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| | === Run Tumble motion === | | === Run Tumble motion === |
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| - | {| {{table}}
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| - | | align="center" style="background:#f0f0f0;"|'''Attribute'''
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| - | | align="center" style="background:#f0f0f0;"|'''Value'''
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| - | | align="center" style="background:#f0f0f0;"|'''Strain'''
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| - | | align="center" style="background:#f0f0f0;"|'''Justification'''
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| - | | align="center" style="background:#f0f0f0;"|'''Reference'''
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| - | |-
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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 the attractant aspartate of around 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. 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. E. coli cells can adapt to Aspartate concentrations over ~5 orders of magnitude. Wild type E. coli cells can detect <10nM of Asp and respond to gradients upto 1mM of Asp. detect small changes in concentration ( 0.1%) via temporal comparisons ( 4 s) over a large range ( 10-8 to 10-3 M)||\"http://www.pdn.cam.ac.uk/groups/comp-cell/ConfSpread.html Overview of Mathematical approaches used to model bacterial chemotaxis I: The single cell. www.pdn.cam.ac.uk/groups/comp-cell/Biophysics.html Competitive and Cooperative Interactions in Receptor Signalling Complexes http://www.jbc.org/cgi/reprint/281/41/30512\"
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| - | | Temporal comparison of chemotactic gradient||4 seconds||N/A||past second has positive weighting, previous 3 seconds have negative weighting. E. coli compares the current concentration over the proceeding one second to the concentration observed over the previous 3 s. The memory thus lasts approximately 3 s. Bacterial cells evaluate changes in signal concentrations by a temporal mechanism, in particular by comparing their average number of bound receptors over the past 1 s with their average number during the previous 3 s. In models by Segall et al and Schnitzer, cells compare their average receptor occupancy between 4 and 1 s ago c 1–4 to the average receptor occupancy during the last second c 0–1. Henceforth we will refer to this difference as the biaser b= c 0–1 - c 1–4. If b>0, the cell reduces the tumbling rate from the ambient value by||Temporal comparisions in bacterial chemotaxis http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=387059&blobtype=pdf 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
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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 filaments 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 2.3 m and a diameter of 0.4 m) 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). This therefore suggests that the tumbling angle has bidirectionality??||Berg and Brown Nature 239, 500 - 504 (27 October 1972) http://www.nature.com/nature/journal/v239/n5374/pdf/239500a0.pdf Emonet Bioinformatics 2005 21(11):2714-2721 http://bioinformatics.oxfordjournals.org/cgi/reprint/21/11/2714 Darnton, N. C., Turner. L., Rojevsky. S., Berg. H. C., 2007 On Torque and tumbling in swimming Escherichia coli J. Bacteriol 189(5) 1756-1764. http://jb.asm.org/cgi/reprint/189/5/1756
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| - | | 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 deg rather than 90 deg.
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| - | |-
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| - | | 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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| - | |-
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| - | | Tumbling time||0.14±0.19s||AW405||Exponential distribution fitted (stated to be exponential by Berg and Brown) using only the mean tumble length (not STDEV).||Berg and Brown Nature 239, 500 - 504 (27 October 1972) http://www.nature.com/nature/journal/v239/n5374/pdf/239500a0.pdf
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| - | | Relationship between tumbling angle and time||||||||
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| - | |-
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| - | | Speed while Tumbling||0μm.s-1||AW405||Berg and Brown noted that AW405 slowed/stopped while tumbling.||Berg and Brown Nature 239, 500 - 504 (27 October 1972) http://www.nature.com/nature/journal/v239/n5374/pdf/239500a0.pdf
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| - | |-
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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 (Berg & Turner, 1990)||Berg and Brown Nature 239, 500 - 504 (27 October 1972) http://www.nature.com/nature/journal/v239/n5374/pdf/239500a0.pdf http://www.springerlink.com/content/d8u27q8430202342/ http://www.pdn.cam.ac.uk/groups/comp-cell/Biophysics.html
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| - | |-
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| - | | 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||Berg and Brown Nature 239, 500 - 504 (27 October 1972) http://www.nature.com/nature/journal/v239/n5374/pdf/239500a0.pdf
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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 Phenylalanine ( the recruitment chemoattractant) 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.||Berg and Brown Nature 239, 500 - 504 (27 October 1972) http://www.nature.com/nature/journal/v239/n5374/pdf/239500a0.pdf http://parts2.mit.edu/wiki/index.php/University_of_California_San_Francisco_2006
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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||Berg and Brown Nature 239, 500 - 504 (27 October 1972) http://www.nature.com/nature/journal/v239/n5374/pdf/239500a0.pdf
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| - | |-
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| - | |
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| - | |}
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| - |
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| - |
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| - | {| {{table}}
| |
| - | | align="center" style="background:#f0f0f0;"|'''Attribute'''
| |
| - | | align="center" style="background:#f0f0f0;"|'''Value'''
| |
| - | | align="center" style="background:#f0f0f0;"|'''Strain'''
| |
| - | | align="center" style="background:#f0f0f0;"|'''Justification'''
| |
| - | | align="center" style="background:#f0f0f0;"|'''Reference'''
| |
| - | |-
| |
| - | | 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 the attractant aspartate of around 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. 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. E. coli cells can adapt to Aspartate concentrations over ~5 orders of magnitude. Wild type E. coli cells can detect <10nM of Asp and respond to gradients upto 1mM of Asp. detect small changes in concentration ( 0.1%) via temporal comparisons ( 4 s) over a large range ( 10-8 to 10-3 M)||\"http://www.pdn.cam.ac.uk/groups/comp-cell/ConfSpread.html
| |
| - | Overview of Mathematical approaches used to model bacterial chemotaxis I: The single cell. Www.pdn.cam.ac.uk/groups/comp-cell/Biophysics.html
| |
| - | Competitive and Cooperative Interactions in Receptor
| |
| - | |-
| |
| - | | Signalling Complexes http://www.jbc.org/cgi/reprint/281/41/30512\"
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| - | |-
| |
| - | | Temporal comparison of chemotactic gradient||4 seconds||N/A||past second has positive weighting, previous 3 seconds have negative weighting. E. coli compares the current concentration over the proceeding one second to the concentration observed over the previous 3 s. The memory thus lasts approximately 3 s. Bacterial cells evaluate changes in signal concentrations by a temporal mechanism, in particular by comparing their average number of bound receptors over the past 1 s with their average number during the previous 3 s. In models by Segall et al and Schnitzer, cells compare their average receptor occupancy between 4 and 1 s ago c 1–4 to the average receptor occupancy during the last second c 0–1. Henceforth we will refer to this difference as the biaser b= c 0–1 - c 1–4. If b>0, the cell reduces the tumbling rate from the ambient value by||Temporal comparisions in bacterial chemotaxis http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=387059&blobtype=pdf 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
| |
| - | |-
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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 filaments 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 2.3 m and a diameter of 0.4 m) 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). This therefore suggests that the tumbling angle has bidirectionality??||Berg and Brown Nature 239, 500 - 504 (27 October 1972) http://www.nature.com/nature/journal/v239/n5374/pdf/239500a0.pdf Emonet Bioinformatics 2005 21(11):2714-2721 http://bioinformatics.oxfordjournals.org/cgi/reprint/21/11/2714 Darnton, N. C., Turner. L., Rojevsky. S., Berg. H. C., 2007 On Torque and tumbling in swimming Escherichia coli J. Bacteriol 189(5) 1756-1764. http://jb.asm.org/cgi/reprint/189/5/1756
| |
| - | |-
| |
| - | | 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 deg rather than 90 deg.
| |
| - | |-
| |
| - | |
| |
| - | |-
| |
| - | |
| |
| - | |-
| |
| - | | 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 time||0.14±0.19s||AW405||Exponential distribution fitted (stated to be exponential by Berg and Brown) using only the mean tumble length (not STDEV).||Berg and Brown Nature 239, 500 - 504 (27 October 1972) http://www.nature.com/nature/journal/v239/n5374/pdf/239500a0.pdf
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| - | |-
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| - | | Relationship between tumbling angle and time||||||||
| |
| - | |-
| |
| - | | Speed while Tumbling||0μm.s-1||AW405||Berg and Brown noted that AW405 slowed/stopped while tumbling.||Berg and Brown Nature 239, 500 - 504 (27 October 1972) http://www.nature.com/nature/journal/v239/n5374/pdf/239500a0.pdf
| |
| - | |-
| |
| - | | 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 (Berg & Turner, 1990)||Berg and Brown Nature 239, 500 - 504 (27 October 1972) http://www.nature.com/nature/journal/v239/n5374/pdf/239500a0.pdf http://www.springerlink.com/content/d8u27q8430202342/ http://www.pdn.cam.ac.uk/groups/comp-cell/Biophysics.html
| |
| - | |-
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| - | | 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||Berg and Brown Nature 239, 500 - 504 (27 October 1972) http://www.nature.com/nature/journal/v239/n5374/pdf/239500a0.pdf
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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 Phenylalanine ( the recruitment chemoattractant) 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.||Berg and Brown Nature 239, 500 - 504 (27 October 1972) http://www.nature.com/nature/journal/v239/n5374/pdf/239500a0.pdf http://parts2.mit.edu/wiki/index.php/University_of_California_San_Francisco_2006
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| - | |-
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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||Berg and Brown Nature 239, 500 - 504 (27 October 1972) http://www.nature.com/nature/journal/v239/n5374/pdf/239500a0.pdf
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| - | |-
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| - | |
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| - | |}
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| | === Swimming Machinery === | | === Swimming Machinery === |
"
