Team:LCG-UNAM-Mexico/Modeling

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          <td width="165" bgcolor="#5C743D"><a href="https://2008.igem.org/Team:LCG-UNAM-Mexico/Modeling" class="navText">Modeling</a></td>
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          <td class="pageName">Modeling</td>
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        </tr>
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        <tr>
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          <td class="bodyText"><p align="justify"><br>
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            We are  using MatLab to simulate our system. We have already done a first approximation which did not contain real parameteres. However, we tried to keep the system consistent within itself. Don't know what we're talking about? Take a look at our <a href="https://2008.igem.org/Team:LCG-UNAM-Mexico/Project" title="Project Description">project description</a>. </p>
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            <p><strong>Metabolites</strong></p>
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            <table width="585" border="0">
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              <tr>
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                <td width="132"><ol>
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                  <li> AiiA</li>
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                  <li>AHL</li>
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                  <li>LuxR</li>
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                  <li>AHL:LuxR</li>
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                  <li>cI*</li>
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                  <li>ρ</li>
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                  <li>ρ:cI*</li>
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                  <li>RcnA</li>
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                  <li>Ni[int]</li>
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                  <li>Ni[ext]</li>
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                  <li>Unk</li>
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                </ol>                </td>
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                <td width="443" valign="top"><p>Acyl-Homoserine Lactone Lactonase<br>
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                  Acyl-Homoserine Lactone<br>
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                  Transcriptional Activator<br>
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                  Complex formed by AHL and LuxR<br>
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                  λ phage repressor (cI) modified with a LVA tail for quick degradation<br>
 +
                  <em>rcnA</em> promoter<br>
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                  Complex formed by cI* repressor and <em>rcnA</em> promoter <br>
 +
                  <em>Escherichia coli</em> nickel efflux pump<br>
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                  Intracellular nickel<br>
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                  Extracellular nickel
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                  <br>
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                  Unknown nickel import channel <br>
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                </p>
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                </td>
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              </tr>
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            </table>
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            <p><strong>Reactions</strong></p>
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            <table width="585" border="0">
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              <tr>
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                <td width="206" valign="top"><ol>
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                    <li>AiiA + AHL <strong>-&gt;</strong> AiiA </li>
 +
                    <li>AHL + LuxR <strong>&lt;--&gt;</strong> AHL:LuxR </li>
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                    <li>AHL:LuxR <strong>-&gt;</strong> AHL:LuxR + cI*</li>
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                    <li>cI* <strong>-&gt;</strong> Ø</li>
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                    <li>ρ + cI* <strong>&lt;-&gt;</strong> ρ:cI*</li>
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                    <li>ρ <strong>-&gt;</strong> ρ + RcnA</li>
 +
                    <li>RcnA + Ni[int] <strong>-&gt;</strong> RcnA + Ni[ext]</li>
 +
                    <li>RcnA <strong>-&gt;</strong> Ø</li>
 +
                    <li>Unk +  Ni[ext] <strong>-&gt;</strong> Unk + Ni[int]</li>
 +
                </ol></td>
 +
                <td width="369" valign="top"><p>Degradation of AHL by AiiA<br>
 +
                  Complex formation and dissociation between AHL and LuxR<br>
 +
                  Transcription activation
 +
                of cI* by AHL and LuxR complex<br>
 +
                Natural degradation of cI*<br>
 +
                Complex formation and dissociation between
 +
ρ and cI*<br>
 +
                RcnA production<br>
 +
                Nickel efflux by RcnA<br>
 +
                Natural degradation of RcnA
 +
                <br>
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                Nickel import by the unknown channel
 +
</p></td>
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              </tr>
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            </table>
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            <p><strong>Assumptions</strong></p>
 +
            <ol>
 +
              <li>
 +
                <div align="justify"><strong>Once  there is nickel in the medium, RcnR no longer participates in the pump’s  regulation.</strong> If there’s nickel in the medium, we can assume that  RcnR is always coupled with a Ni molecule, so it will not be capable of  repressing RcnA (The few RcnR molecules in the cell will cause noise, but this  will be indistinguishable from the pump’s normal behavior).</div>
 +
              </li>
 +
              <li>
 +
                <div align="justify"><strong>All  decrease in AHL concentration is due to AiiA.</strong> We consider the  natural degradation of AHL to be unimportant given the time taken to make the  analysis (AHL half-life is long, from 3 to 24 hours).</div>
 +
              </li>
 +
              <li>
 +
                <div align="justify"><strong>The  change in the transcription of cI* is only dependent on AHL concentration.</strong> There’s  a basal production of cI*, however the change will always be due to the AHL  concentration given that production of LuxR is constitutive. </div>
 +
              </li>
 +
              <li>
 +
                <div align="justify"><strong>It is a  homogeneous system.</strong> This means that the coefficients of the equations are  constant (so we don’t have compartmentalization). </div>
 +
              </li>
 +
              <li>
 +
                <div align="justify"><strong>The  quantity of nickel used by the cell is negligible compared to the  concentrations in and out of the cell.</strong> This means we don’t  need to include an equation describing the change in the Ni concentration due  to cell consumption in the time used by the experiment.</div>
 +
              </li>
 +
              <li>
 +
                <div align="justify"><strong>The  production of RcnR, LuxR and AiiA is constitutive and their concentrations have  reached the steady state.</strong> </div>
 +
              </li>
 +
              <li>
 +
                <div align="justify"><strong>NikABCDE  will not play a role in our model.</strong> NikABCDE serves to import nickel to  the cell, however it only works in anaerobic conditions and our experiment will  be made in aerobic conditions. This therefore implies that the nickel import  will only take place by the unknown mechanism, which nonetheless is constant  and constitutive.</div>
 +
              </li>
 +
            </ol>
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            <p align="justify" class="Estilo1">We still need to state here, why can we assume  these things?</p></td>
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          <td class="bodyText"><p>--- - -  --- -- -- -- -- -- -- --  - ------ -----. --- ------ --- ---- -- --- ----- -- -- -- ------ ---- ---- - -- - ---- - ----- ---- ---, - ----- --- ----- ---- ---- ---- -- --- --- --- --- -- ---- ---------- - ------ ---- - - ---- - ----- ---- ---, - ----- --- ----- ---- ---- ---- -- --- --- --- --- -- ---- ---------- - ------ ---- --- ----- --- - ---- - ----- ---- ---, - ----- - ---- - ----- ---- ---, - ----- --- ----- ---- ---- ---- -- --- --- --- --- -- ---- ---------- - ------ ---- --- ---.
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--- ----- ---- ---- ---- -- --- --- --- --- -- ---- ---------- - ------ ---- --- --- - ---- - ----- ---- ---, - ----- --- ----- ---- ---- ---- -- --- --- --- --- -- ---- ---------- - ------ ---- --- ----.</p>
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<p>--- - -  --- -- -- -- -- -- -- --  - ------ -----. --- ------ --- ---- -- --- ----- -- -- -- ------ ---- ---- - -- - ---- - ----- ---- ---, - ----- --- ----- ---- ---- ---- -- --- --- --- --- -- ---- ---------- - ------ ---- - - ---- - ----- ---- ---, - ----- --- ----- ---- ---- ---- ---- --- --- --- --- -- ------- - -- -- - - ---------- - ------ ---- - - ---- - ----- ---- ---, - ----- --- ----- ---- ---- ---- -- --- --- --- --- -- ---- --------- --- --- --- --- -- ---- ---------- - ------ ---- --- ----- --- - ---- - ----- ---- ---, - ----- - ---- - ----- ---- ---, - ----- --- ----- ---- ---- ---- -- --- --- --- --- -- ---- ---------- - ------ ---- --- ---.
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--- ----- ---- ---- ---- -- --- --- --- --- -- ---- ---------- - ------ ---- --- --- - ---- - ----- ---- ---, - ----- --- ----- ---- ---- ---- -- --- --- --- --- -- ---- ---------- - ------ ---- --- ----.</p>
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<p>--- - -  --- -- -- -- -- -- -- --  - ------ -----. --- ------ --- ---- -- --- ----- -- -- -- ------ ---- ---- - -- - ---- - ----- ---- ---, - ----- --- ----- ---- ---- ---- - - ------ ---- --- ----- --- - ---- - ----- ---- ---, - ----- - ---- - ----- ---- ---, - ----- --- ----- ---- ---- ---- -- --- --- --- --- -- ---- ---------- - ------ ---- --- ---.
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--- ----- ---- ---- ---- -- --- --- --- --- -- ---- ---------- - ------ ---- --- --- - ---- - ----- ---- ---, - ----- --- ----- ---- ---- ---- -- --- --- --- --- -- ---- ---------- - ------ ---- --- ----.</p>
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Revision as of 01:53, 1 August 2008

LCG-UNAM-MexicoTeam

Header image
iGEM 2008 TEAM
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Modeling


We are using MatLab to simulate our system. We have already done a first approximation which did not contain real parameteres. However, we tried to keep the system consistent within itself. Don't know what we're talking about? Take a look at our project description.

Metabolites

  1. AiiA
  2. AHL
  3. LuxR
  4. AHL:LuxR
  5. cI*
  6. ρ
  7. ρ:cI*
  8. RcnA
  9. Ni[int]
  10. Ni[ext]
  11. Unk

Acyl-Homoserine Lactone Lactonase
Acyl-Homoserine Lactone
Transcriptional Activator
Complex formed by AHL and LuxR
λ phage repressor (cI) modified with a LVA tail for quick degradation
rcnA promoter
Complex formed by cI* repressor and rcnA promoter
Escherichia coli nickel efflux pump
Intracellular nickel
Extracellular nickel
Unknown nickel import channel

Reactions

  1. AiiA + AHL -> AiiA
  2. AHL + LuxR <--> AHL:LuxR
  3. AHL:LuxR -> AHL:LuxR + cI*
  4. cI* -> Ø
  5. ρ + cI* <-> ρ:cI*
  6. ρ -> ρ + RcnA
  7. RcnA + Ni[int] -> RcnA + Ni[ext]
  8. RcnA -> Ø
  9. Unk + Ni[ext] -> Unk + Ni[int]

Degradation of AHL by AiiA
Complex formation and dissociation between AHL and LuxR
Transcription activation of cI* by AHL and LuxR complex
Natural degradation of cI*
Complex formation and dissociation between ρ and cI*
RcnA production
Nickel efflux by RcnA
Natural degradation of RcnA
Nickel import by the unknown channel

Assumptions

  1. Once there is nickel in the medium, RcnR no longer participates in the pump’s regulation. If there’s nickel in the medium, we can assume that RcnR is always coupled with a Ni molecule, so it will not be capable of repressing RcnA (The few RcnR molecules in the cell will cause noise, but this will be indistinguishable from the pump’s normal behavior).
  2. All decrease in AHL concentration is due to AiiA. We consider the natural degradation of AHL to be unimportant given the time taken to make the analysis (AHL half-life is long, from 3 to 24 hours).
  3. The change in the transcription of cI* is only dependent on AHL concentration. There’s a basal production of cI*, however the change will always be due to the AHL concentration given that production of LuxR is constitutive.
  4. It is a homogeneous system. This means that the coefficients of the equations are constant (so we don’t have compartmentalization).
  5. The quantity of nickel used by the cell is negligible compared to the concentrations in and out of the cell. This means we don’t need to include an equation describing the change in the Ni concentration due to cell consumption in the time used by the experiment.
  6. The production of RcnR, LuxR and AiiA is constitutive and their concentrations have reached the steady state.
  7. NikABCDE will not play a role in our model. NikABCDE serves to import nickel to the cell, however it only works in anaerobic conditions and our experiment will be made in aerobic conditions. This therefore implies that the nickel import will only take place by the unknown mechanism, which nonetheless is constant and constitutive.

We still need to state here, why can we assume these things?
Modeling_sub

--- - - --- -- -- -- -- -- -- -- - ------ -----. --- ------ --- ---- -- --- ----- -- -- -- ------ ---- ---- - -- - ---- - ----- ---- ---, - ----- --- ----- ---- ---- ---- -- --- --- --- --- -- ---- ---------- - ------ ---- - - ---- - ----- ---- ---, - ----- --- ----- ---- ---- ---- -- --- --- --- --- -- ---- ---------- - ------ ---- --- ----- --- - ---- - ----- ---- ---, - ----- - ---- - ----- ---- ---, - ----- --- ----- ---- ---- ---- -- --- --- --- --- -- ---- ---------- - ------ ---- --- ---. --- ----- ---- ---- ---- -- --- --- --- --- -- ---- ---------- - ------ ---- --- --- - ---- - ----- ---- ---, - ----- --- ----- ---- ---- ---- -- --- --- --- --- -- ---- ---------- - ------ ---- --- ----.

--- - - --- -- -- -- -- -- -- -- - ------ -----. --- ------ --- ---- -- --- ----- -- -- -- ------ ---- ---- - -- - ---- - ----- ---- ---, - ----- --- ----- ---- ---- ---- -- --- --- --- --- -- ---- ---------- - ------ ---- - - ---- - ----- ---- ---, - ----- --- ----- ---- ---- ---- ---- --- --- --- --- -- ------- - -- -- - - ---------- - ------ ---- - - ---- - ----- ---- ---, - ----- --- ----- ---- ---- ---- -- --- --- --- --- -- ---- --------- --- --- --- --- -- ---- ---------- - ------ ---- --- ----- --- - ---- - ----- ---- ---, - ----- - ---- - ----- ---- ---, - ----- --- ----- ---- ---- ---- -- --- --- --- --- -- ---- ---------- - ------ ---- --- ---. --- ----- ---- ---- ---- -- --- --- --- --- -- ---- ---------- - ------ ---- --- --- - ---- - ----- ---- ---, - ----- --- ----- ---- ---- ---- -- --- --- --- --- -- ---- ---------- - ------ ---- --- ----.

--- - - --- -- -- -- -- -- -- -- - ------ -----. --- ------ --- ---- -- --- ----- -- -- -- ------ ---- ---- - -- - ---- - ----- ---- ---, - ----- --- ----- ---- ---- ---- - - ------ ---- --- ----- --- - ---- - ----- ---- ---, - ----- - ---- - ----- ---- ---, - ----- --- ----- ---- ---- ---- -- --- --- --- --- -- ---- ---------- - ------ ---- --- ---. --- ----- ---- ---- ---- -- --- --- --- --- -- ---- ---------- - ------ ---- --- --- - ---- - ----- ---- ---, - ----- --- ----- ---- ---- ---- -- --- --- --- --- -- ---- ---------- - ------ ---- --- ----.

 
 
             
LCG-UNAM-MexicoTeam
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Modeling

--- - - --- -- -- -- -- -- -- -- - ------ -----. --- ------ --- ---- -- --- ----- -- -- -- ------ ---- ---- - -- - ---- - ----- ---- ---, - ----- --- ----- ---- ---- ---- -- --- --- --- --- -- ---- ---------- - ------ ---- --- ----.
Modeling_sub

--- - - --- -- -- -- -- -- -- -- - ------ -----. --- ------ --- ---- -- --- ----- -- -- -- ------ ---- ---- - -- - ---- - ----- ---- ---, - ----- --- ----- ---- ---- ---- -- --- --- --- --- -- ---- ---------- - ------ ---- - - ---- - ----- ---- ---, - ----- --- ----- ---- ---- ---- -- --- --- --- --- -- ---- ---------- - ------ ---- --- ----- --- - ---- - ----- ---- ---, - ----- - ---- - ----- ---- ---, - ----- --- ----- ---- ---- ---- -- --- --- --- --- -- ---- ---------- - ------ ---- --- ---. --- ----- ---- ---- ---- -- --- --- --- --- -- ---- ---------- - ------ ---- --- --- - ---- - ----- ---- ---, - ----- --- ----- ---- ---- ---- -- --- --- --- --- -- ---- ---------- - ------ ---- --- ----.

--- - - --- -- -- -- -- -- -- -- - ------ -----. --- ------ --- ---- -- --- ----- -- -- -- ------ ---- ---- - -- - ---- - ----- ---- ---, - ----- --- ----- ---- ---- ---- -- --- --- --- --- -- ---- ---------- - ------ ---- - - ---- - ----- ---- ---, - ----- --- ----- ---- ---- ---- ---- --- --- --- --- -- ------- - -- -- - - ---------- - ------ ---- - - ---- - ----- ---- ---, - ----- --- ----- ---- ---- ---- -- --- --- --- --- -- ---- --------- --- --- --- --- -- ---- ---------- - ------ ---- --- ----- --- - ---- - ----- ---- ---, - ----- - ---- - ----- ---- ---, - ----- --- ----- ---- ---- ---- -- --- --- --- --- -- ---- ---------- - ------ ---- --- ---. --- ----- ---- ---- ---- -- --- --- --- --- -- ---- ---------- - ------ ---- --- --- - ---- - ----- ---- ---, - ----- --- ----- ---- ---- ---- -- --- --- --- --- -- ---- ---------- - ------ ---- --- ----.

--- - - --- -- -- -- -- -- -- -- - ------ -----. --- ------ --- ---- -- --- ----- -- -- -- ------ ---- ---- - -- - ---- - ----- ---- ---, - ----- --- ----- ---- ---- ---- - - ------ ---- --- ----- --- - ---- - ----- ---- ---, - ----- - ---- - ----- ---- ---, - ----- --- ----- ---- ---- ---- -- --- --- --- --- -- ---- ---------- - ------ ---- --- ---. --- ----- ---- ---- ---- -- --- --- --- --- -- ---- ---------- - ------ ---- --- --- - ---- - ----- ---- ---, - ----- --- ----- ---- ---- ---- -- --- --- --- --- -- ---- ---------- - ------ ---- --- ----.

 
 
             

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