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Team:Groningen/Notebook
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| + | =='''Starting up'''== | ||
| + | In March we started with brainstorms once a week. During these metings we decided on a project. We had a lot of different ideas. In May we decided to focus on three of the ideas we had: | ||
| + | *Using flagellar rotation of Bacteria to make a pump of liquid inside a tube. | ||
| + | *Making ''E. coli'' have a memory of events, like light inputs. | ||
| + | *Make a cellular automata in ''E. coli'' for instance ''Conway`s game of life''. | ||
| - | + | The first idea was hard to make in the 2 or 3 months we had. Here we needed to have bacteria attach to a surface and also have the same orientation in order to have the movement of liquid in the same direction. This topic would probably take us longer than 3 months, so we decided not to move on with it. | |
| + | For the memory idea we wanted the ''E. coli'' insert a small piece of DNA into a plasmid after it got an input. There is a phage system which put an insert inside a certain code in the DNA. However the problem is that we need bacteria to have all just 1 insert at the same time. Moreover we wanted more than one input behind eachother and the bacteria getting inputs in the same order inside a plasmid. This last is probably really hard to obtain, and not possible in the amount of time we have. | ||
| + | The last idea, making a cellular automata seemed to be our best option, since we really like to make a system inside ''E. coli'' and have a nice object to model. | ||
| + | =='''Making the system'''== | ||
| - | '' | + | =='''The labwork'''== |
| + | '''The parts''' | ||
| + | In June we started to transform ''E. coli's'' with the parts. We used the strain DH5alpha, since these we already present at the university. However, we obtained hardly any colony's. We solved this problem by using Invitrogen's Top10 competent cells and making Top10 cells competent ourselves. Still we didn't have a lot of colony's, but we obtained quite some parts. The last parts we really needed for the system, were requested from iGEM HQ. | ||
| + | |||
| + | '''Cloning the parts together''' | ||
| + | |||
| + | Parts were assembled according to the [http://partsregistry.org/Assembly:Standard_assembly <font color=#dd0000>Standard Assembly from the parts registry</font color>] site. When we had to assemble a small part to a big part, the big part was ligated into the vector containing the small part. | ||
| + | |||
| + | '''Media''' | ||
| + | |||
| + | For testing how HSL could diffuse trough the media we wanted to use two parts, [http://partsregistry.org/Part:BBa_F1610 <font color=#dd0000>BBa_F1610</font color>] as sender device and [http://partsregistry.org/Part:BBa_T9002 <font color=#dd0000>BBa_T9002</font color>] as receiver device. Unfortunately the sender device from the registry seems to be wrong (Restriction / PCR /Sequence analysis confirms this), therefor we used the sender device from the Ron Weiss group. In TY browth medium we observed really high GFP background from part [http://partsregistry.org/Part:BBa_T9002 <font color=#dd0000>BBa_T9002</font color>] even without induction. By using [http://openwetware.org/wiki/Neidhardt_EZ_Rich_Defined EZ rich defined medium] the background was reduced. For further measurements we decided to use EZ medium. | ||
| + | |||
| + | =='''The model'''== | ||
| - | |||
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Latest revision as of 12:10, 16 September 2008
Starting up
In March we started with brainstorms once a week. During these metings we decided on a project. We had a lot of different ideas. In May we decided to focus on three of the ideas we had:
- Using flagellar rotation of Bacteria to make a pump of liquid inside a tube.
- Making E. coli have a memory of events, like light inputs.
- Make a cellular automata in E. coli for instance Conway`s game of life.
The first idea was hard to make in the 2 or 3 months we had. Here we needed to have bacteria attach to a surface and also have the same orientation in order to have the movement of liquid in the same direction. This topic would probably take us longer than 3 months, so we decided not to move on with it.
For the memory idea we wanted the E. coli insert a small piece of DNA into a plasmid after it got an input. There is a phage system which put an insert inside a certain code in the DNA. However the problem is that we need bacteria to have all just 1 insert at the same time. Moreover we wanted more than one input behind eachother and the bacteria getting inputs in the same order inside a plasmid. This last is probably really hard to obtain, and not possible in the amount of time we have.
The last idea, making a cellular automata seemed to be our best option, since we really like to make a system inside E. coli and have a nice object to model.
Making the system
The labwork
The parts
In June we started to transform E. coli's with the parts. We used the strain DH5alpha, since these we already present at the university. However, we obtained hardly any colony's. We solved this problem by using Invitrogen's Top10 competent cells and making Top10 cells competent ourselves. Still we didn't have a lot of colony's, but we obtained quite some parts. The last parts we really needed for the system, were requested from iGEM HQ.
Cloning the parts together
Parts were assembled according to the [http://partsregistry.org/Assembly:Standard_assembly Standard Assembly from the parts registry] site. When we had to assemble a small part to a big part, the big part was ligated into the vector containing the small part.
Media
For testing how HSL could diffuse trough the media we wanted to use two parts, [http://partsregistry.org/Part:BBa_F1610 BBa_F1610] as sender device and [http://partsregistry.org/Part:BBa_T9002 BBa_T9002] as receiver device. Unfortunately the sender device from the registry seems to be wrong (Restriction / PCR /Sequence analysis confirms this), therefor we used the sender device from the Ron Weiss group. In TY browth medium we observed really high GFP background from part [http://partsregistry.org/Part:BBa_T9002 BBa_T9002] even without induction. By using [http://openwetware.org/wiki/Neidhardt_EZ_Rich_Defined EZ rich defined medium] the background was reduced. For further measurements we decided to use EZ medium.
The model
