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Team:KULeuven/13 August 2008
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=== Wet Lab === | === Wet Lab === | ||
| - | + | We tested the ligations (using PCR and gel electrophoresis) of the following parts: [http://partsregistry.org/Part:BBa_J23109 J23109]+[http://partsregistry.org/Part:BBa_J23032 J23032], [http://partsregistry.org/Part:BBa_I712074 I712074]+[http://partsregistry.org/Part:BBa_J23032 J23032], [http://partsregistry.org/Part:BBa_K145015 K145015]+[http://partsregistry.org/Part:BBa_B0015 B0015], [http://partsregistry.org/Part:BBa_R0062 R0062]+[http://partsregistry.org/Part:BBa_B0032 B0032], [http://partsregistry.org/Part:BBa_R0084 R0084]+[http://partsregistry.org/Part:BBa_J23022 J23022] and [http://partsregistry.org/Part:BBa_C0012 C0012]+[http://partsregistry.org/Part:BBa_B0015 B0015]. They seemed to have been ligated properly. After that, we digested these ligations for the next step in the ligation process. | |
| - | + | ||
| - | + | We miniprepped the following parts: [http://partsregistry.org/Part:BBa_C0060 C0060]+[http://partsregistry.org/Part:BBa_B0015 B0015], [http://partsregistry.org/Part:BBa_C0040 C0040]+[http://partsregistry.org/Part:BBa_B0015 B0015] and [http://partsregistry.org/Part:BBa_J23100 J23100]+[http://partsregistry.org/Part:BBa_B0032 B0032]. They will be tested tomorrow. | |
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| + | We continued to make the T7 polymerase with UmuD tag. Therefore we used PCR in two steps. The first step worked, but the second one didn't. There might be something wrong with the primer (it was a very long one). | ||
=== Dry Lab === | === Dry Lab === | ||
| - | == Modeling == | + | ==== Modeling ==== |
We seem to be on a streak this week as we finally solved the T7 issue as T7 transcription rates have finally been estimated realistically. Things are looking up again in this haunted week :) | We seem to be on a streak this week as we finally solved the T7 issue as T7 transcription rates have finally been estimated realistically. Things are looking up again in this haunted week :) | ||
| - | Later however we encountered some weird stuff while simulating the entire system. Even without any light, the HSL-LuxR complex would still build up (extremely slow though) and would ultimately kill our cell. There appears to be a tiny flux of HSL through a tiny background amount of LuxI. The HSL produced quickly encounters LuxR transcription factors to which it binds. This binding protects the HSL from any background lactonase here (which has a much higher dissociation constant). When HSL does dissociate from the high affinity LuxR, either through degradation of the protein or through regular dissociation it will quickly be taken up again by another LuxR molecule because they're constantly produced due to the constitutive promoter. | + | Later, however, we encountered some weird stuff while simulating the entire system. Even without any light, the HSL-LuxR complex would still build up (extremely slow though) and would ultimately kill our cell. There appears to be a tiny flux of HSL through a tiny background amount of LuxI. The HSL produced quickly encounters LuxR transcription factors to which it binds. This binding protects the HSL from any background lactonase here (which has a much higher dissociation constant). When HSL does dissociate from the high affinity LuxR, either through degradation of the protein or through regular dissociation it will quickly be taken up again by another LuxR molecule because they're constantly produced due to the constitutive promoter. |
We solved this issue as well by putting the LuxR under a P22 c2 repressable promoter (= output of memory in OFF state) | We solved this issue as well by putting the LuxR under a P22 c2 repressable promoter (= output of memory in OFF state) | ||
At the end of the day we decided to try and put LuxR together with ccdB under control of the hybrid P22 c2 - LuxR promoter tomorrow. We'll see how the system behaves. Exciting ... ;) | At the end of the day we decided to try and put LuxR together with ccdB under control of the hybrid P22 c2 - LuxR promoter tomorrow. We'll see how the system behaves. Exciting ... ;) | ||
| - | == Wiki == | + | ==== Wiki ==== |
Dilbert is in tha house, wiki tabs plugin fixed for IE... finally. | Dilbert is in tha house, wiki tabs plugin fixed for IE... finally. | ||
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Latest revision as of 12:37, 11 October 2008
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Contents |
Lab Work
Wet Lab
We tested the ligations (using PCR and gel electrophoresis) of the following parts: [http://partsregistry.org/Part:BBa_J23109 J23109]+[http://partsregistry.org/Part:BBa_J23032 J23032], [http://partsregistry.org/Part:BBa_I712074 I712074]+[http://partsregistry.org/Part:BBa_J23032 J23032], [http://partsregistry.org/Part:BBa_K145015 K145015]+[http://partsregistry.org/Part:BBa_B0015 B0015], [http://partsregistry.org/Part:BBa_R0062 R0062]+[http://partsregistry.org/Part:BBa_B0032 B0032], [http://partsregistry.org/Part:BBa_R0084 R0084]+[http://partsregistry.org/Part:BBa_J23022 J23022] and [http://partsregistry.org/Part:BBa_C0012 C0012]+[http://partsregistry.org/Part:BBa_B0015 B0015]. They seemed to have been ligated properly. After that, we digested these ligations for the next step in the ligation process.
We miniprepped the following parts: [http://partsregistry.org/Part:BBa_C0060 C0060]+[http://partsregistry.org/Part:BBa_B0015 B0015], [http://partsregistry.org/Part:BBa_C0040 C0040]+[http://partsregistry.org/Part:BBa_B0015 B0015] and [http://partsregistry.org/Part:BBa_J23100 J23100]+[http://partsregistry.org/Part:BBa_B0032 B0032]. They will be tested tomorrow.
We continued to make the T7 polymerase with UmuD tag. Therefore we used PCR in two steps. The first step worked, but the second one didn't. There might be something wrong with the primer (it was a very long one).
Dry Lab
Modeling
We seem to be on a streak this week as we finally solved the T7 issue as T7 transcription rates have finally been estimated realistically. Things are looking up again in this haunted week :)
Later, however, we encountered some weird stuff while simulating the entire system. Even without any light, the HSL-LuxR complex would still build up (extremely slow though) and would ultimately kill our cell. There appears to be a tiny flux of HSL through a tiny background amount of LuxI. The HSL produced quickly encounters LuxR transcription factors to which it binds. This binding protects the HSL from any background lactonase here (which has a much higher dissociation constant). When HSL does dissociate from the high affinity LuxR, either through degradation of the protein or through regular dissociation it will quickly be taken up again by another LuxR molecule because they're constantly produced due to the constitutive promoter. We solved this issue as well by putting the LuxR under a P22 c2 repressable promoter (= output of memory in OFF state)
At the end of the day we decided to try and put LuxR together with ccdB under control of the hybrid P22 c2 - LuxR promoter tomorrow. We'll see how the system behaves. Exciting ... ;)
Wiki
Dilbert is in tha house, wiki tabs plugin fixed for IE... finally.
