Difference between revisions of "Part:BBa K818000:Experience"

Revision as of 17:11, 30 September 2013

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Applications of BBa_K818000

This backbone plasmid was used as primary backbone for all constructs in team Groningen 2012 project: the Food Warden. For further info: [http://2012.igem.org/Team:Groningen/OurBiobrick iGEM Groningen 2012 biobrick page]

User Reviews

UNIQ8019025a57343375-partinfo-00000000-QINU

No part name specified with partinfo tag. Newcastle University iGEM 2013

This BioBrick was designed to be used as an integration backbone for the ‘’B. subtilis’’ by integrating at the ‘’sacA’’ region of the endogenous chromosome via double crossover. The Groningen iGEM 2012 team has showed that this BioBrick can be replicated in ‘’E. coli’’, however have not showed any results/characterisation that this backbone can integrate correctly in ‘’B. subtilis’’.

We transformed this backbone into ‘’B. subtilis’’ but as can be seen in Figure 1, no colonies were found on the ‘’B. subtilis’’ str. 168 + pSac-Cm derived integration plasmid, however the positive control ‘’B. subtilis’’ str.168 + pGFPrrnB (integrates at amyE) did work, which suggested that this backbone was not integrated.

Plate 1: B. Subtilis str. 168 transformed with switch BioBrick.	Plate 2: B.subtilis str. 168 transformed with pGFPrrnB (positive control).
Plate 3: B. subtilis str. 168 no transformation (negative control).	Figure 1. Plates of B. Subtilis str. 168 transformed with switch BioBrick, pGFPrrnB (positive control) and water (negative control).

We repeated the transformations using higher concentration of plasmids 5ug, 10ug, and 15ug and plated them onto the LB + 5ug/ml Chloramphenicol plates. The results Figure 2, shows that there were colonies growing on the 10ug and 15ug plates.

10 minutes	30 minutes
60 minutes	120 minutes
240 minutes	Figure 4. Negative control: Fluorescence microscopy showing how sfGFP expession changes with time on addition of 0mM IPTG in B.subtilis containing our HBsu-sfGFP BioBrick.

To test for integration, we used the Phenol red Sucrose test; the media where the transformants from the 10ug and 15ug plates were inoculated showed the same results as the control (‘’B. subtilis’’ + pGFPrrnB) with pH ranging between 4.6 – 5.2 suggesting that they could utilized sucrose as their carbon source and produced the acid by products, Figure 3.

Figure 3. Display the pH of each samples following the Phenol Red Sucrose test on overnight grown culture in LB + 1% Sucrose media.

We then sequenced the backbone and found out that there were 49 mutations which include SNV, deletions and insertions.Table 1 display the mutations found on the sequence.

Table 1. Shows all the mutations found in the BBa_K818000 backbone.

Table 2. Shows list of mutations found in the BBa_K818000 backbone, including the position, region and type of mutations after analysing the initial sequencing and the sequencing of highly mutated regions. Table 2. Shows list of mutations found in the BBa_K818000 backbone, including the position, region and type of mutations after analysing the initial sequencing and the sequencing of highly mutated regions.

The results from both sequencing run proved to show similar mutations were found on this backbone, most of the mutations occurred in the sacA integration regions. These results explained the reason why this pSac-Cm derived integration backbone for ‘’B.subtilis’’ were not working.

To get round this problem, we align the sequence of this BioBrick to the Integration vector pSac-Cm sequence from the (Middleton, R., Hofmeister, A. New shuttle vectors for ectopic insertion of genes into Bacillus subtilis. Plasmid Volume 51, Issue 3, May 2004, Pages 238–245). The results showed that the sequence that the Groningen team 2012 put up on the registry was correct. This suggests that the plasmid that they have submitted and the sequence they provided did not match. By using the correct sequence to generate this integration plasmid we will be able to make this part functional not just in ‘’E. coli’’ but also ‘’B. subtilis.

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@@ Line 105: / Line 105: @@
 Figure 3. Display the pH of each samples following the Phenol Red Sucrose test on overnight grown culture in LB + 1% Sucrose media.
-We then sequenced the backbone and found out that there were 49 mutations which include SNV, deletions and insertions.
+We then sequenced the backbone and found out that there were 49 mutations which include SNV, deletions and insertions.Table 1 display the mutations found on the sequence.
 [[File:BareCillus_Gro_mutations.jpg|700px]]
+Table 1. Shows all the mutations found in the BBa_K818000 backbone.
-Table 1 display the mutations found on the sequence.
+Table 2. Shows list of mutations found in the BBa_K818000 backbone, including the position, region and type of mutations after analysing the initial sequencing and the sequencing of highly mutated regions.
 [[File:BareCillus Gro sumseq.jpg|700px]]
 Table 2. Shows list of mutations found in the BBa_K818000 backbone, including the position, region and type of mutations after analysing the initial sequencing and the sequencing of highly mutated regions.
 The results from both sequencing run proved to show similar mutations were found on this backbone, most of the mutations occurred in the sacA integration regions. These results explained the reason why this pSac-Cm derived integration backbone for ‘’B.subtilis’’ were not working.