br>
 
5. Remove the supernatant.<br>
−
6. Add 1 mL of LB containing Amp and Kan, and centrifuge at 5000x g, 1 min, 25 ℃ <br>
+
6. Suspend the pellet in 1 mL of LB containing Amp and Kan, and centrifuge at 5000x g, 1 min, 25 ℃ <br>
 
7. Remove the supernatant.<br>
 
7. Remove the supernatant.<br>
 
8. Suspend the pellet in 1 mL of LB containing Amp and Kan, and centrifuge at 5000x g, 1 min, 25 ℃ <br>
 
8. Suspend the pellet in 1 mL of LB containing Amp and Kan, and centrifuge at 5000x g, 1 min, 25 ℃ <br>
 
9. Remove the supernatant.<br>
 
9. Remove the supernatant.<br>
−
10. Add 1 mL of LB containing Amp and Kan, and suspend.<br>
+
10. Suspend the pellet in 1 mL of LB containing Amp and Kan.<br>
 
11. Add 30 microL of suspension in the following medium.<br>
 
11. Add 30 microL of suspension in the following medium.<br>
 
<span style="margin-left: 20px;">① 3 mL of LB containing Amp, Kan, glucose (final concentration of mass of glucose is 0.5 %) and 30 microL of sterile water<br>
 
<span style="margin-left: 20px;">① 3 mL of LB containing Amp, Kan, glucose (final concentration of mass of glucose is 0.5 %) and 30 microL of sterile water<br>
−
<span style="margin-left: 20px;">② 3 mL of LB containing Amp, Kan and 30 microL of 2 mM　arabinose (final concentration of arabinose is 20 microM)<br>
+
<span style="margin-left: 20px;">② 3 mL of LB containing Amp, Kan and 30 microL of 2 mM arabinose (final concentration of arabinose is 20 microM)<br>
 
<span style="margin-left: 20px;">③ 3 mL of LB containing Amp, Kan and 30 microL of 20 mM arabinose (final concentration of arabinose is 200 microM)<br>
 
<span style="margin-left: 20px;">③ 3 mL of LB containing Amp, Kan and 30 microL of 20 mM arabinose (final concentration of arabinose is 200 microM)<br>
 
<span style="margin-left: 20px;">④ 3 mL of LB containing Amp, Kan and 30 microL of 500 mM arabinose (final concentration of arabinose is 5 mM)<br>
 
<span style="margin-left: 20px;">④ 3 mL of LB containing Amp, Kan and 30 microL of 500 mM arabinose (final concentration of arabinose is 5 mM)<br>
−
<span style="margin-left: 20px;">※ As for C and D, the suspension were added only in medium ① and ④. <br>
 
 
12. Incubate the samples at 37 ℃, shaking at 180 rpm for 6.5 hours. (Measure OD590 of all the samples every hour.)<br>
 
12. Incubate the samples at 37 ℃, shaking at 180 rpm for 6.5 hours. (Measure OD590 of all the samples every hour.)<br>
 
13. After the incubation, take the samples, and centrifuge at 9000x g, 1min, 4℃.<br>
 
13. After the incubation, take the samples, and centrifuge at 9000x g, 1min, 4℃.<br>
Line 41: Line 40:
 
17. Use flow cytometer to measure the fluorescence of GFP. (We used BD FACSCaliburTM Flow Cytometer of Becton, Dickenson and Company.)<br>
 
17. Use flow cytometer to measure the fluorescence of GFP. (We used BD FACSCaliburTM Flow Cytometer of Becton, Dickenson and Company.)<br>
  
−
===Applications of BBa_K1632003===
+
=====Results=====
 +
 
 +
[[Image:Tokyo_Tech_fim_switch_TT_FimB_assay_Results.png |thumb|center|700px|<b>Fig. 1. </b>The histograms of the samples measured by flow cytometer]]<br>
 +
 
 +
=====Discussion=====
 +
We tried to confirm that ''fim'' switch(Tokyo_Tech/J23119) is bidirectically inverted in the presence of FimB(wild-type) by using GFP as a reporter, under 4 different concentrations of arabinose. In the medium with 0 M arabinose, we supplemented the medium with 0.5 % glucose in order to repress the leakage in the PBAD/''araC'' promoter. Fig. 2 shows the histograms of the samples measured by the flow cytometer. In the results of the reporter cell (1), when the Induction of FimB(wild-type) expression increases, the fluorescence intensity decreases. From this fact, we confirmed that the fim switch(Tokyo_Tech/J23119) is inverted from [ON] state to [OFF] state by FimB(wild-type). From the result of the reporter cell (2), when the expression amount of FimB(wild-type) increases, the expression amount of GFP in the reporter cell (2) increases. From this fact, we confirmed that the fim switch(Tokyo_Tech/J23119) is inverted from [OFF] state to [ON] state by FimB(wild-type). From the results of the two reporter cells (1) and (2), we successfully confirmed that FimB(wild-type) inverts the fim switch from [ON] state to [OFF] state and from [OFF] state to [ON] state.<br>
 +
The result of the reporter cell (2) shows that when the concentration of arabinose is increased to 0〜20 microM, the fluorescence intensity increases. This shows the function of FimB(wild-type) inverting the ''fim'' switch(wild-type) from [OFF] state to [ON] state. However, when the arabinose concentration is excess (5mM), the fluorescence intensity decreases. According to [1], this is caused by the excess increase of the inversion rate of the ''fim'' switch. When the inversion rate is too high, there is not enough time for transcription initiation. Consequently, the GFP expression decreases.
 +
 
 +
 
 +
<br><br><br><br><br>
 +
 
 +
====Invertion assay with FimE====
 +
 
 +
=====1. Construction=====
 +
 
 +
All the samples were DH5alpha strain with antibiotic resistance to ampicillin and kanamycin.<br>
 +
 
 +
(1) PBAD/''araC''_''fimE''(wild-type) (pSB6A1) + ''fim'' switch[default ON](Tokyo_Tech/J23119)_gfp (pSB3K3) <br>
 +
(2) PBAD/''araC''_''fimE''(wild-type) (pSB6A1) + ''fim'' switch[default OFF](Tokyo_Tech/J23119)_gfp (pSB3K3) <br>
 +
(3) pSB6A1 + ''fim'' switch[default ON](Tokyo_Tech/J23119)_gfp (pSB3K3) …positive control 1<br>
 +
(4) pSB6A1 + ''fim'' switch[default OFF](Tokyo_Tech/J23119)_gfp (pSB3K3) …negative control 1<br>
 +
(5) PBAD/''araC''_''fimE''(wild-type) (pSB6A1) + J23119_gfp (pSB3K3) …positive control 2 <br>
 +
(6) PBAD/''araC''_''fimE''(wild-type) (pSB6A1) + rbs_gfp (pSB3K3) …negative control 2 <br>
 +
 
 +
=====2. Assay protocol=====
 +
 
 +
1. Prepare overnight cultures for each sample in 3 mL of LB medium containing ampicillin (50 microg / mL), kanamycin (30 microg / mL) and glucose (final concentration is 0.5 %) at 37 ℃ for 12h.<br>
 +
2. Make a 1:100 dilution in 3 mL of fresh LB containing Amp, Kan and glucose (final concentration is 0.5 %).<br>
 +
3. Incubate the cells at 37 ℃, shaking at 180 rpm until the observed OD590 reaches 0.4 (Fresh Culture).<br>
 +
4. After the incubation, take 1 mL of the samples, and centrifuge at 5000x g, 1 min, 25 ℃ <br>
 +
5. Remove the supernatant.<br>
 +
6. Suspend the pellet in 1 mL of LB containing Amp and Kan, and centrifuge at 5000x g, 1 min, 25 ℃ <br>
 +
7. Remove the supernatant.<br>
 +
8. Suspend the pellet in 1 mL of LB containing Amp and Kan, and centrifuge at 5000x g, 1 min, 25 ℃ <br>
 +
9. Remove the supernatant.<br>
 +
10. Suspend the pellet in 1mL of LB containing Amp and Kan.<br>
 +
11. Add 30 microL of suspension in the following medium.<br>
 +
<span style="margin-left: 20px;">① 3 mL of LB containing Amp, Kan, glucose (final concentration is 0.5 %) and 30 microL sterile water<br>
 +
<span style="margin-left: 20px;">② 3 mL of LB containing Amp, Kan and 30 microL of 500 mM arabinose (final concentration of arabinose is 5 mM)<br>
 +
12. Incubate the samples at 37 ℃ for 6 hours, shaking at 180 rpm. (Measure the OD590 of all the samples every hour.)<br>
 +
13. After the incubation, take the samples, and centrifuge at 9000x g, 1min, 4℃.<br>
 +
14. Remove the supernatant.<br>
 +
15. Add 1 mL of filtered PBS (phosphate-buffered saline) and suspend. (The ideal of OD is 0.3)<br>
 +
16. Dispense all of each suspension into a disposable tube through a cell strainer.<br>
 +
17. Use flow cytometer to measure the fluorescence of GFP. (We used BD FACSCaliburTM Flow Cytometer of Becton, Dickenson and Company.)<br>
 +
 
 +
=====Results=====
 +
 
 +
[[Image:Tokyo_Tech_fim_switch_TT_FimE_assay_Results.png |thumb|center|700px|<b>Fig. 2. </b>The histograms of the samples measured by flow cytometer]]<br>
 +
 
 +
=====Discussion=====
 +
We tried to confirm that'' fim'' switch(Tokyo_Tech/J23119) is predominantly inverted in the presence of FimE(wild-type) by using GFP as a reporter, under 2 different concentrations of arabinose. In the medium with 0 M arabinose, we supplemented the medium with 0.5 % glucose in order to repress the leakage in the PBAD/''araC'' promoter. Fig.2 shows the histograms of the samples measured by the flow cytometer. In the results of the reporter cell (1), when the induction of FimE(wild-type) expression increases, the fluorescence intensity decreases. From this fact, we confirmed that the ''fim'' switch(Tokyo_Tech/J23119) is inverted from [ON] state to [OFF] state by FimE(wild-type). From the result of reporter cell (2), when the expression amount of FimB(wild-type) increases, the expression amount of GFP in the reporter cell (2) increases. From this fact, we confirmed that the ''fim'' switch(Tokyo_Tech/J23119) is inverted from [OFF] state to [ON] state by FimE(wild-type) that does not invert the''fim'' switch(wild-type) from [OFF] state to [ON] state. From this result, the inversion of ''fim'' switch(Tokyo_Tech/J23119) by FimE was not confirmed correctly. In this assay, the FimE protein inverts ''fim'' switch from [ON] state to [OFF] state and [OFF] state to [ON] state. In other words, the FimE protein works as the FimB protein.
 +
 
 +
===More information===
 +
 
 +
For more information, see [[http://2015.igem.org/Team:Tokyo_Tech/Project Our work in Tokyo_Tech 2015 wiki]],  [[http://2015.igem.org/Team:Tokyo_Tech/Experiment/ssrA_tag_degradation_assay About ssrA-tag]],  [[http://2015.igem.org/Team:Tokyo_Tech/Experiment/Overview_of_fim_inversion_system About ''fim'' inversion system]]
 +
 
 +
===Applications of BBa_K1632002===
  
 
===User Reviews===
 
===User Reviews===
−
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<!-- DON'T DELETE --><partinfo>BBa_K1632002 StartReviews</partinfo>
 
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<partinfo>BBa_K1632003 AddReview number</partinfo>
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<partinfo>BBa_K1632002 AddReview number</partinfo>
 
<I>Username</I>
 
<I>Username</I>
 
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Latest revision as of 03:56, 19 September 2015

Materials and Methods

Invertion assay with FimB

1. Construction

All the samples were DH5alpha strain with antibiotic resistance to ampicillin and kanamycin.

(1) PBAD/araC_fimB(wild-type) (pSB6A1) + fim switch[default ON](Tokyo_Tech/J23119)_gfp (pSB3K3)
(2) PBAD/araC_fimB(wild-type) (pSB6A1) + fim switch[default OFF](Tokyo_Tech/J23119)_gfp (pSB3K3)
(3) pSB6A1 + fim switch[default ON](Tokyo_Tech/J23119)_gfp (pSB3K3) …positive control 1
(4) pSB6A1 + fim switch[default OFF](Tokyo_Tech/J23119)_gfp (pSB3K3) …negative control 1
(5) PBAD/araC_fimB(wild-type) (pSB6A1) + J23119_gfp(pSB3K3) …positive control 2
(6) PBAD/araC_fimB(wild-type) (pSB6A1) + rbs_gfp(pSB3K3) …negative control 2

2. Assay protocol

1. Prepare overnight cultures for each sample in 3 mL of LB medium containing ampicillin (50 microg / mL), kanamycin (30 microg / mL) and glucose (final concentration is 0.5 %) at 37 ℃ for 12h.
2. Make a 1:100 dilution in 3 mL of fresh LB containing Amp, Kan and glucose (final concentration is 0.5 %).
3. Incubate the cells at 37 ℃, shaking at 180 rpm until the observed OD590 reaches 0.4 (Fresh Culture).
4. After the incubation, take 1 mL of the samples, and centrifuge at 5000x g, 1 min, 25 ℃
5. Remove the supernatant.
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.
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.
10. Suspend the pellet in 1 mL of LB containing Amp and Kan.
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 %) 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. Incubate the samples at 37 ℃, shaking at 180 rpm for 6.5 hours. (Measure OD590 of all the samples every hour.)
13. After the incubation, take the samples, and centrifuge at 9000x g, 1min, 4℃.
14. Remove the supernatant.
15. Add 1 mL of filtered PBS (phosphate-buffered saline) and suspend. (The ideal of OD is 0.3)
16. Dispense all of each suspension into a disposable tube through a cell strainer.
17. Use flow cytometer to measure the fluorescence of GFP. (We used BD FACSCaliburTM Flow Cytometer of Becton, Dickenson and Company.)

Results
Fig. 1. The histograms of the samples measured by flow cytometer

Discussion

We tried to confirm that fim switch(Tokyo_Tech/J23119) is bidirectically inverted in the presence of FimB(wild-type) by using GFP as a reporter, under 4 different concentrations of arabinose. In the medium with 0 M arabinose, we supplemented the medium with 0.5 % glucose in order to repress the leakage in the PBAD/araC promoter. Fig. 2 shows the histograms of the samples measured by the flow cytometer. In the results of the reporter cell (1), when the Induction of FimB(wild-type) expression increases, the fluorescence intensity decreases. From this fact, we confirmed that the fim switch(Tokyo_Tech/J23119) is inverted from [ON] state to [OFF] state by FimB(wild-type). From the result of the reporter cell (2), when the expression amount of FimB(wild-type) increases, the expression amount of GFP in the reporter cell (2) increases. From this fact, we confirmed that the fim switch(Tokyo_Tech/J23119) is inverted from [OFF] state to [ON] state by FimB(wild-type). From the results of the two reporter cells (1) and (2), we successfully confirmed that FimB(wild-type) inverts the fim switch from [ON] state to [OFF] state and from [OFF] state to [ON] state.
The result of the reporter cell (2) shows that when the concentration of arabinose is increased to 0〜20 microM, the fluorescence intensity increases. This shows the function of FimB(wild-type) inverting the fim switch(wild-type) from [OFF] state to [ON] state. However, when the arabinose concentration is excess (5mM), the fluorescence intensity decreases. According to [1], this is caused by the excess increase of the inversion rate of the fim switch. When the inversion rate is too high, there is not enough time for transcription initiation. Consequently, the GFP expression decreases.







Invertion assay with FimE

1. Construction

All the samples were DH5alpha strain with antibiotic resistance to ampicillin and kanamycin.

(1) PBAD/araC_fimE(wild-type) (pSB6A1) + fim switch[default ON](Tokyo_Tech/J23119)_gfp (pSB3K3)
(2) PBAD/araC_fimE(wild-type) (pSB6A1) + fim switch[default OFF](Tokyo_Tech/J23119)_gfp (pSB3K3)
(3) pSB6A1 + fim switch[default ON](Tokyo_Tech/J23119)_gfp (pSB3K3) …positive control 1
(4) pSB6A1 + fim switch[default OFF](Tokyo_Tech/J23119)_gfp (pSB3K3) …negative control 1
(5) PBAD/araC_fimE(wild-type) (pSB6A1) + J23119_gfp (pSB3K3) …positive control 2
(6) PBAD/araC_fimE(wild-type) (pSB6A1) + rbs_gfp (pSB3K3) …negative control 2

2. Assay protocol

1. Prepare overnight cultures for each sample in 3 mL of LB medium containing ampicillin (50 microg / mL), kanamycin (30 microg / mL) and glucose (final concentration is 0.5 %) at 37 ℃ for 12h.
2. Make a 1:100 dilution in 3 mL of fresh LB containing Amp, Kan and glucose (final concentration is 0.5 %).
3. Incubate the cells at 37 ℃, shaking at 180 rpm until the observed OD590 reaches 0.4 (Fresh Culture).
4. After the incubation, take 1 mL of the samples, and centrifuge at 5000x g, 1 min, 25 ℃
5. Remove the supernatant.
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.
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.
10. Suspend the pellet in 1mL of LB containing Amp and Kan.
11. Add 30 microL of suspension in the following medium.
① 3 mL of LB containing Amp, Kan, glucose (final concentration is 0.5 %) and 30 microL sterile water
② 3 mL of LB containing Amp, Kan and 30 microL of 500 mM arabinose (final concentration of arabinose is 5 mM)
12. Incubate the samples at 37 ℃ for 6 hours, shaking at 180 rpm. (Measure the OD590 of all the samples every hour.)
13. After the incubation, take the samples, and centrifuge at 9000x g, 1min, 4℃.
14. Remove the supernatant.
15. Add 1 mL of filtered PBS (phosphate-buffered saline) and suspend. (The ideal of OD is 0.3)
16. Dispense all of each suspension into a disposable tube through a cell strainer.
17. Use flow cytometer to measure the fluorescence of GFP. (We used BD FACSCaliburTM Flow Cytometer of Becton, Dickenson and Company.)

Results
Fig. 2. The histograms of the samples measured by flow cytometer

Discussion

We tried to confirm that fim switch(Tokyo_Tech/J23119) is predominantly inverted in the presence of FimE(wild-type) by using GFP as a reporter, under 2 different concentrations of arabinose. In the medium with 0 M arabinose, we supplemented the medium with 0.5 % glucose in order to repress the leakage in the PBAD/araC promoter. Fig.2 shows the histograms of the samples measured by the flow cytometer. In the results of the reporter cell (1), when the induction of FimE(wild-type) expression increases, the fluorescence intensity decreases. From this fact, we confirmed that the fim switch(Tokyo_Tech/J23119) is inverted from [ON] state to [OFF] state by FimE(wild-type). From the result of reporter cell (2), when the expression amount of FimB(wild-type) increases, the expression amount of GFP in the reporter cell (2) increases. From this fact, we confirmed that the fim switch(Tokyo_Tech/J23119) is inverted from [OFF] state to [ON] state by FimE(wild-type) that does not invert thefim switch(wild-type) from [OFF] state to [ON] state. From this result, the inversion of fim switch(Tokyo_Tech/J23119) by FimE was not confirmed correctly. In this assay, the FimE protein inverts fim switch from [ON] state to [OFF] state and [OFF] state to [ON] state. In other words, the FimE protein works as the FimB protein.

More information

For more information, see http://2015.igem.org/Team:Tokyo_Tech/Project Our work in Tokyo_Tech 2015 wiki, http://2015.igem.org/Team:Tokyo_Tech/Experiment/ssrA_tag_degradation_assay About ssrA-tag, http://2015.igem.org/Team:Tokyo_Tech/Experiment/Overview_of_fim_inversion_system About ''fim'' inversion system

Applications of BBa_K1632002

User Reviews

UNIQ566b3351853d7dfe-partinfo-00000000-QINU UNIQ566b3351853d7dfe-partinfo-00000001-QINU