Revision as of 18:12, 20 September 2012

Module 3: Degradation

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.

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 testtestselkjalsfdkjalfkjs;lkdjf;laksjdf;laksjdf;lakjs;dljaf;slkdjfazlskdj;falskjd
Nahr	0.0	Produced all the time, transcription depends on
POPinNahR	0.0	Hill function
Lin	0.0

Number	Reaction	Reaction rate (molecules/sec)	Notes
R1	PE + POPex ↔ PEPOPex	Forward: 1000 Backward: 1	Pops have 1000 times greater tendency to adhere to plastic than float free in the ocean
R2	POPex ↔ POPin	Forward: 0.6 Backward: 0.4	Based on membrane permeability: diffusion gradient
R3	POPin + mRNA.Nahr → POPin.mRNA.Nahr	Forward: 1 Backward: 0.0001	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	Forward: 0.088 Backward: 0.6	Transcription rate of NahR in molecules/sec (for NahR size 909 bp², transcription rate in E.coli 80bp/sec)
R4	POPinmRNANahr → POPinmRNANahr.Psal	Forward: 78200 Backward: 0.191
R5	POPexmRNANahr.Psal → Lin.mRNA	0.054	Transcription rate of Laccase in molecules/sec (for laccase size 1500 bp¹, transcription rate in E.coli 80bp/sec)
R6	Lin.mRNA → Lin	0.04	Translation rate of Laccase in molecules/sec (for laccase size 500 aa, translation rate in E.coli 20aa/sec)
R11	Lin → Lindegp	0.03
R7	Lin → Lex	Forward: 0.9 Backward: 0.1
R8	Lex → PEdegp	Vm: 0.01 Km: 0.114

We ran three simulations in SimBiology, each over a different timespan:

comment here?

1. Laccase size: http://partsregistry.org/Part:BBa_K729002

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

3. 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

4. Teuten E, Saquing J, Knappe D et al. (2009) Transport and release of chemicals from plastics to the environment and to wildlife. Philosophical transactions of the Royal Society of London 364: 2027-2045

8. Young K, Silver LL (1991) Leakage of periplasmic enzymes from envA1 strains of Escherichia coli. J Bacteriol. 173: 3609–3614

11.Van A, Rochman C, Flores E, Hill K, Vargas E, Vargas S, Hoh E (2012) Persistent organic pollutants in plastic marine debris found on beaches in San Diego, California. Chemosphere 86: 258-263

12. Santo M, Weitsman R, Sivan A (2012) The role of the copper-binding enzyme - laccase - in the biodegradation of polyethylene by the actinomycete Rhodococcus ruber. International Biodeterioration & Biodegradation 208: 1-7

POPS & PLASTIC QUANTITITES

Rios L, Moore C, Jones P (2007) Persistent organic pollutants carried by synthetic polymers in the ocean environment. Marine Pollution BulletinI/i> 54: 1230–1237

Takada H, et al (2010) Global distribution of organic micropollutants in marine plastics. Report to Algalita Marine Research Institute

Heskett M, Takada H, Yamashita R, Yuyama M, Ito M, Geok YB, Ogata Y, Kwan C, Heckhausen A, Taylor H, Powell T, Morishige C, Young D, Patterson H, Robertson B, Bailey E, Mermoz J (2012) Measurement of persistent organic pollutants (POPs) in plastic resin pellets from remote islands: Toward establishment of background concentrations for International Pellet Watch. <i>Marine Pollution Bulletin 64: 445-448

4. SALYCITATE

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

5. LACCASE

Ding Z, Peng L, Chen Y, Zhang L, Gu Z, Shi G, Zhang K (2012) Production and characterization of thermostable laccase from the mushroom, Ganoderma lucidum, using submerged fermentation. African Journal of Microbiology Research 6: 1147-1157. DOI: 10.5897/AJMR11.1257

6 Kunamneni A, Plou FJ, Ballesteros A, and Alcalde M. Laccases and their applications: A patent review. Departamento de Biocatálisis, Instituto de Catálisis y Petroleoquímica, CSIC, Cantoblanco, 28049 Madrid, Spain.

7. BRENDA: EC 1.10.3.2 – laccase

8. E.COLI MEMBRANE PERMEABILITY

Heskett M, Takada H, Yamashita R, Yuyama M, Ito M, Geok YB, Ogata Y, Kwan C, Heckhausen A, Taylor H, Powell T, Morishige C, Young D, Patterson H, Robertson B, Bailey E, Mermoz J (2012) Measurement of persistent organic pollutants (POPs) in plastic resin pellets from remote islands: Toward establishment of background concentrations for International Pellet Watch. Marine Pollution Bulletin 64: 445-448 is this right? This is what’s on excel

7. DIFFERENT REGULATOR SYSTEMS Wang B, Papamichail D, Mueller S, Skiena S (2007) Two Proteins for the Price of One: The Design of Maximally Compressed Coding Sequences. DOI: 10.1.1.174.6416

@@ Line 74: / Line 74: @@
 . Santo M, Weitsman R, Sivan A (2012) The role of the copper-binding enzyme - laccase - in the biodegradation of polyethylene by the actinomycete <i>Rhodococcus ruber.  International Biodeterioration & Biodegradation</i> 208: 1-7
+POPS & PLASTIC QUANTITITES
+Rios L, Moore C, Jones P (2007) Persistent organic pollutants carried by synthetic polymers in the ocean environment.  <i>Marine Pollution BulletinI/i> 54: 1230–1237
+Takada H, et al (2010) Global distribution of organic micropollutants in marine plastics.  Report to Algalita Marine Research Institute
+Heskett M, Takada H, Yamashita R, Yuyama M, Ito M, Geok YB, Ogata Y, Kwan C, Heckhausen A, Taylor H, Powell T, Morishige C, Young D, Patterson H, Robertson B, Bailey E, Mermoz J (2012) Measurement of persistent organic pollutants (POPs) in plastic resin pellets from remote islands: Toward establishment of background concentrations for International Pellet Watch.  <i>Marine Pollution Bulletin</i> 64: 445-448
+. SALYCITATE
+Park H, Lim W, Shin H (2005) In vitro binding of purified NahR regulatory protein with promoter Psal. <i>Biochimica et Biophysica Acta</i> 1775: 247-255
+. LACCASE
+Ding Z, Peng L, Chen Y, Zhang L, Gu Z, Shi G, Zhang K (2012) Production and characterization of thermostable laccase from the mushroom, Ganoderma lucidum, using submerged fermentation.  <i>African Journal of Microbiology Research</i> 6: 1147-1157.  DOI: 10.5897/AJMR11.1257
+Kunamneni A, Plou FJ, Ballesteros A, and Alcalde M. Laccases and their applications: A patent review.  Departamento de Biocatálisis, Instituto de Catálisis y Petroleoquímica, CSIC, Cantoblanco, 28049 Madrid, Spain.
+. BRENDA: EC 1.10.3.2 – laccase
+. E.COLI MEMBRANE PERMEABILITY
+Heskett M, Takada H, Yamashita R, Yuyama M, Ito M, Geok YB, Ogata Y, Kwan C, Heckhausen A, Taylor H, Powell T, Morishige C, Young D, Patterson H, Robertson B, Bailey E, Mermoz J (2012) Measurement of persistent organic pollutants (POPs) in plastic resin pellets from remote islands: Toward establishment of background concentrations for International Pellet Watch.   <i>Marine Pollution Bulletin</i> 64: 445-448                 is this right? This is what’s on excel
+. DIFFERENT REGULATOR SYSTEMS
+Wang B, Papamichail D, Mueller S, Skiena S (2007) Two Proteins for the Price of One: The Design of Maximally Compressed Coding Sequences.  DOI: 10.1.1.174.6416
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Revision as of 18:12, 20 September 2012

Module 3: Degradation

Modelling