Team:UC Davis/Adding secretion

From 2009.igem.org

(Difference between revisions)

Revision as of 07:15, 24 September 2009

Adding Secretion

Adding Secretion:

General model for secretion Secretion Models Why test different genes

General model for secretion system:

Advantages of having several models:

In our secretion system, we are using two genes with different sizes as our target secretion genes, GFP being short in length and Luciferase being comparably long would test our secretion system and its ability to secrete small and large proteins.
Testing multiple different combinations; Signal Sequence alone, Signal Sequence plus ompA/INPNC and ompA/INPNC alone, would help us find the best combination for our secretion system based on their secretion ability and rank them from strongest to weakest in strength (in this specific system).

Secretion Models:
Click on a specific model for more information:

Why test different genes in our secretion system?

There is wide range of genes present in our environment. Therefore, it is important to measure our secretion system’s ability to secrete genes of various sizes.

Molecular data on some proteins

	Molecular Wieght	Number of residues	Number of polypeptide
Cytochrome c (human)	13,000	104	1
Ribonuclease A(bovine pancreas)	13,700	124	1
Serum albumin (human)	68,500	609	1

(Page 128, third edition “Lehninger Principles of Biochemistry” by David L. Nelson and Michael M. Cox)

@@ Line 2: / Line 2: @@
 <head>
 <meta content="text/html;charset=ISO-8859-1" http-equiv="Content-Type">
-<title></title>
+<title>Adding Secretion</title>
 </head>
-<body>
+<body style="color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);"
+alink="#ee0000" link="#0000ee" vlink="#551a8b">
 <div style="text-align: center;"><b style="color: rgb(255, 255, 153);"><span
 style="font-size: 13.5pt; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;;"><big><big><big><big><a
@@ Line 15: / Line 16: @@
 alt="" src="https://static.igem.org/mediawiki/2009/d/d1/UCDAVIS_PIC4.png"
 style="border: 0px solid ; width: 82px; height: 36px;"></big></big></big></big></span></b></a><b
+style="color: rgb(255, 255, 153);"><span
+style="font-size: 13.5pt; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;;"></span></b><b
 style="color: rgb(255, 255, 153);"><span
 style="font-size: 13.5pt; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;;"></span></b><b
@@ Line 35: / Line 38: @@
 href="https://2009.igem.org/Team:UC_Davis/Part1"><img alt=""
 src="https://static.igem.org/mediawiki/2009/a/a6/UCDAVIS_PIC6.png"
-style="border: 0px solid ; width: 78px; height: 37px;"></a>&nbsp;<a
+style="border: 0px solid ; width: 78px; height: 37px;"></a>&nbsp;</big></big></big></big></span></b></div>
-href="https://2009.igem.org/Team:UC_Davis/Contact1"><img alt=""
+<hr
-src="https://static.igem.org/mediawiki/2009/1/1d/UCDAVIS_PIC7.png"
+style="width: 100%; height: 2px; background-color: rgb(255, 255, 255);">
-style="border: 0px solid ; width: 83px; height: 37px;"></a></big></big></big></big></span></b><b
+<div style="text-align: left; background-color: rgb(255, 255, 255);"><big
-style="color: rgb(0, 0, 0);"><span
+style="text-decoration: underline;"><big><span
-style="font-size: 13.5pt; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;;"></span></b><br>
+style="font-weight: bold;"><big><small>Adding Secretion:</small></big></span></big></big><br>
+<div style="text-align: center;"><big style="font-weight: bold;"><a
+href="#general_model">General model for secretion</a>&nbsp;&nbsp;&nbsp;&nbsp;
+<a href="#secretion_model">Secretion Models</a>&nbsp;&nbsp;&nbsp;&nbsp;
+<a href="#different_genes">Why test different genes</a></big><br>
+<hr style="width: 100%; height: 2px;"><big
+style="text-decoration: underline;"><big><span
+style="font-weight: bold;"></span></big></big></div>
+<p class="MsoNormal" style="line-height: normal;"><span
+style="font-size: 12pt; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;;"><o:p></o:p></span></p>
+<b><u><span
+style="font-size: 20pt; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;;"></span></u></b><big
+style="text-decoration: underline;"><big><span
+style="font-weight: bold;"></span></big></big>
+<div style="text-align: center;"><big><big><big><span
+style="font-weight: bold;"><small><span
+style="text-decoration: underline; background-color: rgb(255, 255, 0);"><a
+name="general_model"></a>General
+model for secretion system:<br>
+<img
+style="width: 242px; height: 58px; background-color: rgb(255, 255, 255);"
+alt=""
+src="https://static.igem.org/mediawiki/2009/4/4e/UCDAVIS_PROMOTER_1.png"><img
+style="width: 89px; height: 81px; background-color: rgb(255, 255, 255);"
+alt="" src="https://static.igem.org/mediawiki/2009/1/15/UCDAVIS_RBS1.png"><img
+style="width: 106px; height: 56px; background-color: rgb(255, 255, 255);"
+alt=""
+src="https://static.igem.org/mediawiki/2009/9/95/UCDAVIS_SECRETION.png"><img
+style="width: 94px; height: 69px; background-color: rgb(255, 255, 255);"
+alt="" src="https://static.igem.org/mediawiki/2009/9/9d/UCDAVIS_SS1.png"><img
+style="width: 106px; height: 59px; background-color: rgb(255, 255, 255);"
+alt="" src="https://static.igem.org/mediawiki/2009/0/0c/UCDAVIS_GENE1.png"><img
+style="width: 134px; height: 66px; background-color: rgb(255, 255, 255);"
+alt="" src="https://static.igem.org/mediawiki/2009/c/c0/UCDAVIS_6HIS.png"><img
+style="width: 94px; height: 83px; background-color: rgb(255, 255, 255);"
+alt="" src="https://static.igem.org/mediawiki/2009/c/ca/UCDAVIS_STOP.png"><br>
+<br>
+</span></small></span></big></big></big>
+<p class="MsoNormal"
+style="margin-bottom: 0.0001pt; line-height: normal; text-align: center;"><b><span
+style="font-size: 12pt; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;;">Advantages
+of having several models:</span></b><b><span
+style="font-size: 12pt; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;;"><o:p></o:p></span></b></p>
+<div style="text-align: left;"></div>
+<p class="MsoNormal" style="line-height: normal; text-align: left;"><span
+style="font-size: 12pt; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;;">&nbsp;&nbsp;&nbsp;
+&nbsp;&nbsp; In
+our secretion system, we are using two genes with different sizes as
+our target
+secretion genes, GFP being short in length and Luciferase being
+comparably long
+would test our secretion system and its ability to secrete small and
+large
+proteins. <br>
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Testing multiple different combinations;
+Signal
+Sequence alone, Signal Sequence plus ompA/INPNC and ompA/INPNC alone,
+would
+help us find the best combination for our secretion system based on
+their
+secretion ability and rank them from strongest to weakest in strength
+(in this
+specific system).</span></p>
+<big><big><big><span style="font-weight: bold;"><small><span
+style="text-decoration: underline; background-color: rgb(255, 255, 0);"></span></small></span></big></big></big><br>
+<div style="text-align: left;">
+<hr style="width: 100%; height: 2px;"><big><small><big
+style="font-weight: bold;"><span style="text-decoration: underline;"><small><big><a
+name="secretion_model"></a>Secretion
+Models:</big><br>
+</small></span></big><span style="font-style: italic;">Click on a
+specific model for more information:</span><big
+style="font-weight: bold;"><span style="text-decoration: underline;"><small><br>
+</small></span></big><span style="font-style: italic;"><big><span
+style="text-decoration: underline;"><small></small></span></big></span></small></big>
+<div style="text-align: center;"><big><span style="font-weight: bold;"></span></big><big><span
+style="font-weight: bold;"><a href="UCDAVIS_Model%201.html"><img alt=""
+src="https://static.igem.org/mediawiki/2009/b/ba/UCDAVIS_PIC12.png"
+style="border: 0px solid ; width: 95px; height: 63px;"></a><a
+href="UCDAVIS_Model%202.html"><img alt=""
+src="https://static.igem.org/mediawiki/2009/a/a4/UCDAVIS_PIC13.png"
+style="border: 0px solid ; width: 95px; height: 63px;"></a><a
+href="UCDAVIS_Model%203.html"><img alt=""
+src="https://static.igem.org/mediawiki/2009/9/9a/UCDAVIS_PIC14.png"
+style="border: 0px solid ; width: 95px; height: 63px;"></a><a
+href="UCDAVIS_Model%204.html"><img alt=""
+src="https://static.igem.org/mediawiki/2009/b/ba/UCDAVIS_PIC15.png"
+style="border: 0px solid ; width: 95px; height: 63px;"></a><a
+href="UCDAVIS_Model%205.html"><img alt=""
+src="https://static.igem.org/mediawiki/2009/5/5d/UCDAVIS_PIC16.png"
+style="border: 0px solid ; width: 95px; height: 63px;"></a>&nbsp;&nbsp;&nbsp;
+</span><span style="font-style: italic;"><big><span
+style="text-decoration: underline; font-weight: bold;"></span></big></span></big><br>
 </div>
-<hr style="width: 100%; height: 2px;"><b style="color: rgb(0, 0, 0);"><span
+<div style="text-align: center;"><big><span style="font-style: italic;"><big><span
-style="text-decoration: underline;">Adding secretion:</span><br>
+style="text-decoration: underline; font-weight: bold;"></span></big></span></big></div>
-</b>
+<big><span style="font-style: italic;"></span></big><span
+style="text-decoration: underline;"><span style="font-weight: bold;"></span></span><br>
+<big><span style="font-style: italic;"></span></big>
+<p class="MsoNormal"><b><span
+style="font-size: 13.5pt; line-height: 115%; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;;"><o:p></o:p></span></b></p>
+<big><big style="font-weight: bold;"><small></small>
+</big></big>
+<hr style="width: 100%; height: 2px;">
+<div style="text-align: left;"><b><u><span
+style="font-size: 20pt; line-height: 115%; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;;"><small><a
+name="different_genes"></a>Why
+test different genes in our secretion system?</small><o:p></o:p></span></u></b></div>
+<p class="MsoNormal"><b><span
+style="font-size: 13.5pt; line-height: 115%; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;;"><span
+style="">&nbsp;&nbsp;&nbsp;&nbsp; </span></span></b><span
+style="font-size: 13.5pt; line-height: 115%; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;;"><small>There
+is wide range of genes present in our environment. Therefore, it is
+important
+to measure our secretion system’s ability to secrete genes of various
+sizes.</small></span><b><span
+style="font-size: 13.5pt; line-height: 115%; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;;"><big><span
+style="text-decoration: underline;"><br>
+</span></big></span></b></p>
+<div style="text-align: center;"><b><span
+style="font-size: 13.5pt; line-height: 115%; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;;"><big><span
+style="text-decoration: underline;">Molecular data on some proteins</span></big><o:p></o:p></span></b></div>
+<div style="text-align: center;"></div>
+<div style="text-align: center;"></div>
+<table class="MsoNormalTable"
+style="border: medium none ; border-collapse: collapse; text-align: left; margin-left: auto; margin-right: auto; width: 597px; height: 264px;"
+border="1" cellpadding="0" cellspacing="0">
+<tbody>
+<tr style="">
+<td
+style="border: 1pt solid black; padding: 0in 5.4pt; width: 125.15pt; background-color: rgb(0, 0, 153); color: rgb(255, 255, 0);"
+valign="top" width="167">
+<p class="MsoNormal"
+style="margin-bottom: 0.0001pt; line-height: normal;"><b><span
+style="font-size: 14pt; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;;"><o:p>&nbsp;</o:p></span></b></p>
+</td>
+<td
+style="border-style: solid solid solid none; border-color: black black black -moz-use-text-color; border-width: 1pt 1pt 1pt medium; padding: 0in 5.4pt; width: 117.9pt; background-color: rgb(0, 0, 153); color: rgb(255, 255, 0);"
+valign="top" width="157"><small><small> </small></small>
+<p class="MsoNormal"
+style="margin-bottom: 0.0001pt; line-height: normal;"><small><small><b><span
+style="font-size: 14pt; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;;">Molecular
+Wieght<o:p></o:p></span></b></small></small></p>
+<small><small> </small></small></td>
+<td
+style="border-style: solid solid solid none; border-color: black black black -moz-use-text-color; border-width: 1pt 1pt 1pt medium; padding: 0in 5.4pt; width: 117.5pt; background-color: rgb(0, 0, 153); color: rgb(255, 255, 0);"
+valign="top" width="157"><small> </small>
+<p class="MsoNormal"
+style="margin-bottom: 0.0001pt; line-height: normal;"><small><b><span
+style="font-size: 14pt; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;;">Number
+of residues<o:p></o:p></span></b></small></p>
+<small> </small></td>
+<td
+style="border-style: solid solid solid none; border-color: black black black -moz-use-text-color; border-width: 1pt 1pt 1pt medium; padding: 0in 5.4pt; width: 118.25pt; background-color: rgb(0, 0, 153); color: rgb(255, 255, 0);"
+valign="top" width="158">
+<p class="MsoNormal"
+style="margin-bottom: 0.0001pt; line-height: normal;"><b><span
+style="font-size: 14pt; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;;">Number
+of polypeptide<o:p></o:p></span></b></p>
+</td>
+</tr>
+<tr style="">
+<td
+style="border-style: none solid solid; border-color: -moz-use-text-color black black; border-width: medium 1pt 1pt; padding: 0in 5.4pt; width: 125.15pt; background-color: rgb(0, 0, 153); color: rgb(255, 255, 0);"
+valign="top" width="167">
+<p class="MsoNormal"
+style="margin-bottom: 0.0001pt; line-height: normal;"><b><span
+style="font-size: 14pt; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;;">Cytochrome
+<i>c </i>(human)<o:p></o:p></span></b></p>
+</td>
+<td
+style="border-style: none solid solid none; border-color: -moz-use-text-color black black -moz-use-text-color; border-width: medium 1pt 1pt medium; padding: 0in 5.4pt; width: 117.9pt; background-color: rgb(0, 0, 153); color: rgb(255, 255, 0);"
+valign="top" width="157"><small> </small>
+<p class="MsoNormal"
+style="margin-bottom: 0.0001pt; line-height: normal;"><small><b><span
+style="font-size: 14pt; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;;">13,000<o:p></o:p></span></b></small></p>
+<small> </small></td>
+<td
+style="border-style: none solid solid none; border-color: -moz-use-text-color black black -moz-use-text-color; border-width: medium 1pt 1pt medium; padding: 0in 5.4pt; width: 117.5pt; background-color: rgb(0, 0, 153); color: rgb(255, 255, 0);"
+valign="top" width="157">
+<p class="MsoNormal"
+style="margin-bottom: 0.0001pt; line-height: normal;"><b><span
+style="font-size: 14pt; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;;">104<o:p></o:p></span></b></p>
+</td>
+<td
+style="border-style: none solid solid none; border-color: -moz-use-text-color black black -moz-use-text-color; border-width: medium 1pt 1pt medium; padding: 0in 5.4pt; width: 118.25pt; background-color: rgb(0, 0, 153); color: rgb(255, 255, 0);"
+valign="top" width="158">
+<p class="MsoNormal"
+style="margin-bottom: 0.0001pt; line-height: normal;"><b><span
+style="font-size: 14pt; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;;">1<o:p></o:p></span></b></p>
+</td>
+</tr>
+<tr style="height: 51.25pt;">
+<td
+style="border-style: none solid solid; border-color: -moz-use-text-color black black; border-width: medium 1pt 1pt; padding: 0in 5.4pt; width: 125.15pt; height: 51.25pt; background-color: rgb(0, 0, 153); color: rgb(255, 255, 0);"
+valign="top" width="167">
+<p class="MsoNormal"
+style="margin-bottom: 0.0001pt; line-height: normal;"><b><span
+style="font-size: 14pt; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;;">Ribonuclease
+A(bovine pancreas)<o:p></o:p></span></b></p>
+</td>
+<td
+style="border-style: none solid solid none; border-color: -moz-use-text-color black black -moz-use-text-color; border-width: medium 1pt 1pt medium; padding: 0in 5.4pt; width: 117.9pt; height: 51.25pt; background-color: rgb(0, 0, 153); color: rgb(255, 255, 0);"
+valign="top" width="157">
+<p class="MsoNormal"
+style="margin-bottom: 0.0001pt; line-height: normal;"><b><span
+style="font-size: 14pt; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;;">13,700<o:p></o:p></span></b></p>
+</td>
+<td
+style="border-style: none solid solid none; border-color: -moz-use-text-color black black -moz-use-text-color; border-width: medium 1pt 1pt medium; padding: 0in 5.4pt; width: 117.5pt; height: 51.25pt; background-color: rgb(0, 0, 153); color: rgb(255, 255, 0);"
+valign="top" width="157">
+<p class="MsoNormal"
+style="margin-bottom: 0.0001pt; line-height: normal;"><b><span
+style="font-size: 14pt; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;;">124<o:p></o:p></span></b></p>
+</td>
+<td
+style="border-style: none solid solid none; border-color: -moz-use-text-color black black -moz-use-text-color; border-width: medium 1pt 1pt medium; padding: 0in 5.4pt; width: 118.25pt; height: 51.25pt; background-color: rgb(0, 0, 153); color: rgb(255, 255, 0);"
+valign="top" width="158">
+<p class="MsoNormal"
+style="margin-bottom: 0.0001pt; line-height: normal;"><b><span
+style="font-size: 14pt; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;;">1<o:p></o:p></span></b></p>
+</td>
+</tr>
+<tr style="">
+<td
+style="border-style: none solid solid; border-color: -moz-use-text-color black black; border-width: medium 1pt 1pt; padding: 0in 5.4pt; width: 125.15pt; background-color: rgb(0, 0, 153); color: rgb(255, 255, 0);"
+valign="top" width="167">
+<p class="MsoNormal"
+style="margin-bottom: 0.0001pt; line-height: normal;"><b><span
+style="font-size: 14pt; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;;">Serum
+albumin (human)<o:p></o:p></span></b></p>
+</td>
+<td
+style="border-style: none solid solid none; border-color: -moz-use-text-color black black -moz-use-text-color; border-width: medium 1pt 1pt medium; padding: 0in 5.4pt; width: 117.9pt; background-color: rgb(0, 0, 153); color: rgb(255, 255, 0);"
+valign="top" width="157">
+<p class="MsoNormal"
+style="margin-bottom: 0.0001pt; line-height: normal;"><b><span
+style="font-size: 14pt; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;;">68,500<o:p></o:p></span></b></p>
+</td>
+<td
+style="border-style: none solid solid none; border-color: -moz-use-text-color black black -moz-use-text-color; border-width: medium 1pt 1pt medium; padding: 0in 5.4pt; width: 117.5pt; background-color: rgb(0, 0, 153); color: rgb(255, 255, 0);"
+valign="top" width="157">
+<p class="MsoNormal"
+style="margin-bottom: 0.0001pt; line-height: normal;"><b><span
+style="font-size: 14pt; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;;">609<o:p></o:p></span></b></p>
+</td>
+<td
+style="border-style: none solid solid none; border-color: -moz-use-text-color black black -moz-use-text-color; border-width: medium 1pt 1pt medium; padding: 0in 5.4pt; width: 118.25pt; background-color: rgb(0, 0, 153); color: rgb(255, 255, 0);"
+valign="top" width="158">
+<p class="MsoNormal"
+style="margin-bottom: 0.0001pt; line-height: normal;"><b><span
+style="font-size: 14pt; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;;">1<o:p></o:p></span></b></p>
+</td>
+</tr>
+</tbody>
+</table>
+<p style="text-align: center;" class="MsoNormal"><b><span
+style="font-size: 13.5pt; line-height: 115%; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;;">(Page
+, third edition “Lehninger
+Principles of Biochemistry” by David L. Nelson and Michael M. Cox)</span></b><b><span
+style="font-size: 14pt; line-height: 115%; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;;"><o:p>
 <br>
+</o:p></span></b></p>
+<div style="text-align: center;"></div>
+<p style="text-align: center;" class="MsoNormal"><b><span
+style="font-size: 14pt; line-height: 115%; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;;"><br
+style="">
+<!--[if !supportLineBreakNewLine]--><br style="">
+<!--[endif]--></span></b><b><u><span
+style="font-size: 12pt; line-height: 115%; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;;"><o:p></o:p></span></u></b></p>
+<big style="text-decoration: underline;"><big><span
+style="font-weight: bold;"></span></big></big></div>
+</div>
+<div style="text-align: center;"><br>
+<big style="text-decoration: underline;"><big><span
+style="font-weight: bold;"></span></big></big></div>
+</div>
 </body>
 </html>