Revision as of 15:22, 21 September 2012

Module 1: Detection

Modelling

As our detection module is so closely tied up with our degradation module, our cell model for this module examines the hypothetical expression of GFP on detection of POPs. This allows us to assess the efficacy of detection as a stand-alone module before we look at its performance when incorporated into our system.

Our cell model for detection was created in SimBiology. This MathWorks software is a MATLAB extension that allows specification of the species, reactions, and compartments that make up a system - in our case, the cell and the external environment - and to run simulations on the specified system. For this module, we are interested in detection response, which we represent here as GFP production. The model is composed of two compartments:

-External represents the constant association and disassociation of persistent organic pollutants (POPs) that takes place in the ocean.

-Cell represents the reactions taking place inside the cell

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)
GFP	0.0	Green fluorescent protein
GFPmRNA	0.0	GFP mRNA product

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 ocean⁵
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	0.04	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

Our model shows the expected output - production of GFP on detection of persistent organic pollutants. With this in mind and satisfied that our deModule_3/Modelling|cell model for degradation]]

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

3. To follow

4. To follow

5. 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

6. https://2011.igem.org/Team:Peking_S/project/wire/harvest

7. http://www.xbase.ac.uk/genome/azoarcus-sp-bh72/NC_008702/azo2419;nahR1/viewer

8. http://kirschner.med.harvard.edu/files/bionumbers/fundamentalBioNumbersHandout.pdf

9. Park H, Lim W, Shin H (2005) In vitro binding of purified NahR regulatory protein with promoter Psal. Biochimica et Biophysica Acta 1775: 247-255

10. http://partsregistry.org/wiki/index.php?title=Part:BBa_I13522

11. To follow

@@ Line 10: / Line 10: @@
 [[File:detectionnet.jpg]]
-Note that this model is very similar to our [[Team:University_College_London/Module_3/Modelling|cell model for degradation]].  This model, however, looks only at detection response - modelled here by GFP production - and ignores the production and action of laccase.
+Our cell model for detection was created in SimBiology.  This MathWorks software is a MATLAB extension that allows specification of the species, reactions, and compartments that make up a system - in our case, the cell and the external environment - and to run simulations on the specified system.  For this module, we are interested in detection response, which we represent here as GFP production.  The model is composed of two compartments:
 -External represents the constant association and disassociation of persistent organic pollutants (POPs) that takes place in the ocean.
@@ Line 68: / Line 68: @@
 [[File:detectiongraph.jpg]]
-Our model shows the expected output - production of GFP on detection of persistent organic pollutants. With this in mind and satisfied that our detection module worked as expected in silico, we
+Our model shows the expected output - production of GFP on detection of persistent organic pollutants. With this in mind and satisfied that our deModule_3/Modelling|cell model for degradation]]
 == References ==

Team:University College London/Module 1/Modelling

From 2012.igem.org