Team:Tokyo Tech/Project

From 2008.igem.org

(Difference between revisions)
(→We want to make a Coli Touch!)
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== We want to make a Coli Touch! ==
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We try to construct a bacterial `touch panel’ which is colored by the pressure.  
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We name it Coli. touch.<br/>
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;*'''why pressure ?'''
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:In iGEM, genetic circuits responded by various inputs -- for example, heat, small molecule, and light -- have been constructed. However, a pressure-responsive genetic circuit had not been constructed yet. Therefore, we constructed a pressure responsive circuit using a pressure-inducible promoter.<br/>
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;*Pressure inducible promoter - Plac
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:The affinity of LacI for the lac operator is known to decrease due to a tetramer to dimer transition of LacI
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<p class=MsoNormal><b style='mso-bidi-font-weight:normal'><u><span lang=EN-US
 +
style='font-size:14.0pt'>Our project<o:p></o:p></span></u></b></p>
 +
 
 +
<p class=MsoNormal style='text-indent:5.25pt;mso-char-indent-count:.5'><span
 +
lang=EN-US>We want to make a <i style='mso-bidi-font-style:normal'>Coli Touch!!</i></span></p>
 +
 
 +
<p class=MsoNormal><span style='font-family:"ＭＳ 明朝","serif";mso-ascii-font-family:
 +
Century;mso-hansi-font-family:Century'>→</span><span lang=EN-US>We try to
 +
construct a bacterial ‘touch panel’ which is colored by the pressure. </span></p>
 +
 
 +
<p class=MsoNormal style='text-indent:10.5pt;mso-char-indent-count:1.0'><span
 +
lang=EN-US>We name it <i>Coli touch.</i></span></p>
 +
 
 +
<p class=MsoNormal><span lang=EN-US><o:p>&nbsp;</o:p></span></p>
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<! Why pressure?>
 +
 
 +
 
 +
<p class=MsoNormal><b style='mso-bidi-font-weight:normal'><u><span lang=EN-US
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style='font-size:14.0pt'>Why pressure?<o:p></o:p></span></u></b></p>
 +
 
 +
<p class=MsoNormal style='text-indent:5.25pt;mso-char-indent-count:.5'><span
 +
lang=EN-US>Example of input style to genetic circuit</span></p>
 +
 
 +
<p class=MsoNormal style='text-indent:10.5pt;mso-char-indent-count:1.0'><span
 +
lang=EN-US>- Heat: thermal gradient </span></p>
 +
 
 +
<p class=MsoNormal style='text-indent:10.5pt;mso-char-indent-count:1.0'><span
 +
lang=EN-US>- Small molecule: concentration gradient</span></p>
 +
 
 +
<p class=MsoNormal style='text-indent:10.5pt;mso-char-indent-count:1.0'><span
 +
lang=EN-US>- Light: strength depend on location of container</span></p>
 +
 
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<p class=MsoNormal><span lang=EN-US><span
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style='mso-spacerun:yes'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 +
</span></span></p>
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 +
<p class=MsoNormal><span lang=EN-US><span
 +
style='mso-spacerun:yes'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 +
<IMG src="https://static.igem.org/mediawiki/2008/b/be/Tech_%E7%9F%A2%E5%8D%B0.jpg" align="middle">&nbsp;&nbsp;</span>Difficulty in uniform introduction</span></p>
 +
 
 +
<p class=MsoNormal><span lang=EN-US><o:p>&nbsp;</o:p></span></p>
 +
 
 +
<p class=MsoNormal><span lang=EN-US><span style='mso-spacerun:yes'>&nbsp;
 +
</span><span style='color:red'>Press!</span><span
 +
style='mso-spacerun:yes'>&nbsp; </span>Confirmatory experiment </span></p>
 +
 
 +
<p class=MsoNormal><span lang=EN-US>Prospect of technological application!! </span></p>
 +
 
 +
<p class=MsoNormal><span lang=EN-US><o:p>&nbsp;</o:p></span></p>
 +
 
 +
<p class=MsoNormal><b style='mso-bidi-font-weight:normal'><u><span lang=EN-US>Pressure
 +
inducible promoter - P<sub>lac </sub><o:p></o:p></span></u></b></p>
 +
 
 +
<p class=MsoNormal style='text-indent:5.25pt;mso-char-indent-count:.5'><span
 +
lang=EN-US>The affinity of LacI for the lac operator is known to decrease due
 +
to a tetramer to dimer transition of LacI </span></p>
 +
<IMG src="https://static.igem.org/mediawiki/2008/b/bd/Test.jpg" alt="[サンプルの絵]" width="300">
 +
 
 +
 
 +
<! strategy>
 +
 
 +
 
 +
<p class=MsoNormal><b style='mso-bidi-font-weight:normal'><u><span lang=EN-US
 +
style='font-size:14.0pt'>Strategy<o:p></o:p></span></u></b></p>
 +
 
 +
<IMG src="https://static.igem.org/mediawiki/2008/c/cf/Test2.jpg" alt="[サンプルの絵]" width="700">
 +
 
 +
 
 +
<! Equipment. Instrument for pressure experiment>
 +
 
 +
 
 +
<p class=MsoNormal><b style='mso-bidi-font-weight:normal'><u><span lang=EN-US
 +
style='font-size:14.0pt'>Equipment. Instrument for pressure experiment<o:p></o:p></span></u></b></p>
 +
 
 +
<IMG src="https://static.igem.org/mediawiki/2008/a/a3/Tech_kaatu.jpg" align="middle" width="500">
 +
 
 +
<p class=MsoNormal style='text-indent:5.25pt;mso-char-indent-count:.5'><span
 +
lang=EN-US>Fig 4: Fig4-1 is a pressure vessel. Fig4-4 is a pressurizing system.
 +
Fig4-2 show a inside of the vessel. The inside is filled with water and the
 +
withstand pressure container is put into the inside. Fig4-3 show a water bath
 +
placed some vessel.</span></p>
 +
 
 +
<! 1.Construction>
 +
<p class=MsoNormal><b style='mso-bidi-font-weight:normal'><u><span lang=EN-US>Strategy
 +
1.Construction<o:p></o:p></span></u></b></p>
 +
 
 +
<p class=MsoNormal><span lang=EN-US><o:p>&nbsp;</o:p></span></p>
 +
 
 +
<p class=MsoNormal><span lang=EN-US><o:p>&nbsp;</o:p></span></p>
 +
 
 +
<p class=MsoNormal><span lang=EN-US><o:p>&nbsp;</o:p></span></p>
 +
 
 +
<p class=MsoNormal><span lang=EN-US><o:p>&nbsp;</o:p></span></p>
 +
 
 +
<p class=MsoNormal><b style='mso-bidi-font-weight:normal'><span lang=EN-US>Confirmatory
 +
experiment<o:p></o:p></span></b></p>
 +
 
 +
<IMG src="https://static.igem.org/mediawiki/2008/6/6b/Tech_plac_g1.jpg" align="middle">
 +
<p class=MsoNormal><b style='mso-bidi-font-weight:normal'><u><span lang=EN-US
 +
style='font-size:14.0pt'>Stratagy 2. Basic device<o:p></o:p></span></u></b></p>
 +
 
 +
<p class=MsoNormal><span lang=EN-US><o:p>&nbsp;</o:p></span></p>
 +
 
 +
<p class=MsoNormal><span lang=EN-US><o:p>&nbsp;</o:p></span></p>
 +
 
 +
<p class=MsoNormal><span lang=EN-US><o:p>&nbsp;</o:p></span></p>
 +
 
 +
<p class=MsoNormal><span lang=EN-US><o:p>&nbsp;</o:p></span></p>
 +
 
 +
<p class=MsoNormal><span lang=EN-US><o:p>&nbsp;</o:p></span></p>
 +
 
 +
<p class=MsoNormal><span lang=EN-US><o:p>&nbsp;</o:p></span></p>
 +
 
 +
<p class=MsoNormal><span lang=EN-US><o:p>&nbsp;</o:p></span></p>
 +
 
 +
<p class=MsoNormal><b style='mso-bidi-font-weight:normal'><u><span lang=EN-US
 +
style='font-size:14.0pt'>Stratagy 3. Development of low pressure inducible
 +
promoter <o:p></o:p></span></u></b></p>
 +
 
 +
<p class=MsoNormal><span lang=EN-US>We performed random mutagenesis to lac
 +
promoter and tried to screen promoters with FACS.</span></p>
 +
 
 +
<p class=MsoNormal><span lang=EN-US><o:p>&nbsp;</o:p></span></p>
 +
 
 +
<p class=MsoNormal><span lang=EN-US><o:p>&nbsp;</o:p></span></p>
 +
 
 +
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 +
 
 +
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 +
 
 +
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 +
 
 +
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 +
 
 +
<p class=MsoNormal><span lang=EN-US><o:p>&nbsp;</o:p></span></p>
 +
 
 +
<p class=MsoNormal><span lang=EN-US>Strategy for Isolation of promoters </span></p>
 +
 
 +
<p class=MsoNormal><span lang=EN-US><o:p>&nbsp;</o:p></span></p>
 +
 
 +
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 +
 
 +
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 +
 
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 +
 
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 +
 
 +
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 +
 
 +
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 +
 
 +
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 +
 
 +
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 +
 
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 +
 
 +
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 +
 
 +
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 +
 
 +
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 +
 
 +
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 +
 
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 +
 
 +
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 +
 
 +
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 +
 
 +
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 +
 
 +
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 +
 
 +
<p class=MsoNormal><span lang=EN-US><o:p>&nbsp;</o:p></span></p>
 +
 
 +
<p class=MsoNormal><b style='mso-bidi-font-weight:normal'><span lang=EN-US>Future
 +
work<o:p></o:p></span></b></p>
 +
 
 +
<p class=MsoNormal style='margin-left:36.0pt;text-indent:-18.0pt;mso-list:l0 level1 lfo2;
 +
tab-stops:list 36.0pt'><![if !supportLists]><span lang=EN-US style='font-family:
 +
"Arial","sans-serif";mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>&#8226;<span
 +
style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
 +
lang=EN-US>try Step 2 and 3</span></p>
 +
 
 +
<p class=MsoNormal style='margin-left:36.0pt;text-indent:-18.0pt;mso-list:l0 level1 lfo2;
 +
tab-stops:list 36.0pt'><![if !supportLists]><span lang=EN-US style='font-family:
 +
"Arial","sans-serif";mso-fareast-font-family:Arial'><span style='mso-list:Ignore'>&#8226;<span
 +
style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><![endif]><span
 +
lang=EN-US>characterize isolated promoters </span></p>
 +
 
 +
<p class=MsoNormal><span lang=EN-US><o:p>&nbsp;</o:p></span></p>
 +
 
 +
<p class=MsoNormal><b style='mso-bidi-font-weight:normal'><u><span lang=EN-US>4.Genetic
 +
toggle switch to implement rewritable function <o:p></o:p></span></u></b></p>
 +
 
 +
<p class=MsoNormal><span lang=EN-US><o:p>&nbsp;</o:p></span></p>
 +
 
 +
<p class=MsoNormal><span lang=EN-US><o:p>&nbsp;</o:p></span></p>
 +
 
 +
<p class=MsoNormal><span lang=EN-US><o:p>&nbsp;</o:p></span></p>
 +
 
 +
<p class=MsoNormal><span lang=EN-US><o:p>&nbsp;</o:p></span></p>
 +
 
 +
<p class=MsoNormal><span lang=EN-US><o:p>&nbsp;</o:p></span></p>
 +
 
 +
<p class=MsoNormal><span lang=EN-US><o:p>&nbsp;</o:p></span></p>
 +
 
 +
<p class=MsoNormal><span lang=EN-US><o:p>&nbsp;</o:p></span></p>
 +
 
 +
<p class=MsoNormal><span style='font-family:"ＭＳ 明朝","serif";mso-ascii-font-family:
 +
Century;mso-hansi-font-family:Century'>・</span><span lang=EN-US> genetic toggle
 +
switch</span></p>
 +
 
 +
<p class=MsoNormal><span lang=EN-US><span
 +
style='mso-spacerun:yes'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>- Writable
 +
function</span></p>
 +
 
 +
<p class=MsoNormal><span lang=EN-US>P<sub>lac</sub> is induced under 30 MPa
 +
pressure</span></p>
 +
 
 +
<p class=MsoNormal><span lang=EN-US>(P<sub>L </sub>is not induced by 30 MPa
 +
pressure)</span></p>
 +
 
 +
<p class=MsoNormal><span lang=EN-US>Express GFP, CI, and CI represses P<sub>L </sub></span></p>
 +
 
 +
<p class=MsoNormal><span lang=EN-US>→ bright !! </span></p>
 +
 
 +
<p class=MsoNormal><span lang=EN-US>- Erasable function</span></p>
 +
 
 +
<p class=MsoNormal><span lang=EN-US>P<sub>L</sub> is induced by heat</span></p>
 +
 
 +
<p class=MsoNormal><span lang=EN-US>Express LacI, P<sub>lac </sub>represses GFP
 +
</span></p>
 +
 
 +
<p class=MsoNormal><span lang=EN-US>→ go out little by little…</span></p>
 +
 
 +
<p class=MsoNormal><span lang=EN-US><o:p>&nbsp;</o:p></span></p>
 +
 
 +
<p class=MsoNormal><span lang=EN-US>Future work</span></p>
 +
 
 +
<p class=MsoNormal><span lang=EN-US><span
 +
style='mso-spacerun:yes'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>- Identify
 +
pressure model parameter from experimental data</span></p>
 +
 
 +
<p class=MsoNormal><span lang=EN-US><span
 +
style='mso-spacerun:yes'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>- Simulate
 +
pressure induction by pressure model and estimate </span></p>
 +
 
 +
<p class=MsoNormal><span lang=EN-US><span
 +
style='mso-spacerun:yes'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 +
</span>promoter-RBS strength to implement rewritable function</span></p>
 +
 
 +
<p class=MsoNormal><span lang=EN-US><o:p>&nbsp;</o:p></span></p>
 +
 
 +
<p class=MsoNormal><span lang=EN-US><o:p>&nbsp;</o:p></span></p>
 +
 
 +
<p class=MsoNormal><span lang=EN-US><o:p>&nbsp;</o:p></span></p>
 +
 
 +
<p class=MsoNormal><span lang=EN-US><o:p>&nbsp;</o:p></span></p>
 +
 
 +
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 +
 
 +
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 +
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 +
 
 +
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 +
 
 +
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 +
 
 +
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 +
 
 +
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 +
 
 +
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 +
 
 +
<p class=MsoNormal><b style='mso-bidi-font-weight:normal'><span lang=EN-US>Mathematical</span></b><b
 +
style='mso-bidi-font-weight:normal'><span style='font-family:"ＭＳ 明朝","serif";
 +
mso-ascii-font-family:Century;mso-hansi-font-family:Century'>　</span><span
 +
lang=EN-US>model <o:p></o:p></span></b></p>
 +
 
 +
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 +
 
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 +
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 +
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 +
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 +
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== Project Details==
== Project Details==

Revision as of 20:32, 20 October 2008

Project

Code name Rising Sun

E.coli UKIYO-E

This project aims to make UKIYO-E by E.coli. UKIYO-E is a genre of Japanese woodblock prints.



You can write a background of your team here. Give us a background of your team, the members, etc. Or tell us more about something of your choosing.
Tokyotech.jpg
Tell us more about your project. Give us background. Use this is the abstract of your project. Be descriptive but concise (1-2 paragraphs)
Team Example 2
Home The Team The Project Parts Submitted to the Registry Modeling Notebook

(Or you can choose different headings. But you must have a team page, a project page, and a notebook page.)


Our project

We want to make a Coli Touch!!

→We try to construct a bacterial ‘touch panel’ which is colored by the pressure.

We name it Coli touch.

 

Why pressure?

Example of input style to genetic circuit

- Heat: thermal gradient

- Small molecule: concentration gradient

- Light: strength depend on location of container

        

           Difficulty in uniform introduction

 

  Press!  Confirmatory experiment

Prospect of technological application!!

 

Pressure inducible promoter - Plac

The affinity of LacI for the lac operator is known to decrease due to a tetramer to dimer transition of LacI

[サンプルの絵]

Strategy

[サンプルの絵]

Equipment. Instrument for pressure experiment

Fig 4: Fig4-1 is a pressure vessel. Fig4-4 is a pressurizing system. Fig4-2 show a inside of the vessel. The inside is filled with water and the withstand pressure container is put into the inside. Fig4-3 show a water bath placed some vessel.

Strategy 1.Construction

 

 

 

 

Confirmatory experiment

Stratagy 2. Basic device

 

 

 

 

 

 

 

Stratagy 3. Development of low pressure inducible promoter

We performed random mutagenesis to lac promoter and tried to screen promoters with FACS.

 

 

 

 

 

 

 

Strategy for Isolation of promoters

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Future work

•       try Step 2 and 3

•       characterize isolated promoters

 

4.Genetic toggle switch to implement rewritable function

 

 

 

 

 

 

 

・ genetic toggle switch

       - Writable function

Plac is induced under 30 MPa pressure

(PL is not induced by 30 MPa pressure)

Express GFP, CI, and CI represses PL

→ bright !!

- Erasable function

PL is induced by heat

Express LacI, Plac represses GFP

→ go out little by little…

 

Future work

      - Identify pressure model parameter from experimental data

      - Simulate pressure induction by pressure model and estimate

        promoter-RBS strength to implement rewritable function

 

 

 

 

 

 

 

 

 

 

 

 

Mathematical　model

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Contents

Project Details

Part 2

The Experiments

Part 3

Results

Retrieved from "http://2008.igem.org/Team:Tokyo_Tech/Project"