Team:KULeuven/11 August 2008

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Latest revision as of 12:17, 11 October 2008

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Lab Work

Wet Lab

We did a PCR on the following ligations: [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]. [http://partsregistry.org/Part:BBa_R0084 R0084]+[http://partsregistry.org/Part:BBa_B0032 B0032] did not give any colonies. This is the second time. Tomorrow we are going to ligate these parts again.

We continued to construct the T7 polymerase with UmuD tag using PCR. We used the gel extract of the first PCR as a template and 1077/1079 as primers. However, it failed. After we loaded the PCR product on gel, we could only see a smear.

We electroporated 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].

We miniprepped the liquid cultures we made last week. After that, we cut [http://partsregistry.org/Part:BBa_C0060 C0060], [http://partsregistry.org/Part:BBa_C0062 C0062], [http://partsregistry.org/Part:BBa_R0040 R0040] with EcoRI and SpeI. [http://partsregistry.org/Part:BBa_F1610 F1610] was cut with EcoRI and [http://partsregistry.org/Part:BBa_B0032 B0032] was cut with XbaI.

Dry Lab

Modeling

DAY OF THE MODEL REVIEW

We found a small (but important) mistake in our model: the efficiency of the rbs for the translation of LacI was set to only 0.05 while all the other efficienties of the rbs that are incorporated in the lock3d were put on 0.167. This makes a serious difference in the final result and not in a good way: the amount of produced LuxI (and following HSL/HSL_LuxR-complex) is reduced a lot! We we're able to slightly repair this new fact by increasing the efficiency of the rbs of translation of LuxI to maximal, but this doesn't completely fix the problem. It only results in the formation of 2 to 3 molecules of ccdB in the cell which might not be lethal enough...

It seems there's been quite a big misunderstanding between mathematical modellers and biochemical modellers which has resulted in yet another mistake in the model. This time it might be more severe, because after a fast repair, the preliminary results indicate that the timer-capabilities have completely vanished...

Let's hope that the night will bring some good idea's!

Wiki

Commenced building the Homepage (in the Zandbak), primary concern is whether lending the style of the KULeuven homepage is allowed, keeping in mind the conflict we had with the logo before. We have our own custom made Google searchbox that searches through the KULeuven wiki pages.

Quote of the day

“It is better to be roughly right than precisely wrong” - [J.M. Keynes]

Remarks

Multicroc is gesloten tot 27 aug!

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+{{:Team:KULeuven/Tools/Styling}}
+{{:Team:KULeuven/Tools/Header}}
 {{:Team:KULeuven/Tools/New_Day/Date_Retriever}}
@@ Line 4: / Line 7: @@
 === Wet Lab ===
+We did a PCR on the following ligations: [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]. [http://partsregistry.org/Part:BBa_R0084 R0084]+[http://partsregistry.org/Part:BBa_B0032 B0032] did not give any colonies. This is the second time. Tomorrow we are going to ligate these parts again.
+We continued to construct the T7 polymerase with UmuD tag using PCR. We used the gel extract of the first PCR as a template and 1077/1079 as primers. However, it failed. After we loaded the PCR product on gel, we could only see a smear.
+We electroporated 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].
+We miniprepped the liquid cultures we made last week. After that, we cut [http://partsregistry.org/Part:BBa_C0060 C0060], [http://partsregistry.org/Part:BBa_C0062 C0062], [http://partsregistry.org/Part:BBa_R0040 R0040] with ''Eco''RI and ''Spe''I. [http://partsregistry.org/Part:BBa_F1610 F1610] was cut with ''Eco''RI and [http://partsregistry.org/Part:BBa_B0032 B0032] was cut with ''Xba''I.
 === Dry Lab ===
-== Modeling ==
+==== Modeling ====
+DAY OF THE MODEL REVIEW
+We found a small (but important) mistake in our model: the efficiency of the rbs for the translation of LacI was set to only 0.05 while all the other efficienties of the rbs that are incorporated in the lock3d were put on 0.167. This makes a serious difference in the final result and not in a good way: the amount of produced LuxI (and following HSL/HSL_LuxR-complex) is reduced a lot! We we're able to slightly repair this new fact by increasing the efficiency of the rbs of translation of LuxI to maximal, but this doesn't completely fix the problem. It only results in the formation of 2 to 3 molecules of ccdB in the cell which might not be lethal enough...
+It seems there's been quite a big misunderstanding between mathematical modellers and biochemical modellers which has resulted in yet another mistake in the model. This time it might be more severe, because after a fast repair, the preliminary results indicate that the timer-capabilities have completely vanished...
+Let's hope that the night will bring some good idea's!
-We found a small (but important) mistake in our model: the efficiency of the rbs for the translation of LacI was set to ony 0.05 while all the other efficienties of the rbs that are incorporated in the lock3d were put on 0.167. This makes a serious difference in the final result and not in a good way: the amount of produced LuxI (and following HSL/HSL_LuxR-complex) is reduced a lot! We we're able to slightly repair this new fact by increasing the efficiency of the rbs of translation of LuxI to maximal, but this doesn't completely fix the problem. It only results in the formation of 2 to 3 molecules of ccdB in the cell which might not be lethal enough...
+==== Wiki ====
-== Wiki ==
+Commenced building the Homepage (in the Zandbak), primary concern is whether lending the style of the KULeuven homepage is allowed, keeping in mind the conflict we had with the logo before. We have our own custom made Google searchbox that searches through the KULeuven wiki pages.
 == Quote of the day ==