Team:Tokyo-NoKoGen

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               </div>
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<div id="index">
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                     <h1 id="index_title"></h1>
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            <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>
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               <div id="main">
               <div id="main">
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  <img id="mainback" src="https://static.igem.org/mediawiki/2013/f/fd/Twinkle_coli.png">
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  <img id="mainback" src="https://static.igem.org/mediawiki/2013/3/36/Twinklecoliaaa.PNG">
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<p style="text-indent:2em">
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<BR>
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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 for deepening our knowledge of circadian rhythms, understanding genetic network and signal transfer.</p>
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<BR>
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<BR>
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<BR>
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<p align=center><font size=7><strong>Introduction</strong></font></p></font>
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<BR>
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<hr>
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<hr size="3" width="(60%)" align="left"noshade>
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</hr>
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<div style="text-align:right">
 
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<img src="https://2013.igem.org/File:Circadian_rhythm.PNG" width="20" height="20" alt="">
 
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</div>
 
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<BR>
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<p style="text-indent:2em"><font size=5>
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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>
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<BR>
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<div style="text-align:center">
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<img src="https://static.igem.org/mediawiki/2013/0/0d/Circadian_rhythm.PNG", height="300", width="450",alt="">
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</div>
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<BR>
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<div style="text-align:center"><font size=3>
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Fig.1 Circadian rhythm</font>
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</div>
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<p style="text-indent:1em">
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Oscillator is expected to be used for various applications.</p>
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<BR>
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<p style="text-indent:1em">
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Therefore, desired features of oscillator are:</p>
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<p style="text-indent:4em">
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<strong>
 +
1. Variation in types</strong></p>
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<p style="text-indent:4em">
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<strong>
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2. Feasibility in designing and controlling</strong></p>
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<BR>
<p style="text-indent:2em">
<p style="text-indent:2em">
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Oscillator is expected to be used for various applications. It needs to be available in various types and can be made and controlled easily. </p>
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However, existing protein oscillator does not satisfy the above requirements.</p>
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<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">
<p style="text-indent:2em">
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However, there are several problems of existing oscillator using protein.
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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>
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<p style="text-indent:3em">
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1. There are only a few types of repressor proteins, which make it harder to make a sophisticated circuit in one cell.
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<p style="text-indent:3em">
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2. Protein requires several steps for maturation, which makes it difficult to design and control oscillator.
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<p style="text-indent:2em">
<p style="text-indent:2em">
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The first problem 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 that can be made in one cell is not many.  
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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>
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<BR>
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<p style="text-indent:4em"><font size=3>
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　　　　　　　　　　　　　　　　　　　　　　　　　　　　　　　　　　　　　　　　　　  Fig. 2 Steps of protein expression</font></p>
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<BR>
<p style="text-indent:2em">
<p style="text-indent:2em">
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Another problem 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.  
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To satisfy the requirements, we propose the New type of oscillator circuit – <span style="color:#ff0000">RNA oscillator</span>.</p>
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<p style="text-indent:2em">
<p style="text-indent:2em">
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For the solutions of these problems and for the applications, we decided to construct the New type of oscillator circuit – RNA Oscillator.　We named the E. coli which has this function TwinklE. Coli.
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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">
<p style="text-indent:2em">
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　Whereas there are only a few types of proteins that can be used for construction of protein oscillator, Many kinds of RNA oscillators can be constructed by changing a few base pair. Therefore, it will allow us to construct a multiple and orthogonal oscillators in one cell.
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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>
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<img src="https://static.igem.org/mediawiki/2013/5/57/ProteinRNA.PNG",height="200",width="200",alt="">
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<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">
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<p style="text-indent:1em"><font size=3>
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Fig.3 Steps of protein expression and RNA transcription　　　　　  　　Fig.4 RNA is easy to modify</font>
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<BR>
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<BR>
<p style="text-indent:2em">
<p style="text-indent:2em">
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Another advantage is that, although protein has several steps until degradation, RNA does not have the steps of translation, modification and degradation that are needed for proteins, and RNAs degradation occurs fast. 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 pair, and hence change the strength of base pairs binding.
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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">
<p style="text-indent:2em">
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The feature of our RNA oscillator is using Hammerhead ribozyme (HHR). HHR is a ribozyme which has the ability of self-cleavage. When self-cleavage occurs, the downstream sequence from the cleavage site is cleaved into smaller pieces. We constructed RNA oscillator by making HHR whose self-cleavage activity can be controlled by RNA binding.
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Therefore, it can be used for combination with diverse mechanisms.
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<p style="text-indent:2em">
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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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Additionally, we expect the RNA oscillator to be put into practice by combination with diverse mechanisms. For example, we can make systems of automatic control with counter system, change output from RNA to protein with reporter circuit, and reset the oscillation with light sensor. We think that the combination with RNA oscillator can be applied for drug delivery and bioremediation.
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 +
<p style="text-indent:2em">
 +
In this way, the ability to combine with various mechanisms can be used for controlling complex systems such as drug delivery.</p>
 +
<p style="text-indent:2em">
 +
We named the E. coli which has this ability <strong>Twinkle.coli</strong> because of its brilliant future.
 +
</p>
 +
<div style="text-align:center">
 +
<img src="https://static.igem.org/mediawiki/2013/0/0e/Twinklecokikuuuuu.PNG", height="300", width="350", alt="">
 +
<BR>
 +
<BR>
 +
<BR>
 +
<div style="text-align:center"><font size=3>
 +
Fig.5 Twinkle. coli</font>
 +
</div>
 +
</div>
</p>
</p>

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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