Latest revision as of 23:15, 27 September 2013

Glyoxylate Shunt Module's Notebook

June 2013

Week 4

Design primers for aceA, aceB, MLS and EF-1alpha promoter extraction
Mini prepped pCMV/myc/mito
Extracted BW25113 genome
PCR out aceA and aceB for Biobrick
PCR out MLS for fuse with aceA and aceB
PCR out aceA and aceB to fuse with MLS

July 2013

Week 1

Transformed iDUET101a
Mini prepped transformant and do digestion check
Make glycerol stock out of iDUET101a
Extract out pSB1C3 from BBa_J04450 using gel extraction with XbaI and PstI
Extract E. coli BW25113 genome

Week 2

Ligation of aceA and aceB with pSB1C3
Transformed aceA-pSB1C3 and aceB-pSB1C3
Screen out colonies for aceA-pSB1C3 and aceB-pSB1C3 and do digestion check
aceB-pSB1C3 confirmed and proceed with sequencing
aceB-pSB1C3 partial sequence confirmed

Week 3

Extracted out more pSB1C3 from BBa_J04450
PCR out aceA with standard prefix and suffix
Digestion of aceA with XbaI and PstI
Ligate with pSB1C3
Screen colonies and do digestion check
aceA-pSB1C3 confirmed and proceed with sequencing
aceA-pSB1C3 partial sequence confirmed
Help Chloe do digestion check for Pef-1alpha-pSB1C3

Week 4

Extraction of Pef-1alpha for Biobrick
Extract out more pSB1C3 from BBa_J04450
Digestion of Pef-1alpha with EcoRI and PstI
Ligation of Pef-1alpha with pSB1C3
Transformed Pef-1alpha-pSB1C3 construct
Screen colonies and do digestion check
Weird bands show up, do colony PCR to confirm whether Pef-1alpha is ligated
Colony PCR showed that Pef-1alpha is there
Colony PCR with VF2 and VR primers didn’t give any result

August 2013

Week 1

Practice Gibson Assembly using known DNA and Gibson assembly mix
Extract MLS, Pef-1alpha, aceB and polyadenylation sequence using PCR

Week 2

Help Chloe do digestion check of pCMV-aceA
pCMV-aceA construct confirmed
Redo making Pef-1alpha-pSB1C3 construct
Create PMT construct for western blotting training
PMT construct made proceed with western blotting:

Week 3

Build construct for Pef-1alpha characterization
Pcmv – GFP, Pef-1alpha – GFP construct, Pcmv – mCherry, Pef-1alpha – mCherry constructs
Individual DNA was extracted using PCR
Assembled using Gibson Assembly

Week 4

Troubleshooting for Pef-1alpha characterization constructs
Use Gibson Assembly to make Pef-1alpha – pSB1C3 for submission

September 2013

Week 1

Give Pcmv-aceA to group 1 to transfect
Pef-1alpha – pSB1C3 constructed
Digestion checks and sequenced
Improvement of existing Biobrick: J176171 primer designs for J176171 to engineer with standard prefix in RFC10 and RFC25 formats
Found that J176171 are heat unstable and degrades after denaturation

Week 2

Receive transfected HEK293 cell from Group 1
Do western blotting with mouse anti c-myc antibody as primary antibody and anti-mouse HRP as secondary antibody
Western blotting showed that AceA is expressed in HEK293 cell in contrast to the negative control
Build construct for Pef-1alpha characterization: Pef-1alpha – GFP – polyadenylation sequence – pSB1C3
Improvement of existing Biobrick: J176171 primer designs to extract GFP with engineered complementary sequence of J176171

Week 3

Extract GFP in RFC10 and RFC25 format
Heat sensitivity test of J176171 at temperatures range from 40 to 50 degrees Celsius for Gibson Assembly

Week 4

Content 1

Week 5

Content 1

@@ Line 50: / Line 50: @@
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 #title{border: solid 2px;border-radius:15px;width:90%;padding:15px;margin-left:50px;margin-bottom:25px;}
+#iGEM_Logo{
+width:100px;
+height:80px;
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+right:10px;
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+#hkust_Logo{
+width:60px;
+height:80px;
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+top:60px;
+z-index:+15;
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 </head>
 <body>
+           <a href="https://2013.igem.org/Main_Page"><img id="iGEM_Logo" src="https://static.igem.org/mediawiki/2013/4/46/Igem_qgem_logo.png"></a>
+<a href="http://www.ust.hk/eng/index.htm"><img id="hkust_Logo" src="https://static.igem.org/mediawiki/2013/5/55/Hkust_logo.gif"></a>
 <ol class="pos_fixed">
+<li><a href="https://2013.igem.org/Team:Hong_Kong_HKUST/notebook">Notebook</a></li>
 <li><a href="https://2013.igem.org/Team:Hong_Kong_HKUST/notebook/mod1">Module 1</a></li>
 <li><a href="https://2013.igem.org/Team:Hong_Kong_HKUST/notebook/mod2">Module 2</a></li>
-<li><a href="https://2013.igem.org/Team:Hong_Kong_HKUST/notebook/mod3">Module 3</a></il>
+<li><a href="https://2013.igem.org/Team:Hong_Kong_HKUST/notebook/mod3">Module 3</a></li>
+<li><a href="https://2013.igem.org/Team:Hong_Kong_HKUST/notebook/mod4">Module 4</a></il>
 </ol>
 <a href=https://2013.igem.org/Team:Hong_Kong_HKUST><center><div id="kepala" style="height:121px;width:100%;"><img src="https://static.igem.org/mediawiki/igem.org/c/c7/BANNER1_%281%29.png" style="height:121px;width:100%;align:middle;"></div></center></a>
@@ Line 303: / Line 325: @@
 <li><a href="https://2013.igem.org/Team:Hong_Kong_HKUST/abstract">Abstract</a></li>
 <li><a href="https://2013.igem.org/Team:Hong_Kong_HKUST/modules">Modules Description</a></li>
+<li><a href="https://2013.igem.org/Team:Hong_Kong_HKUST/data">Data Page</a></li>
 <li><a href="https://2013.igem.org/Team:Hong_Kong_HKUST/Parts">Parts</a></li>
 <li><a href="https://2013.igem.org/Team:Hong_Kong_HKUST/characterization">Characterization</a></li>
-<li><a href="https://2013.igem.org/Team:Hong_Kong_HKUST/modelling">Modeling</a></li>
 <li><a href="https://2013.igem.org/Team:Hong_Kong_HKUST/results">Result</a></li>
+<li><a href="https://2013.igem.org/Team:Hong_Kong_HKUST/future">Future Work</a></li>
 </ul>
 </li>
@@ Line 315: / Line 338: @@
 <li><a href="https://2013.igem.org/Team:Hong_Kong_HKUST/protocols">Protocols</a></li>
 <li><a href="https://2013.igem.org/Team:Hong_Kong_HKUST/safety">Safety</a></li>
-<li><a href="https://2013.igem.org/Team:Hong_Kong_HKUST/future">Future Work</a></li>
 </ul>
 </li>
@@ Line 328: / Line 351: @@
 <li><a href="https://2013.igem.org/Team:Hong_Kong_HKUST/hp">Human Practice</a>
 <ul>
-<li><a href="https://2013.igem.org/Team:Hong_Kong_HKUST/hp/interview">Interviews</a></li>
 <li><a href="https://2013.igem.org/Team:Hong_Kong_HKUST/hp/cp">Country Profile</a></li>
 <li><a href="https://2013.igem.org/Team:Hong_Kong_HKUST/hp/blog">Blog</a></li>
-<li><a href="https://2013.igem.org/Team:Hong_Kong_HKUST/hp/article">Article</a></li>
+<li><a href="https://2013.igem.org/Team:Hong_Kong_HKUST/hp/interview">Interviews</a></li>
+<li><a href="https://2013.igem.org/Team:Hong_Kong_HKUST/hp/article/genet">Article</a></li>
 <li><a href="https://2013.igem.org/Team:Hong_Kong_HKUST/hp/video">Videos</a></li>
 <li><a href="https://2013.igem.org/Team:Hong_Kong_HKUST/hp/presentation">Presentations</a></li>
@@ Line 341: / Line 364: @@
 </div>
 <br><br><br><br><br><br><br><br>
-<div id="title"><h3>Glyoxylate Shunt Module's Notebook</h3></div>
+<div id="title"><center><h3>Glyoxylate Shunt Module's Notebook</h3></center></div>
 <div id="flight">
   <div id="satu" align="center"> <h1>June 2013</h1>
@@ Line 348: / Line 371: @@
        <a href='#' class='head'>Week 4</a>
        <div class='content' align="left">
-<p><br>Design primers for aceA, aceB, MLS and EF1a extraction<br />
+<p><br>Design primers for <i>aceA</i>, <i>aceB</i>, MLS and EF-1alpha promoter extraction<br />
    Mini prepped pCMV/myc/mito<br />
    Extracted BW25113 genome<br />
-   PCR out aceA and aceB for Biobrick<br />
+   PCR out <i>aceA</i> and <i>aceB</i> for Biobrick<br />
-   PCR out MLS for fuse with aceA and aceB<br />
+   PCR out MLS for fuse with <i>aceA</i> and <i>aceB</i><br />
-   PCR out aceA and aceB to fuse with MLS</p><br>
+   PCR out <i>aceA</i> and <i>aceB</i> to fuse with MLS</p><br>
        </div>
        </div>
@@ Line 365: / Line 388: @@
        <div class='content' align="left">
 <p>&nbsp;</p>
-<p>Transformed iDUET101<br />
+<p>Transformed iDUET101a<br />
    Mini prepped transformant and do digestion check<br />
-   Make glycerol stock out of iDUET101<br />
+   Make glycerol stock out of iDUET101a<br />
-   Extract out Psb1C3 from BBa_J04450 using gel extraction with XbaI and PstI<br />
+   Extract out pSB1C3 from <a href="http://parts.igem.org/Part:BBa_J04450">BBa_J04450</a> using gel extraction with XbaI and PstI<br />
    Extract <i>E. coli</i> BW25113 genome</p>
 <p>&nbsp;</p>
@@ Line 378: / Line 401: @@
        <div class='content' align="left">
 <p>&nbsp;</p>
-<p>Ligation of aceA and aceB with pSB1c3<br />
+<p>Ligation of <i>aceA</i> and <i>aceB</i> with pSB1C3<br />
-   Transformed aceA-pSB1C3 and aceB-pSB1C3<br />
+   Transformed <i>aceA</i>-pSB1C3 and <i>aceB</i>-pSB1C3<br />
-   Screen out colonies for aceA-pSB1C3 and aceB-pSB1C3 and do digestion check<br />
+   Screen out colonies for <i>aceA</i>-pSB1C3 and <i>aceB</i>-pSB1C3 and do digestion check<br />
-   aceB-pSB1C3 confirmed and proceed with sequencing<br />
+   <i>aceB</i>-pSB1C3 confirmed and proceed with sequencing<br />
-aceB-pSB1C3 partial sequence confirmed</p>
+<i>aceB</i>-pSB1C3 partial sequence confirmed</p>
 <p>&nbsp;</p>
        </div>
@@ Line 391: / Line 414: @@
        <div class='content' align="left">
 <p>&nbsp;</p>
-<p>Extracted out more Psb1c3 from BBa_J04450<br />
+<p>Extracted out more pSB1C3 from BBa_J04450<br />
-   PCR out aceA with standard prefix and suffix<br />
+   PCR out <i>aceA</i> with standard prefix and suffix<br />
-   Digestion of aceA with XbaI and PstI<br />
+   Digestion of <i>aceA</i> with XbaI and PstI<br />
    Ligate with pSB1C3<br />
    Screen colonies and do digestion check<br />
-   aceA-pSB1C3 confirmed and proceed with sequencing<br />
+   <i>aceA</i>-pSB1C3 confirmed and proceed with sequencing<br />
-   aceA-pSB1C3 partial sequence confirmed<br />
+   <i>aceA</i>-pSB1C3 partial sequence confirmed<br />
-   Help Chloe do digestion check for EF1a-pSB1C3</p>
+   Help Chloe do digestion check for P<i>ef-1alpha</i>-pSB1C3</p>
 <p>&nbsp;</p>
        </div>
@@ Line 407: / Line 430: @@
        <div class='content' align="left">
 <p>&nbsp;</p>
-<p>Extraction of EF1a for Biobrick<br />
+<p>Extraction of P<i>ef-1alpha</i> for Biobrick<br />
    Extract out more pSB1C3 from BBa_J04450<br />
-   Digestion of EF1a with EcoRI and PstI<br />
+   Digestion of P<i>ef-1alpha</i> with EcoRI and PstI<br />
-   Ligation of EF1a with pSB1c3<br />
+   Ligation of P<i>ef-1alpha</i> with pSB1C3<br />
-   Transformed EF1a-pSB1C3 construct<br />
+   Transformed P<i>ef-1alpha</i>-pSB1C3 construct<br />
    Screen colonies and do digestion check<br />
-   Weird bands show up, do colony PCR to confirm whether EF1a is ligated<br />
+   Weird bands show up, do colony PCR to confirm whether P<i>ef-1alpha</i> is ligated<br />
-   Colony PCR showed that EF1a is there<br />
+   Colony PCR showed that P<i>ef-1alpha</i> is there<br />
    Colony PCR with VF2 and VR primers didn&rsquo;t give any result</p>
 <p>&nbsp;</p>
@@ Line 428: / Line 451: @@
 <p>&nbsp;</p>
 <p>Practice Gibson Assembly using known DNA and Gibson assembly mix<br />
-Extract MLS, EF-1alpha, <em>aceB</em> and polyadenylation sequence using PCR </p>
+Extract MLS, P<i>ef-1alpha</i>, <i>aceB</i> and polyadenylation sequence using PCR </p>
 <p>&nbsp;</p>
        </div>
@@ Line 436: / Line 459: @@
        <div class='content' align="left">
 <p>&nbsp;</p>
-<p>Help Chloe do digestion check of aceA-pCMV<br />
+<p>Help Chloe do digestion check of pCMV-<i>aceA</i><br />
-   aceA-pCMV construct confirmed<br />
+   pCMV-<i>aceA</i> construct confirmed<br />
-   Redo making EF1a-pSB1C3 construct<br />
+   Redo making P<i>ef-1alpha</i>-pSB1C3 construct<br />
    Create PMT construct for western blotting training<br />
    PMT construct made proceed with western blotting:</p>
@@ Line 448: / Line 471: @@
        <div class='content' align="left">
 <p>&nbsp;</p>
-<p>Build construct for EF-1alpha characterization<br />
+<p>Build construct for P<i>ef-1alpha</i> characterization<br />
-   CMV – GFP, EF-1alpha – GFP construct, CMV – mCherry, EF-1alpha – mCherry constructs<br />
+   P<i>cmv</i> – GFP, P<i>ef-1alpha</i> – GFP construct, P<i>cmv</i> – mCherry, P<i>ef-1alpha</i> – mCherry constructs<br />
    Individual DNA was extracted using PCR <br />
    Assembled using Gibson Assembly</p>
@@ Line 459: / Line 482: @@
        <div class='content' align="left">
 <p>&nbsp;</p>
-<p>Troubleshooting for EF-1alpha characterization constructs<br />
+<p>Troubleshooting for P<i>ef-1alpha</i> characterization constructs<br />
-   Use Gibson Assembly to make EF-1alpha – pSB1C3 for submission</p>
+   Use Gibson Assembly to make P<i>ef-1alpha</i> – pSB1C3 for submission</p>
 <p>&nbsp;</p>
        </div>
@@ Line 471: / Line 494: @@
        <div class='content' align="left">
 <p>&nbsp;</p>
-<p>Give aceA-pCMV to group 1 to transfect <br />
+<p>Give P<i>cmv</i>-<i>aceA</i> to group 1 to transfect <br />
-   EF-1alpha – pSB1C3 constructed <br />
+   P<i>ef-1alpha</i> – pSB1C3 constructed <br />
    Digestion checks and sequenced<br />
    Improvement of existing Biobrick: J176171 primer designs for J176171 to engineer with standard prefix in RFC10 and RFC25 formats<br />
-   Found that J176171 are heat sensitive and degrades after denaturation</p>
+   Found that J176171 are heat unstable and degrades after denaturation</p>
 <p>&nbsp;</p>
        </div>
@@ Line 483: / Line 506: @@
        <div class='content' align="left">
 <p>&nbsp;</p>
-<p>Receive transfected  HEK293 cell from Group 1<br />
+<p>Receive transfected HEK293 cell from Group 1<br />
-   Do western blotting with mouse anti c-myc  antibody as primary antibody and anti-mouse HRP as secondary antibody<br />
+   Do western blotting with mouse anti c-myc antibody as primary antibody and anti-mouse HRP as secondary antibody<br />
-   Western blotting showed that aceA is expressed in HEK293 cell in contrast to the negative control<br />
+   Western blotting showed that AceA is expressed in HEK293 cell in contrast to the negative control<br />
-   Build construct for EF-1alpha characterization: EF-1alpha – GFP – polyadenylation sequence – pSB1C3 <br />
+   Build construct for P<i>ef-1alpha</i> characterization: P<i>ef-1alpha</i> – GFP – polyadenylation sequence – pSB1C3 <br />
    Improvement of existing Biobrick: J176171 primer designs to extract GFP with engineered complementary sequence of J176171</p>
 <p>&nbsp;</p>

Team:Hong Kong HKUST/notebook/mod4

From 2013.igem.org

Latest revision as of 23:15, 27 September 2013

Glyoxylate Shunt Module's Notebook

June 2013

July 2013

August 2013

September 2013