Team:St Andrews/Procedure

From 2012.igem.org

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         <dt>date and gene</dt>   
         <dt>date and gene</dt>   
         <dd>result</dd>  
         <dd>result</dd>  
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        <dt>date and gene</dt>   
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         <dd>result</dd>  
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<dt>29/6/12 ELO7 L. major</dt>   
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         <dt>23/7/12 Δ12 Syn. in pET-15b and 20b</dt>   
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         <dd><p><ul>After showing successful insertion of <i>L. major</i> Δ6 elongase in pET-15b, the sample was sent off for sequencing. Unfortunately, the gene sequenced was not the Δ6 elongase we were hoping to find, but a <i>T. brucei</i> mevalonate kinase, which was previously inserted in the pET-15b vectors we had been using. Thus, we digested some fresh pET-15b to be used in the future.</ul></p>
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        <p><ul><a data-toggle="modal" href="#modal6" class="btn btn-primary btn-mini">Sequence</a>
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<div class="modal hide" id="modal6">
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  <div class="modal-header">
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    <button type="button" class="close" data-dismiss="modal">×</button>
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    <h3>ELO6 in pET-15b</h3>
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  </div>
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  <div class="modal-body">
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    <p>GnanTTTGTTtAcTttaagaaggagaTATACCATGGGcAGCAGCCATcatCATcatcaTCACAGCAGCGGCCTggtGCCG
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CGCGGCagCCATATGGTCGTGGCATCGtgTCCGGGAAAAGTGCTGATTCTTGGTGGTTAcCTAATAGttGAGGAGCCAAA
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TGTTGGTATTTCCGTAGGAACAACCGCGCGCTTCGTGACACGTGTGGCGTCgtgGAAAAAATGCTCTGATGGAAAGTGTC
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GAGTGCACATCGTCTCGTCACAGTTCAACAAggaGTTTACGTTTGAATGCGCGGCTGAAGAGGACAGTGATTCCACTATC
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AAGATTGTGCAATTAGAGGGTGCACCATCGCCGTTTCTCTTCTACGGTATTTTGTACTCGGTTGCCGGCGCTCTATTATT
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TGGTGGTGATATTTTTCGTGATGTTACCCTAGAGTTGTTGGCGGATAACGATTTCTACAGCCAAAGGAATTATTTGGAGT
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CCCAAGGCAAGCCGGTGACCGCAGCCAACCTGCGGCTCATCCCCCGTTATACGCCCCTCTTGGGGGAGGTTTCCAAAACT
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GGTCTAGGATCTTCAGCGGCAATGACCACTAGTGTCGTAGCGTGCCTGCTCCAACTTTTTGTTTTTGATTCGAAGAAAAA
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CAATGCCACTGAGTCCGTGGAGAGGGCACCGGAGCTACCTCTACGTTTGGAGGATGTAACAGAGTTCATTCATCGTATTA
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GTCAGGTTGCCCACTGCGTAGCACAGGGAAAAGTGgGGAGCGGGTTTGATGTCTACACGGCCACGTTCGGGACGTGTGTG
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TACCGACGGTTCTCCGCACGCGTGCTGGAnAAGCTCGTAAAGGgtAATGAACCTCCGAAGCGCGTCGCTATTCCTCTTTT
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ACGTGAGTGTGTCGAGACGGATGAAGTGTGgGTTCAGAGGATACcCTtccGGCTTCCTACCGGGTTGCAGCTTCTTTTAG
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GGGATGTACACAAGGGAGgAacaGAAAcACCTGGCATGGTGTcgaAGGTCATGTCatgnnagnggTCGGTGACCacGGAC
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CCcAACAGnttgnggnnnngantTcCCATgnntAAT
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</p>
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  </div>
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  <div class="modal-footer">
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    <a href="#" class="btn" data-dismiss="modal">Close</a>
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    </div>
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</div></ul>
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</ul></p></dd>
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         <dt>23/7/12 Δ12 Syn.</dt>   
         <dd><p><ul>15b forward gave 0 nucleotides</ul></p>
         <dd><p><ul>15b forward gave 0 nucleotides</ul></p>
             <p><ul>15b reverse gave 0 nucleotides</ul></p>
             <p><ul>15b reverse gave 0 nucleotides</ul></p>

Revision as of 15:14, 27 July 2012

Lab Book

Procedure

date
what we did
date
what we did
date
what we did

anyone really keen to write this up, up to protein visualization? Don't forget to mention the differing restriction enzymes and vectors of each team. I can add in links to the protocols page.

Please also refer to our Protocols page.


 

 

 

 

 

 

 

 

 

 

 
Sequences   Primers   Sequencing results   Lipid analysis
 

Start from lipid extraction

primers, sequence results


 
Sequences
 

Δ12 T. Cruzi Δ12 Synechocystis Δ15 Synechocystis Δ6 Synechocystis ELO 6 L. major
 

 
Primers
 

All primers are notated 5' to 3'.
 

Δ12 T. Cruzi forward
Δ12 T. Cruzi reverse
Δ12 Synechocystis forward
Δ12 Synechocystis reverse
Δ15 Synechocystis forward

Δ15 Synechocystis reverse
Δ6 Synechocystis forward
Δ6 Synechocystis reverse


 

When using the pET-duet vector, we needed additionally primers for the alternative restriction sites and His-tags.

ELO6 L. major forward
Δ15 T. Cruzi forward
Δ6 T. Cruzi forward
Δ6 T. Cruzi reverse
Δ12 T. Cruzi forward
Δ12 T. Cruzi reverse

 
Sequencing results
 
date and gene
result
date and gene
result
29/6/12 ELO7 L. major

    After showing successful insertion of L. major Δ6 elongase in pET-15b, the sample was sent off for sequencing. Unfortunately, the gene sequenced was not the Δ6 elongase we were hoping to find, but a T. brucei mevalonate kinase, which was previously inserted in the pET-15b vectors we had been using. Thus, we digested some fresh pET-15b to be used in the future.

    Sequence

23/7/12 Δ12 Syn.

    15b forward gave 0 nucleotides

    15b reverse gave 0 nucleotides

    20b forward gave a 41 nucleotide result.

    Sequence

    A BLAST search showed this to be compatible with Crocosphaera watsonii (genome shotgun sequence, 21%), a diazotrophic cyanobacteria. Add in relations to synechocystis.

    20b reverse gave 0 nucleotides


 

 
Lipid analysis
 

 

 

 

 

 

 

 

 

who knows what those Metal Mickies are up to. Eating nachos in the Whey Pat most likely. MEGA LOLS (all caps, with a Z).


 

PrimersDigestionTransformation


 
Primers
 

All primers are notated 5' to 3'.
 

Ni forward
Ni reverse
Ni2 forward
Ni2 reverse
.

Pd forward
Pd reverse
Pt forward
Pt reverse


 

For primer annealing in the PCR, the primer sequences were combined in the following way:

  • GST Forward and Ni Reverse
  • GST Forward and Ni2 Reverse
  • GST Forward and Pd Reverse
  • GST Forward and Pt Reverse

  •  
    Digestion
     

    pGEX-6P-1 was cut using EcoR1(954) and Xho1 (975)


     
    Transformation
     

    pGEX vector with insert transformed into DH5α E. coli cells to replicate.

    pGEX vector with G-Block insert transformed into DH5α E. coli cells to replicate.


     

    pGEX vector with insert transformed into BL21 E. coli cells for protein expression.

    pGEX vector with G-Block insert transformed into BL21 E. coli cells for protein expression.


     

     

     

     

     

     

     

    Back to top

    University of St Andrews, 2012.

    Contact us: igem2012@st-andrews.ac.uk, Twitter, Facebook

    This iGEM team has been funded by the MSD Scottish Life Sciences Fund. The opinions expressed by this iGEM team are those of the team members and do not necessarily represent those of Merck Sharp & Dohme Limited, nor its Affiliates.