Team:TMU-Tokyo

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This is our project descriptions.
 
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In this year, we paid attention to site-specific recombination system. A lot of living things use this system in various ways. In site-specific recombination, insertion, deficiency, and an inversion happen and those happening frequency change with kinds of enzyme or recombination site.
 
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Then, we tried to create the new system which can respond to a broader situation by using two or more different site-specific recombination mechanisms.
 
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  <h1>Project description<h1>
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    <td><p>In the iGEM, most teams have inserted their Biobrick parts or devices into plasmids and have used them. It is true that there are many good points to use plasmids, for instance, it is easy to do transformation, and it is convenient to use high copy plasmid when you want to get high amount of gene expression. However, there are some bad points to use plasmids too. For example, when the reproduction starting point of plural plasmids are covered, they can’t be put in <i>E.coli</i> at the same time. Also it is difficult to control closely expression of the genes which are in .plasmids.</p>
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<p>Therefore, in this year, our team tried to establish and standardize a new method to insert Biobrick parts or devices in a genome of <i>E.coli</i> and use them. Also, according to this method, we really inserted the device which we designed in a genome of <i>E.coli</i> and functionalized it.</p>
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          <tr  height="30"><td align="center"><b>Standardization</b> －New method, “Breakthrough”－</td></tr>
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          <tr height="200"><td style="padding:3px 7px;"><p><a href="https://2013.igem.org/Team:TMU-Tokyo/Project/NEWS" >In order to insert Biobricks in a genome of <i>E.coli</i> and functionalize them, we established a new and interesting method and standardize it. In this new method named “Breakthrough”, we constructed all of our parts by over rap extension PCR and inserted these PCR products into a genome of <i>E.coli</i> by lambda bacteriophage recombination system named ”RED”. Also we designed a new parts which to improve the present designated vector (pSB1C3). With this part, it can be easily to do cloning the parts which made by PCR.<br>
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Additionally, we standardized this method so that other iGEMers could use it. So<u> we’ll apply for New Standard prize.</u>
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            <tr  height="30"><td align="center"><b>Implementation</b>　―Genomic Pythagorean Device－</a></td></tr>
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          <p><a href="https://2013.igem.org/Team:TMU-Tokyo/Project/Pythagorean_Device" >  According to the method that we spoke in the right, we really inserted the device named “Genomic Pythagorean Device”, which we designed into a genome of <i>E.coli</i>. “Pythagorean Device” is very famous in Japan because Japanese famous educational TV program "Pythagorean Switch" introduces various Pythagorean Devices. They are known as "Rube Goldberg machines" in the US. Pythagorean Devices are deliberately over-engineered or overdone systems that perform very simple task in very complicated process, and they usually include some chain reactions. We constructed “Pythagorean Device” in a genome of <i>E.coli</i> and checked whether it functioned properly.</a></p></td></tr>
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|align="center"|[[Team:TMU-Tokyo | Team TMU-Tokyo]]
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!align="center"|[[Team:TMU-Tokyo|Home]]
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!align="center"|[[Team:TMU-Tokyo/Team|Team]]
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!align="center"|[https://igem.org/Team.cgi?year=2013&team_name=TMU-Tokyo Official Team Profile]
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!align="center"|[[Team:TMU-Tokyo/Project|Project]]
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!align="center"|[[Team:TMU-Tokyo/Parts|Parts Submitted to the Registry]]
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!align="center"|[[Team:TMU-Tokyo/Modeling|Modeling]]
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!align="center"|[[Team:TMU-Tokyo/Notebook|Notebook]]
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!align="center"|[[Team:TMU-Tokyo/Safety|Safety]]
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!align="center"|[[Team:TMU-Tokyo/Attributions|Attributions]]
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        <td class="boximg" rowspan="2" ><a href="https://2013.igem.org/Team:TMU-Tokyo/Project/Idea">
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                                        <img src="https://static.igem.org/mediawiki/igem.org/9/9b/TMU-Idea.png"
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        <td  colspan="2" rowspan="2">
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                    <li>What is our goal?</li>
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                    <li>Why is there a need for our project?</li>
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                    <li>Why do we  insert parts in a genome? </td>
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        <td class="boximg" rowspan="2"><a href="https://2013.igem.org/Team:TMU-Tokyo/Parts">
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                                        <img src="https://static.igem.org/mediawiki/igem.org/0/0c/TMUParts.png"
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                                        onmouseover="this.src='https://static.igem.org/mediawiki/igem.org/2/2e/TMUParts_af.png';"
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                                        onmouseout="this.src='https://static.igem.org/mediawiki/igem.org/0/0c/TMUParts.png';"></td>
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        <td  colspan="2" rowspan="2">
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          <li>What Biobrick parts did we design ?</li>
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          <li>Which parts did we submit ?</li>
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          <li>Did our parts work ?</li> </td>
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        </tr>
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        <tr>
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        <tr>
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        <td ></td>
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        <td class="boximg" rowspan="2"><a href="https://2013.igem.org/Team:TMU-Tokyo/Project/Future_Plan">
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                                        <img src="https://static.igem.org/mediawiki/igem.org/1/11/TMUArrow.png"
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                                        onmouseover="this.src='https://static.igem.org/mediawiki/igem.org/f/fe/TMUArrow_af.png';"
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                                        onmouseout="this.src='https://static.igem.org/mediawiki/igem.org/1/11/TMUArrow.png';"></a></td>
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        <td  colspan="2" rowspan="2">
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          <li>What kind of application is imaginable ?</li>
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          <li>What is necessary to improve our project ?</li>
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        <td ></td>
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      <td class="boximg" rowspan="2"><a href="https://2013.igem.org/Team:TMU-Tokyo/HumanPractice">
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                                      <img src="https://static.igem.org/mediawiki/igem.org/c/c8/TMUHeart.png"
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                                        onmouseover="this.src='https://static.igem.org/mediawiki/igem.org/3/32/TMUHeart_af.png';"
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                                        onmouseout="this.src='https://static.igem.org/mediawiki/igem.org/c/c8/TMUHeart.png';"></a></td>
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        <td  colspan="2" rowspan="2">
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          <li>What did we do to promote Synthetic Biology?</li>
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          </td>
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        <td class="boximg" rowspan="2"><a href="https://2013.igem.org/Team:TMU-Tokyo/Safety">
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                                      <img src="https://static.igem.org/mediawiki/igem.org/2/23/TMUSafety.png"
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                                        onmouseover="this.src='https://static.igem.org/mediawiki/igem.org/5/5a/TMUSafety_af.png';"
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                                        onmouseout="this.src='https://static.igem.org/mediawiki/igem.org/2/23/TMUSafety.png';"></a></td>
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        <td  colspan="2" rowspan="2">
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          <li>What did we do for securing of safety ?</li>
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          </td>
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        </tr>
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        <tr>
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        <td ></td>
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        <td class="boximg" rowspan="2"><a href="https://2013.igem.org/Team:TMU-Tokyo/Achievement">
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                                      <img src="https://static.igem.org/mediawiki/igem.org/5/52/TMUTrophy.png"
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                                        onmouseover="this.src='https://static.igem.org/mediawiki/igem.org/a/a2/TMUTrophy_af.png';"
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                                        onmouseout="this.src='https://static.igem.org/mediawiki/igem.org/5/52/TMUTrophy.png';"></a></td>
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        <td  colspan="2" rowspan="2">
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          <li>What did we achieve in our project ?</li>
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          </td>
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        </tr>
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        <tr>
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        </tr>
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        <tr>
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        <td ></td>
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  <h1>Sponsors</h1>
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<A href="http://www.promega.co.jp/index.html"><IMg src="https://static.igem.org/mediawiki/2013/f/f9/Promega_logo_c.gif"></A>
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<A href="http://lne.st"><IMG Src="https://static.igem.org/mediawiki/2013/8/89/Lnest-logo3_03.png" border="0"height="60">
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</A>
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<A href="http://mendel-science.com/"><IMG Src="http://igemtmu.net/2011/menderu.png" border="0">
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</A>
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<A href="http://www.cosmobio.co.jp"><IMG Src="http://igemtmu.net/2011/kosumo.png" border="0">
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</A>
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<A href="http://www.mbl.co.jp/"><IMG Src="https://static.igem.org/mediawiki/2012/f/f2/Mbl.gif" border="0">
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<A href="http://www.tmu.ac.jp/"><IMG Src="https://static.igem.org/mediawiki/2012/c/c6/TMUlogo.png" border="0">
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</A>
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<A href="http://www.comp.tmu.ac.jp/dousoukai/"><IMG Src="https://static.igem.org/mediawiki/2012/e/e1/Dousoukai.sp.jpg" border="0">
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<a href="http://www.ikedarika.co.jp/"><img src="https://static.igem.org/mediawiki/igem.org/c/c2/Ikeda_logo.gif" >
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      <h1>contact us!!</h1>
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      <Hr>
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    <p  align="center" hspace="20"><a href="https://www.facebook.com/TmUnigem"><img src="https://static.igem.org/mediawiki/igem.org/6/66/TMUFacebook02.jpg" ></a></p>
 +
    <span style="line-height:50%"><Br></span> 
 +
    <p><img  vspace="20" src="https://static.igem.org/mediawiki/igem.org/5/50/TMUGmail-Icon.png">tmutokyo.igem@gmail.com</p>
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Latest revision as of 02:49, 28 September 2013



Project description

In the iGEM, most teams have inserted their Biobrick parts or devices into plasmids and have used them. It is true that there are many good points to use plasmids, for instance, it is easy to do transformation, and it is convenient to use high copy plasmid when you want to get high amount of gene expression. However, there are some bad points to use plasmids too. For example, when the reproduction starting point of plural plasmids are covered, they can’t be put in E.coli at the same time. Also it is difficult to control closely expression of the genes which are in .plasmids.

Therefore, in this year, our team tried to establish and standardize a new method to insert Biobrick parts or devices in a genome of E.coli and use them. Also, according to this method, we really inserted the device which we designed in a genome of E.coli and functionalized it.


Standardization －New method, “Breakthrough”－

In order to insert Biobricks in a genome of E.coli and functionalize them, we established a new and interesting method and standardize it. In this new method named “Breakthrough”, we constructed all of our parts by over rap extension PCR and inserted these PCR products into a genome of E.coli by lambda bacteriophage recombination system named ”RED”. Also we designed a new parts which to improve the present designated vector (pSB1C3). With this part, it can be easily to do cloning the parts which made by PCR.
Additionally, we standardized this method so that other iGEMers could use it. So we’ll apply for New Standard prize.

Implementation　―Genomic Pythagorean Device－

According to the method that we spoke in the right, we really inserted the device named “Genomic Pythagorean Device”, which we designed into a genome of E.coli. “Pythagorean Device” is very famous in Japan because Japanese famous educational TV program "Pythagorean Switch" introduces various Pythagorean Devices. They are known as "Rube Goldberg machines" in the US. Pythagorean Devices are deliberately over-engineered or overdone systems that perform very simple task in very complicated process, and they usually include some chain reactions. We constructed “Pythagorean Device” in a genome of E.coli and checked whether it functioned properly.

　
  • What is our goal?
  • Why is there a need for our project?
  • Why do we insert parts in a genome?
  • What Biobrick parts did we design ?
  • Which parts did we submit ?
  • Did our parts work ?
    		•
  • What kind of application is imaginable ?
  • What is necessary to improve our project ?
    		•
  • What did we do to promote Synthetic Biology?
    		•
  • What did we do for securing of safety ?
    		•
  • What did we achieve in our project ?
    		•


    Sponsors

    contact us!!

    tmutokyo.igem@gmail.com

    Retrieved from "http://2013.igem.org/Team:TMU-Tokyo"