Team:WashU StLouis/Project/nif
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+ | |||
+ | <div class="floating-menu"> | ||
+ | <h3>Home</h3> | ||
+ | <a href="#1">Introduction</a> | ||
+ | <a href="#2">Overview</a> | ||
+ | <a href="#3">Phase 1</a> | ||
+ | <a href="#4">Phase 2</a> | ||
+ | <a href="#5">Phase 3</a> | ||
+ | <a href="#6">Results</a> | ||
+ | <a href="#7">Citation</a> | ||
+ | </div> | ||
<!-- here ends the section that changes the default wiki template to a white full width background --> | <!-- here ends the section that changes the default wiki template to a white full width background --> | ||
- | <table | + | <!-- beginning of your page --> |
+ | |||
+ | <!--float-menu --> | ||
+ | |||
+ | <table | ||
+ | style="text-align: left; width: 80%; margin-left: auto; margin-right: auto;" | ||
border="0" cellpadding="5" cellspacing="5"> | border="0" cellpadding="5" cellspacing="5"> | ||
+ | <tbody> | ||
<tr> | <tr> | ||
- | <td | + | <td style="vertical-align: top;"> |
- | + | ||
- | + | ||
<div style="text-align: center;"> | <div style="text-align: center;"> | ||
- | <h1> | + | <h1>Transferring the <span style="font-style: italic;">nif</span> |
+ | cluster from <span style="font-style: italic;">Cyanothece </span>sp. | ||
+ | 51142 into <span style="font-style: italic;">Escherichia coli</span></h1> | ||
+ | Caroline Focht, Richard Hongyi Li<br><a name="1"></a> | ||
+ | <h3>Introduction</h3> | ||
</div> | </div> | ||
Nitrogen is abundant in the earth’s atmosphere but, unlike carbon, | Nitrogen is abundant in the earth’s atmosphere but, unlike carbon, | ||
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<br> | <br> | ||
<div style="text-align: center;"> | <div style="text-align: center;"> | ||
- | < | + | <h3>Objectives</h3> |
</div> | </div> | ||
Rapidly growing, with high survival rate in environment, <span | Rapidly growing, with high survival rate in environment, <span | ||
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of our team. <br> | of our team. <br> | ||
<br> | <br> | ||
- | <div style="text-align: center;"> | + | <div style="text-align: center;"><a name="2"></a> |
- | < | + | <h3>Overview</h3> |
</div> | </div> | ||
Our project consisted of three different phases. <br> | Our project consisted of three different phases. <br> | ||
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style="font-style: italic;">E. coli</span> strains<br> | style="font-style: italic;">E. coli</span> strains<br> | ||
Phase 2: Determine the optimal conditions for cell survival with | Phase 2: Determine the optimal conditions for cell survival with | ||
- | plasmid pNif51142 in <span style="font-style: italic;">E. coli</span><br> | + | plasmid pNif51142 in <span style="font-style: italic;">E. coli</span><br>< |
Phase 3: Measure nitrogen fixation activity under determined optimal | Phase 3: Measure nitrogen fixation activity under determined optimal | ||
conditions in <span style="font-style: italic;">E. coli</span> strains<br> | conditions in <span style="font-style: italic;">E. coli</span> strains<br> | ||
<br> | <br> | ||
- | <br> | + | <br><a name="3"></a> |
<div style="text-align: center; font-weight: bold;">Phase 1: | <div style="text-align: center; font-weight: bold;">Phase 1: | ||
Electro-Transformation of plasmid pNif51142 into <span | Electro-Transformation of plasmid pNif51142 into <span | ||
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<br> | <br> | ||
<table | <table | ||
- | style="text-align: left; width: | + | style="text-align: left; width: 100%; margin-left: auto; margin-right: auto; height: 551px;" |
border="0" cellpadding="5" cellspacing="5"> | border="0" cellpadding="5" cellspacing="5"> | ||
<tbody> | <tbody> | ||
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all the necessary genes for nitrogen fixation<br> | all the necessary genes for nitrogen fixation<br> | ||
</td> | </td> | ||
- | <td style="vertical-align: middle; text-align: justify;">Due to | + | <td style="vertical-align: middle; text-align: justify;">Due |
+ | to | ||
the large size of the plasmid pNif51142, 37,630bp, it was very | the large size of the plasmid pNif51142, 37,630bp, it was very | ||
challenging to transform it into E. coli strains. <br> | challenging to transform it into E. coli strains. <br> | ||
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</tbody> | </tbody> | ||
</table> | </table> | ||
- | <br> | + | <br><a name="4"></a> |
<div style="text-align: center;"><span style="font-weight: bold;">Phase | <div style="text-align: center;"><span style="font-weight: bold;">Phase | ||
2: Determine the optimal conditions for cell survival with plasmid | 2: Determine the optimal conditions for cell survival with plasmid | ||
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<span style="font-weight: bold;">Strains | <span style="font-weight: bold;">Strains | ||
of <span style="font-style: italic;">E. coli</span></span>: JM109, | of <span style="font-style: italic;">E. coli</span></span>: JM109, | ||
- | BL21(DE3), WM1788, DH5α <br> | + | BL21(DE3), WM1788, Top 10 DH5α <br> |
<br> | <br> | ||
<table | <table | ||
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<tbody> | <tbody> | ||
<tr> | <tr> | ||
- | <td | + | <td>Target<br> |
Strain <br> | Strain <br> | ||
</td> | </td> | ||
- | <td | + | <td>JM109 <br> |
</td> | </td> | ||
- | <td | + | <td>BL21(DE3) <br> |
</td> | </td> | ||
- | <td | + | <td>WM1788</td> |
- | <td | + | <td>Top 10<br> |
+ | </td> | ||
+ | <td>DH5α</td> | ||
</tr> | </tr> | ||
<tr> | <tr> | ||
- | <td | + | <td>Experimental Plates <br> |
</td> | </td> | ||
- | <td | + | <td>JM 109 strain w/ plasmid<br> |
<br> | <br> | ||
Antibiotic <br> | Antibiotic <br> | ||
</td> | </td> | ||
- | <td | + | <td>BL21(DE3) strain w/ plasmid<br> |
<br> | <br> | ||
Antibiotic</td> | Antibiotic</td> | ||
- | <td | + | <td>WM1788 strain w/ plasmid<br> |
<br> | <br> | ||
Antibiotic <br> | Antibiotic <br> | ||
</td> | </td> | ||
- | <td | + | <td>Top 10 strain w/ plasmid<br> |
+ | <br> | ||
+ | Antibiotic<br> | ||
+ | </td> | ||
+ | <td>DH5α strain w/ plasmid<br> | ||
<br> | <br> | ||
Antibiotic</td> | Antibiotic</td> | ||
</tr> | </tr> | ||
<tr> | <tr> | ||
- | <td | + | <td>Positive Control</td> |
- | <td | + | <td>JM 109 strain w/o plasmid<br> |
<br> | <br> | ||
No antibiotic</td> | No antibiotic</td> | ||
- | <td | + | <td>BL21(DE3) strain w/o plasmid<br> |
<br> | <br> | ||
No antibiotic</td> | No antibiotic</td> | ||
- | <td | + | <td> WM1788 strain w/o plasmid<br> |
<br> | <br> | ||
No antibiotic</td> | No antibiotic</td> | ||
- | <td | + | <td>Top 10 straing w/o plasmid<br> |
+ | <br> | ||
+ | No Antibiotic<br> | ||
+ | </td> | ||
+ | <td>DH5α strain w/o plasmid<br> | ||
<br> | <br> | ||
No antibiotic</td> | No antibiotic</td> | ||
</tr> | </tr> | ||
<tr> | <tr> | ||
- | <td | + | <td>Negative Control <br> |
</td> | </td> | ||
- | <td | + | <td> JM 109 strain w/o plasmid<br> |
<br> | <br> | ||
Antibiotic</td> | Antibiotic</td> | ||
- | <td | + | <td>BL21(DE3) strain w/o |
+ | plasmid <br> | ||
<br> | <br> | ||
Antibiotic</td> | Antibiotic</td> | ||
- | <td | + | <td>WM1788 strain w/o plasmid<br> |
<br> | <br> | ||
Antibiotic</td> | Antibiotic</td> | ||
- | <td | + | <td>Top 10 strain w/o plasmid<br> |
+ | <br> | ||
+ | Antibiotic<br> | ||
+ | </td> | ||
+ | <td>DH5α strain w/out plasmid<br> | ||
<br> | <br> | ||
Antibiotic</td> | Antibiotic</td> | ||
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</tbody> | </tbody> | ||
</table> | </table> | ||
- | < | + | <div style="text-align: center;"> |
<table | <table | ||
- | style="text-align: left; width: | + | style="text-align: left; width: 100%; margin-left: auto; margin-right: auto;" |
border="0" cellpadding="5" cellspacing="5"> | border="0" cellpadding="5" cellspacing="5"> | ||
<tbody> | <tbody> | ||
<tr> | <tr> | ||
- | <td style="vertical-align: top; | + | <td style="vertical-align: top; width: 70%;"><img |
- | style="width: | + | style="width: 100%;" alt="Nitrogenase Poisoning" |
- | src="https://static.igem.org/mediawiki/2014/ | + | src="https://static.igem.org/mediawiki/2014/e/e1/WashU_Nitrogenase_Poisoning.jpg"> |
+ | Figure above modified from [5]: The nitrogenase enzyme is deactivated | ||
+ | in the presence of oxygen</td> | ||
+ | <td style="vertical-align: top; width: 30%;"><img | ||
+ | style="width: 100%;" | ||
+ | alt="Bottles of LB media used for culturing strains" | ||
+ | src="https://static.igem.org/mediawiki/2014/f/f5/WashU_Culturing_Ecoli.jpg">Figure: | ||
+ | Bottles of LB used for innoculating <i>E.coli</i> strains</td> | ||
+ | </tr> | ||
+ | </tbody> | ||
+ | </table> | ||
<br> | <br> | ||
- | </ | + | </div> |
- | + | Due | |
+ | to the | ||
oxidative properties of oxygen, most nitrogenases are | oxidative properties of oxygen, most nitrogenases are | ||
irreversibly inhibited by dioxygen, which degradatively oxidizes the | irreversibly inhibited by dioxygen, which degradatively oxidizes the | ||
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Anaerobic were both determined not for cell growth but for nitrogenase | Anaerobic were both determined not for cell growth but for nitrogenase | ||
activity testing, which is the next phase.<br> | activity testing, which is the next phase.<br> | ||
- | < | + | <br><a name="5"></a> |
- | < | + | <div style="text-align: center; font-weight: bold;">Phase 3: |
- | </ | + | Measure |
- | + | ||
- | + | ||
- | <div style="text-align: center; font-weight: bold;">Phase 3: Measure | + | |
nitrogen fixation activity under determined optimal conditions in E. | nitrogen fixation activity under determined optimal conditions in E. | ||
coli strains<br> | coli strains<br> | ||
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border="0" cellpadding="5" cellspacing="5"> | border="0" cellpadding="5" cellspacing="5"> | ||
<tbody> | <tbody> | ||
- | <tr> | + | <tr align="justify"> |
- | <td style="vertical-align: | + | <td colspan="1" rowspan="1" style="vertical-align: middle;">We |
used an Acetylene Reduction Assay to examine the nitrogenase | used an Acetylene Reduction Assay to examine the nitrogenase | ||
activity | activity | ||
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OD600 values.<br> | OD600 values.<br> | ||
<br> | <br> | ||
+ | Acetylene (C2H2) has an triple bond similar to that of atmospheric | ||
+ | nitrogen (N2). Because of this structural similarity, the nitrogenase | ||
+ | enzyme can cleave the triple bond in acetylene just as it would cleave | ||
+ | the triple bond in N2. Ethylene (C2H4) is produced from this enzymatic | ||
+ | activity, so a gas chromatograph can be used to detect the presence of | ||
+ | ethylene and, consequently, nitrogenase activity.<br> | ||
<br> | <br> | ||
- | <span style="font-weight: bold;">Results:</span><br> | + | <table |
- | 1) Of the | + | style="text-align: left; width: 100%; margin-left: auto; margin-right: auto;" |
+ | border="0" cellpadding="5" cellspacing="5"> | ||
+ | <tbody> | ||
+ | <tr> | ||
+ | <td style="vertical-align: top; width: 60%;"><br> | ||
+ | <br> | ||
+ | <div style="text-align: center;"><img | ||
+ | style="width: 100%;" alt="Acetylene Production Apparatus" | ||
+ | src="https://static.igem.org/mediawiki/2014/7/7d/WashU_Acetylene_Production_Apparatus.jpg">Figure | ||
+ | above: This is the apparatus for Acetylene Proeduction</div> | ||
+ | </td> | ||
+ | <td | ||
+ | style="vertical-align: top; width: 40%; text-align: center;"><img | ||
+ | style="width: 100%;" alt="GC Machine" | ||
+ | src="https://static.igem.org/mediawiki/2014/2/28/WashU_GC_Machine.jpg">The | ||
+ | injection ports of Gas phase GC machine used for Acetylene Reduction | ||
+ | Assay</td> | ||
+ | </tr> | ||
+ | </tbody> | ||
+ | </table> | ||
+ | <br> | ||
+ | Materials: <br> | ||
+ | 1-2 small fragments of calcium carbide (CaC2)<br> | ||
+ | Water<br> | ||
+ | <br> | ||
+ | Procedure<br> | ||
+ | <ol> | ||
+ | <li>Place small amount of calcium carbide in sealed flask</li> | ||
+ | <li>Fill the adjacent test tube with water</li> | ||
+ | <li>Inject a small amount (<1 mL) of water into the flask with | ||
+ | a syringe</li> | ||
+ | <li>After the water level in the test tube becomes | ||
+ | constant, draw some of the gas in the headspace of the flask | ||
+ | (acetylene) out and inject it into the sealed bottle with the culture</li> | ||
+ | <li>Using a gas chromatograph, determine the initial | ||
+ | ethylene peak</li> | ||
+ | <li>Test the bottle again after 3 hours</li> | ||
+ | </ol> | ||
+ | <br> | ||
+ | <br> | ||
+ | Growing cultures for Acetylene Reduction Assay:<br> | ||
+ | After deciding to culture the strains in an M9 medium before performing | ||
+ | the assay, the experimenters encountered a few setbacks in the | ||
+ | preparation of that medium. After a couple of days of trial and error, | ||
+ | a protocol was established that produced a viable M9 medium. To create | ||
+ | the 100 mL of 10X M9 stock solution, 0.026 g CaCl2·H2O, 0.030 g | ||
+ | MgSO4,10.4 g Na2HPO4, 3.4 g KH2PO4, and 4 g glucose were dissolved in | ||
+ | the appropriate volume of water. The resulting solution was then | ||
+ | filtered for sterility. 100 mL of a 1000X supplemental stock solution | ||
+ | was prepared by dissolving 0.3 g MnSO4, 7.6 g Na2MoO4*2H2O, 0.010 g | ||
+ | p-aminobenzoic acid, and 0.005 g biotin in the appropriate volume of | ||
+ | water. A 100X ferric citrate solution was also prepared by dissolving | ||
+ | 0.36 g Ferric citrate in water to create 100 mL of solution. The viable | ||
+ | M9 medium was prepared by mixing the appropriate volumes of these | ||
+ | solutions together along with a glutamine solution for all cultures as | ||
+ | a nitrogen source and kanamycin for the experimental tubes and bottles. | ||
+ | After observing their growth, DH5α and Top 10 were eliminated due to | ||
+ | their inability to grow well in the medium, and all experiments | ||
+ | proceeded with the JM109, BL21, and WM1788 wild types and mutants. <br> | ||
+ | </td> | ||
+ | </tr> | ||
+ | <tr align="center"> | ||
+ | <td colspan="1" rowspan="1" style="vertical-align: top;"><img | ||
+ | style="width: 800px; height: 476px;" | ||
+ | alt="Acetylene reduction assay results" | ||
+ | src="https://static.igem.org/mediawiki/2014/f/ff/WashU_ARA_results.png"></td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td colspan="1" rowspan="1" style="vertical-align: top;"> | ||
+ | <table | ||
+ | style="text-align: left; width: 100%; height: 271px; margin-left: auto; margin-right: auto;" | ||
+ | border="0" cellpadding="5" cellspacing="5"> | ||
+ | <tbody> | ||
+ | <tr> | ||
+ | <td style="vertical-align: top;"><br><a name="6"></a> | ||
+ | <div style="text-align: justify;"><span | ||
+ | style="font-weight: bold;">Results:</span><br> | ||
+ | 1) Of the five <span style="font-style: italic;">E. coli</span> | ||
strains tested, JM109 and WM1788 showed strongest nitrogenase activity.<br> | strains tested, JM109 and WM1788 showed strongest nitrogenase activity.<br> | ||
<br> | <br> | ||
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<br> | <br> | ||
3) Optimal conditions determined: <br> | 3) Optimal conditions determined: <br> | ||
- | <ul> | + | </div> |
+ | <ul style="text-align: justify;"> | ||
<li>glucose as carbon-source</li> | <li>glucose as carbon-source</li> | ||
<li>glutamate as | <li>glutamate as | ||
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</ul> | </ul> | ||
</td> | </td> | ||
- | < | + | </tr> |
- | + | </tbody> | |
- | + | </table> | |
- | + | ||
</td> | </td> | ||
</tr> | </tr> | ||
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</table> | </table> | ||
<div style="text-align: center;"> | <div style="text-align: center;"> | ||
- | < | + | <a name="7"></a><h3>Citation</h3> |
</div> | </div> | ||
1: Christian Rogers, Giles E. D. Oldroyd. Journal of Experimental | 1: Christian Rogers, Giles E. D. Oldroyd. Journal of Experimental | ||
Line 315: | Line 443: | ||
3: Liying Wang, Ray Dixon. PLOS Genetics., 2013 Oct 17; 9(10): 3865–3876<br> | 3: Liying Wang, Ray Dixon. PLOS Genetics., 2013 Oct 17; 9(10): 3865–3876<br> | ||
4: Temme, Zhao, Voigt. PNAS., 2012 March 23; 109(18): 7085–7090<br> | 4: Temme, Zhao, Voigt. PNAS., 2012 March 23; 109(18): 7085–7090<br> | ||
- | < | + | 5: Dixon, Kahn. <span style="font-style: italic;">Genetic Regulation |
- | < | + | of Biological Nitrogen Fixation. </span>Nature Reviews. August 2004, |
- | < | + | Vol 2. P. 621-631.<br> |
</td> | </td> | ||
</tr> | </tr> | ||
+ | </tbody> | ||
</table> | </table> | ||
</html> | </html> | ||
{{:Team:WashU_StLouis/footer}} | {{:Team:WashU_StLouis/footer}} |
Latest revision as of 22:31, 17 October 2014