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+ | |||
+ | <body> | ||
+ | |||
+ | <div> | ||
+ | |||
+ | <a href="https://2016.igem.org/Team:Pasteur_Paris/Microbiology"><h2><B>Microbiology Notebook</B></h2><a/> | ||
+ | </div> | ||
+ | |||
+ | <div id="home"> | ||
+ | <center></a><a href="https://2016.igem.org/Team:Pasteur_Paris/Microbiology"><img src="https://static.igem.org/mediawiki/2016/5/5a/Labwork_pasteur.png" width="40%" alt=""/></img></a></center> | ||
+ | </div> | ||
+ | |||
+ | |||
+ | <div id="week15"> | ||
+ | <p><h5><B>Week 15</B></h5></p> | ||
+ | <p><h3><B>September 12, 2016:</B></h3></p> | ||
+ | <p> | ||
+ | <a href="#exp1"><h4> 242. Digestion of the plasmid pSB1C3 </h4></a></br> | ||
+ | </p> | ||
+ | <p><h3><B>September 15, 2016:</B></h3></p> | ||
+ | <p> | ||
+ | <a href="#exp2"><h4> 243. Measure the amount of DNA extracted from the miniprep </h4></a></br> | ||
+ | |||
+ | <a href="#exp3"><h4> 244. Digestion of the plasmid pSB1C3 and inserts A1/A2/B1/B2/C1/C2/D1/D2/E1/E2 </h4></a></br> | ||
+ | <a href="#exp4"><h4> 245. Electrophoresis on agarose gel</h4></a></br> | ||
+ | <a href="#exp5"><h4> 246. DNA extraction</h4></a></br> | ||
+ | </p> | ||
+ | <p><h3><B>September 16, 2016:</B></h3></p> | ||
+ | <p> | ||
+ | <a href="#exp6"><h4> 247. Measure the amount of DNA extracted from the miniprep </h4></a></br> | ||
+ | </p> | ||
+ | |||
+ | |||
+ | |||
+ | <div class="lightbox" id="exp1"> | ||
+ | <figure> | ||
+ | <a href="#" class="closemsg"></a> | ||
+ | <figcaption> | ||
+ | <p> | ||
+ | <U> Aim:</U> To have the right restriction sites to perform the ligation and the cloning.</br> | ||
+ | We choose appropriate restriction sites based on our inserts.</br></br> | ||
+ | <U> Protocol:</U> follow in this <a href="https://static.igem.org/mediawiki/2016/a/ab/T--Pasteur_Paris--Restriction_digestion_protocol.pdf">link</a><br/><br/> | ||
+ | <U>What we did in the lab:</U></br> | ||
+ | <U>Materials:</U></br> | ||
+ | • Restriction enzymes: Xba I, Spe I (New England Biolabs, NEB)</br> | ||
+ | • Restriction enzyme buffers </br> | ||
+ | • 37°C water bath</br> | ||
+ | • UV spectrophotometer</br> | ||
+ | • pSB1C3 (48ng/µl)</br></br> | ||
+ | |||
+ | <U>Method:</U></br> | ||
+ | 1. Mix all the reagents and let digest during 1 hour at 37°C </br> | ||
+ |  ⚠ Big volumes must be added first!</br> | ||
+ | |||
+ | <table> | ||
+ | <caption align="bottom" align="center"><i><p> <U>Table 143</U></p></i></caption> | ||
+ | <thead> | ||
+ | <tr> | ||
+ | <th>Reactants</th> | ||
+ | <th>pSB1C3</th> | ||
+ | </tr> | ||
+ | </thead> | ||
+ | <tbody> | ||
+ | <tr> | ||
+ | <td align="center"; valign="center"><strong><p>Vol<sub>DNA</sub></p></strong></td> | ||
+ | <td align="center"; valign="center">25 µl </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td align="center"; valign="center"><strong><p>Vol<sub>XbaI</sub></p></strong></td> | ||
+ | <td align="center"; valign="center">10 µl </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td align="center"; valign="center"><strong><p>Vol<sub>SpeI</sub></p></strong></td> | ||
+ | <td align="center"; valign="center">10 µl </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td align="center"; valign="center"><strong><p>Vol<sub> buffer (10X) (Cutsmart) </sub></p></strong></td> | ||
+ | <td align="center"; valign="center">5 µl </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td align="center"; valign="center"><strong><p>Vol<sub>total</sub></p></strong></td> | ||
+ | <td align="center"; valign="center">50 µl </td> | ||
+ | </tr> | ||
+ | </tbody> | ||
+ | </table><br/> | ||
+ | |||
+ | 2. Incubate 10 min at 65°C to inactivate the enzymes.</br> | ||
+ | 3. Add 2 µl of rSAP in order to perform the dephosphorylation.</br> | ||
+ | 3. Store at -20°C</br> | ||
+ | <br/><br/><br/> | ||
+ | </p> | ||
+ | </figcaption> | ||
+ | </figure> | ||
+ | </div> | ||
+ | |||
+ | |||
+ | <div class="lightbox" id="exp2"> | ||
+ | <figure> | ||
+ | <a href="#" class="closemsg"></a> | ||
+ | <figcaption> | ||
+ | <p> | ||
+ | <U> Aim:</U> Measure the quantity of plasmid using a Nanodrop (Thermofisher)</br></br> | ||
+ | |||
+ | <U>What we did in the lab:</U></br> | ||
+ | <U>Materials:</U></br> | ||
+ | • Nanodrop (Thermofisher)</br> | ||
+ | • Elution buffer from QIAGEN kit</br> | ||
+ | • Microbiology equipment (Follow this link)</br></br> | ||
+ | |||
+ | <U>Method:</U></br> | ||
+ | 1. Analyze absorbance at 260 nm</br> | ||
+ | 2. Clean the Nanodrop with water</br> | ||
+ | 3. Make the blank with 1μl of elution buffer</br> | ||
+ | 4. Put 1μl of your sample on the Nanodrop</br> | ||
+ | 5. Make the measure and clean the Nanodrop between each measure</br></br> | ||
+ | |||
+ | <U>Results:</U></br> | ||
+ | <table> | ||
+ | <caption align="bottom" align="center"><i><p> <U>Table 144 :</U> Absorbance </p></i></caption> | ||
+ | <thead> | ||
+ | <tr> | ||
+ | <th>Absorbance at 260nm</th> | ||
+ | <th>A260/280</th> | ||
+ | <th>Concentration (ng/µl )</th> | ||
+ | </tr> | ||
+ | </thead> | ||
+ | <tbody> | ||
+ | <tr> | ||
+ | <td align="center"; valign="center"><strong><p>pSB1C3 (1)</p></strong></td> | ||
+ | <td align="center"; valign="center">1.94</td> | ||
+ | <td align="center"; valign="center">115.7</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td align="center"; valign="center"><strong><p>pSB1C3 (2)</p></strong></td> | ||
+ | <td align="center"; valign="center">1.93</td> | ||
+ | <td align="center"; valign="center">13.0</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td align="center"; valign="center"><strong><p>B1-col6</p></strong></td> | ||
+ | <td align="center"; valign="center">1.88</td> | ||
+ | <td align="center"; valign="center">393.3</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td align="center"; valign="center"><strong><p>B1-col8<sub>(diluted 1/2)</sub></p></strong></td> | ||
+ | <td align="center"; valign="center">1.93</td> | ||
+ | <td align="center"; valign="center">74.1</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td align="center"; valign="center"><strong><p>B2-col7</p></strong></td> | ||
+ | <td align="center"; valign="center">1.89 </td> | ||
+ | <td align="center"; valign="center">84.8</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td align="center"; valign="center"><strong><p>B2-col9</p></strong></td> | ||
+ | <td align="center"; valign="center">1.90 </td> | ||
+ | <td align="center"; valign="center">307.1</td> | ||
+ | </tr> | ||
+ | </tbody> | ||
+ | </table><br/> | ||
+ | <br/><br/><br/> | ||
+ | </p> | ||
+ | </figcaption> | ||
+ | </figure> | ||
+ | </div> | ||
+ | |||
+ | |||
+ | <div class="lightbox" id="exp3"> | ||
+ | <figure> | ||
+ | <a href="#" class="closemsg"></a> | ||
+ | <figcaption> | ||
+ | <p> | ||
+ | <U> Aim:</U> To have the right restriction sites to perform the ligation and the cloning.</br> | ||
+ | We choose appropriate restriction sites based on our inserts.</br></br> | ||
+ | <U> Protocol:</U> follow in this <a href="https://static.igem.org/mediawiki/2016/a/ab/T--Pasteur_Paris--Restriction_digestion_protocol.pdf">link</a><br/><br/> | ||
+ | <U>What we did in the lab:</U></br> | ||
+ | <U>Materials:</U></br> | ||
+ | • Restriction enzymes: Xba I, Spe I (New England Biolabs, NEB)</br> | ||
+ | • Restriction enzyme buffers </br> | ||
+ | • 37°C water bath</br> | ||
+ | • UV spectrophotometer</br> | ||
+ | • pSB1C3 (48ng/µl)</br></br> | ||
+ | |||
+ | <U>Method:</U></br> | ||
+ | Mix all the reagents and let digest during 1 hour at 37°C </br></br> | ||
+ |   ⚠ Big volumes must be added first!</br></br> | ||
+ | |||
+ | |||
+ | <table> | ||
+ | <caption align="bottom" align="center"><i><p> <U>Table 145</U></p></i></caption> | ||
+ | <thead> | ||
+ | <tr> | ||
+ | <th>Reactants</th> | ||
+ | <th>Each sample</th> | ||
+ | <th>Global mix</th> | ||
+ | </tr> | ||
+ | </thead> | ||
+ | <tbody> | ||
+ | <tr> | ||
+ | <td align="center"; valign="center"><strong><p>Vol<sub>DNA</sub></p></strong></td> | ||
+ | <td align="center"; valign="center">25 µl </td> | ||
+ | <td align="center"; valign="center">0 µl </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td align="center"; valign="center"><strong><p>Vol<sub>XbaI </sub></p></strong></td> | ||
+ | <td align="center"; valign="center">1 µl </td> | ||
+ | <td align="center"; valign="center">18 µl </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td align="center"; valign="center"><strong><p>Vol<sub>SpeI</sub></p></strong></td> | ||
+ | <td align="center"; valign="center">0.5 µl </td> | ||
+ | <td align="center"; valign="center">9 µl </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td align="center"; valign="center"><strong><p>Vol<sub>buffer 2.1</sub></p></strong></td> | ||
+ | <td align="center"; valign="center">5 µl </td> | ||
+ | <td align="center"; valign="center">90 µl </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td align="center"; valign="center"><strong><p>Vol<sub>H<span>2</span>O</sub></p></strong></td> | ||
+ | <td align="center"; valign="center">18.5 µl </td> | ||
+ | <td align="center"; valign="center">333 µl </td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td align="center"; valign="center"><strong><p>Vol<sub>total</sub></p></strong></td> | ||
+ | <td align="center"; valign="center">50 µl </td> | ||
+ | <td align="center"; valign="center">450 µl </td> | ||
+ | </tbody> | ||
+ | </table><br/> | ||
+ | |||
+ | 2. Incubate 10 min at 65°C to inactivate the enzymes.</br> | ||
+ | 3. Add 2 µl of rSAP in order to perform the dephosphorylation.</br> | ||
+ | 3. Store at -20°C</br> | ||
+ | <br/><br/><br/> | ||
+ | </p> | ||
+ | </figcaption> | ||
+ | </figure> | ||
+ | </div> | ||
+ | |||
+ | |||
+ | |||
+ | <div class="lightbox" id="exp4"> | ||
+ | <figure> | ||
+ | <a href="#" class="closemsg"></a> | ||
+ | <figcaption> | ||
+ | <p> | ||
+ | <U> Aim:</U> This step check the digestion efficiency of B1 (2 tubes)/B2 (2 tubes)/ C1 / C2 / A1 / A2 / D2 / E1 / E2.</br> Moreover, the inserts will be purified during this step because they will be extracted from the gel.</br><br/> | ||
+ | <U> Protocol:</U> follow in this <a href="https://static.igem.org/mediawiki/2016/6/60/T--Pasteur_Paris--Gel_electrophoresis_protocol.pdf">link</a><br/><br/> | ||
+ | <U>What we did in the lab:</U></br> | ||
+ | <U>Materials:</U></br> | ||
+ | • Electrophoresis cuve</br> | ||
+ | • TAE 1X</br> | ||
+ | • Gene ruler (Thermoscientific 1kb plus)</br> | ||
+ | • Loading dye</br> | ||
+ | • Agarose</br> | ||
+ | • UV table </br> | ||
+ | • Ethidium bromide drops (EB)</br></br> | ||
+ | |||
+ | |||
+ | <U>Method:</U></br> Each well will contain 25 µl of DNA and 6 µl of Loading Dye. Follow the next deposit table :</br></br> | ||
+ | |||
+ | Line 1:</br> | ||
+ | Ladder (6 µl) | Ø | B2-col7 | Ø | B2-col9 | Ø | B1-col6 | Ø | B1-col9 | Ø | C1 | Ø | C2</br></br> | ||
+ | |||
+ | Line 2:</br> | ||
+ | Ladder (6 µl) | Ø | D2 | Ø | E1 | Ø | E2 | Ø | pSB1C€3 | Ø | A1 | Ø | A2</br></br> | ||
+ | |||
+ | </p> | ||
+ | </figcaption> | ||
+ | </figure> | ||
+ | </div> | ||
+ | |||
+ | |||
+ | |||
+ | |||
+ | <div class="lightbox" id="exp5"> | ||
+ | <figure> | ||
+ | <a href="#" class="closemsg"></a> | ||
+ | <figcaption> | ||
+ | <p> | ||
+ | <U> Aim:</U> To perform a gel extraction to isolate insert DNA purified from its plasmid thanks to the migration. We use the gel made before with inserts B1 (2 tubes)/B2 (2 tubes)/ C1 / C2 / A1 / A2 / D2 / E1 / E2 but we only extract B2 bands.</br> </br> | ||
+ | <U> Protocol:</U> follow in this <a href="https://static.igem.org/mediawiki/2016/d/d5/T--Pasteur_Paris--Miniprep_protocol.pdf">link</a><br/><br/> | ||
+ | <U>What we did in the lab:</U></br> | ||
+ | <U>Materials:</U></br> | ||
+ | • Scalpel</br> | ||
+ | • 2 ml Eppendorfs</br> | ||
+ | • Balance</br> | ||
+ | • UV table</br> | ||
+ | • Microbiology equipment (type of incubator, Bunsen burner, water bath, etc… Follow this <a href="https://2016.igem.org/Team:Pasteur_Paris/Science">link</a>) | ||
+ | • QIAGEN Gel Extraction Kit</br> | ||
+ | </br></br> | ||
+ | <U>Method:</U></br> | ||
+ |   ⚠ Be aware of the risks! UV light burns the eyes and skin so make sure you have the right protection</br> | ||
+ | |||
+ | Follow QIAGEN Kit steps according to the next tables for the volumes of QG buffer. </br></br> | ||
+ | |||
+ | <table> | ||
+ | <caption align="bottom" align="center"><i><p> <U>Table 146 :</U> Masses </p></i></caption> | ||
+ | <thead> | ||
+ | <tr> | ||
+ | <th>Insert</th> | ||
+ | <th>Mass of gel (mg)</th> | ||
+ | <th>Volume of QG Buffer (µl)</th> | ||
+ | </tr> | ||
+ | </thead> | ||
+ | <tbody> | ||
+ | <tr> | ||
+ | <td align="center"; valign="center"><strong><p>B2-col7</p></strong></td> | ||
+ | <td align="center"; valign="center">190</td> | ||
+ | <td align="center"; valign="center">570</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td align="center"; valign="center"><strong><p>B2-col9</p></strong></td> | ||
+ | <td align="center"; valign="center">170</td> | ||
+ | <td align="center"; valign="center">510</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td align="center"; valign="center"><strong><p>B1-col6</p></strong></td> | ||
+ | <td align="center"; valign="center">80</td> | ||
+ | <td align="center"; valign="center">240</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td align="center"; valign="center"><strong><p>B1-col8</p></strong></td> | ||
+ | <td align="center"; valign="center">140</td> | ||
+ | <td align="center"; valign="center">420</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td align="center"; valign="center"><strong><p>C1</p></strong></td> | ||
+ | <td align="center"; valign="center">150</td> | ||
+ | <td align="center"; valign="center">450</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td align="center"; valign="center"><strong><p>C2</p></strong></td> | ||
+ | <td align="center"; valign="center">130</td> | ||
+ | <td align="center"; valign="center">390</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td align="center"; valign="center"><strong><p>D2</p></strong></td> | ||
+ | <td align="center"; valign="center">150</td> | ||
+ | <td align="center"; valign="center">450</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td align="center"; valign="center"><strong><p>E1</p></strong></td> | ||
+ | <td align="center"; valign="center">150</td> | ||
+ | <td align="center"; valign="center">450</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td align="center"; valign="center"><strong><p>E2</p></strong></td> | ||
+ | <td align="center"; valign="center">180</td> | ||
+ | <td align="center"; valign="center">540</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td align="center"; valign="center"><strong><p>pSB1C3</p></strong></td> | ||
+ | <td align="center"; valign="center">210</td> | ||
+ | <td align="center"; valign="center">630</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td align="center"; valign="center"><strong><p>A1</p></strong></td> | ||
+ | <td align="center"; valign="center">170</td> | ||
+ | <td align="center"; valign="center">510</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td align="center"; valign="center"><strong><p>A2</p></strong></td> | ||
+ | <td align="center"; valign="center">210</td> | ||
+ | <td align="center"; valign="center">630</td> | ||
+ | </tr> | ||
+ | </tbody> | ||
+ | </table> | ||
+ | <br/><br/><br/> | ||
+ | </p> | ||
+ | </figcaption> | ||
+ | </figure> | ||
+ | </div> | ||
+ | |||
+ | |||
+ | <div class="lightbox" id="exp6"> | ||
+ | <figure> | ||
+ | <a href="#" class="closemsg"></a> | ||
+ | <figcaption> | ||
+ | <p> | ||
+ | <U> Aim:</U> Measure the quantity of plasmid using a Nanodrop (Thermofisher)</br> | ||
+ | |||
+ | <U>What we did in the lab:</U></br> | ||
+ | <U>Materials:</U></br> | ||
+ | • Nanodrop (Thermofisher)</br> | ||
+ | • Elution buffer from QIAGEN kit</br> | ||
+ | • Microbiology equipment (type of incubator, Bunsen burner, water bath, etc… Follow this <a href="https://2016.igem.org/Team:Pasteur_Paris/Science">link</a>) <br/><br/> | ||
+ | |||
+ | <U>Method:</U></br> | ||
+ | 1. Analyze absorbance at 260nm</br> | ||
+ | 2. Clean the Nanodrop with water</br> | ||
+ | 3. Make the blank with 1μl of elution buffer</br> | ||
+ | 4. Put 1ul of your sample on the Nanodrop</br> | ||
+ | 5. Make the measure and clean the Nanodrop between each measure</br></br> | ||
+ | |||
+ | <U>Results:</U></br> | ||
+ | |||
+ | <table> | ||
+ | <caption align="bottom" align="center"><i><p> <U>Table 147 :</U> Absorbance </p></i></caption> | ||
+ | <thead> | ||
+ | <tr> | ||
+ | <th>Absorbance at 260 nm</th> | ||
+ | <th>A260/280</th> | ||
+ | <th>Concentration (ng/µl)</th> | ||
+ | </tr> | ||
+ | </thead> | ||
+ | <tbody> | ||
+ | <tr> | ||
+ | <td align="center"; valign="center"><strong><p>B2-col7</p></strong></td> | ||
+ | <td align="center"; valign="center">2.12</td> | ||
+ | <td align="center"; valign="center">3.7</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td align="center"; valign="center"><strong><p>B2-col9</p></strong></td> | ||
+ | <td align="center"; valign="center">2.19</td> | ||
+ | <td>5.3</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td align="center"; valign="center"><strong><p>B1-col6</p></strong></td> | ||
+ | <td align="center"; valign="center">2.04</td> | ||
+ | <td align="center"; valign="center">3.2</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td align="center"; valign="center"><strong><p>B1-col8</p></strong></td> | ||
+ | <td align="center"; valign="center">1.98</td> | ||
+ | <td align="center"; valign="center">3.7</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td align="center"; valign="center"><strong><p>C1</p></strong></td> | ||
+ | <td align="center"; valign="center">1.78 </td> | ||
+ | <td align="center"; valign="center">5.0</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td align="center"; valign="center"><strong><p>C2</p></strong></td> | ||
+ | <td align="center"; valign="center">1.90 </td> | ||
+ | <td align="center"; valign="center">307.1</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td align="center"; valign="center"><strong><p>D2</p></strong></td> | ||
+ | <td align="center"; valign="center">1.84 </td> | ||
+ | <td align="center"; valign="center">5.2</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td align="center"; valign="center"><strong><p>E1</p></strong></td> | ||
+ | <td align="center"; valign="center">2.30 </td> | ||
+ | <td align="center"; valign="center">3.9</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td align="center"; valign="center"><strong><p>E2</p></strong></td> | ||
+ | <td align="center"; valign="center">2.17 </td> | ||
+ | <td align="center"; valign="center">3.8</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td align="center"; valign="center"><strong><p>pSB1C3</p></strong></td> | ||
+ | <td align="center"; valign="center">1.98</td> | ||
+ | <td align="center"; valign="center">13.1</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td align="center"; valign="center"><strong><p>A1</p></strong></td> | ||
+ | <td align="center"; valign="center">2.11</td> | ||
+ | <td align="center"; valign="center">4.8</td> | ||
+ | </tr> | ||
+ | <tr> | ||
+ | <td align="center"; valign="center"><strong><p>A2</p></strong></td> | ||
+ | <td align="center"; valign="center">2.45</td> | ||
+ | <td align="center"; valign="center">4.3</td> | ||
+ | </tr> | ||
+ | </tbody> | ||
+ | </table><br/> | ||
+ | </br></br></br> | ||
+ | |||
+ | </p> | ||
+ | </figcaption> | ||
+ | </figure> | ||
+ | </div> | ||
+ | |||
+ | |||
+ | </body> | ||
+ | </html> |