Difference between revisions of "Team:TAS Taipei/Modeling"

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                             <p>There are four ways to measure cataract severity (how blurred the lens is):
 
                             <p>There are four ways to measure cataract severity (how blurred the lens is):
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          <li>Lens Optical Cataract Scale III (LOCS) - a scale from 0-6 used by physicians.</li>
 
          <li>Lens Optical Cataract Scale III (LOCS) - a scale from 0-6 used by physicians.</li>
 
          <li>Opacity (%) - used to calculate the LOC scale</li>
 
          <li>Opacity (%) - used to calculate the LOC scale</li>
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     <h4>Assumptions</h4>
 
     <h4>Assumptions</h4>
 
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                                       <li>Definition of crystallin damage: Crystallin damage is proportional to the concentration of hydrogen peroxide, and the time of exposure. This is a valid assumption, supported by the fact that the reaction between cysteine (molecules on crystallin) and hydrogen peroxide is linear. </li>
 
                                       <li>Definition of crystallin damage: Crystallin damage is proportional to the concentration of hydrogen peroxide, and the time of exposure. This is a valid assumption, supported by the fact that the reaction between cysteine (molecules on crystallin) and hydrogen peroxide is linear. </li>
 
                                       <li>We assume that the amount of crystallin is far greater than the amount oxidized. Our product is meant for long-term cataract prevention and minor treatment, and is not suggested for patients with extremely severe cataracts. </li>
 
                                       <li>We assume that the amount of crystallin is far greater than the amount oxidized. Our product is meant for long-term cataract prevention and minor treatment, and is not suggested for patients with extremely severe cataracts. </li>

Revision as of 12:41, 17 September 2016

Modeling - TAS Taipei iGEM Wiki




COUNTERACTS

Modeling

Overall Modeling Abstract

Abstract

Our goal is simple: produce GSR/25HC, package it into nanoparticles, and transport into the lens. GSR/25HC is released over time, which decreases H2O2 concentration, reduces crystallin damage, and prevents cataracts. Our models approach these steps in reverse order, starting with our desired goal, and working backwards to understand the entire process.

Achievements

  • Bridged the gap between the medical, biological, and chemical measurement of crystallin damage.
  • Predicted impact of adding GSR and 25HC on the amount of crystallin damage in the lens.
  • Created Nanoparticle Customizer for user to find a full treatment plan.
  • Generalized Customizer to allow other iGEM teams to predict any nanoparticle drug delivery
  • Analyzed sensitivity of prototype, and suggested insights into optimal manufacturing of prototype.
  • Experimental data used to develop Models 1 and 3.

Outline

Introduction

Why Model?

In the lab, biologists are often unable to test everything experimentally. For example, in our cataracts project, cataract prevention occurs in the long-term, from 20-50 years. Obviously, although short experiments can provide us an idea of what prevention may look like, the power of computational biology allows us to model into the future. As a result, our modeling has been crucial in developing a prototype.

Focus

Most iGEM teams perform modeling on gene expression, which we accomplish in model 5. However, as our construct is not directly placed into the eyes, how our synthesized protein impacts the eyes after it is seperately transported is much more interesting. As a result, we spent the majority of our models on understanding the impacts on the eye.

Guiding Questions

  1. How much GSR do we want inside the lens?
  2. How do we use nanoparticles to control the amount of GSR in the lens?
  3. How do we synthesize GSR, package into NP, and send it into the eye?

Model 1: Crystallin Damage

Abstract

In our experiments, absorbance measurements are meaningless without understanding how severe a cataract that absorbance measurement means. We use literature research to relate LOCS, the physician's scale of cataract severity) to absorbance, which is how we quantified crystallin damage in experiments. We use experimental data to understand how crystallin damage can be quantified by measuring absorbance. With this model, we can calculate how much crystallin damage we have to limit to reduce LOCS to an acceptable level.

Purpose

How much do we need to limit crystallin damage so surgery is not needed?

Background

There are four ways to measure cataract severity (how blurred the lens is):

  1. Lens Optical Cataract Scale III (LOCS) - a scale from 0-6 used by physicians.
  2. Opacity (%) - used to calculate the LOC scale
  3. Absorbance at 397.5 nm - measurable in the lab.
  4. Crystallin Damage - used to quantify how much crystallin has been reacted with hydrogen peroxide to create insoluble, damaged crystallin. The following definition of crystallin damage is used:
\[c.d.(t) = \int_{0}^{\infty} [H_2O_2]_t dt\]

In other words, 1 unit of crystallin damage, in M-h, is equal to the damage caused by 1 molar concentration of hydrogen peroxide reacting crystallin in the eyes for 1 hour.

LOCS Scale







Assumptions

  1. Definition of crystallin damage: Crystallin damage is proportional to the concentration of hydrogen peroxide, and the time of exposure. This is a valid assumption, supported by the fact that the reaction between cysteine (molecules on crystallin) and hydrogen peroxide is linear.
  2. We assume that the amount of crystallin is far greater than the amount oxidized. Our product is meant for long-term cataract prevention and minor treatment, and is not suggested for patients with extremely severe cataracts.
  3. When the experiments diluted the cataract lens protein, the amount of crystallin is diluted. However, the final absorbance of degraded crystallin is also diluted, so we assume any errors in absorbance is canceled out.
  4. We assume that fish and human lens contain similar crystallin proteins.

Part 1 Results

Table 1: Data obtained from XXX relating each value of the LOCS scale, to opacity values.
LOCS 0.0 0.5 1.0 2.0 3.0 4.0 5.0 6.0
Degree None Trace Mild Surgery Suggested Moderate Severe Very Severe
Opacity (%) 0.34 4.24 5.80 18.88 23.60 49.14 65.61 90+
Absorbance (a.u.) 0.001 0.019 0.026 0.091 0.117 0.294 0.464 1.3+

We wish to remain below clinically significant levels, so we will reach attempt to lower the LOCS rating of a cataract to below grade 2.5, which means we want to control GSR such that the crystallin damage results in less than 0.108 a.u. at absorbance at 397.5 nm.

Menu 3

Eaque ipsa quae ab illo inventore veritatis et quasi architecto beatae vitae dicta sunt explicabo.

Conclusion

To make sure LOCS rating remains under 2.5, which has equivalent absorbance value of 0.108 a.u, we must add enough GSR to decrease crystallin damage until it is below 1.941 M-h.

To make sure LOCS rating remains under 1.0, which has equivalent absorbance value of 0.0299 a.u., we must add enough GSR to decrease crystallin damage until it is below 1.220 M-h.

Model 2: GSR/H2O2

Abstract

Abstract

Purpose

Purpose

Background

There are three quantifiers of how severe cataract formation is, two are measurable, one is not.

  1. Absorbance @ 397.5 nm, which is measured with lab equipment.
  2. LOCS scale, subjectively measured by physicians on a scale from 0 - 6.
  3. Crystallin Damage, which we define as the following (for any time $t$)

\[c.d.(t) = \int_{0}^{\infty} [H_2O_2]_t dt\]

In other words, 1 unit of crystallin damage, in M-h, is equal to the damage caused by 1 molar concentration of hydrogen peroxide reacting crystallin in the eyes for 1 hour.

In making this definition, we assume that crystallin damage is directly proportional to the amount of time crystallin is exposed to hydrogen peroxide. Hydrogen peroxide causes damage by forming disulfide bridges within cysteine molecules on crystallin. This changes the structure of crystallin, causing misfolding and cataract damage. Our linear assumption is valid because the rate for this reaction is first order with respect to hydrogen peroxide concentration.

Method

We will relate the three by doing the following:

  1. Relate LOCS scale to opacity via literature research.
  2. Relate opacity to light transmittance via literature research.
  3. Relate light transmittance to absorbance via physical calculations.
  4. Relate absorbance to crystallin damage via experimental data.

Part 1 Results

Table 1: Data obtained from XXX relating each value of the LOCS scale, to opacity values.
LOCS 0.0 0.5 1.0 2.0 3.0 4.0 5.0 6.0
Degree None Trace Mild Surgery Suggested Moderate Severe Very Severe
Opacity (%) 0.34 4.24 5.80 18.88 23.60 49.14 65.61 90+
Absorbance (a.u.) 0.001 0.019 0.026 0.091 0.117 0.294 0.464 1.3+

We wish to remain below clinically significant levels, so we will reach attempt to lower the LOCS rating of a cataract to below grade 2.5, which means we want to control GSR such that the crystallin damage results in less than 0.108 a.u. at absorbance at 397.5 nm.

Menu 3

Eaque ipsa quae ab illo inventore veritatis et quasi architecto beatae vitae dicta sunt explicabo.

Conclusion

Conclusion

Model 3: Nanoparticles

Abstract

Abstract

Purpose

Purpose

Background

There are three quantifiers of how severe cataract formation is, two are measurable, one is not.

  1. Absorbance @ 397.5 nm, which is measured with lab equipment.
  2. LOCS scale, subjectively measured by physicians on a scale from 0 - 6.
  3. Crystallin Damage, which we define as the following (for any time $t$)

\[c.d.(t) = \int_{0}^{\infty} [H_2O_2]_t dt\]

In other words, 1 unit of crystallin damage, in M-h, is equal to the damage caused by 1 molar concentration of hydrogen peroxide reacting crystallin in the eyes for 1 hour.

In making this definition, we assume that crystallin damage is directly proportional to the amount of time crystallin is exposed to hydrogen peroxide. Hydrogen peroxide causes damage by forming disulfide bridges within cysteine molecules on crystallin. This changes the structure of crystallin, causing misfolding and cataract damage. Our linear assumption is valid because the rate for this reaction is first order with respect to hydrogen peroxide concentration.

Method

We will relate the three by doing the following:

  1. Relate LOCS scale to opacity via literature research.
  2. Relate opacity to light transmittance via literature research.
  3. Relate light transmittance to absorbance via physical calculations.
  4. Relate absorbance to crystallin damage via experimental data.

Part 1 Results

Table 1: Data obtained from XXX relating each value of the LOCS scale, to opacity values.
LOCS 0.0 0.5 1.0 2.0 3.0 4.0 5.0 6.0
Degree None Trace Mild Surgery Suggested Moderate Severe Very Severe
Opacity (%) 0.34 4.24 5.80 18.88 23.60 49.14 65.61 90+
Absorbance (a.u.) 0.001 0.019 0.026 0.091 0.117 0.294 0.464 1.3+

We wish to remain below clinically significant levels, so we will reach attempt to lower the LOCS rating of a cataract to below grade 2.5, which means we want to control GSR such that the crystallin damage results in less than 0.108 a.u. at absorbance at 397.5 nm.

Menu 3

Eaque ipsa quae ab illo inventore veritatis et quasi architecto beatae vitae dicta sunt explicabo.

Conclusion

Conclusion

Model 4: Eyedrops

Abstract

Abstract

Purpose

Purpose

Background

There are three quantifiers of how severe cataract formation is, two are measurable, one is not.

  1. Absorbance @ 397.5 nm, which is measured with lab equipment.
  2. LOCS scale, subjectively measured by physicians on a scale from 0 - 6.
  3. Crystallin Damage, which we define as the following (for any time $t$)

\[c.d.(t) = \int_{0}^{\infty} [H_2O_2]_t dt\]

In other words, 1 unit of crystallin damage, in M-h, is equal to the damage caused by 1 molar concentration of hydrogen peroxide reacting crystallin in the eyes for 1 hour.

In making this definition, we assume that crystallin damage is directly proportional to the amount of time crystallin is exposed to hydrogen peroxide. Hydrogen peroxide causes damage by forming disulfide bridges within cysteine molecules on crystallin. This changes the structure of crystallin, causing misfolding and cataract damage. Our linear assumption is valid because the rate for this reaction is first order with respect to hydrogen peroxide concentration.

Method

We will relate the three by doing the following:

  1. Relate LOCS scale to opacity via literature research.
  2. Relate opacity to light transmittance via literature research.
  3. Relate light transmittance to absorbance via physical calculations.
  4. Relate absorbance to crystallin damage via experimental data.

Part 1 Results

Table 1: Data obtained from XXX relating each value of the LOCS scale, to opacity values.
LOCS 0.0 0.5 1.0 2.0 3.0 4.0 5.0 6.0
Degree None Trace Mild Surgery Suggested Moderate Severe Very Severe
Opacity (%) 0.34 4.24 5.80 18.88 23.60 49.14 65.61 90+
Absorbance (a.u.) 0.001 0.019 0.026 0.091 0.117 0.294 0.464 1.3+

We wish to remain below clinically significant levels, so we will reach attempt to lower the LOCS rating of a cataract to below grade 2.5, which means we want to control GSR such that the crystallin damage results in less than 0.108 a.u. at absorbance at 397.5 nm.

Menu 3

Eaque ipsa quae ab illo inventore veritatis et quasi architecto beatae vitae dicta sunt explicabo.

Conclusion

Conclusion

Conclusion

Yay

Citations












Prevention

GSR Eyedrop

Treatment

25HC Eyedrop

LOCS: 0

Eyedrops