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

From OpenWetWare
Jump to navigationJump to search
No edit summary
 
(2 intermediate revisions by one other user not shown)
Line 16: Line 16:
===September 28th===
===September 28th===


We could not get a good result of the bistable system so that we change several part of the system.
We could not get a good result for the bistable system so we changed several parts 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 introduced 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 changed the concentration of "D to V" and "N to X", which are always the same concentrations.
We also kept these tubes in 42°C.
We incubated these tubes at 42°C.


*The Experiment of VII
*VII Experiment


[[Image:Biomod_2012_UTokyo_UT-Komaba_Experiment_IndirectBistableVII.png|center|The concept of the experiment VII]]
[[Image:Biomod_2012_UTokyo_UT-Komaba_Experiment_IndirectBistableVII.png|center|The concept of the experiment VII]]


In the experiment, we first input templates CvII, CXII, V to inhX, X to inhV and DNA VII.
In this experiment, we first input templates CvII, CXII, V to inhX, X to inhV and starts the system with VII.
After putting them in PCR for several hours, we put DNA NII and observe the change of the concentration of VII.
After keeping them in a PCR machine at 42°C for several hours, we put DNA NII and observe the change of the concentration of VII.
We want to know which concentration of XII decreases most radically.
The purpose of the experiment is to find out the best concentration of N to X.
The purpose of the experiment is to find out the best concentration of D to V and N to X.
The concentration would be introduced to the bistable system so that we can change the state from "VII" to "XII".  
The concentration would be introduced to the bistable system so that we can change the state from "there is VII" to "there is XII".  




*The Experiment of XII
*XII Experiment


[[Image:Biomod_2012_UTokyo_UT-Komaba_Experiment_IndirectBistableXII.png|center|The concept of the experiment XII]]
[[Image:Biomod_2012_UTokyo_UT-Komaba_Experiment_IndirectBistableXII.png|center|The concept of the experiment XII]]


This one is the opposite experiment of VII.
This one is the counterpart of the previous experiment.
We first input the same templates and DNA XII.
We first input the same templates and DNA XII.
After putting them in PCR for several hours, we put DNA NII and observe the change of the concentration of XII.
After reaching the stable state, we add DNA DII and observe the change of the concentration of XII.
The purpose of the experiment is to find out the best concentration of D to V and N to X.
The purpose of the experiment is to find out the best concentration of D to V.
The concentration would be introduced to the bistable system so that we can change the state from "there is XII" to "there is VII".


[[Biomod/2012/UTokyo/UT-Komaba/Experiment/Lab_Notes#September_28th|More Information]]
[[Biomod/2012/UTokyo/UT-Komaba/Experiment/Lab_Notes#September_28th|More Information]]
Line 47: Line 45:
===October 1st===
===October 1st===


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


Line 58: Line 56:
We lowered the concentratinons of '''D to V''', and '''N to X'''.
We lowered the concentratinons of '''D to V''', and '''N to X'''.
Today, we conducted the same experiment as yesterday. We fixed the concentration of CVII, therefore the purpose of this experiment was to find out the ideal concentration of "'''X to inhV'''".
Today, we conducted the same experiment as yesterday. We fixed the concentration of CVII, therefore the purpose of this experiment was to find out the ideal concentration of "'''X to inhV'''".
We kept these tubes in 42°C, and switched states by injecting '''DII''' or '''VII'''.
We kept these tubes at 42°C, and switched states by injecting '''DII''' or '''NII'''.


[[Biomod/2012/UTokyo/UT-Komaba/Experiment/Lab_Notes#October_2nd|More Information]]
[[Biomod/2012/UTokyo/UT-Komaba/Experiment/Lab_Notes#October_2nd|More Information]]
Line 65: Line 63:


In the experiment, we investigated the best temperature for the bistable system.
In the experiment, we investigated the best temperature for the bistable system.
We made two solutions, one starts from "X" and the other from "Y", and observed them at 6 different temperatures, 41.6, 42.5, 43.8, 45.6, 46.8 and 47.6°C.
We made two solutions, one starts from "XII" and the other from "VII", and observed them at 6 different temperatures, 41.6, 42.5, 43.8, 45.6, 46.8 and 47.6°C.
We successfully switched the state once, but we failed the second switch.
We successfully switched the state once, but we failed the second switch.


[[Biomod/2012/UTokyo/UT-Komaba/Experiment/Lab_Notes#October_3rd|More Information]]
[[Biomod/2012/UTokyo/UT-Komaba/Experiment/Lab_Notes#October_3rd|More Information]]
__NOEDITSECTION__

Latest revision as of 02:19, 28 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 we changed the system into this indirect bistable system. Since an input of C or D indirectly increase the concentration of A or B, concentrations do not change rapidly and radically. We only input C or D, not A or B. As the diagram above shows, inputs C and D indirectly affect the cycle of the bistable system. The purpose of the experiment is to attain proper data about concentrations. This experiment is only for searching the best concentration, and we will eventually use the bistable system for the DNA tablet.

Experiment

September 28th

We could not get a good result for the bistable system so we changed several parts of the system. We introduced two types of DNA, "DII" and "NII", and two types of templates, "D to V" and "N to X" in the system. We changed the concentration of "D to V" and "N to X", which are always the same concentrations. We incubated these tubes at 42°C.

  • VII Experiment
The concept of the experiment VII
The concept of the experiment VII

In this experiment, we first input templates CvII, CXII, V to inhX, X to inhV and starts the system with VII. After keeping them in a PCR machine at 42°C for several hours, we put DNA NII and observe the change of the concentration of VII. The purpose of the experiment is to find out the best concentration of N to X. The concentration would be introduced to the bistable system so that we can change the state from "VII" to "XII".


  • XII Experiment
The concept of the experiment XII
The concept of the experiment XII

This one is the counterpart of the previous experiment. We first input the same templates and DNA XII. After reaching the stable state, we add DNA DII and observe the change of the concentration of XII. The purpose of the experiment is to find out the best concentration of D to V.

More Information


October 1st

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

More Information

October 2nd

We lowered the concentratinons of D to V, and N to X. Today, we conducted the same experiment as yesterday. We fixed the concentration of CVII, therefore the purpose of this experiment was to find out the ideal concentration of "X to inhV". We kept these tubes at 42°C, and switched states by injecting DII or NII.

More Information

October 3rd

In the experiment, we investigated the best temperature for the bistable system. We made two solutions, one starts from "XII" and the other from "VII", and observed them at 6 different temperatures, 41.6, 42.5, 43.8, 45.6, 46.8 and 47.6°C. We successfully switched the state once, but we failed the second switch.

More Information


Retrieved from "https://openwetware.org/mediawiki/index.php?title=Biomod/2012/UTokyo/UT-Komaba/Experiment/Indirect_Bistable&oldid=648859"