Team:Tokyo-NoKoGen

From 2013.igem.org

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                    <a href="https://2013.igem.org/Team:Tokyo-NoKoGen"><img class="title" src="NoKoGen_material/title2.png"></a> 
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                     <a href="https://2013.igem.org"><img class="iGEM2013" src="NoKoGen_material/iGEM2013.png"></a>   
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                     <a href="https://2013.igem.org"><img class="iGEM" src="https://static.igem.org/mediawiki/2013/5/58/IGEM.png"></a>   
               </div>
               </div>
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                         <td class="notebook"><a href="https://2013.igem.org/Team:Tokyo-NoKoGen/Notebook"><span class="notebook"></span></a></td>
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                         <td class="achievement"><a href="https://2013.igem.org/Team:Tokyo-NoKoGen/Achievement"><span class="achievement"></span></a></td>
                     </tbody>
                     </tbody>
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                     </table>   
   
   
               </div>
               </div>
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<div id="index">
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              <div id="index">
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                     <img class="logo" src="NoKoGen_material/Tシャツ5.png">
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                     <h1 id="index_title">INDEX</h1>
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                     <h1 id="index_title"></h1>
            <ul id="contents">
            <ul id="contents">
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                <a href="#abstract"><li><strong>Abstract</strong></li></a>
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                <a href="https://2013.igem.org/Team:Tokyo-NoKoGen/oscillator"><li><a href="#diary"><strong>RNA oscillator</a></strong></li></a>
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                <li><strong></strong></li>
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                <a href="https://2013.igem.org/Team:Tokyo-NoKoGen/scaffold"><li><strong>RNA scaffold</strong></li></a>
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                <li><strong></strong></li>
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                <a href="https://2013.igem.org/Team:Tokyo-NoKoGen/light"><li><strong>Light sensor</strong></li></a>
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                <li><strong></strong></li>
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                <a href="https://2013.igem.org/Team:Tokyo-NoKoGen/modeling"><li><strong>Modeling</strong></li></a>
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                <li><strong></strong></li>
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-
                <li><strong></strong></li>
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            </ul>
            </ul>
   
   
               </div>
               </div>
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               <div id="main">
               <div id="main">
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                    <img id="mainback" src="NoKoGen_material/twinkle_coli.png">
 
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                    <h1 id="abstract">Abstract</h1>
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<img id="mainback" src="https://static.igem.org/mediawiki/2013/3/36/Twinklecoliaaa.PNG">
 +
 
 +
<BR>
 +
<BR>
 +
<BR>
 +
<BR>
 +
<p align=center><font size=7><strong>Introduction</strong></font></p></font>
 +
<BR>
 +
<hr>
 +
<hr size="3" width="(60%)" align="left"noshade>
 +
</hr>
 +
 
 +
 
 +
<BR>
 +
<p style="text-indent:2em"><font size=5>
 +
We all have a biological clock which controls the periodicity of</p>many physiological functions such as blood pressure, body</p>temperature and</p> concentration of hormones. The systems that generate circadian rhythms</p> are called oscillator. Oscillator has been researched fordeepening our</p> knowledge of circadian rhythms, understanding genetic network and signal</p> transfer.</p>
 +
<BR>
 +
 
 +
<div style="text-align:center">
 +
<img src="https://static.igem.org/mediawiki/2013/0/0d/Circadian_rhythm.PNG", height="300", width="450",alt="">
 +
</div>
 +
<BR>
 +
<div style="text-align:center"><font size=3>
 +
Fig.1 Circadian rhythm</font>
 +
</div>
 +
<p style="text-indent:1em">
 +
Oscillator is expected to be used for various applications.</p>
 +
<BR>
 +
<p style="text-indent:1em">
 +
Therefore, desired features of oscillator are:</p>
 +
<p style="text-indent:4em">
 +
<strong>
 +
1. Variation in types</strong></p>
 +
<p style="text-indent:4em">
 +
<strong>
 +
2. Feasibility in designing and controlling</strong></p>
 +
<BR>
 +
<p style="text-indent:2em">
 +
However, existing protein oscillator does not satisfy the above requirements.</p>
 +
<img src="https://static.igem.org/mediawiki/2013/9/91/Protein.PNG",height="200", width="200"alt="" style="float:right">
 +
<p style="text-indent:2em">
 +
The first difficulty of protein oscillator is the small type of the protein. Because the number of repressor proteins and promoters are limited, the variation of protein oscillator is not many. </p>
 +
<p style="text-indent:2em">
 +
Another difficulty of protein oscillator is the component, the protein. Protein requires several steps; transcription and translation, protein modification, folding, and degradation. When we want to construct or control such protein oscillator, we have to genetically engineer to change the transcriptional efficiency, translational efficiency and degradation ability. Therefore, it is difficult to design such gene circuits that can express the repressors periodically. </p>
 +
<BR>
 +
<p style="text-indent:4em"><font size=3>
 +
　　　　　　　　　　　　　　　　　　　　　　　　　　　　　　　　　　　　　　　　　　  Fig. 2 Steps of protein expression</font></p>
 +
<BR>
 +
<p style="text-indent:2em">
 +
To satisfy the requirements, we propose the New type of oscillator circuit – <span style="color:#ff0000">RNA oscillator</span>.</p>
 +
 
 +
<p style="text-indent:2em">
 +
Whereas there are only a few types of proteins that can be used for the construction of protein oscillator, many kinds of oscillators can be constructed with RNA by changing a few base. Therefore, it will allow us to construct a multiple and orthogonal oscillators.</p>
 +
<p style="text-indent:2em">
 +
Another advantage is that, although protein has several steps until degradation, RNA has no steps of translation, modification and time-consuming degradation. Therefore, RNA oscillator can be designed and controlled by only changing the transcriptional efficiency and binding ability. It is easy to change the binding ability of RNA because all we have to do is to alter the base, and hence change the strength of base pairs binding.</p>
 +
 
 +
<img src="https://static.igem.org/mediawiki/2013/5/57/ProteinRNA.PNG",height="200",width="200",alt="">
 +
 
 +
<img src="https://static.igem.org/mediawiki/2013/6/61/%E3%82%AD%E3%83%A3%E3%83%97%E3%83%81%E3%83%A3aa.PNG", height="300", width="350", alt="",style="float:right">
 +
<p style="text-indent:1em"><font size=3>
 +
Fig.3 Steps of protein expression and RNA transcription　　　　　  　　Fig.4 RNA is easy to modify</font>
 +
<BR>
 +
<BR>
 +
<p style="text-indent:2em">
 +
Like this, RNA meets the necessary standards for:</p>
 +
 
 +
<p style="text-indent:4em">
 +
<strong>
 +
1. Variation in types</strong></p>
 +
<p style="text-indent:4em">
 +
<strong>
 +
2. Feasibility in designing and controlling</strong></p>
 +
<BR>
 +
<p style="text-indent:2em">
 +
Therefore, it can be used for combination with diverse mechanisms.
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For example, we can change output signals from RNA to other ones such as protein with reporter circuit, and control the oscillation with light sensor.</p>
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In this way, the ability to combine with various mechanisms can be used for controlling complex systems such as drug delivery.</p>
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We named the E. coli which has this ability <strong>Twinkle.coli</strong> because of its brilliant future.
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<img src="https://static.igem.org/mediawiki/2013/0/0e/Twinklecokikuuuuu.PNG", height="300", width="350", alt="">
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Fig.5 Twinkle. coli</font>
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                    <h2>-Fast cycle! Fast response!-</h2>
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                    <p>　This year, we will create Twinkle.coli! Twinkle.coli blinks luminescence like a firefly. To construct it, we need a circuit that oscillates at a short cycle and a fast responsive system. To make oscillating circuit of a short cycle, we designed RNA based oscillator. Some genetic oscillator circuits have been already created and reported. In such common circuits, the oscillation is generated by the expression of inducer and repressor proteins, creating positive and negative feedbacks. As The problem with these oscillators is that because they use proteins to move the oscillation, it takes time for proteins to be transcribed to mRNA, which then needs to be translated to amino acid, and folded into protein, we have to shorten the cycle to make Twinkle coli. To accomplish it, avoid such problem, we chose RNA as a repressor.</p>
 
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                     <p>　The key point in our RNA oscillator is the use of RNA responsible self-cleavage ribozyme, which can control and be controlled by other RNA. To make a fast responsive system, we use the concept of RNA scaffold. When RNA is transcribed as an output from the oscillator, the already translated and existing luciferase and GFP in the cytoplasm bind the transcribed RNA, and BRET occurs which is a shift in luminescence. </p>
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Latest revision as of 03:40, 28 September 2013

Team:Tokyo-NoKoGen - 2013.igem.org





Introduction



We all have a biological clock which controls the periodicity of

many physiological functions such as blood pressure, body

temperature and

concentration of hormones. The systems that generate circadian rhythms

are called oscillator. Oscillator has been researched fordeepening our

knowledge of circadian rhythms, understanding genetic network and signal

transfer.



Fig.1 Circadian rhythm

Oscillator is expected to be used for various applications.


Therefore, desired features of oscillator are:

1. Variation in types

2. Feasibility in designing and controlling


However, existing protein oscillator does not satisfy the above requirements.

The first difficulty of protein oscillator is the small type of the protein. Because the number of repressor proteins and promoters are limited, the variation of protein oscillator is not many.

Another difficulty of protein oscillator is the component, the protein. Protein requires several steps; transcription and translation, protein modification, folding, and degradation. When we want to construct or control such protein oscillator, we have to genetically engineer to change the transcriptional efficiency, translational efficiency and degradation ability. Therefore, it is difficult to design such gene circuits that can express the repressors periodically.


　　　　　　　　　　　　　　　　　　　　　　　　　　　　　　　　　　　　　　　　　　 Fig. 2 Steps of protein expression


To satisfy the requirements, we propose the New type of oscillator circuit – RNA oscillator.

Whereas there are only a few types of proteins that can be used for the construction of protein oscillator, many kinds of oscillators can be constructed with RNA by changing a few base. Therefore, it will allow us to construct a multiple and orthogonal oscillators.

Another advantage is that, although protein has several steps until degradation, RNA has no steps of translation, modification and time-consuming degradation. Therefore, RNA oscillator can be designed and controlled by only changing the transcriptional efficiency and binding ability. It is easy to change the binding ability of RNA because all we have to do is to alter the base, and hence change the strength of base pairs binding.

Fig.3 Steps of protein expression and RNA transcription　　　　　 　　Fig.4 RNA is easy to modify

Like this, RNA meets the necessary standards for:

1. Variation in types

2. Feasibility in designing and controlling


Therefore, it can be used for combination with diverse mechanisms. For example, we can change output signals from RNA to other ones such as protein with reporter circuit, and control the oscillation with light sensor.

In this way, the ability to combine with various mechanisms can be used for controlling complex systems such as drug delivery.

We named the E. coli which has this ability Twinkle.coli because of its brilliant future.




Fig.5 Twinkle. coli

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