Team:USP-Brazil/Model:RFPVisibility

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<div style="background: rgba(255,255,255,0.90); padding-right: 10px;">
<div style="background: rgba(255,255,255,0.90); padding-right: 10px;">
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<h2>RFP Visual Contrast Analysis</h2>
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<h3>Stating the problem</h3>
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<p>Here is the problem: we are trying to build a &#8220;machine&#8221; to detect methanol in alcoholic drinks using a genetically modified yeast to produce RFP (Red Fluorescent Protein) through methanol consumption. The chosen yeast was <i>Pichia pastoris</i>, especially because its
 +
natural ability to interact with methanol due to the presence of an
 +
<i>AOX</i> promoter.</p>
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<h2>RFP Visibility</h2>
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<p>Among the questions we need to answer in order to accomplish this
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<h3>Defining the problem</h3>
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task, is the simple question about how do we &#8220;see&#8221; RFP signal
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<p>The first question for the modeling group was: could we see the the red protein (RFP) with the naked eye? To answer this question, we tried to relate the visual contrast and the brightness of RFP. First we need a formula for contrast:</p>
+
that would be produced by methanol induction. To address this question
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$$ C(x) = \left| \frac{I(x)-I_B(x)}{I_B(x)} \right| $$
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we make use of some mathematical notions of visual contrast and brightness.</p>
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<p>where <i>C</i> is the contrast, <i>I</i> and <i>I<sub>B</sub></i> are the luminous intensity of the object we are trying to see, i.e. the protein, and the background and <i>x</i> is the distance between the protein and the viewer</p>
+
 +
<h3>Definitions</h3>
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<p>Let's define more precisely the meaning of visual contrast:</p>
 +
<p><b>Visual Contrast:</b> Consider some object placed at a distance <i>x</i> from
 +
an observer and emitting light with a certain intensity. This light
 +
is measured by the observer and called <i>I(x)</i>. Suppose the background
 +
light intensity measured by the observer is <i>I<sub>B</sub>(x)</i>.</p>
 +
<p>We define the Visual Contrast (<i>C</i>) as:</p>
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<p style="text-align:center;"><a href="https://2013.igem.org/Team:USP-Brazil/Model:RFPVisibility">RFP Visibility</a> | <a href="#">Deterministic Model</a> | <a href="#">Stochastic Model</a></p>
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<div style="margin: 20px auto; width: 266px; height: 44px; background: url('https://static.igem.org/mediawiki/2013/9/9b/USPBrFormulasRFP.png') center top;">&nbsp;</div>
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<p><b>Quantum Yield and Molar Extinction Coefficient:</b> The brightness of a
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FP (Fluorescent Protein) is proportional to the product of its Quantum
 +
Yield and its Molar Extinction Coefficient (MEC).</p>
 +
<p>The QY is defined by the rate of emitted fotons and absorbed fotons
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and we call it <i>&Phi;</i>.</p>
 +
 
 +
<div style="margin: 20px auto; width: 266px; height: 41px; background: url('https://static.igem.org/mediawiki/2013/9/9b/USPBrFormulasRFP.png') center -58px;">&nbsp;</div>
 +
 
 +
<p>The MEC, defined as the absorption force per mol per centimeter <i>(M<sup>-1</sup>cm<sup>-1</sup>)</i>, is a property of the FP's chemical structure and we call it <i>&epsilon;</i>.</p>
 +
 
 +
<p><b>Beer-Lambert Law:</b> Consider an object placed at <i>x<sub>0</sub>=0</i> emitting
 +
light. Call <i>I(x)</i> the light intensity at a distance <i>x</i>. The Beer-Lambert
 +
law says the light intensity distant <i>x</i> from <i>x<sub>0</sub></i> suffers an
 +
exponential attenuation:</p>
 +
 
 +
<div style="margin: 20px auto; width: 266px; height: 40px; background: url('https://static.igem.org/mediawiki/2013/9/9b/USPBrFormulasRFP.png') center -118px;">&nbsp;</div>
 +
 
 +
<p>Where <i>A</i> is the Total Absorptivity of the medium where the object
 +
is placed, <i>c<sub>i</sub></i> are the absorbing components and <i>&epsilon;<sub>i</sub></i>
 +
are their respective MECs.</p>
 +
 
 +
<h3>Putting it all together</h3>
 +
<p>Well, there is a natural link between the concepts described above.
 +
To see this we need to describe the intensity produced by the RFP
 +
through its QY and MEC, than we estimate the environment conditions
 +
and choose a desired contrast and determine the necessary concentration
 +
of RFP to achieve this.</p>
 +
 
 +
<p>Looking closely to the relevant quantity concerning the RFP, we can
 +
interpret the product <i>&Phi;&epsilon;</i> as the number of fotons absorbed
 +
and transformed in red light per mol of RFP per centimeter of distance.</p>
 +
 
 +
<p>In normal environment we don't need to be concerned about the frequency
 +
of interaction of a RFP molecule and a foton because there are fotons
 +
in abundance. So we can come up with a simple formula to the intensity
 +
produced by concentration of RFP in a certain container of size
 +
<i>D</i>.</p>
 +
 
 +
<div style="margin: 20px auto; width: 266px; height: 20px; background: url('https://static.igem.org/mediawiki/2013/9/9b/USPBrFormulasRFP.png') center -176px;">&nbsp;</div>
 +
 
 +
<p>Where <i>I<sub>B</sub></i> represents the background (locally homogeneous) light
 +
intensity and <i>[RFP]</i> the RFP concentration. This formula states
 +
that all the background light inside the container with RFP is transformed
 +
in red light and the intensity is adjusted by the factor <i>&Phi;&epsilon; D[RFP]</i>.</p>
 +
 
 +
<p>Inserting this in the definition of visual contrast</p>
 +
 
 +
<div style="margin: 20px auto; width: 266px; height: 44px; background: url('https://static.igem.org/mediawiki/2013/9/9b/USPBrFormulasRFP.png') center -223px;">&nbsp;</div>
 +
 
 +
<p>and extending the homogeneity of background light intensity we can
 +
treat <i>I<sub>B</sub>(x)=I<sub>B</sub></i> for all possible values of <i>x</i>. This leads
 +
us to</p>
 +
 
 +
<div style="margin: 20px auto; width: 266px; height: 22px; background: url('https://static.igem.org/mediawiki/2013/9/9b/USPBrFormulasRFP.png') center -286px;">&nbsp;</div>
 +
 
 +
<p>Here <i>A</i> represents the atmospheric air absorptivity. And finally,
 +
the RFP concentration can be determined</p>
 +
 
 +
<div style="margin: 20px auto; width: 266px; height: 39px; background: url('https://static.igem.org/mediawiki/2013/9/9b/USPBrFormulasRFP.png') center -334px;">&nbsp;</div>
 +
 
 +
<h3>Giving an estimate</h3>
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<p>Now, we can use our knowledge about the human vision limits and about
 +
the RFP to estimate the RFP concentration necessary for it to be seen.
 +
To this end, we make two additional hypothesis and <i>A&nbsp;=0.5&nbsp;m<sup>-1</sup></i>
 +
and <i>x=1 m</i>, i.e., the atmospheric air absorbs half the light it
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interacts per meter and the observer will measure at 1 meter from
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the RFP container. Our data is:</p>
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<ul>
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<li>RFP mCherry QY: <i>&Phi;=0,22</i></li>
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<li>RFP mCherry MEC: <i>&epsilon;=72000</i></li>
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<li>Visual contrast: <i>C=0,10</i></li>
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<li><i>D&sim;2 cm</i></li>
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</ul>
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<p>The value for <i>D</i> was chosen to represent a cylindrical flask with
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<i>2 cm</i> diameter. The value for <i>C</i> is a mean calculated from
 +
data from [1]. Therefore, <b>[RFP] &sim; 8.9 &times; 10<sup>-5</sup>mols</b></p>
 +
 
 +
 
 +
 
 +
 
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<h3>Conclusion</h3>
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<p>With these results we can compare the RFP production rate of <i>Pichia
 +
pastoris</i> with the photostability of our RFP to determine whether we will
 +
be able to see the RFP produced in different conditions. However, more
 +
specific data will be required to proceed.</p>
 +
 
 +
<div class="cf">
 +
<p style="float: left;"><a href="https://2013.igem.org/Team:USP-Brazil/Modeling"><i class="icon-circle-arrow-left"></i> Back to Modeling overview</a></p>
 +
<p style="float: right;"><a href="https://2013.igem.org/Team:USP-Brazil/Model:Deterministic">See the deterministic model <i class="icon-circle-arrow-right"></i></a></p>
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</div>
 +
 
 +
 
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<h4 style="color:grey;">References</h4>
 +
<p style="color:grey;">[1] Contrast Thresholds of the Human Eye - H. RICHARD BLACKWELL -JOURNAL OF THE OPTICAL
 +
SOCIETY OF AMERICA VOLUME 36, NUMBER 11 NOVEMBER, 1946</p>
 +
 
 +
 
 +
<p style="text-align:center;">RFP Visibility | <a href="https://2013.igem.org/Team:USP-Brazil/Model:Deterministic">Deterministic Model</a> | <a href="https://2013.igem.org/Team:USP-Brazil/Model:Stochastic">Stochastic Model</a></p>

Latest revision as of 01:28, 28 September 2013

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Modelling

RFP Visual Contrast Analysis

Stating the problem

Here is the problem: we are trying to build a “machine” to detect methanol in alcoholic drinks using a genetically modified yeast to produce RFP (Red Fluorescent Protein) through methanol consumption. The chosen yeast was Pichia pastoris, especially because its natural ability to interact with methanol due to the presence of an AOX promoter.

Among the questions we need to answer in order to accomplish this task, is the simple question about how do we “see” RFP signal that would be produced by methanol induction. To address this question we make use of some mathematical notions of visual contrast and brightness.

Definitions

Let's define more precisely the meaning of visual contrast:

Visual Contrast: Consider some object placed at a distance x from an observer and emitting light with a certain intensity. This light is measured by the observer and called I(x). Suppose the background light intensity measured by the observer is IB(x).

We define the Visual Contrast (C) as:

 

Quantum Yield and Molar Extinction Coefficient: The brightness of a FP (Fluorescent Protein) is proportional to the product of its Quantum Yield and its Molar Extinction Coefficient (MEC).

The QY is defined by the rate of emitted fotons and absorbed fotons and we call it Φ.

 

The MEC, defined as the absorption force per mol per centimeter (M-1cm-1), is a property of the FP's chemical structure and we call it ε.

Beer-Lambert Law: Consider an object placed at x0=0 emitting light. Call I(x) the light intensity at a distance x. The Beer-Lambert law says the light intensity distant x from x0 suffers an exponential attenuation:

 

Where A is the Total Absorptivity of the medium where the object is placed, ci are the absorbing components and εi are their respective MECs.

Putting it all together

Well, there is a natural link between the concepts described above. To see this we need to describe the intensity produced by the RFP through its QY and MEC, than we estimate the environment conditions and choose a desired contrast and determine the necessary concentration of RFP to achieve this.

Looking closely to the relevant quantity concerning the RFP, we can interpret the product Φε as the number of fotons absorbed and transformed in red light per mol of RFP per centimeter of distance.

In normal environment we don't need to be concerned about the frequency of interaction of a RFP molecule and a foton because there are fotons in abundance. So we can come up with a simple formula to the intensity produced by concentration of RFP in a certain container of size D.

 

Where IB represents the background (locally homogeneous) light intensity and [RFP] the RFP concentration. This formula states that all the background light inside the container with RFP is transformed in red light and the intensity is adjusted by the factor Φε D[RFP].

Inserting this in the definition of visual contrast

 

and extending the homogeneity of background light intensity we can treat IB(x)=IB for all possible values of x. This leads us to

 

Here A represents the atmospheric air absorptivity. And finally, the RFP concentration can be determined

 

Giving an estimate

Now, we can use our knowledge about the human vision limits and about the RFP to estimate the RFP concentration necessary for it to be seen. To this end, we make two additional hypothesis and A =0.5 m-1 and x=1 m, i.e., the atmospheric air absorbs half the light it interacts per meter and the observer will measure at 1 meter from the RFP container. Our data is:

  • RFP mCherry QY: Φ=0,22
  • RFP mCherry MEC: ε=72000
  • Visual contrast: C=0,10
  • D∼2 cm

The value for D was chosen to represent a cylindrical flask with 2 cm diameter. The value for C is a mean calculated from data from [1]. Therefore, [RFP] ∼ 8.9 × 10-5mols

Conclusion

With these results we can compare the RFP production rate of Pichia pastoris with the photostability of our RFP to determine whether we will be able to see the RFP produced in different conditions. However, more specific data will be required to proceed.

References

[1] Contrast Thresholds of the Human Eye - H. RICHARD BLACKWELL -JOURNAL OF THE OPTICAL SOCIETY OF AMERICA VOLUME 36, NUMBER 11 NOVEMBER, 1946

RFP Visibility | Deterministic Model | Stochastic Model

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