Team:KULeuven/30 July 2008

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Latest revision as of 13:09, 7 October 2008

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Lab Work

Wet Lab

Letting XbaI doing its job during the night, gave a positive outcome. These parts ([http://partsregistry.org/Part:BBa_J23032 J23032] and [http://partsregistry.org/Part:BBa_B0015 B0015]) were then cut with EcoRI, separated on gel and purified. Now that we had some useful digests, we could start some ligations: [http://partsregistry.org/Part:BBa_C0040 C0040]+[http://partsregistry.org/Part:BBa_B0015 B0015], [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] and [http://partsregistry.org/Part:BBa_E0022 E0022]+[http://partsregistry.org/Part:BBa_B0015 B0015]. After the previous success of the overnight digest with XbaI, we made some new ones: [http://partsregistry.org/Part:BBa_J23032 J23032], [http://partsregistry.org/Part:BBa_B0015 B0015], [http://partsregistry.org/Part:BBa_J23022 J23022], [http://partsregistry.org/Part:BBa_B0032 B0032] and [http://partsregistry.org/Part:BBa_F1610 F1610].

The digest of [http://partsregistry.org/Part:BBa_R0084 R0084]+[http://partsregistry.org/Part:BBa_B0032 B0032] with EcoRI and SpeI was loaded on a gel, but no fragment of 145bp was observed. This means that the ligation probably failed.

We punched out the DNA of the new memory and checked the concentration with the nanodrop. Despite the doubtful results we did try to electroporate these parts into Top10 cells.

In the evening we prepared some liquid cultures of the following parts: [http://partsregistry.org/Part:BBa_C0062 C0062], [http://partsregistry.org/Part:BBa_R0062 R0062], [http://partsregistry.org/Part:BBa_P1010 P1010], [http://partsregistry.org/Part:BBa_R0011 R0011], [http://partsregistry.org/Part:BBa_C0060 C0060], [http://partsregistry.org/Part:BBa_I712022 I712022], [http://partsregistry.org/Part:BBa_C0012 C0012], [http://partsregistry.org/Part:BBa_B0015 B0015] and [http://partsregistry.org/Part:BBa_F1610 F1610]. They will be miniprepped and digested tomorrow.

Dry Lab

General

Tomorrow, primers for checking the EnvZ::KmR mutation will be completed with the help of Sigrid. The Restriction Cut Sites seems not be in the same place as indicated in the Japanese paper.

Modeling

All the CellDesigner and Matlab models as the model pictures are updated. Everything is now ready for some extra simulations and a sensitivity analysis for the different models...

Wiki

We worked further on the detailed descriptions of the project. More attention will go to figures and easy reading.

New drop-down navigation bar has been posted, allowing subsubmenu's that toggle. Hacks have been added to conform with the most important browsers (IE, Mozilla, Safari). If any trouble occur, mail me (avdmeers).

Some bugs have been fixed in notebook.

Started making div stuff for homepage in case Imperial College's style is wanted.

Remarks

Tippenvulwedstrijd:
Hanne: 1'36"
Maarten: 1'42"
Stefanie: 1'49"

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 === Wet Lab ===
-*Letting ''Xba''I doing its job during the night, gave a positive outcome. These parts (B0015, J23032) were then cut with ''Eco''RI, separated on gel and purified. The following ligations were made: C0040+B0015, J23109+J23032, I712074+J23032, E0022+B0015.
+Letting ''Xba''I doing its job during the night, gave a positive outcome. These parts ([http://partsregistry.org/Part:BBa_J23032 J23032] and [http://partsregistry.org/Part:BBa_B0015 B0015]) were then cut with ''Eco''RI, separated on gel and purified. Now that we had some useful digests, we could start some ligations: [http://partsregistry.org/Part:BBa_C0040 C0040]+[http://partsregistry.org/Part:BBa_B0015 B0015], [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] and [http://partsregistry.org/Part:BBa_E0022 E0022]+[http://partsregistry.org/Part:BBa_B0015 B0015]. After the previous success of the overnight digest with ''Xba''I, we made some new ones: [http://partsregistry.org/Part:BBa_J23032 J23032], [http://partsregistry.org/Part:BBa_B0015 B0015], [http://partsregistry.org/Part:BBa_J23022 J23022], [http://partsregistry.org/Part:BBa_B0032 B0032] and [http://partsregistry.org/Part:BBa_F1610 F1610].
-*R0084 + B0032 were separated on a gel, but there was no fragment of 145bp was obeserved => so no ligation
-*Fluid cultures were prepared with the following parts: C0062, R0062, P1010, R0011, C0060, I712022.
+The digest of [http://partsregistry.org/Part:BBa_R0084 R0084]+[http://partsregistry.org/Part:BBa_B0032 B0032] with ''Eco''RI and ''Spe''I was loaded on a gel, but no fragment of 145bp was observed. This means that the ligation probably failed.
-*New digests with ''Xba''I were made with: B0015, B0032, J23022, J23032.
+We punched out the DNA of the new memory and checked the concentration with the nanodrop. Despite the doubtful results we did try to electroporate these parts into Top10 cells.
+In the evening we prepared some liquid cultures of the following parts: [http://partsregistry.org/Part:BBa_C0062 C0062], [http://partsregistry.org/Part:BBa_R0062 R0062], [http://partsregistry.org/Part:BBa_P1010 P1010], [http://partsregistry.org/Part:BBa_R0011 R0011], [http://partsregistry.org/Part:BBa_C0060 C0060], [http://partsregistry.org/Part:BBa_I712022 I712022], [http://partsregistry.org/Part:BBa_C0012 C0012], [http://partsregistry.org/Part:BBa_B0015 B0015] and [http://partsregistry.org/Part:BBa_F1610 F1610]. They will be miniprepped and digested tomorrow.
 === Dry Lab ===
-I worked further on the detailed descriptions of the project. More attention will go to figures and easy reading.
-Tomorrow, primers for checking the EnvZ::KmR mutation will be completed with the help of Sigrid. The Restriction Cut Sites seem not be on the same place as indicated in the Japanese paper.
+==== General ====
-== Modeling ==
+Tomorrow, primers for checking the EnvZ::KmR mutation will be completed with the help of Sigrid. The Restriction Cut Sites seems not be in the same place as indicated in the Japanese paper.
+==== Modeling ====
 All the CellDesigner and Matlab models as the model pictures are updated. Everything is now ready for some extra simulations and a sensitivity analysis for the different models...
-== Wiki ==
+==== Wiki ====
+We worked further on the detailed descriptions of the project. More attention will go to figures and easy reading.
 New drop-down navigation bar has been posted, allowing subsubmenu's that toggle. Hacks have been added to conform with the most important browsers (IE, Mozilla, Safari). If any trouble occur, mail me (avdmeers).