Team:Tokyo Tech

From 2008.igem.org

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project description
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'''''E.coli UKIYO-E'''''
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This project aims to make ''UKIYO-E'' by E.coli.  
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''UKIYO-E'' is a genre of Japanese woodblock prints.
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We will make this by pressure responsive E.coli.
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</head>
-
==Project Description==
 
-
'''Our goal is to make "UKIYO-E" by pressure responsive E.coli.'''
 
-
''UKIYO-E'' is a genre of Japanese woodblock prints.
+
<! *********************************************************************************************>
-
Pressure is nessesary to make ''UKIYO-E''. Then, we decided to make pressure responsive E.coli.
+
-
We will make pressure responsive E.coli by using ***. 
+
 +
<! *********************************************************************************************>
 +
<! *********************************************************************************************>
 +
<! *********************************************************************************************>
-
{|align="justify"
 
-
|<!-- 表示されない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. -->
 
-
|[[Image:Tokyotech.jpg|200px|center|frame]]
 
-
|-
 
-
|
 
-
<!-- 表示されない''Tell us more about your project.  Give us background.  Use this is the abstract of your project.  Be descriptive but concise (1-2 paragraphs)'' -->
 
-
|
 
-
|-
 
-
|
 
-
|align="center"|[[Team:Tokyo_Tech | Team Example 2]]
 
-
|}
 
-
<!--- The Mission, Experiments --->
+
<body lang=JA style='tab-interval:42.0pt;text-justify-trim:punctuation'>
 +
 
 +
<div class=Section1 style='layout-grid:18.0pt'>
 +
 
 +
<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>
 +
 
 +
<table width="100%" border="0" cellspacing="0" cellpadding="0">
 +
        <tr>
 +
          <td class="a" width="3%">　</td>
 +
          <td class="a">
 +
<p class=MsoNormal><span
 +
lang=EN-US>Until iGEM2007, input style was only heat, small molecule and light. These input
 +
style have problems. For example, Heat input occur thermal gradient, small
 +
molecule input occur concentration gradient, light input depend on location of a
 +
container. So, we thought input style except these. That is “press”. Press input
 +
has an advantage that input signal travel uniformly in a container.</i></span></p>
 +
<td class="a" width="3%">　</td>
 +
        </tr>
 +
      </table>
 +
 
 +
<! Why pressure?>
 +
 
 +
 
 +
<p class=MsoNormal><b style='mso-bidi-font-weight:normal'><u><span lang=EN-US
 +
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>
 +
 
 +
<p class=MsoNormal><span lang=EN-US><span
 +
style='mso-spacerun:yes'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 +
</span></span></p>
 +
 
 +
<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">
 +
 
 +
<small><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></small>
 +
<! ---------------------------------------------------------------------------------------------------------->
 +
<! 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>
 +
 
 +
<IMG src="https://static.igem.org/mediawiki/2008/6/63/Tech_constraction.jpg" align="middle">
 +
 
 +
<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">
 +
<small><p class=MsoNormal style='text-indent:5.25pt;mso-char-indent-count:.5'><span
 +
lang=EN-US>Fig1:Pressure-response of Plac-GFP under several pressures measured by flow cytometer</span></p></small>
 +
 
 +
<! ---------------------------------------------------------------------------------------------------------->
 +
 
 +
<IMG src="https://static.igem.org/mediawiki/2008/e/e5/Tech_pic_30.jpg" >&nbsp;<IMG src="https://static.igem.org/mediawiki/2008/a/a2/Tech_pic_rp.jpg" height="241">&nbsp;<IMG src="https://static.igem.org/mediawiki/2008/f/f6/Tech_pic_nega.jpg" height="241">
 +
 
 +
<small><p class=MsoNormal style='text-indent:5.25pt;mso-char-indent-count:.5'><span
 +
lang=EN-US>Fig2-1:Plac-GFP under 30MPa&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Fig2-2:Plac-GFP under 0.1MPa&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Fig2-3:⊿-GFP under 30MPa</span></p></small>
 +
 
 +
<! ---------------------------------------------------------------------------------------------------------->
 +
<p class=MsoNormal><b style='mso-bidi-font-weight:normal'><u><span lang=EN-US
 +
style='font-size:14.0pt'>Stratagy 2. Basic device</span></u></b></p>
 +
 
 +
<IMG src="https://static.igem.org/mediawiki/2008/9/9d/Tech_youki.jpg" align="middle" width="500" >
 +
 
 +
<! --------------------------------------------------------------------------------------------------------->
 +
<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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 +
 
 +
<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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== Project Details==
 +
 
 +
 
 +
 
 +
 
 +
 
 +
=== Part 2 ===
 +
 
 +
 
 +
 
 +
 
 +
 
 +
=== The Experiments ===
 +
 
 +
 
 +
 
 +
 
 +
=== Part 3 ===
{| style="color:#1b2c8a;background-color:#0c6;" cellpadding="3" cellspacing="1" border="1" bordercolor="#fff" width="62%" align="center"
{| style="color:#1b2c8a;background-color:#0c6;" cellpadding="3" cellspacing="1" border="1" bordercolor="#fff" width="62%" align="center"

Revision as of 22:30, 21 October 2008

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.

　

Until iGEM2007, input style was only heat, small molecule and light. These input style have problems. For example, Heat input occur thermal gradient, small molecule input occur concentration gradient, light input depend on location of a container. So, we thought input style except these. That is “press”. Press input has an advantage that input signal travel uniformly in a container.

　

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

Fig1:Pressure-response of Plac-GFP under several pressures measured by flow cytometer

   

Fig2-1:Plac-GFP under 30MPa       Fig2-2:Plac-GFP under 0.1MPa       Fig2-3:⊿-GFP under 30MPa

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

Home The Team The Project Parts Submitted to the Registry Modeling Notebook Japanese
Retrieved from "http://2008.igem.org/Team:Tokyo_Tech"