Team:BCCS-Bristol/Modeling-Parameters

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* [[Team:BCCS-Bristol/Modeling-Parameters#Bacteria|'''Bacteria''']]
* [[Team:BCCS-Bristol/Modeling-Parameters#Bacteria|'''Bacteria''']]
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* [[Team:BCCS-Bristol/Modeling-Parameters#Run Tumble motion|'''Run Tumble Motion''']]
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* [[Team:BCCS-Bristol/Modeling-Parameters#Run_Tumble_Motion|'''Run Tumble motion''']]
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* [[Team:BCCS-Bristol/Modeling-Parameters#Swimming Machinery|'''Swimming Machinery''']]
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* [[Team:BCCS-Bristol/Modeling-Parameters#GRN_Modelling|'''GRN Modelling''']]
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* [[Team:BCCS-Bristol/Modeling-Parameters#Properties of the media|'''Properties of the Media''']]
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* [[Team:BCCS-Bristol/Modeling-Parameters#Intracellular modelling|'''Intracellular Modelling''']]
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=== Bacteria ===
=== Bacteria ===
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*Vary strain to strain.
*Vary strain to strain.
*Experimental methods
*Experimental methods
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Many papers give different and variable speeds (mainly for AW405 ~20&#956;ms<sup>-1</sup>). The speed itself is nearly uniform during the run. May need to measure experimentally, don't know under what conditions University of Alberta. Alberta value is higher than other values, but probably because MG1655 is a motile strain.
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Various papers give different speeds for E. coli (most papers provide information on AW405 with a speed of ~20&#956;ms<sup>-1</sup>). The speed itself is nearly uniform during the run. The wet lab may need to measure this experimentally as we are unaware of the conditions that the speed for MG1655 was obtained. Alberta's value is higher than other values, but this probably because MG1655 is a motile strain.
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||[http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi University of Alberta], [http://www3.interscience.wiley.com/cgi-bin/fulltext/71003069/PDFSTART A Method for Measuring Bacterial Chemotaxis Parameters in a Microcapillary]
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||[http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi University of Alberta] <br> [http://www3.interscience.wiley.com/cgi-bin/fulltext/71003069/PDFSTART A Method for Measuring Bacterial Chemotaxis Parameters in a Microcapillary]
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|}
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| align="center" width="30%" style="background:#f0f0f0;"|'''Reference'''
| align="center" width="30%" style="background:#f0f0f0;"|'''Reference'''
|-
|-
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| Aspartate concentration detected by E. coli||Over ~5 orders of magnitude, 10nM up to 10mM. Can detect changes of as little as ~0.1%||N/A||Most computer simulations of the chemotaxis pathway based on experimentally determined rates and concentrations predict a minimum detectable concentration of Aspartate at ~200 nM. However, experiments performed by Segall et al. in 1986, (in which E. coli cells are tethered to a coverslip were exposed to small quantities of chemoattractant delivered iontophoretically.) indicated that a change in receptor occupancy of as little as 1/600 could produce an detectable change in swimming behaviour. With a K<sub>d</sub> of 1 µM, this corresponds to a minimum detectable concentration of about 2 nM Aspartate. Wild type E. coli cells can detect <10nM of Asp and respond to Asp concentrations of upto 1mM,(responding to over ~5 orders of magnitude). E. coli detect small changes in concentration of 0.1% via temporal comparisons (4s) over a large range ( 10<sup>-8</sup> to 10<sup>-3</sup> M)||[http://www.jbc.org/cgi/reprint/281/41/30512 Competitive and Cooperative Interactions in Receptor Signalling Complexes]
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| Aspartate concentration detected by E. coli||Over ~5 orders of magnitude, 10nM up to 10mM. Can detect changes of as little as ~0.1%||N/A||E. coli detect small changes in concentration of 0.1% via temporal comparisons (4s) over a large range ( 10<sup>-8</sup> to 10<sup>-3</sup> ). Most computer simulations of chemotaxis are based on experimentally determined rates and concentrations. As a result they predict that the minimum detectable concentration of Aspartate is at ~200 nM. Experiments performed by Segall et al. in 1986, exposed tethered E. coli cells to iontophoretically delivered quantities of chemoattractant. These experiments indicated that a change in receptor occupancy of as little as 1/600 could produce an detectable change in swimming behaviour. With a K<sub>d</sub> of 1 µM, this corresponds to a minimum detectable concentration of about 2 nM Aspartate. Wild type E. coli cells can detect <10nM of Asp and respond to Asp concentrations of upto 1mM,(responding to over ~5 orders of magnitude). M)||[http://www.jbc.org/cgi/reprint/281/41/30512 Competitive and Cooperative Interactions in Receptor Signalling Complexes]
|-
|-
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| Temporal comparison of chemotactic gradient||4 seconds||N/A||The past second has positive weighting, the previous 3 seconds have negative weighting. E coli compares these concentrations (average occupancy of the receptors over the 4s). Models reflecting this have been developed by Segall et al and Schnitzer, cells compare their average receptor occupancy between 4 and 1 s ago  c<sub>1-4</sub> to the average receptor occupancy during the last second  c<sub>0-1</sub> . Hence b= c<sub>0-1</sub>  -  c<sub>1-4</sub> .  If b>0, the cell reduces the tumbling rate to T<sub>tumbling</sub> from the ambient value T<sub>0</sub> , 1s<sup>-1</sup> e.g. b>0 don't tumble. b< 0, tumble at a rate of 1s<sup>-1</sup> ||[http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=387059&blobtype=pdf Temporal comparisons in bacterial chemotaxis] [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TBN-4CVRC68-2&_user=121739&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_version=1&_urlVersion=0&_userid=121739&md5=470c7fd73fb9ebf4ca43342f365e221f#sec5.1 Quantitative analysis of signalling networks], [http://web.mit.edu/biophysics/papers/PNAS2003b.pdf Motility of Escherichia coli cells in clusters formed by chemotactic aggregation]
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| Temporal comparison of chemotactic gradient||4 seconds||N/A||The past second has positive weighting, the previous 3 seconds have negative weighting. E coli compares past and present concentrations by comparing the average occupancy of the receptors over the 4s. Models reflecting this system have been developed by Segall et al and Schnitzer, cells compare their average receptor occupancy between 4 and 1 s ago  c<sub>1-4</sub> to the average receptor occupancy during the last second  c<sub>0-1</sub> . Hence b= c<sub>0-1</sub>  -  c<sub>1-4</sub> .  If b>0, the cell reduces the tumbling rate to T<sub>tumbling</sub> from the ambient value T<sub>0</sub> , 1s<sup>-1</sup> e.g. b>0 don't tumble. b< 0, tumble at a rate of 1s<sup>-1</sup> ||[http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=387059&blobtype=pdf Temporal comparisons in bacterial chemotaxis]<br> [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TBN-4CVRC68-2&_user=121739&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_version=1&_urlVersion=0&_userid=121739&md5=470c7fd73fb9ebf4ca43342f365e221f#sec5.1 Quantitative analysis of signalling networks] <br> [http://web.mit.edu/biophysics/papers/PNAS2003b.pdf Motility of Escherichia coli cells in clusters formed by chemotactic aggregation]
|-
|-
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| Tumbling angle||Shape parameter 4 Scale parameter 18.32 Location parameter -4.6||AW405||Appears not to be dependant on the concentration gradient of chemoattractants/repellents. Nor is there correlation between the length of the run and the change in direction. Used a gamma distribution that fitted the data of Berg and Brown. Non-normality observed by several groups. Suggestions that non-normality was only due to the experimental methods used e.g. in the capillary tube. Tumbling can cause a change in direction when as few as one flagella moves out of the bundle. The flagella on transition from the bundle to release go from normal (a left-handed helix with a pitch of 2.3m and a diameter of 0.4m) to semi coiled (a right-handed helix with half the normal pitch but normal amplitude) and then curly (a right-handed helix with half the normal pitch and half the normal amplitude).||[http://www.nature.com/nature/journal/v239/n5374/pdf/239500a0.pdf Chemotaxis in E. coli anaylsed by three-dimensions],  [http://bioinformatics.oxfordjournals.org/cgi/reprint/21/11/2714 AgentCell: a digital single-cell assay for bacterial chemotaxis],  [http://jb.asm.org/cgi/reprint/189/5/1756 On Torque and tumbling in swimming Escherichia coli]
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| Tumbling angle||Shape parameter 4 Scale parameter 18.32 Location parameter -4.6||AW405||The tumble angle appears not to be dependant on the concentration gradient of chemoattractants/repellents. Nor is there correlation between the length of the run and the change in direction. The program uses a gamma distribution that fits the data collected by Berg and Brown. Several groups though, have observed that the tumble angle is not noramlly distributed but suggest that non-normality was only due to the experimental methods used e.g. in the capillary tube. Tumbling can cause a change in direction when as few as one flagella moves out of the bundle. ||[http://www.nature.com/nature/journal/v239/n5374/pdf/239500a0.pdf Chemotaxis in E. coli anaylsed by three-dimensions] <br> [http://bioinformatics.oxfordjournals.org/cgi/reprint/21/11/2714 AgentCell: a digital single-cell assay for bacterial chemotaxis] <br> [http://jb.asm.org/cgi/reprint/189/5/1756 On Torque and tumbling in swimming Escherichia coli]
|-
|-
| Tumble angle direction||Bidirectional||AW405||Personal communication with Howard Berg. 'The direction is random, more or less, but there is a slight forward bias. It varies from tumble to tumble.  The turn-angle distribution peaks at 68° rather than 90°. Tumbles turn out to be more complex than believed in 1972.  Motors switch independently, and a tumble can occur if one or just a few motors change their directions of rotation.  Tumbles are short, as judged by the tracking microscope, because they involve filament physics rather than motor physics:  a transformation in polymorphic form, following motor reversal, from normal to semi-coiled.  See  Darnton, N.C., Turner, L., Rojevsky, S. and Berg, H.C.  On torque and tumbling in swimming Escherichia coli, J. Bacteriol. 189, 1756-1764 (2007).'||
| Tumble angle direction||Bidirectional||AW405||Personal communication with Howard Berg. 'The direction is random, more or less, but there is a slight forward bias. It varies from tumble to tumble.  The turn-angle distribution peaks at 68° rather than 90°. Tumbles turn out to be more complex than believed in 1972.  Motors switch independently, and a tumble can occur if one or just a few motors change their directions of rotation.  Tumbles are short, as judged by the tracking microscope, because they involve filament physics rather than motor physics:  a transformation in polymorphic form, following motor reversal, from normal to semi-coiled.  See  Darnton, N.C., Turner, L., Rojevsky, S. and Berg, H.C.  On torque and tumbling in swimming Escherichia coli, J. Bacteriol. 189, 1756-1764 (2007).'||
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| Speed while Tumbling||0μm.s<sup>-1</sup>||AW405||Berg and Brown noted that AW405 slowed/stopped while tumbling.||[http://www.nature.com/nature/journal/v239/n5374/pdf/239500a0.pdf Chemotaxis in E. Coli anaylsed by three-dimensional tracking]   
| Speed while Tumbling||0μm.s<sup>-1</sup>||AW405||Berg and Brown noted that AW405 slowed/stopped while tumbling.||[http://www.nature.com/nature/journal/v239/n5374/pdf/239500a0.pdf Chemotaxis in E. Coli anaylsed by three-dimensional tracking]   
|-
|-
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| Drift during run||23±23°||AW405||Drift was observed. It is what would be expected from rotational diffusion. (at 2.7cp at 32ºC drift was 23±23°). Rotational Brownian motion cause the cell to veer off course, so that in between tumbles the probability density function f of the swimming direction e evolves according to the Fokker-Planck equation.  Drift velocity in steep gradient of attractant ~7 µm.s<sup>-1</sup>(Berg & Turner, 1990)||[http://www.nature.com/nature/journal/v239/n5374/pdf/239500a0.pdf Chemotaxis in E. Coli anaylsed by three-dimensional tracking]
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| Drift during run||23±23°||AW405||Drift was observed. It is what would be expected from rotational diffusion. (at 2.7cp at 32ºC drift was 23±23°). Rotational Brownian motion cause the cell to veer off course, so that in between tumbles the probability density function f of the swimming direction e evolves according to the Fokker-Planck equation.  Drift velocity in steep gradient of attractant ~7 µm.s<sup>-1</sup>(Berg & Turner, 1990. Note our model did not include the effects of drift||[http://www.nature.com/nature/journal/v239/n5374/pdf/239500a0.pdf Chemotaxis in E. Coli anaylsed by three-dimensional tracking] <br> [http://www.springerlink.com/content/d8u27q8430202342/ Persistence of direction increases the drift velocity of run and tumble chemotaxis] <br> [http://www.pdn.cam.ac.uk/groups/comp-cell/Biophysics.html Bray computer modelling]
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|-[http://www.springerlink.com/content/d8u27q8430202342/ Persistence of direction increases the drift velocity of run and tumble chemotaxis], [http://www.pdn.cam.ac.uk/groups/comp-cell/Biophysics.html Bray computer modelling]
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|-
|-
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| Thrust||Down an Asp gradient 0.41pN, Up an Asp gradient 0.4387pN ||AW405||Average thrust =0.41pN. In the Berg and Brown paper it states that the speed of the bacteria up an aspartate chemotactic gradient increases by 7%. Therefore in our model we shall use the following; thrust DOWN the Asp gradient =0.41pN, up the Asp gradient = 0.4387pN. ||[http://www.nature.com/nature/journal/v239/n5374/pdf/239500a0.pdf Chemotaxis in E. Coli anaylsed by three-dimensional tracking], [http://jb.asm.org/cgi/reprint/189/5/1756.pdf On Torque and Tumbling in Swimming E. coli]
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| Thrust||Down an Asp gradient 0.41pN, Up an Asp gradient 0.4387pN ||AW405||Average thrust =0.41pN. In the Berg and Brown paper it states that the speed of the bacteria up an aspartate chemotactic gradient increases by 7%. Therefore in our model we shall use the following; thrust DOWN the Asp gradient =0.41pN, up the Asp gradient = 0.4387pN. Data was obtained from 32 AW405s, a strain which has provided the majority of our previous parameters but is not as motile as MG1655. The value was obtained at 23ºC in viscosity 0.93 and 3.07 cP for motility buffer and motility buffer with 0.18% methylcellulose, respectively. The standard deviation is not used as the speed is fixed at 50µm.s<sup>-1</sup> . 0.57pN is the average thrust generated in strain HCB30 (a non tumbling strain). The thrust value was obtained when the imposed flow (U) U=0 at 23ºC. O.41pN was calculated using the resistance force theory treating the flagellar bundle as a single filament. The body was assumed to be prolate elipsoid using values roughly similar to ours, 2μm for length and 0.86μm for diameter. ||[http://www.nature.com/nature/journal/v239/n5374/pdf/239500a0.pdf Chemotaxis in E. Coli anaylsed by three-dimensional tracking] <br> [http://jb.asm.org/cgi/reprint/189/5/1756.pdf On Torque and Tumbling in Swimming E. coli]<br> [http://www.pnas.org/content/103/37/13712.full.pdf+html Swimming efficiency of bacterium E. coli.]
|-
|-
| Isotropic run lengths||0.86±1.18s||AW405||Exponential distribution fitted, this is only an approximate and does not fit exactly (see fig.4 Berg and Brown) The standard deviation is the standard deviation of the mean and has not been used in the exponential distribution||[http://www.nature.com/nature/journal/v239/n5374/pdf/239500a0.pdf Chemotaxis in E. Coli anaylsed by three-dimensional tracking]
| Isotropic run lengths||0.86±1.18s||AW405||Exponential distribution fitted, this is only an approximate and does not fit exactly (see fig.4 Berg and Brown) The standard deviation is the standard deviation of the mean and has not been used in the exponential distribution||[http://www.nature.com/nature/journal/v239/n5374/pdf/239500a0.pdf Chemotaxis in E. Coli anaylsed by three-dimensional tracking]
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|-
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| Run length UP Aspartate gradient||1.07±1.80s||AW405||Exponential distribution fitted, this is only an approximate and does not fit exactly (see fig.6, Berg and Brown). The standard deviation is the standard deviation of the mean and has not been used in the exponential distribution. If Phenylalanine is going to be used as the recruitment chemoattractant it utilises a mutant of the Tar receptor. The mutant Tar receptor has been shown to have comparable chemotactic response to the wild type and therefore the values used for the run lengths of aspartate can also be used for phenylalanine.||[http://www.nature.com/nature/journal/v239/n5374/pdf/239500a0.pdf Chemotaxis in E. Coli anaylsed by three-dimensional tracking], [http://parts2.mit.edu/wiki/index.php/University_of_California_San_Francisco_2006 UCSF wiki]
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| Run length UP Aspartate gradient||1.07±1.80s||AW405||Exponential distribution fitted, this is only an approximate and does not fit exactly (see fig.6, Berg and Brown). The standard deviation is the standard deviation of the mean and has not been used in the exponential distribution. ||[http://www.nature.com/nature/journal/v239/n5374/pdf/239500a0.pdf Chemotaxis in E. Coli anaylsed by three-dimensional tracking] <br> [http://parts2.mit.edu/wiki/index.php/University_of_California_San_Francisco_2006 UCSF wiki]
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| Run length DOWN Aspartate gradient||0.8±1.38s||AW405||Exponential distribution fitted, this is only an approximate and does not fit exactly (see fig.6, Berg and Brown) The standard deviation is the standard deviation of the mean and has not been used in the exponential distribution||[http://www.nature.com/nature/journal/v239/n5374/pdf/239500a0.pdf Chemotaxis in E. Coli anaylsed by three-dimensional tracking]
| Run length DOWN Aspartate gradient||0.8±1.38s||AW405||Exponential distribution fitted, this is only an approximate and does not fit exactly (see fig.6, Berg and Brown) The standard deviation is the standard deviation of the mean and has not been used in the exponential distribution||[http://www.nature.com/nature/journal/v239/n5374/pdf/239500a0.pdf Chemotaxis in E. Coli anaylsed by three-dimensional tracking]
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|}
 
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=== Swimming Machinery ===
 
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{| class="bccstable"
 
-
| align="center" width="10%" style="background:#f0f0f0;"|'''Attribute'''
 
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| align="center" width="10%" style="background:#f0f0f0;"|'''Value'''
 
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| align="center" width="10%" style="background:#f0f0f0;"|'''Strain'''
 
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| align="center" width="40%" style="background:#f0f0f0;"|'''Justification'''
 
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| align="center" width="30%" style="background:#f0f0f0;"|'''Reference'''
 
|-
|-
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| Average thrust ||0.41±0.23 pN||AW405||0.41±0.23 pN ( standard deviation for 32 bacteria) was obtained from strain AW405, a strain which has provided the majority of our previous parameters but is not MG1655 which is more motile. The value was obtained at 23ºC in viscosity 0.93 and 3.07 cP for motility buffer and motility buffer with 0.18% methylcellulose, respectively. The standard deviation is not used as the speed is fixed at 50µm.s<sup>-1</sup> . 0.57pN is the average thrust generated in strain HCB30 (a non tumbling strain). The thrust value was obtained when the imposed flow (U) U=0 at 23ºC. O.41pN was calculated using the resistance force theory treating the flagellar bundle as a single filament. The body was assumed to be prolate elipsoid using values roughly similar to ours, 2μm for length and 0.86μm for diameter.||[http://jb.asm.org/cgi/reprint/189/5/1756 On Torque and Tumbling in swimming Escherichia coli] [http://www.pnas.org/content/103/37/13712.full.pdf+html Swimming efficiency of bacterium E. coli.]
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| Viscosity||Viscosity of water is 1.002cP at 20°C||N/A||At present the medium being used by the lab is still be discussed. Currently though the medium most resembles water and therefore the water's viscosity value can be used. This allows us to assume that the medium is Newtonian (dilute aqueous medium that doesn’t contain long unbranched molecules such as methylcellulose or polyvinylpyrrolidone. Note that methlycellulose does not alter the run and tumble statistics, only bundle and motor rotation rates are affected by the addition of methylcellulose). If agar were to be used then the medium would be Non-Newtonian. Even though it would be Non- Newtonian John Hogan in passing said that we could assume it is Newtonian.||[http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.biochem.72.121801.161737 The rotary motor of bacterial flagella.], [http://jb.asm.org/cgi/reprint/189/5/1756.pdf On Torque and Tumbling in swimming Escherichia coli]
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|-
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| Motor Switching ||20% of motor switches fail to translate to changes in swimming behaviour||N/A||The change in states of the motor don't always translate to changes in swimming behaviour. It was assumed by the modelling paper that 20% fail to translate to a switch when swimming e.g. CCW->CW. Not CW->CCW||[http://bioinformatics.oxfordjournals.org/cgi/reprint/21/11/2714 AgentCell: a digital single-cell assay for bacterial chemotaxis]
 
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|}
|}
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===Properties of the Media===
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=== GRN Modelling ===
{| class="bccstable"
{| class="bccstable"
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| align="center" width="10%" style="background:#f0f0f0;"|'''Attribute'''
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| align="center" width="10%" style="background:#f0f0f0;"|'''Parameter'''
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| align="center" width="10%" style="background:#f0f0f0;"|'''Value'''
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| align="center" width="20%" style="background:#f0f0f0;"|'''Value'''
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| align="center" width="10%" style="background:#f0f0f0;"|'''Strain'''
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| align="center" width="40%" style="background:#f0f0f0;"|'''Description'''
-
| align="center" width="40%" style="background:#f0f0f0;"|'''Justification'''
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| align="center" width="30%" style="background:#f0f0f0;"|'''Reference'''
| align="center" width="30%" style="background:#f0f0f0;"|'''Reference'''
|-
|-
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| Viscosity||Viscosity of water is 1.002cP at 20°C||N/A||At present the medium being used by the lab is still be discussed. Currently though the medium most resembles water and therefore the water's viscosity value can be used. This allows us to assume that the medium is Newtonian (dilute aqueous medium that doesn’t contain long unbranched molecules such as methylcellulose or polyvinylpyrrolidone. Note that methlycellulose does not alter the run and tumble statistics, only bundle and motor rotation rates are affected by the addition of methylcellulose). If agar were to be used then the medium would be Non-Newtonian. Even though it would be Non- Newtonian John Hogan in passing said that we could assume it is Newtonian.||[http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.biochem.72.121801.161737 The rotary motor of bacterial flagella.],  [http://jb.asm.org/cgi/reprint/189/5/1756.pdf On Torque and Tumbling in swimming Escherichia coli]
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| C<sub>pMax<sub> ||Unknown (varied in the program)||Maximal CpxR protein concentration||||
|-
|-
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| Diffusion coefficient of Aspartate.||0.033 cm<sup>2</sup> .h<sup>-1</sup> ||N/A||0.033 cm<sup>2</sup> .h<sup>-1</sup> is for Aspartate at 22°C in 0.15% agar. Another value from the literature, 0.9 x10<sup>-5</sup>  cm<sup>2</sup> .s<sup>-1</sup> , is for aspartate at 35°C in 0.3% agar. To calculate diffusion coefficients the following formula can be used D=RT/6πNvr where: R is the gas constant, T is the absolute temperature (Kelvin), N is the number of molecules in a mole, 6 x10<sup>23</sup> , v is the viscosition of the solvent (e.g. 0.001 for water), r= radius of the particle. This formula could be used to calculate the diffusion coefficient at the viscosity used in our experiments.||[http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=1300146&blobtype=pdf Chemotactic Responses of Escherichia coli to Small Jumps of Photoreleased L-Aspartate] [http://www.pnas.org/content/96/20/11346.full.pdf\" Response tuning in bacterial chemotaxis]
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| k<sub>Cp<sub> ||0.075min<sup>-1<sup> <br> ESTIMATED ||Maximal transcription rate of pCpxR promoter || [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=11830644 Surface Sensing and Adhesion of Escherichia Coli controlled by the cpx-signalling pathway.]
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|-
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| Diffusion coefficient of Phenylalanine.||3.58 x 10<sup>-4</sup> cm<sup>2</sup> . min<sup>-1</sup> ||N/A||This value is for phenylalanine in aqueous phase at 25ºC. ||[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TGK-3W38497-D&_user=121739&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000010018&_version=1&_urlVersion=0&_userid=121739&md5=316e71596cb388d2a0cf0de7c15f84fe#fd16 Extraction and re-extraction of phenylalanine by cationic reversed micelles in hollow fibre contactors]
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| theta<sub>Cpx<sub> ||1 x 10<sup>-9</sup> M <br> ESTIMATED ||Threshold for pCpxR promoter Hill Function || [https://2008.igem.org/team:kuleuven iGEM 2008 KULeuven ]||
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|-
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| m<sub>Cpx<sub> ||1.0 || Co-operativity of pCpxR promoter Hill function ||||
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=== Intracellular Modelling ===
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|-
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| d<sub>Im<sub> || 3.6 x 10<sup>-1</sup>  min<sup>-1<sup> || Degradation rate of GFP mRNA ||[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      Systems Analysis of a quorum sensing network: Design constraints imposed by the functional requirements, network topology and kinetic constants.]
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{| class="bccstable"
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|-
-
| align="center" width="10%" style="background:#f0f0f0;"|'''Attribute'''
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| k<sub>Ip<sub> || 9.6 x 10<sup>-1</sup>  min<sup>-1<sup> || Rate of LuxI protein translation || [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      Systems Analysis of a quorum sensing network: Design constraints imposed by the functional requirements, network topology and kinetic constants.]
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| align="center" width="10%" style="background:#f0f0f0;"|'''Value'''
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|-
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| align="center" width="10%" style="background:#f0f0f0;"|'''Strain'''
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| d<sub>Ip<sub> || 1.67 x 10<sup>-2</sup>  min<sup>-1<sup> || Degradation rate of LuxI protein || [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      Systems Analysis of a quorum sensing network: Design constraints imposed by the functional requirements, network topology and kinetic constants.]
-
| align="center" width="40%" style="background:#f0f0f0;"|'''Justification'''
+
|-
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| align="center" width="30%" style="background:#f0f0f0;"|'''Reference'''
+
| d<sub>Gm<sub> || 1.65 x 10<sup>-3</sup> min<sup>-1<sup> || Degradation rate of GFP protein || [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T36-42HFN5W-11&_user=121739&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000010018&_version=1&_urlVersion=0&_userid=121739&md5=38be996fd7eb7dc4e71179e9d721b298 Efficient GFP mutations profoundly affect mRNA transcription and translation rates ]
 +
|-
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| k<sub>Gp<sub> || 2.4 x 10<sup>-1</sup> min<sup>-1<sup> || Rate of GFP protein translation || [http://www.springerlink.com/content/p14488p56p37n602/  Quantitative measurement of green fluorescent protein expression]
 +
|-
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| d<sub>Gp<sub> || 2.14 x 10<sup>-4</sup> min<sup>-1<sup> || Degradation rate of GFP protein || [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      Systems Analysis of a quorum sensing network: Design constraints imposed by the functional requirements, network topology and kinetic constants.]
 +
|-
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| A<sub>prod<sub> || 3.6 min<sup>-1<sup> || AHL production rate per LuxI enzyme ||[[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      Systems Analysis of a quorum sensing network: Design constraints imposed by the functional requirements, network topology and kinetic constants.]
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|-
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| d<sub>A<sub> || 1 x 10<sup>-2</sup> min<sup>-1<sup> || Degradation rate of AHL molecule ||[http://www.nature.com/nature/journal/v434/n7037/full/nature03461.html A synthetic multicellular system for programmed pattern formation ]
 +
|-
 +
| D<sub>A<sub> || 0.23s<sup>-1<sup> || Diffusion coefficient of AHL || [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      Systems Analysis of a quorum sensing network: Design constraints imposed by the functional requirements, network topology and kinetic constants.]
 +
|-
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| k<sub>Tp<sub> || 0.08min<sup>-1<sup> || Maximal Transcription rate of ptetR promoter || [https://2007.igem.org/Imperial/imperial/cell-free/characterisation iGEM 2007Imperial College London]
 +
|-
 +
| d<sub>Rm<sub> || 3.6 x 10<sup>-1</sup> min<sup>-1<sup> || Degradation rate of LuxR mRNA || [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      Systems Analysis of a quorum sensing network: Design constraints imposed by the functional requirements, network topology and kinetic constants.]
 +
|-
 +
| k<sub>Rp<sub> || 9.6 x 10<sup>-1</sup> min<sup>-1<sup> || Rate of Lux protein translation || [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      Systems Analysis of a quorum sensing network: Design constraints imposed by the functional requirements, network topology and kinetic constants.]
|-
|-
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| T||taxis receptor MW (kDa) = 58-60||RP437||Receptor (total) = 15000±1700, Tsr + Tar = 14000±1700, Trg = 440±70. Value was determined in RP437 strain in rich medium. Note that cellular amounts vary 10 fold but the stiochiometric ratios only vary 30%. Segall et al. 1986 assumed that there was 600 Tar receptors per cell (determined in RP437- a strain often used in chemotaxis studies)||[http://jb.asm.org/cgi/reprint/186/12/3687?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&author1=hazelbauer&searchid=1&FIRSTINDEX=0&resourcetype=HWCIT Cellular Stoichiometry of the Components of the Chemotaxis Signaling Complex], [http://www.pdn.cam.ac.uk/groups/comp-cell/Rates.html Bray Computer Modelling group], [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=387059&blobtype=pdf Temporal comparisons in bacterial chemotaxis ]
+
| d<sub>Rp<sub> || 2.31 x 10<sup>-2</sup> min<sup>-1<sup> || Degration rate of LuxR protein ||[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      Systems Analysis of a quorum sensing network: Design constraints imposed by the functional requirements, network topology and kinetic constants.]
|-
|-
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| R||CheR MW (kDa) = 33||RP437||140 ± 10. Value was determined in RP437 strain in rich medium.||[http://jb.asm.org/cgi/reprint/186/12/3687?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&author1=hazelbauer&searchid=1&FIRSTINDEX=0&resourcetype=HWCIT Cellular Stoichiometry of the Components of the Chemotaxis Signaling], [http://www.pdn.cam.ac.uk/groups/comp-cell/Rates.html Bray Computer Modelling Group]  
+
| k<sub>LuxR<sub> || 0.11 min<sup>-1<sup> || Maximal transcription rate of LuxR promoter || [https://2008.igem.org/team:kuleuven iGEM 2008 KULeuven ]
|-
|-
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| B||CheB MW (kDa) = 37||RP437||240 ± 10,  Value was determined in RP437 strain in rich medium.||[http://jb.asm.org/cgi/reprint/186/12/3687?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&author1=hazelbauer&searchid=1&FIRSTINDEX=0&resourcetype=HWCIT Cellular Stoichiometry of the Components of the Chemotaxis Signaling], [http://www.pdn.cam.ac.uk/groups/comp-cell/Rates.html Bray Computer Modelling Group]  
+
| theta<sub>LuxR<sub> || 1.5 x 10<sup>-9</sup> M || Threshold for LuxR pR promoter Hill function || [https://2008.igem.org/team:kuleuven iGEM 2008 KULeuven ]
|-
|-
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| W||CheW MW (kDa) = 18||RP437||6700 ± 890,  Value was determined in RP437 strain in rich medium.||[http://jb.asm.org/cgi/reprint/186/12/3687?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&author1=hazelbauer&searchid=1&FIRSTINDEX=0&resourcetype=HWCIT Cellular Stoichiometry of the Components of the Chemotaxis Signaling], [http://www.pdn.cam.ac.uk/groups/comp-cell/Rates.html Bray Computer Modelling Group]
+
| m<sub>LuxR<sub> || 1.6 || Co-operativity of LuxpR promoter Hill function || [https://2008.igem.org/team:kuleuven iGEM 2008 KULeuven ]
|-
|-
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| A||CheA MW (kDa) = 71||RP437||CheA (total) =6700±1100, CheA (long) 4500±940, CheA (short) = 2200±520. The “short” form of kinase CheA results from an alternative translational start site in E. coli approximately 90 codons interior to the start site that generates the “long” form, CheAL. CheZ does still bind CheAs protein. Modest differences in growth phase can have significant effects on cellular content of chemotaxis components, as previously documented by Wang and Matsumura for CheAL and CheAS ||[http://jb.asm.org/cgi/reprint/186/12/3687?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&author1=hazelbauer&searchid=1&FIRSTINDEX=0&resourcetype=HWCIT Cellular Stoichiometry of the Components of the Chemotaxis Signaling], [http://www.pdn.cam.ac.uk/groups/comp-cell/Rates.html Bray Computer Modelling Group]
+
| rho<sub>C<sub> || 0.5 micro M<sup>-3</sup> min<sup>-1</sup> || LuxR/AHL dimerisation ||[http://www.nature.com/nature/journal/v434/n7037/full/nature03461.html A synthetic multicellular system for programmed pattern formation ]
|-
|-
-
| Y||CheY MW (kDa) = 14||Ratio of CheY:CheZ =2.3:1 ||Values for AW405 6850±1300 molecules/cell (or 27.2±5.2µM) for RP437 2750±275 (or 9.1±0.9µM). Tethering and swimming assays suggest ~30% of CheY is phosphorylated (Alon et al., 1998). Values in the literature for the same and different strains differ greatly but the ratios of CheY:CheZ are very similar (2.3:1). As the swarming ability between AW405 and RP347 are very similar it shows that the ratio rather than the actual numerical value of molecules per cell is the deciding factor. The different values between papers for the same species can be attributed to differences in protein expression and cell volume (this is very dependant on how the cells are grown). The lack of regulated conditions for cell growth mean that any value used in modelling will not be accurate. As the majority of values for molecules per cell are for RP347 use values for RP437|| [http://jb.asm.org/cgi/reprint/180/19/5123 CheZ Has No Effect on Flagellar Motors Activated by CheY13DK106YW ], [http://www.pdn.cam.ac.uk/groups/comp-cell/Rates.html Bray Computer Modelling Group], [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1170757 Response regulator output in bacterial chemotaxis]
+
| d<sub>C<sub> || 0.0231 min<sup>-1<sup> || Degradation rate of mCherry  mRNA ||[http://www.nature.com/nature/journal/v434/n7037/full/nature03461.html A synthetic multicellular system for programmed pattern formation ]
|-
|-
-
| Z||CheZ MW (kDa) = 24||24||3050 ±580 (12.1±2.3µM) (AW405), 1170 ± 170 (3.9±0.5µM) (RP437) the different values between papers for the same species can be attributed to differences in protein expression and cell volume (this is very dependant on how the cells are grown). The lack of regulated conditions for cell growth mean that any value used in modelling will not be accurate. As the majority of values for molecules per cell are for RP347 use values for RP437||[http://jb.asm.org/cgi/reprint/180/19/5123 CheZ Has No Effect on Flagellar Motors Activated by CheY13DK106YW ]
+
| d<sub>Mm<sub> || 1.65 x 10<sup>-3</sup> min<sup>-1<sup> || Degradation rate of LuxR/AHL complex ||Due to difficulty in finding mCherry modelling parameters, exsisting GFP parameters have been used. ||
|-
|-
-
| M||FliM MW (kDa) = 38||38||37±13 copies per flagella. Determined in salmonella but the value has be used by other groups when referring to E. coli||[http://jb.asm.org/cgi/content/abstract/178/1/258?ijkey=b6d6fd8a1c8564ac118449c4acdff535727e46d6&keytype2=tf_ipsecsha FliG and FliM distribution in the Salmonella typhimurium cell and flagellar basal bodies]
+
| k<sub>Mp<sub> || 2.4 x 10<sup>-1</sup> min<sup>-1<sup> || Rate of mCherry protein translation || Due to difficulty in finding mCherry modelling parameters, exsisting GFP parameters have been used. ||
|-
|-
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| a||aspartate||N/A||N/A||
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| d<sub>Mp<sub> || 2.14 x 10<sup>-4</sup> min<sup>-1<sup> || Degradation rate of mCherry protein || Due to difficulty in finding mCherry modelling parameters, exsisting GFP parameters have been used. ||
|}
|}

Latest revision as of 15:38, 26 September 2008

Home The Team The Project Submitted Parts Modelling Wet Lab Calendar Miscellaneous


Modelling Parameters

Bacteria

Attribute Value Strain Justification Reference
Length2μmMG1655Values come from the University of Alberta’s datasheet on MG1655, produced to aid modelling. There is variability in size between strains - for instance, AW405 length varies between 1.5±0.2μm. But University of Alberta datasheet is specifically for MG1655.[http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi University of Alberta]
Diameter0.8μmMG1655[http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi University of Alberta]
ShapeCircle r =0.714μmMG1655Actually rod-like. A circle with r= 0.714μm will have equivalent surface area to rod-like.[http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi University of Alberta]
Mass1.02x10-13gMG1655Given 1x10-12g for cell wet weight. Dividing this by gravity (=9.81) gives mass. [http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi University of Alberta]
Swimming Speed50μms-1MG1655University Alberta's datasheet gives 50μms-1. However, Swimming speed is affected by:
  • Viscosity (as viscosity increases the speed increases to some maximum, then decreases as the viscosity increases further. E.coli (strain:KL227 of length: 1.0μm and diameter: 0.5μm) maximum speed occurs at viscosity 8cp.
  • Temperature
  • Culture medium
  • Vary strain to strain.
  • Experimental methods

Various papers give different speeds for E. coli (most papers provide information on AW405 with a speed of ~20μms-1). The speed itself is nearly uniform during the run. The wet lab may need to measure this experimentally as we are unaware of the conditions that the speed for MG1655 was obtained. Alberta's value is higher than other values, but this probably because MG1655 is a motile strain.

[http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi University of Alberta]
[http://www3.interscience.wiley.com/cgi-bin/fulltext/71003069/PDFSTART A Method for Measuring Bacterial Chemotaxis Parameters in a Microcapillary]

Run Tumble Motion

Attribute Value Strain Justification Reference
Aspartate concentration detected by E. coliOver ~5 orders of magnitude, 10nM up to 10mM. Can detect changes of as little as ~0.1%N/AE. coli detect small changes in concentration of 0.1% via temporal comparisons (4s) over a large range ( 10-8 to 10-3 ). Most computer simulations of chemotaxis are based on experimentally determined rates and concentrations. As a result they predict that the minimum detectable concentration of Aspartate is at ~200 nM. Experiments performed by Segall et al. in 1986, exposed tethered E. coli cells to iontophoretically delivered quantities of chemoattractant. These experiments indicated that a change in receptor occupancy of as little as 1/600 could produce an detectable change in swimming behaviour. With a Kd of 1 µM, this corresponds to a minimum detectable concentration of about 2 nM Aspartate. Wild type E. coli cells can detect <10nM of Asp and respond to Asp concentrations of upto 1mM,(responding to over ~5 orders of magnitude). M)[http://www.jbc.org/cgi/reprint/281/41/30512 Competitive and Cooperative Interactions in Receptor Signalling Complexes]
Temporal comparison of chemotactic gradient4 secondsN/AThe past second has positive weighting, the previous 3 seconds have negative weighting. E coli compares past and present concentrations by comparing the average occupancy of the receptors over the 4s. Models reflecting this system have been developed by Segall et al and Schnitzer, cells compare their average receptor occupancy between 4 and 1 s ago c1-4 to the average receptor occupancy during the last second c0-1 . Hence b= c0-1 - c1-4 . If b>0, the cell reduces the tumbling rate to Ttumbling from the ambient value T0 , 1s-1 e.g. b>0 don't tumble. b< 0, tumble at a rate of 1s-1 [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=387059&blobtype=pdf Temporal comparisons in bacterial chemotaxis]
[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TBN-4CVRC68-2&_user=121739&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_version=1&_urlVersion=0&_userid=121739&md5=470c7fd73fb9ebf4ca43342f365e221f#sec5.1 Quantitative analysis of signalling networks]
[http://web.mit.edu/biophysics/papers/PNAS2003b.pdf Motility of Escherichia coli cells in clusters formed by chemotactic aggregation]
Tumbling angleShape parameter 4 Scale parameter 18.32 Location parameter -4.6AW405The tumble angle appears not to be dependant on the concentration gradient of chemoattractants/repellents. Nor is there correlation between the length of the run and the change in direction. The program uses a gamma distribution that fits the data collected by Berg and Brown. Several groups though, have observed that the tumble angle is not noramlly distributed but suggest that non-normality was only due to the experimental methods used e.g. in the capillary tube. Tumbling can cause a change in direction when as few as one flagella moves out of the bundle. [http://www.nature.com/nature/journal/v239/n5374/pdf/239500a0.pdf Chemotaxis in E. coli anaylsed by three-dimensions]
[http://bioinformatics.oxfordjournals.org/cgi/reprint/21/11/2714 AgentCell: a digital single-cell assay for bacterial chemotaxis]
[http://jb.asm.org/cgi/reprint/189/5/1756 On Torque and tumbling in swimming Escherichia coli]
Tumble angle directionBidirectionalAW405Personal communication with Howard Berg. 'The direction is random, more or less, but there is a slight forward bias. It varies from tumble to tumble. The turn-angle distribution peaks at 68° rather than 90°. Tumbles turn out to be more complex than believed in 1972. Motors switch independently, and a tumble can occur if one or just a few motors change their directions of rotation. Tumbles are short, as judged by the tracking microscope, because they involve filament physics rather than motor physics: a transformation in polymorphic form, following motor reversal, from normal to semi-coiled. See Darnton, N.C., Turner, L., Rojevsky, S. and Berg, H.C. On torque and tumbling in swimming Escherichia coli, J. Bacteriol. 189, 1756-1764 (2007).'
Tumbling time0.14±0.19sAW405Exponential distribution fitted (stated to be exponential by Berg and Brown) using only the mean tumble length (not STDEV).[http://www.nature.com/nature/journal/v239/n5374/pdf/239500a0.pdf Chemotaxis in E. Coli anaylsed by three-dimensional tracking]
Relationship between tumbling angle and time
Speed while Tumbling0μm.s-1AW405Berg and Brown noted that AW405 slowed/stopped while tumbling.[http://www.nature.com/nature/journal/v239/n5374/pdf/239500a0.pdf Chemotaxis in E. Coli anaylsed by three-dimensional tracking]
Drift during run23±23°AW405Drift was observed. It is what would be expected from rotational diffusion. (at 2.7cp at 32ºC drift was 23±23°). Rotational Brownian motion cause the cell to veer off course, so that in between tumbles the probability density function f of the swimming direction e evolves according to the Fokker-Planck equation. Drift velocity in steep gradient of attractant ~7 µm.s-1(Berg & Turner, 1990. Note our model did not include the effects of drift[http://www.nature.com/nature/journal/v239/n5374/pdf/239500a0.pdf Chemotaxis in E. Coli anaylsed by three-dimensional tracking]
[http://www.springerlink.com/content/d8u27q8430202342/ Persistence of direction increases the drift velocity of run and tumble chemotaxis]
[http://www.pdn.cam.ac.uk/groups/comp-cell/Biophysics.html Bray computer modelling]
ThrustDown an Asp gradient 0.41pN, Up an Asp gradient 0.4387pN AW405Average thrust =0.41pN. In the Berg and Brown paper it states that the speed of the bacteria up an aspartate chemotactic gradient increases by 7%. Therefore in our model we shall use the following; thrust DOWN the Asp gradient =0.41pN, up the Asp gradient = 0.4387pN. Data was obtained from 32 AW405s, a strain which has provided the majority of our previous parameters but is not as motile as MG1655. The value was obtained at 23ºC in viscosity 0.93 and 3.07 cP for motility buffer and motility buffer with 0.18% methylcellulose, respectively. The standard deviation is not used as the speed is fixed at 50µm.s-1 . 0.57pN is the average thrust generated in strain HCB30 (a non tumbling strain). The thrust value was obtained when the imposed flow (U) U=0 at 23ºC. O.41pN was calculated using the resistance force theory treating the flagellar bundle as a single filament. The body was assumed to be prolate elipsoid using values roughly similar to ours, 2μm for length and 0.86μm for diameter. [http://www.nature.com/nature/journal/v239/n5374/pdf/239500a0.pdf Chemotaxis in E. Coli anaylsed by three-dimensional tracking]
[http://jb.asm.org/cgi/reprint/189/5/1756.pdf On Torque and Tumbling in Swimming E. coli]
[http://www.pnas.org/content/103/37/13712.full.pdf+html Swimming efficiency of bacterium E. coli.]
Isotropic run lengths0.86±1.18sAW405Exponential distribution fitted, this is only an approximate and does not fit exactly (see fig.4 Berg and Brown) The standard deviation is the standard deviation of the mean and has not been used in the exponential distribution[http://www.nature.com/nature/journal/v239/n5374/pdf/239500a0.pdf Chemotaxis in E. Coli anaylsed by three-dimensional tracking]
Run length UP Aspartate gradient1.07±1.80sAW405Exponential distribution fitted, this is only an approximate and does not fit exactly (see fig.6, Berg and Brown). The standard deviation is the standard deviation of the mean and has not been used in the exponential distribution. [http://www.nature.com/nature/journal/v239/n5374/pdf/239500a0.pdf Chemotaxis in E. Coli anaylsed by three-dimensional tracking]
[http://parts2.mit.edu/wiki/index.php/University_of_California_San_Francisco_2006 UCSF wiki]
Run length DOWN Aspartate gradient0.8±1.38sAW405Exponential distribution fitted, this is only an approximate and does not fit exactly (see fig.6, Berg and Brown) The standard deviation is the standard deviation of the mean and has not been used in the exponential distribution[http://www.nature.com/nature/journal/v239/n5374/pdf/239500a0.pdf Chemotaxis in E. Coli anaylsed by three-dimensional tracking]
ViscosityViscosity of water is 1.002cP at 20°CN/AAt present the medium being used by the lab is still be discussed. Currently though the medium most resembles water and therefore the water's viscosity value can be used. This allows us to assume that the medium is Newtonian (dilute aqueous medium that doesn’t contain long unbranched molecules such as methylcellulose or polyvinylpyrrolidone. Note that methlycellulose does not alter the run and tumble statistics, only bundle and motor rotation rates are affected by the addition of methylcellulose). If agar were to be used then the medium would be Non-Newtonian. Even though it would be Non- Newtonian John Hogan in passing said that we could assume it is Newtonian.[http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.biochem.72.121801.161737 The rotary motor of bacterial flagella.], [http://jb.asm.org/cgi/reprint/189/5/1756.pdf On Torque and Tumbling in swimming Escherichia coli]

GRN Modelling

Parameter Value Description Reference
CpMax Unknown (varied in the program)Maximal CpxR protein concentration
kCp 0.075min-1
ESTIMATED 		Maximal transcription rate of pCpxR promoter [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=11830644 Surface Sensing and Adhesion of Escherichia Coli controlled by the cpx-signalling pathway.]
thetaCpx 1 x 10-9 M
ESTIMATED 		Threshold for pCpxR promoter Hill Function iGEM 2008 KULeuven
mCpx 1.0 Co-operativity of pCpxR promoter Hill function
dIm 3.6 x 10-1 min-1 Degradation rate of GFP mRNA [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 Systems Analysis of a quorum sensing network: Design constraints imposed by the functional requirements, network topology and kinetic constants.]
kIp 9.6 x 10-1 min-1 Rate of LuxI protein translation [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 Systems Analysis of a quorum sensing network: Design constraints imposed by the functional requirements, network topology and kinetic constants.]
dIp 1.67 x 10-2 min-1 Degradation rate of LuxI protein [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 Systems Analysis of a quorum sensing network: Design constraints imposed by the functional requirements, network topology and kinetic constants.]
dGm 1.65 x 10-3 min-1 Degradation rate of GFP protein [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T36-42HFN5W-11&_user=121739&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000010018&_version=1&_urlVersion=0&_userid=121739&md5=38be996fd7eb7dc4e71179e9d721b298 Efficient GFP mutations profoundly affect mRNA transcription and translation rates ]
kGp 2.4 x 10-1 min-1 Rate of GFP protein translation [http://www.springerlink.com/content/p14488p56p37n602/ Quantitative measurement of green fluorescent protein expression]
dGp 2.14 x 10-4 min-1 Degradation rate of GFP protein [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 Systems Analysis of a quorum sensing network: Design constraints imposed by the functional requirements, network topology and kinetic constants.]
Aprod 3.6 min-1 AHL production rate per LuxI enzyme [[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 Systems Analysis of a quorum sensing network: Design constraints imposed by the functional requirements, network topology and kinetic constants.]
dA 1 x 10-2 min-1 Degradation rate of AHL molecule [http://www.nature.com/nature/journal/v434/n7037/full/nature03461.html A synthetic multicellular system for programmed pattern formation ]
DA 0.23s-1 Diffusion coefficient of AHL [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 Systems Analysis of a quorum sensing network: Design constraints imposed by the functional requirements, network topology and kinetic constants.]
kTp 0.08min-1 Maximal Transcription rate of ptetR promoter iGEM 2007Imperial College London
dRm 3.6 x 10-1 min-1 Degradation rate of LuxR mRNA [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 Systems Analysis of a quorum sensing network: Design constraints imposed by the functional requirements, network topology and kinetic constants.]
kRp 9.6 x 10-1 min-1 Rate of Lux protein translation [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 Systems Analysis of a quorum sensing network: Design constraints imposed by the functional requirements, network topology and kinetic constants.]
dRp 2.31 x 10-2 min-1 Degration rate of LuxR protein [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 Systems Analysis of a quorum sensing network: Design constraints imposed by the functional requirements, network topology and kinetic constants.]
kLuxR 0.11 min-1 Maximal transcription rate of LuxR promoter iGEM 2008 KULeuven
thetaLuxR 1.5 x 10-9 M Threshold for LuxR pR promoter Hill function iGEM 2008 KULeuven
mLuxR 1.6 Co-operativity of LuxpR promoter Hill function iGEM 2008 KULeuven
rhoC 0.5 micro M-3 min-1 LuxR/AHL dimerisation [http://www.nature.com/nature/journal/v434/n7037/full/nature03461.html A synthetic multicellular system for programmed pattern formation ]
dC 0.0231 min-1 Degradation rate of mCherry mRNA [http://www.nature.com/nature/journal/v434/n7037/full/nature03461.html A synthetic multicellular system for programmed pattern formation ]
dMm 1.65 x 10-3 min-1 Degradation rate of LuxR/AHL complex Due to difficulty in finding mCherry modelling parameters, exsisting GFP parameters have been used.
kMp 2.4 x 10-1 min-1 Rate of mCherry protein translation Due to difficulty in finding mCherry modelling parameters, exsisting GFP parameters have been used.
dMp 2.14 x 10-4 min-1 Degradation rate of mCherry protein Due to difficulty in finding mCherry modelling parameters, exsisting GFP parameters have been used.

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