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

Revision as of 06:57, 18 September 2015

Technion 2015 HS Team's Wiki

Constant name	Description	Value	units	Reference
c1	aa_in,A_in → nothing rate, k_cat	1678.2	min^-1	1. 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.
c2	A_in → nothing rate	0.6	min^-1	>http://www.nature.com/nature/journal/v434/n7037/full/nature03461.html
c2'	AHL cell-external degradation	4.81E-04	min^-1	http://www.springerlink.com/content/v36128k24t558820/
c3	L_in,A_in → [L_in+A_in] rate	8.40E-03	mol^-1min^-1	http://goryachev.bio.ed.ac.uk/goryachev/sites/sbsweb2.bio.ed.ac.uk.goryachev/files/pdf/BioSys0206.pdf
c4	LA_in → L_in,A_in rate	0.6	min^-1	http://goryachev.bio.ed.ac.uk/goryachev/sites/sbsweb2.bio.ed.ac.uk.goryachev/files/pdf/BioSys0206.pdf
c5	LA_in,LA_in → LA2_in rate	6.00E-03	mol^-1min^-1	http://goryachev.bio.ed.ac.uk/goryachev/sites/sbsweb2.bio.ed.ac.uk.goryachev/files/pdf/BioSys0206.pdf
c6	LA2_in → LA_in,LA_in rate	0.6	min^-1	Weber M., Buceta J., Dynamics of the quorum sensing switch: stochastic and non-stationary effects, BMC Systems Biology, 2013
c7	a0,LA2_in → a1 rate	10	MIN^-1	Weber M., Buceta J., Dynamics of the quorum sensing switch: stochastic and non-stationary effects, BMC Systems Biology, 2013
c8	a1 → a0,LA2 rate	2	min^-1	Weber M., Buceta J., Dynamics of the quorum sensing switch: stochastic and non-stationary effects, BMC Systems Biology, 2013
c9	TRLV → nothing rate	0.0692	min^-1	https://2011.igem.org/Team:ETH_Zurich/Modeling/Parameters
c10	[b0+TRLV_in] → b1 rate	10	min^-1	estimated
c11	b1 → b0,TRLV rate	2	min^-1	estimated
c12	ccdb_in → nothing rate	4.60E-03	min^-1	https://2008.igem.org/Team:KULeuven/Model/Cell_Death#Parameters_2
c12'	rfp_in→ 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
c13	X produciong rate	1	min^-1	Depends 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
c14	L_in producing rate	5.00E-09	Mmin^-1	Basu S., Gerchman Y., Collins C.H., Arnold F.H., Weiss R., A synthetic multicellular system for programmed pattern formation, Nature, 2005
c15	L_in → nothing rate	0.0231	min^-1	http://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
c16	aa_in producing rate	5.00E-09	Mmin^-1	estimated
c17	aa_in → nothing rate	0.072	min^-1	http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.126.9114&rep=rep1&type=pdf
c18	k_m of aiia+A->nothing	3.72E-18	mol	https://2008.igem.org/Team:LCG-UNAM-Mexico/Parameters
v1	TRLV producing without LA2	3.90E-24	mol/min	http://www.nature.com/nbt/journal/v22/n11/full/nbt1021.html
v2	TRLV producing with LA2	3.90E-21	mol/min	http://www.nature.com/nbt/journal/v22/n11/full/nbt1021.html
u1	ccdb producing without TRLV	1.00E-24	mol/min	estimated
u2	ccdb producing with TRLV	1.00E-21	mol/min	estimated
u1'	rfp producing without TRLV	1.00E-24	mol/min	estimated
u2'	rfp producing with TRLV	1.00E-21	mol/min	estimated
Arbs	A_RBS of TRLV producing	1	A.U.	estimated
Brbs	B_RBS of ccdb producing	1	A.U.	estimated
Nmax		22400000	Unitless
A₀	Concetration of AHL in the Tube	1E(-2 ~ -9)	M	The concentration range we tested in the lab.
N₀		100000	Unitless	Estimated
tot_a	number of Lux Promoter binding sites, which is equal to the number of plasmids in the cell	600	Unitless	Our 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
tot_b	number of Lux Promoter binding sites, which is equal to the number of plasmids in the cell	600	Unitless	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
total time		18*60	min
D	diffusion constants AHL	24	Min^-1	http://goryachev.bio.ed.ac.uk/goryachev/sites/sbsweb2.bio.ed.ac.uk.goryachev/files/pdf/BioSys0206.pdf
V_in	volume of one E.Coli	2.00E-15	dm³	http://bionumbers.hms.harvard.edu/KeyNumbers.aspx
P	1E-5 ~ 1E -5	1.00E-05	Unitless
T+	Cell cycle time, with plasmid	28	Unitless	Estimated. 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 plasmid	23	Unitless	Estimated. 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

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 </style><table class="tableizer-table">
-<tr class="tableizer-firstrow"><th>Constant name</th><th>Description</th><th>Value</th><th>units</th><th>Reference</th></tr>
+<tr class="tableizer-firstrow"><th>Constant name</th><th>Description</th><th>Value</th><th>units</th><th style="width:40%">Reference</th></tr>
   <tr><td>c1</td><td>aa<sub>in</sub>,A<sub>in</sub> &#8594; nothing rate, k<sub>cat</sub></td><td>1678.2</td><td>min<sup>-1</sup></td><td>1. 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.</td></tr>
   <tr><td>c2</td><td>A<sub>in</sub> &#8594; nothing rate</td><td>0.6</td><td>min<sup>-1</sup></td><td>><a href="http://www.nature.com/nature/journal/v434/n7037/full/nature03461.html">http://www.nature.com/nature/journal/v434/n7037/full/nature03461.html</a></td></tr>