From 2011.igem.org

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Latest revision as of 18:41, 28 October 2011

Notebook - September

Lab Notes

July August
September
October

Protocol

Brainstorm

Lab Notes - October

Biobrick Group

Week13

Day

Note

Sept.26th Monday

•Miniprep: Rush-3,-4,-12
•Run the gel of digestion test results:
RFP+YFP+1K3-7,-16

•PCR amplify: Rush-3,-4,-12
•Sample and test the intensity of fluorescence once or twice an hour during the growth of E.coli

Sept.27th Tuesday

•Ligate and transform:
RFP+YFP+CFP+1C3 RFP+YFP+1C3

•PCR amplify:20H
•Cut: Rush Bone,22B

Sept.28th Wednesday

•Cultivate: DH5αwith Device CFP,RFP,YFP and without any device
•Ligate and purify:Rush+22B
•Cut and purify:
the product of the ligation

•Run the gel: Digested Rush and 22B,Lig1
•Self-ligate:Digested Lig
•Colony PCR: RFP+YFP+CFP+1C3
•Cut and purify: RFP+YFP+1K3,12I

Sept.29th Thursday

•Ligate and transform: RFP+YFP+1K3&1C3,
RFP+YFP&1C3
•Colony PCR:RFP+YFP+CFP+1C3
•Preserve the colony on the plate

•Plate the ligation results: RFP+1C3,
RFP+YFP+CFP+1C3
Colony PCR:RFP+YFP+1C3
RFP+YFP+CFP+1C3
•Cultivate the above

Sept.30th Friday

•Colony PCR: Rush-Lig

Oct.1st Saturday

•Colony PCR: Failed
•MIniprep: 10I

•Cut: 10I+22B,20J,1T3
•Ligate:10I+22B+1T3

•Cultivate:2I,2M

Oct.2nd Sunday

•Transform the ligation results:
22B+10I(1T3),20J+10I(1T3)
•Miniprep and Preserve:2M,2I

•Cut:fdhf,Vgb,2M,2I
•Purify:RFP+YFP+CFP+1C3

•Ligate and transform:
RFP+YFP+CFP&1A3k
fdhf+2M&1K3,Vgb+2I&1K3

Week14

Day

Note

Oct.3rd Monday

•Colony PCR

Oct.4th Tuesday

•Cut:RBS+20J
•Cultivate:fdhf+2M-1,-2,-3,-4
Vgb+2I-1,-222B+10I-1,-2
•Ligate and purify:RBS+20J& 1C3

•Cut:RBS+20J
•Ligate:2M+20J&10I to 1K3
•Transform:2M+20J+10I,Vgb+1C3
•Cultivate:22B+10I-1,-2

•Miniprep and cut: fdhf+2M,Vgb+2I
•Cut:fdhf+2M,20H

Oct.5th Wednesday

•Cultivate:Vgb+2I 1-6
•Ligate:fdhf+20H& 1K3

•Transform:fdhf+20H
•Cut:2M+20J

Oct.6th Thurday

Finishing the wiki

Oct.7th Friday

making poster

Oct.8th Saturday

•Miniprep and test:
Vgb,fdhf+20H+1K3 1-4

•Colony PCR

Oct.9th Sunday

•Digestion test and run the gel to test the results:
20J+10I -1,-2,-4
22B+10I -1,-2,-3,-4 Vgb+1C3
Fdhf+2M+20H -1,-2,-3,-4 Vgb+2I -1,-2,-5

•Colony PCR:fdhf+2M+20H 5-14
•Cultivate:fdhf+2M+20H 5-14
•Cut:fdhf+2M,20H

Week15

Day

Note

Oct.10th Monday

•Ligate:Fdhf+2M&20H to 1C3
•Cultivate:16L+Device C

•Cut:Vgb+2I,22B+10I
•Ligate:Vgb+2I&22B+10I to1C3

Oct.11th Tuesday

•Cultivate:20H,22B+10I-1,20J+10I-1,-4

•Miniprep and cut:
fdhf+2M+20H+1K3 5-14

Oct.12th Wednesday

•Miniprep: fdhf+20H-10,20H,22B+10I, 20J+10I-1,-4 fdhf+2I+20H,

•Cut and run the gel: Vgb+2I-5,
22B+10I,20J+10I,1C3 backbone

Oct.13th Thursday

•Cut and run the gel to test the ligate results

Oct.14th Friday

•Regional Jamboree @ HKUST

Oct.15th Saturday

•Regional Jamboree @ HKUST

Oct.16th Sunday

•Regional Jamboree @ HKUST

We are the Champion!!!

Week16

Day

Note

Oct.17th Monday

•Rest

Oct.18th Tuesday

•Rest

Oct.19th Wednesday

•Transform: Kit Plate 1 18E&18I, Kit Plate 4 7K& 7M

Oct.20th Thursday

•Transform: Kit Plate 4 7K
•Colony PCR and run the gel:23L 1-6

Oct.21st Friday

•Transform:7K
•Cultivate:7M,18I,18E,23L pSB1A3,1K3,1C3 backbone

•Cut and test the resistance: 22M+10I
•Colony PCR:7M 1-7,18E 1-6,18I 1-6

Oct. 22nd Saturday

•Cultivate:pSB1C3-5,23L-1,-2,7M-1
•Cultivate:7K,10I,22M,18E,18I
•Colony PCR:18E 1-6,18I 1-6
•Test the reagent for PCR several times

•Miniprep and digestion test: 7M,23L,1K3,1A3,1C3
•Digestion and run the gel: 7M,22M+10I-2,1K3

Oct.23rd Sunday

•Cut:7M,22M+10I
•Digestion test:18I,18E

•Ligate and transform: 7M+22M+10I& 1K3

Week17

Day

Note

Oct.24th Monday

•Transform: Kit Plate 4 8G,8I Kit Plate 1 1F
•Culture yeast & B. subtilis

•Colony PCR and run the gel: 7M+22M+10I+1K3 1-25
•Cultivate:8G,1F,8I

Oct.25th Tuesday

•Miniprep:7M+22M+10I+1K3
•Colony PCR:8I,8G,1F
•Cut:7M+22M+10I+1K3,1C3 backbone

•Cultivate:7K
•Ligate:7M+22M+10I& 1C3
•Genome DNA extraction from yeast & B. subtilis
•PCR condition pre-test for alsS & Adh2

Oct.26th Wednesday

•Cultivate:8G,8I,1F,7M,18E,18I
•Transform:7M+22M+10I+1C3 7M+22M+10I+1K3-2
•Reserve:7M+22M+10I+1K3,8G,8I, 1F,7M,18E,18I

•Miniprep:8G
•Cultivate:7M+22M+10I+1C3，2J
•Testify PCR results on gel
•Clean-up alsS PCR product
•Re-pre-test PCR condition for Adh2

Oct.27th Thursday

•PCR producing Adh2
•alsS ES double-digestion
•purification both

Oct.28th Friday

Oct. 29th Saturday

Oct.30th Sunday

Biofilm Group

3rd Oct

18 Oct

Biofilm formation of AI2+rainbofilm device without induction of AI2 for 48 hours.

19 Oct

Co-transformation of AHL and rainbofilm device.

20 Oct

Observation of rainbofilm. Maximum thickness is 14 micrometer.

22 Oct

Biofilm formation with or without AI2 (by arabinose induction of part BBa_K091191) for 48, 36, 24 hours.

24 Oct

Laser confocal observation of biofilm. Used too much water to wash away salt crystals and although thick biofilm is observed before washing but very thin biofilm is observed under laser confocal.

25 Oct

Biofilm formation with rainbofilm DH5alpha without quorum sensing for 48 hours. Colony PCR of 20 JM109 AI2-rainbofilm co-transformaion. Non has rainbofilm plasmid successfully transformed.

26 Oct

18 AI2-rainbofilm JM109 and 20 AHL-rainbofilm DH5alpha colony PCR. Number 5,6,14 of AI2 and number 5,8,11 of AHL have both plasmids.

27 Oct

Biofilm formation with AI2, AHL induced in rainbofilm DH5alpha AHL, DH5alpha AI2 and JM109 AI2.

Top

@@ Line 1: / Line 1: @@
+{{Template:Zjucss_modeling}}
+{{Template:Zjucss_global}}
+{{Template:Zjucss_template2}}
 <html xmlns="http://www.w3.org/1999/xhtml">
 <head>
@@ Line 14: / Line 17: @@
 	rel='stylesheet' type='text/css'>
-<link href="http://zjuchina.tk/modeling.css" rel="stylesheet" type="text/css">
+<!-- include the Tools -->
-<link href="http://zjuchina.tk/global.css" rel="stylesheet" type="text/css">
-<link href="http://zjuchina.tk/template2.css" rel="stylesheet" type="text/css"><!-- include the Tools -->
 <script src="http://cdn.jquerytools.org/1.2.6/full/jquery.tools.min.js"></script>
@@ Line 130: / Line 129: @@
 </a> <a href="https://2011.igem.org/Team:ZJU-China/September.html">September<br />
 </a>
-<a style="color:#0068b1" href="https://2011.igem.org/Team:ZJU-China/October.html">October</a></div>
+<a href="https://2011.igem.org/Team:ZJU-China/October.html">October</a></div>
 <h4>Protocol</h4>
@@ Line 294: / Line 293: @@
 			cellpadding="1">
-			<td width="191"></td>
+			<td width="191">•Colony PCR</td>
@@ Line 306: / Line 305: @@
 		<td id="sheetleft">Oct.4th Tuesday</td>
 		<td>
-		<table id="intable" width="600" border="0" cellspacing="0"
+		<table id="intable"  border="0" cellspacing="0"
 			cellpadding="1">
-			<td width="414"></td>
+			<td >•Cut:RBS+20J<br/>•Cultivate:fdhf+2M-1,-2,-3,-4<br/>Vgb+2I-1,-222B+10I-1,-2<br/>•Ligate and purify:RBS+20J& 1C3 </td>
-			<td width="182"></td>
+			<td >•Cut:RBS+20J<br/>•Ligate:2M+20J&10I to 1K3<br/>•Transform:2M+20J+10I,Vgb+1C3<br/>•Cultivate:22B+10I-1,-2</td>
+<td>•Miniprep and cut: fdhf+2M,Vgb+2I<br/>•Cut:fdhf+2M,20H</td>
 		</table>
 		</td>
@@ Line 317: / Line 316: @@
 		<td id="sheetleft">Oct.5th Wednesday</td>
 		<td>
-		<table width="609" border="0" cellspacing="0" cellpadding="1">
+		<table  border="0" cellspacing="0" cellpadding="1">
 			<tr>
-				<td width="607"></td>
+				<td >•Cultivate:Vgb+2I 1-6<br/>•Ligate:fdhf+20H& 1K3 </td>
+<td>•Transform:fdhf+20H<br/>•Cut:2M+20J</td>
 			</tr>
 		</table>
@@ Line 328: / Line 327: @@
 		<td id="sheetleft">Oct.6th Thurday</td>
 		<td>
-		<table width="597" border="0" cellspacing="0" cellpadding="1">
+		<table  border="0" cellspacing="0" cellpadding="1">
 			<tr>
-				<td width="297"></td>
+				<td>Finishing the wiki</td>
-				<td width="140"></td>
+				<td></td>
-				<td width="154"></td>
 			</tr>
 		</table>
@@ Line 343: / Line 342: @@
 		<table width="612" border="0" cellspacing="0" cellpadding="1">
 			<tr>
-				<td width="335"></td>
+				<td >making poster</td>
-				<td width="273"></td>
 			</tr>
@@ Line 353: / Line 352: @@
 		<td id="sheetleft">Oct.8th Saturday</td>
 		<td>
-		<table width="610" border="0" cellspacing="0" cellpadding="1">
+		<table  border="0" cellspacing="0" cellpadding="1">
 			<tr>
-				<td width="161"></td>
+				<td >•Miniprep and test:<br/>Vgb,fdhf+20H+1K3 1-4</td>
-				<td width="162"></td>
+				<td >•Colony PCR</td>
-				<td width="148"></td>
-				<td width="131"></td>
 			</tr>
 		</table>
@@ Line 366: / Line 364: @@
 		<td id="sheetleft">Oct.9th Sunday</td>
 		<td>
-		<table width="608" border="0" cellspacing="0" cellpadding="1">
+		<table  border="0" cellspacing="0" cellpadding="1">
 			<tr>
-				<td width="244"></td>
+				<td >•Digestion test and run the gel to test the results:<br/>20J+10I -1,-2,-4<br/>22B+10I -1,-2,-3,-4 Vgb+1C3<br/>Fdhf+2M+20H -1,-2,-3,-4 Vgb+2I -1,-2,-5</td>
-				<td width="164"></td>
+				<td >•Colony PCR:fdhf+2M+20H 5-14<br/>•Cultivate:fdhf+2M+20H 5-14<br/>•Cut:fdhf+2M,20H</td>
-				<td width="194"></td>
 			</tr>
 		</table>
@@ Line 391: / Line 389: @@
 			cellpadding="1">
 			<tr>
-				<td ></td>
+				<td >•Ligate:Fdhf+2M&20H to 1C3<br/>•Cultivate:16L+Device C</td>
-				<td></td>
+				<td>•Cut:Vgb+2I,22B+10I<br/>•Ligate:Vgb+2I&22B+10I to1C3</td>
-				<td></td>
 			</tr>
 		</table>
@@ Line 403: / Line 401: @@
 		<table id="intable3" border="0" cellspacing="0" cellpadding="1">
 			<tr>
-				<td></td>
+				<td>•Cultivate:20H,22B+10I-1,20J+10I-1,-4 </td>
-				<td></td>
+				<td>•Miniprep and cut:<br/>fdhf+2M+20H+1K3 5-14</td>
 			</tr>
 		</table>
@@ Line 412: / Line 410: @@
 		<td id="sheetleft3">Oct.12th Wednesday</td>
 		<td>
-		<table width="600" border="0" cellspacing="0" cellpadding="1">
+		<table  border="0" cellspacing="0" cellpadding="1">
 			<tr>
-				<td></td>
+				<td>•Miniprep: fdhf+20H-10,20H,22B+10I, 20J+10I-1,-4 fdhf+2I+20H,</td>
+                <td>•Cut and run the gel: Vgb+2I-5,<br/>22B+10I,20J+10I,1C3 backbone</td>
 			</tr>
 		</table>
@@ Line 422: / Line 421: @@
 		<td id="sheetleft3">Oct.13th Thursday</td>
 		<td>
-		<table width="618" border="0" cellspacing="0" cellpadding="1">
+		<table  border="0" cellspacing="0" cellpadding="1">
 			<tr>
-				<td></td>
+				<td>•Cut and run the gel to test the ligate results</td>
-				<td></td>
-				<td></td>
 			</tr>
 		</table>
@@ Line 436: / Line 435: @@
 		<table width="600" border="0" cellspacing="0" cellpadding="1">
 			<tr>
-				<td></td>
+				<td>•Regional Jamboree @ HKUST</td>
 				<td></td>
 				<td></td>
@@ Line 448: / Line 447: @@
 		<table width="620" border="0" cellspacing="0" cellpadding="1">
 			<tr>
-				<td width="169"></td>
+				<td>•Regional Jamboree @ HKUST</td>
 				<td width="225"></td>
 				<td width="220"></td>
@@ Line 460: / Line 459: @@
 		<table width="620" border="0" cellspacing="0" cellpadding="1">
 			<tr>
-				<td width="120"></td>
+				<td>•Regional Jamboree @ HKUST </td>
-				<td></td>
+				<td>We are the Champion!!!</td>
 				<td></td>
 			</tr>
@@ Line 481: / Line 480: @@
 			cellpadding="1">
 			<tr>
-				<td></td>
+				<td>•Rest</td>
 			</tr>
 		</table>
@@ Line 492: / Line 491: @@
 			cellpadding="1">
 			<tr>
-				<td width="189"></td>
+				<td width="189">•Rest</td>
 			</tr>
 		</table>
@@ Line 502: / Line 501: @@
 		<table width="603" border="0" cellspacing="0" cellpadding="1">
 			<tr>
-				<td></td>
+				<td>•Transform: Kit Plate 1 18E&18I, Kit Plate 4 7K& 7M </td>
 			</tr>
 		</table>
@@ Line 512: / Line 511: @@
 		<table width="611" border="0" cellspacing="0" cellpadding="1">
 			<tr>
-				<td ></td>
+				<td >•Transform: Kit Plate 4 7K<br/>•Colony PCR and run the gel:23L 1-6</td>
 			</tr>
 		</table>
@@ Line 520: / Line 519: @@
 		<td id="sheetleft2">Oct.21st Friday</td>
 		<td>
-		<table width="600" border="0" cellspacing="0" cellpadding="1">
+		<table border="0" cellspacing="0" cellpadding="1">
 			<tr>
-				<td></td>
+				<td>•Transform:7K <br/>•Cultivate:7M,18I,18E,23L pSB1A3,1K3,1C3 backbone</td>
+                <td>•Cut and test the resistance: 22M+10I<br/>•Colony PCR:7M 1-7,18E 1-6,18I 1-6</td>
 			</tr>
 		</table>
@@ Line 530: / Line 530: @@
 		<td id="sheetleft2">Oct. 22nd Saturday</td>
 		<td>
-		<table width="604" border="0" cellspacing="0" cellpadding="1">
+		<table  border="0" cellspacing="0" cellpadding="1">
 			<tr>
-				<td ></td>
+				<td >•Cultivate:pSB1C3-5,23L-1,-2,7M-1<br/>
+                •Cultivate:7K,10I,22M,18E,18I<br/>•Colony PCR:18E 1-6,18I 1-6 <br/>•Test the reagent for PCR several times</td>
+                <td>•Miniprep and digestion test: 7M,23L,1K3,1A3,1C3<br/>•Digestion and run the gel: 7M,22M+10I-2,1K3</td>
 			</tr>
 		</table>
@@ Line 542: / Line 544: @@
 		<table width="613" border="0" cellspacing="0" cellpadding="1">
 			<tr>
-				<td ></td>
+				<td >•Cut:7M,22M+10I<br/>•Digestion test:18I,18E</td>
+                <td>•Ligate and transform: 7M+22M+10I& 1K3 </td>
 			</tr>
 		</table>
@@ Line 561: / Line 564: @@
 			cellpadding="1">
 			<tr>
-				<td></td>
+				<td>•Transform: Kit Plate 4 8G,8I Kit Plate 1 1F <br/>
+               •Culture yeast & B. subtilis</td>
+                <td>•Colony PCR and run the gel: 7M+22M+10I+1K3 1-25<br/>•Cultivate:8G,1F,8I</td>
 			</tr>
 		</table>
@@ Line 569: / Line 574: @@
 		<td id="sheetleft2">Oct.25th Tuesday</td>
 		<td>
-		<table id="intable2" width="601" border="0" cellspacing="0"
+		<table id="intable2" border="0" cellspacing="0"
 			cellpadding="1">
 			<tr>
-				<td width="189"></td>
+				<td>•Miniprep:7M+22M+10I+1K3<br/>•Colony PCR:8I,8G,1F<br/>•Cut:7M+22M+10I+1K3,1C3 backbone</td>
+                <td>•Cultivate:7K<br/>•Ligate:7M+22M+10I& 1C3<br/> •Genome DNA extraction from yeast & B. subtilis<br/> •PCR condition pre-test for alsS & Adh2</td>
 			</tr>
 		</table>
@@ Line 580: / Line 586: @@
 		<td id="sheetleft2">Oct.26th Wednesday</td>
 		<td>
-		<table width="603" border="0" cellspacing="0" cellpadding="1">
+		<table border="0" cellspacing="0" cellpadding="1">
 			<tr>
-				<td></td>
+				<td>•Cultivate:8G,8I,1F,7M,18E,18I<br/>•Transform:7M+22M+10I+1C3 7M+22M+10I+1K3-2<br/>•Reserve:7M+22M+10I+1K3,8G,8I, 1F,7M,18E,18I</td>
+                <td>•Miniprep:8G<br/>•Cultivate:7M+22M+10I+1C3，2J<br/>•Testify PCR results on gel<br/>•Clean-up alsS PCR product<br/>•Re-pre-test PCR condition for Adh2</td>
 			</tr>
 		</table>
@@ Line 589: / Line 596: @@
 	<tr>
 		<td id="sheetleft2">Oct.27th Thursday</td>
-		<td>
+		<td><table width="611" border="0" cellspacing="0" cellpadding="1">
-		<table width="611" border="0" cellspacing="0" cellpadding="1">
+		  <tr>
-			<tr>
+		    <td > •PCR producing Adh2<br/>•alsS ES double-digestion<br/>•purification both</td>
-				<td ></td>
+		    </tr>
-			</tr>
+		  </table></td>
-		</table>
-		</td>
 	</tr>
 	<tr>
@@ Line 650: / Line 655: @@
 </div>
 <div class="block" id="nsheet">
-<h1>4th Oct</h1>
+<h1>18 Oct</h1>
-<p></p>
+<p>Biofilm formation of AI2+rainbofilm device without induction of AI2 for 48 hours.</p>
 </div>
 <div class="block" id="nsheet">
-<h1>6th Oct</h1>
+<h1>19 Oct</h1>
-<p></p>
+<p>Co-transformation of AHL and rainbofilm device.</p>
 </div>
 <div class="block" id="nsheet">
-<h1>12th Oct</h1>
+<h1>20 Oct</h1>
-<p></p>
+<p>Observation of rainbofilm. Maximum thickness is 14 micrometer.</p>
 </div>
 <div class="block" id="nsheet">
-<h1>15th Oct</h1>
+<h1>22 Oct</h1>
-<p></p>
+<p>Biofilm formation with or without AI2 (by arabinose induction of part BBa_K091191)
+for 48, 36, 24 hours.</p>
 </div>
 <div class="block" id="nsheet">
-<h1>16th Oct</h1>
+<h1>24 Oct</h1>
-<p></p>
+<p>Laser confocal observation of biofilm. Used too much water to wash away salt
+crystals and although thick biofilm is observed before washing but very thin biofilm is
+observed under laser confocal.</p>
 </div>
 <div class="block" id="nsheet">
-<h1>17th Oct</h1>
+<h1>25 Oct</h1>
-<p></p>
+<p>Biofilm formation with rainbofilm DH5alpha without quorum sensing for 48 hours.
+Colony PCR of 20 JM109 AI2-rainbofilm co-transformaion. Non has rainbofilm plasmid
+successfully transformed.</p>
 </div>
 <div class="block" id="nsheet">
-<h1>20th Oct</h1>
+<h1>26 Oct</h1>
-<p></p>
+<p>18 AI2-rainbofilm JM109 and 20 AHL-rainbofilm DH5alpha colony PCR. Number
+,6,14 of AI2 and number 5,8,11 of AHL have both plasmids.</p>
+</div>
+<div class="block" id="nsheet">
+<h1>27 Oct</h1>
+<p>Biofilm formation with AI2, AHL induced in rainbofilm DH5alpha AHL, DH5alpha
+AI2 and JM109 AI2.</p>
 </div>
 </div>
 <script type="text/javascript">