Team:KULeuven/5 September 2008

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Latest revision as of 01:35, 30 October 2008

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Lab Work

Wet Lab

We had a very happy day in the lab today and this is what we did:

We put the digests of [http://partsregistry.org/Part:BBa_R0011 R0011]+[http://partsregistry.org/Part:BBa_B0033 B0033], [http://partsregistry.org/Part:BBa_K145001 K145001]+[http://partsregistry.org/Part:BBa_B0015 B0015], [http://partsregistry.org/Part:BBa_K145150 K145150] and [http://partsregistry.org/Part:BBa_K145013 K145013] on gel. They seemed OK and so we extracted them out of the gel.
We made a miniprep and digest of the following parts:
cut with EcoRI and SpeI -> [http://partsregistry.org/Part:BBa_R0040 R0040]+[http://partsregistry.org/Part:BBa_B0033 B0033], [http://partsregistry.org/Part:BBa_B0014 B0014]+[http://partsregistry.org/Part:BBa_B0033 B0033], [http://partsregistry.org/Part:BBa_R0053 R0053]+[http://partsregistry.org/Part:BBa_P0152 P0152], [http://partsregistry.org/Part:BBa_R0040 R0040]+[http://partsregistry.org/Part:BBa_J23066 J23066] and [http://partsregistry.org/Part:BBa_R1052 R1052].

cut with XbaI -> [http://partsregistry.org/Part:BBa_R0040 R0040]+[http://partsregistry.org/Part:BBa_E0240 E0240], [http://partsregistry.org/Part:BBa_C0056 C0056]+[http://partsregistry.org/Part:BBa_B0015 B0015] and [http://partsregistry.org/Part:BBa_C0061 C0061]+[http://partsregistry.org/Part:BBa_B0015 B0015].
We made a glycerolstock of the ligations that have suceeded so far [http://partsregistry.org/Part:BBa_C0040 C0040]+[http://partsregistry.org/Part:BBa_B0015 B0015], [http://partsregistry.org/Part:BBa_C0060 C0060]+[http://partsregistry.org/Part:BBa_B0015 B0015], [http://partsregistry.org/Part:BBa_C0012 C0012]+[http://partsregistry.org/Part:BBa_B0015 B0015], [http://partsregistry.org/Part:BBa_K145015 K145015]+[http://partsregistry.org/Part:BBa_B0015 B0015], [http://partsregistry.org/Part:BBa_R0040 R0040]+[http://partsregistry.org/Part:BBa_E0240 E0240], [http://partsregistry.org/Part:BBa_K145151 K145151]+[http://partsregistry.org/Part:BBa_B0015 B0015].
We set up the following ligations: [http://partsregistry.org/Part:BBa_K145150 K145150]+[http://partsregistry.org/Part:pSB1A2 pSB1A2], [http://partsregistry.org/Part:BBa_K145150 K145150]+[http://partsregistry.org/Part:BBa_E0240 E0240], [http://partsregistry.org/Part:BBa_K145150 K145150]+[http://partsregistry.org/Part:BBa_B0034 B0034], [http://partsregistry.org/Part:BBa_K145013 K145013]+[http://partsregistry.org/Part:pSB1A2 pSB1A2] and (B0014+B0033)+(K145151+B0015).
Unfortunately, there were also some failures. The PCR for T7 polymerase with UmuD tag failed again. The result of the PCR test of the transduction was also a bit dodgy and the digest of R1052 resulted in a smear (but apparently it is a crappy part). A final attempt to construct T7 polymerase with UmuD tag was started (PCR).

But the most exciting thing today, were our flourescent colonies! We constructed two OUTPUT-subsystems containing GFP with and without LVA tag, as can be seen in this picture. On the left side GFP with LVA tag (our part K145015): less fluorescent. On the right side GFP without LVA tag (part E0240): more fluorescent. This means that our output and GFP-LVA work - hurrah!

Final Schemes so far:

Dry Lab

Dr. Coli and his danger, ethics, ethics, ethics...

Modeling

SimBiology2Latex Toolbox has been finalized and can be found on the wiki.

MultiCell Toolbox has entered it's final design stages. A preview of the GUI can be found on the wiki.

Some more work on diffusion has been done. Sensitivity Analyses is still a pain in the ***.

Wiki

Homepage has been revamped, removing a lot of bugs. IE fixes still need to follow. Components bar has been fixed.

@@ Line 1: / Line 1: @@
+{{:Team:KULeuven/Tools/Styling}}
 {{:Team:KULeuven/Tools/Header}}
+{{:Team:KULeuven/Tools/New_Day/Date_Retriever}}
 == Lab Work ==
@@ Line 5: / Line 8: @@
 === Wet Lab ===
-Succes in the Wet Lab: we constructed the OUTPUT-subsystem with GFP with and without LVA-tag, as can be seen in this picture. On the left side GFP with LVA tag (our part K145015): less fluorescent. On the right side GFP without LVA tag (part E0042): more fluorescent.
+We had a very happy day in the lab today and this is what we did:
+* We put the digests of [http://partsregistry.org/Part:BBa_R0011 R0011]+[http://partsregistry.org/Part:BBa_B0033 B0033], [http://partsregistry.org/Part:BBa_K145001 K145001]+[http://partsregistry.org/Part:BBa_B0015 B0015], [http://partsregistry.org/Part:BBa_K145150 K145150] and [http://partsregistry.org/Part:BBa_K145013 K145013] on gel. They seemed OK and so we extracted them out of the gel.
+* We made a miniprep and digest of the following parts: <div style="margin-left:10px;"> cut with ''Eco''RI and ''Spe''I  -> [http://partsregistry.org/Part:BBa_R0040 R0040]+[http://partsregistry.org/Part:BBa_B0033 B0033], [http://partsregistry.org/Part:BBa_B0014 B0014]+[http://partsregistry.org/Part:BBa_B0033 B0033], [http://partsregistry.org/Part:BBa_R0053 R0053]+[http://partsregistry.org/Part:BBa_P0152 P0152],  [http://partsregistry.org/Part:BBa_R0040 R0040]+[http://partsregistry.org/Part:BBa_J23066 J23066] and [http://partsregistry.org/Part:BBa_R1052 R1052]. </div> <div style="margin-left:10px;"> cut with XbaI  -> [http://partsregistry.org/Part:BBa_R0040 R0040]+[http://partsregistry.org/Part:BBa_E0240 E0240], [http://partsregistry.org/Part:BBa_C0056 C0056]+[http://partsregistry.org/Part:BBa_B0015 B0015] and [http://partsregistry.org/Part:BBa_C0061 C0061]+[http://partsregistry.org/Part:BBa_B0015 B0015]. </div>
+* We made a glycerolstock of the ligations that have suceeded so far [http://partsregistry.org/Part:BBa_C0040 C0040]+[http://partsregistry.org/Part:BBa_B0015 B0015], [http://partsregistry.org/Part:BBa_C0060 C0060]+[http://partsregistry.org/Part:BBa_B0015 B0015], [http://partsregistry.org/Part:BBa_C0012 C0012]+[http://partsregistry.org/Part:BBa_B0015 B0015], [http://partsregistry.org/Part:BBa_K145015 K145015]+[http://partsregistry.org/Part:BBa_B0015 B0015], [http://partsregistry.org/Part:BBa_R0040 R0040]+[http://partsregistry.org/Part:BBa_E0240 E0240], [http://partsregistry.org/Part:BBa_K145151 K145151]+[http://partsregistry.org/Part:BBa_B0015 B0015].
+* We set up the following ligations: [http://partsregistry.org/Part:BBa_K145150 K145150]+[http://partsregistry.org/Part:pSB1A2 pSB1A2], [http://partsregistry.org/Part:BBa_K145150 K145150]+[http://partsregistry.org/Part:BBa_E0240 E0240], [http://partsregistry.org/Part:BBa_K145150 K145150]+[http://partsregistry.org/Part:BBa_B0034 B0034], [http://partsregistry.org/Part:BBa_K145013 K145013]+[http://partsregistry.org/Part:pSB1A2 pSB1A2] and (B0014+B0033)+(K145151+B0015).
+* Unfortunately, there were also some failures. The PCR for T7 polymerase with UmuD tag failed again. The result of the PCR test of the transduction was also a bit dodgy and the digest of R1052 resulted in a smear (but apparently it is a crappy part). A final attempt to construct T7 polymerase with UmuD tag was started (PCR).
+But the most exciting thing today, were our flourescent colonies! We constructed two OUTPUT-subsystems containing GFP with and without LVA tag, as can be seen in this picture. On the left side GFP with LVA tag (our part K145015): less fluorescent. On the right side GFP without LVA tag (part E0240): more fluorescent. This means that our output and GFP-LVA work - hurrah!
 [[Image:DSC02957.JPG|center|800px]]
-Final Scheme till so far:
-[[Image:5sept final.PNG|center|700px]]
-Parallel Scheme till so far:
+Final Schemes so far:
-[[Image:5sept parallel.PNG|center|700px]]
+[[Image:5sept final.PNG|left|thumb|370px]]
+[[Image:5sept parallel.PNG|right|thumb|385px]]
+<br>
-NOT THAT MUCH MORE PARTS TO FINISH!!!!
-* We MiniPrepped a few ligations and part R1052.
-* We continued the digestion of K145001+B0015 and put R0011+B0032, K145150, K145013 on gel.
-* We digested some more parts (R0053+P0152, R0040+B0033, R0040+J23066, B0014+B0033, R1052 with ''Eco''RI and ''Spe''I; C0061+B0015, C0056+B0015, R0040+E0240 with ''Xba''I). Only R1052 didn't cut well.
-* A glycerolstock was made of successful ligations: C0012+B0015, C0060+B0015, C0040+B0015, R0040+E0240 and xxx
-* The PCR we did yesterday (transduction and T7) was put on gel, but they both were not correct.
-* We tried again to do a PCR of the T7 polymerase with UmuD tag.
-* We set up some more ligations: K145150+pSB1A2, 145150+E0240, K145150+B0034, K145013+pSB1A2, B0014+B0033+K145151+B0015
 === Dry Lab ===
@@ Line 43: / Line 44: @@
 Homepage has been revamped, removing a lot of bugs. IE fixes still need to follow. Components bar has been fixed.
-== Remarks ==
-== Strip of the day ==
-{{:Team:KULeuven/Tools/New_Day/Date_Retriever}}