Team:UNAM Genomics Mexico/Parts

From 2012.igem.org

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The aminoglycoside antibiotic resistance gene (aadA +)[3,4] of pHP45 was originally carried on a 1.7-kb PvuII-HindIII fragment from the R100.1 plasmid[5]. Plasmid pHP45Ω was constructed in Pierre Prentki and Henry M. Krisch, 1984 [5] as stated in NCBI[6] with this fragment. The addA sequence can be found in [7, 8 ], it is confirmed to be the one contained in pHP45Ω[9] and the complete sequence of pHP45Ω plasmid can be found in [10, 11].
 +
 +
Hawaii 2008 iGEM team [12] attempted before to construct a similar cassette [13] but didn’t succeed. For iGEM UNAM Genomics México 2012 project [14], the Ω Cassette was used in the design of an OR logic gate[15] using a recently described new type of communication system between ''Bacillus Subtilis'' cells called Nanotubes[16].
 +
<br>
 +
<br>
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<table cellspacing="0" cellpadding="0">
 +
  <tr>
 +
    <td width="209">Spectino    [ng/microliter] </td>
 +
    <td width="83">T0</td>
 +
    <td width="83">T30</td>
 +
    <td width="83">T60</td>
 +
    <td width="83">T90</td>
 +
    <td width="83">T120</td>
 +
    <td width="83">T150</td>
 +
    <td width="83">T180</td>
 +
    <td width="83">T210</td>
 +
    <td width="83">T240</td>
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  </tr>
 +
  <tr>
 +
    <td align="right">0</td>
 +
    <td align="right">0.049</td>
 +
    <td align="right">0.129</td>
 +
    <td align="right">0.274</td>
 +
    <td align="right">0.448</td>
 +
    <td align="right">0.573</td>
 +
    <td align="right">0.736</td>
 +
    <td align="right">0.967</td>
 +
    <td align="right">0.967</td>
 +
    <td align="right">1.088</td>
 +
  </tr>
 +
  <tr>
 +
    <td align="right">2.6</td>
 +
    <td align="right">0.051</td>
 +
    <td align="right">0.086</td>
 +
    <td align="right">0.208</td>
 +
    <td align="right">0.384</td>
 +
    <td align="right">0.531</td>
 +
    <td align="right">0.664</td>
 +
    <td align="right">0.925</td>
 +
    <td align="right">1.002</td>
 +
    <td align="right">1.096</td>
 +
  </tr>
 +
  <tr>
 +
    <td align="right">3</td>
 +
    <td align="right">0.048</td>
 +
    <td align="right">0.098</td>
 +
    <td align="right">0.23</td>
 +
    <td align="right">0.421</td>
 +
    <td align="right">0.556</td>
 +
    <td align="right">0.726</td>
 +
    <td align="right">0.873</td>
 +
    <td align="right">1.003</td>
 +
    <td align="right">1.056</td>
 +
  </tr>
 +
  <tr>
 +
    <td align="right">3.4</td>
 +
    <td align="right">0.049</td>
 +
    <td align="right">0.102</td>
 +
    <td align="right">0.213</td>
 +
    <td align="right">0.423</td>
 +
    <td align="right">0.574</td>
 +
    <td align="right">0.718</td>
 +
    <td align="right">0.83</td>
 +
    <td align="right">0.959</td>
 +
    <td align="right">1.073</td>
 +
  </tr>
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  <tr>
 +
    <td align="right">3.6</td>
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    <td align="right">0.048</td>
 +
    <td align="right">0.101</td>
 +
    <td align="right">0.211</td>
 +
    <td align="right">0.397</td>
 +
    <td align="right">0.528</td>
 +
    <td align="right">0.687</td>
 +
    <td align="right">0.833</td>
 +
    <td align="right">0.963</td>
 +
    <td align="right">1.026</td>
 +
  </tr>
 +
  <tr>
 +
    <td align="right">3.8</td>
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    <td align="right">0.046</td>
 +
    <td align="right">0.101</td>
 +
    <td align="right">0.209</td>
 +
    <td align="right">0.392</td>
 +
    <td align="right">0.532</td>
 +
    <td align="right">0.671</td>
 +
    <td align="right">0.706</td>
 +
    <td align="right">0.955</td>
 +
    <td align="right">1.009</td>
 +
  </tr>
 +
</table>
 +
 +
[[Image:Unamgenomicsomegacassete1.png]]
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Second Repetition <br>
 +
<table cellspacing="0" cellpadding="0">
 +
  <tr>
 +
    <td width="209">Spectino    [ng/microliter]</td>
 +
    <td width="83">T0</td>
 +
    <td width="83">T30</td>
 +
    <td width="83">T60</td>
 +
    <td width="83">T90</td>
 +
    <td width="83">T120</td>
 +
    <td width="83">T150</td>
 +
    <td width="83">T180</td>
 +
    <td width="83">T210</td>
 +
    <td width="83">T240</td>
 +
  </tr>
 +
  <tr>
 +
    <td align="right">0</td>
 +
    <td align="right">0.065</td>
 +
    <td align="right">0.12</td>
 +
    <td align="right">0.261</td>
 +
    <td align="right">0.435</td>
 +
    <td align="right">0.57</td>
 +
    <td align="right">0.742</td>
 +
    <td align="right">0.939</td>
 +
    <td align="right">0.966</td>
 +
    <td align="right">1.083</td>
 +
  </tr>
 +
  <tr>
 +
    <td align="right">2.6</td>
 +
    <td align="right">0.045</td>
 +
    <td align="right">0.095</td>
 +
    <td align="right">0.263</td>
 +
    <td align="right">0.408</td>
 +
    <td align="right">0.541</td>
 +
    <td align="right">0.7</td>
 +
    <td align="right">0.897</td>
 +
    <td align="right">0.988</td>
 +
    <td align="right">1.07</td>
 +
  </tr>
 +
  <tr>
 +
    <td align="right">3</td>
 +
    <td align="right">0.048</td>
 +
    <td align="right">0.111</td>
 +
    <td align="right">0.219</td>
 +
    <td align="right">0.428</td>
 +
    <td align="right">0.55</td>
 +
    <td align="right">0.709</td>
 +
    <td align="right">0.851</td>
 +
    <td align="right">1</td>
 +
    <td align="right">1.043</td>
 +
  </tr>
 +
  <tr>
 +
    <td align="right">3.4</td>
 +
    <td align="right">0.048</td>
 +
    <td align="right">0.094</td>
 +
    <td align="right">0.192</td>
 +
    <td align="right">0.371</td>
 +
    <td align="right">0.534</td>
 +
    <td align="right">0.697</td>
 +
    <td align="right">0.844</td>
 +
    <td align="right">0.989</td>
 +
    <td align="right">1.036</td>
 +
  </tr>
 +
  <tr>
 +
    <td align="right">3.6</td>
 +
    <td align="right">0.04</td>
 +
    <td align="right">0.101</td>
 +
    <td align="right">0.214</td>
 +
    <td align="right">0.407</td>
 +
    <td align="right">0.542</td>
 +
    <td align="right">0.679</td>
 +
    <td align="right">0.853</td>
 +
    <td align="right">0.951</td>
 +
    <td align="right">1.067</td>
 +
  </tr>
 +
  <tr>
 +
    <td align="right">3.8</td>
 +
    <td align="right">0.049</td>
 +
    <td align="right">0.102</td>
 +
    <td align="right">0.211</td>
 +
    <td align="right">0.4</td>
 +
    <td align="right">0.552</td>
 +
    <td align="right">0.691</td>
 +
    <td align="right">0.83</td>
 +
    <td align="right">1</td>
 +
    <td align="right">1.006</td>
 +
  </tr>
 +
</table>
 +
 +
 +
[[Image:Unamgenomicsomegacassete2png.png]]
 +
===REFERENCES===
 +
<br>
 +
[1] http://www.shigen.nig.ac.jp/ecoli/strain/cvectorDetailAction.do?cvectorId=147<br>
 +
[2] https://2012.igem.org/Team:UNAM_Genomics_Mexico/Notebook/ANDSugar <br>
 +
[3] http://www.ihop-net.org/UniPub/iHOP/bng/174343.html<br>
 +
[4] http://www.wikigenes.org/e/gene/e/1238687.html<br>
 +
[5] Pierre Prentki and Henry M. Krisch (1984). In vitro insertional mutagenesis with a selectable DNA fragment. Gene, 29:303-313<br>
 +
[6] http://www.ncbi.nlm.nih.gov/nuccore/K02163<br>
 +
[7] http://www.uniprot.org/uniprot/P0AG05<br>
 +
[8] http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&term=1446561<br>
 +
[9] Nancye C. Clark, Ørjan Olsvik, Jana M. Swenson, Carol A. Spiegel and Fred C. Tenover(1999) Detection of a Streptomycin/Spectinomycin Adenylyltransferase Gene ( aadA) in Enterococcus faecalis. Antimicrob. Agents Chemother. 43(1):157.<br>
 +
[10] http://www.ncbi.nlm.nih.gov/nuccore/207855?report=fasta<br>
 +
[11] Pierre Prentki, Anna Bind and Andrée Epstein (1991). Plasmid vectors for selecting ISI-promoted deletions in cloned DNA: sequence analysis of the omega interposon. Gene, 103:17-23.<br>
 +
[12] https://2008.igem.org/Team:Hawaii<br>
 +
[13] https://2008.igem.org/Team:Hawaii/Construction_of_Omega_Interposon_BioBrick<br>
 +
[14] https://2012.igem.org/Team:UNAM_Genomics_Mexico<br>
 +
[15] Link con la página de descripción general del sistema o el de la parte del OR<br>
 +
[16] Dubey GP, Ben-Yehuda S. (2011) Intercellular nanotubes mediate bacterial communication. Cell.;144(4) :590-600<br>
<br />
<br />

Revision as of 00:40, 26 October 2012


UNAM-Genomics_Mexico


Our Parts






<groupparts>iGEM012 UNAM_Genomics_Mexico</groupparts>


The aminoglycoside antibiotic resistance gene (aadA +)[3,4] of pHP45 was originally carried on a 1.7-kb PvuII-HindIII fragment from the R100.1 plasmid[5]. Plasmid pHP45Ω was constructed in Pierre Prentki and Henry M. Krisch, 1984 [5] as stated in NCBI[6] with this fragment. The addA sequence can be found in [7, 8 ], it is confirmed to be the one contained in pHP45Ω[9] and the complete sequence of pHP45Ω plasmid can be found in [10, 11].

Hawaii 2008 iGEM team [12] attempted before to construct a similar cassette [13] but didn’t succeed. For iGEM UNAM Genomics México 2012 project [14], the Ω Cassette was used in the design of an OR logic gate[15] using a recently described new type of communication system between Bacillus Subtilis cells called Nanotubes[16].

Spectino [ng/microliter]  T0 T30 T60 T90 T120 T150 T180 T210 T240
0 0.049 0.129 0.274 0.448 0.573 0.736 0.967 0.967 1.088
2.6 0.051 0.086 0.208 0.384 0.531 0.664 0.925 1.002 1.096
3 0.048 0.098 0.23 0.421 0.556 0.726 0.873 1.003 1.056
3.4 0.049 0.102 0.213 0.423 0.574 0.718 0.83 0.959 1.073
3.6 0.048 0.101 0.211 0.397 0.528 0.687 0.833 0.963 1.026
3.8 0.046 0.101 0.209 0.392 0.532 0.671 0.706 0.955 1.009

Unamgenomicsomegacassete1.png


Second Repetition

Spectino [ng/microliter] T0 T30 T60 T90 T120 T150 T180 T210 T240
0 0.065 0.12 0.261 0.435 0.57 0.742 0.939 0.966 1.083
2.6 0.045 0.095 0.263 0.408 0.541 0.7 0.897 0.988 1.07
3 0.048 0.111 0.219 0.428 0.55 0.709 0.851 1 1.043
3.4 0.048 0.094 0.192 0.371 0.534 0.697 0.844 0.989 1.036
3.6 0.04 0.101 0.214 0.407 0.542 0.679 0.853 0.951 1.067
3.8 0.049 0.102 0.211 0.4 0.552 0.691 0.83 1 1.006


File:Unamgenomicsomegacassete2png.png

REFERENCES


[1] http://www.shigen.nig.ac.jp/ecoli/strain/cvectorDetailAction.do?cvectorId=147
[2] https://2012.igem.org/Team:UNAM_Genomics_Mexico/Notebook/ANDSugar
[3] http://www.ihop-net.org/UniPub/iHOP/bng/174343.html
[4] http://www.wikigenes.org/e/gene/e/1238687.html
[5] Pierre Prentki and Henry M. Krisch (1984). In vitro insertional mutagenesis with a selectable DNA fragment. Gene, 29:303-313
[6] http://www.ncbi.nlm.nih.gov/nuccore/K02163
[7] http://www.uniprot.org/uniprot/P0AG05
[8] http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&term=1446561
[9] Nancye C. Clark, Ørjan Olsvik, Jana M. Swenson, Carol A. Spiegel and Fred C. Tenover(1999) Detection of a Streptomycin/Spectinomycin Adenylyltransferase Gene ( aadA) in Enterococcus faecalis. Antimicrob. Agents Chemother. 43(1):157.
[10] http://www.ncbi.nlm.nih.gov/nuccore/207855?report=fasta
[11] Pierre Prentki, Anna Bind and Andrée Epstein (1991). Plasmid vectors for selecting ISI-promoted deletions in cloned DNA: sequence analysis of the omega interposon. Gene, 103:17-23.
[12] https://2008.igem.org/Team:Hawaii
[13] https://2008.igem.org/Team:Hawaii/Construction_of_Omega_Interposon_BioBrick
[14] https://2012.igem.org/Team:UNAM_Genomics_Mexico
[15] Link con la página de descripción general del sistema o el de la parte del OR
[16] Dubey GP, Ben-Yehuda S. (2011) Intercellular nanotubes mediate bacterial communication. Cell.;144(4) :590-600



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