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Team:KULeuven/23 July 2008
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=== Wet Lab === | === Wet Lab === | ||
| - | Stefanie and | + | Stefanie and Hanne prepared liquid cultures of the plates with the cells we received from iGEM. We also started on the glycerol stock. Tomorrow we'll continue to make a glycerol stock of all the parts. |
| - | + | ||
| + | Elke, Nathalie and Jan started with cutting and pasting to test the output. We miniprepped [http://partsregistry.org/Part:BBa_R0084 R0084], [http://partsregistry.org/Part:BBa_B0032 B0032], [http://partsregistry.org/Part:BBa_E0022 E0022] and [http://partsregistry.org/Part:BBa_B0015 B0015], checked their concentration, made the right digest and separated them on gel. Only [http://partsregistry.org/Part:BBa_B0032 B0032] and [http://partsregistry.org/Part:BBa_E0022 E0022] were cut by the enzymes and the correct pieces could be cut out for the ligation. | ||
=== Dry Lab === | === Dry Lab === | ||
| + | |||
| + | ==== General ==== | ||
One big question: is the stop codon in the scar a problem in linking a tag and a protein coding region? The BioBricks of [http://partsregistry.org/wiki/index.php?title=Part:BBa_I712043 Ljubljana] prove not, but is this correct? | One big question: is the stop codon in the scar a problem in linking a tag and a protein coding region? The BioBricks of [http://partsregistry.org/wiki/index.php?title=Part:BBa_I712043 Ljubljana] prove not, but is this correct? | ||
| - | == Modeling == | + | ==== Modeling ==== |
| - | Modeling wiki has been updated, [[Team:KULeuven/Model/Output | Output]], [[Team:KULeuven/Model/Cell_Death | Cell Death]], [[Team:KULeuven/Model/Inverter | Inverter]], [[Team:KULeuven/Model/Memory | Memory]], [[Team:KULeuven/Model/Filter | Filter]], [[Team:KULeuven/Model/Pulse_Generator | Pulse Generator]](still need | + | Modeling wiki has been updated, [[Team:KULeuven/Model/Output | Output]], [[Team:KULeuven/Model/Cell_Death | Cell Death]], [[Team:KULeuven/Model/Inverter | Inverter]], [[Team:KULeuven/Model/Memory | Memory]], [[Team:KULeuven/Model/Filter | Filter]], [[Team:KULeuven/Model/Pulse_Generator | Pulse Generator]] have been revised (they still need a parameter check though), graphs of both CellDesigner and Matlab were added. We made a pdf file containing the ODE equations and other stuff. |
| - | I'm affraid we will have to come back on our decision to simply remove the | + | I'm affraid we will have to come back on our decision to simply remove the pulse generator and put the lactonase production after the filter. The problem is that the key-lock system is so leaky that there is a continuous lactonase production. Even when this production is very small (low efficiency of rbs for lactonase), an equilibrium will be achieved between lactonase, HSL --> HSL_LuxR-complex and LuxR. The result is a constant amount of LuxR which is still large enough to repress the production of ccdB, so we can never achieve cell death! Tomorrow we will have to take another look at our pulse generator and see what this component can add to the system. |
| - | + | Downside: not all the parameters have been found yet (and Jonas is absent). | |
Latest revision as of 13:05, 7 October 2008
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Contents |
Lab Work
Wet Lab
Stefanie and Hanne prepared liquid cultures of the plates with the cells we received from iGEM. We also started on the glycerol stock. Tomorrow we'll continue to make a glycerol stock of all the parts.
Elke, Nathalie and Jan started with cutting and pasting to test the output. We miniprepped [http://partsregistry.org/Part:BBa_R0084 R0084], [http://partsregistry.org/Part:BBa_B0032 B0032], [http://partsregistry.org/Part:BBa_E0022 E0022] and [http://partsregistry.org/Part:BBa_B0015 B0015], checked their concentration, made the right digest and separated them on gel. Only [http://partsregistry.org/Part:BBa_B0032 B0032] and [http://partsregistry.org/Part:BBa_E0022 E0022] were cut by the enzymes and the correct pieces could be cut out for the ligation.
Dry Lab
General
One big question: is the stop codon in the scar a problem in linking a tag and a protein coding region? The BioBricks of [http://partsregistry.org/wiki/index.php?title=Part:BBa_I712043 Ljubljana] prove not, but is this correct?
Modeling
Modeling wiki has been updated, Output, Cell Death, Inverter, Memory, Filter, Pulse Generator have been revised (they still need a parameter check though), graphs of both CellDesigner and Matlab were added. We made a pdf file containing the ODE equations and other stuff.
I'm affraid we will have to come back on our decision to simply remove the pulse generator and put the lactonase production after the filter. The problem is that the key-lock system is so leaky that there is a continuous lactonase production. Even when this production is very small (low efficiency of rbs for lactonase), an equilibrium will be achieved between lactonase, HSL --> HSL_LuxR-complex and LuxR. The result is a constant amount of LuxR which is still large enough to repress the production of ccdB, so we can never achieve cell death! Tomorrow we will have to take another look at our pulse generator and see what this component can add to the system.
Downside: not all the parameters have been found yet (and Jonas is absent).
