Team:Macquarie Australia/Results

From 2012.igem.org

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<p><center>To quickly skip to the section that you wish to read, click on the links below.</p></center>
<p><center>To quickly skip to the section that you wish to read, click on the links below.</p></center>
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<th colspan="2"><center><h2>Sequencing Data</h2></center></th>
 
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<a href="#5"><h3>Heme Oxygenase</h3></a>
 
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<a href="#6"><h3>Bacteriophytochromes</h3></a>
 
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<center><h2>Results</h2></center>
<center><h2>Results</h2></center>
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<a href=#3><h3>Bacteriophytochromes</h3></a>
<a href=#3><h3>Bacteriophytochromes</h3></a>
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<th colspan="2"><center><h2>Sequencing Data</h2></center></th>
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<td>
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<a href="#5"><h3>Heme Oxygenase</h3></a>
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</td>
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<td>
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<a href="#6"><h3>Bacteriophytochromes</h3></a>
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<th colspan="2"><center><h2>Characterisation</h2></center></th>
<th colspan="2"><center><h2>Characterisation</h2></center></th>
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<center><a name="1"><h3>Heme Oxygenase</h3></center>
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<center><a name="1"><h3>Heme Oxygenase Results</h3></center>
<p>We produced a Heme oxygenase that was codon optimize for <i>E. coli</i>. The Gibson assembly of the T7 promoter containing Heme Oxygenase was successful. The transformation was successful with numerous colonies grown using Chloramphenicol as the selecting agent. Six colonies were selected and then they were sequenced before digestion with EcoR1 and Spe1. The sequencing suggested that all of the colonies contained the plasmid with a Heme oxygenase identical to the original protein sequence. The gel containing the digested Heme Oxygenase bearing plasmid can be seen in Figure 1.</p><br>
<p>We produced a Heme oxygenase that was codon optimize for <i>E. coli</i>. The Gibson assembly of the T7 promoter containing Heme Oxygenase was successful. The transformation was successful with numerous colonies grown using Chloramphenicol as the selecting agent. Six colonies were selected and then they were sequenced before digestion with EcoR1 and Spe1. The sequencing suggested that all of the colonies contained the plasmid with a Heme oxygenase identical to the original protein sequence. The gel containing the digested Heme Oxygenase bearing plasmid can be seen in Figure 1.</p><br>
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  and the heme oxygenese gene (Green Box). We used a 1kb ladder.
  and the heme oxygenese gene (Green Box). We used a 1kb ladder.
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<center><a name="5"><h3>Heme Oxygenase Sequencing Results</h3></center>
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<p>The plasmid was sequencing using the forward and reverse primers for the BioBricks. We performed Blastx pipeline to determine if there was a significant change in the protein sequence.</p>
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<center><table border="3" cellpadding="4" cellspacing="0">
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<tr><td>Sample</td><td>Proposed Identity</td> <td>e-value</td><td>MaxID</td></tr>
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<tr><td>1C-6F</td><td>Heme Oxygenase (Synechocystic sp. PCC603)</td><td>7e-176</td><td>99%</td></tr>
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<tr><td>1C-6R</td><td>Heme Oxygenase (Synechocystic sp. PCC603)</td><td>1e-171</td><td>99%</td></tr>
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<tr><td>1C-4F</td><td>Heme Oxygenase (Synechocystic sp. PCC603)</td><td>4e-176</td><td>99%</td></tr>
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<tr><td>1C-4R</td><td>Heme Oxygenase (Synechocystic sp. PCC603)</td><td>6e-172</td><td>99%</td></tr>
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<tr><td>1C-5F</td><td>Heme Oxygenase (Synechocystic sp. PCC603)</td><td>1e-23</td><td>92%</td></tr>
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<tr><td>1C-5F</td><td>Heme Oxygenase (Synechocystic sp. PCC603)</td><td>6e-172</td><td>99%</td></tr></table></center>
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<p>Given that this was the source of our gene, we proposed that the sequencing result was accurate. We then compared to the original gBlock sequence and determined that the sequencing was accurate and confirmed the identity of the plasmid.</p>
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<center><a name="2"><h3>Characterisation of Heme Oxygenase</h3></center>
<center><a name="2"><h3>Characterisation of Heme Oxygenase</h3></center>
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<center><a name="3"><h3>Bacteriophytochromes</h3></center>
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<center><a name="3"><h3>Bacteriophytochromes Results</h3></center>
<p>Like the Heme Oxygenase, the bacteriophytochromes from <i>Deinococcus radiodurans</i> and <i>Agrobacterium tumefaciens</i> were optimised for use in <i>E. Coli</i>.</p>
<p>Like the Heme Oxygenase, the bacteriophytochromes from <i>Deinococcus radiodurans</i> and <i>Agrobacterium tumefaciens</i> were optimised for use in <i>E. Coli</i>.</p>
<hr>
<hr>
<center><a name="4"><h3>Bacteriophytochrome Characterisation</h3></center>
<center><a name="4"><h3>Bacteriophytochrome Characterisation</h3></center>

Revision as of 02:24, 25 September 2012



Results and Characterisation

To quickly skip to the section that you wish to read, click on the links below.

Results

Heme Oxygenase

Bacteriophytochromes

Sequencing Data

Heme Oxygenase

Bacteriophytochromes

Characterisation

Heme Oxygenase

Bacteriophytochromes


Heme Oxygenase Results

We produced a Heme oxygenase that was codon optimize for E. coli. The Gibson assembly of the T7 promoter containing Heme Oxygenase was successful. The transformation was successful with numerous colonies grown using Chloramphenicol as the selecting agent. Six colonies were selected and then they were sequenced before digestion with EcoR1 and Spe1. The sequencing suggested that all of the colonies contained the plasmid with a Heme oxygenase identical to the original protein sequence. The gel containing the digested Heme Oxygenase bearing plasmid can be seen in Figure 1.


Figure 1: The restriction digest showing the linearised plasmid backbone (Black Box)
and the heme oxygenese gene (Green Box). We used a 1kb ladder.

Heme Oxygenase Sequencing Results

The plasmid was sequencing using the forward and reverse primers for the BioBricks. We performed Blastx pipeline to determine if there was a significant change in the protein sequence.

SampleProposed Identity e-valueMaxID
1C-6FHeme Oxygenase (Synechocystic sp. PCC603)7e-17699%
1C-6RHeme Oxygenase (Synechocystic sp. PCC603)1e-17199%
1C-4FHeme Oxygenase (Synechocystic sp. PCC603)4e-17699%
1C-4RHeme Oxygenase (Synechocystic sp. PCC603)6e-17299%
1C-5FHeme Oxygenase (Synechocystic sp. PCC603)1e-2392%
1C-5FHeme Oxygenase (Synechocystic sp. PCC603)6e-17299%

Given that this was the source of our gene, we proposed that the sequencing result was accurate. We then compared to the original gBlock sequence and determined that the sequencing was accurate and confirmed the identity of the plasmid.


Characterisation of Heme Oxygenase

The T7 bearing Heme Oxygenase produced was characterised to determine if it was functional. BL21 E. coli was transformed with the plasmid, selected for using chloramphenicol and a culture was inoculated. The culture was then induced with ALA (d-aminolevulinic acid) for the heme pathway and IPTG to promote protein production. They were incubate overnight and the cells were spun down. We observed a functional Heme Oxygenase and the cells appeared a vibrant green after induction by ALA and IPTG.


Bacteriophytochromes Results

Like the Heme Oxygenase, the bacteriophytochromes from Deinococcus radiodurans and Agrobacterium tumefaciens were optimised for use in E. Coli.


Bacteriophytochrome Characterisation