Team:University College London/Module 2/Modelling

From 2012.igem.org

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References:
 
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==Species ==
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{| class="bigtable"
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|-
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! Species!! Initial value (molecules) !! Notes
 +
|-
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| PE|| 0.044 || Polyethylene found in North Pacific Gyre (value per cubic metre)<sup>1,2</sup>
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|-
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| POPex || 0.0 || Persistent organic pollutants (ex = extracellular) that are not adhered to plastic surface
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|-
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| PEPOPex || 9.24E-5 || Persistent organic pollutants (ex = extracellular) that are adhered to the plastic surface<sup>3</sup>
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|-
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| POPin || 0.5 || Persistent organic pollutants (in = intracellular) assumed from <i>E. coli</i> membrane permeability <sup>4</sup>
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|-
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| mRNANahR || 0.0|| NahR mRNA product
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|-
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| POPinNahR || 0.0|| Complex of the above two molecules
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|-
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| POPinNahRpSal || 0.0 || Complex of the above molecule and pSal (promoter that induces laccase transcription)
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|-
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| mRNACurli || 0.0 || Polycistronic mRNA as it codes for more than one protein, in reality curli cluster contains five or more proteins, in our model mRNA is present as ??CsgE??<sup>5</sup>
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|-
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| CsgA || 0.0 || One of the polypeptides that is coded for in curli cluster, it is a structural component secreted in subunits outside of the cell
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|-
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| CsgB || 0.0 || One of the polypeptides that is coded for in curli cluster, it is secreted outside of the cell allowing polymerization of CsgA
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|-
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| Fibril || Result of CsgA and CsgB interaction
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|}
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==Reactions taking place in the model==
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{| class="bigtable"
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|-
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! Number !! Reaction !! Reaction rate (molecules/sec) !! Notes
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|-
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| R1 || PE + POPex ↔ PEPOPex || Forward: 1000 <br /> Backward: 1 || Pops have 1000 to 10000 times greater tendency to adhere to plastic than float free in the ocean<sup>6</sup>
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|-
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| R2 || POPex ↔ POPin || Forward: 0.6 <br /> Backward: 0.4 || Based on membrane permeability<sup>4</sup>: diffusion gradient
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|-
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| R3 || POPin + mRNA.Nahr → POPin.mRNA.Nahr || Forward: 1 <br /> Backward: 0.0001 || Based on the assumption that the chemical structure/size of POPs is similar to salycilate<sup>6</sup>.  Salycilate binds to the NahR mRNA product, which complex then binds to the pSal promoter.
 +
|-
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| R7 || 0 → mRNA.Nahr || Forward: 0.088 <br /> Backward: 0.6 || Transcription rate of NahR in molecules/sec (for NahR size 909 bp<sup>7</sup>, transcription rate in E.coli 80bp/sec<sup>8</sup>) under constitutive promoter control
 +
|-
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| R4 || POPinmRNANahr → POPinmRNANahr.Psal || Forward: 78200 <br /> Backward: 0.191 <sup>9</sup> || NahR to pSal binding based on the assumption that POP-NahR binding has no effect on NahR-pSal binding
 +
|-
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| R5 || POPexmRNANahr.Psal → GFP.mRNA|| 0.11 || Transcription rate of GFP in molecules/sec (for GFP size 720bp<sup>10</sup>, transcription rate in E.coli 80bp/sec<sup>8</sup>)
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|-
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| R6 || GFP.mRNA → GFP|| 0.084 || Translation rate of GFP in molecules/sec (for GFP size 240aa<sup>10</sup>, translation rate in E.coli 20aa/sec<sup>8</sup>)
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|-
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| R9 || GFP.mRNA → 0 || 0.03 || Degradation rate of GFP mRNA product<sup>11</sup> must be taken into account due to suboptimal conditions
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|}
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== Results ==
 +
 +
To follow
 +
 +
== References ==
 +
1. Goldstein M, Rosenberg M, Cheng L (2012) Increased oceanic microplastic debris enhances oviposition in an endemic pelagic insect. <i>Biology Letters</i> 10.1098
 +
 +
2. Andrady AL (2011) Microplastics in the marine environment. Marine Pollution Bulletin 62: 1596-1605
Shala AA, Restrepo S, Gonzalez Barrios AF (2011) A network model for biofilm development in Escherichia coli K-12.  <i> Theoretical Biology and Medical Modelling </i> 8: 34 doi:10.1186/1742-4682-8-34
Shala AA, Restrepo S, Gonzalez Barrios AF (2011) A network model for biofilm development in Escherichia coli K-12.  <i> Theoretical Biology and Medical Modelling </i> 8: 34 doi:10.1186/1742-4682-8-34
 +
 +
3. To follow
 +
 +
4. To follow
 +
 +
5. Nenninger AA, Robinson LS, Hammer ND, Epstein EA, Badtke MP, Hultgren SJ, Chapman MR (2011) CsgE is a curli secretion specificity factor that prevents amyloid fibre aggregation.  <i>Mol Microbiol</i> 81: 486-499
 +
 +
6. Mato Y, Isobe T, Takada H, Kanehiro H, Ohtake C, Kaminuma T (2001) Plastic Resin Pellets as a Transport Medium for Toxic Chemicals in the Marine Environment. Environ. Sci. Technol. 35: 318-324
 +
Walsh DM, Lomakin A, Benedek GB, Condron MM, Teplow DB (1997) Amyloid b-Protein Fibrillogenesis: Detection of a protofibrillar intermediate.  <i> The Journal of Biological Chemistry </i> 272: 22364–22372
Walsh DM, Lomakin A, Benedek GB, Condron MM, Teplow DB (1997) Amyloid b-Protein Fibrillogenesis: Detection of a protofibrillar intermediate.  <i> The Journal of Biological Chemistry </i> 272: 22364–22372

Revision as of 16:30, 21 September 2012

Contents

Module 2: Aggregation

Description | Design | Construction | Characterisation | Shear Device | Modelling | Results | Conclusions

Modelling

In addition to our gene network model for this module, we have come up with a system of equations which describe the strength of our adhesive biofilms under shear force stress.

Aggnet.png


Species

Species Initial value (molecules) Notes
PE 0.044 Polyethylene found in North Pacific Gyre (value per cubic metre)1,2
POPex 0.0 Persistent organic pollutants (ex = extracellular) that are not adhered to plastic surface
PEPOPex 9.24E-5 Persistent organic pollutants (ex = extracellular) that are adhered to the plastic surface3
POPin 0.5 Persistent organic pollutants (in = intracellular) assumed from E. coli membrane permeability 4
mRNANahR 0.0 NahR mRNA product
POPinNahR 0.0 Complex of the above two molecules
POPinNahRpSal 0.0 Complex of the above molecule and pSal (promoter that induces laccase transcription)
mRNACurli 0.0 Polycistronic mRNA as it codes for more than one protein, in reality curli cluster contains five or more proteins, in our model mRNA is present as ??CsgE??5
CsgA 0.0 One of the polypeptides that is coded for in curli cluster, it is a structural component secreted in subunits outside of the cell
CsgB 0.0 One of the polypeptides that is coded for in curli cluster, it is secreted outside of the cell allowing polymerization of CsgA
Fibril Result of CsgA and CsgB interaction

Reactions taking place in the model

Number Reaction Reaction rate (molecules/sec) Notes
R1 PE + POPex ↔ PEPOPex Forward: 1000
Backward: 1 		Pops have 1000 to 10000 times greater tendency to adhere to plastic than float free in the ocean6
R2 POPex ↔ POPin Forward: 0.6
Backward: 0.4 		Based on membrane permeability4: diffusion gradient
R3 POPin + mRNA.Nahr → POPin.mRNA.Nahr Forward: 1
Backward: 0.0001 		Based on the assumption that the chemical structure/size of POPs is similar to salycilate6. Salycilate binds to the NahR mRNA product, which complex then binds to the pSal promoter.
R7 0 → mRNA.Nahr Forward: 0.088
Backward: 0.6 		Transcription rate of NahR in molecules/sec (for NahR size 909 bp7, transcription rate in E.coli 80bp/sec8) under constitutive promoter control
R4 POPinmRNANahr → POPinmRNANahr.Psal Forward: 78200
Backward: 0.191 9 		NahR to pSal binding based on the assumption that POP-NahR binding has no effect on NahR-pSal binding
R5 POPexmRNANahr.Psal → GFP.mRNA 0.11 Transcription rate of GFP in molecules/sec (for GFP size 720bp10, transcription rate in E.coli 80bp/sec8)
R6 GFP.mRNA → GFP 0.084 Translation rate of GFP in molecules/sec (for GFP size 240aa10, translation rate in E.coli 20aa/sec8)
R9 GFP.mRNA → 0 0.03 Degradation rate of GFP mRNA product11 must be taken into account due to suboptimal conditions

Results

To follow

References

1. Goldstein M, Rosenberg M, Cheng L (2012) Increased oceanic microplastic debris enhances oviposition in an endemic pelagic insect. Biology Letters 10.1098

2. Andrady AL (2011) Microplastics in the marine environment. Marine Pollution Bulletin 62: 1596-1605 Shala AA, Restrepo S, Gonzalez Barrios AF (2011) A network model for biofilm development in Escherichia coli K-12. Theoretical Biology and Medical Modelling 8: 34 doi:10.1186/1742-4682-8-34

3. To follow

4. To follow

5. Nenninger AA, Robinson LS, Hammer ND, Epstein EA, Badtke MP, Hultgren SJ, Chapman MR (2011) CsgE is a curli secretion specificity factor that prevents amyloid fibre aggregation. Mol Microbiol 81: 486-499

6. Mato Y, Isobe T, Takada H, Kanehiro H, Ohtake C, Kaminuma T (2001) Plastic Resin Pellets as a Transport Medium for Toxic Chemicals in the Marine Environment. Environ. Sci. Technol. 35: 318-324


Walsh DM, Lomakin A, Benedek GB, Condron MM, Teplow DB (1997) Amyloid b-Protein Fibrillogenesis: Detection of a protofibrillar intermediate. The Journal of Biological Chemistry 272: 22364–22372

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