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 :

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

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

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.