Biomod/2012/UTokyo/UT-Komaba/Experiment/Indirect Bistable: Difference between revisions

From OpenWetWare
Jump to navigationJump to search
No edit summary
No edit summary
Line 11: Line 11:
The purpose of the experiment is to attain proper data of concentrations.
The purpose of the experiment is to attain proper data of concentrations.


==Experiment==
===September 28th===
We could not get a good result of the bistable system so that we change several part of the system.
We introduce two types of DNA, "DII" and "NII", and two types of templates, "D to V" and "N to X" in the system.
We change the concentration of "D to V" and "N to X", which are always the saame concentration.
We also kept these tubes in 42°C.
*The Experiment of XII
(µL)
{|
! !!BST !! NBI !! tt-RecJ !! DTT !! BSA !! Smix 4x !! V to inhX !! X to inhv !! dTTP !! XII !! CxII !! CvII !! D to V !! N to X !! mQ !! Total Amount
|-
| 2.5nM || 0.17 || 0.84 || 0.32 || 0.21 || 0.21 || 5.25 || 0.42 || 0.32 || 0.21 || 0.11 || 0.11 || 0.42 || 0.05 || 0.05 || 12.20 ||21.00
|-
| 5.0nM || 0.17 || 0.84 || 0.32 || 0.21 || 0.21 || 5.25 || 0.42 || 0.32 || 0.21 || 0.11 || 0.11 || 0.42 || 0.11 || 0.11 || 12.08 ||21.00
|-
| 7.5nM || 0.17 || 0.84 || 0.32 || 0.21 || 0.21 || 5.25 || 0.42 || 0.32 || 0.21 || 0.11 || 0.11 || 0.42 || 0.16 || 0.16 || 11.98 ||21.00
|-
| 10.0nM ||0.17 || 0.84 || 0.32 || 0.21 || 0.21 || 5.25 || 0.42 || 0.32 || 0.21 || 0.11 || 0.11 || 0.42 || 0.21 || 0.21 || 11.88 ||21.00
|}
*The Experiment of VII
(µL)
{|
! !!BST !! NBI !! tt-RecJ !! DTT !! BSA !! Smix 4x !! V to inhX !! X to inhv !! dTTP !! VII !! CxII !! CvII !! D to V !! N to X !! mQ !! Total Amount
|-
| 2.5nM || 0.17 || 0.84 || 0.32 || 0.21 || 0.21 || 5.25 || 0.42 || 0.32 || 0.21 || 0.11 || 0.11 || 0.42 || 0.05 || 0.05 || 12.20 ||21.00
|-
| 5.0nM || 0.17 || 0.84 || 0.32 || 0.21 || 0.21 || 5.25 || 0.42 || 0.32 || 0.21 || 0.11 || 0.11 || 0.42 || 0.11 || 0.11 || 12.08 ||21.00
|-
| 7.5nM || 0.17 || 0.84 || 0.32 || 0.21 || 0.21 || 5.25 || 0.42 || 0.32 || 0.21 || 0.11 || 0.11 || 0.42 || 0.16 || 0.16 || 11.98 ||21.00
|-
| 10.0nM ||0.17 || 0.84 || 0.32 || 0.21 || 0.21 || 5.25 || 0.42 || 0.32 || 0.21 || 0.11 || 0.11 || 0.42 || 0.21 || 0.21 || 11.88 ||21.00
|}
When several hours had passed since we put these tubes in PCR, we put DII in tubes of X and NII in that of V so that the concentration of X or V might not change radically.
After putting DNAs, we kept them in PCR.


==Experiment==
 
===October 1st===
 
We conducted the same experiment as what we did in September 28th.
We got enough information about the experiment of VII, so we only conducted that of VII.
The purpose of the experiment is to find out the best condition of the experiment of XII.
We changed the concentration of CvII and X to inhV and compared the results.
 
*The Concentration of X to inhV: 10.00nM.
 
(µL)
{|
! !!BST !! NBI !! tt-RecJ !! DTT !! BSA !! Smix 4x !! V to inhX !! X to inhv !! dTTP !! XII !! CxII !! CvII !! D to V !! N to X !! mQ !! Total Amount
|-
| CvII: 20.00nM || 0.16 || 0.80 || 0.30 || 0.20 || 0.20 || 5.00 || 0.40 || 0.20 || 0.20 || 0.10 || 0.10 || 0.40 || 0.20 || 0.20 || 11.54 ||20.00
|-
| CvII: 22.50nM || 0.16 || 0.80 || 0.30 || 0.20 || 0.20 || 5.00 || 0.40 || 0.20 || 0.20 || 0.10 || 0.10 || 0.45 || 0.20 || 0.20 || 11.49 ||20.00
|-
| CvII: 25.00nM || 0.16 || 0.80 || 0.30 || 0.20 || 0.20 || 5.00 || 0.40 || 0.20 || 0.20 || 0.10 || 0.10 || 0.50 || 0.20 || 0.20 || 11.44 ||20.00
|}
 
 
*The Concentration of X to inhV: 15.00nM
 
(µL)
{|
! !!BST !! NBI !! tt-RecJ !! DTT !! BSA !! Smix 4x !! V to inhX !! X to inhv !! dTTP !! XII !! CxII !! CvII !! D to V !! N to X !! mQ !! Total Amount
|-
| CvII: 20.00nM || 0.16 || 0.80 || 0.30 || 0.20 || 0.20 || 5.00 || 0.40 || 0.30 || 0.20 || 0.10 || 0.10 || 0.40 || 0.20 || 0.20 || 11.44 ||20.00
|-
| CvII: 22.50nM || 0.16 || 0.80 || 0.30 || 0.20 || 0.20 || 5.00 || 0.40 || 0.30 || 0.20 || 0.10 || 0.10 || 0.45 || 0.20 || 0.20 || 11.39 ||20.00
|-
| CvII: 25.00nM || 0.16 || 0.80 || 0.30 || 0.20 || 0.20 || 5.00 || 0.40 || 0.30 || 0.20 || 0.10 || 0.10 || 0.50 || 0.20 || 0.20 || 11.34 ||20.00
|}

Revision as of 10:49, 21 October 2012

<html>

<style type="text/css"> <!--

  1. column-one {display:none; width:0px;}
  2. column-content {margin: 0;}

.container{background-color: #ffffff; margin-top:0px} .OWWNBcpCurrentDateFilled {display: none;}

  1. globalWrapper{margin: 0 auto; padding: 0; width: 900px;}


.firstHeading {display:none; width:0px;}

  1. content {margin-left: 0; padding: 0; border: none;}
  2. sidebar-main {display:none; width:0px;}
  3. footer{position: center; margin: 0;}


body { 

 margin: 0;
font-family: Calibri, Verdana, helvetica, sans-serif;
 background: url(http://openwetware.org/images/2/21/Biomod-2012-ut-komaba-Metal-texture.jpg) darkgray repeat-y;

}

  1. content {
  margin: 0;

}

/*title*/

  1. title{
 margin: 10px 0;
 padding: auto;
 background-color: black;
 text-align :center;

}

  1. navi ul {
 font-size: 12px;
 margin: 0 0 30px;
 padding: 0;
 text-align:center;
 height: 30px;
 background-color: black}
  1. navi ul li {
 list-style-type: none;
 float: left;
 padding: 0;
 margin: 0;
 display: block}
  1. navi ul li a {
 display: block;
 width: 100px;
 line-height: 30px;
 text-decoration: none;
 text-align: center;
 color: #ffffff;
 background-color: black;

}

  1. navi ul li a:hover {
 background-color: gainsboro;
 color: black;

}


  1. bodyContent{
 width: 800px;
 margin: auto;
 padding: 50px;
 background: url("http://openwetware.org/images/c/c2/Biomod_2012_UToyko_UT-Komaba_background.png") white repeat-y;
 font-size: 140%;

}

  1. toc{
 font-size: 80%;

}

/* table */ table { 

 border: solid 1px black;
 border-collapse: collapse;
 border-spacing: 0;

}

table.noborder, table.noborder th, table.noborder td{ 

 border: none;

}

table th{ 

 border: solid 1px black;
 padding: 1px 5px;
 color: white;
 background-color: darkgray;
 text-align: center;

}

table td{ 

 border: solid 1px black;
 padding: 1px 5px;
 text-align: center;

}

table.tdleft td{ 

 text-align: left;

}


h1,h2,h3,h4 { 

 font-family: serif;
 clear: both;

}

table.dialog{ 

 border: none;

}

table.dialog th{ 

 border: none;
 padding-top: 0px;
 background-color: white;
 color: black;
 text-decolation: bold;
 text-align: left;

}

table.dialog td{ 

 border: none;
 padding: 5px 0;
 text-align: left;

}

--> </style>

<div id="title"><img src="http://openwetware.org/images/4/47/Biomod_2012_UTokyo_UT-Komaba_Top.png" alt="DNA tablet" width="800" height="120" onClick="this.src='http://openwetware.org/images/7/7d/BIOMOD_2012_UTokyo_UT-Komaba_title-animation.gif'"/></div>

<div id="navi"> <ul> 

 <li><a href="/wiki/Biomod/2012/UTokyo/UT-Komaba">Home</a></li>
 <li><a href="/wiki/Biomod/2012/UTokyo/UT-Komaba/Idea">Idea</a></li>
 <li><a href="/wiki/Biomod/2012/UTokyo/UT-Komaba/Simulation">Simulation</a></li>
 <li><a href="/wiki/Biomod/2012/UTokyo/UT-Komaba/Experiment">Experiment</a></li>
 <li><a href="/wiki/Biomod/2012/UTokyo/UT-Komaba/Progress">Progress</a></li>
 <li><a href="/wiki/Biomod/2012/UTokyo/UT-Komaba/Episode">Episode</a></li>
 <li><a href="/wiki/Biomod/2012/UTokyo/UT-Komaba/Team">Team</a></li>
 <li><a href="/wiki/Biomod/2012/UTokyo/UT-Komaba/Supplementary">Supplementary</a></li>

</ul> </div>

</html>

Concept

Indirect Bistable Concept
Indirect Bistable Concept

We could not get enough information from normal bistable sytem experiment so that we change the system into indirect bistable system. That is because input of C or D indirectly increase the concentration of A or B so that the concentrations do not change rapidly and radically. We only input C or D, not A or B. As the diagram above, input C and D indirectly affect the cycle of bistable system. The purpose of the experiment is to attain proper data of concentrations.

Experiment

September 28th

We could not get a good result of the bistable system so that we change several part of the system. We introduce two types of DNA, "DII" and "NII", and two types of templates, "D to V" and "N to X" in the system. We change the concentration of "D to V" and "N to X", which are always the saame concentration. We also kept these tubes in 42°C.

  • The Experiment of XII

(µL)

BST NBI tt-RecJ DTT BSA Smix 4x V to inhX X to inhv dTTP XII CxII CvII D to V N to X mQ Total Amount
2.5nM 0.17 0.84 0.32 0.21 0.21 5.25 0.42 0.32 0.21 0.11 0.11 0.42 0.05 0.05 12.20 21.00
5.0nM 0.17 0.84 0.32 0.21 0.21 5.25 0.42 0.32 0.21 0.11 0.11 0.42 0.11 0.11 12.08 21.00
7.5nM 0.17 0.84 0.32 0.21 0.21 5.25 0.42 0.32 0.21 0.11 0.11 0.42 0.16 0.16 11.98 21.00
10.0nM 0.17 0.84 0.32 0.21 0.21 5.25 0.42 0.32 0.21 0.11 0.11 0.42 0.21 0.21 11.88 21.00


  • The Experiment of VII

(µL)

BST NBI tt-RecJ DTT BSA Smix 4x V to inhX X to inhv dTTP VII CxII CvII D to V N to X mQ Total Amount
2.5nM 0.17 0.84 0.32 0.21 0.21 5.25 0.42 0.32 0.21 0.11 0.11 0.42 0.05 0.05 12.20 21.00
5.0nM 0.17 0.84 0.32 0.21 0.21 5.25 0.42 0.32 0.21 0.11 0.11 0.42 0.11 0.11 12.08 21.00
7.5nM 0.17 0.84 0.32 0.21 0.21 5.25 0.42 0.32 0.21 0.11 0.11 0.42 0.16 0.16 11.98 21.00
10.0nM 0.17 0.84 0.32 0.21 0.21 5.25 0.42 0.32 0.21 0.11 0.11 0.42 0.21 0.21 11.88 21.00


When several hours had passed since we put these tubes in PCR, we put DII in tubes of X and NII in that of V so that the concentration of X or V might not change radically. After putting DNAs, we kept them in PCR.


October 1st

We conducted the same experiment as what we did in September 28th. We got enough information about the experiment of VII, so we only conducted that of VII. The purpose of the experiment is to find out the best condition of the experiment of XII. We changed the concentration of CvII and X to inhV and compared the results.

  • The Concentration of X to inhV: 10.00nM.

(µL)

BST NBI tt-RecJ DTT BSA Smix 4x V to inhX X to inhv dTTP XII CxII CvII D to V N to X mQ Total Amount
CvII: 20.00nM 0.16 0.80 0.30 0.20 0.20 5.00 0.40 0.20 0.20 0.10 0.10 0.40 0.20 0.20 11.54 20.00
CvII: 22.50nM 0.16 0.80 0.30 0.20 0.20 5.00 0.40 0.20 0.20 0.10 0.10 0.45 0.20 0.20 11.49 20.00
CvII: 25.00nM 0.16 0.80 0.30 0.20 0.20 5.00 0.40 0.20 0.20 0.10 0.10 0.50 0.20 0.20 11.44 20.00


  • The Concentration of X to inhV: 15.00nM

(µL)

BST NBI tt-RecJ DTT BSA Smix 4x V to inhX X to inhv dTTP XII CxII CvII D to V N to X mQ Total Amount
CvII: 20.00nM 0.16 0.80 0.30 0.20 0.20 5.00 0.40 0.30 0.20 0.10 0.10 0.40 0.20 0.20 11.44 20.00
CvII: 22.50nM 0.16 0.80 0.30 0.20 0.20 5.00 0.40 0.30 0.20 0.10 0.10 0.45 0.20 0.20 11.39 20.00
CvII: 25.00nM 0.16 0.80 0.30 0.20 0.20 5.00 0.40 0.30 0.20 0.10 0.10 0.50 0.20 0.20 11.34 20.00
Retrieved from "https://openwetware.org/mediawiki/index.php?title=Biomod/2012/UTokyo/UT-Komaba/Experiment/Indirect_Bistable&oldid=638053"