Team:Tokyo-NoKoGen

From 2013.igem.org

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            <ul id="contents">
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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>
                <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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                <a href="https://2013.igem.org/Team:Tokyo-NoKoGen/scaffold"><li><strong>RNA scaffold<strong></li></a>
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                <a href="https://2013.igem.org/Team:Tokyo-NoKoGen/scaffold"><li><strong>RNA scaffold</strong></li></a>
                <a href="https://2013.igem.org/Team:Tokyo-NoKoGen/light"><li><strong>Light sensor</strong></li></a>
                <a href="https://2013.igem.org/Team:Tokyo-NoKoGen/light"><li><strong>Light sensor</strong></li></a>
                <a href="https://2013.igem.org/Team:Tokyo-NoKoGen/modeling"><li><strong>Modeling</strong></li></a>
                <a href="https://2013.igem.org/Team:Tokyo-NoKoGen/modeling"><li><strong>Modeling</strong></li></a>
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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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<BR>
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<p align=center><font size=7>Introduction</font></p></font>
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<p align=center><font size=7><strong>Introduction</strong></font></p></font>
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<hr size="3" width="(60%)" align="left"noshade>
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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 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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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>
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<div style="text-align:center">
<div style="text-align:center">
<img src="https://static.igem.org/mediawiki/2013/0/0d/Circadian_rhythm.PNG", height="300", width="450",alt="">
<img src="https://static.igem.org/mediawiki/2013/0/0d/Circadian_rhythm.PNG", height="300", width="450",alt="">
</div>
</div>
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<p style="text-indent:2em">
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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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<p style="text-indent:1em">
Oscillator is expected to be used for various applications.</p>
Oscillator is expected to be used for various applications.</p>
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<p style="text-indent:1em">
Therefore, desired features of oscillator are:</p>
Therefore, desired features of oscillator are:</p>
<p style="text-indent:4em">
<p style="text-indent:4em">
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1. Variation in types</p>
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<strong>
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1. Variation in types</strong></p>
<p style="text-indent:4em">
<p style="text-indent:4em">
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2. Feasibility in designing and controlling</p>
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<strong>
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2. Feasibility in designing and controlling</strong></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">
<img src="https://static.igem.org/mediawiki/2013/9/91/Protein.PNG",height="200", width="200"alt="" style="float:right">
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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 is not many. </p>
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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>
<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. </p>
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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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<p style="text-indent:4em"><font size=3>
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                                            Fig. 2 Steps of protein expression</font></p>
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To satisfy the requirements, we propose the New type of oscillator circuit – RNA oscillator.</p>
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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">
<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.</p>
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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>
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<p style="text-indent:2em">
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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 pair, and hence change the strength of base pairs binding.</p>
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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="300",width="300",alt="">
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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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<p style="text-indent:2em">
<p style="text-indent:2em">
Like this, RNA meets the necessary standards for:</p>
Like this, RNA meets the necessary standards for:</p>
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<p style="text-indent:4em">
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1. Variation in types</p>
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<strong>
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1. Variation in types</strong></p>
<p style="text-indent:4em">
<p style="text-indent:4em">
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2. Feasibility in designing and controlling</p>
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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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Therefore, it can be used for combination with diverse mechanisms.</p>
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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.</p>
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>
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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<p style="text-indent:2em">
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We named the E. coli which has this function TwinklE.coli because of its brilliant future.
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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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</p>
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<div style="text-align:center">
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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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<div style="text-align:center"><font size=3>
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Fig.5 Twinkle. coli</font>
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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