Team:KAIST-Korea/Projects/report 4-Test

From 2011.igem.org

(Difference between revisions)
 
(134 intermediate revisions not shown)
Line 38: Line 38:
}
}
 +
#Content{
 +
        position: relative;
 +
        color: white;
 +
        left: 200px;
 +
        top: -590px;
 +
        width:740px;
 +
        border:3px solid white;
 +
        padding:10px;
 +
}
-
 
+
h1{color:white;}
-
 
+
</style>
</style>
Line 84: Line 92:
<br>
<br>
-
<div style="position:relative; left:270px; top:-580px;">
+
<div id="Content">
-
<table border="1">
+
<h1>&nbsp; Introduction </h1><br />
-
<tr>
+
<p>&nbsp; The human eyes cannot perceive objects that are smaller than a certain size. Also, they cannot recognize light whose intensity is lower than an inherent threshold. We take these limitations into account to determine the number of fluorescent proteins that must accumulate before we can notice any fluorescence, and establish the minimum circular area required for us to perceive any fluorescence.</p>
-
<td>row 1, cell 1</td>
+
<br /><br />
-
<td>row 1, cell 2</td>
+
<h1>&nbsp; Objective </h1><br /><br />
-
</tr>
+
<p>&nbsp; Investigate concentration required for an amount of fluorescent protein in the E.coli that makes light from E.coli be visible for human.</p>
-
<tr>
+
<br /><br />
-
<td>row 2, cell 1</td>
+
<h1>&nbsp; Background </h1><br /><br />
-
<td>row 2, cell 2</td>
+
<p>&nbsp; Human has the limits in vision. For our objective, we have to know about the limit of recognizing size of objects in human vision. This limit is called the ‘Minimum visible acuity’. The exact definition of minimum visible acuity is the minimum size of object that the human eyes can discern. In the table 1 Types of visual acuity(reference 1), the value of detection acuity(red box), ~1.0 arc second, is the minimum visible acuity that we take.</p>
-
</tr>
+
      <br />
-
</table>
+
      <div style="border:2px solid gray; padding-right:7px; ">
 +
          <img src="https://static.igem.org/mediawiki/2011/d/dc/Table_report4.jpg" width=737; />
 +
          <p>&nbsp; Table : Types of visual acuity <sup> 1 </sup></p>
 +
      </div>
 +
      <br />
 +
<p>&nbsp; We assume that the E. coli is in a darkroom for discovering the minimum number of fluorescent protein. In this reason, we use 0.1 lx, the minimum intensity of light that cone cells in human can perceive. <sup>2</sup> In fig1 (a), There is a brief picture for minimum visible acuity. We choose that 1 second is the basic time scale, so have to know the number of fluorescent protein per 1 second. By our research, The range of the photon emitted time is wide, from
 +
    <img src="https://static.igem.org/mediawiki/2011/3/35/%EC%88%98%EC%8B%9D1.png" width=45; height=20; />
 +
      to <img src="https://static.igem.org/mediawiki/2011/b/b4/%EC%88%98%EC%8B%9D2.png" width=45; height=24; />
 +
Although it hasn’t any theoretical reason, we choose the photon emitted time by a fluorescent protein,
 +
    <img src="https://static.igem.org/mediawiki/2011/3/35/%EC%88%98%EC%8B%9D1.png" width=45; height=20; /> .<sup>3</sup>
 +
&nbsp; We will proceed this modeling by using the energy of photons for relating the light and the number of fluorescent protein. One of the unit for light is lm(lumen) and this unit is transformed to J(joule) in
 +
    <img src="https://static.igem.org/mediawiki/2011/3/37/%EC%88%98%EC%8B%9D3.png" width=180; height=24; /><sup>4</sup>
 +
&nbsp; In fig1 (b), There are two values that we will use.
 +
</p>
 +
<br /><br />
 +
<h1>&nbsp; Analysis & Result </h1><br /><br />
 +
<p>&nbsp; For achieving our objective, first we assume that the pictures by E.coli are located at 1 meter from human eyes. From the Background, minimum visible acuity of human is ~1.0 arc second. ~1.0 arc sec, equivalent to
 +
      <img src="https://static.igem.org/mediawiki/2011/a/a2/%EC%88%98%EC%8B%9D4.png" width=50; height=35; />
 +
, is a very small quantity and therefore can be approximated as
 +
      <img src="https://static.igem.org/mediawiki/2011/5/58/%EC%88%98%EC%8B%9D5.png" width=60; height=35; />
 +
. Hence, the smallest object at a distance 1 meter away discernable to the human eye occupies
 +
      <img src="https://static.igem.org/mediawiki/2011/b/ba/%EC%88%98%EC%8B%9D6.png" width=80; height=35; />
 +
of area. Additional explanation by illustration will follow in fig1 (a). Then, we calculate the number of fluorescent protein per second in the discernable area,
 +
      <img src="https://static.igem.org/mediawiki/2011/b/ba/%EC%88%98%EC%8B%9D6.png" width=80; height=35; />.
 +
The cone cells in the human retina recognize green, yellow, red, blue emitted by the GFP, YFP, RYP, and CYP. They detect light with intensity greater than 0.1 lux. Therefore, objects must emit light with
 +
      <img src="https://static.igem.org/mediawiki/2011/a/a9/%EC%88%98%EC%8B%9D7.png" width=320; height=50; />
 +
of luminous flux if they are to be discernable at a meter away. The energy of a photon emitted by a single GFP is
 +
      <img src="https://static.igem.org/mediawiki/2011/9/9b/%EC%88%98%EC%8B%9D8.png" width=400; height=50; />
 +
. Because it takes about
 +
      <img src="https://static.igem.org/mediawiki/2011/3/35/%EC%88%98%EC%8B%9D1.png" width=45; height=20; />
 +
for a fluorescent protein to emit a photon, approximately
 +
      <img src="https://static.igem.org/mediawiki/2011/3/31/%EC%88%98%EC%8B%9D9.png" width=45; height=20; />
 +
photons are emitted per second. Thus, the energy emitted by a GFP per second is
 +
      <img src="https://static.igem.org/mediawiki/2011/1/10/%EC%88%98%EC%8B%9D10.png" width=320; height=40; />
 +
. In order to satisfy this value, we need
 +
      <img src="https://static.igem.org/mediawiki/2011/3/3f/%EC%88%98%EC%8B%9D12.png" width=120; height=20; />
 +
fluorescent proteins per second in
 +
      <img src="https://static.igem.org/mediawiki/2011/b/ba/%EC%88%98%EC%8B%9D6.png" width=80; height=35; />
 +
. Unfortunately, it’s not sure that the photon emitted time is
 +
      <img src="https://static.igem.org/mediawiki/2011/3/35/%EC%88%98%EC%8B%9D1.png" width=40; height=20; />
 +
. We cannot get any scientific basis for our choice. If we get any theoretical basis for our choice or other reliable value, this result will be more credible.
 +
</p>
 +
<br />
 +
      <div style="border:2px solid gray; padding-right:7px; ">
 +
          <img src="https://static.igem.org/mediawiki/2011/c/c8/Fig1-report4.png" width=737; />
 +
      </div>
 +
<br /><br />
 +
<h1> &nbsp; Conclusion </h1></br /><br />
 +
<p>Dividing
 +
      <img src="https://static.igem.org/mediawiki/2011/b/ba/%EC%88%98%EC%8B%9D6.png" width=80; height=50; />
 +
by the two dimensional area of E. coli yields
 +
      <img src="https://static.igem.org/mediawiki/2011/9/91/%EC%88%98%EC%8B%9D11.png" width=90; height=40; />
 +
E. coli. In conclusion, the human eye can perceive color if each E. coli in
 +
      <img src="https://static.igem.org/mediawiki/2011/b/ba/%EC%88%98%EC%8B%9D6.png" width=80; height=50; />
 +
of area produces 0.00257 fluorescent proteins. In other words, 1000 E. coli must make a total of 3 fluorescent proteins. In real life, however, more fluorescent proteins will need to be produced because light emanating from the background may mask the emitted light. This result corroborates the validity of the assumption, used in session 5, that fluorescent proteins produce color instantly upon translation.
 +
</p><br />
</div>
</div>
-
<!--
 
-
<div style="float:left;left:270px;position:relative;top:-580px;width:65%";>
 
-
<p style="color:white;">
 
-
1. Overview </br>
 
-
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
-
Our system, E.Casso is composed of two modules. Each module is a different strain of E. coli. We introduced the modules into disparate strains of E.coli because it is usually easier to engineer something by adopting the ‘divide and conquer’ strategy. The modules perform the following tasks: The first type (Brush E. coli) produces signals that determine the color among green, cyan, yellow, and red generated by adjacent, second type of E. coli. This is achieved through an inherent mechanism by which E. coli naturally communicate with each other, the quorum sensing. By exchanging signaling molecules termed quorum, E. coli can coordinate gene expression as a colony according to its local density. The second type (Dyestuff E. coli) receives quorum from the first type and produces corresponding fluorescent proteins. It also amplifies the signal made by the type 1 module and propagates it to the surrounding E. coli. In essence, we utilize cell-cell communication to coordinate the collective behavior of E. coli.
 
-
</br>
 
-
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;   
 
-
This is akin to soaking a brush with any one of four colors and compressing it firmly against a point on a paper. As time goes by, the blob of paint on the paper will spread. Our genetically engineered E. coli will draw abstract paintings in a similar manner.
 
-
</br>
 
-
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;   
 
-
The modeling procedure is divided into four parts.
 
-
</br>
 
-
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
-
A.Modeling the production of quorum by the first type of E. coli (Brush E. coli): Objective – observe that Brush E. coli produce enough quorums per some interval of time.
 
-
</br>
 
-
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
-
B.Modeling the diffusion of quorum: Objective – note the time scale in which quorum propagates from Brush E. coli to Dyestuff E. coli.
 
-
</br>
 
-
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
-
C.Modeling the production of fluorescent proteins by the Dyestuff E. coli upon receiving quorum and projecting the time it takes for a noticeable amount of fluorescence to accumulate: Objective – observe the time it takes for enough fluorescence to build up.
 
-
</br>
 
-
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 
-
D.Modeling how the variation in E. coli distribution affects the final outcome: Objective – note how the ratio of the two E. coli and the method of seeding affect the resultant painting.
 
-
</p>
 
-
<div id ="modeling picture" style="left:-170px;position:absolute;top:-50px";>
 
-
<img src="https://static.igem.org/mediawiki/2011/thumb/3/3c/Modeling.png/192px-Modeling.png" width = 200; height=600;/>
 
-
</div>
 
-
</div>
 
-
//-->
 
</body>
</body>
</html>
</html>

Latest revision as of 17:36, 11 July 2011





















  Introduction


  The human eyes cannot perceive objects that are smaller than a certain size. Also, they cannot recognize light whose intensity is lower than an inherent threshold. We take these limitations into account to determine the number of fluorescent proteins that must accumulate before we can notice any fluorescence, and establish the minimum circular area required for us to perceive any fluorescence.



  Objective



  Investigate concentration required for an amount of fluorescent protein in the E.coli that makes light from E.coli be visible for human.



  Background



  Human has the limits in vision. For our objective, we have to know about the limit of recognizing size of objects in human vision. This limit is called the ‘Minimum visible acuity’. The exact definition of minimum visible acuity is the minimum size of object that the human eyes can discern. In the table 1 Types of visual acuity(reference 1), the value of detection acuity(red box), ~1.0 arc second, is the minimum visible acuity that we take.


  Table : Types of visual acuity 1


  We assume that the E. coli is in a darkroom for discovering the minimum number of fluorescent protein. In this reason, we use 0.1 lx, the minimum intensity of light that cone cells in human can perceive. 2 In fig1 (a), There is a brief picture for minimum visible acuity. We choose that 1 second is the basic time scale, so have to know the number of fluorescent protein per 1 second. By our research, The range of the photon emitted time is wide, from to Although it hasn’t any theoretical reason, we choose the photon emitted time by a fluorescent protein, .3   We will proceed this modeling by using the energy of photons for relating the light and the number of fluorescent protein. One of the unit for light is lm(lumen) and this unit is transformed to J(joule) in 4   In fig1 (b), There are two values that we will use.



  Analysis & Result



  For achieving our objective, first we assume that the pictures by E.coli are located at 1 meter from human eyes. From the Background, minimum visible acuity of human is ~1.0 arc second. ~1.0 arc sec, equivalent to , is a very small quantity and therefore can be approximated as . Hence, the smallest object at a distance 1 meter away discernable to the human eye occupies of area. Additional explanation by illustration will follow in fig1 (a). Then, we calculate the number of fluorescent protein per second in the discernable area, . The cone cells in the human retina recognize green, yellow, red, blue emitted by the GFP, YFP, RYP, and CYP. They detect light with intensity greater than 0.1 lux. Therefore, objects must emit light with of luminous flux if they are to be discernable at a meter away. The energy of a photon emitted by a single GFP is . Because it takes about for a fluorescent protein to emit a photon, approximately photons are emitted per second. Thus, the energy emitted by a GFP per second is . In order to satisfy this value, we need fluorescent proteins per second in . Unfortunately, it’s not sure that the photon emitted time is . We cannot get any scientific basis for our choice. If we get any theoretical basis for our choice or other reliable value, this result will be more credible.




  Conclusion



Dividing by the two dimensional area of E. coli yields E. coli. In conclusion, the human eye can perceive color if each E. coli in of area produces 0.00257 fluorescent proteins. In other words, 1000 E. coli must make a total of 3 fluorescent proteins. In real life, however, more fluorescent proteins will need to be produced because light emanating from the background may mask the emitted light. This result corroborates the validity of the assumption, used in session 5, that fluorescent proteins produce color instantly upon translation.