Team:KULeuven/5 September 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 9: / Line 9: @@
 We had a very happy day in the lab today and this is what we did:
-* We put the digests of R0011+B0033, K145001+B0015, K145150 and K145013 on gel. They seemed OK and so we extracted them out of the gel.
+* 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  -> R0053+P0152, R0040+B0033, R0040+J23066, B0014+B0033 and R1052. </div> <div style="margin-left:10px;"> cut with XbaI  -> R0040+E0240, C0061+B0015 and C0056+B0015. </div>
+* 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 (C0040+B0014, C0060+B0015, C0012+B0015, K145015+B0015, K145151+B0015 and R0040+E0240).
+* 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: K145150+pSB1A2, K145150+E0240, K145150+B0034, K145013+pSB1A2 and (B0014+B0033)+(K145151+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).
@@ Line 21: / Line 21: @@
-Final Scheme so far:
+Final Schemes so far:
-[[Image:5sept final.PNG|center|700px]]
+[[Image:5sept final.PNG|left|thumb|370px]]
+[[Image:5sept parallel.PNG|right|thumb|385px]]
-Parallel Scheme so far:
-[[Image:5sept parallel.PNG|center|700px]]
-NOT THAT MUCH MORE PARTS TO FINISH!!!!
 === Dry Lab ===