Team:Alberta/Project/Modeling

From 2009.igem.org

(Difference between revisions)
Line 1: Line 1:
{{:Team:Alberta/Template3}}
{{:Team:Alberta/Template3}}
 +
<html>
 +
<head>
 +
<style type="text/css">
 +
.b1f, .b2f, .b3f, .b4f{font-size:1px; overflow:hidden; display:block;}
 +
.b1f {height:1px; background:#ADED7C; margin:0 5px;}
 +
.b2f {height:1px; background:#ADED7C; margin:0 3px;}
 +
.b3f {height:1px; background:#ADED7C; margin:0 2px;}
 +
.b4f {height:2px; background:#ADED7C; margin:0 1px;}
 +
.content {background: #ADED7C;}
 +
.content div {margin-left: 5px;}
 +
</style>
 +
</head>
 +
 +
<div class="all">
 +
<div style="background:#FFFFFF">
 +
 +
<!-- adjust table width, main background and padding between cells and edge of background -->
 +
 +
 +
<table width=75% style="background:#FFFFFF; padding:2px;">
 +
 +
<tr>
 +
<td style="height: 400; padding-left: 10px; padding-right: 10px; padding-top: 11px;">
 +
    <b class="b1f"></b><b class="b2f"></b><b class="b3f"></b><b class="b4f"></b>
 +
    <div class="Outreach">
 +
    <div style="height: 400; background:#FFFFFF; colorou line-height:100% padding: 3px 0px;">
 +
    <h1>Why build a minimal genome?</h1>
 +
 +
<!-- <div align="justify" style="padding-left:20px; padding-right:20px"> -->
 +
<div align="justify">
 +
 +
<font size="2">
 +
<P>Genomes are complex! Determining how simplified a genome can become enriches our understanding of the function and interactions of cellular components. Simplified cells can be used as a well characterized chasses for synthetic biology. Moreover, a simplified cell can be used to study cellular processes in a controlled, characterized genetic background. Finally, developing a minimal genome requires us to develop and optimize molecular methods of genome assembly. These methods can be then applied to other high through put biology. </P>
 +
 +
</font></div>
 +
 +
      </div></div>
 +
<b class="b4f"></b><b class="b3f"></b><b class="b2f"></b><b class="b1f"></b>
 +
    </td>
 +
  </tr>
 +
 +
<tr>
 +
<td style="height: 400; padding-left: 10px; padding-right: 10px; padding-top: 11px;">
 +
    <b class="b1f"></b><b class="b2f"></b><b class="b3f"></b><b class="b4f"></b>
 +
    <div class="Why We Need Bioinformatics">
 +
    <div style="height: 400; background:#FFFFFF; colorou line-height:100% padding: 3px 0px;">
 +
    <h1>Why We Need Bioinformatics</h1>
 +
 +
<!-- <div align="justify" style="padding-left:20px; padding-right:20px"> -->
 +
<div align="justify">
 +
 +
<font size="2">
 +
 +
<b> The size and complexity of the genome make bioinformatics analysis essential. We used bioinformatics to accomplish the following: </b>
 +
 +
<P> - review lists of essential genes in the literature and existing databases and compile a preliminary essential gene list </P>
 +
<P> - model the metabolic reactions and net growth rate of E.coli with given gene sets. This identified additional metabolic genes essential to a minimal genome. </P>
 +
<P> - identify knock out combinations that could be tested in the wet lab, to verify the accuracy of our metabolic model. </P>
 +
<P> - select standardized promoters and terminators that would replace the natural promoters and terminators of essential genes. </P>
 +
<P> - determine which promoter should be used with which gene, by analyzing expression level data. </P>
 +
<P> - design primers to amplify all essential genes from genomic DNA. </P>
 +
 +
<b> These steps have all been completed, and are described on the following pages. </b>
 +
 +
<P>
 +
</font></div>
 +
 +
      </div></div>
 +
<b class="b4f"></b><b class="b3f"></b><b class="b2f"></b><b class="b1f"></b>
 +
    </td>
 +
  </tr>
 +
 +
 +
 +
</table>
 +
</div>
 +
</HTML>
 +
 +
<html>
 +
<head>
 +
<style type="text/css">
 +
.b1f, .b2f, .b3f, .b4f{font-size:1px; overflow:hidden; display:block;}
 +
.b1f {height:1px; background:#ADED7C; margin:0 5px;}
 +
.b2f {height:1px; background:#ADED7C; margin:0 3px;}
 +
.b3f {height:1px; background:#ADED7C; margin:0 2px;}
 +
.b4f {height:2px; background:#ADED7C; margin:0 1px;}
 +
.content {background: #ADED7C;}
 +
.content div {margin-left: 5px;}
 +
</style>
 +
</head>
 +
 +
<div class="all">
 +
<div style="background:#FFFFFF">
 +
 +
<!-- adjust table width, main background and padding between cells and edge of background -->
 +
 +
 +
<table width=75% style="background:#FFFFFF; padding:2px;">
 +
 +
<tr>
 +
<td style="height: 400; padding-left: 10px; padding-right: 10px; padding-top: 11px;">
 +
    <b class="b1f"></b><b class="b2f"></b><b class="b3f"></b><b class="b4f"></b>
 +
    <div class="Outreach">
 +
    <div style="height: 400; background:#FFFFFF; colorou line-height:100% padding: 3px 0px;">
 +
    <h1>Constraint Based Flux Analysis – Cobra Toolbox and SBML</h1>
 +
 +
<!-- <div align="justify" style="padding-left:20px; padding-right:20px"> -->
 +
<div align="justify">
 +
 +
<font size="2">

Revision as of 18:48, 14 September 2009

University of Alberta - BioBytes










































































































Why build a minimal genome?

Genomes are complex! Determining how simplified a genome can become enriches our understanding of the function and interactions of cellular components. Simplified cells can be used as a well characterized chasses for synthetic biology. Moreover, a simplified cell can be used to study cellular processes in a controlled, characterized genetic background. Finally, developing a minimal genome requires us to develop and optimize molecular methods of genome assembly. These methods can be then applied to other high through put biology.

Why We Need Bioinformatics

The size and complexity of the genome make bioinformatics analysis essential. We used bioinformatics to accomplish the following:

- review lists of essential genes in the literature and existing databases and compile a preliminary essential gene list

- model the metabolic reactions and net growth rate of E.coli with given gene sets. This identified additional metabolic genes essential to a minimal genome.

- identify knock out combinations that could be tested in the wet lab, to verify the accuracy of our metabolic model.

- select standardized promoters and terminators that would replace the natural promoters and terminators of essential genes.

- determine which promoter should be used with which gene, by analyzing expression level data.

- design primers to amplify all essential genes from genomic DNA.

These steps have all been completed, and are described on the following pages.

Constraint Based Flux Analysis – Cobra Toolbox and SBML