Team:Paris Saclay/Notebook/July/17

From 2013.igem.org

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==='''A - Aerobic/Anaerobic regulation system'''===
==='''A - Aerobic/Anaerobic regulation system'''===
-
===='''Objective : obtaining Bba_K1155003, Bba_K1155007'''====
+
===='''Objective : obtaining BBa_K1155003, BBa_K1155007'''====
-
===='''1 - Electrophoresis  of digestions of Bba_B0015, Bba_B0017, Bba_I732019 by EcoRI/PstI'''====
+
===='''1 - Electrophoresis  of digestions of BBa_B0015, BBa_B0017, BBa_I732019 by EcoRI/PstI'''====
Anaïs, Sheng
Anaïs, Sheng
 +
 +
* BBa_B0015, BBa_B0017 :
{|
{|
-
| style="width:350px;border:1px solid black;" |[[]]
+
| style="width:350px;border:1px solid black;" |[[File:Psgel11707.jpg|300px]]
| style="width:350px;border:1px solid black;vertical-align:top;" |
| style="width:350px;border:1px solid black;vertical-align:top;" |
-
* Well 1 : 5µL Bba_I732019 digested by EcoRI/PstI+1µl of 6X loading dye
+
* Well 1 : 2µL BBa_B0015+1µL of 6X loading dye
-
* Well 2 : 6µL DNA Ladder
+
* Well 2 : 2µL BBa_B0015+1µL of 6X loading dye
 +
* Well 3 : 2µL BBa_B0015+1µL of 6X loading dye
 +
* Well 4 : 6µL DNA Ladder
 +
* Well 5 : 2µL BBa_B0017+1µL of 6X loading dye
 +
* Well 6 : 2µL BBa_B0017+1µL of 6X loading dye
 +
* Well 7 : 2µL BBa_B0017+1µL of 6X loading dye
* Gel : 1%
* Gel : 1%
|}
|}
Expected sizes :  
Expected sizes :  
-
* RBS-LacZ-term : ...
+
* BBa_B0015 digested by EcoRI/PstI : 500bp
 +
* BBa_B0017 digested by EcoRI/PstI : 500bp
{|
{|
-
| style="width:350px;border:1px solid black;" |[[]]
+
| style="border:1px solid black;padding:5px;background-color:#DEDEDE;" |
 +
We obtain fragments at the right size. We will do a PCR of them.
 +
|}
 +
 
 +
{|
 +
| style="width:350px;border:1px solid black;" |[[File:Psgel31707.jpg|300px]]
| style="width:350px;border:1px solid black;vertical-align:top;" |
| style="width:350px;border:1px solid black;vertical-align:top;" |
-
* Well 1 : 2µL Bba_B0015+1µl of 6X loading dye
+
* Well 1 : 5µL BBa_I732019 digested by EcoRI/PstI+1µL of 6X loading dye
-
* Well 2 : 2µL Bba_B0015+1µl of 6X loading dye
+
* Well 2 : 6µL DNA Ladder
-
* Well 3 : 2µL Bba_B0015+1µl of 6X loading dye
+
-
* Well 4 : 6µL DNA Ladder
+
-
* Well 5 : 2µL Bba_B0017+1µl of 6X loading dye
+
-
* Well 6 : 2µL Bba_B0017+1µl of 6X loading dye
+
-
* Well 7 : 2µL Bba_B0017+1µl of 6X loading dye
+
* Gel : 1%
* Gel : 1%
|}
|}
Expected sizes :  
Expected sizes :  
-
* Bba_B0015 digested by EcoRI/PstI : ...
+
* BBa_I732019 : 3230bp
-
* Bba_B0017 digested by EcoRI/PstI : ...
+
 +
{|
 +
| style="border:1px solid black;padding:5px;background-color:#DEDEDE;" |
 +
We didn't obtain fragments at the right size. We will use BBa_I732017.
 +
|}
 +
==='''B - PCB sensor system'''===
 +
===='''Objective : obtaining BBa_K1155001, BBa_K1155002 and BphR2'''====
 +
===='''1 - Stock of BBa_K1155001'''====
 +
Anaïs, Sheng
 +
Used quantities :
 +
* BBa_K1155001 confirmed : 1 mL
 +
* Glycerol : 500µL glycerol.
 +
 +
We stocked them at -20°C.
 +
 +
===='''2 - Extraction of BBa_K1155001 from DH5α'''====
 +
 +
Anaïs, Sheng
 +
Protocol : [[Team:Paris_Saclay/extraction|Hight copy plamid extraction]]
=='''Modeling'''==
=='''Modeling'''==
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Ethic about open source:<br>
Ethic about open source:<br>
-Hsim is not an open source software, it belongs to the University of Paris Sud. However, it is a free software, we can download it free.<br>
-Hsim is not an open source software, it belongs to the University of Paris Sud. However, it is a free software, we can download it free.<br>
-
 
<br>
<br>
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|[[Team:Paris_Saclay/Notebook|<big>Back to calendar</big>]]
|[[Team:Paris_Saclay/Notebook|<big>Back to calendar</big>]]
-
|[[Team:Paris Saclay/Notebook/July/18|<big>next day</big>]]
+
|[[Team:Paris Saclay/Notebook/July/18|<big>Next day</big>]]
|}
|}
{{Team:Paris_Saclay/incl_fin}}
{{Team:Paris_Saclay/incl_fin}}

Latest revision as of 00:11, 5 October 2013

Navigation Home Team Project Labwork Notebook Human practices

Contents

Notebook : July 17

Lab work

A - Aerobic/Anaerobic regulation system

Objective : obtaining BBa_K1155003, BBa_K1155007

1 - Electrophoresis of digestions of BBa_B0015, BBa_B0017, BBa_I732019 by EcoRI/PstI

Anaïs, Sheng

  • BBa_B0015, BBa_B0017 :
Psgel11707.jpg
  • Well 1 : 2µL BBa_B0015+1µL of 6X loading dye
  • Well 2 : 2µL BBa_B0015+1µL of 6X loading dye
  • Well 3 : 2µL BBa_B0015+1µL of 6X loading dye
  • Well 4 : 6µL DNA Ladder
  • Well 5 : 2µL BBa_B0017+1µL of 6X loading dye
  • Well 6 : 2µL BBa_B0017+1µL of 6X loading dye
  • Well 7 : 2µL BBa_B0017+1µL of 6X loading dye
  • Gel : 1%

Expected sizes :

  • BBa_B0015 digested by EcoRI/PstI : 500bp
  • BBa_B0017 digested by EcoRI/PstI : 500bp

We obtain fragments at the right size. We will do a PCR of them.

Psgel31707.jpg
  • Well 1 : 5µL BBa_I732019 digested by EcoRI/PstI+1µL of 6X loading dye
  • Well 2 : 6µL DNA Ladder
  • Gel : 1%

Expected sizes :

  • BBa_I732019 : 3230bp

We didn't obtain fragments at the right size. We will use BBa_I732017.

B - PCB sensor system

Objective : obtaining BBa_K1155001, BBa_K1155002 and BphR2

1 - Stock of BBa_K1155001

Anaïs, Sheng

Used quantities :

  • BBa_K1155001 confirmed : 1 mL
  • Glycerol : 500µL glycerol.

We stocked them at -20°C.

2 - Extraction of BBa_K1155001 from DH5α

Anaïs, Sheng

Protocol : Hight copy plamid extraction

Modeling

Meeting memo
Meeting Date: 17/07/2013
Meeting participants: Patrick Amar, Claire Toffano-Nioche, Abdou Mouhtare, Damir Damipator, Gabriel Gallin, Zhou Yi
Recorder: Zhou Yi

Hsim:
-Hsim is created for bio-chemical reaction simulation, it demonstrates bio-chemical systems which the scientists are already known.

-The molecules are simulated as spheres (in 2D or 3D). Initial positions and size of sphere are configurable.

-example of a Hsim command:
B + V -> R + V [probability]

-Molecules diffusion are simulated by movements of spheres, if the distance between two centers of the spheres is less than the sum of 2 radium, we consider that will lead to a collision.

-Computer takes a random sample and compare it to the probability which is specified in equation. If the value exceeds the threshold, we consider that the reaction takes place.

-Probability of success is associated with kinetics of reaction which depends on concentrations of molecules varying during the reaction.

-Time unit is 100ms. So movement of spheres is discreet.
-Spheres move randomly but could follow some stochastic rules (like Brownian movement).

Ethic about open source:
-Hsim is not an open source software, it belongs to the University of Paris Sud. However, it is a free software, we can download it free.


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