Team:Tokyo-NoKoGen

From 2013.igem.org

(Difference between revisions)
 
(247 intermediate revisions not shown)
Line 351: Line 351:
float: left;
float: left;
width:490px;
width:490px;
-
height:1000px;
+
height:4000px;
background: url("https://static.igem.org/mediawiki/2013/a/a5/Header_index_kiso4.png") 0px -250px no-repeat ;
background: url("https://static.igem.org/mediawiki/2013/a/a5/Header_index_kiso4.png") 0px -250px no-repeat ;
}
}
Line 380: Line 380:
float: left;
float: left;
width:820px;
width:820px;
-
height:1000px;
+
height:4000px;
background: url("https://static.igem.org/mediawiki/2013/a/a5/Header_index_kiso4.png") -490px -250px no-repeat;
background: url("https://static.igem.org/mediawiki/2013/a/a5/Header_index_kiso4.png") -490px -250px no-repeat;
Line 388: Line 388:
float: left;
float: left;
width: 100px;
width: 100px;
-
height: 1000px;
+
height: 4000px;
background: url("https://static.igem.org/mediawiki/2013/a/a5/Header_index_kiso4.png") -1310px -250px no-repeat;
background: url("https://static.igem.org/mediawiki/2013/a/a5/Header_index_kiso4.png") -1310px -250px no-repeat;
}
}
Line 396: Line 396:
width: 1410px;
width: 1410px;
height: 700px;
height: 700px;
-
background: url( "https://static.igem.org/mediawiki/2013/a/a5/Header_index_kiso4.png") 0px -2578px no-repeat;
+
background: url( "https://static.igem.org/mediawiki/2013/a/a5/Header_index_kiso4.png") 0px -9300px no-repeat;
}
}
Line 502: Line 502:
   
   
               </div>
               </div>
-
 
+
<div id="index">
-
              <div id="index">
+
                      
                      
                      
                      
                     <h1 id="index_title"></h1>
                     <h1 id="index_title"></h1>
            <ul id="contents">
            <ul id="contents">
-
                <a href="#abstract"><li><strong>Abstract</strong></li></a>
+
                <a href="https://2013.igem.org/Team:Tokyo-NoKoGen/oscillator"><li><a href="#diary"><strong>RNA oscillator</a></strong></li></a>
-
                <li><strong></strong></li>
+
                <a href="https://2013.igem.org/Team:Tokyo-NoKoGen/scaffold"><li><strong>RNA scaffold</strong></li></a>
-
                <li><strong></strong></li>
+
                <a href="https://2013.igem.org/Team:Tokyo-NoKoGen/light"><li><strong>Light sensor</strong></li></a>
-
                <li><strong></strong></li>
+
                <a href="https://2013.igem.org/Team:Tokyo-NoKoGen/modeling"><li><strong>Modeling</strong></li></a>
-
                <li><strong></strong></li>
+
               
-
                <li><strong></strong></li>
+
            </ul>
            </ul>
   
   
               </div>
               </div>
 +
              <div id="main">
-
              <div id="main">
+
<img id="mainback" src="https://static.igem.org/mediawiki/2013/3/36/Twinklecoliaaa.PNG">
-
<img id="mainback" src="https://static.igem.org/mediawiki/2013/f/fd/Twinkle_coli.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>
-
<p>生体内にはサーカディアンリズムが存在している。脳波やホルモン分泌、体温や血圧の日内変動はこの体内時計によって制御されている。このように、周期を出すものを一般的にオシレータという。
 
-
オシレータは、現在まで、サーカディアンリズムや遺伝子ネットワーク、シグナル伝達のより深い理解をするために研究されてきた。タンパク質の発現を周期的に制御できることから、今後ドラッグデリバリーやバイオレメディエーションへ利用できる可能性が考えられている。
 
-
そこで私たちは、このオシレータが今後、様々なものと組み合わせて応用できるのではないかと思い、オシレータに着目した。
 
-
We all have a biological clock which controls the periodicity of many physiological functions such as blood pressure, body temperature and concentraion 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. As it can control protein expressions periodically, its application is thought to be used for drug delivery and bioremediation.
 
-
Oscillator can be applicable to be used in combination with wide variety of things, and that is why we focused on oscillator circuit.
 
 +
<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>
-
しかし、既存のプロテインオシレータにはいくつかの問題点があった。それは、
+
<div style="text-align:center">
-
・リプレッサータンパク質の種類が少ないということ（＝一細胞内での系の数が限られること）
+
<img src="https://static.igem.org/mediawiki/2013/0/0d/Circadian_rhythm.PNG", height="300", width="450",alt="">
-
・オシレータの設計・コントロールが困難であるということ
+
</div>
-
である。
+
<BR>
-
However, there are several problems of existing oscillator using protein.
+
<div style="text-align:center"><font size=3>
-
1. There are only a few types of repressor proteins, which make it harder to make a sophisticated circuit in one cell.
+
Fig.1 Circadian rhythm</font>
-
2. Protein requires several steps for maturation, which makes it difficult to design and control oscillator.
+
</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>
-
プロテインオシレータは、タンパク質によってオシレーションを引き起こすものであるため、そのプロモータやリプレッサータンパク質の種類には限界がある。
+
<img src="https://static.igem.org/mediawiki/2013/5/57/ProteinRNA.PNG",height="200",width="200",alt="">
-
また、プロテインオシレータには、mRNAの転写・タンパク質の翻訳,(フォールディング,修飾？),分解といったステップが存在する。プロテインオシレータを構築・コントロールする際は、このステップの各々の効率（転写効率や翻訳効率・分解能の調節）を遺伝子操作によって行わなくてはならない。このため、互いを制御しあい、発現量が互い違いとなるようなオシレーションを起こすような、希望のタンパク質(遺伝子回路)を設計することは非常に難しい。
+
-
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.  
+
-
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.
+
 +
<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>
-
この問題点を解決し、今後の応用に役立てるべく、わたしたちはRNAオシレータを構築し、モジュール化?することにした。この機能を持たせた大腸菌を、私たちはTwinklE. Coliと呼びます。
+
<p style="text-indent:4em">
-
For the solutions of these problems, we decided to construct the New type of Oscillator circuit – RNA Oscillator.　We named the E. coli which has this function TwinklE. Coli.
+
<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.
 +
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>
 +
<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>
-
プロテインオシレータが、使えるタンパク質の種類が限られているのに対して、RNAオシレータは、その構造上、塩基を変更し結合能を変えるだけで何種類ものオシレータをつくることができます。このことによって、一つの細胞内において多様な系を構築することが可能となるのです。
 
-
また、プロテインオシレータには、mRNAの転写・タンパク質の翻訳,(フォールディング,修飾？),分解といったステップが存在するのに対して、RNAオシレータには、・・・ため、特異的な結合部分の塩基のみを変更し、その転写効率と結合能を変えるだけでオシレーションの設計・コントロールを行うことが可能なのです。
 
-
　Whereas there is few proteins that are suitable for construction of oscillator, Many kinds of RNA oscillators can be easily constructed by changing its sequenses. Therefore, it will allow us to construct a multiple and orthogonal oscillators in one cell.
 
-
Moreover, since RNA oscillator does not have the steps of translation, modification and optimization of RNA oscillator is easier than the oscillator using proteins that requires translation. 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 sequence.
 
-
さらに、私たちのRNAオシレータの最大の特徴は、HHRを用いている点である。
 
-
HHRは自己切断活性を持つリボザイムであり、切断が起こると切断部位より下流の配列が切り出される。私たちは、RNAに応答して切断活性が制御されるHHRを用いることによって、RNAオシレータを構築した。
 
-
The greatest 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.
 
-
私たちはこのRNAオシレータを構築するだけでなく、様々なものと組み合わせることによる応用利用を期待した。例えば、・・・といったものを使って、・・・・。
 
-
カウンター
 
-
レポーター
 
-
ライトセンサー
 
-
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.</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

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