http://2010.igem.org/wiki/index.php?title=Team:TU_Delft/Project/rbs-characterization&feed=atom&action=historyTeam:TU Delft/Project/rbs-characterization - Revision history2024-03-29T12:15:49ZRevision history for this page on the wikiMediaWiki 1.16.5http://2010.igem.org/wiki/index.php?title=Team:TU_Delft/Project/rbs-characterization&diff=136796&oldid=prevMvoges: /* Ribosome Binding Site Characterization */2010-10-24T19:59:20Z<p><span class="autocomment">Ribosome Binding Site Characterization</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>A ribosomal binding site sequence is a specific mRNA sequence that folds in such a way that it attracts the ribosome. This ribosome binds to the mRNA molecule and starts translation of the mRNA into protein.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>A ribosomal binding site sequence is a specific mRNA sequence that folds in such a way that it attracts the ribosome. This ribosome binds to the mRNA molecule and starts translation of the mRNA into protein.</div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">[[Image:TUDelft_bottleneck.png|100px|right|a bottleneck]]</del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>As with many synthetically implemented pathways, the rate of conversion through the pathway is highly influenced by the expression levels of the proteins involved. While the way in which these protein levels have their influence on the rates is not yet fully understood, the simple bottle-neck explanation has generally been accepted in the community. </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>As with many synthetically implemented pathways, the rate of conversion through the pathway is highly influenced by the expression levels of the proteins involved. While the way in which these protein levels have their influence on the rates is not yet fully understood, the simple bottle-neck explanation has generally been accepted in the community. </div></td></tr>
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</table>Mvogeshttp://2010.igem.org/wiki/index.php?title=Team:TU_Delft/Project/rbs-characterization&diff=136788&oldid=prevMvoges: /* Ribosome Binding Site Characterization */2010-10-24T19:58:25Z<p><span class="autocomment">Ribosome Binding Site Characterization</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>A ribosomal binding site sequence is a specific mRNA sequence that folds in such a way that it attracts the ribosome. This ribosome binds to the mRNA molecule and starts translation of the mRNA into protein.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>A ribosomal binding site sequence is a specific mRNA sequence that folds in such a way that it attracts the ribosome. This ribosome binds to the mRNA molecule and starts translation of the mRNA into protein.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>[[Image:TUDelft_bottleneck.png|100px|right|<del class="diffchange diffchange-inline">molecules through </del>a bottleneck]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>[[Image:TUDelft_bottleneck.png|100px|right|a bottleneck]]</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>As with many synthetically implemented pathways, the rate of conversion through the pathway is highly influenced by the expression levels of the proteins involved. While the way in which these protein levels have their influence on the rates is not yet fully understood, the simple bottle-neck explanation has generally been accepted in the community. </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>As with many synthetically implemented pathways, the rate of conversion through the pathway is highly influenced by the expression levels of the proteins involved. While the way in which these protein levels have their influence on the rates is not yet fully understood, the simple bottle-neck explanation has generally been accepted in the community. </div></td></tr>
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</table>Mvogeshttp://2010.igem.org/wiki/index.php?title=Team:TU_Delft/Project/rbs-characterization&diff=136781&oldid=prevMvoges: /* Ribosome Binding Site Characterization */2010-10-24T19:57:12Z<p><span class="autocomment">Ribosome Binding Site Characterization</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>A ribosomal binding site sequence is a specific mRNA sequence that folds in such a way that it attracts the ribosome. This ribosome binds to the mRNA molecule and starts translation of the mRNA into protein.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>A ribosomal binding site sequence is a specific mRNA sequence that folds in such a way that it attracts the ribosome. This ribosome binds to the mRNA molecule and starts translation of the mRNA into protein.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>[[Image:TUDelft_bottleneck.png|100px|right<del class="diffchange diffchange-inline">]</del>molecules through a bottleneck]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>[[Image:TUDelft_bottleneck.png|100px|right<ins class="diffchange diffchange-inline">|</ins>molecules through a bottleneck<ins class="diffchange diffchange-inline">]</ins>]</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>As with many synthetically implemented pathways, the rate of conversion through the pathway is highly influenced by the expression levels of the proteins involved. While the way in which these protein levels have their influence on the rates is not yet fully understood, the simple bottle-neck explanation has generally been accepted in the community. </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>As with many synthetically implemented pathways, the rate of conversion through the pathway is highly influenced by the expression levels of the proteins involved. While the way in which these protein levels have their influence on the rates is not yet fully understood, the simple bottle-neck explanation has generally been accepted in the community. </div></td></tr>
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</table>Mvogeshttp://2010.igem.org/wiki/index.php?title=Team:TU_Delft/Project/rbs-characterization&diff=136774&oldid=prevMvoges: /* Ribosome Binding Site Characterization */2010-10-24T19:56:01Z<p><span class="autocomment">Ribosome Binding Site Characterization</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>A ribosomal binding site sequence is a specific mRNA sequence that folds in such a way that it attracts the ribosome. This ribosome binds to the mRNA molecule and starts translation of the mRNA into protein.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>A ribosomal binding site sequence is a specific mRNA sequence that folds in such a way that it attracts the ribosome. This ribosome binds to the mRNA molecule and starts translation of the mRNA into protein.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>[[Image:TUDelft_bottleneck.png|<del class="diffchange diffchange-inline">300px</del>|right]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>[[Image:TUDelft_bottleneck.png|<ins class="diffchange diffchange-inline">100px</ins>|right]<ins class="diffchange diffchange-inline">molecules through a bottleneck</ins>]</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>As with many synthetically implemented pathways, the rate of conversion through the pathway is highly influenced by the expression levels of the proteins involved. While the way in which these protein levels have their influence on the rates is not yet fully understood, the simple bottle-neck explanation has generally been accepted in the community. </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>As with many synthetically implemented pathways, the rate of conversion through the pathway is highly influenced by the expression levels of the proteins involved. While the way in which these protein levels have their influence on the rates is not yet fully understood, the simple bottle-neck explanation has generally been accepted in the community. </div></td></tr>
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</table>Mvogeshttp://2010.igem.org/wiki/index.php?title=Team:TU_Delft/Project/rbs-characterization&diff=136756&oldid=prevMvoges: /* Ribosome Binding Site Characterization */2010-10-24T19:52:28Z<p><span class="autocomment">Ribosome Binding Site Characterization</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>A ribosomal binding site sequence is a specific mRNA sequence that folds in such a way that it attracts the ribosome. This ribosome binds to the mRNA molecule and starts translation of the mRNA into protein.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>A ribosomal binding site sequence is a specific mRNA sequence that folds in such a way that it attracts the ribosome. This ribosome binds to the mRNA molecule and starts translation of the mRNA into protein.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">[[Image:TUDelft_bottleneck.png|300px|right]]</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>As with many synthetically implemented pathways, the rate of conversion through the pathway is highly influenced by the expression levels of the proteins involved. While the way in which these protein levels have their influence on the rates is not yet fully understood, the simple bottle-neck explanation has generally been accepted in the community. </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>As with many synthetically implemented pathways, the rate of conversion through the pathway is highly influenced by the expression levels of the proteins involved. While the way in which these protein levels have their influence on the rates is not yet fully understood, the simple bottle-neck explanation has generally been accepted in the community. </div></td></tr>
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</table>Mvogeshttp://2010.igem.org/wiki/index.php?title=Team:TU_Delft/Project/rbs-characterization&diff=124074&oldid=prevRavandervalk: /* Ribosome Binding Site Characterization */2010-10-23T11:31:11Z<p><span class="autocomment">Ribosome Binding Site Characterization</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>A perfect way to implement this variation in the alkane degradation pathway is by using ribosome binding sites with varying strengths. This led to the characterization of the ribosome initiation strengths of five Anderson RBS family members.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>A perfect way to implement this variation in the alkane degradation pathway is by using ribosome binding sites with varying strengths. This led to the characterization of the ribosome initiation strengths of five Anderson RBS family members.</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><html><center><img src="https://static.igem.org/mediawiki/2010/0/00/TU_Delft_project_navigation.jpg" usemap="#projectnavigation" border="0" /></center><map id="projectnavigation" name="projectnavigation"><area shape="rect" alt="Characterization" title="" coords="309,3,591,45" href="https://2010.igem.org/Team:TU_Delft#page=Project/rbs-characterization/characterization" target="" /><area shape="rect" alt="Results" title="" coords="609,3,891,44" href="https://2010.igem.org/Team:TU_Delft#page=Project/rbs-characterization/results" target="" /><area shape="rect" alt="Parts" title="" coords="9,3,290,44" href="https://2010.igem.org/Team:TU_Delft#page=Project/rbs-characterization/parts" target="" /></map></html></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><html><center><img src="https://static.igem.org/mediawiki/2010/0/00/TU_Delft_project_navigation.jpg" usemap="#projectnavigation" border="0" /></center><map id="projectnavigation" name="projectnavigation"><area shape="rect" alt="Characterization" title="" coords="309,3,591,45" href="https://2010.igem.org/Team:TU_Delft#page=Project/rbs-characterization/characterization" target="" /><area shape="rect" alt="Results" title="" coords="609,3,891,44" href="https://2010.igem.org/Team:TU_Delft#page=Project/rbs-characterization/results" target="" /><area shape="rect" alt="Parts" title="" coords="9,3,290,44" href="https://2010.igem.org/Team:TU_Delft#page=Project/rbs-characterization/parts" target="" /></map></html></div></td></tr>
</table>Ravandervalkhttp://2010.igem.org/wiki/index.php?title=Team:TU_Delft/Project/rbs-characterization&diff=124071&oldid=prevRavandervalk: /* Ribosome Binding Site Characterization */2010-10-23T11:30:30Z<p><span class="autocomment">Ribosome Binding Site Characterization</span></p>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">===Continue reading===</del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><html><center><img src="https://static.igem.org/mediawiki/2010/0/00/TU_Delft_project_navigation.jpg" usemap="#projectnavigation" border="0" /></center><map id="projectnavigation" name="projectnavigation"><area shape="rect" alt="Characterization" title="" coords="309,3,591,45" href="https://2010.igem.org/Team:TU_Delft#page=Project/rbs-characterization/characterization" target="" /><area shape="rect" alt="Results" title="" coords="609,3,891,44" href="https://2010.igem.org/Team:TU_Delft#page=Project/rbs-characterization/results" target="" /><area shape="rect" alt="Parts" title="" coords="9,3,290,44" href="https://2010.igem.org/Team:TU_Delft#page=Project/rbs-characterization/parts" target="" /></map></html></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><html><center><img src="https://static.igem.org/mediawiki/2010/0/00/TU_Delft_project_navigation.jpg" usemap="#projectnavigation" border="0" /></center><map id="projectnavigation" name="projectnavigation"><area shape="rect" alt="Characterization" title="" coords="309,3,591,45" href="https://2010.igem.org/Team:TU_Delft#page=Project/rbs-characterization/characterization" target="" /><area shape="rect" alt="Results" title="" coords="609,3,891,44" href="https://2010.igem.org/Team:TU_Delft#page=Project/rbs-characterization/results" target="" /><area shape="rect" alt="Parts" title="" coords="9,3,290,44" href="https://2010.igem.org/Team:TU_Delft#page=Project/rbs-characterization/parts" target="" /></map></html></div></td></tr>
</table>Ravandervalkhttp://2010.igem.org/wiki/index.php?title=Team:TU_Delft/Project/rbs-characterization&diff=123923&oldid=prevMvoges: /* Ribosome Binding Site Characterization */2010-10-23T10:50:12Z<p><span class="autocomment">Ribosome Binding Site Characterization</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>As with many synthetically implemented pathways, the rate of conversion through the pathway is highly influenced by the expression levels of the proteins involved. While the way in which these protein levels have their influence on the rates is not yet fully understood, the simple bottle-neck explanation has generally been accepted in the community. </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>As with many synthetically implemented pathways, the rate of conversion through the pathway is highly influenced by the expression levels of the proteins involved. While the way in which these protein levels have their influence on the rates is not yet fully understood, the simple bottle-neck explanation has generally been accepted in the community. </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">For example, consider </del>the following pathway: </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">Consider </ins>the following pathway: </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>#alkane → alkanol ; catalyzed by LadA</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>#alkane → alkanol ; catalyzed by LadA</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>#alkanol → alkanal ; catalyzed by ADH</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>#alkanol → alkanal ; catalyzed by ADH</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>#alkanal → alkanoic acid ; catalyzed by ALDH</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>#alkanal → alkanoic acid ; catalyzed by ALDH</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>If the protein expression level of ALDH is lower than that of ADH, a build-up of alkanal occurs, which will be toxic to the cell. Thus, in implementing our alkane degradation pathway we aimed to increase the protein levels in accordance with the conversion steps.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>If<ins class="diffchange diffchange-inline">, for example, </ins>the protein expression level of ALDH is lower than that of ADH, a build-up of alkanal occurs, which will be toxic to the cell. Thus, in implementing our alkane degradation pathway we aimed to increase the protein levels in accordance with the conversion steps.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>A perfect way to implement this variation in the alkane degradation pathway is by using ribosome binding sites with varying strengths. This led to the characterization of the ribosome initiation strengths of five Anderson RBS family members.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>A perfect way to implement this variation in the alkane degradation pathway is by using ribosome binding sites with varying strengths. This led to the characterization of the ribosome initiation strengths of five Anderson RBS family members.</div></td></tr>
</table>Mvogeshttp://2010.igem.org/wiki/index.php?title=Team:TU_Delft/Project/rbs-characterization&diff=120857&oldid=prevMvoges: /* Ribosome Binding Site Characterization */2010-10-22T17:48:14Z<p><span class="autocomment">Ribosome Binding Site Characterization</span></p>
<table style="background-color: white; color:black;">
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<td colspan='2' style="background-color: white; color:black;">Revision as of 17:48, 22 October 2010</td>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>As with many synthetically implemented pathways, the rate of conversion through the pathway is highly influenced by the expression levels of the proteins involved. While the way in which these protein levels have their influence on the rates is not yet fully understood, the simple bottle-neck explanation has generally been accepted in the community. </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>As with many synthetically implemented pathways, the rate of conversion through the pathway is highly influenced by the expression levels of the proteins involved. While the way in which these protein levels have their influence on the rates is not yet fully understood, the simple bottle-neck explanation has generally been accepted in the community. </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>For example, consider the pathway <del class="diffchange diffchange-inline">A </del>→ <del class="diffchange diffchange-inline">B, where </del>the protein expression level of <del class="diffchange diffchange-inline">B </del>is lower than that of <del class="diffchange diffchange-inline">A, due to the slower conversion by B</del>, a build-up of <del class="diffchange diffchange-inline">intermediates </del>occurs, which <del class="diffchange diffchange-inline">could </del>be <del class="diffchange diffchange-inline">detrimental </del>to the cell <del class="diffchange diffchange-inline">(depending on the toxicity of the intermediate)</del>. Thus, in implementing our alkane degradation pathway we aimed to increase the protein levels in accordance with the conversion steps.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>For example, consider the <ins class="diffchange diffchange-inline">following </ins>pathway<ins class="diffchange diffchange-inline">: </ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">#alkane </ins>→ <ins class="diffchange diffchange-inline">alkanol ; catalyzed by LadA</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">#alkanol → alkanal ; catalyzed by ADH</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">#alkanal → alkanoic acid ; catalyzed by ALDH</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">If </ins>the protein expression level of <ins class="diffchange diffchange-inline">ALDH </ins>is lower than that of <ins class="diffchange diffchange-inline">ADH</ins>, a build-up of <ins class="diffchange diffchange-inline">alkanal </ins>occurs, which <ins class="diffchange diffchange-inline">will </ins>be <ins class="diffchange diffchange-inline">toxic </ins>to the cell. Thus, in implementing our alkane degradation pathway we aimed to increase the protein levels in accordance with the conversion steps.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> </div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">In order </del>to <del class="diffchange diffchange-inline">achieve </del>this the ribosome initiation strengths of five Anderson RBS family members <del class="diffchange diffchange-inline">were characterized. By varying only the RBS sequence in a protein generator construct the dependence of the expression level of the encoded protein on the RBS sequence could be determined by simple fluorescence and biomass curve analysis</del>.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">A perfect way </ins>to <ins class="diffchange diffchange-inline">implement </ins>this <ins class="diffchange diffchange-inline">variation in the alkane degradation pathway is by using ribosome binding sites with varying strengths. This led to the characterization of </ins>the ribosome initiation strengths of five Anderson RBS family members.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
</table>Mvogeshttp://2010.igem.org/wiki/index.php?title=Team:TU_Delft/Project/rbs-characterization&diff=120830&oldid=prevMvoges: /* Ribosome Binding Site Characterization */2010-10-22T17:32:49Z<p><span class="autocomment">Ribosome Binding Site Characterization</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Ribosome Binding Site Characterization==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Ribosome Binding Site Characterization==</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:TUDelft_RBS.png|300px|right]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:TUDelft_RBS.png|300px|right]]</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">Part of our project is to measure the effect of various ribosome </del>binding site <del class="diffchange diffchange-inline">(RBS) sequences. A RBS </del>sequence is a specific mRNA sequence that folds in such a way that it attracts the ribosome. This ribosome binds to the mRNA molecule and starts translation of the mRNA into protein. <del class="diffchange diffchange-inline">Accurate information </del>on <del class="diffchange diffchange-inline">how well this binding </del>occurs (<del class="diffchange diffchange-inline">The binding strength</del>) <del class="diffchange diffchange-inline">can </del>be <del class="diffchange diffchange-inline">very useful when designing new biological systems</del>.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">A ribosomal </ins>binding site sequence is a specific mRNA sequence that folds in such a way that it attracts the ribosome. This ribosome binds to the mRNA molecule and starts translation of the mRNA into protein.</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">As with many synthetically implemented pathways, the rate of conversion through the pathway is highly influenced by the expression levels of the proteins involved. While the way in which these protein levels have their influence </ins>on <ins class="diffchange diffchange-inline">the rates is not yet fully understood, the simple bottle-neck explanation has generally been accepted in the community. </ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">For example, consider the pathway A → B, where the protein expression level of B is lower than that of A, due to the slower conversion by B, a build-up of intermediates </ins>occurs<ins class="diffchange diffchange-inline">, which could be detrimental to the cell </ins>(<ins class="diffchange diffchange-inline">depending on the toxicity of the intermediate</ins>)<ins class="diffchange diffchange-inline">. Thus, in implementing our alkane degradation pathway we aimed to increase the protein levels in accordance with the conversion steps.</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"> </ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">In order to achieve this the ribosome initiation strengths of five Anderson RBS family members were characterized. By varying only the RBS sequence in a protein generator construct the dependence of the expression level of the encoded protein on the RBS sequence could </ins>be <ins class="diffchange diffchange-inline">determined by simple fluorescence and biomass curve analysis</ins>.</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
</table>Mvoges