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| <li><a href="https://2014.igem.org/Team:Tokyo_Tech/Experiment/C4HSL-dependent_3OC12HSL_production" style="width:400px; margin-left:-135px;">C4HSL-dependent 3OC12HSL production</a></li> | | <li><a href="https://2014.igem.org/Team:Tokyo_Tech/Experiment/C4HSL-dependent_3OC12HSL_production" style="width:400px; margin-left:-135px;">C4HSL-dependent 3OC12HSL production</a></li> |
| <li><a href="https://2014.igem.org/Team:Tokyo_Tech/Experiment/3OC12HSL-dependent_C4HSL_production" style="width:400px; margin-left:-135px;">3OC12HSL-dependent C4HSL production</a></li> | | <li><a href="https://2014.igem.org/Team:Tokyo_Tech/Experiment/3OC12HSL-dependent_C4HSL_production" style="width:400px; margin-left:-135px;">3OC12HSL-dependent C4HSL production</a></li> |
- | <li><a href="https://2014.igem.org/Team:Tokyo_Tech/Experiment/Symbiosis_confirmation_by_co-culture" style="width:400px; margin-left:-135px;">Symbiosis confirmation by co-culture </a></li> | + | <li><a href="https://2014.igem.org/Team:Tokyo_Tech/Experiment/Symbiosis_confirmation_by_co-culture" style="width:400px; margin-left:-135px;">Mutualism Confirmation ~Co-culture Assay~</a></li> |
| </ul> | | </ul> |
| </li> | | </li> |
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| <p align="center"><span class="title-small">Contents</span></p> | | <p align="center"><span class="title-small">Contents</span></p> |
| <p align="left" class="info-24"><a href="#Introduction">1. Introduction </a></p> | | <p align="left" class="info-24"><a href="#Introduction">1. Introduction </a></p> |
- | <p align="left" class="info-24"><a href="#Summary">2. Summary of the experiments</a></p> | + | <p align="left" class="info-24"><a href="#Summary">2. Summary of the Experiments</a></p> |
| <p align="left" class="info-18"><a href="#Summary">2-1. 3OC12HSL-dependent CmR expression</a></p> | | <p align="left" class="info-18"><a href="#Summary">2-1. 3OC12HSL-dependent CmR expression</a></p> |
| <p align="left" class="info-18"><a href="#2.2">2-2. 3OC12HSL-dependent C4HSL production</a></p> | | <p align="left" class="info-18"><a href="#2.2">2-2. 3OC12HSL-dependent C4HSL production</a></p> |
| <p align="left" class="info-24"><a href="#Results">3. Results </a></p> | | <p align="left" class="info-24"><a href="#Results">3. Results </a></p> |
- | <p align="left" class="info-18"><a href="#Results">3.1. 3OC12HSL-depemdent CmR expression</a></p> | + | <p align="left" class="info-18"><a href="#Results">3.1. 3OC12HSL-dependent CmR expression</a></p> |
| <p align="left" class="info-18"><a href="#3.2">3.2. 3OC12HSL-dependent C4HSL production</a></p> | | <p align="left" class="info-18"><a href="#3.2">3.2. 3OC12HSL-dependent C4HSL production</a></p> |
- | <p align="left" class="info-24"><a href="#Materials">4. Materials and methods</a></p> | + | <p align="left" class="info-24"><a href="#Materials">4. Materials and Methods</a></p> |
| <p align="left" class="info-18"><a href="#4.1">4.1. Construction</a></p> | | <p align="left" class="info-18"><a href="#4.1">4.1. Construction</a></p> |
| <p align="left" class="info-18"><a href="#4.2">4.2. Assay Protocol </a></p> | | <p align="left" class="info-18"><a href="#4.2">4.2. Assay Protocol </a></p> |
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| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td><p class="info-18">We designed signal-dependent signal production in our system by using signaling molecules and antibiotics resistance gene. In our bank story, we used signaling molecules 3OC12HSL as products.</p></td> | + | <td><p class="info-18">We designed a signal-dependent signal production in our system by using signaling molecules and antibiotics resistance gene. In our bank story, we used signaling molecule 3OC12HSL as product.</p></td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td><p class="info-18">For construction of the 3OC12HSL-dependent chloramphenicol resistance (CmR) and C4HSL production module, we constructed a new part Plux-CmR-RhlI (<a href="http://parts.igem.org/Part:BBa_K1529797">BBa_K1529797</a>). Plux-CmR-RhlI cell is an engineered E. coli that contains a 3OC12HSL-dependent RhlI generator and a constitutive LuxR generator. As a constitutive LuxR generator, we used Ptet-LuxR. In our bank story, this part imitates the function of Customer. (Fig. 3-4-1-1.) We confirmed that 3OC12HSL-dependent growth by measuring the optical density, and 3OC12HSL-dependent C4HSL production by using reporter cell.</p></td> | + | <td><p class="info-18">For construction of the 3OC12HSL-dependent chloramphenicol resistance gene product(CmR) and C4HSL production module, we constructed a new part Plux-CmR-RhlI (<a href="http://parts.igem.org/Part:BBa_K1529797">BBa_K1529797</a>). Plux-CmR-RhlI cell is an engineered <i>E. coli</i> that contains 3OC12HSL-dependent RhlI generator and a constitutive LuxR generator. As a constitutive LuxR generator, we used Ptet-LuxR. In our bank story, this part imitates the function of Customer. (Fig. 3-4-1-1) We confirmed the 3OC12HSL-dependent growth by measuring the optical density, and 3OC12HSL-dependent C4HSL production by using reporter cell.</p></td> |
| </tr> | | </tr> |
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| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td><div align="center"><strong>Fig. 3-4-1-1. </strong>Genetic Circuit of Customer <i>E. coli</i></div></td> | + | <td><div align="center"><strong>Fig. 3-4-1-1. </strong>Genetic Circuit of Customer</div></td> |
| </tr> | | </tr> |
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| <td> </td> | | <td> </td> |
| </tr> | | </tr> |
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| </tr> | | </tr> |
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- | <td><div align="center"> <strong>Fig. 3-4-2-1.</strong> 3OC12HSL-dependent CmR expression assay Flow Chart </div></td> | + | <td><div align="center"> <strong>Fig. 3-4-2-1.</strong> 3OC12HSL-dependent CmR expression assay flow chart </div></td> |
| </tr><tr> | | </tr><tr> |
- | <td><p class="info-18">We confirmed the function of 3OC12HSL-dependent CmR expression by measuring optical density of the cell cultures containing chloramphenicol. </p> | + | <td><p class="info-18">We confirmed the function of 3OC12HSL-dependent CmR expression by measuring the optical density of the cell cultures containing chloramphenicol.(Fig. 3-4-2-1) </p> |
- | <p class="info-18"> In this experiment we prepared two plasmids, A and B. (See Fig. 3-4-2-2.) Right after the 3OC12HSL induction, we added chloramphenicol into the medium containing Customer cell. We measured optical density for about 8 h to estimate the concentration of the cell. </p> | + | <p class="info-18"> In this experiment, we prepared two plasmids A and B (See Fig. 3-4-2-2).Right after the 3OC12HSL induction, we added chloramphenicol into the medium including Customer cell. We measured the optical density for about eight hours to estimate the concentration of the cell. </p> |
| </td> | | </td> |
| </tr> | | </tr> |
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| </tr> | | </tr> |
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- | <td><div align="center"><strong>Fig. 3-4-2-3.</strong> 3OC12HSL-dependent C4HSL production assay Flow Chart</div></td> | + | <td><div align="center"><strong>Fig. 3-4-2-3.</strong> 3OC12HSL-dependent C4HSL production assay flow chart</div></td> |
| </tr> | | </tr> |
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- | <td><p class="info-18">We performed a reporter assay by using reporter cell C, D and E to characterize the function of 3OC12HSL-dependent C4HSL production. Plux-CmR-RhlI cell containing constitutive LuxR generator express RhlI and produce C4HSL (RhlI) in the presence of 3OC12HSL. Since C4HSL is excreted to the culture, the supernatant of the sender cell contains C4HSL when the part works as expected.</td> | + | <td><p class="info-18">We performed a reporter assay by using reporter cell C, D and E to characterize the function of 3OC12HSL-dependent C4HSL production. Plux-CmR-RhlI cell containing constitutive LuxR generator expresses RhlI and produces C4HSL (RhlI) in the presence of 3OC12HSL. Since C4HSL is excreted to the culture, the supernatant of the sender cell contains C4HSL when this part works as expected.</td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td><p class="info-18"> Reporter cells was incubated in the supernatant of the culture of sender cell. When there are C4HSL in the supernatant, reporter cell expresses GFP. We checked the fluorescence intensity of reporter cell to confirm of the production of C4HSL.The fluorescence intensity of the reporter cell was measured by Flow Cytometer.</p></td> | + | <td><p class="info-18"> The reporter cell was incubated in the supernatant of the culture of the sender cell. When there are C4HSL in the supernatant, the reporter cell expresses GFP.(Fig. 3-4-2-3) We checked the fluorescence intensity of the reporter cell to confirm the production of C4HSL. The fluorescence intensity of the reporter cell was measured by flow cytometer.</p></td> |
| </tr> | | </tr> |
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- | <td><p class="info-18">We prepared the following conditions for the induction of reporter cells. (PlacIq-CmR cell was used as the negative control of RhlI.)</p></td> | + | <td><p class="info-18">We prepared the following conditions for the induction of the reporter cells. (PlacIq-CmR cell was used as the negative control of RhlI. See Fig.3-4-2-4)</p></td> |
| </tr> | | </tr> |
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- | <td class="info-18">(1)Culture containing sender A (Plux-CmR-RhlI) with 3OC12HSL induction</td> | + | <td class="info-18">(1) Culture containing sender A (Plux-CmR-RhlI) with 3OC12HSL induction</td> |
| </tr> | | </tr> |
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- | <td class="info-18">(4)Culture containing sender B (PlacIq-CmR) without induction </td> | + | <td class="info-18">(4) Culture containing sender B (PlacIq-CmR) without induction </td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td class="info-18">(5)5 microM of artificial C4HSL in LB medium </td> | + | <td class="info-18">(5)5 microM of synthetic C4HSL in LB medium </td> |
| </tr> | | </tr> |
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- | <td class="info-18">(6)DMSO in LB medium </td> | + | <td class="info-18">(6) DMSO in LB medium </td> |
| </tr> | | </tr> |
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- | <td><h1>3-1. 3OC12HSL-depemdent CmR expression assay</h1></td> | + | <td><h1>3-1. 3OC12HSL-dependent CmR expression assay</h1></td> |
| </tr> | | </tr> |
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| <td><p class="info-18">We tested two types of culture condition which contains different concentration of chloramphenicol(Cm). (0 and 100 microg / mL)</p> | | <td><p class="info-18">We tested two types of culture condition which contains different concentration of chloramphenicol(Cm). (0 and 100 microg / mL)</p> |
- | <p class="info-18"><strong>Fig.3-4-3-1.</strong> and <strong>Fig.3-4-3-2.</strong>show the condition in the absence and the presence of chloramphenicol, respectively.</p> | + | <p class="info-18">Fig. 3-4-3-1 and Fig. 3-4-3-2 show the condition in the absence and the presence of chloramphenicol, respectively.</p> |
- | <p class="info-18"><strong>Fig.3-4-3-1.</strong> shows that every cell can grow in the absence of chloramphenicol.</p></td> | + | <p class="info-18">Fig. 3-4-3-1 shows that every cell can grow in the absence of chloramphenicol.</p></td> |
| </tr> | | </tr> |
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| </tr> | | </tr> |
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- | <td><div align="center"><strong>Fig.3-4-3-2.</strong> 3OC12HSL-dependent Customer growth in 100 microg / mL chloramphenicol</div></td> | + | <td><div align="center"><strong>Fig. 3-4-3-2.</strong> 3OC12HSL-dependent Customer growth in 100 microg / mL chloramphenicol</div></td> |
| </tr> | | </tr> |
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- | <td><p class="info-18">On the other hand, in the presence of chloramphenicol, the cell containing Plux-CmR-RhlI can grow only when induced by 3OC12HSL. Without the induction of 3OC12HSL, the cell cannot express CmR and cannot grow in the presence of chloramphenicol. As a result, we confirmed that Plux-CmR-RhlI expressed CmR when induced by 3OC12HSL as expected.</p></td> | + | <td><p class="info-18">On the other hand, in the presence of chloramphenicol, the cell containing Plux-CmR-RhlI can grow only when it was induced by 3OC12HSL. Without the induction of 3OC12HSL, the cell cannot express CmR and cannot grow in the presence of chloramphenicol. As a result, we confirmed that Plux-CmR-RhlI expressed CmR when induced by 3OC12HSL as expected.</p></td> |
| </tr> | | </tr> |
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- | <td><p class="info-18"><strong>Fig. 3-4-3-3.</strong>shows the fluorescence intensities generated by reporter cells. When the reporter cell C (Plux-CmR-RhlI) was incubated in the condition (1) (the culture of the induced Customer cell), the fluorescence intensity of the reporter cell increased. Comparing the results of condition (1) and (2), reporter cell in the supernatant of (1) had 95-fold higher fluorescence intensity.</p> | + | <td><p class="info-18">Fig. 3-4-3-3 shows the fluorescence intensities generated by reporter cells. When the reporter cell C (Plux-CmR-RhlI) was incubated in the condition (1) (the culture of the induced Customer cell), the fluorescence intensity of the reporter cell increased. Comparing the results of condition (1) and (2), reporter cell in the supernatant of (1) had 95-fold higher fluorescence intensity.</p> |
| <p class="info-18">This result indicates that Customer cell produced C4HSL in response to 3OC12HSL induction by the function of Plux-CmR-RhlI.</p> | | <p class="info-18">This result indicates that Customer cell produced C4HSL in response to 3OC12HSL induction by the function of Plux-CmR-RhlI.</p> |
| <p class="info-18">From this experiment, we confirmed that a new part Plux-CmR-RhlI synthesized C4HSL (RhlI) as expected.</p></td> | | <p class="info-18">From this experiment, we confirmed that a new part Plux-CmR-RhlI synthesized C4HSL (RhlI) as expected.</p></td> |
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- | <td><div align="center"><strong>Fig.3-4-3-3.</strong> Customer excretes C4HSL when C12HSL exists</div></td> | + | <td><div align="center"><strong>Fig. 3-4-3-3.</strong> Customer excretes C4HSL when C12HSL exists</div></td> |
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- | <td><div align="center"><a href="https://2014.igem.org/File:Tokyo_Tech_3-4-4-1.png"><img src="https://static.igem.org/mediawiki/2014/5/5f/Tokyo_Tech_3-4-4-1.png" width="500" height="86" /></a></div></td> | + | <td><div align="center"><a href="https://2014.igem.org/File:Tokyo_Tech_3-4-4-1.png"><img src="https://static.igem.org/mediawiki/2014/5/5f/Tokyo_Tech_3-4-4-1.png" width="500" /></a></div></td> |
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- | <td><div align="center"> <strong>Fig. 3-4-4-1. </strong></div></td> | + | <td><div align="center"> <strong>Fig. 3-4-4-1. </strong></div></td> |
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- | <td><div align="center"><a href="https://2014.igem.org/File:Tokyo_Tech_3-4-4-2.png"><img src="https://static.igem.org/mediawiki/2014/7/74/Tokyo_Tech_3-4-4-2.png" width="500" height="86" /></a></div></td> | + | <td><div align="center"><a href="https://2014.igem.org/File:Tokyo_Tech_3-4-4-2.png"><img src="https://static.igem.org/mediawiki/2014/7/74/Tokyo_Tech_3-4-4-2.png" width="500" /></a></div></td> |
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- | <td><div align="center"><a href="https://2014.igem.org/File:Tokyo_Tech_3-4-4-3.png"><img src="https://static.igem.org/mediawiki/2014/8/88/Tokyo_Tech_3-4-4-3.png" width="500" height="86" /></a></div></td> | + | <td><div align="center"><a href="https://2014.igem.org/File:Tokyo_Tech_3-4-4-3.png"><img src="https://static.igem.org/mediawiki/2014/8/88/Tokyo_Tech_3-4-4-3.png" width="500" /></a></div></td> |
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- | <td><div align="center"><a href="https://2014.igem.org/File:Tokyo_Tech_3-4-4-4.png"><img src="https://static.igem.org/mediawiki/2014/8/8b/Tokyo_Tech_3-4-4-4.png" width="500" height="86" /></a></div></td> | + | <td><div align="center"><a href="https://2014.igem.org/File:Tokyo_Tech_3-4-4-4.png"><img src="https://static.igem.org/mediawiki/2014/8/8b/Tokyo_Tech_3-4-4-4.png" width="500" /></a></div></td> |
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- | <td><div align="center"><a href="https://2014.igem.org/File:Tokyo_Tech_3-4-4-5.png"><img src="https://static.igem.org/mediawiki/2014/b/b7/Tokyo_Tech_3-4-4-5.png" width="500" height="122" /></a></div></td> | + | <td><div align="center"><a href="https://2014.igem.org/File:Tokyo_Tech_3-4-4-5.png"><img src="https://static.igem.org/mediawiki/2014/b/b7/Tokyo_Tech_3-4-4-5.png" width="500" /></a></div></td> |
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- | <td><div align="center"><strong>Fig. 3-3-4-5.</strong></div></td> | + | <td><div align="center"><strong>Fig. 3-4-4-5.</strong></div></td> |
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- | <td><div align="center"><a href="https://2014.igem.org/File:Tokyo_Tech_3-4-4-6.png"><img src="https://static.igem.org/mediawiki/2014/a/a8/Tokyo_Tech_3-4-4-6.png" width="500" height="122" /></a></div></td> | + | <td><div align="center"><a href="https://2014.igem.org/File:Tokyo_Tech_3-4-4-6.png"><img src="https://static.igem.org/mediawiki/2014/a/a8/Tokyo_Tech_3-4-4-6.png" width="500" /></a></div></td> |
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- | <td><div align="center"><a href="https://2014.igem.org/File:Tokyo_Tech_3-4-4-7.png"><img src="https://static.igem.org/mediawiki/2014/b/b3/Tokyo_Tech_3-4-4-7.png" width="500" height="125" /></a></div></td> | + | <td><div align="center"><a href="https://2014.igem.org/File:Tokyo_Tech_3-4-4-7.png"><img src="https://static.igem.org/mediawiki/2014/b/b3/Tokyo_Tech_3-4-4-7.png" width="500" /></a></div></td> |
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- | <td><div align="center">Fig. 3-4-4-7.</div></td> | + | <td><div align="center"><strong>Fig. 3-4-4-7.</strong></div></td> |
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- | <td class="info-18"> 1) 3 mL of LB containing Amp and Kan + 30 microL C4HSL (final concentration is 500 microM)</td> | + | <td colspan="2" class="info-18" style="text-indent:50px;">1) 3 mL of LB containing Amp and Kan + 30 microL C4HSL (final concentration is 500 microM)</td> |
| </tr> | | </tr> |
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- | <td class="info-18"> 2) 3 mL of LB containing Amp and Kan + 30 microL DMSO</td> | + | <td colspan="2" class="info-18" style="text-indent:50px;">2) 3 mL of LB containing Amp and Kan + 30 microL DMSO</td> |
| </tr> | | </tr> |
| | | |
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- | <td class="info-18"> 3) 3 mL of LB containing Amp, Kan and Cm (final concentration is 100microg / mL) + 30 microL C4HSL (final concentration is 500 microM)</td> | + | <td colspan="2" class="info-18" style="text-indent:50px;">3) 3 mL of LB containing Amp, Kan and Cm (final concentration is 100microg / mL) + 30 microL C4HSL (final concentration is 500 microM)</td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td class="info-18"> 4) 3 mL of LB containing Amp, Kan and Cm (final concentration is 100microg / mL) + 30 microL DMSO</td> | + | <td colspan="2" class="info-18" style="text-indent:50px;">4) 3 mL of LB containing Amp, Kan and Cm (final concentration is 100microg / mL) + 30 microL DMSO</td> |
| </tr> | | </tr> |
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- | <td class="info-18"> a) Add 30 microL of 500 microM 3OC12HSL to 3 mL LB containing Amp and Kan</td> | + | <td colspan="2" class="info-18" style="text-indent:50px;">a) Add 30 microL of 500 microM 3OC12HSL to 3 mL LB containing Amp and Kan</td> |
| </tr> | | </tr> |
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- | <td class="info-18"> b) Add 30 microL DMSO to 3 mL LB containing Amp and Kan</td> | + | <td colspan="2" class="info-18" style="text-indent:50px;">b) Add 30 microL DMSO to 3 mL LB containing Amp and Kan</td> |
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| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td class="info-18"> 1) 2.7 mL filtrate of Aa +300 microL LB</td> | + | <td colspan="2" class="info-18" style="text-indent:50px;">1) 2.7 mL filtrate of Aa +300 microL LB</td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td class="info-18"> 2) 2.7 mL filtrate of Ab +300 microL LB</td> | + | <td colspan="2" class="info-18" style="text-indent:50px;">2) 2.7 mL filtrate of Ab +300 microL LB</td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td class="info-18"> 3) 2.7 mL filtrate of Ba +300 microL LB</td> | + | <td colspan="2" class="info-18" style="text-indent:50px;">3) 2.7 mL filtrate of Ba +300 microL LB</td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td class="info-18"> 4) 2.7 mL filtrate of Bb +300 microL LB</td> | + | <td colspan="2" class="info-18" style="text-indent:50px;">4) 2.7 mL filtrate of Bb +300 microL LB</td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td class="info-18"> 5) 3 mL LB + 500 microM C4HSL 30 microM (final concentration is 5 microM)</td> | + | <td colspan="2" class="info-18" style="text-indent:50px;">5) 3 mL LB + 500 microM C4HSL 30 microM (final concentration is 5 microM)</td> |
| </tr> | | </tr> |
| <tr> | | <tr> |
- | <td class="info-18"> 6) 3 mL LB + DMSO 30 microL</td> | + | <td colspan="2" class="info-18" style="text-indent:50px;">6) 3 mL LB + DMSO 30 microL</td> |
| </tr> | | </tr> |
| <tr> | | <tr> |