Team:Bonn/Notebook

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Lab Notebook

This is an overview on what we did in our lab, including our standard lab protocols.

Summary

Our lab work started in May and after a few first successful transformations we came across our greatest issue: all our experiments with the LOVTAP plasmid from the distribution failed. A long time of troubleshooting followed since LOV is our main component. Finally, we switched to a non-BioBrick LOV with two PstI sites instead of using the distribution. Our work with the other parts could be resumed and we finished the final ligation for the LOV-ccdB and Lov-LacZalpha fusion constructs. But we could not remove the two PstI restriction sites. Additionally we removed one PstI restriction site from the single LOV domain for the fusion system.

LOVTAP

We used 2 month for the troubleshooting of our LOVTAP sample from the distribution plate. The first experiments with our LOVTAP plasmid were misinterpreted. We thought our problems lay in the restrictions, PCR or our transformation. In fact, restriction and transformation worked well with all the other plasmids. We also sent out the plasmid for sequencing. We could not get sequencing results matching any part of the LOVTAP plasmid at all but had a contamination with another sequence. Finally we asked two other German iGEM teams (LMU Munich and Darmstadt) for a sample of their distribution plate LOVTAP. This samples did not lead to good sequencing results either and showed the same pattern of degeneration. In the end we used LOVTAP-pCal-n (modified) instead of the Biobrick.

Highlights by date

May 2012

23.05.

Starting our lab work with creating chemo-competent DH5α bacteria.

31.05.

First successful transformation of iGEM plasmids (pLac, Lac1, LOVTap, J23119, LacZα, ccdB, RBS32 and the double terminator). XL1-blue bacteria turned out to be much more competent than our DH5α, so we used these from now on.

June 2012

04.06.

Midi-Preps of iGEM plasmids from our distribution kit.

06.06. - 08.06.

First restrictions, some of them were successful.

08.06. - 03.07.

PCR, transformation and restriction troubleshooting to find the issue in our LOVTAP transformation.

July 2012

04.07.

Sequencing results of all our biobricks are available: Sequence is okay for RBS32, LacZα, pLac and our double-terminator. A frameshift was found in LacI plasmid. LOVTAP was contaminated with another sequence.

later that month...

Further troubleshooting and optimization of our standard procedures.

August 2012

06.08.

First application of the 3A assembly, following the official iGEM protocol. (we used a different one before).

Restrictions of LacZalpha-pSB1AK3, ccdB-pSB1A2, TT-pSB1AK3, pSB1C3
Ligations to LacZalpha-TT-pSB1C3 and ccdB-TT-pSB1C3

Midi-Preparation of LOVTAP-pCal-n (wt) - we later used this construct for testing reasons only.

we got LOVTAP-pCal-n(wt) and LovTAP-pCal-n(mod) from the Sosnick Lab and used it instead of the BioBrick.

07.08.

Transformation of constructs prepared the day before.

08.08.

Restriction analysis of our first completed constructs: LacZα-TT-pSB1C3 and ccdB-TT-pSB1C3
Started work on constructs J23119-lacI-pSB1C3 and pLac-RBS32-pSB1K3

10.08.

Sequencing of our first constructs (LacZα-TT-pSB1C3 and ccdB-TT-pSB1C3) for verification.
First successful PCR of wildtype-LOV (test for future experiments)
Midi-Preps of LOVTAP-pCal-n (Mutant) and mazF-pBAD

16.08.

Work on constructs pLac-RBS32-ccdB-TT-pSB1A3 and pLac-RBS32-LacZα-TT-pSB1A3 started

21.08.

Successful PCR-amplification of mod-LOV

22.08. - 28.08.

First trial of ligation to form the new constructs pLac-RBS32-LOV-Ccdb-TT-pSB1C3 and pLac-RBS32-LOV-ccdB-TT-pSB1C3

29.08.

Gel-purification of the pSB1C3 fragment, which was cut with EcoRI and SpeI before, for usage in the pLac-RBS32-LOV-pSB1C3 construct.

23.08. - 28.08.

Creation/finalization of constructs J23119-LacI-pSB1C3 and J23119-LacI-pSBA3

September 2012

05.09. - 07.09.

Formation of construct pLac-RBS32-LOV-pSB1C3

06.09.

Successful PCR-amplification of mazF fragment
Constructs mazF-pSB1C3 and mazF-TT-pSB1C3 completed

10.09. - 11.09.

Succesful mutagenesis PCR: pLac-LOV-pSB1C3 and LOV-pSB1C3, first of two PCRs to make the LOV part BioBrick compliant

13.09. - 24.09.

New constructs:

pLac-RBS32-LOV-ccdB-TT-pSB1C3
pLac-RBS32-LOV-LacZalpha-TT-pSB1C3

Protocols

You can find the protocols we used at our protocols page

@@ Line 6: / Line 6: @@
 !align="center"|[[Team:Bonn/Team|<span style="color:#4f8dde;">Team]]
 !align="center"|[[Team:Bonn/Project|<span style="color:#4f8dde;">Project]]
-!align="center"|[[Team:Bonn/Activities|<span style="color:#4f8dde;">Activities]]
+!align="center"|[[Team:Bonn/Activities|<span style="color:#4f8dde;">Other Activities]]
 !align="center"|[[Team:Bonn/Parts|<span style="color:#4f8dde;">Parts Submitted to the Registry]]
 !align="center"|[[Team:Bonn/Notebook|<span style="color:#005186;">Notebook]]
@@ Line 20: / Line 20: @@
 == '''Lab Notebook''' ==
-A compilation over what we did in our lab, including the [[Team:Bonn/Protocols|standard protocols]] we used.
+This is an overview on what we did in our lab, including our [[Team:Bonn/Protocols|standard lab protocols]].
 === Summary ===
-Our lab work started in May and after the first successful transformations we came across our greatest issue: The LovTap of our distribution-kit isn't what it is supposed to be. A long time of troubleshooting followed as Lov is our main component. Finally, we switched to the wild-type Lov instead of using the BioBrick (which was broken for us and the teams who sent us samples of their Lov distribution-kit plasmids), which has two PstI cutting sites to be removed. Our work with the other parts could be resumed and we started the restrictions and ligations of our final constructs.
+Our lab work started in May and after a few first successful transformations we came across our greatest issue: all our experiments with the LOVTAP plasmid from the distribution failed. A long time of troubleshooting followed since LOV is our main component. Finally, we switched to a non-BioBrick LOV with two ''PstI'' sites instead of using the distribution. Our work with the other parts could be resumed and we finished the final ligation for the LOV-ccdB and Lov-LacZalpha fusion constructs. But we could not remove the two ''PstI'' restriction sites. Additionally we removed one ''PstI'' restriction site from the single LOV domain for the fusion system.
-=== Results ===
+=== LOVTAP ===
-'''Lov-Ccdb - Lov Kills''': Ccdb (gyrase inhibitor) induces cell-dead when released by Lov after activation with ~450nm light. For this project, we finished the constructs ''pLac-RBS32-Lov-Ccdb-TT-pSB1C3'', as effective part, and ''pLac-RBS32-LacZalpha-TT-pSB1C3'', our control vector.
+We used 2 month for the troubleshooting of our LOVTAP sample from the distribution plate.
+The first experiments with our LOVTAP plasmid were misinterpreted. We thought our problems lay in the restrictions, PCR or our transformation. In fact, restriction and transformation worked well with all the other plasmids. We also sent out the plasmid for sequencing. We could not get sequencing results matching any part of the LOVTAP plasmid at all but had a contamination with another sequence. Finally we asked two other German iGEM teams (LMU Munich and Darmstadt) for a sample of their distribution plate LOVTAP. This samples did not lead to good sequencing results either and showed the same pattern of degeneration.
-'''Lov-LacZα - Lov Blues:''' When treated with blue light, Lov releases a part of β-Galactosidase, which completes the enzyme (other parts are floating in the cytosol) and induces the conversion of X-Gal to a blue-coloured product. We finished the corresponding part ''pLac-RBS32-Lov-LacZalpha-TT-pSB1C3'' and the control vector ''pLac-RBS32-LacZalpha-TT-pSB1C3'' for this.
+In the end we used LOVTAP-pCal-n (modified) instead of the Biobrick.
-'''Lov-MazF - Lov Cuts:''' If activated through light, the nuclease MazF becomes active. For this aspect we created the parts ''MazF-pSB1C3'' and ''MazF-TT-pSB1C3''. The issue itself isn't completed at time.
-'''Fusion Kit:''' We created the following parts to create fusion proteins with Lov:
-Lov-pSB1C3 - with 1 PstI restriction site
-pLac-RBS32-LOV-pSB1C3 - with  1PstI restriction site
-All Lov samples we use still contain two PstI restriction sites inside the Lov. We are currently working on a mutagenesis PCR to remove them, but this issue hasn't been completed yet.
 === Highlights by date ===
@@ Line 44: / Line 36: @@
 ==== May 2012 ====
-===== 23.05 =====
+===== 23.05. =====
-Starting our lab work with preparing some media like SOB and SOC and creating chemo-competent DH5α bacteria.
+Starting our lab work with creating chemo-competent DH5α bacteria.
-===== 31.05 =====
+===== 31.05. =====
-First successful transformation of iGEM plasmids (pLac, Lac1, LovTap, J23119, LacZα, ccdB, RBS32 and the double terminator). XL1-blue bacteria turned out to be much more competent than our DH5α, so we used these from now on.
+First successful transformation of iGEM plasmids (pLac, Lac1, LOVTap, J23119, LacZα, ccdB, RBS32 and the double terminator). XL1-blue bacteria turned out to be much more competent than our DH5α, so we used these from now on.
 ==== June 2012 ====
-===== 04.06 =====
+===== 04.06. =====
 Midi-Preps of iGEM plasmids from our distribution kit.
-===== 06.06 - 08.06 =====
+===== 06.06. - 08.06. =====
-First restrictions, some of them were successful. The failure on our LovTAP plasmid was misinterpreted: We thought we had problems with the restriction, PCR or our transformation, but in fact the iGEM LOV biobrick was broken.
+First restrictions, some of them were successful.
-===== 08.06 - 03.07 =====
+===== 08.06. - 03.07. =====
-PCR, transformation and restriction troubleshooting to find the issue in our LovTAP transformation. All tests and modifications of our protocols failed for the LovTAP plasmid, but worked out with other biobricks and sample plasmids. So we finally send the LovTAP iGEM plasmid to a company for sequencing.
+PCR, transformation and restriction troubleshooting to find the issue in our LOVTAP transformation.
 ==== July 2012 ====
-===== 04.07 =====
+===== 04.07. =====
-Sequencing results of all our biobricks are available: Sequence is okay for RBS32, LacZα, pLac and our double-terminator. A frameshift was found in lacI plasmid.
+Sequencing results of all our biobricks are available: Sequence is okay for RBS32, LacZα, pLac and our double-terminator. A frameshift was found in LacI plasmid.
-LovTAP was contaminated with another sequence as the found sequence didn't match the desired one at all.
+LOVTAP was contaminated with another sequence.
-===== later this month... =====
-Further troubleshooting and optimization of our standard procedures. We also tried to figure out if only our distribution plate contained the broken LOV, so we asked other iGEM teams to provide us with samples from their plates. We did transformations and sequencing, but these LOV plasmids showed the same pattern of degeneration our LOV did.
+===== later that month... =====
+Further troubleshooting and optimization of our standard procedures.
 ==== August 2012 ====
-===== 06.08 =====
+===== 06.08. =====
 First application of the 3A assembly, following the official iGEM protocol. (we used a different one before).
 * Restrictions of LacZalpha-pSB1AK3, ccdB-pSB1A2, TT-pSB1AK3, pSB1C3
 * Ligations to LacZalpha-TT-pSB1C3 and ccdB-TT-pSB1C3
-Midi-Preparation of LovTAP-pCal-n (wt) - we later used this construct for testing reasons only.
+Midi-Preparation of LOVTAP-pCal-n (wt) - we later used this construct for testing reasons only.
+*we got LOVTAP-pCal-n(wt) and LovTAP-pCal-n(mod) from the Sosnick Lab and used it instead of the BioBrick.
-===== 07.08 =====
+===== 07.08. =====
 Transformation of constructs prepared the day before.
-===== 08.08 =====
+===== 08.08. =====
-* Restriction analysis of constructs LacZα-TT-pSB1C3 and ccdB-TT-pSB1C3
+* Restriction analysis of our first completed constructs: LacZα-TT-pSB1C3 and ccdB-TT-pSB1C3
 * Started work on constructs J23119-lacI-pSB1C3 and pLac-RBS32-pSB1K3
-===== 10.08 =====
+===== 10.08. =====
 * Sequencing of our first constructs (LacZα-TT-pSB1C3 and ccdB-TT-pSB1C3) for verification.
 * First successful PCR of wildtype-LOV (test for future experiments)
-* Midi-Preps of LovTAP-pCal-n (Mutant) and mazF-pBAD
+* Midi-Preps of LOVTAP-pCal-n (Mutant) and mazF-pBAD
-===== 16.08 =====
+===== 16.08. =====
-Work on constructs pLac-RBS32-Ccdb-TT-pSB1A3 and pLac-RBS32-LacZα-TT-pSB1A3 started
+Work on constructs pLac-RBS32-ccdB-TT-pSB1A3 and pLac-RBS32-LacZα-TT-pSB1A3 started
-===== 21.08 =====
+===== 21.08. =====
-Successful amplification of mod-LOV
+Successful PCR-amplification of mod-LOV
-===== 22.08- 28.08 =====
+===== 22.08. - 28.08. =====
-First trial of ligation to form the new constructs pLac-RBS32-LOV-Ccdb-TT-pSB1C3 and pLac-RBS32-LOV-Ccdb-TT-pSB1C3
+First trial of ligation to form the new constructs pLac-RBS32-LOV-Ccdb-TT-pSB1C3 and pLac-RBS32-LOV-ccdB-TT-pSB1C3
-===== 29.08 =====
+===== 29.08. =====
-Purification of the pSB1C3 fragment, which was cut with EcoRI and SpeI before, for usage in the pLac-RBS32-LOV-pSB1C3 construct.
+Gel-purification of the pSB1C3 fragment, which was cut with ''EcoRI'' and ''SpeI'' before, for usage in the pLac-RBS32-LOV-pSB1C3 construct.
-===== 23.08-28.08 =====
+===== 23.08. - 28.08. =====
 Creation/finalization of constructs J23119-LacI-pSB1C3 and J23119-LacI-pSBA3
 ==== September 2012 ====
-===== 05.09-07.09 =====
+===== 05.09. - 07.09. =====
 Formation of construct pLac-RBS32-LOV-pSB1C3
-===== 06.09 =====
+===== 06.09. =====
-* Successful amplification of MazF fragment
+* Successful PCR-amplification of mazF fragment
-* Constructs MazF-pSB1C3 and MazF-TT-pSB1C3 completed
+* Constructs mazF-pSB1C3 and mazF-TT-pSB1C3 completed
-===== 10.09 - 11.09 =====
+===== 10.09. - 11.09. =====
-Mutagenesis PCR No 1: pLac-LOV-pSB1C3 and LOV-pSB1C3 to make the LOV part BioBrick compliant
+Succesful mutagenesis PCR: pLac-LOV-pSB1C3 and LOV-pSB1C3, first of two PCRs to make the LOV part BioBrick compliant
-===== 13.09 - 24.09 =====
+===== 13.09. - 24.09. =====
 New constructs:
-* pLac-RBS32-LOV-Ccdb-TT-pSB1C3
+* pLac-RBS32-LOV-ccdB-TT-pSB1C3
 * pLac-RBS32-LOV-LacZalpha-TT-pSB1C3
 === Protocols ===
-You can find the Protocols we used at our [[Team:Bonn/Protocols|Protocols page]]
+You can find the protocols we used at our [[Team:Bonn/Protocols|protocols page]]