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Team:MIT/Organizational Daily Notebook - Revision history
2024-03-29T01:25:28Z
Revision history for this page on the wiki
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Smouradi: /* AUG 1 */
2008-08-01T21:10:22Z
<p><span class="autocomment">AUG 1</span></p>
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<td colspan='2' style="background-color: white; color:black;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black;">Revision as of 21:10, 1 August 2008</td>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>1. Overview</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>1. Overview</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline"> </del>Large synthetic biology -> food overview</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">* </ins>Large synthetic biology -> food overview</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline"> </del>Our goal</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">* </ins>Our goal</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline"> </del>Why important</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">* </ins>Why important</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline"> </del>Teeth</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">**</ins>Teeth</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline"> </del>Globally</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">**</ins>Globally</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline"> </del>Plan of Attack</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">*</ins>Plan of Attack</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline"> </del>forming DNA</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">** </ins>forming DNA</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline"> </del>lactobacillus bulgaricus</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">** </ins>lactobacillus bulgaricus</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline"> </del>binding assay</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">** </ins>binding assay</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;"><div>2. Binding Assay</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>2. Binding Assay</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline"> </del>New method</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">*</ins>New method</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline"> </del>(Controls to prove eficacy of method)</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">** </ins>(Controls to prove eficacy of method)</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;"><div>3. DNA work</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>3. DNA work</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline"> </del>Gene construct</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">* </ins>Gene construct</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline"> </del>Brief reason for parts in teh construct</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">** </ins>Brief reason for parts in teh construct</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline"> </del>signal seq for l.bulgaricus</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">*** </ins>signal seq for l.bulgaricus</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline"> </del>Promoter</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">*</ins>Promoter</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline"> </del>characterizing bad T7</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">**</ins>characterizing bad T7</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline"> </del>BioBricks</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">*</ins>BioBricks</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;"><div>4. L.bulgaricus</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>4. L.bulgaricus</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline"> </del>Transforming</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">* </ins>Transforming</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline"> </del>Restriction Mechanism</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">**</ins>Restriction Mechanism</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline"> </del>Emphasize how hard it is</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">**</ins>Emphasize how hard it is</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;"><div>5. Final results</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>5. Final results</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>7. Final overview</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>7. Final overview</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline"> </del>This is specific, but applies to a lot strains / peptides</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">*</ins>This is specific, but applies to a lot strains / peptides</div></td></tr>
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Smouradi
http://2008.igem.org/wiki/index.php?title=Team:MIT/Organizational_Daily_Notebook&diff=26460&oldid=prev
Smouradi: /* JUN 24 */
2008-08-01T21:08:03Z
<p><span class="autocomment">JUN 24</span></p>
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<td colspan='2' style="background-color: white; color:black;">Revision as of 21:08, 1 August 2008</td>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==JUN 24==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==JUN 24==</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*Ordered MRS broth and agar for L.bulgaricus from Difco</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*Ordered MRS broth and agar for L.bulgaricus from Difco</div></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;"></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 style="color: red; font-weight: bold; text-decoration: none;">==AUG 1==</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 style="color: red; font-weight: bold; text-decoration: none;">*Initial outline for powerpoint: </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 style="color: red; font-weight: bold; text-decoration: none;"></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 style="color: red; font-weight: bold; text-decoration: none;">1. Overview</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 style="color: red; font-weight: bold; text-decoration: none;"> Large synthetic biology -> food overview</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 style="color: red; font-weight: bold; text-decoration: none;"> Our goal</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 style="color: red; font-weight: bold; text-decoration: none;"> Why important</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 style="color: red; font-weight: bold; text-decoration: none;"> Teeth</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 style="color: red; font-weight: bold; text-decoration: none;"> Globally</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 style="color: red; font-weight: bold; text-decoration: none;"> Plan of Attack</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 style="color: red; font-weight: bold; text-decoration: none;"> forming DNA</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 style="color: red; font-weight: bold; text-decoration: none;"> lactobacillus bulgaricus</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 style="color: red; font-weight: bold; text-decoration: none;"> binding assay</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 style="color: red; font-weight: bold; text-decoration: none;"></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 style="color: red; font-weight: bold; text-decoration: none;">2. Binding Assay</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 style="color: red; font-weight: bold; text-decoration: none;"> New method</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 style="color: red; font-weight: bold; text-decoration: none;"> (Controls to prove eficacy of method)</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 style="color: red; font-weight: bold; text-decoration: none;"></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 style="color: red; font-weight: bold; text-decoration: none;">3. DNA work</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 style="color: red; font-weight: bold; text-decoration: none;"> Gene construct</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 style="color: red; font-weight: bold; text-decoration: none;"> Brief reason for parts in teh construct</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 style="color: red; font-weight: bold; text-decoration: none;"> signal seq for l.bulgaricus</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 style="color: red; font-weight: bold; text-decoration: none;"> Promoter</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 style="color: red; font-weight: bold; text-decoration: none;"> characterizing bad T7</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 style="color: red; font-weight: bold; text-decoration: none;"> BioBricks</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 style="color: red; font-weight: bold; text-decoration: none;"></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 style="color: red; font-weight: bold; text-decoration: none;">4. L.bulgaricus</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 style="color: red; font-weight: bold; text-decoration: none;"> Transforming</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 style="color: red; font-weight: bold; text-decoration: none;"> Restriction Mechanism</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 style="color: red; font-weight: bold; text-decoration: none;"> Emphasize how hard it is</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 style="color: red; font-weight: bold; text-decoration: none;"></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 style="color: red; font-weight: bold; text-decoration: none;">5. Final results</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 style="color: red; font-weight: bold; text-decoration: none;"></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 style="color: red; font-weight: bold; text-decoration: none;">6. Our contribution (biobricks, l.bulgaricus, binding assay for cells)</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 style="color: red; font-weight: bold; text-decoration: none;"></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 style="color: red; font-weight: bold; text-decoration: none;">7. Final overview</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 style="color: red; font-weight: bold; text-decoration: none;"> This is specific, but applies to a lot strains / peptides</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 style="color: red; font-weight: bold; text-decoration: none;"></ins></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>
Smouradi
http://2008.igem.org/wiki/index.php?title=Team:MIT/Organizational_Daily_Notebook&diff=8957&oldid=prev
Aang: New page: <!--- The Mission, Experiments ---> {| style="color:#1b2c8a;background-color:#0c6;" cellpadding="3" cellspacing="1" border="1" bordercolor="#fff" width="62%" align="center" !align="center...
2008-06-25T20:44:36Z
<p>New page: <!--- The Mission, Experiments ---> {| style="color:#1b2c8a;background-color:#0c6;" cellpadding="3" cellspacing="1" border="1" bordercolor="#fff" width="62%" align="center" !align="center...</p>
<p><b>New page</b></p><div><!--- The Mission, Experiments ---><br />
<br />
{| style="color:#1b2c8a;background-color:#0c6;" cellpadding="3" cellspacing="1" border="1" bordercolor="#fff" width="62%" align="center"<br />
!align="center"|[[Team:MIT|Home]]<br />
!align="center"|[[Team:MIT/Team|The Team]]<br />
!align="center"|[[Team:MIT/Project|The Project]]<br />
!align="center"|[[Team:MIT/Parts|Parts Submitted to the Registry]]<br />
!align="center"|[[Team:MIT/Modeling|Modeling]]<br />
!align="center"|[[Team:MIT/Notebook|Notebook]]<br />
|}<br />
<br />
==[[BRAINSTORMING]]==<br />
<br />
==PROTOCOLS==<br />
<br />
*[http://openwetware.org/wiki/MIT_iGEM_T4_and_Quick_Ligation DNA Ligations]<br />
*[http://openwetware.org/wiki/MIT_iGEM_Top10_ChemComp_Ecoli_transformation_protocol#Regular_Transformation_protocol_for_Top10_cells Top10 chem competent cell transformation]<br />
*[http://web.mit.edu/biopolymers/www/DNA.html DNA sequencing]<br />
*[http://openwetware.org/wiki/Endy_pcr PCR]<br />
*[http://openwetware.org/wiki/MIT_iGEM_Agarose_Gels Running DNA Gels]<br />
*[http://openwetware.org/wiki/MIT_iGEM_Restriction_Digests Restriction Digests]<br />
*[http://openwetware.org/wiki/Endy:Preparing_Antibiotic_Stocks Preparing Antibiotic Stocks]<br />
<br />
==JUN 10==<br />
[[Image:System_diagram_pic.jpg]]<br />
<br />
==JUN 16==<br />
<br />
<br />
<br />
===Summary of individual tasks to research:===<br />
# S. Mutans metabolism pathway-Asad<br />
# L. bulgaricus metabolism pathway-Allin<br />
# secretion (full or partial)-John<br />
# other secretion systems (introduction of)-Sara<br />
# T7 as a promoter (L. bulgaricus)-Prarthna<br />
# L. bulgaricus transformation/protocols-Derek<br />
# binding assay protocols-Andrew<br />
<br />
===Linear Sequence/Design===<br />
Ex-promoter-RBS-ATG-signal-epitope-p1025-linker (TEV cleavage site)-GFP-His-TAATAA-termination-SP (see top of page)<br />
*Base pairs: 35-10-3-90-30-60-45-700-15-6-8<br />
*potential eptiopes<br />
**FLAG (Asp-Tyr-Lys-Asp-Asp-Asp-Asp-Lys)<br />
**C-myc (E Q K L I S E E D L)<br />
**HA (Y P Y D U P D Y A: #2)<br />
<br />
===DNA/Plasmid Editor===<br />
*http://www.biology.utah.edu/jorgensen/wayned/ape/<br />
===Peptide Sequence Manipulations===<br />
*http://slam.bs.jhmi.edu/gd/<br />
<br />
===Primer Analyzer Tool (check temperature & GC content)===<br />
*http://www.idtdna.com/analyzer/Applications/OligoAnalyzer/Default.aspx<br />
<br />
# primers should be 17-28 bases in length; <br />
# base composition should be 50-60% (G+C); <br />
# primers should end (3') in a G or C, or CG or GC: this prevents "breathing" of ends and increases efficiency of priming; <br />
# Tms between 55-80oC are preferred; <br />
# 3'-ends of primers should not be complementary (ie. base pair), as otherwise primer dimers will be synthesised preferentially to any other product; <br />
# primer self-complementarity (ability to form 2o structures such as hairpins) should be avoided; <br />
# runs of three or more Cs or Gs at the 3'-ends of primers may promote mispriming at G or C-rich sequences (because of stability of annealing), and should be avoided. <br />
**http://bioweb.uwlax.edu/GenWeb/Molecular/Seq_Anal/Primer_Design/primer_design.htm<br />
<br />
===Parts/Construction===<br />
#Construction<br />
##GFP<br />
##Synthetic peptide<br />
##L. bulgaricus vector<br />
#Assay<br />
#L. bulgaricus<br />
#S. Mutans<br />
===To Do/To Buy:===<br />
*finalize DNA sequence<br />
*primer<br />
*synthesis<br />
*reagents<br />
<br />
===TEV Protease cut site===<br />
<br />
* Amino Acid Sequence : Glu-Asn-Leu-Tyr-Phe-Gln-Gly (Cuts between Gln-Gly)<br />
* Base Pair Sequence: GAAAACCTGTACTTCCAGGGT<br />
<br />
<br />
<br />
==JUN 17==<br />
===Links to sites from individual research topics===<br />
*T7 as a promoter in L. bulgaricus/Other viable promoter options<br />
**LacS promoter<br />
***http://www.patentstorm.us/patents/5639644/description.html<br />
***http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=161534<br />
**http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=123959<br />
**http://jb.asm.org/cgi/content/full/184/4/928<br />
*Secretion signal peptide<br />
**[http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=178052&blobtype=pdf cleavage site]<br />
<br />
===P4 Revised===<br />
[[image:P4-4.jpg]]<br />
**reverse sequence: CTG CAG CGG CCG CTA CTA GTA AGA GAA TAT AAA AAG CCA GAT TAT TAA TCC GGC TTT TTT ATT ATT TTT ATT AGT GGT GAT GGT GAT GAT GTT TGT ATA GTT CAT CCA TGC<br />
**length = 111 bp<br />
**melting temp = 69.6 C<br />
**GC content % = 36.0<br />
<br />
==JUN 18==<br />
* [[../lbulgaricus |''Lactobacillus delbrueckii'' subsp. ''bulgaricus'' Information & Protocols]]<br />
<br />
* [[../toothbindingassay | Tooth binding assay protocol]]<br />
<br />
*http://www.freewebs.com/naguiar/ (S. mutans Information)<br />
<br />
*http://pubs.acs.org/cgi-bin/abstract.cgi/jafcau/2002/50/i05/abs/jf010958t.html (S. mutans adsorption to HA Beads)<br />
<br />
*http://www.blackwell-synergy.com/doi/full/10.1111/j.1399-302X.2007.00412.x (Influence of Starch and Sucrose on S. mutans)<br />
<br />
===Friday Meeting breakdown===<br />
#Andrew: primers<br />
#Derek: L. bulgaricus procedures<br />
#Allin: metabolism<br />
#John: binding assay<br />
#Sara: secretion<br />
#Asad: S. Mutans/Binding Assay<br />
#Prarthna: promoters<br />
<br />
==JUN 20==<br />
<br />
Powerpoint [linked here]<br />
<br />
==JUN 24==<br />
*Ordered MRS broth and agar for L.bulgaricus from Difco<br />
<br />
<br />
<!--- The Mission, Experiments ---><br />
<br />
{| style="color:#1b2c8a;background-color:#0c6;" cellpadding="3" cellspacing="1" border="1" bordercolor="#fff" width="62%" align="center"<br />
!align="center"|[[Team:MIT|Home]]<br />
!align="center"|[[Team:MIT/Team|The Team]]<br />
!align="center"|[[Team:MIT/Project|The Project]]<br />
!align="center"|[[Team:MIT/Parts|Parts Submitted to the Registry]]<br />
!align="center"|[[Team:MIT/Modeling|Modeling]]<br />
!align="center"|[[Team:MIT/Notebook|Notebook]]<br />
|}</div>
Aang