Difference between revisions of "Team:Technion HS Israel/Modelling/Parameters"

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Revision as of 18:13, 18 September 2015

Technion 2015 HS Team's Wiki

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Constant nameDescriptionValueunitsReference
c1aain,Ain → nothing rate, kcat1678.2min-11. Wang LH et al. (2004) Specificity and Enzyme Kinetics of the Quorum-quenching N-Acyl Homoserine Lactone Lactonase (AHL-Lactonase). J Biol Chem 279:4, 13645-13651.
c2Ain → nothing rate0.6min-1>http://www.nature.com/nature/journal/v434/n7037/full/nature03461.html
c2'AHL cell-external degradation4.81E-04min-1http://www.springerlink.com/content/v36128k24t558820/
c3Lin,Ain → [Lin+Ain] rate8.40E-03mol-1min-1http://goryachev.bio.ed.ac.uk/goryachev/sites/sbsweb2.bio.ed.ac.uk.goryachev/files/pdf/BioSys0206.pdf
c4LAin → Lin,Ain rate0.6min-1http://goryachev.bio.ed.ac.uk/goryachev/sites/sbsweb2.bio.ed.ac.uk.goryachev/files/pdf/BioSys0206.pdf
c5LAin,LAin → LA2in rate6.00E-03mol-1min-1http://goryachev.bio.ed.ac.uk/goryachev/sites/sbsweb2.bio.ed.ac.uk.goryachev/files/pdf/BioSys0206.pdf
c6LA2in → LAin,LAin rate0.6min-1Weber M., Buceta J., Dynamics of the quorum sensing switch: stochastic and non-stationary effects, BMC Systems Biology, 2013
c7a0,LA2in → a1 rate10MIN-1Weber M., Buceta J., Dynamics of the quorum sensing switch: stochastic and non-stationary effects, BMC Systems Biology, 2013
c8a1 → a0,LA2 rate2min-1Weber M., Buceta J., Dynamics of the quorum sensing switch: stochastic and non-stationary effects, BMC Systems Biology, 2013
c9TRLV → nothing rate0.0692min-1https://2011.igem.org/Team:ETH_Zurich/Modeling/Parameters
c10[b0+TRLVin] → b1 rate10min-1estimated
c11b1 → b0,TRLV rate2min-1estimated
c12ccdbin → nothing rate4.60E-03min-1https://2008.igem.org/Team:KULeuven/Model/Cell_Death#Parameters_2
c12'rfpin→ nothing rate  Michael Halter, Alex Tona, Kiran Bhadriraju, Anne L. Plant, John T. Elliott,Automated Live Cell Imaging of Green Fluorescent Protein Degradation in Individual Fibroblasts,Cytometry Part A, Volume 71A Issue 10, 2007
c13X produciong rate1min-1Depends on the enzyme in question (Remember that our system is generic), and changes the result only up to a constant. Therefore, when we study the behaviour of the system its value has no significance
c14Lin producing rate5.00E-09Mmin-1Basu S., Gerchman Y., Collins C.H., Arnold F.H., Weiss R., A synthetic multicellular system for programmed pattern formation, Nature, 2005
c15Lin → nothing rate0.0231min-1http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T2K-4H4T39N-1&_user=121739&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_version=1&_urlVersion=0&_userid=121739&md5=08a37acb41420b0e80d3cde6ead4a347
c16aain producing rate5.00E-09Mmin-1estimated
c17aain → nothing rate0.072min-1http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.126.9114&rep=rep1&type=pdf
c18km of aiia+A->nothing3.72E-18molhttps://2008.igem.org/Team:LCG-UNAM-Mexico/Parameters
v1TRLV producing without LA23.90E-24mol/minhttp://www.nature.com/nbt/journal/v22/n11/full/nbt1021.html
v2TRLV producing with LA23.90E-21mol/minhttp://www.nature.com/nbt/journal/v22/n11/full/nbt1021.html
u1ccdb producing without TRLV1.00E-24mol/minestimated
u2ccdb producing with TRLV1.00E-21mol/minestimated
u1'rfp producing without TRLV1.00E-24mol/minestimated
u2'rfp producing with TRLV1.00E-21mol/minestimated
ArbsARBS of TRLV producing1A.U.estimated
BrbsBRBS of ccdb producing1A.U.estimated
Nmax 22400000Unitless 
A0Concetration of AHL in the Tube1E(-2 ~ -9)MThe concentration range we tested in the lab.
N0 100000UnitlessEstimated
totanumber of Lux Promoter binding sites, which is equal to the number of plasmids in the cell600UnitlessOur origion of replication is pMB1 and it is a pUC derived. Copy number comes from: https://www.qiagen.com/il/resources/technologies/plasmid-resource-center/growth%20of%20bacterial%20cultures#Origins%20of%20replication%20and%20copy%20numbers%20of%20various%20plasmids%20and%20cosmids
totbnumber of Lux Promoter binding sites, which is equal to the number of plasmids in the cell600Unitlesshttps://www.qiagen.com/il/resources/technologies/plasmid-resource-center/growth%20of%20bacterial%20cultures#Origins%20of%20replication%20and%20copy%20numbers%20of%20various%20plasmids%20and%20cosmids
total time 18*60min 
Ddiffusion constants AHL24Min-1http://goryachev.bio.ed.ac.uk/goryachev/sites/sbsweb2.bio.ed.ac.uk.goryachev/files/pdf/BioSys0206.pdf
Vinvolume of one E.Coli2.00E-15dm3http://bionumbers.hms.harvard.edu/KeyNumbers.aspx
P1E-5 ~ 1E -51.00E-05Unitless 
T+Cell cycle time, with plasmid28UnitlessEstimated. This number takes into account the effect of the plasmid on the cycle time. http://textbookofbacteriology.net/growth_3.html
T-Cell cycle time, without plasmid23UnitlessEstimated. This number takes into account the effect of the antibiotics on the metabolism and thus on the cycle time. http://textbookofbacteriology.net/growth_3.html