Team:UNAM Genomics Mexico/Notebook/ANDSugar

From 2012.igem.org

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{{:Template:Team:UNAM_Genomics_Mexico/webhtml| content=
{{:Template:Team:UNAM_Genomics_Mexico/webhtml| content=
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__NOTOC__
<br />
<br />
-
<center><h1>'''Arabinose/Xylose AND Gate'''</h1></center>
+
<center><h1>'''Arabinose/Xylose AND Gate Notebook'''</h1></center>
<br />
<br />
<br />
<br />
-
<table border="0"  height="150" cellspacing="15" bgcolor="transparent" id="tablecontentbg">
+
<table border="0"  height="150" cellspacing="15" bgcolor="transparent" id="tablecontentbg" cellpadding="20">
<tr>
<tr>
-
<td id="leftcolumn2">Nanotubes!!</td>
+
<td id="leftcolumn2"><center>2 [[Team:UNAM_Genomics_Mexico/Notebook/ANDSugar#JUNE | '''JUNE''']] </center> <br />
-
<td  id="contentcolumn2">The logic</td>
+
<br />
-
<td id="rightcolumn2">Random info</td>
+
2.1 [[Team:UNAM_Genomics_Mexico/Notebook/ANDSugar#06.2F07.2F12 |06/07/12]] <br />
 +
2.2 [[Team:UNAM_Genomics_Mexico/Notebook/ANDSugar#06.2F12.2F12 |06/12/12]] <br />
 +
2.3 [[Team:UNAM_Genomics_Mexico/Notebook/ANDSugar#06.2F13.2F12 |06/13/12]] <br />
 +
2.4 [[Team:UNAM_Genomics_Mexico/Notebook/ANDSugar#06.2F14.2F12 |06/14/12]] <br />
 +
2.5 [[Team:UNAM_Genomics_Mexico/Notebook/ANDSugar#06.2F15.2F12 |06/15/12]] <br />
 +
2.6 [[Team:UNAM_Genomics_Mexico/Notebook/ANDSugar#06.2F18.2F12 |06/18/12]] <br />
 +
2.7 [[Team:UNAM_Genomics_Mexico/Notebook/ANDSugar#06.2F19.2F12 |06/19/12]] <br />
 +
2.8 [[Team:UNAM_Genomics_Mexico/Notebook/ANDSugar#06.2F22.2F12 |06/22/12]] <br />
 +
2.9 [[Team:UNAM_Genomics_Mexico/Notebook/ANDSugar#06.2F25.2F12 |06/25/12]] <br />
 +
2.10 [[Team:UNAM_Genomics_Mexico/Notebook/ANDSugar#06.2F26.2F12 |06/26/12]] <br />
 +
2.11 [[Team:UNAM_Genomics_Mexico/Notebook/ANDSugar#06.2F27.2F12 |06/27/12]] <br />
 +
2.12 [[Team:UNAM_Genomics_Mexico/Notebook/ANDSugar#06.2F29.2F12 |06/29/12]] <br />
 +
</td>
 +
 
 +
<td id="contentcolumn2"><center>3 [[Team:UNAM_Genomics_Mexico/Notebook/ANDSugar#JULY | '''JULY''']] </center> <br />
 +
<br />
 +
3.1[[Team:UNAM_Genomics_Mexico/Notebook/ANDSugar#07.2F03.2F12 | 07/03/12]] <br />
 +
3.2 [[Team:UNAM_Genomics_Mexico/Notebook/ANDSugar#07.2F04.2F12 | 07/04/12]] <br />
 +
3.3 [[Team:UNAM_Genomics_Mexico/Notebook/ANDSugar#07.2F06.2F12 | 07/06/12]] <br />
 +
3.4 [[Team:UNAM_Genomics_Mexico/Notebook/ANDSugar#07.2F07.2F12 | 07/07/12]] <br />
 +
3.5 [[Team:UNAM_Genomics_Mexico/Notebook/ANDSugar#07.2F08.2F12 | 07/08/12]] <br />
 +
3.6 [[Team:UNAM_Genomics_Mexico/Notebook/ANDSugar#07.2F09.2F12 | 07/09/12]] <br />
 +
3.7 [[Team:UNAM_Genomics_Mexico/Notebook/ANDSugar#07.2F10.2F12 | 07/10/12]] <br />
 +
3.8 [[Team:UNAM_Genomics_Mexico/Notebook/ANDSugar#07.2F11.2F12 | 07/11/12]] <br />
 +
3.9 [[Team:UNAM_Genomics_Mexico/Notebook/ANDSugar#07.2F12.2F12 | 07/12/12]] <br />
 +
3.10 [[Team:UNAM_Genomics_Mexico/Notebook/ANDSugar#07.2F13.2F12 | 07/13/12]] <br />
 +
3.11 [[Team:UNAM_Genomics_Mexico/Notebook/ANDSugar#07.2F14.2F12 | 07/14/12]] <br />
 +
3.12 [[Team:UNAM_Genomics_Mexico/Notebook/ANDSugar#07.2F16.2F12 | 07/16/12]] <br />
 +
3.13 [[Team:UNAM_Genomics_Mexico/Notebook/ANDSugar#07.2F17.2F12 | 07/17/12]] <br />
 +
3.14 [[Team:UNAM_Genomics_Mexico/Notebook/ANDSugar#07.2F18.2F12 | 07/18/12]] <br />
 +
3.15 [[Team:UNAM_Genomics_Mexico/Notebook/ANDSugar#07.2F19.2F12 | 07/19/12]] <br />
 +
3.16 [[Team:UNAM_Genomics_Mexico/Notebook/ANDSugar#07.2F20.2F12 | 07/20/12]] <br />
 +
3.17 [[Team:UNAM_Genomics_Mexico/Notebook/ANDSugar#07.2F23.2F12 | 07/23/12]] <br />
 +
3.18 [[Team:UNAM_Genomics_Mexico/Notebook/ANDSugar#07.2F24.2F12 | 07/24/12]] <br />
 +
3.19 [[Team:UNAM_Genomics_Mexico/Notebook/ANDSugar#07.2F25.2F12 | 07/25/12]] <br />
 +
3.20 [[Team:UNAM_Genomics_Mexico/Notebook/ANDSugar#07.2F26.2F12 | 07/26/12]] <br />
 +
3.21 [[Team:UNAM_Genomics_Mexico/Notebook/ANDSugar#07.2F27.2F12 | 07/27/12]] <br />
 +
3.22 [[Team:UNAM_Genomics_Mexico/Notebook/ANDSugar#07.2F30.2F12 | 07/30/12]] <br />
 +
3.23 [[Team:UNAM_Genomics_Mexico/Notebook/ANDSugar#07.2F31.2F12 | 07/31/12]] <br />
 +
</td>
 +
 
 +
<td id="rightcolumn2"><center>4 [[Team:UNAM_Genomics_Mexico/Notebook/ANDSugar#AUGUST | '''AUGUST''']] </center> <br />
 +
<br />
 +
4.1 [[Team:UNAM_Genomics_Mexico/Notebook/ANDSugar#08.2F01.2F12 | 08/01/12]] <br />
 +
4.2 [[Team:UNAM_Genomics_Mexico/Notebook/ANDSugar#08.2F02.2F12 | 08/02/12]] <br />
 +
4.3 [[Team:UNAM_Genomics_Mexico/Notebook/ANDSugar#08.2F03.2F12 | 08/03/12]] <br />
 +
4.4 [[Team:UNAM_Genomics_Mexico/Notebook/ANDSugar#08.2F06.2F12 | 08/06/12]] <br />
 +
4.5 [[Team:UNAM_Genomics_Mexico/Notebook/ANDSugar#08.2F08.2F12 | 08/08/12]] <br />
 +
4.6 [[Team:UNAM_Genomics_Mexico/Notebook/ANDSugar#08.2F09.2F12 | 08/09/12]] <br />
 +
4.7 [[Team:UNAM_Genomics_Mexico/Notebook/ANDSugar#08.2F10.2F12 | 08/10/12]] <br />
 +
4.8 [[Team:UNAM_Genomics_Mexico/Notebook/ANDSugar#08.2F13.2F12 | 08/13/12]] <br />
 +
4.9 [[Team:UNAM_Genomics_Mexico/Notebook/ANDSugar#08.2F16.2F12 | 08/16/12]] <br />
 +
4.10 [[Team:UNAM_Genomics_Mexico/Notebook/ANDSugar#08.2F20.2F12 | 08/20/12]] <br />
 +
4.11 [[Team:UNAM_Genomics_Mexico/Notebook/ANDSugar#08.2F21.2F12 | 08/21/12]] <br />
 +
4.12 [[Team:UNAM_Genomics_Mexico/Notebook/ANDSugar#08.2F22.2F12 | 08/22/12]] <br />
 +
4.13 [[Team:UNAM_Genomics_Mexico/Notebook/ANDSugar#08.2F23.2F12 | 08/23/12]] <br />
 +
4.14 [[Team:UNAM_Genomics_Mexico/Notebook/ANDSugar#08.2F24.2F12 | 08/24/12]] <br />
 +
4.15 [[Team:UNAM_Genomics_Mexico/Notebook/ANDSugar#08.2F25.2F12 | 08/25/12]] <br />
 +
4.16 [[Team:UNAM_Genomics_Mexico/Notebook/ANDSugar#08.2F28.2F12 | 08/28/12]] <br />
 +
4.17 [[Team:UNAM_Genomics_Mexico/Notebook/ANDSugar#08.2F29.2F12 | 08/29/12]] <br />
 +
4.18 [[Team:UNAM_Genomics_Mexico/Notebook/ANDSugar#08.2F30.2F12 | 08/30/12]] <br />
 +
4.19 [[Team:UNAM_Genomics_Mexico/Notebook/ANDSugar#08.2F31.2F12 | 08/31/12]] <br />
 +
</td>
 +
</tr>
 +
 
 +
<tr>
 +
<td id="leftcolumn2"><center>5 [[Team:UNAM_Genomics_Mexico/Notebook/ANDSugar#SEPTEMBER | '''SEPTEMBER''']] </center> <br />
 +
<br />
 +
5.1 [[Team:UNAM_Genomics_Mexico/Notebook/ANDSugar#09.2F01.2F12 | 09/01/12]] <br />
 +
5.2 [[Team:UNAM_Genomics_Mexico/Notebook/ANDSugar#09.2F02.2F12 | 09/03/12]] <br />
 +
5.3 [[Team:UNAM_Genomics_Mexico/Notebook/ANDSugar#09.2F04.2F12 | 09/04/12]] <br />
 +
5.4 [[Team:UNAM_Genomics_Mexico/Notebook/ANDSugar#09.2F05.2F12 | 09/05/12]] <br />
 +
5.5 [[Team:UNAM_Genomics_Mexico/Notebook/ANDSugar#09.2F06.2F12 | 09/06/12]] <br />
 +
5.6 [[Team:UNAM_Genomics_Mexico/Notebook/ANDSugar#09.2F14.2F12 | 09/14/12]] <br />
 +
5.7 [[Team:UNAM_Genomics_Mexico/Notebook/ANDSugar#09.2F16.2F12 | 09/16/12]]<br />
 +
5.8 [[Team:UNAM_Genomics_Mexico/Notebook/ANDSugar#09.2F17.2F12 | 09/17/12]]<br />
 +
5.9 [[Team:UNAM_Genomics_Mexico/Notebook/ANDSugar#09.2F18.2F12 | 09/18/12]]<br />
 +
5.10 [[Team:UNAM_Genomics_Mexico/Notebook/ANDSugar#09.2F19.2F12 | 09/19/12]]<br />
 +
5.11 [[Team:UNAM_Genomics_Mexico/Notebook/ANDSugar#09.2F19.2F12 | 09/19/12]]<br />
 +
5.12 [[Team:UNAM_Genomics_Mexico/Notebook/ANDSugar#09.2F20.2F12 | 09/20/12]]<br />
 +
5.13 [[Team:UNAM_Genomics_Mexico/Notebook/ANDSugar#09.2F21.2F12 | 09/21/12]]<br />
 +
5.14 [[Team:UNAM_Genomics_Mexico/Notebook/ANDSugar#09.2F22.2F12 | 09/22/12]]<br />
 +
5.15 [[Team:UNAM_Genomics_Mexico/Notebook/ANDSugar#09.2F23.2F12 | 09/23/12]]<br />
 +
5.16 [[Team:UNAM_Genomics_Mexico/Notebook/ANDSugar#09.2F24.2F12 | 09/24/12]]<br />
 +
5.17 [[Team:UNAM_Genomics_Mexico/Notebook/ANDSugar#09.2F26.2F12 | 09/26/12]]<br />
 +
5.18 [[Team:UNAM_Genomics_Mexico/Notebook/ANDSugar#09.2F27.2F12 | 09/27/12]]<br />
 +
 
 +
 
 +
 
 +
</td>
 +
 
 +
<td  id="contentcolumn2">
 +
'''OCTOBER'''<br />
 +
5.19 [[Team:UNAM_Genomics_Mexico/Notebook/ANDSugar#10.2F09.2F12 | 10/09/12]]<br />
 +
5.20 [[Team:UNAM_Genomics_Mexico/Notebook/ANDSugar#10.2F10.2F12 | 10/10/12]]<br />
 +
5.21 [[Team:UNAM_Genomics_Mexico/Notebook/ANDSugar#10.2F11.2F12 | 10/11/12]]<br />
 +
5.22 [[Team:UNAM_Genomics_Mexico/Notebook/ANDSugar#10.2F12.2F12 | 10/12/12]]<br />
 +
5.23 [[Team:UNAM_Genomics_Mexico/Notebook/ANDSugar#10.2F13.2F12 | 10/13/12]]<br />
 +
</td>
 +
 
 +
<td id="rightcolumn2"><center>[[File:UnmagenomicsBacteria sugar.png | 190px]]</center><p> '''On hover the images to see descriptions'''</p><td/>
</tr>
</tr>
</table>
</table>
 +
=JUNE=
=JUNE=
Line 37: Line 138:
plate 2 17E<br />
plate 2 17E<br />
Stock 50 mg/mL<br />
Stock 50 mg/mL<br />
-
E.coli 1/1000<br />
+
''E.coli'' 1/1000<br />
[[Team:UNAM_Genomics_Mexico/Notebook/Protocols#Transformation | TRANSFORMATION PROTOCOL]]. <br />
[[Team:UNAM_Genomics_Mexico/Notebook/Protocols#Transformation | TRANSFORMATION PROTOCOL]]. <br />
We made liquid cultures with colonies [[Team:UNAM_Genomics_Mexico/Notebook/Protocols#Liquid_culture | LIQUID CULTURE]]. <br />
We made liquid cultures with colonies [[Team:UNAM_Genomics_Mexico/Notebook/Protocols#Liquid_culture | LIQUID CULTURE]]. <br />
Line 68: Line 169:
<h2>06/13/12</h2><br />
<h2>06/13/12</h2><br />
We ran gel and extracted from gel [[Team:UNAM_Genomics_Mexico/Notebook/Protocols#Gel_extraction_protocol | LIQUID CULTURE]].<br />
We ran gel and extracted from gel [[Team:UNAM_Genomics_Mexico/Notebook/Protocols#Gel_extraction_protocol | LIQUID CULTURE]].<br />
-
We made liquid cultures [[Team:UNAM_Genomics_Mexico/Notebook/Protocols#Liquid_culture | LIQUID CULTURE]] and lysed [LYSIS PROTOCOL]. <br />
+
We made liquid cultures [[Team:UNAM_Genomics_Mexico/Notebook/Protocols#Liquid_culture | LIQUID CULTURE]] and lysed. <br />
<br />
<br />
<br />
<br />
Line 202: Line 303:
>Ran gels with digestions B0014 with E,X and E,P [[Team:UNAM_Genomics_Mexico/Notebook/Protocols#Gel_electrophoresis | GEL ELECTROPHORESIS PROTOCOL]]. <br />
>Ran gels with digestions B0014 with E,X and E,P [[Team:UNAM_Genomics_Mexico/Notebook/Protocols#Gel_electrophoresis | GEL ELECTROPHORESIS PROTOCOL]]. <br />
-
>Dephosphated B0014 E,X and B0014 E,P [DESPHOPHORYLATION PROTOCOL]. <br />
+
>Dephosphated B0014 E,X and B0014 E,P. <br />
<br />
<br />
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<br />
<br />
<br />
<br />
 +
::::::::::::::::::::::::::::::::::::::[[File:UnamgenomcisUp.png|right | 120px |link=Team:UNAM_Genomics_Mexico/Notebook/ANDSugar#Arabinose.2FXylose_AND_Gate_Notebook]]
 +
=JULY=
=JULY=
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>Did band extractions [[Team:UNAM_Genomics_Mexico/Notebook/Protocols#Gel_extraction_protocol | LIQUID CULTURE]]. <br />
>Did band extractions [[Team:UNAM_Genomics_Mexico/Notebook/Protocols#Gel_extraction_protocol | LIQUID CULTURE]]. <br />
>Stored at -20ºC. <br />
>Stored at -20ºC. <br />
-
>Did PCR to Cassete  ΩSpr/Strr  to add RBS and prefix/suffix [PCR PROTOCOL]. <br />
+
>Did PCR to Cassete  ΩSpr/Strr  to add RBS and prefix/suffix. <br />
>Left digesting with E,S [[Team:UNAM_Genomics_Mexico/Notebook/Protocols#Digestion_protocol_.2820_.C2.B5l.29 | LIQUID CULTURE]]. <br />
>Left digesting with E,S [[Team:UNAM_Genomics_Mexico/Notebook/Protocols#Digestion_protocol_.2820_.C2.B5l.29 | LIQUID CULTURE]]. <br />
<br />
<br />
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<h2>07/04/12</h2><br />
<h2>07/04/12</h2><br />
-
>We dephosphated B0079 S,P, K143001 S,P, K143002 E,X (9.1) [DESPHOPHORYLATION PROTOCOL]. <br />
+
>We dephosphated B0079 S,P, K143001 S,P, K143002 E,X (9.1). <br />
-
>Ligated Cassete  ΩSpr/Strr  +K143002 dephosphated(digested with E,X and E,S) LIGATION PROTOCOL]. <br />
+
>Ligated Cassete  ΩSpr/Strr  +K143002 dephosphated(digested with E,X and E,S). <br />
>Transformed ligation and left overnight plated [[Team:UNAM_Genomics_Mexico/Notebook/Protocols#Transformation | TRANSFORMATION PROTOCOL]]. <br />
>Transformed ligation and left overnight plated [[Team:UNAM_Genomics_Mexico/Notebook/Protocols#Transformation | TRANSFORMATION PROTOCOL]]. <br />
-
>Extracted plasmid PBBR1 GusA in 2 1.5 mL eppendorfs [PLASMID  EXTRACTION (“soft” lysis) PROTOCOL]. <br />
+
>Extracted plasmid PBBR1 GusA in 2 1.5 mL eppendorfs. <br />
>Digested with PstI [[Team:UNAM_Genomics_Mexico/Notebook/Protocols#Digestion_protocol_.2820_.C2.B5l.29 | LIQUID CULTURE]]. <br />
>Digested with PstI [[Team:UNAM_Genomics_Mexico/Notebook/Protocols#Digestion_protocol_.2820_.C2.B5l.29 | LIQUID CULTURE]]. <br />
<br />
<br />
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Did GusA primers dissolution for PCR. <br />
Did GusA primers dissolution for PCR. <br />
GusA PCR <br />
GusA PCR <br />
-
[PCR PROTOCOL] <br />
 
Gel Extraction by kit of lanes 3 and 5 [[Team:UNAM_Genomics_Mexico/Notebook/Protocols#Gel_extraction_protocol | LIQUID CULTURE]]. <br />
Gel Extraction by kit of lanes 3 and 5 [[Team:UNAM_Genomics_Mexico/Notebook/Protocols#Gel_extraction_protocol | LIQUID CULTURE]]. <br />
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•Transformed AraC PCR+ Ω+AmyE 3’ ligation in two tubes [[Team:UNAM_Genomics_Mexico/Notebook/Protocols#Transformation | TRANSFORMATION PROTOCOL]]. <br />
•Transformed AraC PCR+ Ω+AmyE 3’ ligation in two tubes [[Team:UNAM_Genomics_Mexico/Notebook/Protocols#Transformation | TRANSFORMATION PROTOCOL]]. <br />
-
•From pfrc54 liquid cultures (A3) that were grown overnight we extracted plasmid [PLASMID  EXTRACTION (“soft” lysis) PROTOCOL]. <br />
+
•From pfrc54 liquid cultures (A3) that were grown overnight we extracted plasmid. <br />
•Made glycerols from 2 LB Km 30 Sp100 DH5α  Ω+AmyE 3’ plates and from 1 LB Amp100 pfrc54 (A3) plates with control[[Team:UNAM_Genomics_Mexico/Notebook/Protocols#GLYCEROL_PROTOCOL | GLYCEROL PROTOCOL]] . <br />
•Made glycerols from 2 LB Km 30 Sp100 DH5α  Ω+AmyE 3’ plates and from 1 LB Amp100 pfrc54 (A3) plates with control[[Team:UNAM_Genomics_Mexico/Notebook/Protocols#GLYCEROL_PROTOCOL | GLYCEROL PROTOCOL]] . <br />
•Ligated GusA PCR with B0014 E,X desphophorylated [[Team:UNAM_Genomics_Mexico/Notebook/Protocols#Ligation | LIGATION PROTOCOL]]. <br />
•Ligated GusA PCR with B0014 E,X desphophorylated [[Team:UNAM_Genomics_Mexico/Notebook/Protocols#Ligation | LIGATION PROTOCOL]]. <br />
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•Digested Pfrc54 (A3) with S,P [[Team:UNAM_Genomics_Mexico/Notebook/Protocols#Digestion_protocol_.2820_.C2.B5l.29 | LIQUID CULTURE]]. <br />
•Digested Pfrc54 (A3) with S,P [[Team:UNAM_Genomics_Mexico/Notebook/Protocols#Digestion_protocol_.2820_.C2.B5l.29 | LIQUID CULTURE]]. <br />
-
•Desphophorylated  Ω+AmyE 3’ E,X [DESPHOPHORYLATION PROTOCOL]. <br />
+
•Desphophorylated  Ω+AmyE 3’ E,X. <br />
<br />
<br />
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•Transformed with GFP E0040 psBIA2. <br />
•Transformed with GFP E0040 psBIA2. <br />
•Liquid Cultures with ligation: AraC+ Ω+AmyE 3’ for plasmid extraction at night [[Team:UNAM_Genomics_Mexico/Notebook/Protocols#Transformation | TRANSFORMATION PROTOCOL]]. <br />
•Liquid Cultures with ligation: AraC+ Ω+AmyE 3’ for plasmid extraction at night [[Team:UNAM_Genomics_Mexico/Notebook/Protocols#Transformation | TRANSFORMATION PROTOCOL]]. <br />
-
•B. Subtitils competent cells [B.Subtilis group protocol]. <br />
+
•''B. Subtitils'' competent cells. <br />
<br />
<br />
<br />
<br />
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•From 24 AraC+ Ω+AmyE 3’ LB Km 30 Sp 100 DH5α tubes: <br />
•From 24 AraC+ Ω+AmyE 3’ LB Km 30 Sp 100 DH5α tubes: <br />
•Extracted pellets<br />
•Extracted pellets<br />
-
•Extracted plasmids [PLASMID  EXTRACTION (“soft” lysis) PROTOCOL]. <br />
+
•Extracted plasmids. <br />
•Ran gel [[Team:UNAM_Genomics_Mexico/Notebook/Protocols#Gel_electrophoresis | GEL ELECTROPHORESIS PROTOCOL]] . <br /><br />
•Ran gel [[Team:UNAM_Genomics_Mexico/Notebook/Protocols#Gel_electrophoresis | GEL ELECTROPHORESIS PROTOCOL]] . <br /><br />
•From transformed DH5α km 30: <br />
•From transformed DH5α km 30: <br />
Line 547: Line 649:
From these two we: <br />
From these two we: <br />
•Did liquid cultures [[Team:UNAM_Genomics_Mexico/Notebook/Protocols#Liquid_culture | LIQUID CULTURE]]. <br />
•Did liquid cultures [[Team:UNAM_Genomics_Mexico/Notebook/Protocols#Liquid_culture | LIQUID CULTURE]]. <br />
-
•Extracted plasmid [PLASMID  EXTRACTION (“soft” lysis) PROTOCOL]. <br />
+
•Extracted plasmid. <br />
•From the GusA+E0014 transformation we took 24 colonies, did liquid cultures and extracted plasmid  [[Team:UNAM_Genomics_Mexico/Notebook/Protocols#Liquid_culture | LIQUID CULTURE]]. <br />
•From the GusA+E0014 transformation we took 24 colonies, did liquid cultures and extracted plasmid  [[Team:UNAM_Genomics_Mexico/Notebook/Protocols#Liquid_culture | LIQUID CULTURE]]. <br />
•Ran gel with this transformation [[Team:UNAM_Genomics_Mexico/Notebook/Protocols#Gel_electrophoresis | GEL ELECTROPHORESIS PROTOCOL]] . <br />
•Ran gel with this transformation [[Team:UNAM_Genomics_Mexico/Notebook/Protocols#Gel_electrophoresis | GEL ELECTROPHORESIS PROTOCOL]] . <br />
Line 616: Line 718:
•We ran We digested 1 + Ω+AmyE 3’ E,P with Miguel’s enzymes and with Abiel’s enzymes [[Team:UNAM_Genomics_Mexico/Notebook/Protocols#Digestion_protocol_.2820_.C2.B5l.29 | LIQUID CULTURE]]. <br /><br />
•We ran We digested 1 + Ω+AmyE 3’ E,P with Miguel’s enzymes and with Abiel’s enzymes [[Team:UNAM_Genomics_Mexico/Notebook/Protocols#Digestion_protocol_.2820_.C2.B5l.29 | LIQUID CULTURE]]. <br /><br />
•We transformed with ligations AraC+ Ω+AmyE 3’ E and + Ω+AmyE 3’ E [[Team:UNAM_Genomics_Mexico/Notebook/Protocols#Transformation | TRANSFORMATION PROTOCOL]]. <br /><br />
•We transformed with ligations AraC+ Ω+AmyE 3’ E and + Ω+AmyE 3’ E [[Team:UNAM_Genomics_Mexico/Notebook/Protocols#Transformation | TRANSFORMATION PROTOCOL]]. <br /><br />
-
•Extracted plasmids from AraC+ Ω+AmyE 3’ 12,15,21 [PLASMID  EXTRACTION (“soft” lysis) PROTOCOL]. <br /><br />
+
•Extracted plasmids from AraC+ Ω+AmyE 3’ 12,15,21. <br /><br />
•Digested E0040 X,S 2,3,4,5,6; ligations AraC+ Ω+AmyE 3’ E 12,15,21; ligations AraC+ Ω+AmyE 3’ P [[Team:UNAM_Genomics_Mexico/Notebook/Protocols#Digestion_protocol_.2820_.C2.B5l.29 | LIQUID CULTURE]]. <br /><br />
•Digested E0040 X,S 2,3,4,5,6; ligations AraC+ Ω+AmyE 3’ E 12,15,21; ligations AraC+ Ω+AmyE 3’ P [[Team:UNAM_Genomics_Mexico/Notebook/Protocols#Digestion_protocol_.2820_.C2.B5l.29 | LIQUID CULTURE]]. <br /><br />
<br />
<br />
Line 651: Line 753:
<h2>07/23/12</h2><br /><br />
<h2>07/23/12</h2><br /><br />
•From 24 GusA+B0014 tubes (-) we didn’t do anything. <br />
•From 24 GusA+B0014 tubes (-) we didn’t do anything. <br />
-
•From 4 AraC+ Ω+AmyE 3’  we extracted plasmid [PLASMID  EXTRACTION (“soft” lysis) PROTOCOL]. <br />
+
•From 4 AraC+ Ω+AmyE 3’  we extracted plasmid. <br />
•Digested from the 4 AraC+ Ω+AmyE 3’  E,X; X; P and GusA PCR with X,P [[Team:UNAM_Genomics_Mexico/Notebook/Protocols#Digestion_protocol_.2820_.C2.B5l.29 | LIQUID CULTURE]]. <br /><br />
•Digested from the 4 AraC+ Ω+AmyE 3’  E,X; X; P and GusA PCR with X,P [[Team:UNAM_Genomics_Mexico/Notebook/Protocols#Digestion_protocol_.2820_.C2.B5l.29 | LIQUID CULTURE]]. <br /><br />
Line 662: Line 764:
•Ran gel of digested AraC+ Ω+AmyE 3’  1,2,3,4 with E,P  [[Team:UNAM_Genomics_Mexico/Notebook/Protocols#Digestion_protocol_.2820_.C2.B5l.29 | LIQUID CULTURE]]. <br />
•Ran gel of digested AraC+ Ω+AmyE 3’  1,2,3,4 with E,P  [[Team:UNAM_Genomics_Mexico/Notebook/Protocols#Digestion_protocol_.2820_.C2.B5l.29 | LIQUID CULTURE]]. <br />
•Joined B0014 E with X B0014 X with E digestions. <br />
•Joined B0014 E with X B0014 X with E digestions. <br />
-
•Made liquid cultures from 2 days old plated GusA+B0014 and extracted plasmid [[Team:UNAM_Genomics_Mexico/Notebook/Protocols#Liquid_culture | LIQUID CULTURE]] [PLASMID  EXTRACTION (“soft” lysis) PROTOCOL]. Transformed [[Team:UNAM_Genomics_Mexico/Notebook/Protocols#Transformation | TRANSFORMATION PROTOCOL]]. <br />
+
•Made liquid cultures from 2 days old plated GusA+B0014 and extracted plasmid [[Team:UNAM_Genomics_Mexico/Notebook/Protocols#Liquid_culture | LIQUID CULTURE]]. Transformed [[Team:UNAM_Genomics_Mexico/Notebook/Protocols#Transformation | TRANSFORMATION PROTOCOL]]. <br />
•From LasR DH5α make liquid cultures and plate [[Team:UNAM_Genomics_Mexico/Notebook/Protocols#Liquid_culture | LIQUID CULTURE]]. <br />
•From LasR DH5α make liquid cultures and plate [[Team:UNAM_Genomics_Mexico/Notebook/Protocols#Liquid_culture | LIQUID CULTURE]]. <br />
•Digested  Ω+AmyE 3’  with X,P; E,S; C0080 X,P; E,S; S,P [[Team:UNAM_Genomics_Mexico/Notebook/Protocols#Digestion_protocol_.2820_.C2.B5l.29 | LIQUID CULTURE]]. <br />
•Digested  Ω+AmyE 3’  with X,P; E,S; C0080 X,P; E,S; S,P [[Team:UNAM_Genomics_Mexico/Notebook/Protocols#Digestion_protocol_.2820_.C2.B5l.29 | LIQUID CULTURE]]. <br />
Line 690: Line 792:
•From C0179 (LasR) transformation which grew colonies, we made two liquid cultures: DH5α C0179 LB Cb 100 (two cultures) and a control without bacteria [[Team:UNAM_Genomics_Mexico/Notebook/Protocols#Liquid_culture | LIQUID CULTURE]]. <br />
•From C0179 (LasR) transformation which grew colonies, we made two liquid cultures: DH5α C0179 LB Cb 100 (two cultures) and a control without bacteria [[Team:UNAM_Genomics_Mexico/Notebook/Protocols#Liquid_culture | LIQUID CULTURE]]. <br />
-
•We extracted plasmid from 8 C0179 tubes, from 2 tubes of C0179 (Miguel’s transformation), Puc, B.S. control and PSB4AE [PLASMID  EXTRACTION (“soft” lysis) PROTOCOL]. <br />
+
•We extracted plasmid from 8 C0179 tubes, from 2 tubes of C0179 (Miguel’s transformation), Puc, B.S. control and PSB4AE. <br />
•Due to problems with the way we did the transformations of ligations we repeated them: <br />
•Due to problems with the way we did the transformations of ligations we repeated them: <br />
Line 735: Line 837:
<h2>07/31/12</h2><br /><br />
<h2>07/31/12</h2><br /><br />
-
Extracted plasmids from yesterday’s cultures and from K143002 cultures that were in the other lab [PLASMID  EXTRACTION (“soft” lysis) PROTOCOL]. <br />
+
Extracted plasmids from yesterday’s cultures and from K143002 cultures that were in the other lab. <br />
<br />
<br />
<br />
<br />
 +
::::::::::::::::::::::::::::::::::::::[[File:UnamgenomcisUp.png|right | 120px |link=Team:UNAM_Genomics_Mexico/Notebook/ANDSugar#Arabinose.2FXylose_AND_Gate_Notebook]]
=AUGUST=
=AUGUST=
Line 763: Line 866:
<h2>08/02/12</h2><br /><br />
<h2>08/02/12</h2><br /><br />
-
•Extracted plasmids from liquid cultures[PLASMID  EXTRACTION (“soft” lysis) PROTOCOL]: <br />
+
•Extracted plasmids from liquid cultures: <br />
AraC+ Ω+K143002 <br />
AraC+ Ω+K143002 <br />
•GusA+A3<br />
•GusA+A3<br />
Line 812: Line 915:
<br />
<br />
-
<h2>03/08/12</h2><br /><br />
+
<h2>08/03/12</h2><br /><br />
• Ran a gel with: (18) <br />
• Ran a gel with: (18) <br />
Line 960: Line 1,063:
•After running a gel with 14 PCR’s AraC+ Ω+AmyE 3’  and it did not come out as expected, we ran a gel with the ligation AraC+ Ω+AmyE 3’ to select candidate (that weight the same as the ligation) [[Team:UNAM_Genomics_Mexico/Notebook/Protocols#Gel_electrophoresis | GEL ELECTROPHORESIS PROTOCOL]] : (20) <br />
•After running a gel with 14 PCR’s AraC+ Ω+AmyE 3’  and it did not come out as expected, we ran a gel with the ligation AraC+ Ω+AmyE 3’ to select candidate (that weight the same as the ligation) [[Team:UNAM_Genomics_Mexico/Notebook/Protocols#Gel_electrophoresis | GEL ELECTROPHORESIS PROTOCOL]] : (20) <br />
-
•Extracted pasmids form liquid cultures: B0049, B0079+GusA [PLASMID  EXTRACTION (“soft” lysis) PROTOCOL]. <br />
+
•Extracted pasmids form liquid cultures: B0049, B0079+GusA. <br />
•AraC+ Ω+AmyE 3’  undigested didn’t run in the gel as expected, it ran similarly to AraC+ Ω<br />
•AraC+ Ω+AmyE 3’  undigested didn’t run in the gel as expected, it ran similarly to AraC+ Ω<br />
Line 1,002: Line 1,105:
<h2>08/16/12</h2><br />
<h2>08/16/12</h2><br />
-
•Ran a gel with yesterday’s digestions [GEL ELECTROPHORESIS (22)PROTOCOL]: <br />
+
•Ran a gel with yesterday’s digestions: <br />
•Digested: <br />
•Digested: <br />
Line 1,026: Line 1,129:
<h2>08/21/12</h2><br />
<h2>08/21/12</h2><br />
-
•Joined both .6 ml tubes of B0014 EX and B0014 XE in one and dephosphorylated [DEPHOSPHORYLATION PROTOCOL]. <br />
+
•Joined both .6 ml tubes of B0014 EX and B0014 XE in one and dephosphorylated. <br />
-
•Extracted plasmid from the 24 tubes of of ligation K143001+pBad/pXylR [PLASMID  EXTRACTION (“soft” lysis) PROTOCOL]. <br />
+
•Extracted plasmid from the 24 tubes of of ligation K143001+pBad/pXylR. <br />
•Digested  Ω+AmyE 3’  with E,X and + Ω+AmyE 3’  II with E,X (obtained these two from glycerols stored at -80ºC [[Team:UNAM_Genomics_Mexico/Notebook/Protocols#Digestion_protocol_.2820_.C2.B5l.29 | LIQUID CULTURE]]. <br />
•Digested  Ω+AmyE 3’  with E,X and + Ω+AmyE 3’  II with E,X (obtained these two from glycerols stored at -80ºC [[Team:UNAM_Genomics_Mexico/Notebook/Protocols#Digestion_protocol_.2820_.C2.B5l.29 | LIQUID CULTURE]]. <br />
Line 1,045: Line 1,148:
<br /><br />
<br /><br />
</html>
</html>
-
 
-
 
<html>
<html>
<div class='thumbnailWrapper'>
<div class='thumbnailWrapper'>
Line 1,071: Line 1,172:
<h2>08/22/12</h2><br />
<h2>08/22/12</h2><br />
-
•We did 2 PCR’s for A3 [PCR PROTOCOL]. <br />
+
•We did 2 PCR’s for A3. <br />
•Digested K143001+PBad, pXyl with E,S <br /> [[Team:UNAM_Genomics_Mexico/Notebook/Protocols#Digestion_protocol_.2820_.C2.B5l.29 | LIQUID CULTURE]]. (22.1) <br />
•Digested K143001+PBad, pXyl with E,S <br /> [[Team:UNAM_Genomics_Mexico/Notebook/Protocols#Digestion_protocol_.2820_.C2.B5l.29 | LIQUID CULTURE]]. (22.1) <br />
Line 1,093: Line 1,194:
<br />
<br />
 +
<html>
 +
<div class='thumbnailWrapper'>
 +
<ul>
 +
<li>
 +
<img src='https://static.igem.org/mediawiki/2012/7/78/UnamgenomicsandsugarBitacora_23.01.jpg' height="300"/>
 +
<div class='captionazul'>
 +
<p class='captionInside'>1. Ω+AmyE 3’  E,X 6.2<br />
 +
2.Ω+AmyE 3’  II E,X<br />
 +
3.97 ArsR-CzrA<br />
 +
4.98 ArsR-CzrA<br />
 +
5.99 ArsR-CzrA
 +
</p>
 +
</li>
 +
</ul>
 +
</div>
 +
<br /><br />
 +
</html>
 +
<h2>08/23/12</h2><br />
 +
•The negative controls were contaminated. We didn’t manipulate the ones that had grown because of this. <br />
 +
•Ran gel with [[Team:UNAM_Genomics_Mexico/Notebook/Protocols#Gel_electrophoresis | GEL ELECTROPHORESIS PROTOCOL]] : (23.01) <br />
 +
[[Team:UNAM_Genomics_Mexico/Notebook/Protocols#Digestion_protocol_.2820_.C2.B5l.29 | Digestion Protocol]]. <br />
 +
 +
 +
<h2>08/24/12</h2><br />
 +
From plate with ligation E0040+B0014, ligation K143001+pBad,pXyl 10 and 11, and ligation AraC+ Ω+AmyE 3’  6 and 8  we streaked 2 plates for glycerol of each ligation. <br />Repeated ligation B0079+GusA. <br />
 +
 +
Ligated E0040 PCR E,S+B0014 E,X dephospohylated [[Team:UNAM_Genomics_Mexico/Notebook/Protocols#Ligation | LIGATION PROTOCOL]]. <br />
 +
 +
Made 2 new plates from Pveg+XylR ligation and liquid cultures [[Team:UNAM_Genomics_Mexico/Notebook/Protocols#Liquid_culture | LIQUID CULTURE]]. <br />
 +
 +
 +
<h2>08/25/12</h2><br />
 +
Extracted pellet from 16 tubes of pVeg+XylR that were left overnight. <br />
 +
 +
Ligated B0079+GusA and B0040+B0014 [[Team:UNAM_Genomics_Mexico/Notebook/Protocols#Ligation | LIGATION PROTOCOL]]. <br />
 +
 +
 +
<h2>08/28/12</h2><br />
 +
 +
Made liquid cultures from transformations tht were left overnight
 +
-R0079+GusA<br />
 +
-R0079+GusA (-)<br />
 +
-E0040+B0014<br />
 +
-E0040+B0014 (-)<br />
 +
[[Team:UNAM_Genomics_Mexico/Notebook/Protocols#Liquid_culture | LIQUID CULTURE]]. <br />
 +
 +
<html>
 +
<div class='thumbnailWrapper'>
 +
<ul>
 +
<li>
 +
<img src='https://static.igem.org/mediawiki/2012/2/25/UnamgenomicsandsugarBitacora_23.1.jpg' height="300"/>
 +
<div class='captiongray'>
 +
<p class='captionInside'>1. A3 PCR 1. <br />
 +
2. A3 PCR 2. <br />
 +
3. Ω+AmyE 3’  S,P *.<br />
 +
4. Ω+AmyE 3’  S,P . <br />
 +
5. Pveg+XylR E,S 2. <br />
 +
6. Pveg+XylR E,S 3. <br />
 +
7. Pveg+XylR E,S 4. <br />
 +
</p>
 +
</li>
 +
</ul>
 +
</div>
 +
<br /><br />
 +
</html>
 +
 +
<h2>08/29/12</h2><br />
 +
Digested Pveg+XylR 2,3,4 with E,S. <br />
 +
 +
Digested  Ω+AmyE 3’  with S,P [[Team:UNAM_Genomics_Mexico/Notebook/Protocols#Digestion_protocol_.2820_.C2.B5l.29 | DIGESTION]]. <br />
 +
 +
Ran a PCR with A3 PCR (2 .6 ml tubes). <br />
 +
 +
Ran a gel with <br /> [[Team:UNAM_Genomics_Mexico/Notebook/Protocols#Gel_electrophoresis | GEL ELECTROPHORESIS PROTOCOL]] : (23.01) <br />
 +
<br />
 +
 +
<br />
 +
 +
<br />
 +
 +
<br />
 +
 +
<br />
 +
 +
<br />
 +
 +
<br />
 +
 +
<br />
 +
 +
<html>
 +
<div class='thumbnailWrapper'>
 +
<ul>
 +
<li>
 +
<img src='https://static.igem.org/mediawiki/2012/2/2e/UnamgenomicsandsugarBitacoraBitacora_24.jpg' height="300"/>
 +
<div class='captiongray'>
 +
<p class='captionInside'>1-23. E0040 + B0014 colonies<br />
 +
24-29. B0079+GusA 1<br />
 +
30. B0079<br />
 +
</p>
 +
</li>
 +
</ul>
 +
</div>
 +
<br /><br />
 +
</html>
 +
 +
<h2>08/30/12</h2><br />
 +
•Ran a gel [[Team:UNAM_Genomics_Mexico/Notebook/Protocols#Gel_electrophoresis | GEL ELECTROPHORESIS PROTOCOL]] : (24) <br />
 +
 +
 +
•Digested PVeg+XylR 1,5,7,10,13,16 with E,S; E0040+B0014 3,4,5,10,11,19,21,22 with X,P; B0079+GusA 3,4,5 E,S [[Team:UNAM_Genomics_Mexico/Notebook/Protocols#Digestion_protocol_.2820_.C2.B5l.29 | LIQUID CULTURE]]. <br />
 +
<br />
 +
 +
<br />
 +
 +
<br />
 +
 +
<br />
 +
 +
<br />
 +
 +
<br />
 +
 +
<br />
 +
 +
<br />
 +
 +
<br />
 +
 +
<html>
 +
<div class='thumbnailWrapper'>
 +
<ul>
 +
<li>
 +
<img src='https://static.igem.org/mediawiki/2012/3/3d/UnamgenomicsandsugarBitacora_25.jpg' height="300"/>
 +
<div class='captionnaranja'>
 +
<p class='captionInside'>1-3B0079+GusA E,S 3. <br />
 +
4-9. PVeg+XylR  E,S 1. <br />
 +
10-17. E0040+B0014 X,P 3. <br />
 +
18. 1 kb ladder. <br />
 +
</p>
 +
</li>
 +
</ul>
 +
</div>
 +
<br /><br />
 +
</html>
 +
<html>
 +
<div class='thumbnailWrapper'>
 +
<ul>
 +
<li>
 +
<img src='https://static.igem.org/mediawiki/2012/d/d2/UnamgenomicsandsugarBitacora_26.jpg' height="300"/>
 +
<div class='captionrojo'>
 +
<p class='captionInside'>1.A3 PCR. <br />
 +
</p>
 +
</li>
 +
</ul>
 +
</div>
 +
<br /><br />
 +
</html>
 +
<html>
 +
<div class='thumbnailWrapper'>
 +
<ul>
 +
<li>
 +
<img src='https://static.igem.org/mediawiki/2012/7/7b/UnamgenomicsandsugarBitacora_27.jpg' height="300"/>
 +
<div class='captionverde'>
 +
<p class='captionInside'>E0040+B0014 X,P 4 to extract<br />
 +
</p>
 +
</li>
 +
</ul>
 +
</div>
 +
<br /><br />
 +
</html>
 +
<h2>08/31/12</h2><br />
 +
•Ran a gel [[Team:UNAM_Genomics_Mexico/Notebook/Protocols#Gel_electrophoresis | GEL ELECTROPHORESIS PROTOCOL]] : (25) <br />
 +
 +
 +
•Dephosphorylated: <br />
 +
Ω+AmyE 3’  S,P <br />
 +
Ω+AmyE 3’  II S,P <br />
 +
6 AraC+ Ω+AmyE 3’  E,X<br />
 +
8 AraC+ Ω+AmyE 3’  E,X<br />
 +
11 AraC+ Ω+AmyE 3’  E,X<br />
 +
12 AraC+ Ω+AmyE 3’  E,X<br /><br />•Ran a gel with A3 PCR [[Team:UNAM_Genomics_Mexico/Notebook/Protocols#Gel_electrophoresis | GEL ELECTROPHORESIS PROTOCOL]] : (26) <br />
 +
 +
•It was the second time we didn’t obtain a band from A3’s PCR.
 +
 +
•Probably because it had been missing the buffer 2’s ethanol (“blue lid”) from the PCR purification. <br />
 +
 +
•Ran a gel woth E0040+B0014 X,P 4 to extract <br /> [[Team:UNAM_Genomics_Mexico/Notebook/Protocols#Gel_extraction_protocol | Gen extraction protocol]]. <br />
 +
 +
•Did an A3 PCR. <br />
 +
 +
<br />
 +
 +
<br />
 +
 +
<br />
 +
 +
<br />
 +
 +
<br />
 +
::::::::::::::::::::::::::::::::::::::[[File:UnamgenomcisUp.png|right | 120px |link=Team:UNAM_Genomics_Mexico/Notebook/ANDSugar#Arabinose.2FXylose_AND_Gate_Notebook]]
 +
 +
=SEPTEMBER=
 +
 +
<html>
 +
<div class='thumbnailWrapper'>
 +
<ul>
 +
<li>
 +
<img src='https://static.igem.org/mediawiki/2012/b/b8/UnamgenomicsandsugarBitacora_28.jpg' height="300"/>
 +
<div class='captionrosa'>
 +
<p class='captionInside'>1.A3 PCR 1. <br />
 +
2.A3 PCR 2. <br />
 +
3.E0040+B0014 X,P 1. <br />
 +
4.E0040+B0014 X,P 2. <br />
 +
5.Ω+AmyE 3’  dephosphorylated S,P. <br />
 +
6.Ω+AmyE 3’  dephosphorylated S,P II. <br />
 +
7.97 dephosphorylated S,P. <br />
 +
8.98 dephosphorylated S,P. <br />
 +
9.99 dephosphorylated S,P. <br />
 +
10-13. Arac+ Ω+AmyE 3’  dephosphorylated  E,X 12. <br />
 +
14. 1 kb Ladder. <br />
 +
</p>
 +
</li>
 +
</ul>
 +
</div>
 +
<br /><br />
 +
</html>
 +
 +
 +
<h2>09/01/12</h2><br />
 +
•Ran a gel with [[Team:UNAM_Genomics_Mexico/Notebook/Protocols#Gel_electrophoresis | GEL ELECTROPHORESIS PROTOCOL]] : (28) <br />
 +
 +
•Ligated E0040+B0014 X,P 2 +promoter S,P dephosphorylated; K143002 X,P+ Ω+AmyE 3’  dephosphorylated S,P [[Team:UNAM_Genomics_Mexico/Notebook/Protocols#Ligation | LIGATION PROTOCOL]]. <br />
 +
 +
<br />
 +
 +
<br />
 +
 +
<br />
 +
 +
<br />
 +
 +
<h2>09/03/12</h2><br />
 +
 +
•Digested B0079+GusA E,S 3,4,5; PVeg+XylR E,S 1,5,7,10,13,16 [[Team:UNAM_Genomics_Mexico/Notebook/Protocols#Digestion_protocol_.2820_.C2.B5l.29 | LIQUID CULTURE]]. <br />
 +
 +
 +
<h2>09/04/12</h2><br />
 +
•Ran gel with digestions: <br />
 +
B0079+GusA E,S 3,4,5<br />
 +
PVeg+XylR E,S 1,5,7,10,13,16 <br />
 +
[[Team:UNAM_Genomics_Mexico/Notebook/Protocols#Gel_electrophoresis | GEL ELECTROPHORESIS PROTOCOL]] . <br />
 +
 +
•Purified A3 PCR 1,2. <br />
 +
 +
•Ran a gel of A3 PCR <br /> [[Team:UNAM_Genomics_Mexico/Notebook/Protocols#Gel_electrophoresis | GEL ELECTROPHORESIS PROTOCOL]]  and digested with X,P [[Team:UNAM_Genomics_Mexico/Notebook/Protocols#Digestion_protocol_.2820_.C2.B5l.29 | LIQUID CULTURE]]. <br />
 +
 +
•From ligations: PVeg+E0040+B0014, PBad/PXyl+E0040+B0014, B0079+E0040+B0014 only colonies grew in PBad/PXyl+E0040+B0014.
 +
 +
•Plated colonies that grew in a new plate. <br />
 +
 +
•Made liquid cultures of these <br /> [[Team:UNAM_Genomics_Mexico/Notebook/Protocols#Liquid_culture | LIQUID CULTURE]]. <br />
 +
 +
•Repeated the ones that did not grow. <br />
 +
 +
•Digested E0040+B0014 4 with X,P[[Team:UNAM_Genomics_Mexico/Notebook/Protocols#Digestion_protocol_.2820_.C2.B5l.29 | LIQUID CULTURE]]. <br />
 +
 +
•Ran a gel [[Team:UNAM_Genomics_Mexico/Notebook/Protocols#Gel_electrophoresis | GEL ELECTROPHORESIS PROTOCOL]] . <br />
 +
 +
•Extracted from gel [[Team:UNAM_Genomics_Mexico/Notebook/Protocols#Gel_extraction_protocol | LIQUID CULTURE]]. <br />
 +
-BBa_J23101 18E plate 1 plasmid BBa_J61002_2948 bp Amp+<br />
 +
 +
 +
<html>
 +
<div class='thumbnailWrapper'>
 +
<ul>
 +
<li>
 +
<img src='https://static.igem.org/mediawiki/2012/c/c1/UnamgenomicsandsugarBitacora_29.jpg' height="300"/>
 +
<div class='captionaqua'>
 +
<p class='captionInside'>24 PBad/PXyl+E0040+B0014 tubes we extracted <br />
 +
</p>
 +
</li>
 +
</ul>
 +
</div>
 +
<br /><br />
 +
</html>
 +
<html>
 +
<div class='thumbnailWrapper'>
 +
<ul>
 +
<li>
 +
<img src='https://static.igem.org/mediawiki/2012/a/a4/UnamgenomicsandsugarBitacora_30.jpg' height="300"/>
 +
<div class='captionmoradoclaro'>
 +
<p class='captionInside'>1.E0040+B0014 X,P<br />
 +
2.E0040+B0014 X,P<br />
 +
3.PVeg+XylR E<br />
 +
4.B0079+GusA S<br />
 +
5.1 kb plus ladder<br />
 +
Extracted band from 1. and 2
 +
<br />
 +
</p>
 +
</li>
 +
</ul>
 +
</div>
 +
<br /><br />
 +
</html>
 +
<html>
 +
<div class='thumbnailWrapper'>
 +
<ul>
 +
<li>
 +
<img src='https://static.igem.org/mediawiki/2012/7/7d/UnamgenomicsandsugarBitacora_31.jpg' height="300"/>
 +
<div class='captionmorado'>
 +
<p class='captionInside'>Digested B0079+GusA with E,S 4,5; PVeg+XylR with E,S
 +
<br />
 +
</p>
 +
</li>
 +
</ul>
 +
</div>
 +
<br /><br />
 +
</html>
 +
 +
<h2>09/05/12</h2><br />
 +
•From the 24 PBad/PXyl+E0040+B0014 tubes we extracted plasmids  (29)  and ran a gel [[Team:UNAM_Genomics_Mexico/Notebook/Protocols#Gel_extraction_protocol | LIQUID CULTURE]]. <br />
 +
 +
•Extracted plasmid from 2 tubes of E0040+B0014. <br />
 +
 +
•Ran a gel with yesterday’s digestions: <br />
 +
1.E0040+B0014 X,P<br />
 +
2.E0040+B0014 X,P<br />
 +
3.PVeg+XylR E<br />
 +
4.B0079+GusA S<br />
 +
5.1 kb plus ladder<br />
 +
 +
•Extracted band from 1. and 2. [[Team:UNAM_Genomics_Mexico/Notebook/Protocols#Gel_extraction_protocol | LIQUID CULTURE]]. <br />
 +
 +
•Purified A3 PCR from 2 0.6ml tubes 1 and 2. <br />
 +
 +
•1 colony grew from ligation pVeg+E0040+B0014. <br />
 +
 +
•We streaked this in another plate and did liquid cultures <br /> [[Team:UNAM_Genomics_Mexico/Notebook/Protocols#Liquid_culture | LIQUID CULTURE]]. <br />
 +
 +
•To do: <br />
 +
•Ligate B0079 S,P dephosphorylated + E0040+B0014 X,P and  Ω+AmyE 3’  S,P dephosphorylated+ K143001 X,P. <br />
 +
•Digested B0079+GusA with E,S 4,5; PVeg+XylR with E,S 10,13. (31) <br />
 +
<br />
 +
 +
<br />
 +
 +
<br />
 +
 +
<br />
 +
 +
<br />
 +
 +
<br />
 +
 +
<br />
 +
 +
<br />
 +
<html>
 +
<div class='thumbnailWrapper'>
 +
<ul>
 +
<li>
 +
<img src='https://static.igem.org/mediawiki/2012/2/26/UnamgenomicsandsugarBitacora_32.jpg' height="300"/>
 +
<div class='captionazul'>
 +
<p class='captionInside'>•A3 PCR and gel A3 PCR X,P 
 +
<br />
 +
</p>
 +
</li>
 +
</ul>
 +
</div>
 +
<br /><br />
 +
</html>
 +
 +
<br />
 +
 +
<h2>09/06/12</h2><br />
 +
 +
•A3 PCR and gel A3 PCR X,P 1,2. <br />
 +
 +
 +
<h2>09/14/12</h2><br />
 +
 +
•Digested  Ω+AmyE 3’  11,13,18, and 22 with E,X. <br />
 +
•Ligate: <br />
 +
PVeg S,P dephosphorylated+XylR X,P. <br />
 +
PBad p Xyl S,P dephosphorylated + E0040+B0014 X,P. <br />
 +
pSB13C3 E,P dephosphorylated + A3 PCR E,P. <br />
 +
pSB13C3 E,P dephosphorylated + GusA PCR E,P. <br />
 +
pSB13C3 E,P dephosphorylated + XylR E,P. <br />
 +
pSB13C3 E,P dephosphorylated + pVeg E,P. <br />
 +
pSB13C3 E,P dephosphorylated + pBad pXyl E,P. <br />
 +
pSB13C3 E,P dephosphorylated +  Ω PCR E,P. <br />
 +
<br />
 +
 +
<br />
 +
 +
<br />
 +
 +
<br />
 +
 +
<br />
 +
<h2>09/16/12</h2><br />
 +
• Colonies in these plates grew: <br />
 +
- R0079+E0040+B0014 <br />
 +
- pBad/pXyl <br />
 +
- XylR <br />
 +
- pVeg <br />
 +
- A3+E0040+B0014 from colonies 1,3,4,5,6,7,8,9,10,11,12,13,14,15,17 <br />
 +
- pVeg+E0040+B0014 1,2,3,4,5,6,8,9,10,11,12,13,14,15,16 <br />
 +
- pBad/pXyl+E0040+B0014 2 tubes from the same correct colony. <br />
 +
- pVeg+XylR 1,2 <br />
 +
- pBad/pXyl+pSB1C3 1,2 <br />
 +
- XylR+pSB1C3 1,2 <br />
 +
- pVeg+pSB1C3 1,2 <br />
 +
- A3+pSB1C3 1,2 <br />
 +
- GusA+pSB1C3 1,2 <br />
 +
- omegacassette+pSB1C3 1,2 <br />
 +
<br />
 +
• Ran gel from the plasmid extractions that we did yesterday: <br />
 +
- A3+E0040+B0014 1-16 <br />
 +
- pVeg+E0040+B0014 1-16, 18 <br />
 +
- omega cassette+AmyE 3’ 11,13,18,22 <br />
 +
• Digested R0079+E0040+B0014 with E,S. to ligate with AmyE 3’ E,x dephosphorylated. <br />
 +
• Digested omega cassette with E,P. <br />
 +
• Digested pSB1C3 with E,P. <br />
 +
• Made liquid cultures from AmyE 5’ and AmyE 3’. <br />
 +
• Did plasmid extraction from pSB1C3 colonies 3 and 6. <br />
 +
<br />
 +
 +
<h2>09/17/12</h2><br />
 +
• Digested A3+E0040+B0014 colonies 2,3,4,5,6,11 and 16 with E,S. <br />
 +
• Digested pVeg+E0040+B0014 colonies 1,2,3,4,5,9 and 10 with E,S. <br />
 +
• Dephosphorylated omega cassette+AmyE 3’ colonies 13,18 and 22 digested with E,X. <br />
 +
• Digested pBad/pXyl and pVeg with S,P. Then dephosphorylated. <br />
 +
• Digested AmyE 3’ with E,X. Then dephosphorylated. <br />
 +
<br />
 +
 +
<h2>09/18/12</h2><br />
 +
<br />
 +
• Ran gel with: <br />
 +
1. A3 2 E,S <br />
 +
2. A3 3 E,S <br />
 +
3. A3 4 E,S <br />
 +
4. A3 5 E,S <br />
 +
5. A3 6 E,S <br />
 +
6. A3 11 E,S <br />
 +
7. A3 16 E,S <br />
 +
8. E0040+B0014 colony 1 E,X <br />
 +
9. AmyE 5’ E,P <br />
 +
10. AmyE 3’ E,X <br />
 +
11. Omega cassette E,S <br />
 +
12. pSB1C3 E,P <br />
 +
13. ladder <br />
 +
Bottom: <br />
 +
1. pVeg 1 E,S <br />
 +
2. pVeg 2 E,S <br />
 +
3. pVeg 3 E,S <br />
 +
4. pVeg 4 E,S <br />
 +
5. pVeg 5 E,S <br />
 +
6. pVeg 9 E,S <br />
 +
7. pVeg 10 E,S <br />
 +
8. pVeg S,P dephosphorylated <br />
 +
9. pVeg 2 S,P <br />
 +
10. pBad/pXyl S,P <br />
 +
11. XylR X,P <br />
 +
12. R0079+GFP+TT E,S <br />
 +
13. R0079 S,P <br />
 +
14. Ladder <br />
 +
• Dephosphorylated GFP+TT E,X; AmyE 5’ E,X; pSB1C3 E,P; pVeg 2 S,P; pBad/pXyl S,P and R0079 S,P. <br />
 +
<br />
 +
<h2>09/19/12</h2><br />
 +
<br />
 +
• Did PCR from A3 and a 1/50 dilution. <br />
 +
• Ran gel with: <br />
 +
1. pVeg 3 E,P. <br />
 +
2. pVeg 9 E,P. <br />
 +
3. pVeg 10 E,P. <br />
 +
4. pBAd/pXyl 3 E,P. <br />
 +
5. pBAd/pXyl 5 E,P. <br />
 +
6. pBAd/pXyl 1 E,P. <br />
 +
7. A3 3 E,P. <br />
 +
8. A3 4 E,P. <br />
 +
9. XylR 1 E,P. <br />
 +
10. XylR 3 E,P. <br />
 +
11. XylR 8 E,P. <br />
 +
12. pSB1C3 6 E,P. <br />
 +
13. pSB1C3 6 E,P. <br />
 +
14. AmyE 5’ E,S. <br />
 +
15. AmyE 5’ E,S. <br />
 +
16. A3 1/50 PCR. <br />
 +
17. A3 PCR. <br />
 +
18. Ladder <br />
 +
• We did transformations: <br />
 +
- 2 of R0079+GusA <br />
 +
- R0079+GusA control <br />
 +
- 2 of A3+pSB1AK3 <br />
 +
- A3+pSB1AK3 control <br />
 +
- 2 of omega cassette+pSB1C3 <br />
 +
- 2 of GusA+pSB1C3 <br />
 +
• Digested: <br />
 +
- pVeg+pSB1C3 <br />
 +
- pBad/pXyl+pSB1C3 <br />
 +
- XylR+pSB1C3 <br />
 +
- A3+pSB1C3 <br />
 +
With E,P. <br />
 +
• Ran gel with these digestions. <br />
 +
<br />
 +
<h2>09/19/12</h2><br />
 +
• Made liquids cultures from: <br />
 +
- Glicerol of AmyE 5’ <br />
 +
- Glicerol of AmyE 3’ <br />
 +
- pBad/pXyl+pSB1C3 colony 5 <br />
 +
• Made liquid cultures from yesterday transformations: <br />
 +
- R0079+GusA 2 and control <br />
 +
- A3+pSB1AK3 2 and control <br />
 +
- Omega cassette+pSB1C3 2 <br />
 +
- GusA+pSB1C3 2 <br />
 +
• We transformed yesterday ligations: <br />
 +
- pBad/pXyl+pSB1C3 <br />
 +
- XylR+pSB1C3 <br />
 +
- pVeg+pSB1C3 <br />
 +
- A3+pSB1C3 <br />
 +
• Purified A3 PCR with kit, and then, digested with E,P and E,S. <br />
 +
• Ran gel <br />
 +
<br />
 +
<h2>09/20/12</h2><br />
 +
<br />
 +
• Made liquid cultures from transformations: <br />
 +
- Omega cassette+pSB1C3 colony 7 <br />
 +
- 2 of GusA+pSB1C3 colony 32 <br />
 +
- R0079+GusA colony 12 <br />
 +
• Digested A3 1/50 PCR with E,P and E,S. <br />
 +
• Made liquid cultures from R0079+E0040+B0014; pBad/pXyl+E0040+B0014; pVeg+E0040+B0014; A3+E0040+B0014. <br />
 +
• Ligated: <br />
 +
- pBad/pXyl S,P dephosphorylated + E0040+B0014 X,P <br />
 +
- pVeg S,P dephosphorylated + E0040+B0014 X,P <br />
 +
- A3 PCR E,S + E0040+B0014 E,X dephosphorylated. <br />
 +
<br />
 +
<h2>09/21/12</h2><br />
 +
<br />
 +
• Ran gel with: <br />
 +
1. R0079+GFP+TT 1 <br />
 +
2. R0079+GFP+TT <br />
 +
3. pBad/pXyl+pSB1C3 1 <br />
 +
4. pBad/pXyl+pSB1C3 <br />
 +
5. omega cassette+psB1C3 1 <br />
 +
6. omega cassette+psB1C3 <br />
 +
7. pSB1C3 E,P 1 <br />
 +
8. pSB1C3 E,P <br />
 +
9. pSB1C3 E <br />
 +
10. pSB1C3 P <br />
 +
11. A3 1/50 PCR E,P <br />
 +
<br />
 +
 +
<h2>09/22/12</h2><br />
 +
• Ran gel with lysis extractions: <br />
 +
1. GusA+pSB1C3 1 <br />
 +
2. GusA+pSB1C3 2 <br />
 +
3. GusA+pSB1C3 3 <br />
 +
4. GusA+pSB1C3 4 <br />
 +
5. GusA+pSB1C3 5 <br />
 +
6. GusA+pSB1C3 6 <br />
 +
7. GusA+pSB1C3 7 <br />
 +
8. GusA+pSB1C3 8 <br />
 +
9. GusA+pSB1C3 9 <br />
 +
10. GusA+pSB1C3 10 <br />
 +
11. GusA+pSB1C3 11 <br />
 +
12. GusA+pSB1C3 12 <br />
 +
13. pSB1C3 <br />
 +
14. A3+E0040+B0014 1 <br />
 +
15. A3+E0040+B0014 2 <br />
 +
16. A3+E0040+B0014 3 <br />
 +
17. A3+E0040+B0014 4 <br />
 +
18. A3+E0040+B0014 5 <br />
 +
19. A3+E0040+B0014 6 <br />
 +
20. A3+E0040+B0014 7 <br />
 +
21. A3+E0040+B0014 8 <br />
 +
22. A3+E0040+B0014 9 <br />
 +
23. pVeg+E0040+B0014 3 <br />
 +
24. pVeg+E0040+B0014 4 <br />
 +
25. pVeg+E0040+B0014 5 <br />
 +
26. pVeg+E0040+B0014 6 <br />
 +
27. pVeg+E0040+B0014 7 <br />
 +
28. pVeg+E0040+B0014 8 <br />
 +
29. pVeg+E0040+B0014 9 <br />
 +
30. pVeg <br />
 +
31. pBad/pXyl+E0040+B0014 1 <br />
 +
32. pBad/pXyl+E0040+B0014 2 <br />
 +
33. pBad/pXyl+E0040+B0014 3 <br />
 +
34. pBad/pXyl+E0040+B0014 4 <br />
 +
35. pBad/pXyl+E0040+B0014 5 <br />
 +
36. pBad/pXyl+E0040+B0014 6 <br />
 +
37. pBad/pXyl+E0040+B0014 7 <br />
 +
38. pBad/pXyl+E0040+B0014 8 <br />
 +
39. pBad/pXyl+E0040+B0014 9 <br />
 +
40. pBad/pXyl+E0040+B0014 10 <br />
 +
41. pBad/pXyl <br />
 +
42. pVeg+XylR 1 <br />
 +
43. pVeg+XylR 2 <br />
 +
44. pVeg+XylR 3 <br />
 +
45. pVeg+XylR 4 <br />
 +
46. pVeg+XylR 5 <br />
 +
47. pVeg+XylR 6 <br />
 +
48. pVeg+XylR 7 <br />
 +
49. pVeg+XylR 8 <br />
 +
50. omega cassette <br />
 +
<br />
 +
• Ran gel with yesterday digestions: <br />
 +
1. R0079+GFP+TT E,P <br />
 +
2. R0079+GFP+TT E,P <br />
 +
3. Omega cassette+pSB1C3 E,P <br />
 +
4. Omega cassette+pSB1C3 E,P <br />
 +
5. Ladder <br />
 +
6. pBad/pXyl+pSB1C3 <br />
 +
7. pBad/pXyl+pSB1C3 <br />
 +
8. pSB1C3 6 E,P. <br />
 +
9. A3 1/50 PCR E,S <br />
 +
10. pBbak C011 <br />
 +
11. pBbak C012 <br />
 +
12. ladder <br />
 +
<br />
 +
• Did pellet from R0079+GusA. <br />
 +
• Did plasmid extraction from omega cassette+pSB1C3 colonies 1,4,6 and 7. <br />
 +
• Digested them with E,P. <br />
 +
• Digested: <br />
 +
- GusA+pSB1C3 1,3,4,10 and 11 <br />
 +
- A3+E0040+B0014 2,4,7 and 9 <br />
 +
- pVeg+E0040+B0014 4,5 and 6 <br />
 +
- pBad/pXyl+E0040+B0014 3,7 and 10 <br />
 +
- pVeg+XylR 2,4 and 5 <br />
 +
with E,P. <br />
 +
• Made liquid cultures from pVeg+pSB1C3 <br />
 +
• Ligated: <br />
 +
- XylR E,P + pSB1C3 E,P dephosphorylated. <br />
 +
- pVeg E,P + pSB1C3 E,P dephosphorylated. <br />
 +
- A3 1/50 PCR E,P + pSB1C3 E,P dephosphorylated. <br />
 +
- pBad/pXyl S,P dephosphorylated + E0040+B0014 X,P. <br />
 +
- pVeg S,P dephosphorylated + E0040+B0014 X,P. <br />
 +
- A3 1/50 PCR E,S + E0040+B0014 E,X dephosphorylated. <br />
 +
- pVeg S,P dephosphorylated + XylR X,P. <br />
 +
<br />
 +
<h2>09/23/12</h2><br />
 +
<br />
 +
• Ran gel with yesterday digestions: <br />
 +
1. Omega cassette+pSB1C3 1 E,P <br />
 +
2. Omega cassette+pSB1C3 4 E,P <br />
 +
3. Omega cassette+pSB1C3 6 E,P <br />
 +
4. Omega cassette+pSB1C3 7 E,P <br />
 +
5. GusA+pSB1C3 1 E,P <br />
 +
6. GusA+pSB1C3 3 E,P <br />
 +
7. GusA+pSB1C3 4 E,P <br />
 +
8. GusA+pSB1C3 10 E,P <br />
 +
9. GusA+pSB1C3 11 E,P <br />
 +
10. pSB1C3 E,P dephosphorylated <br />
 +
11. pVeg+XylR 2 E,P <br />
 +
12. pVeg+XylR 4 E,P <br />
 +
13. pVeg+XylR 5 E,P <br />
 +
14. pVeg S,P dephosphorylated <br />
 +
15. pVeg+GFP+TT 4 E,P. <br />
 +
16. pVeg+GFP+TT 5 E,P. <br />
 +
17. pVeg+GFP+TT 6 E,P. <br />
 +
18. ladder <br />
 +
Bottom <br />
 +
1. pBad/pXyl+GFP+TT 3 E,P <br />
 +
2. pBad/pXyl+GFP+TT 7 E,P <br />
 +
3. pBad/pXyl+GFP+TT 10 E,P <br />
 +
4. pBad/pXyl S,P dephosphorylated <br />
 +
5. A3+GFP+TT 2 E,P <br />
 +
6. A3+GFP+TT 4 E,P <br />
 +
7. A3+GFP+TT 7 E,P <br />
 +
8. A3+GFP+TT 9 E,P <br />
 +
9. Ladder <br />
 +
<br />
 +
<h2>09/24/12</h2><br />
 +
<br />
 +
• Did PCR from omega cassette+pSB1C3 colonies 1,4,6 and 7. <br />
 +
• Made 1/50 dilutions from these PCR products. <br />
 +
• Ran gel with: <br />
 +
1. Omega cassette+pSB1C3 1/50 PCR 1 <br />
 +
2. Omega cassette+pSB1C3 PCR 1 <br />
 +
3. Omega cassette+pSB1C3 1/50 PCR 4 <br />
 +
4. Omega cassette+pSB1C3 PCR 4 <br />
 +
5. Omega cassette+pSB1C3 1/50 PCR 6 <br />
 +
6. Omega cassette+pSB1C3 PCR 6 <br />
 +
7. Omega cassette+pSB1C3 1/50 PCR 7 <br />
 +
8. Omega cassette+pSB1C3 PCR 7 <br />
 +
9. GusA+pSB1C3 1 P <br />
 +
10. GusA+pSB1C3 3 P <br />
 +
11. GusA+pSB1C3 4 P <br />
 +
12. GusA+pSB1C3 10 P <br />
 +
13. GusA+pSB1C3 11 P <br />
 +
14. pVeg+pSB1C3 6 E,P <br />
 +
15. pVeg+pSB1C3 5 E,P <br />
 +
16. pVeg+pSB1C3 4 E,P <br />
 +
17. pVeg+pSB1C3 3 E,P <br />
 +
18. pVeg+pSB1C3 2 E,P <br />
 +
19. pVeg+pSB1C3 1 E,P <br />
 +
20. ladder <br />
 +
 +
• From yesterday transformations, these didn’t grow: <br />
 +
- pBad/pXyl+E0040+B0014 1 and 2. <br />
 +
- A3+E0040+B0014. <br />
 +
• Made liquid cultures from transformations that did grow: <br />
 +
- pVeg+E0040+B0014. <br />
 +
- pVeg+XylR. <br />
 +
- A3+pSB1C3 <br />
 +
- pVeg+pSB1C3 <br />
 +
- XylR+pSB1C3 <br />
 +
<br />
 +
<h2>09/26/12</h2><br />
 +
<br />
 +
• Did plasmid extractions form liquids cultures: <br />
 +
- 8 of pVeg+pSB1C3 <br />
 +
- 8 of A3 <br />
 +
- 8 of XylR <br />
 +
• Digested them with E,P. <br />
 +
• Ran gel with: <br />
 +
1. Ladder <br />
 +
2. XylR+pSB1C3 1 E,P <br />
 +
3. XylR+pSB1C3 2 E,P <br />
 +
4. XylR+pSB1C3 3 E,P <br />
 +
5. pVeg+pSB1C3 1 E,P <br />
 +
6. pVeg+pSB1C3 3 E,P <br />
 +
7. pVeg+pSB1C3 4 E,P <br />
 +
8. pVeg+pSB1C3 5 E,P <br />
 +
9. pVeg+pSB1C3 6 E,P <br />
 +
10. pVeg+pSB1C3 8 E,P <br />
 +
11. pSB1C3 6 E,P dephosphorylated <br />
 +
12. A3+pSB1C3 1 E,P <br />
 +
13. A3+pSB1C3 3 E,P <br />
 +
14. A3+pSB1C3 4 E,P <br />
 +
15. A3+pSB1C3 5 E,P <br />
 +
16. A3+pSB1C3 6 E,P <br />
 +
17. A3+pSB1C3 8 E,P <br />
 +
18. Ladder <br />
 +
19. P4+E0040+B0014 1 E,X <br />
 +
20. P4+E0040+B0014 7 E,X <br />
 +
<br />
 +
<h2>09/27/12</h2><br />
 +
<br />
 +
• Digested pVeg+XylR colonies 1,4,5 and 6 in pJ209 plasmid with E,S for 3 hours. <br />
 +
• Digested pVeg+E0040+B0014 colonies 7,9,10 and 11 in pasmid pJ209 with E,P. <br />
 +
<br />
 +
<h2>10/09/12</h2><br />
 +
<br />
 +
• Ligated: <br />
 +
- A3 1/50 PCR E,P + pSB1C3 6 E,P dephosphorylated. <br />
 +
- pVeg S,P dephosphorylated + XylR X,P. <br />
 +
- P4+CI+E1010+B0014 E,X dephosphorylated + AmyE 5’+pBad/pXyl E,S. <br />
 +
<br />
 +
<h2>10/10/12</h2><br />
 +
<br />
 +
• Ligated: <br />
 +
- GusA PCR E,P + pSB1C3 6 E,P dephosphorylated. <br />
 +
- pBad/pXyl S,P dephosphorylated + E0040+B0014 X,P. <br />
 +
- pVeg S,P dephosphorylated + E0040+B0014 X,P. <br />
 +
- A3 1/50 PCR E,S + E0040+B0014 E,X dephosphorylated. <br />
 +
• Digested R0079+E0040+B0014 with E,S. <br />
 +
• Digested AmyE 3’ with E,X. Then dephosphorylated. <br />
 +
• Digested pVeg and R0079, A3 with X,P. <br />
 +
• Digested pBad/pSB1C3 with S,P. <br />
 +
<br />
 +
<h2>10/11/12</h2><br />
 +
<br />
 +
• Did plasmid extraction from liquid cultures: <br />
 +
- 2 of AmyE 5’ <br />
 +
- 2 of AmyE 3’ <br />
 +
- 2 of E0040+B0014 <br />
 +
• Ran gel with: <br />
 +
1. A3 1/50 PCR X,P <br />
 +
2. A3 1/50 PCR X,P <br />
 +
3. A3+pSB1C3 6 X,P <br />
 +
4. A3+pSB1C3 6 X,P <br />
 +
5. A3+pSB1C3 8 X,P <br />
 +
6. A3+pSB1C3 8 X,P <br />
 +
7. pVeg X,P <br />
 +
8. pVeg 96 X,P <br />
 +
9. pVeg 96 X,P <br />
 +
10. pVeg+pSB1C3 1 X,P <br />
 +
11. pVeg+pSB1C3 1 X,P <br />
 +
12. pVeg+pSB1C3 3 X,P <br />
 +
13. pVeg+pSB1C3 3 X,P <br />
 +
14. R0079 X,P <br />
 +
15. Ladder <br />
 +
<br />
 +
<h2>10/12/12</h2><br />
 +
<br />
 +
• Ligated:
 +
- AmyE 5’+pBad/pXyl 10 E,S + P4+CI+E1010+TT E,X dephosphorylated. <br />
 +
- AmyE 5’+pBad/pXyl 11 E,S + P4+CI+E1010+TT E,X dephosphorylated. <br />
 +
- AmyE 5’+pBad/pXyl 12 E,S + P4+CI+E1010+TT E,X dephosphorylated. <br />
 +
- pVeg S,P dephosphorylated + XylR X,P. <br />
 +
- A3 1/50 PCR E,P + pSB1C3 E,P dephosphorylated. <br />
 +
<br />
 +
<h2>10/12/12</h2><br />
 +
<br />
 +
• Digested AmyE 5’ with S,P <br />
 +
• Dephosphorylated it. <br />
 +
• Ligated: <br />
 +
- AmyE  5’ S,P dephosphorylated with <br />
 +
- R0079 X,P <br />
 +
- pVeg 96 X,P <br />
 +
- A3 1/50 PCR X,P <br />
 +
- A3+pSB1C3 6 X,P <br />
 +
- R0079+E0040+B0014 <br />
 +
• Ligated pBad/pXyl+pSB1C3 S,P dephosphorylated + E0040+B0014 X,P. <br />
 +
• Ran gel with: <br />
 +
1. A3+pSB1C3 1 <br />
 +
2. A3+pSB1C3 2 <br />
 +
3. A3+pSB1C3 3 <br />
 +
4. A3+pSB1C3 4 <br />
 +
5. A3+pSB1C3 5 <br />
 +
6. A3+pSB1C3 6 <br />
 +
7. A3+pSB1C3 7 <br />
 +
8. A3+pSB1C3 8 <br />
 +
9. A3+pSB1C3 9 <br />
 +
10. A3+pSB1C3 10 <br />
 +
11. A3+pSB1C3 11 <br />
 +
12. A3+pSB1C3 6 control <br />
 +
13. AmyE 5’+P4+CI+E1010+B0014 1 <br />
 +
14. AmyE 5’+P4+CI+E1010+B0014 2 <br />
 +
15. AmyE 5’+P4+CI+E1010+B0014 3 <br />
 +
16. AmyE 5’+P4+CI+E1010+B0014 4 <br />
 +
17. AmyE 5’+P4+CI+E1010+B0014 5 <br />
 +
18. AmyE 5’+P4+CI+E1010+B0014 6 <br />
 +
19. AmyE 5’+P4+CI+E1010+B0014 7 <br />
 +
20. P4+CI+E1010+B0014 1 control <br />
 +
<br />
 +
<h2>10/09/12</h2><br />
 +
<br />
 +
• Ligate: <br />
 +
K143001+pBad/pXyl + p4+CI+E1010+TT E,X dephosphorylated. <br />
 +
• Ligate: <br />
 +
pVeg S,P dephosphorylated + XylR X,P. <br />
 +
• Ligate: <br />
 +
A3 PCR 1/50 E,P + pSB1C3 E,P dephosphorylated <br />
 +
<br />
 +
<h2>10/13/12</h2><br />
<br />
<br />
 +
• Digested AmyE 5’ with S,P. Then dephosphorylated. <br />
 +
• Ligate: <br />
 +
AmyE 5’ S,P dephosphorylated + <br />
 +
- R0079 X,P <br />
 +
- pVeg 96 X,P <br />
 +
- A3 PCR 1/50 X,P <br />
 +
- A3+pSB1C3 colony 6 X,P <br />
 +
- R0079+E0040+B0014 E,X <br />
 +
• Ligate: <br />
 +
pBad/pXyl+pSB1C3 S,P dephosphorylated + E0040+B0014 X,P <br />
 +
• Ran a gel with: <br />
 +
1. A3+pSB1C3 1 <br />
 +
2. A3+pSB1C3 2 <br />
 +
3. A3+pSB1C3 3 <br />
 +
4. A3+pSB1C3 4 <br />
 +
5. A3+pSB1C3 5 <br />
 +
6. A3+pSB1C3 6 <br />
 +
7. A3+pSB1C3 7 <br />
 +
8. A3+pSB1C3 8 <br />
 +
9. A3+pSB1C3 9 <br />
 +
10. A3+pSB1C3 10 <br />
 +
11. A3+pSB1C3 11 <br />
 +
12. A3+pSB1C3 6 control <br />
 +
13. AmyE 5’+P4+CI+E1010+B0014 8 <br />
 +
14. AmyE 5’+P4+CI+E1010+B0014 9 <br />
 +
15. AmyE 5’+P4+CI+E1010+B0014 10 <br />
 +
16. P4+CI+E1010+B0014 1 control <br />
 +
17. pVeg+XylR 1 <br />
 +
18. pVeg+XylR 2 <br />
 +
19. pVeg+XylR 3 <br />
 +
20. pVeg+XylR 4 <br />
 +
21. pVeg+XylR 5 <br />
 +
22. pVeg+XylR 6 <br />
 +
23. pVeg+XylR 7 <br />
 +
24. pVeg+XylR 8 <br />
 +
25. pVeg+XylR 10 <br />
 +
26. pVeg+XylR 11 <br />
 +
27. pVeg+XylR 12 <br />
 +
28. pVeg 96 control <br />
 +
• Ran gel with: <br />
 +
1. A3 1/50 PCR X,P <br />
 +
2. A3+pSB1C3 6 X,P <br />
 +
3. pVeg 96 X,P <br />
 +
4. pVeg+pSB1C3 1 X,P <br />
 +
5. pVeg+pSB1C3 3 X,P <br />
 +
6. R0079 X,P <br />
 +
7. pBad/pXyl+pSB1C3 S,P dephosphorylated <br />
 +
8. ladder <br />
 +
9. Digested: <br />
 +
- A3+pSB1C3 colonies 3,4,5 and 10 with E,P. <br />
 +
- AmyE 5’+pBad/pXyl+P4+CI+E1010*B0014 colonies 1,2,7 and 8 with E,P. <br />
 +
- pVeg+XylR 1,4,5 and 12 with E,P. <br />
 +
• Ran gel with: <br />
 +
1. GFP+TT 1 X,P <br />
 +
2. GFP+TT 1 X,P <br />
 +
3. GFP+TT 1 E,S <br />
 +
4. GFP+TT 1 E,S <br />
 +
5. GFP+TT 2 X,P <br />
 +
6. GFP+TT 2 X,P <br />
 +
7. GFP+TT 2 E,S <br />
 +
8. GFP+TT 2 E,S <br />
 +
9. Ladder  <br />
 +
10. A3 1/50 PCR X,P <br />
 +
11. A3+pSB1C3 6 X,P <br />
 +
12. pVeg 96 X,P <br />
 +
13. pVeg+pSB1C3 1 X,P <br />
 +
14. R0079 X,P <br />
 +
15. AmyE 5’ S,P <br />
 +
<h2>10/16/12</h2><br />
 +
• Made liquid cultures from yesterday transformations: <br />
 +
- AmyE 5’+R0079 <br />
 +
- AmyE 5’+R0079_2 <br />
 +
- AmyE 5’+A3 <br />
 +
- AmyE 5’+pVeg <br />
 +
- pBad/pXyl+E0040+B0014 in pSB1C3 plasmid. <br />
 +
• Digested: <br />
 +
- AmyE 5’+pBad/pXyl+P4+CI+E1010+B0014 colonies 1,2,7 and 8 with E,P. <br />
 +
- pVeg+XylR 1,4,5 and 12 with E,P. <br />
 +
- R0079+GFP+TT and R0079+GFP+TT_2 with X,P. <br />
}}
}}

Latest revision as of 03:52, 27 October 2012


UNAM-Genomics_Mexico


Arabinose/Xylose AND Gate Notebook



2 JUNE


2.1 06/07/12
2.2 06/12/12
2.3 06/13/12
2.4 06/14/12
2.5 06/15/12
2.6 06/18/12
2.7 06/19/12
2.8 06/22/12
2.9 06/25/12
2.10 06/26/12
2.11 06/27/12
2.12 06/29/12

3 JULY


3.1 07/03/12
3.2 07/04/12
3.3 07/06/12
3.4 07/07/12
3.5 07/08/12
3.6 07/09/12
3.7 07/10/12
3.8 07/11/12
3.9 07/12/12
3.10 07/13/12
3.11 07/14/12
3.12 07/16/12
3.13 07/17/12
3.14 07/18/12
3.15 07/19/12
3.16 07/20/12
3.17 07/23/12
3.18 07/24/12
3.19 07/25/12
3.20 07/26/12
3.21 07/27/12
3.22 07/30/12
3.23 07/31/12

4 AUGUST


4.1 08/01/12
4.2 08/02/12
4.3 08/03/12
4.4 08/06/12
4.5 08/08/12
4.6 08/09/12
4.7 08/10/12
4.8 08/13/12
4.9 08/16/12
4.10 08/20/12
4.11 08/21/12
4.12 08/22/12
4.13 08/23/12
4.14 08/24/12
4.15 08/25/12
4.16 08/28/12
4.17 08/29/12
4.18 08/30/12
4.19 08/31/12

5 SEPTEMBER


5.1 09/01/12
5.2 09/03/12
5.3 09/04/12
5.4 09/05/12
5.5 09/06/12
5.6 09/14/12
5.7 09/16/12
5.8 09/17/12
5.9 09/18/12
5.10 09/19/12
5.11 09/19/12
5.12 09/20/12
5.13 09/21/12
5.14 09/22/12
5.15 09/23/12
5.16 09/24/12
5.17 09/26/12
5.18 09/27/12


OCTOBER
5.19 10/09/12
5.20 10/10/12
5.21 10/11/12
5.22 10/12/12
5.23 10/13/12

UnmagenomicsBacteria sugar.png

On hover the images to see descriptions


JUNE



  • 1. 1 kb ladder
    2.E1010



06/07/12


PY BROTH 10g salt/L
PSB2K3 kanamicin
We transformed RFP E1010.
plate 1 18F
plate 2 17E
Stock 50 mg/mL
E.coli 1/1000
TRANSFORMATION PROTOCOL.
We made liquid cultures with colonies LIQUID CULTURE.
We extracted plasmids PLASMID EXTRACTION PROTOCOL.
We ran a gel to check the extraction GEL ELECTROPHORESIS PROTOCOL.




06/12/12


We made glycerols of the bacteria
GLYCEROL PROTOCOL .
We transformed plasmid pHp45 TRANSFORMATION PROTOCOL.

  • 1. 1 kb ladder
    2.E1010



06/13/12


We ran gel and extracted from gel LIQUID CULTURE.
We made liquid cultures LIQUID CULTURE and lysed.














  • 1. 1 kb ladder
    We extracted from gel



06/14/12


We extracted from gel LIQUID CULTURE.
We made glycerols of pHp45 Ω GLYCEROL PROTOCOL .
We transformed PSB2K3 Km (Kanamycin) 5C BBa_J04450 PSB4A5 Am (ampicillin) 1I BBa_J04450 AraC BBa_C0080
2012 14L plate 1 pSB2K3 Km+
2011 14L plate 1 pSB2K3 Km+
2012 14L plate 1 pSB2K3 Km+
TRANSFORMATION PROTOCOL.





  • 1. 1 kb ladder
    pHp45 Ω with E/P
    We extracted from gel



06/15/12


> Digested pHp45 Ω with E/P LIQUID CULTURE.
> We extracted plasmid with kit.
> Ran a gel GEL ELECTROPHORESIS PROTOCOL . (5)
>Extracted from gel LIQUID CULTURE.

ARAC
>From the overnight plate we prepared liquid culture LIQUID CULTURE.
>We left them incubating overnight.
>We left a plate (LB Km DH5α C0080 and a control).





06/18/12


>Plasmid extraction AraC with kit.
>C0080-psB2K3 915 bp
>Streaked 4 LB Km 30 plates DH5α psB2K3.
>It seemed as though there were two different colonies (white) and there had been a mutation. Normally they are red.
>Ran gel with Spr/Strr (eppendorf -20ºC) GEL ELECTROPHORESIS PROTOCOL.
>Made glycerols from one tube of DH5α C0080 Km 50 -> 04.
>Made glycerols from one tube of DH5α PSB4A5 Amp 100 -> 05 GLYCEROL PROTOCOL.
>Digested C0080 X,S.
>Digested B0014 E,P LIQUID CULTURE.


  • 1. 1 kb ladder
    Digested B0014 with E, P and with E,X





06/19/12


>Digested B0014 with E, P and with E,X. LIQUID CULTURE.
>Ran gels with yesterday’s digestions GEL ELECTROPHORESIS PROTOCOL .
2 B0014 E,X and 3 B0014 E,P were discarded because of problems in the preparation.
C0080 is in the first lane.
>Extracted from gel C0080 X,S LIQUID CULTURE.
>Made glycerols from 4 plates LB Km DH5α pSB2K3 GLYCEROL PROTOCOL .
>Take out AmyE 5’ from distribution [DNA KIT PLATE INSTRUCTIONS].
AmyE 5’ 18K plate 3 2010, 2011, 2012
AmyE 3’ 18M plate 3 2010, 2011, 2012
>Digested B0014 with E,X and E,P again LIQUID CULTURE.






06/22/12


>Ran gels with digestions B0014 with E,X and E,P GEL ELECTROPHORESIS PROTOCOL.

>Dephosphated B0014 E,X and B0014 E,P.










06/25/12


>Took LasR BBa_B0079 plate 1 2010,2011,2012 psB1A2 Amp+ from distribution [DNA KIT PLATE INSTRUCTIONS].

06/26/12


>Ran gel with psB2K3 and psB4A5 GEL ELECTROPHORESIS PROTOCOL .

06/27/12


>Transformed with plasmid B0079 1576 bp psB1A2 12A TRANSFORMATION PROTOCOL.
LasR B0079 plasmid Amp+ 12A plate 1 2010,2011
AmyE 5’ BBa_K143001 Km+ 18K plate 3 2010 and 16M, 18K 2011
AmyE 3’ BBa_K143002 Km+ 18M plate 3 2010 and 16O, 18M 2011
AmyE 5’ grew 2 colonies.

06/29/12


>We did a DH5α K143001 Km30 Amp 100 glycerol GLYCEROL PROTOCOL 07.
>We plated twice DH5α K143002 Km 30 Amp 100 + control and twice DH5α B0079 Amp 100 + control
These were both plated in 2 plates each.
They were left overnight since they had not grown by 7:00 pm so the next day glycerols were made.
>Liquid cultures LIQUID CULTURE.

2 tubes DH5α K143001 Km30 Amp 100
2 tubes DH5α K143002 Km30 Amp 100
2 tubes DH5α B0079 Amp 100
1 tube LB Km 30 Amp 100 control
1 tube LB Amp 100 control
>From the 6 tubes we extracted plasmid from kit.


UnamgenomcisUp.png

JULY

07/02/12
>Digestions LIQUID CULTURE.
B0079 digestion with S,P
K143001 with S,P
K143002 with S,P
>PCR’s
•AraC
•Cassete ΩSpr/Strr
PCR PROTOCOL

  • After Cassete ΩSpr/Strr PCR we ran a gel



  • B0079 digestion with S,P
    K143001 with S,P
    K143002 with S,P



07/03/12


>After Cassete ΩSpr/Strr PCR we ran a gel GEL ELECTROPHORESIS PROTOCOL . (8)
>Ran gel with digestions from yesterday. (9)
>Did band extractions LIQUID CULTURE.
>Stored at -20ºC.
>Did PCR to Cassete ΩSpr/Strr to add RBS and prefix/suffix.
>Left digesting with E,S LIQUID CULTURE.






  • We dephosphated B0079 S,P, K143001 S,P, K143002 E,X



07/04/12


>We dephosphated B0079 S,P, K143001 S,P, K143002 E,X (9.1).
>Ligated Cassete ΩSpr/Strr +K143002 dephosphated(digested with E,X and E,S).
>Transformed ligation and left overnight plated TRANSFORMATION PROTOCOL.
>Extracted plasmid PBBR1 GusA in 2 1.5 mL eppendorfs.
>Digested with PstI LIQUID CULTURE.






07/06/12


4 LB Km30 Spec60 DH5α ΩSpr/Strr +K143002 still have not grown.
Ran a gel with yesterday’s digestions to chek if they were done properly (10)
GEL ELECTROPHORESIS PROTOCOL .
Ran another gel with the rest of the samples.
Extracted GusA fragment
LIQUID CULTURE.
Repeated ligation ΩSpr/Strr +K143002 E,X dephosphated LIGATION PROTOCOL.
Repeated ΩSpr/Strr PCR.


07/07/12


Transformed DH5α ΩSpr/Strr +K143002 ligation LIGATION PROTOCOL.
Plated LB Km30 Spec 60 DH5α ΩSpr/Strr +K143002 .


07/08/12


Transformed DH5α ΩSpr/Strr +K143002 ligation LIGATION PROTOCOL.
Plated LB Km30 Spec 60 DH5α ΩSpr/Strr +K143002.



  • We dephosphated B0079 S,P, K143001 S,P, K143002 E,X



  • 1 PCR omega P
    2 PCR omega I
    3 PCR AraC P
    4 PCR AraC I
    5 ladder 1 Kb



07/09/12


From yesterday’s transformations only one colony grew.
From the previous transformation only 2 colonies grew.
These 3 were streaked in 3 plates:
DH5α ΩSpr/Strr +K143002 LB Km 30 Sp 100 1.
DH5α ΩSpr/Strr +K143002 LB Km 30 Sp 100 2.
DH5α ΩSpr/Strr +K143002 LB Km 30 Sp 100 3.
LB Km 30 Sp 100 control.
Did liquid cultures in 3 tubes:
ΩSpr/Strr +K143002 LB Km 30 Sp 100 1.
ΩSpr/Strr +K143002 LB Km 30 Sp 100 2.
ΩSpr/Strr +K143002 LB Km 30 Sp 100 3.
LB Km30 Sp 100 control.
LIQUID CULTURE.

Ran a gel with: (11)
GusA P
PBBR1 GusA
Ω E PCR P
Ω PCR P
Ω PCR I
Ω E
Ω PCR I
GEL ELECTROPHORESIS PROTOCOL
Did GusA primers dissolution for PCR.
GusA PCR
Gel Extraction by kit of lanes 3 and 5 LIQUID CULTURE.

PCR omega P, PCR omega I, PCR AraC P, PCR AraC I
Add 10 μl of each primer (LW and UP).
Add 3 μl of plasmid (P).
Add 30.4 μl buffer.
Add 5 μl Mg.
Add 8 μl DNTp’s.
Add 42.6μl H2O miliQ.
Add 1 μl RTTG polymerase.
Centrifuge (spin) 8 secs.
Add vegetable oil till the eppendorf is full.
Place eppendorf 1 mL in thermocycler.
Run PCR with program “BERNA”.

  • GusA digestions with X,P; Ω+AmyE 3’ with E,X; AraC PCR with E,S



07/10/12


•GusA digestions with X,P; Ω+AmyE 3’ with E,X; AraC PCR with E,S (2 times) DIGESTIONS. (11.2)











07/11/12


•GusA PCR digestions with E,S; Ω+AmyE 3’ with E,X LIQUID CULTURE.
•T.V. AraC PCR+ Ω+AmyE 3’ E,X dephosphated ligation LIGATION PROTOCOL.

  • 1. ladder.
    2. GusA PCR E,S.
    3. Ω+AmyE 3’ with E,X.



07/12/12


•Ran a gel with yesterday’s digestions: (12)

GEL ELECTROPHORESIS PROTOCOL .

•Transformed AraC PCR+ Ω+AmyE 3’ ligation in two tubes TRANSFORMATION PROTOCOL.

•From pfrc54 liquid cultures (A3) that were grown overnight we extracted plasmid.
•Made glycerols from 2 LB Km 30 Sp100 DH5α Ω+AmyE 3’ plates and from 1 LB Amp100 pfrc54 (A3) plates with control GLYCEROL PROTOCOL .
•Ligated GusA PCR with B0014 E,X desphophorylated LIGATION PROTOCOL.

•Digested Pfrc54 (A3) with S,P LIQUID CULTURE.

•Desphophorylated Ω+AmyE 3’ E,X.







  • •Ran gel with pfrc54 S,P



07/13/12



•Ran gel with pfrc54 S,P GEL ELECTROPHORESIS PROTOCOL . (13)
•Transformation of GusA PCR + B0014 ligation TRANSFORMATION PROTOCOL.
•Transformed with GFP E0040 psBIA2.
•Liquid Cultures with ligation: AraC+ Ω+AmyE 3’ for plasmid extraction at night TRANSFORMATION PROTOCOL.
B. Subtitils competent cells.








07/14/12



•From 24 AraC+ Ω+AmyE 3’ LB Km 30 Sp 100 DH5α tubes:
•Extracted pellets
•Extracted plasmids.
•Ran gel GEL ELECTROPHORESIS PROTOCOL .

•From transformed DH5α km 30:
GusA+B0014 DH5α Km50 24 pellets
E0040 DH5α LB Amp100
From these two we:
•Did liquid cultures LIQUID CULTURE.
•Extracted plasmid.
•From the GusA+E0014 transformation we took 24 colonies, did liquid cultures and extracted plasmid LIQUID CULTURE.
•Ran gel with this transformation GEL ELECTROPHORESIS PROTOCOL .



07/16/12



•Digested E,P AraC+ Ω+AmyE 3’
•Ω+AmyE 3’ E,P LIQUID CULTURE.


  • Digested E,P AraC+ Ω+AmyE 3’
    Ω+AmyE 3’ E,P



07/17/12



•Ran gel with yesterday’s digestions LIQUID CULTURE. (14)
•The gel we ran didn’t work, probably because the agarose was not prepared correctly.
•Digested 12, 15, 18, 21 with AraC+ Ω+AmyE 3 with E and also with P’; B0014 with E,X; E0040 with X,S LIQUID CULTURE.











  • •Digested 12, 15, 18, 21 with AraC+ Ω+AmyE 3 with E and also with P’; B0014 with E,X; E0040 with X,S




07/18/12



•From yesterday’s digestions we ran a gel GEL ELECTROPHORESIS PROTOCOL . (15)

•We made liquid cultures of AraC+ Ω+AmyE 3’ 12, 15, 21 LIQUID CULTURE.

•We ligated AraC PCR E,S dephosphated with + Ω+AmyE 3’ LIGATION PROTOCOL.

•We digested 1 + Ω+AmyE 3’ E,P LIQUID CULTURE.

07/19/12



•We ran We digested 1 + Ω+AmyE 3’ E,P with Miguel’s enzymes and with Abiel’s enzymes LIQUID CULTURE.

•We transformed with ligations AraC+ Ω+AmyE 3’ E and + Ω+AmyE 3’ E TRANSFORMATION PROTOCOL.

•Extracted plasmids from AraC+ Ω+AmyE 3’ 12,15,21.

•Digested E0040 X,S 2,3,4,5,6; ligations AraC+ Ω+AmyE 3’ E 12,15,21; ligations AraC+ Ω+AmyE 3’ P LIQUID CULTURE.



  • Digested E0040 X,S 2,3,4,5,6; ligations AraC+ Ω+AmyE 3’ E 12,15,21; ligations AraC+ Ω+AmyE 3’ P



07/20/12



•Ran gel with yesterday’s digestions GEL ELECTROPHORESIS PROTOCOL . (16)
•Transformed GusA+B0014 in two tubes TRANSFORMATION PROTOCOL.
•Made liquid cultures from AraC+ Ω+AmyE 3’s transformation LB Km30 Sp 100 and control LB Km 30 Sp100 LIQUID CULTURE.






07/23/12



•From 24 GusA+B0014 tubes (-) we didn’t do anything.
•From 4 AraC+ Ω+AmyE 3’ we extracted plasmid.
•Digested from the 4 AraC+ Ω+AmyE 3’ E,X; X; P and GusA PCR with X,P LIQUID CULTURE.

07/24/12



•Digested B0014 E with X B0014 X with E
•Digested AraC+ Ω+AmyE 3’ 1,2,3,4 with E,P LIQUID CULTURE.

07/25/12



•Ran gel of digested AraC+ Ω+AmyE 3’ 1,2,3,4 with E,P LIQUID CULTURE.
•Joined B0014 E with X B0014 X with E digestions.
•Made liquid cultures from 2 days old plated GusA+B0014 and extracted plasmid LIQUID CULTURE. Transformed TRANSFORMATION PROTOCOL.
•From LasR DH5α make liquid cultures and plate LIQUID CULTURE.
•Digested Ω+AmyE 3’ with X,P; E,S; C0080 X,P; E,S; S,P LIQUID CULTURE.
•Ligated Gus PCR X,P with B0079 S,P dephosphorylated LIGATION PROTOCOL.


  • 1.Ω+AmyE 3’ X,P
    2. Ω+AmyE 3’ E,S
    3.C0080 X,P
    4.C0080 E,S
    5.C0080 S,P
    6.ladder



07/26/12


•From C0179 (LasR) transformation which grew colonies, we made two liquid cultures: DH5α C0179 LB Cb 100 (two cultures) and a control without bacteria LIQUID CULTURE.

•We extracted plasmid from 8 C0179 tubes, from 2 tubes of C0179 (Miguel’s transformation), Puc, B.S. control and PSB4AE.

•Due to problems with the way we did the transformations of ligations we repeated them:
GusAPCR X,P+ B0079 S,P dephosphorylated

GusAPCR X,P+ B0079 S,P dephosphorylated (-)

GusAPCR X,P+ A3 S,P dephosphorylated

GusAPCR X,P+ A3 S,P dephosphorylated (-)
TRANSFORMATION PROTOCOL.

•Did the following digestions LIQUID CULTURE.
•AraC+ Ω+AmyE 3’ S,P 1,2,3,4
•K143002 X,P
•AraC+ Ω S,P
•C0179 X,S


07/27/12



Ligated AraC+ Ω S,P dephosphorylated + K143002 X,P LIGATION PROTOCOL.

07/30/12



•Transformed with ligations:
•AraC+ Ω dephosphprylated +K143002 X,P
•GusAPCR X,P+ A3 S,P dephosphorylated
•GusAPCR X,P+ B0079 S,P dephosphorylated
•Transformed the following sythesis:
•91996 Pveg 140 bp
•91997 ArsR-CzrA_promoter 1 194 bp
•91998 ArsR-CzrA_promoter 2 221 bp
•91999 ArsR-CzrA_promoter 3 213 bp
•92000 pBad-pXyl 387 bp
•92001 XylR 1117pb
•92002 CI_pro_(NAND_INHIBITOR) 774
•These synthesis come in pJ209 and supposedly come with Chloramphenicol+ and Gentamicin+ resistance, but we discovered that only Chloramphenicol worked. TRANSFORMATION PROTOCOL.

•Make liquid cultures of the following transformations for tomorrow LIQUID CULTURE:
•AraC+ Ω+K143002
•GusA+A3
•GusA+B0079
•Synthesis

07/31/12



Extracted plasmids from yesterday’s cultures and from K143002 cultures that were in the other lab.


UnamgenomcisUp.png

AUGUST

08/01/12



Digested XylR 01 X,P; pBAD-pXyl X,P; Pveg 96 S,P LIQUID CULTURE.


  • 1 PCR GusA I
    2 PCR GusA I
    3 PCR GusA P
    4 PCR GusA P
    5 ladder 1 Kb



08/02/12



•Extracted plasmids from liquid cultures:
AraC+ Ω+K143002
•GusA+A3
•GusA+BBR1

PCR GusA, GusA I, PCR GusA P, PCR GusA I

•Add 10 μl of each primer (LW and UP).
•Add 3 μl of plasmid (P).
•Add 30.4 μl buffer.
•Add 5 μl Mg.
•Add 8 μl DNTp’s.
•Add 42.6μl H2O miliQ.
•Add 1 μl RTTG polymerase.
•Centrifuge (spin) 8 secs.
•Add mineral oil till the eppendorf is full.
•Place eppendorf 1 mL in thermocycler.
•Run PCR with program “BERNA”.



  • 1.GusA PCR 1
    2.GusA PCR 2
    3.A3+GusA 1
    4.A3+GusA 2
    5.A3+GusA 3
    6.P GusA
    7.P GusA 2
    8.Ladder
    9.01
    10.06
    11.96





08/03/12



• Ran a gel with: (18)

GEL ELECTROPHORESIS PROTOCOL .
•Ran another gel to extract with:
1.GusA PCR 1
2.GusA PCR 2
3.00
4.01
GEL ELECTROPHORESIS PROTOCOL .
•Did the following digestions LIQUID CULTURE:

• Ω+K143002 E,X; A3+GusA E,S; GusAPCR X,P

•Extracted GusAPCR X,P digestion LIQUID CULTURE.

•Left the following ligation: AraC+ Ω+K143002 LIGATION PROTOCOL.




  • 1.A3+GusA 2
    2.A3+GusA 3
    3. Ω+AmyE 3’ 2
    4. Ω+AmyE 3’ 3
    5.XylR X,P
    6.pBad-pXyl X,P
    7.GusA PCR X,P




08/06/12



•Made liquid cultures of Ω+K143002 (2 cultures+1 control) and AraC+ Ω+K143002 (2 cultures+1 control) LIQUID CULTURE.
•Ligated GusAPCR X,P+B0079 S,P dephosphorylated LIGATION PROTOCOL.
•Ran a Gel with: (19)









  • Digested 14 tubes of AraC+ Ω+AmyE 3’ E,P



08/08/12


BBa_B0040 6I psB1A2 Amp+ plate 1
Digested 14 tubes of AraC+ Ω+AmyE 3’ E,P LIQUID CULTURE. (19.1)








08/09/12


•From yesterday’s PCR’s :
• E0040 plasmid 1
E0040 plasmid 2
E0040 digested 1
E0040 digested 2
We purified with PCR kit

•Ran a gel GEL ELECTROPHORESIS PROTOCOL .
•Made 14 PCR’s from AraC+ Ω+AmyE 3’.
•From B0079+GusA ligation and B0040 transformation: •Grew colonies.
•Made liquid cultures LIQUID CULTURE.
•Streaked these in a new plate.
•Diluted plasmid E0080 2 1/50.


08/10/12


•Yesterday’s gel did not come out as expected so we repeated the PCR.



  • 1.AraC+ Ω+AmyE 3’
    2-14.AraC+ Ω+AmyE 3’
    15.AraC+ Ω 1
    16.AraC+ Ω 1
    17.AraC+ Ω 1
    18.PCR 1 GFP
    19.PCR GFP




08/13/12


•After running a gel with 14 PCR’s AraC+ Ω+AmyE 3’ and it did not come out as expected, we ran a gel with the ligation AraC+ Ω+AmyE 3’ to select candidate (that weight the same as the ligation) GEL ELECTROPHORESIS PROTOCOL : (20)

•Extracted pasmids form liquid cultures: B0049, B0079+GusA.

•AraC+ Ω+AmyE 3’ undigested didn’t run in the gel as expected, it ran similarly to AraC+ Ω

• We repeated the ligation AraC+ Ω S,P dephosphorylated+K143002 X,P LIGATION PROTOCOL.

• GFP PCR gel came out with two bands one is GFP and the other one are the primers, even after purifying by kit. We joined 2 GFP PCR tubes.

• We ran a gel to extract.




  • 1.6 AraC+ Ω+AmyE 3’ E with P.

    2.8 AraC+ Ω+AmyE 3’ E with P.
    3.11 AraC+ Ω+AmyE 3’ E with P.
    4.12 AraC+ Ω+AmyE 3’ E with P.
    5.6 AraC+ Ω+AmyE 3’ with E,X.
    6.8 AraC+ Ω+AmyE 3’ with E,X.
    7.11 AraC+ Ω+AmyE 3’ with E,X.
    8.12 AraC+ Ω+AmyE 3’ with E,X.
    9.00 pBad/pXyl with S,P.
    10.Ladder.
    11.E0040 PCR E,S to extract the correct band.




08/16/12


•Ran a gel with yesterday’s digestions:

•Digested:
ArSR-CzrA 97 with S,P
ArSR-CzrA 98 with S,P
ArSR-CzrA 99 with S,P
E0040 PCR with E,S
Digestion Protocol.






08/20/12


•Ligated B0079 S,P dephosphorylated + GusA PCR X,P and pVeg S,P dephosphorylated + XylR X,P LIGATION PROTOCOL.


08/21/12


•Joined both .6 ml tubes of B0014 EX and B0014 XE in one and dephosphorylated.
•Extracted plasmid from the 24 tubes of of ligation K143001+pBad/pXylR.
•Digested Ω+AmyE 3’ with E,X and + Ω+AmyE 3’ II with E,X (obtained these two from glycerols stored at -80ºC LIQUID CULTURE.


  • Digested K143001+PBad, pXyl with E,S



  • 1.K143001+PBad, pXyl E,S 10
    2.K143001+PBad, pXyl E,S 11
    3.K143001+PBad, pXyl E,S 12
    4.A3 PCR
    5.A3 PCR
    6.E0040 PCR E,S
    7.B0014 E,X dephosphorylated
    8. Ω+AmyE 3’ E,X
    9. Ω+AmyE 3’ E,X II
    10.Ladder



08/22/12


•We did 2 PCR’s for A3.

•Digested K143001+PBad, pXyl with E,S
LIQUID CULTURE. (22.1)

GEL ELECTROPHORESIS PROTOCOL .
•Did band extraction of:
1. K143001+PBad, pXyl E,S 10
2.K143001+PBad, pXyl E,S 11
3.K143001+PBad, pXyl E,S 12

LIQUID CULTURE.
•Made liquid cultures from E1010+Boo14 that the other lab gave us and did 2 plates for glycerol Km+ LIQUID CULTURE
GLYCEROL PROTOCOL .

•Did 2 plates for glycerol of both K143001+pBad/pXyl 10y11 Km+ and AraC+ Ω+AmyE 3’ 6,8,11,12 Km+ and Spectinomycin+ GLYCEROL PROTOCOL .

•Transformed ligations:
B0079+GusA Amp+
Pveg+XylR Chloramphenicol+ TRANSFORMATION PROTOCOL..


  • 1. Ω+AmyE 3’ E,X 6.2
    2.Ω+AmyE 3’ II E,X
    3.97 ArsR-CzrA
    4.98 ArsR-CzrA
    5.99 ArsR-CzrA



08/23/12


•The negative controls were contaminated. We didn’t manipulate the ones that had grown because of this.
•Ran gel with GEL ELECTROPHORESIS PROTOCOL : (23.01)
Digestion Protocol.


08/24/12


From plate with ligation E0040+B0014, ligation K143001+pBad,pXyl 10 and 11, and ligation AraC+ Ω+AmyE 3’ 6 and 8 we streaked 2 plates for glycerol of each ligation.
Repeated ligation B0079+GusA.

Ligated E0040 PCR E,S+B0014 E,X dephospohylated LIGATION PROTOCOL.

Made 2 new plates from Pveg+XylR ligation and liquid cultures LIQUID CULTURE.


08/25/12


Extracted pellet from 16 tubes of pVeg+XylR that were left overnight.

Ligated B0079+GusA and B0040+B0014 LIGATION PROTOCOL.


08/28/12


Made liquid cultures from transformations tht were left overnight -R0079+GusA
-R0079+GusA (-)
-E0040+B0014
-E0040+B0014 (-)
LIQUID CULTURE.

  • 1. A3 PCR 1.
    2. A3 PCR 2.
    3. Ω+AmyE 3’ S,P *.
    4. Ω+AmyE 3’ S,P .
    5. Pveg+XylR E,S 2.
    6. Pveg+XylR E,S 3.
    7. Pveg+XylR E,S 4.



08/29/12


Digested Pveg+XylR 2,3,4 with E,S.

Digested Ω+AmyE 3’ with S,P DIGESTION.

Ran a PCR with A3 PCR (2 .6 ml tubes).

Ran a gel with
GEL ELECTROPHORESIS PROTOCOL : (23.01)








  • 1-23. E0040 + B0014 colonies
    24-29. B0079+GusA 1
    30. B0079



08/30/12


•Ran a gel GEL ELECTROPHORESIS PROTOCOL : (24)


•Digested PVeg+XylR 1,5,7,10,13,16 with E,S; E0040+B0014 3,4,5,10,11,19,21,22 with X,P; B0079+GusA 3,4,5 E,S LIQUID CULTURE.









  • 1-3B0079+GusA E,S 3.
    4-9. PVeg+XylR E,S 1.
    10-17. E0040+B0014 X,P 3.
    18. 1 kb ladder.



  • 1.A3 PCR.



  • E0040+B0014 X,P 4 to extract



08/31/12


•Ran a gel GEL ELECTROPHORESIS PROTOCOL : (25)


•Dephosphorylated:
Ω+AmyE 3’ S,P
Ω+AmyE 3’ II S,P
6 AraC+ Ω+AmyE 3’ E,X
8 AraC+ Ω+AmyE 3’ E,X
11 AraC+ Ω+AmyE 3’ E,X
12 AraC+ Ω+AmyE 3’ E,X

•Ran a gel with A3 PCR GEL ELECTROPHORESIS PROTOCOL : (26)

•It was the second time we didn’t obtain a band from A3’s PCR.

•Probably because it had been missing the buffer 2’s ethanol (“blue lid”) from the PCR purification.

•Ran a gel woth E0040+B0014 X,P 4 to extract
Gen extraction protocol.

•Did an A3 PCR.






UnamgenomcisUp.png

SEPTEMBER

  • 1.A3 PCR 1.
    2.A3 PCR 2.
    3.E0040+B0014 X,P 1.
    4.E0040+B0014 X,P 2.
    5.Ω+AmyE 3’ dephosphorylated S,P.
    6.Ω+AmyE 3’ dephosphorylated S,P II.
    7.97 dephosphorylated S,P.
    8.98 dephosphorylated S,P.
    9.99 dephosphorylated S,P.
    10-13. Arac+ Ω+AmyE 3’ dephosphorylated E,X 12.
    14. 1 kb Ladder.




09/01/12


•Ran a gel with GEL ELECTROPHORESIS PROTOCOL : (28)

•Ligated E0040+B0014 X,P 2 +promoter S,P dephosphorylated; K143002 X,P+ Ω+AmyE 3’ dephosphorylated S,P LIGATION PROTOCOL.





09/03/12


•Digested B0079+GusA E,S 3,4,5; PVeg+XylR E,S 1,5,7,10,13,16 LIQUID CULTURE.


09/04/12


•Ran gel with digestions:
B0079+GusA E,S 3,4,5
PVeg+XylR E,S 1,5,7,10,13,16
GEL ELECTROPHORESIS PROTOCOL .

•Purified A3 PCR 1,2.

•Ran a gel of A3 PCR
GEL ELECTROPHORESIS PROTOCOL and digested with X,P LIQUID CULTURE.

•From ligations: PVeg+E0040+B0014, PBad/PXyl+E0040+B0014, B0079+E0040+B0014 only colonies grew in PBad/PXyl+E0040+B0014.

•Plated colonies that grew in a new plate.

•Made liquid cultures of these
LIQUID CULTURE.

•Repeated the ones that did not grow.

•Digested E0040+B0014 4 with X,P LIQUID CULTURE.

•Ran a gel GEL ELECTROPHORESIS PROTOCOL .

•Extracted from gel LIQUID CULTURE.
-BBa_J23101 18E plate 1 plasmid BBa_J61002_2948 bp Amp+


  • 24 PBad/PXyl+E0040+B0014 tubes we extracted



  • 1.E0040+B0014 X,P
    2.E0040+B0014 X,P
    3.PVeg+XylR E
    4.B0079+GusA S
    5.1 kb plus ladder
    Extracted band from 1. and 2



  • Digested B0079+GusA with E,S 4,5; PVeg+XylR with E,S



09/05/12


•From the 24 PBad/PXyl+E0040+B0014 tubes we extracted plasmids (29) and ran a gel LIQUID CULTURE.

•Extracted plasmid from 2 tubes of E0040+B0014.

•Ran a gel with yesterday’s digestions:
1.E0040+B0014 X,P
2.E0040+B0014 X,P
3.PVeg+XylR E
4.B0079+GusA S
5.1 kb plus ladder

•Extracted band from 1. and 2. LIQUID CULTURE.

•Purified A3 PCR from 2 0.6ml tubes 1 and 2.

•1 colony grew from ligation pVeg+E0040+B0014.

•We streaked this in another plate and did liquid cultures
LIQUID CULTURE.

•To do:
•Ligate B0079 S,P dephosphorylated + E0040+B0014 X,P and Ω+AmyE 3’ S,P dephosphorylated+ K143001 X,P.
•Digested B0079+GusA with E,S 4,5; PVeg+XylR with E,S 10,13. (31)








  • •A3 PCR and gel A3 PCR X,P




09/06/12


•A3 PCR and gel A3 PCR X,P 1,2.


09/14/12


•Digested Ω+AmyE 3’ 11,13,18, and 22 with E,X.
•Ligate:
PVeg S,P dephosphorylated+XylR X,P.
PBad p Xyl S,P dephosphorylated + E0040+B0014 X,P.
pSB13C3 E,P dephosphorylated + A3 PCR E,P.
pSB13C3 E,P dephosphorylated + GusA PCR E,P.
pSB13C3 E,P dephosphorylated + XylR E,P.
pSB13C3 E,P dephosphorylated + pVeg E,P.
pSB13C3 E,P dephosphorylated + pBad pXyl E,P.
pSB13C3 E,P dephosphorylated + Ω PCR E,P.





09/16/12


• Colonies in these plates grew:
- R0079+E0040+B0014
- pBad/pXyl
- XylR
- pVeg
- A3+E0040+B0014 from colonies 1,3,4,5,6,7,8,9,10,11,12,13,14,15,17
- pVeg+E0040+B0014 1,2,3,4,5,6,8,9,10,11,12,13,14,15,16
- pBad/pXyl+E0040+B0014 2 tubes from the same correct colony.
- pVeg+XylR 1,2
- pBad/pXyl+pSB1C3 1,2
- XylR+pSB1C3 1,2
- pVeg+pSB1C3 1,2
- A3+pSB1C3 1,2
- GusA+pSB1C3 1,2
- omegacassette+pSB1C3 1,2

• Ran gel from the plasmid extractions that we did yesterday:
- A3+E0040+B0014 1-16
- pVeg+E0040+B0014 1-16, 18
- omega cassette+AmyE 3’ 11,13,18,22
• Digested R0079+E0040+B0014 with E,S. to ligate with AmyE 3’ E,x dephosphorylated.
• Digested omega cassette with E,P.
• Digested pSB1C3 with E,P.
• Made liquid cultures from AmyE 5’ and AmyE 3’.
• Did plasmid extraction from pSB1C3 colonies 3 and 6.

09/17/12


• Digested A3+E0040+B0014 colonies 2,3,4,5,6,11 and 16 with E,S.
• Digested pVeg+E0040+B0014 colonies 1,2,3,4,5,9 and 10 with E,S.
• Dephosphorylated omega cassette+AmyE 3’ colonies 13,18 and 22 digested with E,X.
• Digested pBad/pXyl and pVeg with S,P. Then dephosphorylated.
• Digested AmyE 3’ with E,X. Then dephosphorylated.

09/18/12



• Ran gel with:
1. A3 2 E,S
2. A3 3 E,S
3. A3 4 E,S
4. A3 5 E,S
5. A3 6 E,S
6. A3 11 E,S
7. A3 16 E,S
8. E0040+B0014 colony 1 E,X
9. AmyE 5’ E,P
10. AmyE 3’ E,X
11. Omega cassette E,S
12. pSB1C3 E,P
13. ladder
Bottom:
1. pVeg 1 E,S
2. pVeg 2 E,S
3. pVeg 3 E,S
4. pVeg 4 E,S
5. pVeg 5 E,S
6. pVeg 9 E,S
7. pVeg 10 E,S
8. pVeg S,P dephosphorylated
9. pVeg 2 S,P
10. pBad/pXyl S,P
11. XylR X,P
12. R0079+GFP+TT E,S
13. R0079 S,P
14. Ladder
• Dephosphorylated GFP+TT E,X; AmyE 5’ E,X; pSB1C3 E,P; pVeg 2 S,P; pBad/pXyl S,P and R0079 S,P.

09/19/12



• Did PCR from A3 and a 1/50 dilution.
• Ran gel with:
1. pVeg 3 E,P.
2. pVeg 9 E,P.
3. pVeg 10 E,P.
4. pBAd/pXyl 3 E,P.
5. pBAd/pXyl 5 E,P.
6. pBAd/pXyl 1 E,P.
7. A3 3 E,P.
8. A3 4 E,P.
9. XylR 1 E,P.
10. XylR 3 E,P.
11. XylR 8 E,P.
12. pSB1C3 6 E,P.
13. pSB1C3 6 E,P.
14. AmyE 5’ E,S.
15. AmyE 5’ E,S.
16. A3 1/50 PCR.
17. A3 PCR.
18. Ladder
• We did transformations:
- 2 of R0079+GusA
- R0079+GusA control
- 2 of A3+pSB1AK3
- A3+pSB1AK3 control
- 2 of omega cassette+pSB1C3
- 2 of GusA+pSB1C3
• Digested:
- pVeg+pSB1C3
- pBad/pXyl+pSB1C3
- XylR+pSB1C3
- A3+pSB1C3
With E,P.
• Ran gel with these digestions.

09/19/12


• Made liquids cultures from:
- Glicerol of AmyE 5’
- Glicerol of AmyE 3’
- pBad/pXyl+pSB1C3 colony 5
• Made liquid cultures from yesterday transformations:
- R0079+GusA 2 and control
- A3+pSB1AK3 2 and control
- Omega cassette+pSB1C3 2
- GusA+pSB1C3 2
• We transformed yesterday ligations:
- pBad/pXyl+pSB1C3
- XylR+pSB1C3
- pVeg+pSB1C3
- A3+pSB1C3
• Purified A3 PCR with kit, and then, digested with E,P and E,S.
• Ran gel

09/20/12



• Made liquid cultures from transformations:
- Omega cassette+pSB1C3 colony 7
- 2 of GusA+pSB1C3 colony 32
- R0079+GusA colony 12
• Digested A3 1/50 PCR with E,P and E,S.
• Made liquid cultures from R0079+E0040+B0014; pBad/pXyl+E0040+B0014; pVeg+E0040+B0014; A3+E0040+B0014.
• Ligated:
- pBad/pXyl S,P dephosphorylated + E0040+B0014 X,P
- pVeg S,P dephosphorylated + E0040+B0014 X,P
- A3 PCR E,S + E0040+B0014 E,X dephosphorylated.

09/21/12



• Ran gel with:
1. R0079+GFP+TT 1
2. R0079+GFP+TT
3. pBad/pXyl+pSB1C3 1
4. pBad/pXyl+pSB1C3
5. omega cassette+psB1C3 1
6. omega cassette+psB1C3
7. pSB1C3 E,P 1
8. pSB1C3 E,P
9. pSB1C3 E
10. pSB1C3 P
11. A3 1/50 PCR E,P

09/22/12


• Ran gel with lysis extractions:
1. GusA+pSB1C3 1
2. GusA+pSB1C3 2
3. GusA+pSB1C3 3
4. GusA+pSB1C3 4
5. GusA+pSB1C3 5
6. GusA+pSB1C3 6
7. GusA+pSB1C3 7
8. GusA+pSB1C3 8
9. GusA+pSB1C3 9
10. GusA+pSB1C3 10
11. GusA+pSB1C3 11
12. GusA+pSB1C3 12
13. pSB1C3
14. A3+E0040+B0014 1
15. A3+E0040+B0014 2
16. A3+E0040+B0014 3
17. A3+E0040+B0014 4
18. A3+E0040+B0014 5
19. A3+E0040+B0014 6
20. A3+E0040+B0014 7
21. A3+E0040+B0014 8
22. A3+E0040+B0014 9
23. pVeg+E0040+B0014 3
24. pVeg+E0040+B0014 4
25. pVeg+E0040+B0014 5
26. pVeg+E0040+B0014 6
27. pVeg+E0040+B0014 7
28. pVeg+E0040+B0014 8
29. pVeg+E0040+B0014 9
30. pVeg
31. pBad/pXyl+E0040+B0014 1
32. pBad/pXyl+E0040+B0014 2
33. pBad/pXyl+E0040+B0014 3
34. pBad/pXyl+E0040+B0014 4
35. pBad/pXyl+E0040+B0014 5
36. pBad/pXyl+E0040+B0014 6
37. pBad/pXyl+E0040+B0014 7
38. pBad/pXyl+E0040+B0014 8
39. pBad/pXyl+E0040+B0014 9
40. pBad/pXyl+E0040+B0014 10
41. pBad/pXyl
42. pVeg+XylR 1
43. pVeg+XylR 2
44. pVeg+XylR 3
45. pVeg+XylR 4
46. pVeg+XylR 5
47. pVeg+XylR 6
48. pVeg+XylR 7
49. pVeg+XylR 8
50. omega cassette

• Ran gel with yesterday digestions:
1. R0079+GFP+TT E,P
2. R0079+GFP+TT E,P
3. Omega cassette+pSB1C3 E,P
4. Omega cassette+pSB1C3 E,P
5. Ladder
6. pBad/pXyl+pSB1C3
7. pBad/pXyl+pSB1C3
8. pSB1C3 6 E,P.
9. A3 1/50 PCR E,S
10. pBbak C011
11. pBbak C012
12. ladder

• Did pellet from R0079+GusA.
• Did plasmid extraction from omega cassette+pSB1C3 colonies 1,4,6 and 7.
• Digested them with E,P.
• Digested:
- GusA+pSB1C3 1,3,4,10 and 11
- A3+E0040+B0014 2,4,7 and 9
- pVeg+E0040+B0014 4,5 and 6
- pBad/pXyl+E0040+B0014 3,7 and 10
- pVeg+XylR 2,4 and 5
with E,P.
• Made liquid cultures from pVeg+pSB1C3
• Ligated:
- XylR E,P + pSB1C3 E,P dephosphorylated.
- pVeg E,P + pSB1C3 E,P dephosphorylated.
- A3 1/50 PCR E,P + pSB1C3 E,P dephosphorylated.
- pBad/pXyl S,P dephosphorylated + E0040+B0014 X,P.
- pVeg S,P dephosphorylated + E0040+B0014 X,P.
- A3 1/50 PCR E,S + E0040+B0014 E,X dephosphorylated.
- pVeg S,P dephosphorylated + XylR X,P.

09/23/12



• Ran gel with yesterday digestions:
1. Omega cassette+pSB1C3 1 E,P
2. Omega cassette+pSB1C3 4 E,P
3. Omega cassette+pSB1C3 6 E,P
4. Omega cassette+pSB1C3 7 E,P
5. GusA+pSB1C3 1 E,P
6. GusA+pSB1C3 3 E,P
7. GusA+pSB1C3 4 E,P
8. GusA+pSB1C3 10 E,P
9. GusA+pSB1C3 11 E,P
10. pSB1C3 E,P dephosphorylated
11. pVeg+XylR 2 E,P
12. pVeg+XylR 4 E,P
13. pVeg+XylR 5 E,P
14. pVeg S,P dephosphorylated
15. pVeg+GFP+TT 4 E,P.
16. pVeg+GFP+TT 5 E,P.
17. pVeg+GFP+TT 6 E,P.
18. ladder
Bottom
1. pBad/pXyl+GFP+TT 3 E,P
2. pBad/pXyl+GFP+TT 7 E,P
3. pBad/pXyl+GFP+TT 10 E,P
4. pBad/pXyl S,P dephosphorylated
5. A3+GFP+TT 2 E,P
6. A3+GFP+TT 4 E,P
7. A3+GFP+TT 7 E,P
8. A3+GFP+TT 9 E,P
9. Ladder

09/24/12



• Did PCR from omega cassette+pSB1C3 colonies 1,4,6 and 7.
• Made 1/50 dilutions from these PCR products.
• Ran gel with:
1. Omega cassette+pSB1C3 1/50 PCR 1
2. Omega cassette+pSB1C3 PCR 1
3. Omega cassette+pSB1C3 1/50 PCR 4
4. Omega cassette+pSB1C3 PCR 4
5. Omega cassette+pSB1C3 1/50 PCR 6
6. Omega cassette+pSB1C3 PCR 6
7. Omega cassette+pSB1C3 1/50 PCR 7
8. Omega cassette+pSB1C3 PCR 7
9. GusA+pSB1C3 1 P
10. GusA+pSB1C3 3 P
11. GusA+pSB1C3 4 P
12. GusA+pSB1C3 10 P
13. GusA+pSB1C3 11 P
14. pVeg+pSB1C3 6 E,P
15. pVeg+pSB1C3 5 E,P
16. pVeg+pSB1C3 4 E,P
17. pVeg+pSB1C3 3 E,P
18. pVeg+pSB1C3 2 E,P
19. pVeg+pSB1C3 1 E,P
20. ladder

• From yesterday transformations, these didn’t grow:
- pBad/pXyl+E0040+B0014 1 and 2.
- A3+E0040+B0014.
• Made liquid cultures from transformations that did grow:
- pVeg+E0040+B0014.
- pVeg+XylR.
- A3+pSB1C3
- pVeg+pSB1C3
- XylR+pSB1C3

09/26/12



• Did plasmid extractions form liquids cultures:
- 8 of pVeg+pSB1C3
- 8 of A3
- 8 of XylR
• Digested them with E,P.
• Ran gel with:
1. Ladder
2. XylR+pSB1C3 1 E,P
3. XylR+pSB1C3 2 E,P
4. XylR+pSB1C3 3 E,P
5. pVeg+pSB1C3 1 E,P
6. pVeg+pSB1C3 3 E,P
7. pVeg+pSB1C3 4 E,P
8. pVeg+pSB1C3 5 E,P
9. pVeg+pSB1C3 6 E,P
10. pVeg+pSB1C3 8 E,P
11. pSB1C3 6 E,P dephosphorylated
12. A3+pSB1C3 1 E,P
13. A3+pSB1C3 3 E,P
14. A3+pSB1C3 4 E,P
15. A3+pSB1C3 5 E,P
16. A3+pSB1C3 6 E,P
17. A3+pSB1C3 8 E,P
18. Ladder
19. P4+E0040+B0014 1 E,X
20. P4+E0040+B0014 7 E,X

09/27/12



• Digested pVeg+XylR colonies 1,4,5 and 6 in pJ209 plasmid with E,S for 3 hours.
• Digested pVeg+E0040+B0014 colonies 7,9,10 and 11 in pasmid pJ209 with E,P.

10/09/12



• Ligated:
- A3 1/50 PCR E,P + pSB1C3 6 E,P dephosphorylated.
- pVeg S,P dephosphorylated + XylR X,P.
- P4+CI+E1010+B0014 E,X dephosphorylated + AmyE 5’+pBad/pXyl E,S.

10/10/12



• Ligated:
- GusA PCR E,P + pSB1C3 6 E,P dephosphorylated.
- pBad/pXyl S,P dephosphorylated + E0040+B0014 X,P.
- pVeg S,P dephosphorylated + E0040+B0014 X,P.
- A3 1/50 PCR E,S + E0040+B0014 E,X dephosphorylated.
• Digested R0079+E0040+B0014 with E,S.
• Digested AmyE 3’ with E,X. Then dephosphorylated.
• Digested pVeg and R0079, A3 with X,P.
• Digested pBad/pSB1C3 with S,P.

10/11/12



• Did plasmid extraction from liquid cultures:
- 2 of AmyE 5’
- 2 of AmyE 3’
- 2 of E0040+B0014
• Ran gel with:
1. A3 1/50 PCR X,P
2. A3 1/50 PCR X,P
3. A3+pSB1C3 6 X,P
4. A3+pSB1C3 6 X,P
5. A3+pSB1C3 8 X,P
6. A3+pSB1C3 8 X,P
7. pVeg X,P
8. pVeg 96 X,P
9. pVeg 96 X,P
10. pVeg+pSB1C3 1 X,P
11. pVeg+pSB1C3 1 X,P
12. pVeg+pSB1C3 3 X,P
13. pVeg+pSB1C3 3 X,P
14. R0079 X,P
15. Ladder

10/12/12



• Ligated: - AmyE 5’+pBad/pXyl 10 E,S + P4+CI+E1010+TT E,X dephosphorylated.
- AmyE 5’+pBad/pXyl 11 E,S + P4+CI+E1010+TT E,X dephosphorylated.
- AmyE 5’+pBad/pXyl 12 E,S + P4+CI+E1010+TT E,X dephosphorylated.
- pVeg S,P dephosphorylated + XylR X,P.
- A3 1/50 PCR E,P + pSB1C3 E,P dephosphorylated.

10/12/12



• Digested AmyE 5’ with S,P
• Dephosphorylated it.
• Ligated:
- AmyE 5’ S,P dephosphorylated with
- R0079 X,P
- pVeg 96 X,P
- A3 1/50 PCR X,P
- A3+pSB1C3 6 X,P
- R0079+E0040+B0014
• Ligated pBad/pXyl+pSB1C3 S,P dephosphorylated + E0040+B0014 X,P.
• Ran gel with:
1. A3+pSB1C3 1
2. A3+pSB1C3 2
3. A3+pSB1C3 3
4. A3+pSB1C3 4
5. A3+pSB1C3 5
6. A3+pSB1C3 6
7. A3+pSB1C3 7
8. A3+pSB1C3 8
9. A3+pSB1C3 9
10. A3+pSB1C3 10
11. A3+pSB1C3 11
12. A3+pSB1C3 6 control
13. AmyE 5’+P4+CI+E1010+B0014 1
14. AmyE 5’+P4+CI+E1010+B0014 2
15. AmyE 5’+P4+CI+E1010+B0014 3
16. AmyE 5’+P4+CI+E1010+B0014 4
17. AmyE 5’+P4+CI+E1010+B0014 5
18. AmyE 5’+P4+CI+E1010+B0014 6
19. AmyE 5’+P4+CI+E1010+B0014 7
20. P4+CI+E1010+B0014 1 control

10/09/12



• Ligate:
K143001+pBad/pXyl + p4+CI+E1010+TT E,X dephosphorylated.
• Ligate:
pVeg S,P dephosphorylated + XylR X,P.
• Ligate:
A3 PCR 1/50 E,P + pSB1C3 E,P dephosphorylated

10/13/12



• Digested AmyE 5’ with S,P. Then dephosphorylated.
• Ligate:
AmyE 5’ S,P dephosphorylated +
- R0079 X,P
- pVeg 96 X,P
- A3 PCR 1/50 X,P
- A3+pSB1C3 colony 6 X,P
- R0079+E0040+B0014 E,X
• Ligate:
pBad/pXyl+pSB1C3 S,P dephosphorylated + E0040+B0014 X,P

• Ran a gel with:
1. A3+pSB1C3 1
2. A3+pSB1C3 2
3. A3+pSB1C3 3
4. A3+pSB1C3 4
5. A3+pSB1C3 5
6. A3+pSB1C3 6
7. A3+pSB1C3 7
8. A3+pSB1C3 8
9. A3+pSB1C3 9
10. A3+pSB1C3 10
11. A3+pSB1C3 11
12. A3+pSB1C3 6 control
13. AmyE 5’+P4+CI+E1010+B0014 8
14. AmyE 5’+P4+CI+E1010+B0014 9
15. AmyE 5’+P4+CI+E1010+B0014 10
16. P4+CI+E1010+B0014 1 control
17. pVeg+XylR 1
18. pVeg+XylR 2
19. pVeg+XylR 3
20. pVeg+XylR 4
21. pVeg+XylR 5
22. pVeg+XylR 6
23. pVeg+XylR 7
24. pVeg+XylR 8
25. pVeg+XylR 10
26. pVeg+XylR 11
27. pVeg+XylR 12
28. pVeg 96 control

• Ran gel with:
1. A3 1/50 PCR X,P
2. A3+pSB1C3 6 X,P
3. pVeg 96 X,P
4. pVeg+pSB1C3 1 X,P
5. pVeg+pSB1C3 3 X,P
6. R0079 X,P
7. pBad/pXyl+pSB1C3 S,P dephosphorylated
8. ladder
9. Digested:
- A3+pSB1C3 colonies 3,4,5 and 10 with E,P.
- AmyE 5’+pBad/pXyl+P4+CI+E1010*B0014 colonies 1,2,7 and 8 with E,P.
- pVeg+XylR 1,4,5 and 12 with E,P.
• Ran gel with:
1. GFP+TT 1 X,P
2. GFP+TT 1 X,P
3. GFP+TT 1 E,S
4. GFP+TT 1 E,S
5. GFP+TT 2 X,P
6. GFP+TT 2 X,P
7. GFP+TT 2 E,S
8. GFP+TT 2 E,S
9. Ladder
10. A3 1/50 PCR X,P
11. A3+pSB1C3 6 X,P
12. pVeg 96 X,P
13. pVeg+pSB1C3 1 X,P
14. R0079 X,P
15. AmyE 5’ S,P

10/16/12


• Made liquid cultures from yesterday transformations:
- AmyE 5’+R0079
- AmyE 5’+R0079_2
- AmyE 5’+A3
- AmyE 5’+pVeg
- pBad/pXyl+E0040+B0014 in pSB1C3 plasmid.
• Digested:
- AmyE 5’+pBad/pXyl+P4+CI+E1010+B0014 colonies 1,2,7 and 8 with E,P.
- pVeg+XylR 1,4,5 and 12 with E,P.
- R0079+GFP+TT and R0079+GFP+TT_2 with X,P.