Team:Paris Saclay/Notebook/August/29

From 2013.igem.org

(Difference between revisions)
(→2 - Colony PCR of Pfnr wit RBS_AmilCP-Term in DH5α)
(→2 - Electrophoresis to check the digestion of BBa_J04450 by EcoRI/PstI)
 
(33 intermediate revisions not shown)
Line 9: Line 9:
===='''Objective : characterize BBa_K1155000 and BBa_K1155004, BBa_K1155005, BBa_K1155006'''====
===='''Objective : characterize BBa_K1155000 and BBa_K1155004, BBa_K1155005, BBa_K1155006'''====
-
===='''1 - Purification of colony transformed with ligation : NirB with RBS-LacZ-Term in PSB1C3, Pfnr with RBS-Amil CP-Term in PSB1C3 by streaking in aerobic or anaerobic conditions'''====
+
===='''1 - Purification of colonies: NirB with RBS-LacZ-Term in pSB1C3, Pfnr with RBS-AmilCP-Term in pSB1C3 by streaking colonies in aerobic or anaerobic conditions'''====
XiaoJing
XiaoJing
Line 15: Line 15:
{|
{|
| style="border:1px solid black;padding:5px;background-color:#DE;" |
| style="border:1px solid black;padding:5px;background-color:#DE;" |
-
Purification of 08/28/13 didn't work. We have blue colonies for Pfnr with RBS-Amil CP-Term in PSB1C3 in aerobic and anaerobic conditions. We also have blue colonies for NirB with RBS-LacZ-Term in PSB1C3 in anaerobic conditions. We will streak these colonies again.
+
Purification of 08/28/13 didn't work. We have blue colonies for Pndh* with RBS-AmilCP-Term in pSB1C3 in aerobic and anaerobic conditions. We also have blue colonies for NirB with RBS-LacZ-Term in pSB1C3 in anaerobic conditions. We will streak these colonies again.
|}
|}
Line 21: Line 21:
[[File:PsNirB2908.jpg|500px]]
[[File:PsNirB2908.jpg|500px]]
-
We streak :  
+
We streak colonies from construction :  
-
* Pfnr with RBS-Amil CP-Term in PSB1C3 with O2 at 37°C
+
* Pndh* with RBS-Amil CP-Term in pSB1C3 with O2 at 37°C
-
* Pfnr with RBS-Amil CP-Term in PSB1C3 without O2 at 37°C
+
* Pndh* with RBS-Amil CP-Term in pSB1C3 without O2 at 37°C
-
* Pfnr with RBS-Amil CP-Term in PSB1C3 with O2 at 30°C
+
* Pndh* with RBS-Amil CP-Term in pSB1C3 with O2 at 30°C
-
* Pfnr with RBS-Amil CP-Term in PSB1C3 without O2 at 30°C
+
* Pndh* with RBS-Amil CP-Term in pSB1C3 without O2 at 30°C
-
* NirB with RBS-LacZ-Term in PSB1C3 with O2 with Xgal at 37°C
+
* NirB with RBS-LacZ-Term in pSB1C3 with O2 with Xgal at 37°C
-
* NirB with RBS-LacZ-Term in PSB1C3 without O2 with Xgal at 37°C
+
* NirB with RBS-LacZ-Term in pSB1C3 without O2 with Xgal at 37°C
-
We also purify Pfnr with RBS-Amil CP-Term in PSB1C3 in liquid culture at 37°C using :
+
We also purify Pndh* with RBS-AmilCP-Term in pSB1C3 in liquid culture at 37°C using :
-
* Pfnr with RBS-Amil CP-Term in PSB1C3 in aerobic conditions :  
+
* Pndh* with RBS-AmilCP-Term in pSB1C3 in aerobic conditions :  
** LB : 10 mL  
** LB : 10 mL  
** Clone : 1 and 2
** Clone : 1 and 2
-
* Pfnr with RBS-Amil CP-Term in PSB1C3 in anaerobic conditions :  
+
* Pndh* with RBS-AmilCP-Term in pSB1C3 in anaerobic conditions :  
** LB : 50mL
** LB : 50mL
** Clone : 1 and 2
** Clone : 1 and 2
-
===='''2 - Colony PCR of Pfnr with RBS_AmilCP-Term in DH5α'''====
+
===='''2 -  PCR Colony of strain DH5α containing plasmid pSB1C3 with Pndh* and RBS_AmilCP-Term'''====
XiaoJing
XiaoJing
-
We mix our colonies in 20µL of H2O.
+
We resuspend our colonies in 20µL of H2O.
Used quantities :  
Used quantities :  
-
* DNA : 2µL
+
* DNA : 2µL of resuspend colony
-
* Mix : (it was divided in 4 tubes for 4 different colonies for each assembly with 23µL of mix in each tube. We do it twice.)
+
* PCR mix: 23µL  
 +
 
 +
PCR mix:
** Oligo 43 : 14µL
** Oligo 43 : 14µL
** Oligo 44 : 14µL
** Oligo 44 : 14µL
Line 78: Line 80:
** H2O : 9µL
** H2O : 9µL
-
We keep the digestion for 30 minutes at 37°C.
+
We incubatethe digestion for 30 minutes at 37°C.
===='''4 - Electrophoresis to check the digestion of BBa_K1155000 by PstI/SpeI, BBa_K1155003, BBa_K1155007 by Xbal/PstI'''====
===='''4 - Electrophoresis to check the digestion of BBa_K1155000 by PstI/SpeI, BBa_K1155003, BBa_K1155007 by Xbal/PstI'''====
Line 85: Line 87:
{|
{|
-
| style="width:350px;border:1px solid black;" | [[]]
+
| style="width:350px;border:1px solid black;" | [[File:Psgel12908.jpg]]
| style="width:350px;border:1px solid black;vertical-align:top;" |
| style="width:350px;border:1px solid black;vertical-align:top;" |
* Well 1 : 6µL DNA Ladder
* Well 1 : 6µL DNA Ladder
-
* Well 2 : 5µL of RBS-Amil CP-Term clone 9+1µL of 6X loading dye  
+
* Well 2 : 5µL of RBS-AmilCP-Term clone 9 + 1µL of 6X loading dye  
-
* Well 3 : 5µL of RBS-Amil CP-Term clone 12+1µL of 6X loading dye  
+
* Well 3 : 5µL of RBS-AmilCP-Term clone 12 + 1µL of 6X loading dye  
-
* Well 4 : 5µL of RBS-LacZ-Term clone 10+1µL of 6X loading dye  
+
* Well 4 : 5µL of RBS-LacZ-Term clone 10 + 1µL of 6X loading dye  
-
* Well 5 : 5µL of RBS-LacZ-Term clone 11+1µL of 6X loading dye   
+
* Well 5 : 5µL of RBS-LacZ-Term clone 11 + 1µL of 6X loading dye   
-
* Well 6 : 5µL of RBS-LacZ-Term clone 15+1µL of 6X loading dye  
+
* Well 6 : 5µL of RBS-LacZ-Term clone 15 + 1µL of 6X loading dye  
* Gel : 1.0%
* Gel : 1.0%
|}
|}
Line 98: Line 100:
Expected sizes :  
Expected sizes :  
* RBS-LacZ-Term : 3500bp
* RBS-LacZ-Term : 3500bp
-
* RBS-Amil CP-Term :  
+
* RBS-AmilCP-Term : 824bp
-
 
+
-
{|
+
-
| style="width:350px;border:1px solid black;" | [[]]
+
-
| style="width:350px;border:1px solid black;vertical-align:top;" |
+
-
* Well 1 : 6µL DNA Ladder
+
-
* Well 3 : 5µL of Pfnr+1µL of 6X loading dye 
+
-
* Gel : 1.0%
+
-
|}
+
Expected sizes :  
Expected sizes :  
-
* Pfnr :   
+
* Pndh* :  111bp
{|
{|
| style="border:1px solid black;padding:5px;background-color:#DEDEDE;" |
| style="border:1px solid black;padding:5px;background-color:#DEDEDE;" |
-
We obtain fragments at the right size. We will purify them.
+
We obtained fragments at the right size. We will purify them.
|}
|}
Line 123: Line 117:
Nanodrop :  
Nanodrop :  
-
* Pfnr : 26.2ng/µL
+
* Pndh* : 26.2ng/µL
===='''6 - Electrophoresis to check the gel purification of the digestion of BBa_K1155000 by PstI/SpeI, BBa_K1155003, BBa_K1155007 by Xbal/PstI'''====
===='''6 - Electrophoresis to check the gel purification of the digestion of BBa_K1155000 by PstI/SpeI, BBa_K1155003, BBa_K1155007 by Xbal/PstI'''====
Line 130: Line 124:
{|
{|
-
| style="width:350px;border:1px solid black;" | [[]]
+
| style="width:350px;border:1px solid black;" | [[File:Psgel32908.jpg]]
| style="width:350px;border:1px solid black;vertical-align:top;" |
| style="width:350px;border:1px solid black;vertical-align:top;" |
* Well 1 : 6µL DNA Ladder
* Well 1 : 6µL DNA Ladder
-
* Well 2 : 2µL of RBS-LacZ-Term clone 10+1µL of 6X loading dye  
+
* Well 2 : 2µL of RBS-LacZ-Term clone 10 + 1µL of 6X loading dye  
-
* Well 3 : 2µL of RBS-Amil CP-Term clone 9+1µL of 6X loading dye  
+
* Well 3 : 2µL of RBS-AmilCP-Term clone 9 + 1µL of 6X loading dye  
* Gel : 1.0%
* Gel : 1.0%
|}
|}
Line 140: Line 134:
Expected sizes :  
Expected sizes :  
* RBS-LacZ-Term : 3500bp
* RBS-LacZ-Term : 3500bp
-
* RBS-Amil CP-Term :  
+
* RBS-Amil CP-Term : 824bp
{|
{|
| style="border:1px solid black;padding:5px;background-color:#DEDEDE;" |
| style="border:1px solid black;padding:5px;background-color:#DEDEDE;" |
-
We obtain fragments at the right size for RBS-LacZ-Term. We will ligate it.
+
We obtained fragments at the right size for RBS-LacZ-Term. We will ligate it.
|}
|}
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{|
{|
-
| style="width:350px;border:1px solid black;" | [[]]
+
| style="width:350px;border:1px solid black;" | [[File:Psgel42908.jpg]]
| style="width:350px;border:1px solid black;vertical-align:top;" |
| style="width:350px;border:1px solid black;vertical-align:top;" |
* Well 1 : 6µL DNA Ladder
* Well 1 : 6µL DNA Ladder
-
* Well 2 : 5µL of NirB clone 7+1µL of 6X loading dye  
+
* Well 2 : 5µL of PNirB clone 7 + 1µL of 6X loading dye  
-
* Well 3 : 5µL of NarG clone 6+1µL of 6X loading dye  
+
* Well 3 : 5µL of NarG clone 6 + 1µL of 6X loading dye  
-
* Well 4 : 5µL of BBa_K1155006 already digested by SpeI+1µL of 6X loading dye  
+
* Well 4 : 5µL of BBa_K1155006 already digested by SpeI + 1µL of 6X loading dye  
-
* Well 5 : 5µL of BBa_K1155004 already digested by SpeI+1µL of 6X loading dye  
+
* Well 5 : 5µL of BBa_K1155004 already digested by SpeI + 1µL of 6X loading dye  
-
* Well 5 : 5µL of BBa_K1155005 already digested by SpeI+1µL of 6X loading dye   
+
* Well 6 : 5µL of BBa_K1155005 already digested by SpeI + 1µL of 6X loading dye   
* Gel : 1.0%
* Gel : 1.0%
|}
|}
Expected sizes :  
Expected sizes :  
-
* NarK, NarG, NirB : 200bp
+
* NarK, NarG, NirB : 2000bp
{|
{|
| style="border:1px solid black;padding:5px;background-color:#DEDEDE;" |
| style="border:1px solid black;padding:5px;background-color:#DEDEDE;" |
-
We obtain fragments at the right size for NarK. We will ligate it
+
We obtained fragments at the right size for NarK. We will ligate it
-
|}  
+
|}
 +
 
 +
===='''8 - Purification colony of strain MG1655Z1 Δfnr '''====
 +
 
 +
XiaoJing
 +
 
 +
{|
 +
| style="border:1px solid black;padding:5px;background-color:#DE;" |
 +
Culture from 08/28/13 works. We will do a purification of one colonies on plates with kanamycin, ampicilin and chloramphenicol antibiotics.
 +
|}
 +
 
 +
We streaked 4 colonies in each plate but we used the same colony to streak on plates with LB or kanamycin or ampicilin or chloramphenicol antibiotics. We incubate our colonies at 42°C.
-
===='''Objective : obtaining Pfnr, NarK, NarG or NirB and RBS-LacZ-Term or RBS-AmilCP-Term in PSB3K3'''====
+
===='''Objective : obtaining Pfnr, NarK, NarG or NirB and RBS-LacZ-Term or RBS-AmilCP-Term in pSB3K3'''====
===='''1 - Digestion of BBa_J04450 by EcoRI/PstI'''====
===='''1 - Digestion of BBa_J04450 by EcoRI/PstI'''====
Line 185: Line 190:
* PstI FD : 1µL  
* PstI FD : 1µL  
-
We let the digestion at 37°C during 10 minutes.
+
We incubate the digestion at 37°C for 10 minutes.
===='''2 - Electrophoresis to check the digestion of BBa_J04450 by EcoRI/PstI'''====
===='''2 - Electrophoresis to check the digestion of BBa_J04450 by EcoRI/PstI'''====
Line 192: Line 197:
{|
{|
-
| style="width:350px;border:1px solid black;" | [[]]
+
| style="width:350px;border:1px solid black;" | [[File:Psgel52908.jpg]]
| style="width:350px;border:1px solid black;vertical-align:top;" |
| style="width:350px;border:1px solid black;vertical-align:top;" |
* Well 1 : 6µL DNA Ladder
* Well 1 : 6µL DNA Ladder
-
* Well 3 : 5µL of PSB3K3+1µL of 6X loading dye   
+
* Well 3 : 5µL of PSB3K3 + 1µL of 6X loading dye   
* Gel : 1.0%
* Gel : 1.0%
|}
|}
Expected sizes :  
Expected sizes :  
-
* PSB3K3 : 2750bp
+
* pSB3K3 : 2750bp
{|
{|
| style="border:1px solid black;padding:5px;background-color:#DEDEDE;" |
| style="border:1px solid black;padding:5px;background-color:#DEDEDE;" |
-
We obtain fragments at the right size. We will ligate it.
+
We obtained fragments at the right size. We will ligate it.
|}
|}
Line 213: Line 218:
Nanodrop :  
Nanodrop :  
-
* Pfnr : 7.2ng/µL
+
* Pndh* : 7.2ng/µL
-
 
+
==='''A - Aerobic/Anaerobic regulation system / B - PCB sensor system'''===
==='''A - Aerobic/Anaerobic regulation system / B - PCB sensor system'''===
Line 220: Line 224:
===='''Objective : obtaining FRN and BphR2 proteins'''====
===='''Objective : obtaining FRN and BphR2 proteins'''====
-
===='''1 - Colony  PCR of FNR, RBS-FNR and RBS-BphR2 in DH5α'''====
+
===='''1 -   PCR Colony of FNR, RBS-FNR and RBS-BphR2 in DH5α strain'''====
XiaoJing
XiaoJing

Latest revision as of 01:22, 5 October 2013

Navigation Home Team Project Labwork Notebook Human practices

Contents

Notebook : August 29

Lab work

A - Aerobic/Anaerobic regulation system

Objective : characterize BBa_K1155000 and BBa_K1155004, BBa_K1155005, BBa_K1155006

1 - Purification of colonies: NirB with RBS-LacZ-Term in pSB1C3, Pfnr with RBS-AmilCP-Term in pSB1C3 by streaking colonies in aerobic or anaerobic conditions

XiaoJing

Purification of 08/28/13 didn't work. We have blue colonies for Pndh* with RBS-AmilCP-Term in pSB1C3 in aerobic and anaerobic conditions. We also have blue colonies for NirB with RBS-LacZ-Term in pSB1C3 in anaerobic conditions. We will streak these colonies again.

PsPfnr2908.jpg PsNirB2908.jpg

We streak colonies from construction :

  • Pndh* with RBS-Amil CP-Term in pSB1C3 with O2 at 37°C
  • Pndh* with RBS-Amil CP-Term in pSB1C3 without O2 at 37°C
  • Pndh* with RBS-Amil CP-Term in pSB1C3 with O2 at 30°C
  • Pndh* with RBS-Amil CP-Term in pSB1C3 without O2 at 30°C
  • NirB with RBS-LacZ-Term in pSB1C3 with O2 with Xgal at 37°C
  • NirB with RBS-LacZ-Term in pSB1C3 without O2 with Xgal at 37°C

We also purify Pndh* with RBS-AmilCP-Term in pSB1C3 in liquid culture at 37°C using :

  • Pndh* with RBS-AmilCP-Term in pSB1C3 in aerobic conditions :
    • LB : 10 mL
    • Clone : 1 and 2
  • Pndh* with RBS-AmilCP-Term in pSB1C3 in anaerobic conditions :
    • LB : 50mL
    • Clone : 1 and 2

2 - PCR Colony of strain DH5α containing plasmid pSB1C3 with Pndh* and RBS_AmilCP-Term

XiaoJing

We resuspend our colonies in 20µL of H2O.

Used quantities :

  • DNA : 2µL of resuspend colony
  • PCR mix: 23µL

PCR mix:

    • Oligo 43 : 14µL
    • Oligo 44 : 14µL
    • dNTP : 14µL
    • Buffer Dream Taq : 69µL
    • Dream Taq : 5.5µL
    • H2O : 577µL

PsPCR2908.jpg

3 - Digestion of BBa_K1155000, BBa_K1155003, BBa_K1155007 by Xbal/PstI

XiaoJing

We used clone 9 and 12 for BBa_K1155003, clone 10, 11 and 15 for BBa_K1155007

Used quantities :

  • BBa_K1155003, BBa_K1155007
    • DNA : 14µL
    • Buffer FD : 2µL
    • XbaI FD : 2µL
    • PstI FD : 2µL
  • BBa_K1155000 :
    • DNA : 5µL
    • Buffer FD : 2µL
    • SpeI FD : 2µL
    • PstI FD : 2µL
    • H2O : 9µL

We incubatethe digestion for 30 minutes at 37°C.

4 - Electrophoresis to check the digestion of BBa_K1155000 by PstI/SpeI, BBa_K1155003, BBa_K1155007 by Xbal/PstI

XiaoJing

Psgel12908.jpg
  • Well 1 : 6µL DNA Ladder
  • Well 2 : 5µL of RBS-AmilCP-Term clone 9 + 1µL of 6X loading dye
  • Well 3 : 5µL of RBS-AmilCP-Term clone 12 + 1µL of 6X loading dye
  • Well 4 : 5µL of RBS-LacZ-Term clone 10 + 1µL of 6X loading dye
  • Well 5 : 5µL of RBS-LacZ-Term clone 11 + 1µL of 6X loading dye
  • Well 6 : 5µL of RBS-LacZ-Term clone 15 + 1µL of 6X loading dye
  • Gel : 1.0%

Expected sizes :

  • RBS-LacZ-Term : 3500bp
  • RBS-AmilCP-Term : 824bp

Expected sizes :

  • Pndh* : 111bp

We obtained fragments at the right size. We will purify them.

5 - Gel purification of the digestion of BBa_K1155000 by PstI/SpeI, BBa_K1155003, BBa_K1155007 by Xbal/PstI

XiaoJing

Protocol : [http://www.mn-net.com/tabid/1452/default.aspx Gel purification ]

Nanodrop :

  • Pndh* : 26.2ng/µL

6 - Electrophoresis to check the gel purification of the digestion of BBa_K1155000 by PstI/SpeI, BBa_K1155003, BBa_K1155007 by Xbal/PstI

Damir

Psgel32908.jpg
  • Well 1 : 6µL DNA Ladder
  • Well 2 : 2µL of RBS-LacZ-Term clone 10 + 1µL of 6X loading dye
  • Well 3 : 2µL of RBS-AmilCP-Term clone 9 + 1µL of 6X loading dye
  • Gel : 1.0%

Expected sizes :

  • RBS-LacZ-Term : 3500bp
  • RBS-Amil CP-Term : 824bp

We obtained fragments at the right size for RBS-LacZ-Term. We will ligate it.

7 - Electrophoresis to check the digestion of BBa_K1155004, BBa_K1155005, BBa_K1155006 by SpeI/PstI and plasmids already digested by SpeI and after digested by PstI

XiaoJing

Psgel42908.jpg
  • Well 1 : 6µL DNA Ladder
  • Well 2 : 5µL of PNirB clone 7 + 1µL of 6X loading dye
  • Well 3 : 5µL of NarG clone 6 + 1µL of 6X loading dye
  • Well 4 : 5µL of BBa_K1155006 already digested by SpeI + 1µL of 6X loading dye
  • Well 5 : 5µL of BBa_K1155004 already digested by SpeI + 1µL of 6X loading dye
  • Well 6 : 5µL of BBa_K1155005 already digested by SpeI + 1µL of 6X loading dye
  • Gel : 1.0%

Expected sizes :

  • NarK, NarG, NirB : 2000bp

We obtained fragments at the right size for NarK. We will ligate it

8 - Purification colony of strain MG1655Z1 Δfnr

XiaoJing

Culture from 08/28/13 works. We will do a purification of one colonies on plates with kanamycin, ampicilin and chloramphenicol antibiotics.

We streaked 4 colonies in each plate but we used the same colony to streak on plates with LB or kanamycin or ampicilin or chloramphenicol antibiotics. We incubate our colonies at 42°C.

Objective : obtaining Pfnr, NarK, NarG or NirB and RBS-LacZ-Term or RBS-AmilCP-Term in pSB3K3

1 - Digestion of BBa_J04450 by EcoRI/PstI

Anaïs

Used quantities :

  • Buffer FD: 2µL
  • H2O : 5µL
  • DNA : 9µL
  • EcoRI FD : 1µL
  • PstI FD : 1µL

We incubate the digestion at 37°C for 10 minutes.

2 - Electrophoresis to check the digestion of BBa_J04450 by EcoRI/PstI

XiaoJing

Psgel52908.jpg
  • Well 1 : 6µL DNA Ladder
  • Well 3 : 5µL of PSB3K3 + 1µL of 6X loading dye
  • Gel : 1.0%

Expected sizes :

  • pSB3K3 : 2750bp

We obtained fragments at the right size. We will ligate it.

3 - Gel purification of the digestion of BBa_J04450 by PstI/SpeI

XiaoJing

Protocol : [http://www.mn-net.com/tabid/1452/default.aspx Gel purification ]

Nanodrop :

  • Pndh* : 7.2ng/µL

A - Aerobic/Anaerobic regulation system / B - PCB sensor system

Objective : obtaining FRN and BphR2 proteins

1 - PCR Colony of FNR, RBS-FNR and RBS-BphR2 in DH5α strain

XiaoJing

Transformation of 08/28/13 works. We will do a Colony PCR.

We mix our colonies in 20µL of H2O.

Used quantities :

  • DNA : 2µL
  • Mix : (it was divided in 8 tubes for 8 different colonies for each assembly with 23µL of mix in each tube. We do it twice.)
    • Oligo 43 : 27.5µL
    • Oligo 44 : 27.5µL
    • dNTP : 27.5µL
    • Buffer Dream Taq : 137.5µL
    • Dream Taq : 11µL
    • H2O : 1144µL

PsPCR2908.jpg

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