Team:HokkaidoU Japan/Projects/Overview/Background

From 2014.igem.org

(Difference between revisions)
 
(53 intermediate revisions not shown)
Line 1: Line 1:
-
[[Media:Example.ogg]]{{Team:HokkaidoU_Japan/CSS}}
+
{{Team:HokkaidoU_Japan/CSS}}
-
{{Team:HokkaidoU_Japan/Header/CSS}}
+
{{Team:HokkaidoU_Japan/Footer/CSS}}
{{Team:HokkaidoU_Japan/Footer/CSS}}
-
{{Team:HokkaidoU_Japan/LargeDropDown_Projects/CSS}}
+
{{Team:HokkaidoU_Japan/LargeDropDown/CSS}}
 +
{{Team:HokkaidoU_Japan/Top_Header/CSS}}
<html>
<html>
 +
<link href='http://fonts.googleapis.com/css?family=Merriweather' rel='stylesheet' type='text/css'>
 +
<link href='http://fonts.googleapis.com/css?family=Special+Elite' rel='stylesheet' type='text/css'>
<div id="background">
<div id="background">
<!--begin header-->
<!--begin header-->
-
<div id="header-top" style="background-color:#6CC4C1;">
+
<div id="header-top">
 +
<img src="https://static.igem.org/mediawiki/2014/b/bb/HokkaidoU_Header_Top.png">
 +
</div>
 +
<div id="header-bottom">
 +
  <div id="header-bottom-contents">
 +
    <div class="header-title">
 +
      <div class="header-title-top">
 +
      Project Overview
 +
      </div>
 +
      <div class="header-title-bottom">
 +
      Background
 +
      </div>
 +
    </div>
 +
    <div class="header-picture">
 +
      <img src="https://static.igem.org/mediawiki/2014/b/ba/HokkaidoU_Header_mRNA.png">
 +
    </div>
 +
  </div>
 +
</div>
 +
<!--end header-->
 +
<!--begin menu-->
     <div class="box">
     <div class="box">
   <div id="box-wrapper">  
   <div id="box-wrapper">  
Line 12: Line 33:
       <ul id="ldd_menu" class="ldd_menu">
       <ul id="ldd_menu" class="ldd_menu">
                                 <li>
                                 <li>
-
                                 <span class="menu-list" ><a href="https://2014.igem.org/Team:HokkaidoU_Japan"><span style="position:relative; top:10px;">Top</span></a></span>
+
                                 <span class="menu-list" ><a href="https://2014.igem.org/Team:HokkaidoU_Japan"><span style="position:relative; top:10px;" >Top</span></a></span><!-- Increases to 510px in width-->
                                 </li>
                                 </li>
<li class="menu_button">
<li class="menu_button">
Line 18: Line 39:
<div class="ldd_submenu" style="left:-415px; width:970px;">
<div class="ldd_submenu" style="left:-415px; width:970px;">
<ul style="margin-left:20px;">
<ul style="margin-left:20px;">
-
<li class="ldd_heading"><a href="https://2014.igem.org/Team:HokkaidoU_Japan/Projects/Overview/Introduction">Overview</a></li>
+
<li class="ldd_heading"><a href="https://2014.igem.org/Team:HokkaidoU_Japan/Projects/Overview/Background">Overview</a></li>
-
<li class="ldd_contents"><a href="https://2014.igem.org/Team:HokkaidoU_Japan/Projects/Overview/Introduction">Introduction</a></li>
+
<li class="ldd_contents"><a href="https://2014.igem.org/Team:HokkaidoU_Japan/Projects/Overview/Background">Background</a></li>
<li class="ldd_contents"><a href="https://2014.igem.org/Team:HokkaidoU_Japan/Projects/Overview/Background">Background</a></li>
<li class="ldd_contents"><a href="https://2014.igem.org/Team:HokkaidoU_Japan/Projects/Overview/Achievements">Achievements</a></li>
<li class="ldd_contents"><a href="https://2014.igem.org/Team:HokkaidoU_Japan/Projects/Overview/Achievements">Achievements</a></li>
Line 40: Line 60:
<ul>
<ul>
<li class="ldd_heading"><a href="https://2014.igem.org/Team:HokkaidoU_Japan/Projects/Length">Length Variation</a></li>
<li class="ldd_heading"><a href="https://2014.igem.org/Team:HokkaidoU_Japan/Projects/Length">Length Variation</a></li>
-
            <li class="ldd_contents"><a href="">Overview</a></li>
+
            <li class="ldd_contents"><a href="https://2014.igem.org/Team:HokkaidoU_Japan/Projects/Length">Overview</a></li>
                                                             <li class="ldd_contents"><a href="https://2014.igem.org/Team:HokkaidoU_Japan/Projects/Length#Method">Method</a></li>
                                                             <li class="ldd_contents"><a href="https://2014.igem.org/Team:HokkaidoU_Japan/Projects/Length#Method">Method</a></li>
                                                             <li class="ldd_contents"><a href="https://2014.igem.org/Team:HokkaidoU_Japan/Projects/Length#Results">Results</a></li>
                                                             <li class="ldd_contents"><a href="https://2014.igem.org/Team:HokkaidoU_Japan/Projects/Length#Results">Results</a></li>
-
                                                             <li class="ldd_contents"><a href="https://2014.igem.org/Team:HokkaidoU_Japan/Projects/Length#Conclusiton">Conclusion</a></li>
+
                                                             <li class="ldd_contents"><a href="https://2014.igem.org/Team:HokkaidoU_Japan/Projects/Length#Conclusion">Conclusion</a></li>
</ul>
</ul>
<ul>
<ul>
Line 57: Line 77:
<div class="ldd_submenu" style="width:590px; left:-230px;">
<div class="ldd_submenu" style="width:590px; left:-230px;">
<ul style="margin-left:20px;">
<ul style="margin-left:20px;">
-
<li class="ldd_heading"><a href="https://2014.igem.org/Team:HokkaidoU_Japan/Policy_And_Practice/Education">Education</a></li>
+
<li class="ldd_heading"><a href="https://2014.igem.org/Team:HokkaidoU_Japan/Outreach/Univ_festival">Univ. Festival</a></li>
-
<li class="ldd_contents"><a href="https://2014.igem.org/Team:HokkaidoU_Japan/Policy_And_Practice/Education#School_Festival">School Festival</a></li>
+
<li class="ldd_contents"><a href="https://2014.igem.org/Team:HokkaidoU_Japan/Outreach/Univ_festival#Education">Education</a></li>
-
<li class="ldd_contents"><a href="https://2014.igem.org/Team:HokkaidoU_Japan/Policy_And_Practice/Education#High_School">High-school</a></li>
+
<li class="ldd_contents"><a href="https://2014.igem.org/Team:HokkaidoU_Japan/Outreach/Univ_festival#Survey">Survey</a></li>
</ul>
</ul>
<ul>
<ul>
-
<li class="ldd_heading"><a href="https://2014.igem.org/Team:HokkaidoU_Japan/Policy_And_Practice/Survey">Survey</a></li>
+
<li class="ldd_heading"><a href="https://2014.igem.org/Team:HokkaidoU_Japan/Outreach/Survey">High School</a></li>
-
<li class="ldd_contents"><a href="https://2014.igem.org/Team:HokkaidoU_Japan/Policy_And_Practice/Survey#School_Festival">School Festival</a></li>
+
<li class="ldd_contents"><a href="https://2014.igem.org/Team:HokkaidoU_Japan/Outreach/Survey#Education">Education</a></li>
-
<li class="ldd_contents"><a href="https://2014.igem.org/Team:HokkaidoU_Japan/Policy_And_Practice/Survey#High_School">High-school</a></li>
+
<li class="ldd_contents"><a href="https://2014.igem.org/Team:HokkaidoU_Japan/Outreach/Survey#Survey">Survey</a></li>
</ul>
</ul>
<ul>
<ul>
-
<li class="ldd_heading"><a href="https://2014.igem.org/Team:HokkaidoU_Japan/Policy_And_Practice/Discussion">Discussion</a></li>
+
<li class="ldd_heading"><a href="https://2014.igem.org/Team:HokkaidoU_Japan/Outreach/Discussion">Discussion</a></li>
-
<li class="ldd_contents"><a href="https://2014.igem.org/Team:HokkaidoU_Japan/Policy_And_Practice/Discussion#Background">Background</a></li>
+
<li class="ldd_contents"><a href="https://2014.igem.org/Team:HokkaidoU_Japan/Outreach/Discussion#Background">Background</a></li>
-
<li class="ldd_contents"><a href="https://2014.igem.org/Team:HokkaidoU_Japan/Policy_And_Practice/Discussion#Estimation">Evaluation</a></li>
+
<li class="ldd_contents"><a href="https://2014.igem.org/Team:HokkaidoU_Japan/Outreach/Discussion#Evaluation">Evaluation</a></li>
</ul>
</ul>
</div>
</div>
Line 88: Line 108:
     </div>
     </div>
</div>
</div>
-
</div><!-- end box-->
 
-
<div id="header-bottom" style="background-color:#25928E;">
 
-
  <div id="header-bottom-contents">
 
-
  </div>
 
-
</div>
 
-
<!--end header begin menu-->
 
 +
<!--end box-->
<!-- end menu-->
<!-- end menu-->
<!--begin contents-->
<!--begin contents-->
Line 102: Line 117:
       <h1>Background</h1>
       <h1>Background</h1>
       <p>
       <p>
-
       Discovering of non-codingRNA (ncRNA) and reverse transcription of Virus collapsed the Central dogma that was declared by Francis Click.  
+
       Discovering of non-coding RNA (ncRNA) and reverse transcription of virus composes the central dogma that was declared by Francis Crick.  
-
       ncRNA does not encode any proteins, and it had been thought that they don’t have any function.  
+
       Since ncRNAs do not encode any proteins, they had been thought that they don’t have any functions.
-
       However, now we know they have many functions.
+
       However, it was proved that they do have many functions.
-
      For example, some ncRNA reduce the efficiency of translation, while others promote that. (C Claudia <i>et al.</i>, 2012<sup><a href="#cite-1">[1]</a></sup>).       
+
      For example, some ncRNAs reduce the efficiency of translation, while others promote that. (C. Claudia <i>et al.</i>, 2012<sup><a href="#cite-1">[1]</a></sup>).       
       </p>       
       </p>       
       <p>
       <p>
-
       There is ncRNA that is called anti-sense RNA (asRNA).
+
       There are ncRNAs called anti-sense RNA (asRNA), which down-regulate translation. An asRNA has a complement sequence of its target mRNA and reduces the translation efficiency by hybridizing.  
-
      asRNA is a kind of translation down regulate RNA. It has complement sequence of target mRNA, and reduce the translation efficiency by hybridizing.  
+
       asRNA can be easily synthesized, but there is no clear method to make stable, highly efficient asRNA.  
-
       We can synthesize asRNA easily, but there is no clear method to make stable, high efficient asRNA.
+
-
      </p>     
+
-
      <p>
+
-
      In this situation, Nakashima who is a researcher of  AIST (National Institute of Advanced Industrial Science and Technology)
+
-
      discovered asRNA that is sandwiched by 38 base pairs repeated sequence is stable and have high efficiency for translation regulation(N Nakashima <i>et al.</i>, 2006<sup><a href="#cite-2">[2]</a></sup>).
+
       </p>
       </p>
 +
 +
      <div class="fig fig800">
 +
        <img src="https://static.igem.org/mediawiki/2014/9/93/HokkaidoU_Background01.png">
 +
        <div>
 +
        Fig. 1 An asRNA hybridizes with target mRNA and interrupts entry of ribosome.
 +
        </div>
 +
      </div>
 +
     
 +
 +
    <div class="fig fig400">
 +
        <img style="width:300px;" src="https://static.igem.org/mediawiki/2014/f/fd/HokkaidoU_Hstem_RNA.png">
 +
<div>
 +
        Fig. 2 Stem structure stabilizes asRNA
 +
        </div>
 +
      </div>
 +
       
       <p>
       <p>
-
       Many iGEM teams prepare their project using asRNA, but how many teams use the asRNA that is based on a clear design concept?
+
      In this situation, Nakashima and his colleagues discovered asRNA that is sandwiched by 38 base pairs of repeated sequence is stable and regulates translation at a high efficiency (N. Nakashima <i>et al.</i>, 2006<sup><a href="#cite-2">[2]</a></sup>).
-
      So, this year, we provide you a BioBrick standardized asRNA.
+
      </p>
 +
    <p>
 +
       Many iGEM teams prepare their project using asRNA, but how many teams use the asRNA that is designed on clear concepts?
 +
      This year, we provide you a BioBrick standardized procedure to design asRNA.
       </p>
       </p>
 +
      <div class="clearfix"></div>
 +
 +
       <p>
       <p>
-
       This asRNA will assure you that
+
       Our procedure to design asRNAs will assure you that
       </p>
       </p>
-
       <ul>
+
       <ol>
-
         <li>It’s based on a clear design concept.</li>
+
         <li>The asRNA are based on a clear design concept.</li>
-
         <li> It has calculated an ideal second structure.</li>
+
         <li>They are calculated to have ideal second structures.</li>
-
         <li> High translation regulation efficiency based on our results. </li>
+
         <li>They have high efficiency to regulate translation, based on our results. </li>
-
       </ul>
+
       </ol>
       <p>
       <p>
-
       By using such asRNA, we did the projects below.
+
       Using this procedure, we arranged these projects.
       </p>
       </p>
-
       <ul>
+
       <ol>
-
         <li>Construct our asRNA that has modified stem sequence.</li>
+
         <li>Declared a standard procedure to design asRNA that has modified stem sequence.</li>
-
         <li> Construct B0034―most popular RBS― specific asRNA, and regulate translation efficiency generally.</li>
+
         <li>Synthesized B0034 (<a href="http://parts.igem.org/Part:BBa_B0034">BBa_B0034</a>) - most popular RBS - specific asRNA, and widely regulated translation efficiency.</li>
-
         <li> Construct various length asRNA and discover the optimum length of asRNA. </li>
+
         <li>Synthesized various length asRNA and determined the optimum length. </li>
-
       </ul>
+
       </ol>
       <p>
       <p>
-
      In conventional iGEM projects, many teams only transform plasmids, but if you use our asRNA, you can regulate genome gene expression.
+
       Our project provides not only highly efficient asRNA but also brand new viewpoints to your project.
-
       Our project provides not only high efficient asRNA but also new standpoint of your project.
+
      As yet, almost all the projects presented to iGEM have focused on to regulate the behavior of <i>E. coli</i>, only by transforming plasmids.
 +
      But now, you can use our asRNA and regulate expression of the genes which are on genome.
       </p>
       </p>
       <p>
       <p>
-
       We used hybridizing of mRNA and specific asRNA to resemble love of RNA, and named our project “RNA in Love”
+
       Hybridization of a mRNA and a specific asRNA seems like a love story in the RNA world, so we named our project "RNA in love".
-
       Let's watch over RNA in love!
+
       Let’s watch over RNA in love!
       </p>
       </p>
Line 150: Line 183:
<br>
<br>
     <ol class="citation-list">
     <ol class="citation-list">
-
       <li id="cite-1">C Claudia<i>et al.</i> (2012) Long non-coding antisense RNA controls Uchl1 translation through an embedded SINEB2 repeat. Nature 491: 7424 454-</li>
+
       <li id="cite-1">C. Claudia <i>et al.</i> (2012) Long non-coding antisense RNA controls Uchl1 translation through an embedded SINEB2 repeat. Nature 491: 7424 454-</li>
-
    </ol>
+
       <li id="cite-2">N. Nakashima <i>et al.</i> (2006) Paired termini stabilize antisense RNAs and enhance conditional gene silencing in <i>Escherichia coli</i>. Nucleic Acids Res 34: 20 e138</li>
-
    <ol class="citation-list">
+
-
       <li id="cite-2">N Nakashima <i>et al.</i> (2006) Paired termini stabilize antisense RNAs and enhance conditional gene silencing in <i>Escherichia coli</i>. Nucleic Acids Res 34: 20 e138</li>
+
     </ol>
     </ol>
     </div>
     </div>
Line 163: Line 194:
   <div id="footer-content">
   <div id="footer-content">
<div id="footer-logo">
<div id="footer-logo">
-
<a href="http://igemhokkaidou.com/"><img style="height:150px;position:relative;" src="https://static.igem.org/mediawiki/2014/3/39/HokkaidoU_logo_transparent.png"></a>
+
<a href="http://igemhokkaidou.wordpress.com"><img style="height:150px;position:relative;" src="https://static.igem.org/mediawiki/2014/3/39/HokkaidoU_logo_transparent.png"></a>
</div>
</div>
<div id="footer-twitter">
<div id="footer-twitter">

Latest revision as of 15:20, 9 September 2015

Project Overview
Background

Background

Discovering of non-coding RNA (ncRNA) and reverse transcription of virus composes the central dogma that was declared by Francis Crick. Since ncRNAs do not encode any proteins, they had been thought that they don’t have any functions. However, it was proved that they do have many functions. For example, some ncRNAs reduce the efficiency of translation, while others promote that. (C. Claudia et al., 2012[1]).

There are ncRNAs called anti-sense RNA (asRNA), which down-regulate translation. An asRNA has a complement sequence of its target mRNA and reduces the translation efficiency by hybridizing. asRNA can be easily synthesized, but there is no clear method to make stable, highly efficient asRNA.

Fig. 1 An asRNA hybridizes with target mRNA and interrupts entry of ribosome.
Fig. 2 Stem structure stabilizes asRNA

In this situation, Nakashima and his colleagues discovered asRNA that is sandwiched by 38 base pairs of repeated sequence is stable and regulates translation at a high efficiency (N. Nakashima et al., 2006[2]).

Many iGEM teams prepare their project using asRNA, but how many teams use the asRNA that is designed on clear concepts? This year, we provide you a BioBrick standardized procedure to design asRNA.

Our procedure to design asRNAs will assure you that

  1. The asRNA are based on a clear design concept.
  2. They are calculated to have ideal second structures.
  3. They have high efficiency to regulate translation, based on our results.

Using this procedure, we arranged these projects.

  1. Declared a standard procedure to design asRNA that has modified stem sequence.
  2. Synthesized B0034 (BBa_B0034) - most popular RBS - specific asRNA, and widely regulated translation efficiency.
  3. Synthesized various length asRNA and determined the optimum length.

Our project provides not only highly efficient asRNA but also brand new viewpoints to your project. As yet, almost all the projects presented to iGEM have focused on to regulate the behavior of E. coli, only by transforming plasmids. But now, you can use our asRNA and regulate expression of the genes which are on genome.

Hybridization of a mRNA and a specific asRNA seems like a love story in the RNA world, so we named our project "RNA in love". Let’s watch over RNA in love!



  1. C. Claudia et al. (2012) Long non-coding antisense RNA controls Uchl1 translation through an embedded SINEB2 repeat. Nature 491: 7424 454-
  2. N. Nakashima et al. (2006) Paired termini stabilize antisense RNAs and enhance conditional gene silencing in Escherichia coli. Nucleic Acids Res 34: 20 e138