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Revision as of 07:46, 10 September 2016

Modeling - TAS Taipei iGEM Wiki




COUNTERACTS

Modeling

Overall Modeling 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.

In model 1, we quantified crystallin damage, and measured its true impact on light absorbance, to relate it to cataracts. Then in model 2 we modelled how varying amounts of GSR added impacted the amount of crystallin damage, until we found a desirable GSR level for cataract prevention. We examined the degradation of nanoparticles in model 3, and how repeated doses in the long-term contributed to sustain the desirable GSR level. Model 4 accounts for the actual transport of nanoparticles into the highly protected eye, mainly by flooding the eyedrops with GSR so sufficient amounts entered the eyes. Finally, Model 5 is a simple stochastic model for understanding gene expression in a simple circuit.

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

An absorbance measurement is meaningless without knowing how clinically severe it is. Cataract severity is graded on the LOCS scale from 0-6, and our goal is to lower LOCS to 2.0, below the threshold of surgery. We relate measurements made on different scales, from LOCS to opacity, light transmittance, light transmittance, wavelength absorbance, and finally to crystallin damage, a quantity that is useful for our future models.

Purpose

What amount of crystallin damage is acceptable, to not require surgery? This will let us know how much GSR we need to maintain an acceptable amount of crystallin damage that will not require surgery (based on LOCS scale)

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.

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.

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.

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.

Conclusion

Conclusion

Human GzmB Inhibitor ACT3m

HOME

Given our model of Serpina3n, we also wanted to create a model for the protein used in our device, ACT3m. The dataset obtained from the ACT3m paper (Marcet-Palacios et al., 2014) is the result of a colorimetric assay. Data was presented as absorbance values (A405), which correspond to the concentration of free GzmB, at different inhibitor concentrations. The paper used this to prove that their novel ACT3m inhibitor was the strongest out of their entire pool of possible candidates: treatment with ACT3m resulted in the lowest A405 values, which suggests the strongest inhibition of GzmB.

Conclusion

Yay

Citations












Prevention

GSR Eyedrop

Treatment

25HC Eyedrop

LOCS: 0

Eyedrops