Difference between revisions of "Team:NTU-LIHPAO-Taiwan/Notebook"

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font-size: 20px;
 
font-size: 20px;
 
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 +
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 +
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 +
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 +
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 +
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 +
 
 +
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 +
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 +
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 +
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+
 
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Green {
+
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+
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+
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+
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+
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Super {
+
 
vertical-align:super;
+
/*-------------------------------------------*/
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+
 
/*-------------------Media-------------------*/
 
/*-------------------Media-------------------*/
 
/*-------------------------------------------*/
 
/*-------------------------------------------*/
Line 801: Line 806:
 
<ul class="main-Content">
 
<ul class="main-Content">
 
<li>
 
<li>
<span class="title">Months</span>
+
<span class="title">Protocols</span>
 
<ul class="sub-Content">
 
<ul class="sub-Content">
<li><a href="#First1">July</a></li>
+
<li><a href="#First1">Preparation of Competent Cells (<i>E.coli</i>)</a></li>
<li><a href="#First2">August</a></li>
+
<li><a href="#First2">DNA Dissolution</a></li>
<li><a href="#First3">September</a></li>
+
<li><a href="#First3">Agarose Gel Electrophoresis</a></li>
 +
<li><a href="#First4">Gel Extraction</a></li>
 +
<li><a href="#First5">DNA Ligation</a></li>
 +
<li><a href="#First6">Plasmid DNA Extraction Using Alkaline Lysis Method (<i>E.coli</i>)</a></li>
 +
<li><a href="#First7">Transformation(<i>E.coli</i>)</a></li>
 +
<li><a href="#First8">Protein Extraction</a></li>
 +
<li><a href="#First9">SDS-PAGE</a></li>
 +
<li><a href="#First10">Western Blot</a></li>
 +
<li><a href="#First11">Immunostaining</a></li>
 +
<li><a href="#First12">Thawing Caco-2 cells</a></li>
 +
<li><a href="#First13">Freezing Caco-2 cells</a></li>
 +
<li><a href="#First14">Caco2 Cell passage</a></li>
 +
<li><a href="#First15">Seeding in transwell</a></li>
 +
<li><a href="#First16">Measure TEER</a></li>
 
</ul>
 
</ul>
 
</li>
 
</li>
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var sub_Content = main_Contents[i].querySelector(".sub-Content");
 
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sub_Content.style.height = '12rem';
+
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Line 840: Line 858:
 
<div class="ContentBox">
 
<div class="ContentBox">
 
<div class="ContentHolder">
 
<div class="ContentHolder">
<div class="Container_Top1"></div>
 
  
<div class="Container2" id="First1"><div class="Text2">7/4</div></div>
+
<div class="Text1" id="First1"><Red>Preparation of Competent Cells (<i>E.coli</i>)</Red></div>
 +
<div class="Text2">
 +
<Green>Materials and Reagents :</Green>
 +
</div>
 
<div class="Text3">
 
<div class="Text3">
<Green>Manufacture <i>CP<Super>+</Super></i> plate</Green>
+
<ol class="part1">
 +
<li><i>Escherichia coli</i> DH5α</li>
 +
<li>LB broth</li>
 +
<li>TB buffer</li>
 +
<li>DMSO</li>
 +
<li>Liquid nitrogen</li>
 +
</ol>
 
</div>
 
</div>
 
+
<div class="Text2">
 
+
<Green>Equipment :</Green>
<div class="Container2"><div class="Text2">7/6</div></div>
+
</div>
 
<div class="Text3">
 
<div class="Text3">
<Red>Learn how to transform</Red>
+
<ol class="part1">
 +
<li>Ice</li>
 +
<li>Shaker</li>
 +
<li>Spectrometer</li>
 +
<li>Centrifuge</li>
 +
</ol>
 
</div>
 
</div>
 +
<div class="Text2">
 +
<Green>Procedure :</Green>
 +
</div>
 
<div class="Text3">
 
<div class="Text3">
<Green>Suicide Part:</Green>
+
<ol class="part2">
 +
<li>Inoculate 10μL <i>Escherichia coli</i> DH5α into 10mL LB broth (1:1000)</li>
 +
<li>Grow for 12-16 hours at 37℃ with shaking</li>
 +
<li>Inoculate 500μL <i>Escherichia coli</i> DH5α into 50mL LB broth (1:100)</li>
 +
<li>Grow for 2 hours at 37℃ with shaking to O.D.<Sub>600</Sub>=0.4-0.6</li>
 +
<li>Split the cell into two Falcon tubes, both contain 25 mL <i>Escherichia coli</i> DH5α</li>
 +
<li>Centrifuge at 4℃, 3000rpm(800G) for 10 minutes</li>
 +
<li>Discard the supernatant</li>
 +
<li>Resuspend the cell pellet by gently adding 8.5mL TB buffer (1/3 V)</li>
 +
<li>On ice for 10 minutes</li>
 +
<li>Centrifuge at 4℃, 3000rpm(800G) for 10 minutes</li>
 +
<li>Discard the supernatant using pipetman</li>
 +
<li>Resuspend the cell pellet by gently adding 2mL TB buffer (1/12.5 V)</li>
 +
<li>Add 150μL DMSO (7%)</li>
 +
<li>On ice for 10 minutes</li>
 +
<li>Transfer the cell to new eppendorfs with 60μL per tube</li>
 +
<li>Freeze the cell in liquid nitrogen</li>
 +
<li>Store the cell at -80℃</li>
 +
</ol>
 
</div>
 
</div>
<div class="Text3_Sub">
+
<div class="Text1" id="First2"><Red>DNA Dissolution</Red></div>
Transformation of:
+
<div class="Text2">
</div>
+
<Green>Materials and Reagents :</Green>
<div class="Text3_SubSub">
+
</div>
[RBS] (BBa_B0034), [C2] (BBa_C0053)
+
</div>
+
 
+
 
+
<div class="Container2"><div class="Text2">7/7</div></div>
+
 
<div class="Text3">
 
<div class="Text3">
<Red>Learn how to manufacture competent cell</Red>
+
<ol class="part1">
 +
<li>DNA (BioBricks/synthesized)</li>
 +
<li>ddH<Sub>2</Sub>O</li>
 +
</ol>
 
</div>
 
</div>
 +
<div class="Text2">
 +
<Green>Procedure :</Green>
 +
</div>
 
<div class="Text3">
 
<div class="Text3">
<Blue>Manufacture competent cell</Blue>
+
<ol class="part2">
 +
<li>Add 10μL ddH<Sub>2</Sub>O</li>
 +
<li>Wait for 1 minute until the DNA dissolve</li>
 +
<li>Pipet several times and transfer the DNA to an eppendorf</li>
 +
</ol>
 
</div>
 
</div>
 +
<div class="Text1" id="First3"><Red>Agarose Gel Electrophoresis</Red></div>
 +
<div class="Text2">
 +
<Green>Materials and Reagents :</Green>
 +
</div>
 
<div class="Text3">
 
<div class="Text3">
<Green>PYY part:</Green>
+
<ol class="part1">
</div>
+
<li>Agarose</li>
<div class="Text3_Sub">
+
<li>1X TAE</li>
Transformation of:
+
<li>Tracking dye</li>
</div>
+
<li>Marker (1kb/100bp)</li>
<div class="Text3_SubSub">
+
<li>EtBr</li>
[promoter] (BBa_J23100), [signal peptide] (BBa_K554002), [terminator] (BBa_B0015)
+
<li>ddH<Sub>2</Sub>O</li>
</div>
+
</ol>
 +
</div>
 +
<div class="Text2">
 +
<Green>Equipment :</Green>
 +
</div>
 
<div class="Text3">
 
<div class="Text3">
<Green>Suicide Part:</Green>
+
<ol class="part1">
 +
<li>Gel tray</li>
 +
<li>Well comb</li>
 +
<li>Electrophoresis tank</li>
 +
<li>UV detector</li>
 +
</ol>
 
</div>
 
</div>
<div class="Text3_Sub">
+
<div class="Text2">
Transformation of:
+
<Green>Procedure :</Green>
</div>
+
</div>
<div class="Text3_SubSub">
+
[pC1] (BBa_R0051), [pC2] (BBa_R0053), [endolysin] (BBa_K112806), [C1] (BBa_C0051)
+
</div>
+
 
+
 
+
<div class="Container2"><div class="Text2">7/8</div></div>
+
 
<div class="Text3">
 
<div class="Text3">
<Red>Learn how to extract the plasmid</Red>
+
<ol class="part2">
 +
<div class="Text_TitleUnderline">Casting an Agarose Gel (m/v = 1.0% or 1.5%)</div>
 +
<li>Measure out appropriate mass of agarose powder into a serum bottle</li>
 +
<li>Add appropriate volume of 1X TAE</li>
 +
        <li>Let agarose solution cool down to acceptable temperature for bare hands</li>
 +
        <li>Pour the solution into a gel tray with the well comb in place, and push the bubbles away with a pipette tip</li>
 +
        <li>Let sit at room temperature for 30 minutes, until it has completely solidified</li>
 +
<div class="Text_TitleUnderline">Loading Samples and Running the Gel</div>
 +
        <li>Place the gel as well as its tray into the electrophoresis tank containing 1X TAE  </li>
 +
        (Make sure that the surface is higher than the top of the gel and not overflow)
 +
        <li>Mix the samples with tracking dye (1/10 V) sufficiently</li>
 +
        <li>Load the samples into the each well</li>
 +
        <li>Load marker (usually in the first and last lane)</li>
 +
        <li>Set an appropriate voltage (full/half) and run the gel for 15-20 minutes</li>
 +
        <div class="Text_TitleUnderline">Imaging the Gel</div>
 +
        <li>Put the gel into a container filled with 1X TAE and EtBr, staining for 5 minutes</li>
 +
        <li>Replace EtBr solution with water and destain for 3 minutes</li>
 +
        <li>Put the gel in an UV detector and record the result</li>
 +
</ol>
 
</div>
 
</div>
 +
<div class="Text1" id="First4"><Red>Gel Extraction</Red></div>
 +
<div class="Text2">
 +
<Green>Materials and Reagents :</Green>
 +
</div>
 
<div class="Text3">
 
<div class="Text3">
<Red>Learn how to conduct the gel extraction and electrophoresis</Red>
+
<ol class="part1">
</div>
+
<li>Gel/PCR buffer</li>
 +
<li>W1 buffer</li>
 +
<li>Wash buffer</li>
 +
<li>ddH<Sub>2</Sub>O</li>
 +
</ol>
 +
</div>
 +
<div class="Text2">
 +
<Green>Equipment :</Green>
 +
</div>
 
<div class="Text3">
 
<div class="Text3">
<Green>Suicide Part:</Green>
+
<ol class="part1">
 +
<li>Cutter knife</li>
 +
<li>Eppendorf</li>
 +
<li>Vortex mixer</li>
 +
<li>Dry bath incubator</li>
 +
        <li>DF Column & Collection tube</li>
 +
        <li>Mini Centrifuge</li>
 +
        <li>Microcentrifuge</li>
 +
</ol>
 
</div>
 
</div>
<div class="Text3_Sub">
+
<div class="Text2">
Extract the plasmid:
+
<Green>Procedure :</Green>
</div>
+
</div>
<div class="Text3_SubSub">
+
[RBS] (BBa_B0034), [C2] (BBa_C0053)
+
</div>
+
<div class="Text3_Sub">
+
Restriction enzyme:
+
</div>
+
<div class="Text3_SubSub">
+
[RBS] cleave by EcoRI, [C2] cleave by EcoRI and PstI
+
</div>
+
<div class="Text3_Sub">
+
Gel electrophoresis:
+
</div>
+
<div class="Text3_SubSub">
+
[RBS] ----- Result: Failed (Smeared band was too blurred)
+
</div>
+
<div class="Text3_SubSub">
+
[C2] ----- Result: Succeeded
+
</div>
+
<div class="Text3_Sub">
+
Transformation of:
+
</div>
+
<div class="Text3_SubSub">
+
[pC1] (BBa_R0051), [pC2] (BBa_R0053), [endolysin] (BBa_K112806) <b>again</b>
+
</div>
+
 
+
 
+
<div class="Container2"><div class="Text2">7/9</div></div>
+
 
<div class="Text3">
 
<div class="Text3">
<Green>Suicide Part:</Green>
+
<ol class="part2">
</div>
+
        <div class="Text_TitleUnderline">Gel Dissociation</div>
<div class="Text3_Sub">
+
<li>Excise the agarose gel slice containing relevant DNA fragments and remove any extra agarose to minimize the size of the gel slice (<300μL)</li>
Extract the plasmid:
+
<li>Transfer the gel slice to an eppendorf</li>
</div>
+
<li>Add 500μL Gel/PCR buffer to the sample and mix by vortex</li>
<div class="Text3_SubSub">
+
        <li>Incubate at 60℃ for 10-15 minutes to ensure the gel slice has been completely dissolved (invert the tube every 2-3 minutes)</li>
[RBS] (BBa_B0034), [C1] (BBa_C0051), [endolysin] (BBa_K112806)
+
        <li>Cool the dissolved sample mixture to room temperature</li>
</div>
+
        <div class="Text_TitleUnderline">DNA Binding</div>
<div class="Text3_Sub">
+
        <li>Place the DF Column in a 2mL Collection tube</li>
Gel electrophoresis:
+
        <li>Transfer 800μL of the sample mixture to the DF Column</li>
</div>
+
        <li>Discard the flow-through and place the DF Column back in the Collection tube</li>
<div class="Text3_SubSub">
+
        (If the sample mixture is more than 800μL, repeat the DNA binding step)
[RBS] ----- Result: Failed (Smeared band was too blurred)
+
        <div class="Text_TitleUnderline">Wash</div>
</div>
+
        <li>Add 400μL W1 buffer into the DF Column</li>
<div class="Text3_SubSub">
+
        <li>Spin down for approximately 20 seconds</li>
[C1] ----- Result: Succeeded
+
        <li>Discard the flow-through and place the DF Column back in the Collection tube</li>
</div>
+
        <li>Add 600μL wash buffer (contains ethanol) into the DF Column</li>
<div class="Text3_SubSub">
+
        <li>Let stand for 1 minute at room temperature</li>
[endolysin] ----- Result: Failed (Smeared band was too blurred)
+
        <li>Spin down for approximately 30 seconds</li>
</div>
+
        <li>Discard the flow-through and place the DF Column back in the Collection tube</li>
<div class="Text3">
+
        <li>Centrifuge at 12000 rpm for 3 minutes to dry the column matrix</li>
<Green>PYY part:</Green>
+
        (Can be done twice)
</div>
+
        <li>Discard the flow-through</li>
<div class="Text3_Sub">
+
        <div class="Text_TitleUnderline">DNA Elution</div>
Extract the plasmid:
+
        <li>Transfer the dried DF Column to a new eppendorf (cap cut)</li>
</div>
+
        <li>Add 30μL of 37℃ ddH2O into the center of the column matrix</li>
<div class="Text3_SubSub">
+
        <li>Let stand for at least 2 minutes to ensure that ddH2O is completely absorbed</li>
[signal peptide] (BBa_K554002), [terminator] (BBa_B0015)
+
        <li>Centrifuge at 12000 rpm for 2 minutes to elute the purified DNA</li>
 +
        <li>Re-add the subnatant into the center of the column matrix</li>
 +
        <li>Centrifuge at 12000 rpm for 2 minutes to elute the purified DNA</li>
  
 +
</ol>
 
</div>
 
</div>
<div class="Text3_Sub">
+
<div class="Text1" id="First5"><Red>DNA Ligation</Red></div>
Gel electrophoresis:
+
<div class="Text2">
</div>
+
<Green>Materials and Reagents :</Green>
<div class="Text3_SubSub">
+
</div>
[signal peptide] ----- Result: Succeeded
+
</div>
+
<div class="Text3_SubSub">
+
[terminator] ----- Result: Succeeded
+
</div>
+
 
+
 
+
<div class="Container2"><div class="Text2">7/10</div></div>
+
 
<div class="Text3">
 
<div class="Text3">
<Blue>Manufacture <i>CP<Super>+</Super></i> plate</Blue>
+
<ol class="part1">
</div>
+
<li>DNA (insert & vector)</li>
 +
<li>Ligation high ver.2</li>
 +
</ol>
 +
</div>
 +
<div class="Text2">
 +
<Green>Equipment :</Green>
 +
</div>
 
<div class="Text3">
 
<div class="Text3">
<Blue>Manufacture <i>Amp<Super>+</Super></i> plate</Blue>
+
<ol class="part1">
 +
<li>Cooling dry bath incubator</li>
 +
</ol>
 
</div>
 
</div>
 +
<div class="Text2">
 +
<Green>Procedure :</Green>
 +
</div>
 
<div class="Text3">
 
<div class="Text3">
<Green>Suicide Part:</Green>
+
<ol class="part2">
</div>
+
<li>
<div class="Text3_Sub">
+
Table
Gel electrophoresis:
+
<table>
</div>
+
<tr>
<div class="Text3_SubSub">
+
<th>Components</th>
[RBS] (BBa_B0034) ----- Result: Failed (Smeared band was too blurred)
+
<th>Volume (μL)</th>
</div>
+
</tr>
<div class="Text3_SubSub">
+
<tr>
[C2] (BBa_C0053) ----- Result: Succeeded
+
<td>Insert</td>
</div>
+
<td>x</td>
<div class="Text3_Sub">
+
</tr>
Gel extraction:
+
<tr>
</div>
+
<td>Vector</td>
<div class="Text3_SubSub">
+
<td>y</td>
[C2]
+
</tr>
 +
<tr>
 +
<td>Ligation High</td>
 +
<td>1</td>
 +
</tr>
 +
<tr class="alt">
 +
<td>Total</td>
 +
<td>7</td>
 +
</tr>
 +
</table>
 +
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Molar ratio: insert/vector = 3/1
 +
<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; x + y = 6</br>
 +
</li>
 +
<li>Gently mix the solution by pipetting up and down</li>
 +
<li>Incubate
 +
<ol class="part3">
 +
<li>at 16℃ for 2 hours, or</li>
 +
<li>at 37℃ for 1 hour, or</li>
 +
<li>at 4℃ overnight</li>
 +
</ol>
 +
</li>
 +
<li>Proceed with bacterial transformation</li>
 +
</ol>
 
</div>
 
</div>
  
 
+
<div class="Text1" id="First6"><Red>Plasmid DNA Extraction Using Alkaline Lysis Method (<i>E. coli</i>)</Red></div>
<div class="Container2"><div class="Text2">7/11</div></div>
+
<div class="Text2">
 +
<Green>Materials and Reagents :</Green>
 +
</div>
 
<div class="Text3">
 
<div class="Text3">
<Green>Suicide Part:</Green>
+
<ol class="part1">
</div>
+
<li><i>Escherichia coli</i> DH5α (with plasmid)</li>
<div class="Text3_Sub">
+
<li>LB broth</li>
Extract the plasmid:
+
<li>Resuspension solution (MPI, with RNAase)</li>
</div>
+
<li>Lysis solution (MPII)</li>
<div class="Text3_SubSub">
+
<li>Neutralizing solution (MPIII)</li>
[RBS] (BBa_B0034), [C1] (BBa_C0051), [endolysin] (BBa_K112806)
+
<li>Isopropanol</li>
</div>
+
<li>70% ethanol</li>
 +
<li>ddH<Sub>2</Sub>O</li>
 +
</ol>
 +
</div>
 +
<div class="Text2">
 +
<Green>Equipment :</Green>
 +
</div>
 
<div class="Text3">
 
<div class="Text3">
<Green>PYY part:</Green>
+
<ol class="part1">
 +
<li>Shaker</li>
 +
<li>Centrifuge</li>
 +
<li>Vortex mixer</li>
 +
</ol>
 
</div>
 
</div>
<div class="Text3_Sub">
+
<div class="Text2">
Transformation of:
+
<Green>Procedure :</Green>
</div>
+
</div>
<div class="Text3_SubSub">
+
[promoter] (BBa_J23101)
+
</div>
+
 
+
 
+
<div class="Container2"><div class="Text2">7/12</div></div>
+
 
<div class="Text3">
 
<div class="Text3">
<Green>Suicide Part:</Green>
+
<ol class="part2">
 +
        <li>Grow bacteria in LB broth with appropriate antibiotics at 37℃ overnight with shaking</li>
 +
<li>Transfer 1.5mL culture to an eppendorf</li>
 +
<li>Centrifuge at 4℃, 5000rpm for 5 minutes</li>
 +
<li>Discard the supernatant</li>
 +
        <li>Add 150μL of resuspension solution (MPI, with RNAase) into each tube, pipet several times, and vortex to completely resuspend the cell pellet</li>
 +
        <li>Add 150μL of lysis solution (MPII), gently invert the tubes about 20 times, and then let the sample mixture stand at room temperature for 2 minutes</li>
 +
        <li>Add 150μL of neutralizing solution (MPIII) and mix by inverting the tubes about 20 times. Bacterial chromosomal DNA and proteins can be seen as white precipitates</li>
 +
        <li>Centrifuge at 4℃, 15000rpm for 15 minutes</li>
 +
        <li>Carefully transfer 400μL of the supernatant to a new eppendorf</li>
 +
        (Step 8&9 can be done twice)
 +
        <li>Add 400μL (same volume as the supernatant) isopropanol, and shake up the tubes as vigorously as one can</li>
 +
        <li>Centrifuge at 4℃, 15000rpm for 15 minutes</li>
 +
        <li>Discard the supernatant</li>
 +
        <li>Add 200μL of 70% ethanol to wash out the salts</li>
 +
        <li>Centrifuge at 4℃, 15000rpm for 5 minutes</li>
 +
        <li>Discard the supernatant and remove the remains as much as possible with pipetman</li>
 +
        <li>Air dry for about 30 minutes</li>
 +
        <li>Resuspend the DNA pellet with 20μL ddH<Sub>2</Sub>O</li>
 +
</ol>
 
</div>
 
</div>
<div class="Text3_Sub">
+
<div class="Text1" id="First7"><Red>Transformation (<i>E. coli</i>)</Red></div>
Extract the plasmid:
+
<div class="Text2">
</div>
+
<Green>Materials and Reagents :</Green>
<div class="Text3_SubSub">
+
</div>
[pC1] (BBa_R0051)
+
</div>
+
 
+
 
+
<div class="Container2"><div class="Text2">7/13</div></div>
+
 
<div class="Text3">
 
<div class="Text3">
<Green>PYY part:</Green>
+
<ol class="part1">
</div>
+
<li>Competent cell (<i>Escherichia coli</i> DH5α)</li>
<div class="Text3_Sub">
+
<li>LB plate (Amp+/CP+)</li>
Extract the plasmid:
+
</ol>
</div>
+
</div>
<div class="Text3_SubSub">
+
<div class="Text2">
[promoter] (BBa_J23101)
+
<Green>Equipment :</Green>
</div>
+
</div>
<div class="Text3_Sub">
+
Gel electrophoresis (two white colonies & two red colonies):
+
</div>
+
<div class="Text3_SubSub">
+
[promoter] ------ Result: Failed (white colonies didn’t have band, red colonies had band but not the correct size, we speculated that was pollution)
+
 
+
</div>
+
 
+
 
+
<div class="Container2"><div class="Text2">7/20</div></div>
+
 
<div class="Text3">
 
<div class="Text3">
<Red>Discuss about total synthesis</Red>
+
<ol class="part1">
 +
<li>-80℃ refrigerator</li>
 +
<li>Ice</li>
 +
<li>37℃ incubator</li>
 +
<li>Super optimal broth (SOB) (37℃)</li>
 +
<li>Shaker</li>
 +
</ol>
 
</div>
 
</div>
 
+
<div class="Text2">
 
+
<Green>Procedure :</Green>
<div class="Container2"><div class="Text2">7/13</div></div>
+
</div>
 
<div class="Text3">
 
<div class="Text3">
<Green>PYY part:</Green>
+
<ol class="part2">
</div>
+
        <li>Take out the competent cells from -80℃ refrigerator</li>
<div class="Text3_Sub">
+
        <li>Thaw the cells on ice for 5 minutes</li>
Transformation of:
+
        <li>Add 1μL plasmid DNA into the competent cells, and mix gently by pipetting</li>
</div>
+
        <li>On ice for 10 minutes</li>
<div class="Text3_SubSub">
+
        <li>Heat shock at 37℃ for 3 minutes</li>
[terminator] (BBa_B0015)
+
        <li>On ice for 2 minutes</li>
</div>
+
        <li>Add 150μL 37℃ SOB into the mixture</li>
 +
        <li>Place the tube at 37℃ with shaking for 1 hour(Amp+)/4 hours(CP+) respectively</li>
 +
        <li>Spread the cells onto the LB plates (Amp+/ CP+)</li>
 +
        <li>Incubate the plates at 37℃ with shaking for 12-16 hours</li>
  
 
+
</ol>
<div class="Container2"><div class="Text2">7/24</div></div>
+
<div class="Text3">
+
<Red>Discuss our project with professor</Red>
+
 
</div>
 
</div>
 +
<div class="Text1" id="First8"><Red>Protein Extraction</Red></div>
 +
<div class="Text2">
 +
<Green>Materials and Reagents :</Green>
 +
</div>
 
<div class="Text3">
 
<div class="Text3">
<Green>PYY part:</Green>
+
<ol class="part1">
 +
<li>plasmid/ BL21 competent cell</li>
 +
<li>LB plate</li>
 +
<li>LB broth</li>
 +
<li>lysis buffer</li>
 +
</ol>
 
</div>
 
</div>
<div class="Text3_Sub">
+
<div class="Text2">
Extract the plasmid:
+
<Green>Equipment :</Green>
</div>
+
</div>
<div class="Text3_SubSub">
+
[terminator] (BBa_B0015)
+
</div>
+
<div class="Text3_Sub">
+
Gel electrophoresis:
+
</div>
+
<div class="Text3_SubSub">
+
[terminator] ----- Result: Failed
+
</div>
+
 
+
 
+
<div class="Container2"><div class="Text2">7/25</div></div>
+
 
<div class="Text3">
 
<div class="Text3">
<Red>Discuss our problems with Instructor</Red>
+
<ol class="part1">
 +
<li>15/ 50ml conial tube</li>
 +
<li>Shaking incubator</li>
 +
<li>Erlenmeyer flask</li>
 +
<li>Spectrophotometer</li>
 +
<li>Centrifuge</li>
 +
<li>Sonicator</li>
 +
<li>Eppendorf</li>
 +
</ol>
 
</div>
 
</div>
 
+
<div class="Text2">
 
+
<Green>Procedure :</Green>
<div class="Container2"><div class="Text2">7/26</div></div>
+
</div>
 
<div class="Text3">
 
<div class="Text3">
<Green>PYY part:</Green>
+
<ol class="part2">
 +
<li>Transform plamid into BL21 (see transformation)</li>
 +
<li>Pick up a single colony and incubate into 2ml LB/CP medium, then agitate them in a shaking incubator at 37℃ overnight</li>
 +
<li>Pour the culture into 100ml LB/CP medium, then agitate until it reach A<sub>600</sub> of 0.6</li>
 +
<li>Pour the culture into 50ml conical tube, and centrifuge at 8000rpm for 10 min</li>
 +
<li>Store the supernate and the pellets in the centrifuge tubes in a -80℃ freezer</li>
 +
<li>Use 6ml lysis buffer(NP-10) to resuspend the cell pellet and transfer into a 15ml centrifuge tube</li>
 +
<li>Lyse the cell with sonication</li>
 +
<li>Centrifuge 15ml conial tube at 9000rpm for 10 min</li>
 +
<li>Store the supernate as coarse extract</li>
 +
</ol>
 
</div>
 
</div>
<div class="Text3_SubSub">
+
<div class="Text1" id="First9"><Red>SDS-PAGE</Red></div>
Cultured [terminator] again
+
<div class="Text2">
</div>
+
<Green>Materials and Reagents :</Green>
 
+
</div>
 
+
<div class="Container2"><div class="Text2">7/27</div></div>
+
 
<div class="Text3">
 
<div class="Text3">
<Green>PYY part:</Green>
+
<ol class="part1">
</div>
+
<li>Solution A (acrylamide/ bis-acrylamide (29:1) 30% solution)</li>
<div class="Text3_Sub">
+
<li>Solution B (Tris (Tris base, 1.5 M) 90.8 gm; TEMED 1.8 ml; pH = 8.8/ 500ml)</li>
Extract the plasmid:
+
<li>Solution C (Tris (Tris base, 0.5 M) 6.0 gm; TEMED 0.4 ml; pH = 6.7/ 100ml)</li>
</div>
+
<li>10% SDS (1kb/100bp)</li>
<div class="Text3_SubSub">
+
<li>ddH<Sub>2</Sub>O</li>
[terminator] (BBa_B0015)
+
<li>APS</li>
</div>
+
<li>Running buffer (1M Tris 12.5 ml; glysine 7.7g/ 500ml)</li>
<div class="Text3_Sub">
+
<li>Sample buffer(5X) (Tris base, 125mM X5; EDTA2•Na, 2mM X 5; SDS(2% X2); β-mercaptoethanol, 5% X5)</li>
Gel electrophoresis:
+
<li>Protein marker</li>
</div>
+
</ol>
<div class="Text3_SubSub">
+
</div>
[terminator] ----- Result: Succeeded
+
<div class="Text2">
</div>
+
<Green>Equipment :</Green>
 
+
</div>
 
+
<div class="Container2" id="First2"><div class="Text2">8/2</div></div>
+
 
<div class="Text3">
 
<div class="Text3">
<Green>Suicide Part:</Green>
+
<ol class="part1">
 +
<li>Gel Caster</li>
 +
<li>Accessories for each gel</li>
 +
<li>&nbsp;&nbsp;&nbsp;&nbsp;(1) One glass plate</li>
 +
<li>&nbsp;&nbsp;&nbsp;&nbsp;(2) One aluminum notched plate</li>
 +
        <li>&nbsp;&nbsp;&nbsp;&nbsp;(3) Two 0.75-mm thick spacers</li>
 +
        <li>&nbsp;&nbsp;&nbsp;&nbsp;(4) One 0.75-mm thick 10-well comb</li>
 +
        <li>&nbsp;&nbsp;&nbsp;&nbsp;(5) One well-locating decal</li>
 +
<li>Power supply</li>
 +
</ol>
 
</div>
 
</div>
<div class="Text3_Sub">
+
<div class="Text2">
Extract the plasmid:
+
<Green>Procedure :</Green>
</div>
+
</div>
<div class="Text3_SubSub">
+
[RFP](BBa_E1010)
+
</div>
+
<div class="Text3_Sub">
+
Restriction enzyme:
+
</div>
+
<div class="Text3_SubSub">
+
[RFP] cleave by EcoRI and SpeI
+
</div>
+
        <div class="Text3_SubSub">
+
[Cl] cleave by XbaI and PstI
+
</div>
+
        <div class="Text3_SubSub">
+
[pSB1A3] cleave by EcoRI and PstI
+
</div>
+
 
+
 
+
<div class="Container2"><div class="Text2">8/5</div></div>
+
 
<div class="Text3">
 
<div class="Text3">
<Blue>Passaged L.c.393</Blue>
+
<ol class="part2">
 +
<li>Assemble one glass plate and one alumimum plate with  two spacers for each gel module</li>
 +
<li>Prepare the SDS gel solution (see the table below). Two 0.75mm mini gels need approximately 10ml separation gel solution and 5ml stacking solution. Add APS solution at the final step</li>
 +
        <li>Mix the separation gel solution, and add the solution into the gel module until reaching the designated level. Then add isopropanol on the top of the gel. It takes about 40 min to complete the polymerization step</li>
 +
        <li>Remove the isopropanol by using a small strip of filter paper. Fill up the stacking gel solution until reaching the top. Insert comb into the gel solution as soon as possible. It takes 10 min to complete the polymerization step</li>
 +
        <li>Remove the comb and set the gel in the cell buffer dam. Pour the running buffer into the inner chamber and keep pouring after overflow until the buffer surface reaches the required level in the outer chamber</li>
 +
        <li>Use a micropipette to clean up every single well with the running buffer</li>
 +
        <li>Mix protein samples with 1/5 volumes of 5X sample buffer. Heat the mixture at 100oC for 10 min. Let it cool down to room temperature</li>
 +
        <li>Load protein sample and the protein marker into the well</li>
 +
        <li>Run the electrophoresis at 70V for 20 min, and then 150V for 55 min</li>
 +
        <li>Remove the two spacer and lift the glass plate, and remove the stacking gel and the remaining gel is ready for CBR staining and Western blot</li>
 +
</ol>
 
</div>
 
</div>
 
<div class="Text3">
 
<div class="Text3">
<Blue>Manufacture MRS plate</Blue>
+
<table class="Table_Width">
 +
<tr>
 +
<th>(Unit: ml)</th>
 +
<th>Separation gel</th>
 +
<th></th>
 +
<th></th>
 +
<th></th>
 +
<th></th>
 +
<th></th>
 +
<th>Stacking gel</th>
 +
</tr>
 +
<tr>
 +
<td>Percentage</td>
 +
<td>5%</td>
 +
<td>7.5%</td>
 +
<td>10%</td>
 +
<td>12.5%</td>
 +
<td>15%</td>
 +
<td>20%</td>
 +
<td>4%</td>
 +
</tr>
 +
<tr>
 +
<td>Solution A</td>
 +
<td>16.5</td>
 +
<td>2.5</td>
 +
<td>3.35</td>
 +
<td>4.15</td>
 +
<td>5</td>
 +
<td>6.5</td>
 +
<td>0.66</td>
 +
</tr>
 +
<tr>
 +
<td>Solution B</td>
 +
<td>2.5</td>
 +
<td>2.5</td>
 +
<td>2.5</td>
 +
<td>2.5</td>
 +
<td>2.5</td>
 +
<td>2.5</td>
 +
<td>-</td>
 +
</tr>
 +
<tr>
 +
<td>Solution C</td>
 +
<td>-</td>
 +
<td>-</td>
 +
<td>-</td>
 +
<td>-</td>
 +
<td>-</td>
 +
<td>-</td>
 +
<td>1.24</td>
 +
</tr>
 +
<tr>
 +
<td>10% SDS</td>
 +
<td>0.1</td>
 +
<td>0.1</td>
 +
<td>0.1</td>
 +
<td>0.1</td>
 +
<td>0.1</td>
 +
<td>0.1</td>
 +
<td>0.05</td>
 +
</tr>
 +
<tr>
 +
<td>dH<sub>2</sub>O</td>
 +
<td>5.7</td>
 +
<td>4.85</td>
 +
<td>4</td>
 +
<td>3.2</td>
 +
<td>2.35</td>
 +
<td>0.85</td>
 +
<td>2.95</td>
 +
</tr>
 +
<tr>
 +
<td>APS(10%)</td>
 +
<td>0.05</td>
 +
<td>0.05</td>
 +
<td>0.05</td>
 +
<td>0.05</td>
 +
<td>0.05</td>
 +
<td>0.05</td>
 +
<td>0.1</td>
 +
</tr>
 +
<tr class="alt">
 +
<td>Total Volume</td>
 +
<td>10</td>
 +
<td>10</td>
 +
<td>10</td>
 +
<td>10</td>
 +
<td>10</td>
 +
<td>10</td>
 +
<td>5</td>
 +
</tr>
 +
</table>
 
</div>
 
</div>
 +
<div class="Text1" id="First10"><Red>Western Blot</Red></div>
 +
<div class="Text2">
 +
<Green>Materials and Reagents :</Green>
 +
</div>
 
<div class="Text3">
 
<div class="Text3">
<Green>PYY part</Green>
+
<ol class="part1">
</div>
+
<li>Transfer buffer ( Tris 25mM; glycine 0.192M)</li>
<div class="Text3_Sub">
+
<li>Methanol</li>
Redissoluted DNA of total synthesis
+
<li>10 X TBST (1M Tris pH =8.0; Tween 20, 50ml; NaCl 43.5g)</li>
</div>
+
</ol>
<div class="Text3_Sub">
+
</div>
Restriction enzyme:
+
<div class="Text2">
</div>
+
<Green>Equipment :</Green>
        <div class="Text3_SubSub">
+
</div>
[signalpeptide -PYY] cleave by EcoRI and PstI
+
</div>
+
        <div class="Text3_Sub">
+
Ligation:
+
</div>
+
        <div class="Text3_SubSub">
+
[signalpeptide-PYY]+ [pSB1C3]
+
</div>
+
        <div class="Text3_Sub">
+
Transformation
+
</div>
+
 
+
 
+
<div class="Container2"><div class="Text2">8/6</div></div>
+
 
<div class="Text3">
 
<div class="Text3">
<Blue>Passaged L.c.393</Blue>
+
<ol class="part1">
 +
<li>Semi-dry trnasfer cell</li>
 +
<li>PVDF membrane</li>
 +
<li>Nitrocellulose paper</li>
 +
<li>Square Petri dish</li>
 +
<li>Rotary shaker</li>
 +
</ol>
 
</div>
 
</div>
 +
<div class="Text2">
 +
<Green>Procedure :</Green>
 +
</div>
 
<div class="Text3">
 
<div class="Text3">
<Green>PYY part</Green>
+
<ol class="part2">
 +
        <li>Equilibrate the nitrocellulose paper and SDS-PAGE gel by soaking them with transfer buffer</li>
 +
<li>Rinse the PVDF membrane with 100% methanol for a few second and equilibrate it with transfer buffer</li>
 +
<li>Place the elements in the following order onto the semi-dry transfer cell from bottom to top: nitrocellulose paper, PVDF membrane, SDS-PAGE gel, nitrocellulose paper</li>
 +
<li>Set up the current at 0.09A and run for 75 min</li>
 +
</ol>
 
</div>
 
</div>
<div class="Text3_Sub">
+
<div class="Text1" id="First11"><Red>Immunostaining</Red></div>
Restriction enzyme:
+
<div class="Text2">
</div>
+
<Green>Materials and Reagents :</Green>
<div class="Text3_SubSub">
+
</div>
[PYY] cleave by EcoRI and PstI
+
</div>
+
<div class="Text3_SubSub">
+
[TAT-PYY] cleave by EcoRI and PstI
+
</div>
+
<div class="Text3_SubSub">
+
[Y2R] cleave by KpnI and XhoI
+
</div>
+
<div class="Text3_Sub">
+
Ligation:
+
</div>
+
<div class="Text3_SubSub">
+
[PYY]+ [pSB1C3]
+
</div>
+
<div class="Text3_SubSub">
+
[TAT-PYY]+ [pSB1C3]
+
</div>
+
<div class="Text3_SubSub">
+
[Y2R]+[pcDNA]
+
</div>
+
<div class="Text3_Sub">
+
Transformation
+
</div>
+
 
+
 
+
<div class="Container2"><div class="Text2">8/7</div></div>
+
 
<div class="Text3">
 
<div class="Text3">
<Green>PYY part</Green>
+
<ol class="part1">
</div>
+
<li>3% milk</li>
<div class="Text3_Sub">
+
<li>Antibody solution</li>
Gel electrophoresis:
+
<li>Secondary antibody (anti-mouse HRP)</li>
</div>
+
<li>TBST</li>
<div class="Text_underline">
+
<li>Western HRP substrate</li>
Result:
+
</ol>
</div>
+
</div>
<div class="Text3_SubSub">
+
<div class="Text2">
signalpeptide-PYY] ----- Failed (Smeared band was too blurred)
+
<Green>Equipment :</Green>
</div>
+
</div>
<div class="Text3_SubSub">
+
[PYY] ----- Failed (Smeared band was too blurred)
+
</div>
+
<div class="Text3_Sub">
+
Transform again
+
</div>
+
 
+
 
+
<div class="Container2"><div class="Text2">8/10</div></div>
+
 
<div class="Text3">
 
<div class="Text3">
<Blue>Manufacture CP<sup>+</sup> plate</Blue>
+
<ol class="part1">
 +
<li>Square petri dish</li>
 +
<li>Rotary shaker</li>
 +
<li>UVP Biospectrum</li>
 +
</ol>
 
</div>
 
</div>
 +
<div class="Text2">
 +
<Green>Procedure :</Green>
 +
</div>
 
<div class="Text3">
 
<div class="Text3">
<Green>Suicide part</Green>
+
<ol class="part2">
</div>
+
<li>Put the membrane in the square petri dish block the membrane with the 3% milk/TBST at room temperature for 1hr</li>
<div class="Text3_Sub">
+
<li>Discard the milk and replace it with antibody solution(mouse His-probe Antibody) at 4℃ overnight</li>
Gel electrophoresis:
+
        <li>Recycle the antibody solution. Wash the membrane with TBST three times, 5 min each</li>
</div>
+
        <li>Soak membrane into anti-mouse HRP solution for 1 hr</li>
<div class="Text_underline">
+
        <li>Discard the anti-mouse HRP solution and wash it with TBST three times, 5 min each</li>
Result:
+
        <li>Add HRP substrate on the membrane for 1 min</li>
</div>
+
        <li>Soak the membrane into ddH<sub>2</sub>O to remove the substrate</li>
<div class="Text3_SubSub">
+
        <li>Observe the result with UVP Biospectrum</li>
[RFP+Terminator] ----- Failed (Confirmed it was pollution)
+
</ol>
</div>
+
<div class="Text3_SubSub">
+
[Cl+Terminator] ----- Failed
+
</div>
+
<div class="Text3_Sub">
+
Clean up:
+
</div>
+
<div class="Text3_Sub">
+
[RFP+Terminator]
+
 
</div>
 
</div>
 +
<div class="Text1" id="First12"><Red>Thawing Caco-2 cells</Red></div>
 +
<div class="Text2">
 +
<Green>Materials and Reagents :</Green>
 +
</div>
 
<div class="Text3">
 
<div class="Text3">
<Green>PYY part</Green>
+
<ol class="part1">
</div>
+
<li>1 ml frozen Caco-2 cells in cryovial</li>
<div class="Text3_Sub">
+
<li>Cell culture medium (MEM (minimum essential medium) (GIBCOTM #41500-034)/2.2g NaHCO3/ 0.11 g sodium pyruvate/20% FBS/1% PSA) </li>
Clean up:
+
<li>70% ethanol</li>
</div>
+
<li>Trypan blue solution</li>
<div class="Text3_SubSub">
+
</ol>
[signalpeptide-PYY]+ [pSB1A3]
+
</div>
</div>
+
<div class="Text2">
<div class="Text3_SubSub">
+
<Green>Equipment :</Green>
[PYY]+ [pSB1A3]
+
</div>
</div>
+
<div class="Text3_SubSub">
+
[TAT-PYY]+ [pSB1A3]
+
</div>
+
<div class="Text3_SubSub">
+
[Y2R]+[pcDNA]
+
</div>
+
<div class="Text3_Sub">
+
Transformation
+
</div>
+
 
+
 
+
<div class="Container2"><div class="Text2">8/11</div></div>
+
 
<div class="Text3">
 
<div class="Text3">
<Green>Suicide part</Green>
+
<ol class="part1">
</div>
+
<li>Laminar flow hood</li>
<div class="Text3_Sub">
+
<li>Auto pipette</li>
Clean up:
+
<li>Centrifuge</li>
</div>
+
<li>15 ml centrifuge tubes</li>
<div class="Text3_SubSub">
+
<li>10 cm dish</li>
[Cl+Terminator]
+
<li>Hemocytometer</li>
</div>
+
<li>Optical microscope</li>
<div class="Text3_Sub">
+
<li>Suction machine</li>
Gel electrophoresis
+
</ol>
</div>
+
<div class="Text_underline">
+
Result:
+
</div>
+
<div class="Text3_SubSub">
+
[RFP+Terminator]----- Failed (Smeared band was too blurred)
+
</div>
+
<div class="Text3_SubSub">
+
[Cl+Terminator] ----- Failed (Smeared band was too blurred)
+
 
</div>
 
</div>
 +
<div class="Text2">
 +
<Green>Procedure :</Green>
 +
</div>
 
<div class="Text3">
 
<div class="Text3">
<Green>PYY part</Green>
+
<ol class="part2">
 +
<li>Pre-warm medium in 37˚C water bath</li>
 +
<li>Open a laminar flow hood</li>
 +
        <li>Clean materials, reagents and equipments before moving them into the hood</li>
 +
        <li>Thawing Caco-2 cells in 37˚C water bath and transfer the cells into a 15ml centrifuge tube</li>
 +
        <li>Add 9 ml cell culture medium very slowly</li>
 +
        <li>Centrifuge at 1000 rpm for 5 min</li>
 +
        <li>Decant the supernate and resuspend cells with 10 ml cell culture medium</li>
 +
        <li>Mix 10 ul cell suspension and 10 μl trypan blue solution and count total cell number with a hemocytometer</li>
 +
        <li>Add all cell suspension to a 10 cm dish</li>
 +
        <li>Write date, cell line and passage number</li>
 +
        <li>Put the dish into incubator</li>
 +
</ol>
 
</div>
 
</div>
<div class="Text3_Sub">
+
<div class="Text1" id="First13"><Red>Freezing Caco-2 cells</Red></div>
Extract the plasmid:
+
<div class="Text2">
</div>
+
<Green>Materials and Reagents :</Green>
<div class="Text3_SubSub">
+
</div>
[TAT-PYY], [Y2R]
+
</div>
+
 
+
 
+
<div class="Container2"><div class="Text2">8/12</div></div>
+
 
<div class="Text3">
 
<div class="Text3">
<Green>Suicide part</Green>
+
<ol class="part1">
</div>
+
<li>Caco-2 cell in 10 cm dish</li>
<div class="Text3_Sub">
+
<li>Cell culture medium (MEM (minimum essential medium) (GIBCOTM #10370-021)/10% FBS/ 2 mM glutamine</li>
Redissoluted DNA of total synthesis
+
<li>1X PBS (phosphate buffer saline)</li>
</div>
+
<li>0.5% trypsin</li>
<div class="Text3_Sub">
+
<li>Trypan blue solution</li>
Restriction enzyme:
+
<li>70% ethanol</li>
</div>
+
<li>Cell freezing media (50% FBS, 40% cell culture medium, 10% DMSO)</li>
<div class="Text3_SubSub">
+
</ol>
[Lac-RBS] cleave by EcoRI and PstI
+
</div>
</div>
+
<div class="Text2">
<div class="Text3_SubSub">
+
<Green>Equipment :</Green>
[NucA-Terminator] cleave by EcoRI and PstI
+
</div>
</div>
+
<div class="Text3_SubSub">
+
[NIsI] cleave by EcoRI and PstI
+
</div>
+
<div class="Text3_SubSub">
+
[LcSPddhol] cleave by EcoRI and PstI
+
</div>
+
<div class="Text3_Sub">
+
Ligation:
+
</div>
+
<div class="Text3_SubSub">
+
[Lac-RBS]+ [pSB1C3]
+
</div>
+
<div class="Text3_SubSub">
+
[NucA-Terminator]+ [pSB1C3]
+
</div>
+
<div class="Text3_SubSub">
+
[NIsI]+ [pSB1C3]
+
</div>
+
<div class="Text3_SubSub">
+
[LcSPddhol]+ [pSB1C3]
+
</div>
+
<div class="Text3_Sub">
+
Transformation
+
</div>
+
 
<div class="Text3">
 
<div class="Text3">
<Green>PYY part</Green>
+
<ol class="part1">
 +
<li>Laminar flow hood</li>
 +
<li>Auto pipette</li>
 +
<li>Centrifuge</li>
 +
<li>15 ml centrifuge tubes</li>
 +
<li>10 cm dish</li>
 +
<li>Hemocytometer</li>
 +
<li>Optical microscope</li>
 +
<li>Suction machine</li>
 +
<li>Cryovials</li>
 +
<li>Freezing apparatus</li>
 +
<li>-80˚C refrigerator</li>
 +
<li>Liquid nitrogen tank</li>
 +
</ol>
 
</div>
 
</div>
<div class="Text3_Sub">
+
<div class="Text2">
Gel electrophoresis:
+
<Green>Procedure :</Green>
</div>
+
</div>
<div class="Text_underline">
+
Result:
+
</div>
+
<div class="Text3_SubSub">
+
[TAT-PYY]----- Failed(Confirmed it was pollution)
+
</div>
+
<div class="Text3_SubSub">
+
[Cll] ----- Succeeded
+
</div>
+
 
+
 
+
<div class="Container2"><div class="Text2">8/13</div></div>
+
 
<div class="Text3">
 
<div class="Text3">
<Green>Suicide part</Green>
+
<ol class="part2">
</div>
+
<li>Pre-warm medium in 37˚C water bath</li>
<div class="Text3_Sub">
+
<li>Open a laminar flow hood</li>
Extract the plasmid:
+
        <li>Clean materials, reagents and equipments before moving them into the hood</li>
</div>
+
        <li>Take a 10 cm dish with Caco-2 cell</li>
<div class="Text3_SubSub">
+
        <li>Discard the medium with a suction machine</li>
[Lac-RBS]+ [pSB1C3]
+
        <li>Wash the cells with 5 ml PBS</li>
</div>
+
        <li>Add 1 ml 0.5% trypsin and incubate at 37˚C for 7 minutes</li>
<div class="Text3_SubSub">
+
        <li>Wash out all the cells from the surface of the dish by pipetting the fresh complete culture medium (9 ml) all over the surface</li>
[NucA-Terminator]+ [pSB1C3]
+
        <li>Transfer the cell suspension to a 15 ml centrifuge tube</li>
</div>
+
        <li>Mix 10 μl cell suspension and 10 ul trypan blue solution and count total cell number with a hemocytometer</li>
<div class="Text3_SubSub">
+
        <li>Add about 1x10<sup>6</sup> cells per cryovial, and add cell freezing media</li>
[NIsI]+ [pSB1C3]
+
        <li>Freeze the cryovials in a controlled rate freezing apparatus, decreasing the temperature approximately 1°C per minute in a -80°C refrigerator for more than 3 hour, then move them into liquid nitrogen tank</li>
</div>
+
</ol>
<div class="Text3_Sub">
+
Clean up:
+
</div>
+
<div class="Text3_SubSub">
+
[Cl], [terminator], [RFP]
+
</div>
+
<div class="Text3_Sub">
+
Ligation:
+
</div>
+
<div class="Text3_SubSub">
+
[Cl]+ [terminator]
+
</div>
+
<div class="Text3_SubSub">
+
[RFP]+ [terminator]
+
</div>
+
<div class="Text3_Sub">
+
Gel electrophoresis:
+
</div>
+
<div class="Text_underline">
+
Result:
+
</div>
+
<div class="Text3_SubSub">
+
[Cl]+ [terminator] ----- Succeeded
+
</div>
+
<div class="Text3_SubSub">
+
[RFP]+ [terminator] ----- Succeeded
+
 
</div>
 
</div>
 +
<div class="Text1" id="First14"><Red>Caco2 Cell passage</Red></div>
 +
<div class="Text2">
 +
<Green>Materials and Reagents :</Green>
 +
</div>
 
<div class="Text3">
 
<div class="Text3">
<Green>PYY part</Green>
+
<ol class="part1">
</div>
+
<li>Caco-2 cell in 10 cm dish</li>
<div class="Text3_Sub">
+
<li>Cell culture medium (MEM (minimum essential medium) (GIBCOTM #10370-021)/10% FBS/ 2 mM glutamine</li>
Extract the plasmid:
+
<li>1X PBS (phosphate buffer saline)</li>
</div>
+
<li>0.5% trypsin</li>
<div class="Text3_SubSub">
+
<li>Trypan blue solution</li>
[LcSPddhol]+ [pSB1C3]
+
<li>70% ethanol</li>
</div>
+
</ol>
<div class="Text3_Sub">
+
</div>
Clean up:
+
<div class="Text2">
</div>
+
<Green>Equipment :</Green>
<div class="Text3_SubSub">
+
</div>
[TAT-PYY]
+
</div>
+
 
+
 
+
<div class="Container2"><div class="Text2">8/14</div></div>
+
 
<div class="Text3">
 
<div class="Text3">
<Blue>DNA sequencing:</Blue>
+
<ol class="part1">
</div>
+
<li>Laminar flow hood</li>
<div class="Text3_Sub">
+
<li>Auto pipette</li>
[SP-PYY], [PYY], [Y2R], [Lac-RBS], [NucA-Terminator], [NIsI], [LcSPddhol]
+
<li>Centrifuge</li>
 +
<li>15 ml centrifuge tubes</li>
 +
<li>10 cm dish</li>
 +
<li>Hemocytometer</li>
 +
<li>Optical microscope</li>
 +
<li>Suction machine</li>
 +
</ol>
 
</div>
 
</div>
 +
<div class="Text2">
 +
<Green>Procedure :</Green>
 +
</div>
 
<div class="Text3">
 
<div class="Text3">
<Green>Suicide part</Green>
+
<ol class="part2">
 +
<li>Pre-warm medium in 37˚C water bath</li>
 +
<li>Open a laminar flow hood</li>
 +
        <li>Clean materials, reagents and equipments before moving them into the hood</li>
 +
        <li>Take a 10 cm dish with Caco-2 cell</li>
 +
        <li>Discard the medium with a suction machine</li>
 +
        <li>Wash the cells with 5 ml PBS</li>
 +
        <li>Add 1 ml 0.5% trypsin and incubate at 37˚C for 7 minutes</li>
 +
        <li>Wash out all the cells from the surface of the dish by pipetting the fresh complete culture medium (9 ml) all over the surface</li>
 +
        <li>Transfer the cell suspension to a 15 ml centrifuge tube</li>
 +
        <li>Mix 10 ul cell suspension and 10 μl trypan blue solution and count total cell number with a hemocytometer</li>
 +
        <li>Transfer appropriate amounts of cell suspension to new dishes (1/4 X)</li>
 +
        <li>Write date, cell line and passage number</li>
 +
        <li>Put the dish into incubator</li>
 +
</ol>
 
</div>
 
</div>
<div class="Text3_Sub">
+
<div class="Text1" id="First15"><Red>Seeding in transwell</Red></div>
Ligation:
+
<div class="Text2">
</div>
+
<Green>Materials and Reagents :</Green>
<div class="Text3_SubSub">
+
</div>
[Cl]+ [terminator]
+
</div>
+
<div class="Text3_Sub">
+
Gel electrophoresis:
+
</div>
+
<div class="Text_underline">
+
Result:
+
</div>
+
<div class="Text3_SubSub">
+
[Lac-RBS] ----- Succeeded
+
</div>
+
<div class="Text3_SubSub">
+
[NucA-Terminator] ----- Succeeded
+
</div>
+
<div class="Text3_SubSub">
+
[NIsI] ----- Succeeded
+
</div>
+
<div class="Text3_Sub">
+
[LcSPddhol] ----- Succeeded
+
</div>
+
<div class="Text3_Sub">
+
Extract the plasmid:  
+
</div>
+
<div class="Text3_SubSub">
+
[RFP-terminator]
+
</div>
+
 
+
 
+
<div class="Container2"><div class="Text2">8/15</div></div>
+
 
<div class="Text3">
 
<div class="Text3">
<Blue>Passaged L.c.393</Blue>
+
<ol class="part1">
</div>
+
<li>Caco-2 cell in 10 cm dish</li>
 +
<li>Cell culture medium (MEM (minimum essential medium) (GIBCOTM #41500-034)/2.2 g NaHCO3/ 0.11 g sodium pyruvate/20% FBS/1% PSA</li>
 +
<li>1X PBS (phosphate buffer saline)</li>
 +
<li>0.5% trypsin</li>
 +
<li>Trypan blue solution</li>
 +
<li>70% ethanol</li>
 +
</ol>
 +
</div>
 +
<div class="Text2">
 +
<Green>Equipment :</Green>
 +
</div>
 
<div class="Text3">
 
<div class="Text3">
<Green>Suicide part</Green>
+
<ol class="part1">
</div>
+
<li>Laminar flow hood</li>
<div class="Text3_Sub">
+
<li>Auto pipette</li>
Extract the plasmid:
+
<li>Centrifuge</li>
</div>
+
<li>15 ml centrifuge tubes</li>
<div class="Text3_SubSub">
+
<li>10 cm dish</li>
[Cl-terminator]
+
<li>Hemocytometer</li>
</div>
+
<li>Optical microscope</li>
<div class="Text3_Sub">
+
<li>Suction machine</li>
Gel electrophoresis:
+
<li>6-well plate</li>
</div>
+
<li>Millicell plate insert (PIHP03050)</li>
<div class="Text_underline">
+
</ol>
Result:
+
</div>
+
<div class="Text3_SubSub">
+
[RFP-terminator] ----- Succeeded
+
</div>
+
<div class="Text3_SubSub">
+
[Cl-terminator] ----- Succeeded
+
 
</div>
 
</div>
 +
<div class="Text2">
 +
<Green>Procedure :</Green>
 +
</div>
 
<div class="Text3">
 
<div class="Text3">
<Green>PYY part</Green>
+
<ol class="part2">
 +
<li>Open 6-well plate, add 1.5 mL medium to each large well (6 wells) which are going to be used</li>
 +
<li>Add 2 ml PBS/well to other wells</li>
 +
        <li>Put transwell in larger well</li>
 +
        <li>Take a 10 cm dish with Caco-2 cell</li>
 +
        <li>Discard the medium with a suction machine</li>
 +
        <li>Wash the cells with 5 ml PBS</li>
 +
        <li>Add 1 ml 0.5% trypsin and incubate at 37˚C for 7 minutes</li>
 +
        <li>Wash out all the cells from the surface of the dish by pipetting the fresh complete culture medium (9 ml) all over the surface</li>
 +
        <li>Transfer the cell suspension to a 15 ml centrifuge tube</li>
 +
        <li>Mix 10 ul cell suspension and 10 μl trypan blue solution and count total cell number with a hemocytometer</li>
 +
        <li>Cell count: 70/ 2 * orginal volume *100 (*10<sup>4</sup>)= 35 X 10<sup>4</sup> cell/mL (Seeding 42 x 10<sup>4</sup> cell/well)</li>
 +
        <li>Write date, cell line and passage number</li>
 +
        <li>Put the dish into incubator</li>
 +
</ol>
 
</div>
 
</div>
<div class="Text3_Sub">
+
<div class="Text1" id="First16"><Red>Measure TEER</Red></div>
Extract the plasmid:
+
<div class="Text2">
</div>
+
<Green>Materials and Reagents :</Green>
<div class="Text3_SubSub">
+
</div>
[TAT-PYY]
+
</div>
+
<div class="Text3_Sub">
+
Transformation of [TAT-PYY]
+
</div>
+
<div class="Text3_Sub">
+
Restriction enzyme:
+
</div>
+
<div class="Text3_SubSub">
+
[TAT-PYY] cleave by EcoRI and PstI
+
</div>
+
<div class="Text3_Sub">
+
Gel electrophoresis:
+
</div>
+
<div class="Text_underline">
+
Result:
+
</div>
+
<div class="Text3_SubSub">
+
[TAT-PYY] ----- Succeeded
+
</div>
+
 
+
 
+
<div class="Container2"><div class="Text2">8/16</div></div>
+
 
<div class="Text3">
 
<div class="Text3">
<Blue>Passaged L.c.393</Blue>
+
<ol class="part1">
</div>
+
<li>Caco-2 cells seeded in transwell</li>
 +
<li>70% ethanol</li>
 +
</ol>
 +
</div>
 +
<div class="Text2">
 +
<Green>Equipment :</Green>
 +
</div>
 
<div class="Text3">
 
<div class="Text3">
<Blue>Manufacture LB broth</Blue>
+
<ol class="part1">
 +
<li>Laminar flow hood</li>
 +
<li>Millicell ERS</li>
 +
</ol>
 
</div>
 
</div>
 +
<div class="Text2">
 +
<Green>Procedure :</Green>
 +
</div>
 
<div class="Text3">
 
<div class="Text3">
<Blue>Manufacture MRS broth</Blue>
+
<ol class="part2">
</div>
+
<li>Prepare laminar hood for experiment</li>
<div class="Text3">
+
<li>To sterilize electrode of Millicell ERS, soak electrode in 70% alcohol for 15 min, and air dry for 15 sec</li>
<Green>Suicide part</Green>
+
        <li>Measure TEER value of each well (n=3)</li>
</div>
+
</ol>
<div class="Text3_Sub">
+
Restriction enzyme:
+
</div>
+
<div class="Text3_SubSub">
+
[Cl-Terminator] cleave by EcoRI and PstI
+
</div>
+
<div class="Text3_SubSub">
+
[RFP-Terminator] cleave by EcoRI and PstI
+
</div>
+
<div class="Text3">
+
<Green>PYY part</Green>
+
</div>
+
<div class="Text3_Sub">
+
Transformation of [SP-PYY], [PYY], [TAT-PYY]
+
 
</div>
 
</div>
  
  
<div class="Container2"><div class="Text2">8/17</div></div>
 
<div class="Text3">
 
<Green>Suicide part</Green>
 
</div>
 
<div class="Text3_Sub">
 
Ligation:
 
</div>
 
<div class="Text3_SubSub">
 
[plac-RFP-T], [plac-Cl-T]
 
</div>
 
<div class="Text3_Sub">
 
Transformation of [plac-RFP-T], [plac-Cl-T]
 
</div>
 
<div class="Text3">
 
<Green>PYY part</Green>
 
</div>
 
<div class="Text3_Sub">
 
Culture [SP-PYY], [PYY], [TAT-PYY] in BL21 Competent
 
</div>
 
<div class="Text3_Sub">
 
<i>E. coli</i> and Rosetta Competent <i>E. coli</i>
 
</div>
 
 
 
<div class="Container2"><div class="Text2">8/18</div></div>
 
<div class="Text3">
 
<Green>Suicide part</Green>
 
</div>
 
<div class="Text3_Sub">
 
Culture [plac-RFP], [plac-Cl], [NucA] in LB broth
 
</div>
 
<div class="Text3_Sub">
 
Extract the plasmid:
 
</div>
 
<div class="Text3_SubSub">
 
[plac-RFP], [plac-Cl]
 
</div>
 
<div class="Text3_Sub">
 
Gel electrophoresis:
 
</div>
 
<div class="Text_underline">
 
Result:
 
</div>
 
<div class="Text3_SubSub">
 
[plac-RFP] ----- Succeeded
 
</div>
 
<div class="Text3_SubSub">
 
[plac-Cl] ----- Succeeded
 
</div>
 
<div class="Text3">
 
<Green>PYY part</Green>
 
</div>
 
<div class="Text3_Sub">
 
Western blot ([SP-PYY], [PYY], [TAT-PYY]):
 
</div>
 
<div class="Text3_SubSub">
 
Sonication of Competent <i>E. coli</i>
 
</div>
 
 
 
<div class="Container2"><div class="Text2">8/19</div></div>
 
<div class="Text3">
 
<Green>Suicide part</Green>
 
</div>
 
<div class="Text3_Sub">
 
Extract the plasmid:
 
</div>
 
<div class="Text3_SubSub">
 
[NucA]
 
</div>
 
<div class="Text3_Sub">
 
Gel electrophoresis:
 
</div>
 
<div class="Text_underline">
 
Result:
 
</div>
 
<div class="Text3_SubSub">
 
[NucA] ----- Succeeded
 
</div>
 
<div class="Text3">
 
<Green>PYY part</Green>
 
</div>
 
<div class="Text3_Sub">
 
Western blot ([SP-PYY], [PYY], [TAT-PYY]):
 
</div>
 
<div class="Text3_SubSub">
 
SDS-page
 
</div>
 
<div class="Text3_SubSub">
 
Transfer
 
</div>   
 
<div class="Text3_SubSub">
 
Blocking
 
</div>
 
<div class="Text3_SubSub">
 
Primary antibody
 
</div>
 
 
 
<div class="Container2"><div class="Text2">8/20</div></div>
 
<div class="Text3">
 
<Blue>Passaged Caco2 cell</Blue>
 
</div>
 
<div class="Text3">
 
<Green>Suicide part</Green>
 
</div>
 
<div class="Text3_Sub">
 
Gel Purification:
 
</div>
 
<div class="Text3_SubSub">
 
[plac-Cl-T], [pCl-NucA-T]
 
</div>
 
<div class="Text3_Sub">
 
Ligation:
 
</div>
 
<div class="Text3_SubSub">
 
[plac-Cl-T], [pCl-NucA-T]
 
</div>
 
<div class="Text3_Sub">
 
Transformation of [plac-Cl-T], [pCl-NucA-T]
 
</div>
 
<div class="Text3">
 
<Green>PYY part</Green>
 
</div>
 
<div class="Text3_Sub">
 
Western blot ([SP-PYY], [PYY], [TAT-PYY]):
 
</div>
 
<div class="Text3_SubSub">
 
Secondary antibody
 
</div>   
 
<div class="Text3_SubSub">
 
Chemiluminescent detection
 
</div>
 
<div class="Text_underline">
 
Result:
 
</div>
 
<div class="Text3_SubSub">
 
[SP-PYY] ----- Failed (no band displayed)
 
</div>
 
<div class="Text3_SubSub">
 
[PYY] ----- Failed (no band displayed)
 
</div>
 
<div class="Text3_SubSub">
 
[TAT-PYY] ----- Failed (no band displayed)
 
</div>
 
<div class="Text3_Sub">
 
Western blot ([SP-PYY], [PYY], [TAT-PYY]):
 
</div>
 
<div class="Text3_SubSub">
 
SDS-page
 
</div>
 
<div class="Text3_SubSub">
 
Transfer
 
</div>   
 
<div class="Text3_SubSub">
 
Blocking
 
</div>
 
<div class="Text3_SubSub">
 
Primary antibody
 
</div>
 
 
 
<div class="Container2"><div class="Text2">8/21</div></div>
 
<div class="Text3">
 
<Green>Suicide part</Green>
 
</div>
 
<div class="Text3_Sub">
 
Culture [[plac-Cl-T], [pCl-NucA-T] in LB broth
 
</div>
 
<div class="Text3_Sub">
 
Extract the plasmid:
 
</div>
 
<div class="Text3_SubSub">
 
[plac-Cl-T], [pCl-NucA-T]
 
</div>
 
<div class="Text3_Sub">
 
Gel electrophoresis:
 
</div>
 
<div class="Text_underline">
 
Result:
 
</div>
 
<div class="Text3_SubSub">
 
[plac-Cl-T] ----- Succeeded
 
</div>
 
<div class="Text3_SubSub">
 
[pCl-NucA-T] ----- Failed (band was too blurred)
 
</div>
 
<div class="Text3">
 
<Green>PYY part</Green>
 
</div>
 
<div class="Text3_Sub">
 
Western blot ([SP-PYY], [PYY], [TAT-PYY]):
 
</div>
 
<div class="Text3_SubSub">
 
Secondary antibody
 
</div>   
 
<div class="Text3_SubSub">
 
Chemiluminescent detection
 
</div>
 
<div class="Text_underline">
 
Result:
 
</div>
 
<div class="Text3_SubSub">
 
[SP-PYY] ----- Failed (band was too blurred)
 
</div>
 
<div class="Text3_SubSub">
 
[PYY] ----- Failed (no band displayed)
 
</div>
 
<div class="Text3_SubSub">
 
[TAT-PYY] ----- Failed (no band displayed)
 
</div>
 
<div class="Text3_Sub">
 
Transformation of [SP-PYY], [PYY], [TAT-PYY], [RFP] again. (use [RFP] as negative control)
 
</div>
 
<div class="Text3_Sub">
 
Culture [SP-PYY], [PYY], [TAT-PYY] , [RFP] in BL21
 
</div>
 
<div class="Text3_Sub">
 
Competent <i>E. coli</i> and Rosetta Competent <i>E. coli</i>
 
</div>
 
 
 
<div class="Container2"><div class="Text2">8/22</div></div>
 
<div class="Text3">
 
<Green>PYY part</Green>
 
</div>
 
<div class="Text3_Sub">
 
Western blot ([SP-PYY], [PYY], [TAT-PYY] , [RFP]):
 
</div>
 
<div class="Text3_SubSub">
 
Sonication of Competent <i>E. coli</i>
 
</div>
 
 
 
<div class="Container2"><div class="Text2">8/23</div></div>
 
<div class="Text3">
 
<Green>PYY part</Green>
 
</div>
 
<div class="Text3_Sub">
 
Western blot ([SP-PYY], [PYY], [TAT-PYY] , [RFP]):
 
</div>
 
<div class="Text3_SubSub">
 
SDS-page
 
</div>
 
<div class="Text3_SubSub">
 
Transfer
 
</div>   
 
<div class="Text3_SubSub">
 
Blocking
 
</div>
 
<div class="Text3_SubSub">
 
Primary antibody
 
</div>
 
 
 
<div class="Container2"><div class="Text2">8/24</div></div>
 
<div class="Text3">
 
<Green>Suicide part</Green>
 
</div>
 
<div class="Text3_Sub">
 
Restriction enzyme:
 
</div>
 
<div class="Text3_SubSub">
 
[NucA] cleave by SpeI and PstI
 
</div>
 
<div class="Text3">
 
<Green>PYY part</Green>
 
</div>
 
<div class="Text3_Sub">
 
Western blot ([SP-PYY], [PYY], [TAT-PYY]):
 
</div>
 
<div class="Text3_SubSub">
 
Secondary antibody
 
</div>   
 
<div class="Text3_SubSub">
 
Chemiluminescent detection
 
</div>
 
<div class="Text_underline">
 
Result:
 
</div>
 
<div class="Text3_SubSub">
 
[SP-PYY] ----- Failed (band was not specificity)
 
</div>
 
<div class="Text3_SubSub">
 
[PYY] ----- Failed (band was not specificity)
 
</div>
 
<div class="Text3_SubSub">
 
[TAT-PYY] ----- Failed (band was not specificity)
 
</div>
 
<div class="Text3_Sub">
 
Culture [SP-PYY], [PYY], [TAT-PYY] , [RFP]in mini
 
</div>
 
 
 
<div class="Container2"><div class="Text2">8/25</div></div>
 
<div class="Text3">
 
<Green>Suicide part</Green>
 
</div>
 
<div class="Text3_Sub">
 
Restriction enzyme:
 
</div>
 
<div class="Text3_SubSub">
 
[plac-C1-T-backbone] cleave by EcoRI
 
</div>
 
<div class="Text3_Sub">
 
Gel electrophoresis:
 
</div>
 
<div class="Text_underline">
 
Result:
 
</div>
 
<div class="Text3_SubSub">
 
[plac-C1-T] ----- Failed
 
</div>
 
<div class="Text3_Sub">
 
Redissoluted [pJ23102]
 
</div>
 
<div class="Text3_Sub">
 
Transformation of [pCl], [pCll], [RBS], [pJ23102]
 
</div>
 
<div class="Text3_Sub">
 
Culture [pCl], [pCll], [RBS] in LB broth
 
</div>
 
<div class="Text3">
 
<Green>PYY part</Green>
 
</div>
 
<div class="Text3_Sub">
 
Culture [SP-PYY], [PYY], [TAT-PYY] , [RFP] in midi
 
</div>
 
<div class="Text3_Sub">
 
Centrifugal and took the supernatant
 
</div>   
 
<div class="Text3_Sub">
 
Bradford protein assay
 
</div>
 
 
 
<div class="Container2"><div class="Text2">8/26</div></div>
 
<div class="Text3">
 
<Blue>Passaged Caco2 cell</Blue>
 
</div>
 
<div class="Text3">
 
<Green>Suicide part</Green>
 
</div>
 
<div class="Text3_Sub">
 
Ligation:
 
</div>
 
<div class="Text3_SubSub">
 
[plac-Cl-T]
 
</div>
 
<div class="Text3_Sub">
 
Transformation of [plac-Cl-T]
 
</div>
 
<div class="Text3_Sub">
 
Extract the plasmid:
 
</div>
 
<div class="Text3_SubSub">
 
[plac], [pCl], [pCll], [RBS]
 
</div>
 
<div class="Text3">
 
<Green>PYY part</Green>
 
</div>
 
<div class="Text3_Sub">
 
Western blot ([SP-PYY], [PYY], [TAT-PYY], [RFP]):
 
</div>
 
<div class="Text3_SubSub">
 
SDS-page
 
</div>
 
<div class="Text3_SubSub">
 
Transfer
 
</div>   
 
<div class="Text3_SubSub">
 
Blocking
 
</div>
 
<div class="Text3_SubSub">
 
Primary antibody
 
</div>
 
 
 
<div class="Container2"><div class="Text2">8/27</div></div>
 
<div class="Text3">
 
<Green>Suicide part</Green>
 
</div>
 
<div class="Text3_Sub">
 
Transformation of [RBS-Cl-T], [RBS-RFP-T]
 
</div>
 
<div class="Text3_Sub">
 
Culture [plac-Cl-T],[RBS-Cl-T],[RBS-RFP-T],[pJ23102] in LB broth
 
</div>
 
<div class="Text3_Sub">
 
Extract the plasmid:
 
</div>
 
<div class="Text3_SubSub">
 
[plac-Cl-T], [pJ23102]
 
</div>
 
<div class="Text3_Sub">
 
Gel electrophoresis:
 
</div>
 
<div class="Text_underline">
 
Result:
 
</div>
 
<div class="Text3_SubSub">
 
[plac-Cl-T] ----- Succeeded
 
</div>
 
<div class="Text3_SubSub">
 
[pJ23102] ----- Succeeded
 
</div>
 
<div class="Text3_Sub">
 
Restriction enzyme:
 
</div>
 
<div class="Text3_SubSub">
 
[pCl-T] cleave by SpeI and PstI
 
</div>
 
<div class="Text3_Sub">
 
Gel Purification:
 
</div>
 
<div class="Text3_SubSub">
 
[pCll]
 
</div>
 
<div class="Text3">
 
<Green>PYY part</Green>
 
</div>
 
<div class="Text3_Sub">
 
Western blot ([SP-PYY], [PYY], [TAT-PYY], [RFP]):
 
</div>
 
<div class="Text3_SubSub">
 
Secondary antibody
 
</div>
 
<div class="Text3_SubSub">
 
Chemiluminescent detection
 
</div>   
 
<div class="Text_underline">
 
Result:
 
</div>
 
<div class="Text3_SubSub">
 
[SP-PYY] ----- Failed (no band displayed)
 
</div>
 
<div class="Text3_SubSub">
 
[PYY] ----- Failed (no band displayed)
 
</div>
 
<div class="Text3_SubSub">
 
[TAT-PYY] ----- Failed (no band displayed)
 
</div>
 
<div class="Text3_Sub">
 
Transformation of [SP-PYY], [PYY], [TAT-PYY], [RFP] again
 
</div>
 
<div class="Text3_Sub">
 
Culture [SP-PYY], [PYY], [TAT-PYY] , [RFP] in BL21
 
</div>
 
<div class="Text3_Sub">
 
Competent <i>E. coli</i>
 
</div>
 
 
 
<div class="Container2"><div class="Text2">8/28</div></div>
 
<div class="Text3">
 
<Green>Suicide part</Green>
 
</div>
 
<div class="Text3_Sub">
 
Ligation:
 
</div>
 
<div class="Text3_SubSub">
 
[pCIt]+[NucA]
 
</div>
 
<div class="Text3_Sub">
 
Extract the plasmid:
 
</div>
 
<div class="Text3_SubSub">
 
[Cl-T], [RFP-T]
 
</div>
 
<div class="Text3_Sub">
 
Gel electrophoresis:
 
</div>
 
<div class="Text_underline">
 
Result:
 
</div>
 
<div class="Text3_SubSub">
 
[Cl-T] ----- Failed (band size was wrong)
 
</div>
 
  <div class="Text3_SubSub">
 
[RFP-T] ----- Failed (band size was wrong)
 
</div>
 
<div class="Text3_Sub">
 
Restriction enzyme:
 
</div>
 
  <div class="Text3_SubSub">
 
[plac-T] cleave by SpeI and PstI
 
</div>
 
  <div class="Text3_SubSub">
 
[pJ23102] cleave by SpeI and PstI
 
</div>
 
<div class="Text3_Sub">
 
Gel Purification:
 
</div>
 
<div class="Text3_SubSub">
 
[pCI-T]
 
</div>
 
<div class="Text3">
 
<Green>PYY part</Green>
 
</div>
 
<div class="Text3_Sub">
 
Western blot ([SP-PYY], [PYY], [TAT-PYY], [RFP]):
 
</div>
 
<div class="Text3_SubSub">
 
SDS-page
 
</div>
 
<div class="Text3_SubSub">
 
Transfer
 
</div>   
 
<div class="Text3_SubSub">
 
Blocking
 
</div>
 
<div class="Text3_SubSub">
 
Primary antibody
 
</div>
 
 
 
<div class="Container2"><div class="Text2">8/29</div></div>
 
<div class="Text3">
 
<Blue>Passaged Caco2 cell</Blue>
 
</div>
 
<div class="Text3">
 
<Green>Suicide part</Green>
 
</div>
 
<div class="Text3_Sub">
 
Extract the plasmid:
 
</div>
 
<div class="Text3_SubSub">
 
[RBS-Cl-T], [RBS-RFP-T]
 
</div>
 
<div class="Text3">
 
<Green>PYY part</Green>
 
</div>
 
<div class="Text3_Sub">
 
Western blot ([SP-PYY], [PYY], [TAT-PYY], [RFP]):
 
</div>
 
<div class="Text3_SubSub">
 
Secondary antibody
 
</div>
 
<div class="Text3_SubSub">
 
Chemiluminescent detection
 
</div>   
 
<div class="Text_underline">
 
Result:
 
</div>
 
<div class="Text3_SubSub">
 
[SP-PYY] ----- Failed (no band displayed)
 
</div>
 
<div class="Text3_SubSub">
 
[PYY] ----- Failed (no band displayed)
 
</div>
 
<div class="Text3_SubSub">
 
[TAT-PYY] ----- Failed (no band displayed)
 
</div>
 
<div class="Text3_Sub">
 
Histag column([SP-PYY], [PYY], [TAT-PYY] , [RFP])
 
</div>
 
<div class="Text3_Sub">
 
Western blot ([SP-PYY], [PYY], [TAT-PYY], [RFP]):
 
</div>
 
<div class="Text3_SubSub">
 
SDS-page
 
</div>
 
<div class="Text3_SubSub">
 
Transfer
 
</div>   
 
<div class="Text3_SubSub">
 
Blocking
 
</div>
 
<div class="Text3_SubSub">
 
Primary antibody
 
</div>
 
 
 
<div class="Container2"><div class="Text2">8/30</div></div>
 
<div class="Text3">
 
<Green>Suicide part</Green>
 
</div>
 
<div class="Text3_Sub">
 
Extract the plasmid:
 
</div>
 
<div class="Text3_SubSub">
 
[RBS], [pCl]
 
</div>
 
<div class="Text3_Sub">
 
Gel electrophoresis:
 
</div>
 
<div class="Text_underline">
 
Result:
 
</div>
 
<div class="Text3_SubSub">
 
[RBS] ----- Succeeded
 
</div>
 
<div class="Text3_SubSub">
 
[pCl] ----- Failed
 
</div>
 
<div class="Text3">
 
<Green>PYY part</Green>
 
</div>
 
<div class="Text3_Sub">
 
Western blot ([SP-PYY], [PYY], [TAT-PYY], [RFP]):
 
</div>
 
<div class="Text3_SubSub">
 
Secondary antibody
 
</div>
 
<div class="Text3_SubSub">
 
Chemiluminescent detection
 
</div>   
 
<div class="Text_underline">
 
Result:
 
</div>
 
<div class="Text3_SubSub">
 
[SP-PYY] ----- Failed (no band displayed)
 
</div>
 
<div class="Text3_SubSub">
 
[PYY] ----- Failed (no band displayed)
 
</div>
 
<div class="Text3_SubSub">
 
[TAT-PYY] ----- Failed (no band displayed)
 
</div>
 
 
 
<div class="Container2"><div class="Text2">8/31</div></div>
 
<div class="Text3">
 
<Blue>Passaged hek293 cell</Blue>
 
</div>
 
<div class="Text3">
 
<Green>Suicide part</Green>
 
</div>
 
<div class="Text3_Sub">
 
Gel Purification:
 
</div>
 
<div class="Text3_SubSub">
 
[RBS], [CI-T]
 
</div>
 
<div class="Text3">
 
<Green>PYY part</Green>
 
</div>
 
<div class="Text3_Sub">
 
Western blot ([SP-PYY], [PYY], [TAT-PYY], [RFP]):
 
</div>
 
<div class="Text3_SubSub">
 
SDS-page
 
</div>
 
<div class="Text3_SubSub">
 
Transfer
 
</div>   
 
<div class="Text3_SubSub">
 
Blocking
 
</div>
 
<div class="Text3_SubSub">
 
Primary antibody
 
</div>
 
 
 
<div class="Container2" id="First3"><div class="Text2">9/1</div></div>
 
<div class="Text3">
 
<Green>Suicide part</Green>
 
</div>
 
<div class="Text3_Sub">
 
Ligation:
 
</div>
 
<div class="Text3_SubSub">
 
[RBS] + [CI-T]
 
</div>
 
<div class="Text3_Sub">
 
Culture [RBS- CI-T] in LB broth
 
</div>
 
<div class="Text3">
 
<Green>PYY part</Green>
 
</div>
 
<div class="Text3_Sub">
 
Western blot ([SP-PYY], [PYY], [TAT-PYY], [RFP]):
 
</div>
 
<div class="Text3_SubSub">
 
Secondary antibody
 
</div>
 
<div class="Text3_SubSub">
 
Chemiluminescent detection
 
</div>   
 
<div class="Text_underline">
 
Result:
 
</div>
 
<div class="Text3_SubSub">
 
[SP-PYY] ----- Failed (no band displayed)
 
</div>
 
<div class="Text3_SubSub">
 
[PYY] ----- Failed (no band displayed)
 
</div>
 
<div class="Text3_SubSub">
 
[TAT-PYY] ----- Failed (no band displayed)
 
</div>
 
<div class="Text3_Sub">
 
Transformation of [SP-PYY], [PYY], [TAT-PYY], [pETDuet-1]
 
</div>
 
<div class="Text3">
 
<Green>Selection part</Green>
 
</div>
 
<div class="Text3_Sub">
 
Culture [nisI] in MRS broth
 
</div>
 
 
 
<div class="Container2"><div class="Text2">9/2</div></div>
 
<div class="Text3">
 
<Green>Suicide part</Green>
 
</div>
 
<div class="Text3_Sub">
 
Extract the plasmid:
 
</div>
 
<div class="Text3_SubSub">
 
[RBS- CI-T]
 
</div>
 
<div class="Text3_Sub">
 
Gel electrophoresis:
 
</div>
 
<div class="Text_underline">
 
Result:
 
</div>
 
<div class="Text3_SubSub">
 
[RBS- CI-T] ----- Succeeded
 
</div>
 
<div class="Text3">
 
<Green>PYY part</Green>
 
</div>
 
<div class="Text3_Sub">
 
Extract the plasmid:
 
</div>
 
<div class="Text3_SubSub">
 
[SP-PYY], [PYY], [TAT-PYY], [pETDuet-1]
 
</div>
 
<div class="Text3_Sub">
 
Restriction enzyme:
 
</div>
 
<div class="Text3_SubSub">
 
[SP-PYY] cleave by EcoRI
 
</div>
 
<div class="Text3_SubSub">
 
[PYY] cleave by EcoRI
 
</div>
 
<div class="Text3_SubSub">
 
[TAT-PYY] cleave by EcoRI
 
</div>
 
<div class="Text3_SubSub">
 
[pETDuet-1] cleave by EcoRI
 
</div>   
 
<div class="Text3_Sub">
 
Gel electrophoresis:
 
</div>
 
<div class="Text_underline">
 
Result:
 
</div>
 
<div class="Text3_SubSub">
 
[SP-PYY] ----- Succeeded
 
</div>
 
<div class="Text3_SubSub">
 
[PYY] ----- Succeeded
 
</div>
 
<div class="Text3_SubSub">
 
[TAT-PYY] ----- Succeeded
 
</div>
 
<div class="Text3_SubSub">
 
[pETDuet-1] ----- Succeeded
 
</div>
 
<div class="Text3">
 
<Green>Selection part</Green>
 
</div>
 
<div class="Text3_Sub">
 
Nisin Immunity Test
 
</div>
 
<div class="Text3_Sub">
 
Culture [nisI] in LB broth
 
</div>
 
 
 
<div class="Container2"><div class="Text2">9/3</div></div>
 
<div class="Text3">
 
<Green>PYY part</Green>
 
</div>
 
<div class="Text3_Sub">
 
Restriction enzyme:
 
</div>
 
<div class="Text3_SubSub">
 
[SP-PYY] cleave by XbaI and PstI
 
</div>
 
<div class="Text3_SubSub">
 
[PYY] cleave by XbaI and PstI
 
</div>
 
<div class="Text3_SubSub">
 
[TAT-PYY] cleave by XbaI and PstI
 
</div>
 
<div class="Text3_SubSub">
 
[pETDuet-1] cleave by XbaI and PstI
 
</div>
 
<div class="Text3_Sub">
 
Gel electrophoresis:
 
</div>
 
<div class="Text_underline">
 
Result:
 
</div>
 
<div class="Text3_SubSub">
 
[SP-PYY] ----- Failed (small band didn’t display)
 
</div>
 
<div class="Text3_SubSub">
 
[PYY] ----- Failed (small band didn’t display)
 
</div>
 
<div class="Text3_SubSub">
 
[TAT-PYY] ----- Failed(small band didn’t display)
 
</div>
 
<div class="Text3_SubSub">
 
[pETDuet-1] ----- Succeeded
 
</div>
 
<div class="Text3_Sub">
 
Again -->
 
</div>
 
<div class="Text3_Sub">
 
Restriction enzyme:
 
</div>
 
<div class="Text3_SubSub">
 
[SP-PYY] cleave by XbaI and PstI
 
</div>
 
<div class="Text3_SubSub">
 
[PYY] cleave by XbaI and PstI
 
</div>
 
<div class="Text3_SubSub">
 
[TAT-PYY] cleave by XbaI and PstI
 
</div>
 
<div class="Text3_SubSub">
 
[pETDuet-1] cleave by XbaI and PstI
 
</div>
 
<div class="Text3_Sub">
 
Gel electrophoresis:
 
</div>   
 
<div class="Text_underline">
 
Result:
 
</div>
 
<div class="Text3_SubSub">
 
[SP-PYY] ----- Succeeded
 
</div>
 
<div class="Text3_SubSub">
 
[PYY] ----- Succeeded
 
</div>
 
<div class="Text3_SubSub">
 
[TAT-PYY] ----- Succeeded
 
</div>
 
<div class="Text3_SubSub">
 
[pETDuet-1] ----- Succeeded
 
</div>
 
<div class="Text3_Sub">
 
16℃ Ligation 4hr:
 
</div>
 
<div class="Text3_SubSub">
 
[SP-PYY]+ [pETDuet-1] ----- Failed
 
</div>
 
<div class="Text3_SubSub">
 
[PYY]+ [pETDuet-1] ----- Failed
 
</div>
 
<div class="Text3_SubSub">
 
[TAT-PYY]+ [pETDuet-1] ----- Failed
 
</div>
 
<div class="Text3">
 
<Green>Selection part</Green>
 
</div>
 
<div class="Text3_Sub">
 
Extract the plasmid:
 
</div>
 
<div class="Text3_SubSub">
 
[nisI-pSB1C3]
 
</div>
 
<div class="Text3_Sub">
 
Restriction enzyme:
 
</div>
 
<div class="Text3_SubSub">
 
[nisI-pSB1C3] cleave by XbaI and PstI
 
</div>
 
<div class="Text3_Sub">
 
Gel electrophoresis:
 
</div>
 
<div class="Text_underline">
 
Result:
 
</div>
 
<div class="Text3_SubSub">
 
[nisI-pSB1C3] ----- Succeeded
 
</div>
 
<div class="Text3_Sub">
 
Nisin Immunity Test
 
</div>
 
 
 
<div class="Container2"><div class="Text2">9/4</div></div>
 
<div class="Text3">
 
<Green>Suicide part</Green>
 
</div>
 
<div class="Text3_Sub">
 
Ligation:
 
</div>
 
<div class="Text3_SubSub">
 
[pJ23102] + [RBS-CI-T]
 
</div>
 
<div class="Text3_SubSub">
 
[plac] + [RBS-CI-T]
 
</div>
 
<div class="Text3_Sub">
 
Transformation of [pJ23102-RBS-CI-T], [plac-RBS-CI-T]
 
</div>
 
<div class="Text3">
 
<Green>PYY part</Green>
 
</div>
 
<div class="Text3_Sub">
 
Restriction enzyme:
 
</div>
 
<div class="Text3_SubSub">
 
[SP-PYY] cleave by XbaI and PstI
 
</div>
 
<div class="Text3_SubSub">
 
[PYY] cleave by XbaI and PstI
 
</div>
 
<div class="Text3_SubSub">
 
[TAT-PYY] cleave by XbaI and PstI
 
</div>
 
<div class="Text3_SubSub">
 
[pETDuet-1] cleave by XbaI and PstI
 
</div>
 
<div class="Text3_Sub">
 
Gel electrophoresis:
 
</div>   
 
<div class="Text_underline">
 
Result:
 
</div>
 
<div class="Text3_SubSub">
 
[SP-PYY] ----- Succeeded
 
</div>
 
<div class="Text3_SubSub">
 
[PYY] ----- Succeeded
 
</div>
 
<div class="Text3_SubSub">
 
[TAT-PYY] ----- Succeeded
 
</div>
 
<div class="Text3_SubSub">
 
[pETDuet-1] ----- Succeeded
 
</div>
 
<div class="Text3_Sub">
 
Gel Purification:
 
</div>
 
<div class="Text3_SubSub">
 
[SP-PYY], [PYY], [TAT-PYY], [pETDuet-1]
 
</div>
 
<div class="Text3_Sub">
 
16℃ Ligation 4hr:
 
</div>
 
<div class="Text3_SubSub">
 
[SP-PYY]+ [pETDuet-1] ----- Failed
 
</div>
 
<div class="Text3_SubSub">
 
[PYY]+ [pETDuet-1] ----- Failed
 
</div>
 
<div class="Text3_SubSub">
 
[TAT-PYY]+ [pETDuet-1] ----- Failed
 
</div>
 
 
 
<div class="Container2"><div class="Text2">9/5</div></div>
 
<div class="Text3">
 
<Green>Suicide part</Green>
 
</div>
 
<div class="Text3_Sub">
 
Culture[pJ23102-RBS-CI-T], [plac-RBS-CI-T] in LB broth
 
</div>
 
<div class="Text3">
 
<Green>PYY part</Green>
 
</div>
 
<div class="Text3_Sub">
 
Restriction enzyme:
 
</div>
 
<div class="Text3_SubSub">
 
[SP-PYY] cleave by XbaI and PstI
 
</div>
 
<div class="Text3_SubSub">
 
[PYY] cleave by XbaI and PstI
 
</div>
 
<div class="Text3_SubSub">
 
[TAT-PYY] cleave by XbaI and PstI
 
</div>
 
<div class="Text3_SubSub">
 
[pETDuet-1] cleave by XbaI and PstI
 
</div>
 
<div class="Text3_Sub">
 
Gel electrophoresis:
 
</div>   
 
<div class="Text_underline">
 
Result:
 
</div>
 
<div class="Text3_SubSub">
 
[SP-PYY] ----- Succeeded
 
</div>
 
<div class="Text3_SubSub">
 
[PYY] ----- Succeeded
 
</div>
 
<div class="Text3_SubSub">
 
[TAT-PYY] ----- Succeeded
 
</div>
 
<div class="Text3_SubSub">
 
[pETDuet-1] ----- Succeeded
 
</div>
 
<div class="Text3_Sub">
 
Gel Purification:
 
</div>
 
<div class="Text3_SubSub">
 
[SP-PYY], [PYY], [TAT-PYY], [pETDuet-1]
 
</div>
 
<div class="Text3_Sub">
 
16℃ Ligation 4hr:
 
</div>
 
<div class="Text3_SubSub">
 
[SP-PYY]+ [pETDuet-1]
 
</div>
 
<div class="Text3_SubSub">
 
[PYY]+ [pETDuet-1]
 
</div>
 
<div class="Text3_SubSub">
 
[TAT-PYY]+ [pETDuet-1]
 
</div>
 
<div class="Text3_Sub">
 
Transformation of [SP-PYY-pETDuet-1], [PYY-pETDuet-1], [TAT-PYY-pETDuet-1]
 
</div>
 
<div class="Text3_Sub">
 
Transformation of [SP-PYY], [PYY], [TAT-PYY], [pETDuet-1]
 
</div>
 
<div class="Text3_Sub">
 
Measure the resistance of Caco2 cell
 
</div>
 
 
 
<div class="Container2"><div class="Text2">9/6</div></div>
 
<div class="Text3">
 
<Green>Suicide part</Green>
 
</div>
 
<div class="Text3_Sub">
 
Extract the plasmid:
 
</div>
 
<div class="Text3_SubSub">
 
[placE-RBS-CI-T], [pJ23102-RBS-CI-T], [placE]
 
</div>
 
<div class="Text3_Sub">
 
Gel electrophoresis:
 
</div>
 
<div class="Text_underline">
 
Result:
 
</div>
 
<div class="Text3_SubSub">
 
[placE-RBS-CI-T] ----- Failed
 
</div>
 
<div class="Text3_SubSub">
 
[pJ23102-RBS-CI-T] ----- Succeeded
 
</div>
 
<div class="Text3_SubSub">
 
[placE] ----- Succeeded
 
</div>
 
<div class="Text3">
 
<Green>PYY part</Green>
 
</div>
 
<div class="Text3_Sub">
 
Extract the plasmid:
 
</div>
 
<div class="Text3_SubSub">
 
[SP-PYY-pETDuet-1],[PYY-pETDuet-1], [TAT-PYY-pETDuet-1]
 
</div>
 
<div class="Text3_Sub">
 
Restriction enzyme:
 
</div>
 
<div class="Text3_SubSub">
 
[SP-PYY-pETDuet-1] cleave by XbaI and PstI
 
</div>
 
<div class="Text3_SubSub">
 
[PYY-pETDuet-1] cleave by XbaI and PstI
 
</div>
 
<div class="Text3_SubSub">
 
[TAT-PYY-pETDuet-1] cleave by XbaI and PstI
 
</div>
 
<div class="Text3_Sub">
 
Gel electrophoresis:
 
</div>
 
<div class="Text_underline">
 
Result:
 
</div>   
 
<div class="Text3_SubSub">
 
[SP-PYY-pETDuet-1] ----- Failed
 
</div>
 
<div class="Text3_SubSub">
 
[PYY-pETDuet-1] ----- Failed
 
</div>
 
<div class="Text3_SubSub">
 
[TAT-PYY-pETDuet-1] ----- Failed
 
</div>
 
<div class="Text3_Sub">
 
Extract the plasmid:
 
</div>
 
<div class="Text3_SubSub">
 
[SP-PYY], [PYY], [TAT-PYY], [pETDuet-1]
 
</div>
 
<div class="Text3_Sub">
 
Restriction enzyme:
 
</div>
 
<div class="Text3_SubSub">
 
[SP-PYY] cleave by XbaI and PstI
 
</div>
 
<div class="Text3_SubSub">
 
[PYY] cleave by XbaI and PstI
 
</div>
 
<div class="Text3_SubSub">
 
[TAT-PYY] cleave by XbaI and PstI
 
</div>
 
<div class="Text3_SubSub">
 
[pETDuet-1] cleave by XbaI and PstI
 
</div>
 
<div class="Text3_Sub">
 
Gel electrophoresis:
 
</div>
 
<div class="Text_underline">
 
Result:
 
</div>
 
<div class="Text3_SubSub">
 
[SP-PYY-pETDuet-1]-----Failed(Ligation failed)
 
</div>
 
<div class="Text3_SubSub">
 
[PYY-pETDuet-1] ----- Failed(Ligation failed)
 
</div>
 
<div class="Text3_SubSub">
 
[TAT-PYY-pETDuet-1]-----Failed(Ligation failed)
 
</div>
 
<div class="Text3_Sub">
 
Measure the resistance of Caco2 cell
 
</div>
 
 
 
<div class="Container2"><div class="Text2">9/7</div></div>
 
<div class="Text3">
 
<Green>Suicide part</Green>
 
</div>
 
<div class="Text3_Sub">
 
Restriction enzyme:
 
</div>
 
<div class="Text3_SubSub">
 
[placE] cleave by SpeI and PstI
 
</div>
 
<div class="Text3_SubSub">
 
[RBS-CI-T] cleave by XbaI and PstI
 
</div>
 
<div class="Text3_Sub">
 
Transformation of [pCLP7]
 
</div>
 
<div class="Text3_Sub">
 
Restriction enzyme:
 
</div>
 
<div class="Text3_SubSub">
 
[pCLP7] cleave by XbaI and PstI
 
</div>
 
<div class="Text3_SubSub">
 
[nisi] cleave by XbaI and PstI
 
</div>
 
<div class="Text3">
 
<Green>PYY part</Green>
 
</div>
 
<div class="Text3_Sub">
 
Restriction enzyme:
 
</div>
 
<div class="Text3_SubSub">
 
[SP-PYY] cleave by XbaI and PstI
 
</div>
 
<div class="Text3_SubSub">
 
[PYY] cleave by XbaI and PstI
 
</div>
 
<div class="Text3_SubSub">
 
[TAT-PYY] cleave by XbaI and PstI
 
</div>
 
<div class="Text3_SubSub">
 
[pETDuet-1] cleave by XbaI and PstI
 
</div>
 
<div class="Text3_Sub">
 
Restriction enzyme:
 
</div>
 
<div class="Text3_SubSub">
 
[SP-PYY-pETDuet-1] cleave by XbaI and PstI
 
</div>
 
<div class="Text3_SubSub">
 
[PYY-pETDuet-1] cleave by XbaI and PstI
 
</div>
 
<div class="Text3_SubSub">
 
[TAT-PYY-pETDuet-1] cleave by XbaI and PstI
 
</div>
 
<div class="Text3_Sub">
 
Gel electrophoresis:
 
</div>
 
<div class="Text_underline">
 
Result:
 
</div>   
 
<div class="Text3_SubSub">
 
[SP-PYY] ----- Failed(small band didn’t display)
 
</div>
 
<div class="Text3_SubSub">
 
[PYY] ----- Failed(small band didn’t display)
 
</div>
 
<div class="Text3_SubSub">
 
[TAT-PYY] ----- Failed(small band didn’t display)
 
</div>
 
<div class="Text3_SubSub">
 
[pETDuet-1]-----Failed(small band didn’t display)
 
</div>
 
<div class="Text3_SubSub">
 
[SP-PYY-pETDuet-1]-----Failed(Ligation failed)
 
</div>
 
<div class="Text3_SubSub">
 
[PYY-pETDuet-1] ----- Failed(Ligation failed)
 
</div>
 
<div class="Text3_SubSub">
 
[TAT-PYY-pETDuet-1]-----Failed(Ligation failed)
 
</div>
 
<div class="Text3_Sub">
 
Measure the resistance of Caco2 cell
 
</div>
 
<div class="Text3">
 
<Green>Selection part</Green>
 
</div>
 
<div class="Text3_Sub">
 
Construction of the plasmid:
 
</div>
 
<div class="Text3_SubSub">
 
[nisI- pCLP7]
 
</div>
 
<div class="Text3_Sub">
 
Restriction enzyme:
 
</div>
 
<div class="Text3_SubSub">
 
[nisI- pCLP7] cleave by XbaI and PstI
 
</div>
 
<div class="Text3_Sub">
 
Gel electrophoresis:
 
</div>
 
<div class="Text_underline">
 
Result:
 
</div>
 
<div class="Text3_SubSub">
 
[nisI- pCLP7] ----- Succeeded
 
</div>
 
<div class="Text3_Sub">
 
Clean up:
 
</div>
 
<div class="Text3_SubSub">
 
[pCLP7]
 
</div>
 
<div class="Text3_Sub">
 
Ligation:
 
</div>
 
<div class="Text3_SubSub">
 
[nisI] + [pCLP7]
 
</div>
 
<div class="Text3_Sub">
 
Transformation of [nisI- pCLP7]
 
</div>
 
 
 
<div class="Container2"><div class="Text2">9/8</div></div>
 
<div class="Text3">
 
<Green>Suicide part</Green>
 
</div>
 
<div class="Text3_Sub">
 
Restriction enzyme:
 
</div>
 
<div class="Text3_SubSub">
 
[pCLP7] cleave by XbaI and PstI
 
</div>
 
<div class="Text3_SubSub">
 
[plac-RBS-RFP-T] cleave by XbaI and PstI
 
</div>
 
<div class="Text3_Sub">
 
Ligation:
 
</div>
 
<div class="Text3_SubSub">
 
[pCLP7] + [plac-RBS-RFP-T]
 
</div>
 
<div class="Text3_Sub">
 
Manufacture competent cell with [pJ23102-RBS-CI-T]
 
</div>
 
<div class="Text3">
 
<Green>PYY part</Green>
 
</div>
 
<div class="Text3_Sub">
 
Restriction enzyme:
 
</div>
 
<div class="Text3_SubSub">
 
[SP-PYY] cleave by XbaI and PstI
 
</div>
 
<div class="Text3_SubSub">
 
[PYY] cleave by XbaI and PstI
 
</div>
 
<div class="Text3_SubSub">
 
[TAT-PYY] cleave by XbaI and PstI
 
</div>
 
<div class="Text3_SubSub">
 
[pETDuet-1] cleave by XbaI and PstI
 
</div>
 
<div class="Text3_Sub">
 
Gel electrophoresis:
 
</div>
 
<div class="Text_underline">
 
Result:
 
</div>   
 
<div class="Text3_SubSub">
 
[SP-PYY] ----- Succeeded
 
</div>
 
<div class="Text3_SubSub">
 
[PYY] ----- Succeeded
 
</div>
 
<div class="Text3_SubSub">
 
[TAT-PYY] ----- Succeeded
 
</div>
 
<div class="Text3_SubSub">
 
[pETDuet-1]-----Succeeded
 
</div>
 
<div class="Text3_Sub">
 
Gel Purification:
 
</div>
 
<div class="Text3_SubSub">
 
[SP-PYY], [PYY], [TAT-PYY], [pETDuet-1]
 
</div>
 
<div class="Text3_Sub">
 
4℃ Ligation overnight:
 
</div>
 
<div class="Text3_SubSub">
 
[SP-PYY]+ [pETDuet-1]
 
</div>   
 
<div class="Text3_SubSub">
 
[PYY]+ [pETDuet-1]
 
</div>
 
<div class="Text3_SubSub">
 
[TAT-PYY]+ [pETDuet-1]
 
</div>
 
<div class="Text3_Sub">
 
Measure the resistance of Caco2 cell
 
</div>
 
<div class="Text3_Sub">
 
Transfect hek293 cell
 
</div>
 
<div class="Text3">
 
<Green>Selection part</Green>
 
</div>
 
<div class="Text3_Sub">
 
Culture [nisI- pCLP7] in LB broth
 
</div>
 
 
 
<div class="Container2"><div class="Text2">9/9</div></div>
 
<div class="Text3">
 
<Blue>Passaged hek293 cell</Blue>
 
</div>
 
<div class="Text3">
 
<Green>Suicide part</Green>
 
</div>
 
<div class="Text3_Sub">
 
Extract the plasmid:
 
</div>
 
<div class="Text3_SubSub">
 
[pCLP7], [place-RBS-CI-T]
 
</div>
 
<div class="Text3_Sub">
 
Gel electrophoresis:
 
</div>
 
<div class="Text_underline">
 
Result:
 
</div>
 
<div class="Text3_SubSub">
 
[pCLP7] ----- Succeeded
 
</div>
 
<div class="Text3_SubSub">
 
[place-RBS-CI-T]-----Failed(concentration to low)
 
</div>
 
<div class="Text3_Sub">
 
Transformation of [plac-RBS-RFP-T- pCIp]
 
</div>
 
<div class="Text3_Sub">
 
Transformation of [plac-RBS-CI-T-NucA] in competent cell with [pJ23102-RBS-CI-T]
 
</div>
 
<div class="Text3">
 
<Green>PYY part</Green>
 
</div>
 
<div class="Text3_Sub">
 
Transformation of [SP-PYY-pETDuet-1], [PYY-pETDuet-1], [TAT-PYY-pETDuet-1]
 
</div>
 
<div class="Text3_Sub">
 
Restriction enzyme:
 
</div>
 
<div class="Text3_SubSub">
 
[SP-PYY] cleave by XbaI and PstI
 
</div>
 
<div class="Text3_SubSub">
 
[PYY] cleave by XbaI and PstI
 
</div>
 
<div class="Text3_SubSub">
 
[TAT-PYY] cleave by XbaI and PstI
 
</div>
 
<div class="Text3_SubSub">
 
[pETDuet-1] cleave by XbaI and PstI
 
</div>
 
<div class="Text3_Sub">
 
Gel electrophoresis:
 
</div>
 
<div class="Text_underline">
 
Result:
 
</div>   
 
<div class="Text3_SubSub">
 
[SP-PYY] ----- Succeeded
 
</div>
 
<div class="Text3_SubSub">
 
[PYY] ----- Succeeded
 
</div>
 
<div class="Text3_SubSub">
 
[TAT-PYY] ----- Succeeded
 
</div>
 
<div class="Text3_SubSub">
 
[pETDuet-1]-----Succeeded
 
</div>
 
<div class="Text3_Sub">
 
Measure the resistance of Caco2 cell
 
</div>
 
<div class="Text3">
 
<Green>Selection part</Green>
 
</div>
 
<div class="Text3_Sub">
 
Extract the plasmid:
 
</div>
 
<div class="Text3_SubSub">
 
[nisI- pCLP7]
 
</div>
 
<div class="Text3_Sub">
 
Restriction enzyme:
 
</div>
 
<div class="Text3_SubSub">
 
[nisI- pCLP7] cleave by XbaI and PstI
 
</div>
 
<div class="Text3_Sub">
 
Gel electrophoresis:
 
</div>
 
<div class="Text_underline">
 
Result:
 
</div>
 
<div class="Text3_SubSub">
 
[nisI- pCLP7] ----- Failed
 
</div>
 
 
 
<div class="Container2"><div class="Text2">9/10</div></div>
 
<div class="Text3">
 
<Green>Suicide part</Green>
 
</div>
 
<div class="Text3_Sub">
 
Extract the plasmid:
 
</div>
 
<div class="Text3_SubSub">
 
[plac-RBS-RFP-T- pCLP7]
 
</div>
 
<div class="Text3_Sub">
 
Gel electrophoresis:
 
</div>
 
<div class="Text_underline">
 
Result:
 
</div>
 
<div class="Text3_SubSub">
 
[plac-RBS-RFP-T- pCLP7] ----- Failed
 
</div>
 
<div class="Text3_Sub">
 
Manufacture L.casei competent cell
 
</div>
 
<div class="Text3_Sub">
 
Electroporation of [pCIp] in L.casei competent cell
 
</div>
 
<div class="Text3">
 
<Green>PYY part</Green>
 
</div>
 
<div class="Text3_Sub">
 
Gel Purification:
 
</div>
 
<div class="Text3_SubSub">
 
[SP-PYY], [PYY], [TAT-PYY], [pETDuet-1]
 
</div>
 
<div class="Text3_Sub">
 
4℃ Ligation overnight:
 
</div>
 
<div class="Text3_SubSub">
 
[SP-PYY]+ [pETDuet-1]
 
</div>
 
<div class="Text3_SubSub">
 
[PYY]+ [pETDuet-1]
 
</div>
 
<div class="Text3_SubSub">
 
[TAT-PYY]+ [pETDuet-1]
 
</div>
 
<div class="Text3_Sub">
 
Extract the plasmid:
 
</div>
 
<div class="Text3_SubSub">
 
[SP-PYY-pETDuet-1],[PYY-pETDuet-1], [TAT-PYY-pETDuet-1]
 
</div>   
 
<div class="Text3_Sub">
 
Restriction enzyme:
 
</div>
 
<div class="Text3_SubSub">
 
[SP-PYY-pETDuet1] cleave by EcoRI and SpeI
 
</div>
 
<div class="Text3_SubSub">
 
[PYY-pETDuet-1] cleave by EcoRI and SpeI
 
</div>
 
<div class="Text3_SubSub">
 
[TAT-PYY-pETDuet1] cleave by EcoRI and SpeI
 
</div>
 
<div class="Text3_Sub">
 
Gel electrophoresis:
 
</div>
 
<div class="Text_underline">
 
Result:
 
</div>
 
<div class="Text3_SubSub">
 
[SP-PYY-pETDuet-1] ----- Failed
 
</div>
 
<div class="Text3_SubSub">
 
[PYY-pETDuet-1] ----- Failed
 
</div>
 
<div class="Text3_SubSub">
 
[TAT-PYY-pETDuet-1] ----- Failed
 
</div>
 
<div class="Text3_Sub">
 
Restriction enzyme:
 
</div>
 
<div class="Text3_SubSub">
 
[SP-PYY] cleave by XbaI and PstI
 
</div>
 
<div class="Text3_SubSub">
 
[PYY] cleave by XbaI and PstI
 
</div>
 
<div class="Text3_SubSub">
 
[TAT-PYY] cleave by XbaI and PstI
 
</div>
 
<div class="Text3_SubSub">
 
[pETDuet-1] cleave by XbaI and PstI
 
</div>
 
<div class="Text3_Sub">
 
Gel electrophoresis:
 
</div>
 
<div class="Text_underline">
 
Result:
 
</div>
 
<div class="Text3_SubSub">
 
[SP-PYY] ----- Succeeded
 
</div>
 
<div class="Text3_SubSub">
 
[PYY] ----- Succeeded
 
</div>
 
<div class="Text3_SubSub">
 
[TAT-PYY] ----- Succeeded
 
</div>
 
<div class="Text3_SubSub">
 
[pETDuet-1] ----- Succeeded
 
</div>
 
<div class="Text3_Sub">
 
Gel Purification:
 
</div>
 
<div class="Text3_SubSub">
 
[SP-PYY], [PYY], [TAT-PYY], [pETDuet-1]
 
</div>
 
<div class="Text3_Sub">
 
Measure the resistance of Caco2 cell
 
</div>
 
<div class="Text3">
 
<Green>Selection part</Green>
 
</div>
 
<div class="Text3_Sub">
 
Extract the plasmid:
 
</div>
 
<div class="Text3_SubSub">
 
[nisI- pCLP7]
 
</div>
 
<div class="Text3_Sub">
 
Nisin Immunity Test
 
</div>
 
 
 
<div class="Container2"><div class="Text2">9/11</div></div>
 
<div class="Text3">
 
<Green>Suicide part</Green>
 
</div>
 
<div class="Text3_Sub">
 
Extract the plasmid:
 
</div>
 
<div class="Text3_SubSub">
 
[plac+RBS-RFP-T- pCLP7]
 
</div>
 
<div class="Text3_Sub">
 
Gel electrophoresis:
 
</div>
 
<div class="Text_underline">
 
Result:
 
</div>
 
<div class="Text3_SubSub">
 
[plac+RBS-RFP-T- pCLP7] ----- Failed
 
</div>
 
<div class="Text3_Sub">
 
Test electroporation of <i>L.casei</i>
 
</div>
 
<div class="Text3">
 
<Green>PYY part</Green>
 
</div>
 
<div class="Text3_Sub">
 
4℃ Ligation overnight:
 
</div>
 
<div class="Text3_SubSub">
 
[SP-PYY]+ [pETDuet-1]
 
</div>
 
<div class="Text3_SubSub">
 
[PYY]+ [pETDuet-1]
 
</div>
 
<div class="Text3_SubSub">
 
[TAT-PYY]+ [pETDuet-1]
 
</div>
 
<div class="Text3_Sub">
 
Transformation of [SP-PYY-pETDuet-1], [PYY-pETDuet-1], [TAT-PYY-pETDuet-1] in XL1blue
 
</div>
 
<div class="Text3_Sub">
 
Extract the plasmid:
 
</div>   
 
<div class="Text3_SubSub">
 
[SP-PYY-pETDuet-1], [PYY-pETDuet-1], [TAT-PYY-pETDuet-1]
 
</div>
 
<div class="Text3_Sub">
 
Restriction enzyme:
 
</div>
 
<div class="Text3_SubSub">
 
[SP-PYY-pETDuet1] cleave by XbaI and KpnI
 
</div>
 
<div class="Text3_SubSub">
 
[PYY-pETDuet-1] cleave by XbaI and KpnI
 
</div>
 
<div class="Text3_SubSub">
 
[TAT-PYY-pETDuet1] cleave by XbaI and KpnI
 
</div>
 
<div class="Text3_Sub">
 
Gel electrophoresis:
 
</div>
 
<div class="Text_underline">
 
Result:
 
</div>
 
<div class="Text3_SubSub">
 
[SP-PYY-pETDuet-1] ----- Failed
 
</div>
 
<div class="Text3_SubSub">
 
[PYY-pETDuet-1] ----- Failed
 
</div>
 
<div class="Text3_SubSub">
 
[TAT-PYY-pETDuet-1] ----- Failed
 
</div>
 
<div class="Text3_Sub">
 
Extract the plasmid:
 
</div>
 
<div class="Text3_SubSub">
 
[SP-PYY], [PYY], [TAT-PYY], [pETDuet-1]
 
</div>
 
<div class="Text3_Sub">
 
Restriction enzyme:
 
</div>
 
<div class="Text3_SubSub">
 
[SP-PYY] cleave by EcoRI
 
</div>
 
<div class="Text3_SubSub">
 
[PYY] cleave by EcoRI
 
</div>
 
<div class="Text3_SubSub">
 
[TAT-PYY] cleave by EcoRI
 
</div>
 
<div class="Text3_SubSub">
 
[pETDuet-1] cleave by EcoRI
 
</div>
 
<div class="Text3_Sub">
 
Gel electrophoresis:
 
</div>
 
<div class="Text_underline">
 
Result:
 
</div>
 
<div class="Text3_SubSub">
 
[SP-PYY] ----- Succeeded
 
</div>
 
<div class="Text3_SubSub">
 
[PYY] ----- Succeeded
 
</div>
 
<div class="Text3_SubSub">
 
[TAT-PYY] ----- Succeeded
 
</div>
 
<div class="Text3_SubSub">
 
[pETDuet-1] ----- Succeeded
 
</div>
 
<div class="Text3_Sub">
 
Restriction enzyme:
 
</div>
 
<div class="Text3_SubSub">
 
[SP-PYY] cleave by XbaI and PstI
 
</div>
 
<div class="Text3_SubSub">
 
[PYY] cleave by XbaI and PstI
 
</div>
 
<div class="Text3_SubSub">
 
[TAT-PYY] cleave by XbaI and PstI
 
</div>
 
<div class="Text3_SubSub">
 
[pETDuet-1] cleave by XbaI and PstI
 
</div>
 
<div class="Text3_Sub">
 
Gel electrophoresis:
 
</div>
 
<div class="Text_underline">
 
Result:
 
</div>
 
<div class="Text3_SubSub">
 
[SP-PYY] ----- Succeeded
 
</div>
 
<div class="Text3_SubSub">
 
[PYY] ----- Succeeded
 
</div>
 
<div class="Text3_SubSub">
 
[TAT-PYY] ----- Succeeded
 
</div>
 
<div class="Text3_SubSub">
 
[pETDuet-1] ----- Succeeded
 
</div>
 
<div class="Text3_Sub">
 
Gel Purification:
 
</div>
 
<div class="Text3_SubSub">
 
[SP-PYY], [PYY], [TAT-PYY], [pETDuet-1]
 
</div>
 
<div class="Text3_Sub">
 
4℃ Ligation overnight:
 
</div>
 
<div class="Text3_SubSub">
 
[SP-PYY]+ [pETDuet-1]
 
</div>
 
<div class="Text3_SubSub">
 
[PYY]+ [pETDuet-1]
 
</div>
 
<div class="Text3_SubSub">
 
[TAT-PYY]+ [pETDuet-1]
 
</div>
 
<div class="Text3_Sub">
 
Measure the resistance of Caco2 cell
 
</div>
 
<div class="Text3">
 
<Green>Selection part</Green>
 
</div>
 
<div class="Text3_Sub">
 
Nisin Immunity Test
 
</div>
 
 
 
<div class="Container2"><div class="Text2">9/12</div></div>
 
<div class="Text3">
 
<Green>Suicide part</Green>
 
</div>
 
<div class="Text3_Sub">
 
Test absorbance(O.D. 600nm) of E.coli in Suicide circuit
 
</div>
 
<div class="Text3">
 
<Green>PYY part</Green>
 
</div>
 
<div class="Text3_Sub">
 
Extract the plasmid:
 
</div>   
 
<div class="Text3_SubSub">
 
[SP-PYY-pETDuet-1], [PYY-pETDuet-1], [TAT-PYY-pETDuet-1]
 
</div>
 
<div class="Text3_Sub">
 
Restriction enzyme:
 
</div>
 
<div class="Text3_SubSub">
 
[SP-PYY-pETDuet1] cleave by XbaI and KpnI
 
</div>
 
<div class="Text3_SubSub">
 
[PYY-pETDuet-1] cleave by XbaI and KpnI
 
</div>
 
<div class="Text3_SubSub">
 
[TAT-PYY-pETDuet1] cleave by XbaI and KpnI
 
</div>
 
<div class="Text3_Sub">
 
Gel electrophoresis:
 
</div>
 
<div class="Text_underline">
 
Result:
 
</div>
 
<div class="Text3_SubSub">
 
[SP-PYY-pETDuet-1] ----- Failed
 
</div>
 
<div class="Text3_SubSub">
 
[PYY-pETDuet-1] ----- Failed
 
</div>
 
<div class="Text3_SubSub">
 
[TAT-PYY-pETDuet-1] ----- Failed
 
</div>
 
<div class="Text3_Sub">
 
Transformation of [SP-PYY-pETDuet-1], [PYY-pETDuet-1], [TAT-PYY-pETDuet-1] in XL1blue
 
</div>
 
<div class="Text3_Sub">
 
Extract the plasmid:
 
</div>
 
<div class="Text3_SubSub">
 
[SP-PYY-pETDuet-1], [PYY-pETDuet-1], [TAT-PYY-pETDuet-1]
 
</div>
 
<div class="Text3_Sub">
 
Restriction enzyme:
 
</div>
 
<div class="Text3_SubSub">
 
[SP-PYY-pETDuet1] cleave by XbaI and KpnI
 
</div>
 
<div class="Text3_SubSub">
 
[PYY-pETDuet-1] cleave by XbaI and KpnI
 
</div>
 
<div class="Text3_SubSub">
 
[TAT-PYY-pETDuet1] cleave by XbaI and KpnI
 
</div>
 
<div class="Text3_Sub">
 
Gel electrophoresis:
 
</div>
 
<div class="Text_underline">
 
Result:
 
</div>
 
<div class="Text3_SubSub">
 
[SP-PYY-pETDuet-1] ----- Failed
 
</div>
 
<div class="Text3_SubSub">
 
[PYY-pETDuet-1] ----- Failed
 
</div>
 
<div class="Text3_SubSub">
 
[TAT-PYY-pETDuet-1] ----- Failed
 
</div>
 
<div class="Text3">
 
<Green>Selection part</Green>
 
</div>
 
<div class="Text3_Sub">
 
Nisin Immunity Test
 
</div>
 
 
 
<div class="Container2"><div class="Text2">9/13</div></div>
 
<div class="Text3">
 
<Green>PYY part</Green>
 
</div>
 
<div class="Text3_Sub">
 
Extract the plasmid:
 
</div>   
 
<div class="Text3_SubSub">
 
[SP-PYY-pETDuet-1], [PYY-pETDuet-1], [TAT-PYY-pETDuet-1]
 
</div>
 
<div class="Text3_Sub">
 
Restriction enzyme:
 
</div>
 
<div class="Text3_SubSub">
 
[SP-PYY-pETDuet1] cleave by XbaI and KpnI
 
</div>
 
<div class="Text3_SubSub">
 
[PYY-pETDuet-1] cleave by XbaI and KpnI
 
</div>
 
<div class="Text3_SubSub">
 
[TAT-PYY-pETDuet1] cleave by XbaI and KpnI
 
</div>
 
<div class="Text3">
 
<Green>Selection part</Green>
 
</div>
 
<div class="Text3_Sub">
 
Nisin Immunity Test
 
</div>
 
  
  
Line 3,447: Line 1,694:
 
Maintained by the iGEM team NTU-LIHPAO-Taiwan&nbsp;&nbsp;&nbsp;&nbsp;©2015 NTU-LIHPAO-Taiwan
 
Maintained by the iGEM team NTU-LIHPAO-Taiwan&nbsp;&nbsp;&nbsp;&nbsp;©2015 NTU-LIHPAO-Taiwan
 
</div>
 
</div>
 
 
 
 
</div>
 
</div>
 
</div>
 
</div>
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$('html,body').animate({
scrollTop: target.offset().top-55
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Revision as of 21:49, 16 September 2015

NTU-LIHPAO-Taiwan

Preparation of Competent Cells (E.coli)
Materials and Reagents :
  1. Escherichia coli DH5α
  2. LB broth
  3. TB buffer
  4. DMSO
  5. Liquid nitrogen
Equipment :
  1. Ice
  2. Shaker
  3. Spectrometer
  4. Centrifuge
Procedure :
  1. Inoculate 10μL Escherichia coli DH5α into 10mL LB broth (1:1000)
  2. Grow for 12-16 hours at 37℃ with shaking
  3. Inoculate 500μL Escherichia coli DH5α into 50mL LB broth (1:100)
  4. Grow for 2 hours at 37℃ with shaking to O.D.600=0.4-0.6
  5. Split the cell into two Falcon tubes, both contain 25 mL Escherichia coli DH5α
  6. Centrifuge at 4℃, 3000rpm(800G) for 10 minutes
  7. Discard the supernatant
  8. Resuspend the cell pellet by gently adding 8.5mL TB buffer (1/3 V)
  9. On ice for 10 minutes
  10. Centrifuge at 4℃, 3000rpm(800G) for 10 minutes
  11. Discard the supernatant using pipetman
  12. Resuspend the cell pellet by gently adding 2mL TB buffer (1/12.5 V)
  13. Add 150μL DMSO (7%)
  14. On ice for 10 minutes
  15. Transfer the cell to new eppendorfs with 60μL per tube
  16. Freeze the cell in liquid nitrogen
  17. Store the cell at -80℃
DNA Dissolution
Materials and Reagents :
  1. DNA (BioBricks/synthesized)
  2. ddH2O
Procedure :
  1. Add 10μL ddH2O
  2. Wait for 1 minute until the DNA dissolve
  3. Pipet several times and transfer the DNA to an eppendorf
Agarose Gel Electrophoresis
Materials and Reagents :
  1. Agarose
  2. 1X TAE
  3. Tracking dye
  4. Marker (1kb/100bp)
  5. EtBr
  6. ddH2O
Equipment :
  1. Gel tray
  2. Well comb
  3. Electrophoresis tank
  4. UV detector
Procedure :
    Casting an Agarose Gel (m/v = 1.0% or 1.5%)
  1. Measure out appropriate mass of agarose powder into a serum bottle
  2. Add appropriate volume of 1X TAE
  3. Let agarose solution cool down to acceptable temperature for bare hands
  4. Pour the solution into a gel tray with the well comb in place, and push the bubbles away with a pipette tip
  5. Let sit at room temperature for 30 minutes, until it has completely solidified
  6. Loading Samples and Running the Gel
  7. Place the gel as well as its tray into the electrophoresis tank containing 1X TAE
  8. (Make sure that the surface is higher than the top of the gel and not overflow)
  9. Mix the samples with tracking dye (1/10 V) sufficiently
  10. Load the samples into the each well
  11. Load marker (usually in the first and last lane)
  12. Set an appropriate voltage (full/half) and run the gel for 15-20 minutes
  13. Imaging the Gel
  14. Put the gel into a container filled with 1X TAE and EtBr, staining for 5 minutes
  15. Replace EtBr solution with water and destain for 3 minutes
  16. Put the gel in an UV detector and record the result
Gel Extraction
Materials and Reagents :
  1. Gel/PCR buffer
  2. W1 buffer
  3. Wash buffer
  4. ddH2O
Equipment :
  1. Cutter knife
  2. Eppendorf
  3. Vortex mixer
  4. Dry bath incubator
  5. DF Column & Collection tube
  6. Mini Centrifuge
  7. Microcentrifuge
Procedure :
    Gel Dissociation
  1. Excise the agarose gel slice containing relevant DNA fragments and remove any extra agarose to minimize the size of the gel slice (<300μL)
  2. Transfer the gel slice to an eppendorf
  3. Add 500μL Gel/PCR buffer to the sample and mix by vortex
  4. Incubate at 60℃ for 10-15 minutes to ensure the gel slice has been completely dissolved (invert the tube every 2-3 minutes)
  5. Cool the dissolved sample mixture to room temperature
  6. DNA Binding
  7. Place the DF Column in a 2mL Collection tube
  8. Transfer 800μL of the sample mixture to the DF Column
  9. Discard the flow-through and place the DF Column back in the Collection tube
  10. (If the sample mixture is more than 800μL, repeat the DNA binding step)
    Wash
  11. Add 400μL W1 buffer into the DF Column
  12. Spin down for approximately 20 seconds
  13. Discard the flow-through and place the DF Column back in the Collection tube
  14. Add 600μL wash buffer (contains ethanol) into the DF Column
  15. Let stand for 1 minute at room temperature
  16. Spin down for approximately 30 seconds
  17. Discard the flow-through and place the DF Column back in the Collection tube
  18. Centrifuge at 12000 rpm for 3 minutes to dry the column matrix
  19. (Can be done twice)
  20. Discard the flow-through
  21. DNA Elution
  22. Transfer the dried DF Column to a new eppendorf (cap cut)
  23. Add 30μL of 37℃ ddH2O into the center of the column matrix
  24. Let stand for at least 2 minutes to ensure that ddH2O is completely absorbed
  25. Centrifuge at 12000 rpm for 2 minutes to elute the purified DNA
  26. Re-add the subnatant into the center of the column matrix
  27. Centrifuge at 12000 rpm for 2 minutes to elute the purified DNA
DNA Ligation
Materials and Reagents :
  1. DNA (insert & vector)
  2. Ligation high ver.2
Equipment :
  1. Cooling dry bath incubator
Procedure :
  1. Table
    Components Volume (μL)
    Insert x
    Vector y
    Ligation High 1
    Total 7
            Molar ratio: insert/vector = 3/1
            x + y = 6
  2. Gently mix the solution by pipetting up and down
  3. Incubate
    1. at 16℃ for 2 hours, or
    2. at 37℃ for 1 hour, or
    3. at 4℃ overnight
  4. Proceed with bacterial transformation
Plasmid DNA Extraction Using Alkaline Lysis Method (E. coli)
Materials and Reagents :
  1. Escherichia coli DH5α (with plasmid)
  2. LB broth
  3. Resuspension solution (MPI, with RNAase)
  4. Lysis solution (MPII)
  5. Neutralizing solution (MPIII)
  6. Isopropanol
  7. 70% ethanol
  8. ddH2O
Equipment :
  1. Shaker
  2. Centrifuge
  3. Vortex mixer
Procedure :
  1. Grow bacteria in LB broth with appropriate antibiotics at 37℃ overnight with shaking
  2. Transfer 1.5mL culture to an eppendorf
  3. Centrifuge at 4℃, 5000rpm for 5 minutes
  4. Discard the supernatant
  5. Add 150μL of resuspension solution (MPI, with RNAase) into each tube, pipet several times, and vortex to completely resuspend the cell pellet
  6. Add 150μL of lysis solution (MPII), gently invert the tubes about 20 times, and then let the sample mixture stand at room temperature for 2 minutes
  7. Add 150μL of neutralizing solution (MPIII) and mix by inverting the tubes about 20 times. Bacterial chromosomal DNA and proteins can be seen as white precipitates
  8. Centrifuge at 4℃, 15000rpm for 15 minutes
  9. Carefully transfer 400μL of the supernatant to a new eppendorf
  10. (Step 8&9 can be done twice)
  11. Add 400μL (same volume as the supernatant) isopropanol, and shake up the tubes as vigorously as one can
  12. Centrifuge at 4℃, 15000rpm for 15 minutes
  13. Discard the supernatant
  14. Add 200μL of 70% ethanol to wash out the salts
  15. Centrifuge at 4℃, 15000rpm for 5 minutes
  16. Discard the supernatant and remove the remains as much as possible with pipetman
  17. Air dry for about 30 minutes
  18. Resuspend the DNA pellet with 20μL ddH2O
Transformation (E. coli)
Materials and Reagents :
  1. Competent cell (Escherichia coli DH5α)
  2. LB plate (Amp+/CP+)
Equipment :
  1. -80℃ refrigerator
  2. Ice
  3. 37℃ incubator
  4. Super optimal broth (SOB) (37℃)
  5. Shaker
Procedure :
  1. Take out the competent cells from -80℃ refrigerator
  2. Thaw the cells on ice for 5 minutes
  3. Add 1μL plasmid DNA into the competent cells, and mix gently by pipetting
  4. On ice for 10 minutes
  5. Heat shock at 37℃ for 3 minutes
  6. On ice for 2 minutes
  7. Add 150μL 37℃ SOB into the mixture
  8. Place the tube at 37℃ with shaking for 1 hour(Amp+)/4 hours(CP+) respectively
  9. Spread the cells onto the LB plates (Amp+/ CP+)
  10. Incubate the plates at 37℃ with shaking for 12-16 hours
Protein Extraction
Materials and Reagents :
  1. plasmid/ BL21 competent cell
  2. LB plate
  3. LB broth
  4. lysis buffer
Equipment :
  1. 15/ 50ml conial tube
  2. Shaking incubator
  3. Erlenmeyer flask
  4. Spectrophotometer
  5. Centrifuge
  6. Sonicator
  7. Eppendorf
Procedure :
  1. Transform plamid into BL21 (see transformation)
  2. Pick up a single colony and incubate into 2ml LB/CP medium, then agitate them in a shaking incubator at 37℃ overnight
  3. Pour the culture into 100ml LB/CP medium, then agitate until it reach A600 of 0.6
  4. Pour the culture into 50ml conical tube, and centrifuge at 8000rpm for 10 min
  5. Store the supernate and the pellets in the centrifuge tubes in a -80℃ freezer
  6. Use 6ml lysis buffer(NP-10) to resuspend the cell pellet and transfer into a 15ml centrifuge tube
  7. Lyse the cell with sonication
  8. Centrifuge 15ml conial tube at 9000rpm for 10 min
  9. Store the supernate as coarse extract
SDS-PAGE
Materials and Reagents :
  1. Solution A (acrylamide/ bis-acrylamide (29:1) 30% solution)
  2. Solution B (Tris (Tris base, 1.5 M) 90.8 gm; TEMED 1.8 ml; pH = 8.8/ 500ml)
  3. Solution C (Tris (Tris base, 0.5 M) 6.0 gm; TEMED 0.4 ml; pH = 6.7/ 100ml)
  4. 10% SDS (1kb/100bp)
  5. ddH2O
  6. APS
  7. Running buffer (1M Tris 12.5 ml; glysine 7.7g/ 500ml)
  8. Sample buffer(5X) (Tris base, 125mM X5; EDTA2•Na, 2mM X 5; SDS(2% X2); β-mercaptoethanol, 5% X5)
  9. Protein marker
Equipment :
  1. Gel Caster
  2. Accessories for each gel
  3.     (1) One glass plate
  4.     (2) One aluminum notched plate
  5.     (3) Two 0.75-mm thick spacers
  6.     (4) One 0.75-mm thick 10-well comb
  7.     (5) One well-locating decal
  8. Power supply
Procedure :
  1. Assemble one glass plate and one alumimum plate with two spacers for each gel module
  2. Prepare the SDS gel solution (see the table below). Two 0.75mm mini gels need approximately 10ml separation gel solution and 5ml stacking solution. Add APS solution at the final step
  3. Mix the separation gel solution, and add the solution into the gel module until reaching the designated level. Then add isopropanol on the top of the gel. It takes about 40 min to complete the polymerization step
  4. Remove the isopropanol by using a small strip of filter paper. Fill up the stacking gel solution until reaching the top. Insert comb into the gel solution as soon as possible. It takes 10 min to complete the polymerization step
  5. Remove the comb and set the gel in the cell buffer dam. Pour the running buffer into the inner chamber and keep pouring after overflow until the buffer surface reaches the required level in the outer chamber
  6. Use a micropipette to clean up every single well with the running buffer
  7. Mix protein samples with 1/5 volumes of 5X sample buffer. Heat the mixture at 100oC for 10 min. Let it cool down to room temperature
  8. Load protein sample and the protein marker into the well
  9. Run the electrophoresis at 70V for 20 min, and then 150V for 55 min
  10. Remove the two spacer and lift the glass plate, and remove the stacking gel and the remaining gel is ready for CBR staining and Western blot
(Unit: ml) Separation gel Stacking gel
Percentage 5% 7.5% 10% 12.5% 15% 20% 4%
Solution A 16.5 2.5 3.35 4.15 5 6.5 0.66
Solution B 2.5 2.5 2.5 2.5 2.5 2.5 -
Solution C - - - - - - 1.24
10% SDS 0.1 0.1 0.1 0.1 0.1 0.1 0.05
dH2O 5.7 4.85 4 3.2 2.35 0.85 2.95
APS(10%) 0.05 0.05 0.05 0.05 0.05 0.05 0.1
Total Volume 10 10 10 10 10 10 5
Western Blot
Materials and Reagents :
  1. Transfer buffer ( Tris 25mM; glycine 0.192M)
  2. Methanol
  3. 10 X TBST (1M Tris pH =8.0; Tween 20, 50ml; NaCl 43.5g)
Equipment :
  1. Semi-dry trnasfer cell
  2. PVDF membrane
  3. Nitrocellulose paper
  4. Square Petri dish
  5. Rotary shaker
Procedure :
  1. Equilibrate the nitrocellulose paper and SDS-PAGE gel by soaking them with transfer buffer
  2. Rinse the PVDF membrane with 100% methanol for a few second and equilibrate it with transfer buffer
  3. Place the elements in the following order onto the semi-dry transfer cell from bottom to top: nitrocellulose paper, PVDF membrane, SDS-PAGE gel, nitrocellulose paper
  4. Set up the current at 0.09A and run for 75 min
Immunostaining
Materials and Reagents :
  1. 3% milk
  2. Antibody solution
  3. Secondary antibody (anti-mouse HRP)
  4. TBST
  5. Western HRP substrate
Equipment :
  1. Square petri dish
  2. Rotary shaker
  3. UVP Biospectrum
Procedure :
  1. Put the membrane in the square petri dish block the membrane with the 3% milk/TBST at room temperature for 1hr
  2. Discard the milk and replace it with antibody solution(mouse His-probe Antibody) at 4℃ overnight
  3. Recycle the antibody solution. Wash the membrane with TBST three times, 5 min each
  4. Soak membrane into anti-mouse HRP solution for 1 hr
  5. Discard the anti-mouse HRP solution and wash it with TBST three times, 5 min each
  6. Add HRP substrate on the membrane for 1 min
  7. Soak the membrane into ddH2O to remove the substrate
  8. Observe the result with UVP Biospectrum
Thawing Caco-2 cells
Materials and Reagents :
  1. 1 ml frozen Caco-2 cells in cryovial
  2. Cell culture medium (MEM (minimum essential medium) (GIBCOTM #41500-034)/2.2g NaHCO3/ 0.11 g sodium pyruvate/20% FBS/1% PSA)
  3. 70% ethanol
  4. Trypan blue solution
Equipment :
  1. Laminar flow hood
  2. Auto pipette
  3. Centrifuge
  4. 15 ml centrifuge tubes
  5. 10 cm dish
  6. Hemocytometer
  7. Optical microscope
  8. Suction machine
Procedure :
  1. Pre-warm medium in 37˚C water bath
  2. Open a laminar flow hood
  3. Clean materials, reagents and equipments before moving them into the hood
  4. Thawing Caco-2 cells in 37˚C water bath and transfer the cells into a 15ml centrifuge tube
  5. Add 9 ml cell culture medium very slowly
  6. Centrifuge at 1000 rpm for 5 min
  7. Decant the supernate and resuspend cells with 10 ml cell culture medium
  8. Mix 10 ul cell suspension and 10 μl trypan blue solution and count total cell number with a hemocytometer
  9. Add all cell suspension to a 10 cm dish
  10. Write date, cell line and passage number
  11. Put the dish into incubator
Freezing Caco-2 cells
Materials and Reagents :
  1. Caco-2 cell in 10 cm dish
  2. Cell culture medium (MEM (minimum essential medium) (GIBCOTM #10370-021)/10% FBS/ 2 mM glutamine
  3. 1X PBS (phosphate buffer saline)
  4. 0.5% trypsin
  5. Trypan blue solution
  6. 70% ethanol
  7. Cell freezing media (50% FBS, 40% cell culture medium, 10% DMSO)
Equipment :
  1. Laminar flow hood
  2. Auto pipette
  3. Centrifuge
  4. 15 ml centrifuge tubes
  5. 10 cm dish
  6. Hemocytometer
  7. Optical microscope
  8. Suction machine
  9. Cryovials
  10. Freezing apparatus
  11. -80˚C refrigerator
  12. Liquid nitrogen tank
Procedure :
  1. Pre-warm medium in 37˚C water bath
  2. Open a laminar flow hood
  3. Clean materials, reagents and equipments before moving them into the hood
  4. Take a 10 cm dish with Caco-2 cell
  5. Discard the medium with a suction machine
  6. Wash the cells with 5 ml PBS
  7. Add 1 ml 0.5% trypsin and incubate at 37˚C for 7 minutes
  8. Wash out all the cells from the surface of the dish by pipetting the fresh complete culture medium (9 ml) all over the surface
  9. Transfer the cell suspension to a 15 ml centrifuge tube
  10. Mix 10 μl cell suspension and 10 ul trypan blue solution and count total cell number with a hemocytometer
  11. Add about 1x106 cells per cryovial, and add cell freezing media
  12. Freeze the cryovials in a controlled rate freezing apparatus, decreasing the temperature approximately 1°C per minute in a -80°C refrigerator for more than 3 hour, then move them into liquid nitrogen tank
Caco2 Cell passage
Materials and Reagents :
  1. Caco-2 cell in 10 cm dish
  2. Cell culture medium (MEM (minimum essential medium) (GIBCOTM #10370-021)/10% FBS/ 2 mM glutamine
  3. 1X PBS (phosphate buffer saline)
  4. 0.5% trypsin
  5. Trypan blue solution
  6. 70% ethanol
Equipment :
  1. Laminar flow hood
  2. Auto pipette
  3. Centrifuge
  4. 15 ml centrifuge tubes
  5. 10 cm dish
  6. Hemocytometer
  7. Optical microscope
  8. Suction machine
Procedure :
  1. Pre-warm medium in 37˚C water bath
  2. Open a laminar flow hood
  3. Clean materials, reagents and equipments before moving them into the hood
  4. Take a 10 cm dish with Caco-2 cell
  5. Discard the medium with a suction machine
  6. Wash the cells with 5 ml PBS
  7. Add 1 ml 0.5% trypsin and incubate at 37˚C for 7 minutes
  8. Wash out all the cells from the surface of the dish by pipetting the fresh complete culture medium (9 ml) all over the surface
  9. Transfer the cell suspension to a 15 ml centrifuge tube
  10. Mix 10 ul cell suspension and 10 μl trypan blue solution and count total cell number with a hemocytometer
  11. Transfer appropriate amounts of cell suspension to new dishes (1/4 X)
  12. Write date, cell line and passage number
  13. Put the dish into incubator
Seeding in transwell
Materials and Reagents :
  1. Caco-2 cell in 10 cm dish
  2. Cell culture medium (MEM (minimum essential medium) (GIBCOTM #41500-034)/2.2 g NaHCO3/ 0.11 g sodium pyruvate/20% FBS/1% PSA
  3. 1X PBS (phosphate buffer saline)
  4. 0.5% trypsin
  5. Trypan blue solution
  6. 70% ethanol
Equipment :
  1. Laminar flow hood
  2. Auto pipette
  3. Centrifuge
  4. 15 ml centrifuge tubes
  5. 10 cm dish
  6. Hemocytometer
  7. Optical microscope
  8. Suction machine
  9. 6-well plate
  10. Millicell plate insert (PIHP03050)
Procedure :
  1. Open 6-well plate, add 1.5 mL medium to each large well (6 wells) which are going to be used
  2. Add 2 ml PBS/well to other wells
  3. Put transwell in larger well
  4. Take a 10 cm dish with Caco-2 cell
  5. Discard the medium with a suction machine
  6. Wash the cells with 5 ml PBS
  7. Add 1 ml 0.5% trypsin and incubate at 37˚C for 7 minutes
  8. Wash out all the cells from the surface of the dish by pipetting the fresh complete culture medium (9 ml) all over the surface
  9. Transfer the cell suspension to a 15 ml centrifuge tube
  10. Mix 10 ul cell suspension and 10 μl trypan blue solution and count total cell number with a hemocytometer
  11. Cell count: 70/ 2 * orginal volume *100 (*104)= 35 X 104 cell/mL (Seeding 42 x 104 cell/well)
  12. Write date, cell line and passage number
  13. Put the dish into incubator
Measure TEER
Materials and Reagents :
  1. Caco-2 cells seeded in transwell
  2. 70% ethanol
Equipment :
  1. Laminar flow hood
  2. Millicell ERS
Procedure :
  1. Prepare laminar hood for experiment
  2. To sterilize electrode of Millicell ERS, soak electrode in 70% alcohol for 15 min, and air dry for 15 sec
  3. Measure TEER value of each well (n=3)
Maintained by the iGEM team NTU-LIHPAO-Taiwan    ©2015 NTU-LIHPAO-Taiwan