Team:University College London/Module 3/Modelling

From 2012.igem.org

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(→Modelling)
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! Parameter !! Value
! Parameter !! Value
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|-
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| f.PE+POPex-PEPOPex|| Example
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| forward:PE+POPex-PEPOPex|| 1000
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| r.PE+POPEX-PEPOPex|| Example
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| reverse:PE+POPEX-PEPOPex|| 1
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|-
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| f.POPex-POPin|| Example
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| forward:POPex-POPin|| Example
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|-
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| r.POPex-POPin|| Example
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| reverse:POPex-POPin|| Example
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|-
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| f.NahR+POPin-POPinNahR|| Example
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| forward:NahR+POPin-POPinNahR|| Example
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|-
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| r.NahR+POPin-POPinNahr|| Example
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| reverse:NahR+POPin-POPinNahr|| Example
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| POPinNahR-Lin+POPinNahR || Example
| POPinNahR-Lin+POPinNahR || Example
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| Lin-Lex|| Example
| Lin-Lex|| Example
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|-
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| f.Null-NahR|| Example
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| forward:Null-NahR|| Example
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|-
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| r.Null-NahR || Example
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| reverse:Null-NahR || Example
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| PEPOP+Lex-Lex || Example
| PEPOP+Lex-Lex || Example
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{| class="wikitable"
{| class="wikitable"
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! Species!! Initial value !! Notes
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! Species!! Initial value (molecules) !! Notes
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| PE|| Example ||
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| PE|| 0.00345 ||
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| POPEX|| Example ||
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| Lex || 0.0 ||
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| Lex || Example ||
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| PEPOPex || 9.24E-5 ||
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| PEPOPex || Example ||
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| POPin || 0.5 || Dependent on the concentration gradient: when the conc. in is equal to conc. out rate decreases
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|-
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| POPin || Example || Dependent on the concentration gradient: when the conc. in is equal to conc. out rate decreases
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| Nahr || 0.0|| Produced all the time, transcription depends on  
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|-
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| Nahr || Example || Produced all the time, transcription depends on
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| POPinNahR || 0.0|| Hill function
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| POPinNahR || Example || Hill function
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| Lin|| 0.0||
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| Lin|| Example ||
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|}
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| R4 || POPexmRNANahr → POPexmRNANahr.Psal ||  
| R4 || POPexmRNANahr → POPexmRNANahr.Psal ||  
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| R5 || POPexmRNANahr.Psal → Lin.mRNA|| Lin.mRNA → mRNA.degp??
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| R5 || POPexmRNANahr.Psal → Lin.mRNA|| 0.053 - transcription rate of Laccase in molecules/sec (for laccase size 1500 bp, transcription rate in E.coli 80bp/sec
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| R6 || Lin.mRNA → Lin||  
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| R6 || Lin.mRNA → Lin|| 0.053 - translation rate of Laccase in molecules/sec (for laccase size 500 aa, translation rate in E.coli 20aa/sec)
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| R11 || Lin → Lindegp ||
| R11 || Lin → Lindegp ||

Revision as of 15:48, 20 September 2012

Module 3: Degradation

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

Modelling

Our gene network model for this module shows the amount of laccase produced by our bacteria. We have used this prediction to find out how many bacteria would be required per cubic meter of sea water in order to effectively degrade polyethylene-based plastics.

Parameter Value
forward:PE+POPex-PEPOPex 1000
reverse:PE+POPEX-PEPOPex 1
forward:POPex-POPin Example
reverse:POPex-POPin Example
forward:NahR+POPin-POPinNahR Example
reverse:NahR+POPin-POPinNahr Example
POPinNahR-Lin+POPinNahR Example
Lin-Lex Example
Lin-Lex Example
forward:Null-NahR Example
reverse:Null-NahR Example
PEPOP+Lex-Lex Example
Species Initial value (molecules) Notes
PE 0.00345
Lex 0.0
PEPOPex 9.24E-5
POPin 0.5 Dependent on the concentration gradient: when the conc. in is equal to conc. out rate decreases
Nahr 0.0 Produced all the time, transcription depends on
POPinNahR 0.0 Hill function
Lin 0.0
Number Reaction Notes
R1 PE + POPex ↔ PEPOPex Pops have 1000 times greater tendency to adhere to plastic than float free in the ocean
R2 POPex ↔ POPin Based on membrane permeability: diffusion gradient
R3 POPin + mRNA.Nahr → POPin.mRNA.Nahr The chemical structure/size of POPs is similar to salycilate which is the original compound that react to mRNA.Nahr -> 0 (??)
R9 0 → mRNA.Nahr
R4 POPexmRNANahr → POPexmRNANahr.Psal
R5 POPexmRNANahr.Psal → Lin.mRNA 0.053 - transcription rate of Laccase in molecules/sec (for laccase size 1500 bp, transcription rate in E.coli 80bp/sec
R6 Lin.mRNA → Lin 0.053 - translation rate of Laccase in molecules/sec (for laccase size 500 aa, translation rate in E.coli 20aa/sec)
R11 Lin → Lindegp
R7 Lin → Lex
R12 Lex → Lexdegp  ??
R8 Lex → PEdegp

Degradationnet.jpg

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