|
|
Line 1: |
Line 1: |
- | <html>
| |
- | <head>
| |
- | <title>LCG-UNAM-MexicoTeam</title>
| |
- | <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
| |
- | <link rel="stylesheet" href="http://kabah.lcg.unam.mx/~larriola/mm_health_nutr.css" type="text/css" />
| |
- | <script language="JavaScript" type="text/javascript">
| |
- | //--------------- Fecha ---------------
| |
- | var d=new Date();
| |
- | var monthname=new Array("January","February","March","April","May","June","July","August","September","October","November","December");
| |
- | var TODAY = monthname[d.getMonth()] + " " + d.getDate() + ", " + d.getFullYear();
| |
- | //--------------- END Fecha ---------------
| |
- | </script>
| |
- | <style type="text/css">
| |
- | <!--
| |
- | .Estilo1 {color: #5C743D}
| |
- | -->
| |
- | </style>
| |
- | </head>
| |
- | <body bgcolor="#F4FFE4">
| |
- | <table width="82%" border="0" cellspacing="0" cellpadding="0">
| |
- | <tr bgcolor="#D5EDB3">
| |
- | <td colspan="3" rowspan="2"><img src="http://kabah.lcg.unam.mx/~larriola/mm_health_photo.jpg" alt="Header image" width="524" height="143" border="0" /></td>
| |
- | <td height="50" colspan="3" id="logo" valign="bottom" align="center" nowrap="nowrap">LCG-UNAM-Mexico</td>
| |
- | <td width="132" rowspan="2"><img src="http://kabah.lcg.unam.mx/~larriola/TeamLogo_00.jpg" width="120" height="142" /></td>
| |
- | </tr>
| |
| | | |
- | <tr bgcolor="#D5EDB3">
| |
- | <td height="51" colspan="3" id="tagline" valign="top" align="center">iGEM 2008 TEAM</td>
| |
- | </tr>
| |
- |
| |
- | <tr>
| |
- | <td colspan="7" bgcolor="#5C743D"><img src="http://kabah.lcg.unam.mx/~larriola/mm_spacer.gif" alt="" width="1" height="2" border="0" /></td>
| |
- | </tr>
| |
- |
| |
- | <tr>
| |
- | <td colspan="7" bgcolor="#99CC66" background="http://kabah.lcg.unam.mx/~larriola/mm_dashed_line.gif"><img src="http://kabah.lcg.unam.mx/~larriola/mm_dashed_line.gif" alt="line decor" width="4" height="3" border="0" /></td>
| |
- | </tr>
| |
- |
| |
- | <tr bgcolor="#99CC66">
| |
- | <td colspan="7" id="dateformat" height="20"> <script language="JavaScript" type="text/javascript">
| |
- | document.write(TODAY); </script> </td>
| |
- | </tr>
| |
- | <tr>
| |
- | <td colspan="7" bgcolor="#99CC66" background="http://kabah.lcg.unam.mx/~larriola/mm_dashed_line.gif"><img src="http://kabah.lcg.unam.mx/~larriola/mm_dashed_line.gif" alt="line decor" width="4" height="3" border="0" /></td>
| |
- | </tr>
| |
- |
| |
- | <tr>
| |
- | <td colspan="7" bgcolor="#5C743D"><img src="http://kabah.lcg.unam.mx/~larriola/mm_spacer.gif" alt="" width="1" height="2" border="0" /></td>
| |
- | </tr>
| |
- |
| |
- | <tr>
| |
- | <td width="224" valign="top" bgcolor="#5C743D">
| |
- | <table border="0" cellspacing="0" cellpadding="0" width="165" id="navigation">
| |
- | <tr>
| |
- | <td width="165" bgcolor="#5C743D"> <br />
| |
- | <br /></td>
| |
- | </tr>
| |
- | <tr>
| |
- | <td width="165" bgcolor="#5C743D"><a href="https://2008.igem.org/Team:LCG-UNAM-Mexico" class="navText">Home</a></td>
| |
- | </tr>
| |
- | <tr>
| |
- | <td width="165" bgcolor="#5C743D"><a href="https://2008.igem.org/Team:LCG-UNAM-Mexico/Team" class="navText">About Us</a></td>
| |
- | </tr>
| |
- | <tr>
| |
- | <td width="165" bgcolor="#5C743D"><a href="https://2008.igem.org/Team:LCG-UNAM-Mexico/Project" class="navText">Our Project</a></td>
| |
- | </tr>
| |
- | <tr>
| |
- | <td width="165" bgcolor="#5C743D"><a href="https://2008.igem.org/Team:LCG-UNAM-Mexico/Parts" class="navText">Parts Submitted to the Registry</a></td>
| |
- | </tr>
| |
- | <tr>
| |
- | <td width="165" bgcolor="#5C743D"><a href="https://2008.igem.org/Team:LCG-UNAM-Mexico/Modeling" class="navText">Modeling</a></td>
| |
- | </tr>
| |
- | <tr>
| |
- | <td width="165" bgcolor="#5C743D"><a href="https://2008.igem.org/Team:LCG-UNAM-Mexico/Notebook" class="navText">Notebook</a></td>
| |
- | </tr>
| |
- | </table>
| |
- | <br />
| |
- | <br />
| |
- | <br />
| |
- | <br /> </td>
| |
- | <td width="42"> </td>
| |
- | <td colspan="4" valign="top"><img src="http://kabah.lcg.unam.mx/~larriola/mm_spacer.gif" alt="" width="305" height="1" border="0" /><br />
| |
- | <br />
| |
- | <br />
| |
- | <table border="0" cellspacing="0" cellpadding="2" width="590">
| |
- | <tr>
| |
- | <td class="pageName">Modeling</td>
| |
- | </tr>
| |
- | <tr>
| |
- | <td class="bodyText"><p align="justify"><br>
| |
- | 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>
| |
- | <p><strong>Metabolites</strong></p>
| |
- | <table width="585" border="0">
| |
- | <tr>
| |
- | <td width="132"><ol>
| |
- | <li> AiiA</li>
| |
- | <li>AHL</li>
| |
- | <li>LuxR</li>
| |
- | <li>AHL:LuxR</li>
| |
- | <li>cI*</li>
| |
- | <li>ρ</li>
| |
- | <li>ρ:cI*</li>
| |
- | <li>RcnA</li>
| |
- | <li>Ni[int]</li>
| |
- | <li>Ni[ext]</li>
| |
- | <li>Unk</li>
| |
- | </ol> </td>
| |
- | <td width="443" valign="top"><p>Acyl-Homoserine Lactone Lactonase<br>
| |
- | Acyl-Homoserine Lactone<br>
| |
- | Transcriptional Activator<br>
| |
- | Complex formed by AHL and LuxR<br>
| |
- | λ phage repressor (cI) modified with a LVA tail for quick degradation<br>
| |
- | <em>rcnA</em> promoter<br>
| |
- | Complex formed by cI* repressor and <em>rcnA</em> promoter <br>
| |
- | <em>Escherichia coli</em> nickel efflux pump<br>
| |
- | Intracellular nickel<br>
| |
- | Extracellular nickel
| |
- | <br>
| |
- | Unknown nickel import channel <br>
| |
- | </p>
| |
- | </td>
| |
- | </tr>
| |
- | </table>
| |
- | <p> </p>
| |
- | <p><strong>Reactions</strong></p>
| |
- | <table width="585" border="0">
| |
- | <tr>
| |
- | <td width="206" valign="top"><ol>
| |
- | <li>AiiA + AHL <strong>-></strong> AiiA </li>
| |
- | <li>AHL + LuxR <strong><--></strong> AHL:LuxR </li>
| |
- | <li>AHL:LuxR <strong>-></strong> AHL:LuxR + cI*</li>
| |
- | <li>cI* <strong>-></strong> Ø</li>
| |
- | <li>ρ + cI* <strong><-></strong> ρ:cI*</li>
| |
- | <li>ρ <strong>-></strong> ρ + RcnA</li>
| |
- | <li>RcnA + Ni[int] <strong>-></strong> RcnA + Ni[ext]</li>
| |
- | <li>RcnA <strong>-></strong> Ø</li>
| |
- | <li>Unk + Ni[ext] <strong>-></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>
| |
- | Nickel import by the unknown channel
| |
- | </p></td>
| |
- | </tr>
| |
- | </table>
| |
- | <p> </p>
| |
- | <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>
| |
- | <p align="justify" class="Estilo1">We still need to state here, why can we assume these things?</p>
| |
- | </td>
| |
- | </tr>
| |
- | <td class="pageName">Modeling_sub</td>
| |
- | <tr>
| |
- | <td class="bodyText"><p>--- - - --- -- -- -- -- -- -- -- - ------ -----. --- ------ --- ---- -- --- ----- -- -- -- ------ ---- ---- - -- - ---- - ----- ---- ---, - ----- --- ----- ---- ---- ---- -- --- --- --- --- -- ---- ---------- - ------ ---- - - ---- - ----- ---- ---, - ----- --- ----- ---- ---- ---- -- --- --- --- --- -- ---- ---------- - ------ ---- --- ----- --- - ---- - ----- ---- ---, - ----- - ---- - ----- ---- ---, - ----- --- ----- ---- ---- ---- -- --- --- --- --- -- ---- ---------- - ------ ---- --- ---.
| |
- | --- ----- ---- ---- ---- -- --- --- --- --- -- ---- ---------- - ------ ---- --- --- - ---- - ----- ---- ---, - ----- --- ----- ---- ---- ---- -- --- --- --- --- -- ---- ---------- - ------ ---- --- ----.</p>
| |
- | <p>--- - - --- -- -- -- -- -- -- -- - ------ -----. --- ------ --- ---- -- --- ----- -- -- -- ------ ---- ---- - -- - ---- - ----- ---- ---, - ----- --- ----- ---- ---- ---- -- --- --- --- --- -- ---- ---------- - ------ ---- - - ---- - ----- ---- ---, - ----- --- ----- ---- ---- ---- ---- --- --- --- --- -- ------- - -- -- - - ---------- - ------ ---- - - ---- - ----- ---- ---, - ----- --- ----- ---- ---- ---- -- --- --- --- --- -- ---- --------- --- --- --- --- -- ---- ---------- - ------ ---- --- ----- --- - ---- - ----- ---- ---, - ----- - ---- - ----- ---- ---, - ----- --- ----- ---- ---- ---- -- --- --- --- --- -- ---- ---------- - ------ ---- --- ---.
| |
- | --- ----- ---- ---- ---- -- --- --- --- --- -- ---- ---------- - ------ ---- --- --- - ---- - ----- ---- ---, - ----- --- ----- ---- ---- ---- -- --- --- --- --- -- ---- ---------- - ------ ---- --- ----.</p>
| |
- | <p>--- - - --- -- -- -- -- -- -- -- - ------ -----. --- ------ --- ---- -- --- ----- -- -- -- ------ ---- ---- - -- - ---- - ----- ---- ---, - ----- --- ----- ---- ---- ---- - - ------ ---- --- ----- --- - ---- - ----- ---- ---, - ----- - ---- - ----- ---- ---, - ----- --- ----- ---- ---- ---- -- --- --- --- --- -- ---- ---------- - ------ ---- --- ---.
| |
- | --- ----- ---- ---- ---- -- --- --- --- --- -- ---- ---------- - ------ ---- --- --- - ---- - ----- ---- ---, - ----- --- ----- ---- ---- ---- -- --- --- --- --- -- ---- ---------- - ------ ---- --- ----.</p>
| |
- | </td>
| |
- | </tr>
| |
- | </table><br />
| |
- | <br />
| |
- | <td width="132"> </td>
| |
- | </tr>
| |
- | <tr>
| |
- | <td width="224"> </td>
| |
- | <td width="42"> </td>
| |
- | <td width="296"> </td>
| |
- | <td width="135"> </td>
| |
- | <td width="59"> </td>
| |
- | <td width="109"> </td>
| |
- | <td width="132"> </td>
| |
- | </tr>
| |
- | </table>
| |
- | </body>
| |
- | </html>
| |
- | <html>
| |
- | <head>
| |
- | <title>LCG-UNAM-MexicoTeam</title>
| |
- | <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
| |
- | <link rel="stylesheet" href="http://kabah.lcg.unam.mx/~larriola/mm_health_nutr.css" type="text/css" />
| |
- | <script language="JavaScript" type="text/javascript">
| |
- | //--------------- Fecha ---------------
| |
- | var d=new Date();
| |
- | var monthname=new Array("January","February","March","April","May","June","July","August","September","October","November","December");
| |
- | var TODAY = monthname[d.getMonth()] + " " + d.getDate() + ", " + d.getFullYear();
| |
- | //--------------- END Fecha ---------------
| |
- | </script>
| |
- | </head>
| |
- | <body bgcolor="#F4FFE4">
| |
- | <table width="82%" border="0" cellspacing="0" cellpadding="0">
| |
- | <tr bgcolor="#D5EDB3">
| |
- | <td colspan="3" rowspan="2"><img src="http://kabah.lcg.unam.mx/~larriola/mm_health_photo.jpg" alt="Header image" width="524" height="143" border="0" /></td>
| |
- | <td height="50" colspan="3" id="logo" valign="bottom" align="center" nowrap="nowrap">LCG-UNAM-Mexico</td>
| |
- | <td width="132" rowspan="2"><img src="http://kabah.lcg.unam.mx/~larriola/TeamLogo_00.jpg" width="120" height="142" /></td>
| |
- | </tr>
| |
- |
| |
- | <tr bgcolor="#D5EDB3">
| |
- | <td height="51" colspan="3" id="tagline" valign="top" align="center">iGEM 2008 TEAM</td>
| |
- | </tr>
| |
- |
| |
- | <tr>
| |
- | <td colspan="7" bgcolor="#5C743D"><img src="http://kabah.lcg.unam.mx/~larriola/mm_spacer.gif" alt="" width="1" height="2" border="0" /></td>
| |
- | </tr>
| |
- |
| |
- | <tr>
| |
- | <td colspan="7" bgcolor="#99CC66" background="http://kabah.lcg.unam.mx/~larriola/mm_dashed_line.gif"><img src="http://kabah.lcg.unam.mx/~larriola/mm_dashed_line.gif" alt="line decor" width="4" height="3" border="0" /></td>
| |
- | </tr>
| |
- |
| |
- | <tr bgcolor="#99CC66">
| |
- | <td colspan="7" id="dateformat" height="20"> <script language="JavaScript" type="text/javascript">
| |
- | document.write(TODAY); </script> </td>
| |
- | </tr>
| |
- | <tr>
| |
- | <td colspan="7" bgcolor="#99CC66" background="http://kabah.lcg.unam.mx/~larriola/mm_dashed_line.gif"><img src="http://kabah.lcg.unam.mx/~larriola/mm_dashed_line.gif" alt="line decor" width="4" height="3" border="0" /></td>
| |
- | </tr>
| |
- |
| |
- | <tr>
| |
- | <td colspan="7" bgcolor="#5C743D"><img src="http://kabah.lcg.unam.mx/~larriola/mm_spacer.gif" alt="" width="1" height="2" border="0" /></td>
| |
- | </tr>
| |
- |
| |
- | <tr>
| |
- | <td width="224" valign="top" bgcolor="#5C743D">
| |
- | <table border="0" cellspacing="0" cellpadding="0" width="165" id="navigation">
| |
- | <tr>
| |
- | <td width="165" bgcolor="#5C743D"> <br />
| |
- | <br /></td>
| |
- | </tr>
| |
- | <tr>
| |
- | <td width="165" bgcolor="#5C743D"><a href="https://2008.igem.org/Team:LCG-UNAM-Mexico" class="navText">Home</a></td>
| |
- | </tr>
| |
- | <tr>
| |
- | <td width="165" bgcolor="#5C743D"><a href="https://2008.igem.org/Team:LCG-UNAM-Mexico/Team" class="navText">About Us</a></td>
| |
- | </tr>
| |
- | <tr>
| |
- | <td width="165" bgcolor="#5C743D"><a href="https://2008.igem.org/Team:LCG-UNAM-Mexico/Project" class="navText">Our Project</a></td>
| |
- | </tr>
| |
- | <tr>
| |
- | <td width="165" bgcolor="#5C743D"><a href="https://2008.igem.org/Team:LCG-UNAM-Mexico/Parts" class="navText">Parts Submitted to the Registry</a></td>
| |
- | </tr>
| |
- | <tr>
| |
- | <td width="165" bgcolor="#5C743D"><a href="https://2008.igem.org/Team:LCG-UNAM-Mexico/Modeling" class="navText">Modeling</a></td>
| |
- | </tr>
| |
- | <tr>
| |
- | <td width="165" bgcolor="#5C743D"><a href="https://2008.igem.org/Team:LCG-UNAM-Mexico/Notebook" class="navText">Notebook</a></td>
| |
- | </tr>
| |
- | </table>
| |
- | <br />
| |
- | <br />
| |
- | <br />
| |
- | <br /> </td>
| |
- | <td width="42"> </td>
| |
- | <td colspan="4" valign="top"><img src="http://kabah.lcg.unam.mx/~larriola/mm_spacer.gif" alt="" width="305" height="1" border="0" /><br />
| |
- | <br />
| |
- | <br />
| |
- | <table border="0" cellspacing="0" cellpadding="2" width="590">
| |
- | <tr>
| |
- | <td class="pageName">Modeling</td>
| |
- | </tr>
| |
- | <tr>
| |
- | <td class="bodyText"><p>--- - - --- -- -- -- -- -- -- -- - ------ -----. --- ------ --- ---- -- --- ----- -- -- -- ------ ---- ---- - -- - ---- - ----- ---- ---, - ----- --- ----- ---- ---- ---- -- --- --- --- --- -- ---- ---------- - ------ ---- --- ----.</p>
| |
- | </td>
| |
- | </tr>
| |
- | <td class="pageName">Modeling_sub</td>
| |
- | <tr>
| |
- | <td class="bodyText"><p>--- - - --- -- -- -- -- -- -- -- - ------ -----. --- ------ --- ---- -- --- ----- -- -- -- ------ ---- ---- - -- - ---- - ----- ---- ---, - ----- --- ----- ---- ---- ---- -- --- --- --- --- -- ---- ---------- - ------ ---- - - ---- - ----- ---- ---, - ----- --- ----- ---- ---- ---- -- --- --- --- --- -- ---- ---------- - ------ ---- --- ----- --- - ---- - ----- ---- ---, - ----- - ---- - ----- ---- ---, - ----- --- ----- ---- ---- ---- -- --- --- --- --- -- ---- ---------- - ------ ---- --- ---.
| |
- | --- ----- ---- ---- ---- -- --- --- --- --- -- ---- ---------- - ------ ---- --- --- - ---- - ----- ---- ---, - ----- --- ----- ---- ---- ---- -- --- --- --- --- -- ---- ---------- - ------ ---- --- ----.</p>
| |
- | <p>--- - - --- -- -- -- -- -- -- -- - ------ -----. --- ------ --- ---- -- --- ----- -- -- -- ------ ---- ---- - -- - ---- - ----- ---- ---, - ----- --- ----- ---- ---- ---- -- --- --- --- --- -- ---- ---------- - ------ ---- - - ---- - ----- ---- ---, - ----- --- ----- ---- ---- ---- ---- --- --- --- --- -- ------- - -- -- - - ---------- - ------ ---- - - ---- - ----- ---- ---, - ----- --- ----- ---- ---- ---- -- --- --- --- --- -- ---- --------- --- --- --- --- -- ---- ---------- - ------ ---- --- ----- --- - ---- - ----- ---- ---, - ----- - ---- - ----- ---- ---, - ----- --- ----- ---- ---- ---- -- --- --- --- --- -- ---- ---------- - ------ ---- --- ---.
| |
- | --- ----- ---- ---- ---- -- --- --- --- --- -- ---- ---------- - ------ ---- --- --- - ---- - ----- ---- ---, - ----- --- ----- ---- ---- ---- -- --- --- --- --- -- ---- ---------- - ------ ---- --- ----.</p>
| |
- | <p>--- - - --- -- -- -- -- -- -- -- - ------ -----. --- ------ --- ---- -- --- ----- -- -- -- ------ ---- ---- - -- - ---- - ----- ---- ---, - ----- --- ----- ---- ---- ---- - - ------ ---- --- ----- --- - ---- - ----- ---- ---, - ----- - ---- - ----- ---- ---, - ----- --- ----- ---- ---- ---- -- --- --- --- --- -- ---- ---------- - ------ ---- --- ---.
| |
- | --- ----- ---- ---- ---- -- --- --- --- --- -- ---- ---------- - ------ ---- --- --- - ---- - ----- ---- ---, - ----- --- ----- ---- ---- ---- -- --- --- --- --- -- ---- ---------- - ------ ---- --- ----.</p>
| |
- | </td>
| |
- | </tr>
| |
- | </table><br />
| |
- | <br />
| |
- | <td width="132"> </td>
| |
- | </tr>
| |
- | <tr>
| |
- | <td width="224"> </td>
| |
- | <td width="42"> </td>
| |
- | <td width="296"> </td>
| |
- | <td width="135"> </td>
| |
- | <td width="59"> </td>
| |
- | <td width="109"> </td>
| |
- | <td width="132"> </td>
| |
- | </tr>
| |
- | </table>
| |
- | </body>
| |
- | </html>
| |