osmotic up/down shock
DESCRIPTION
Osmotic up/down shock. A summary of Allison’s data 9/3/10. Upshift of Br strain. Histograms of width and length for individual time points to follow with information about average width and number of cells Take home: 1 hour not enough, 2 hours enough. . Br Ala-Pro steady-state. - PowerPoint PPT PresentationTRANSCRIPT
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Osmotic up/down shock
A summary of Allison’s data9/3/10
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Upshift of Br strain
Histograms of width and length for individual time points to follow with information about
average width and number of cells
Take home: 1 hour not enough, 2 hours enough.
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Br Ala-Pro steady-state
570 cells with average width 0.71 microns
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Upshift for 1,2,3,4 hours
Looks like shift takes place between 1hr and 2hrs
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Br upshift 1 hour
447 cells with average width 0.7 microns
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Br upshift 2 hour
622 cells with average width 0.85 microns (fixed this run tonight 9/8/10)
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Br upshift 3 hour
170 cells with average width 0.89 microns
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Br upshift 4 hour
335 cells with average width 0.9 microns
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Downshift of Br strain
Histograms of width and length for individual time points to follow
Take home: 4 hours may or may not be enough.
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Br Glu-Caa steady-state
359 cells with average width 1.05 microns
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Downshift for 2,4 hours
Looks like shift still taking place after 4 hours
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Br downshift 2 hour
1687 cells with average width 0.94 microns
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Br downshift 4 hour
1247 cells with average width 0.86 microns
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Upshift of MG1655 strain
Histograms of width and length for individual time points to follow
Take home: Looks like only small increase in width after 2 hours (slower adjustment than in Br strain).
I’m going to check the analysis to make sure.
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MG1655 Ala-Pro steady-state
323 cells with average width 0.68 microns
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Upshift for 1,2 hours
Looks like shifting very slowly
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MG1655 upshift 1 hour
605 cells with average width 0.71 microns
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MG1655 upshift 2 hour
779 cells with average width 0.7 microns
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Downshift of MG1655 strain
Histograms of width and length for individual time points to follow
Take home: Looks same as Br strain. Needs at least 4 hours.
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MG1655 Glu-Caa steady-state
445 cells with average width 0.97 microns
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Downshift for 2,4 hours
Same as Br, looks like shift is not complete after 4 hours
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MG1655 downshift 2 hours
1298 cells with average width 0.8 microns
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MG1655 downshift 4 hours
1106 cells with average width 0.74 microns
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SummaryStrain # of cells Average width (microns)
Br Ala-Pro steady-state 570 0.71
Br upshift 1 hour 447 0.70
Br upshift 2 hours 622 0.85
Br upshift 3 hours 170 0.89
Br upshift 4 hours 335 0.90
Br Glu-Caa steady-state 359 1.05
Br downshift 2 hours 1687 0.94
Br downshift 4 hours 1247 0.86
MG1655 Ala-Pro steady-state 323 0.68
MG1655 upshift 1 hour 605 0.71
MG1655 upshift 2 hours 779 0.70
MG1655 Glu-Caa steady-state 445 0.97
MG1655 downshift 2 hours 1298 0.80
MG1655 downshift 4 hours 1106 0.74
• Colors are set to match up the same experiments between Br and MG1655 cells• Note the good agreement between the steady-state sizes of the two strains
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Splitting between ceph-treated and non-treated cells…
Take home message: The widths vary systematically, although the ceph-
treated cells are systematically thinner. Incidentally, we’ve seen this
in our own experiments…
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Summary (ceph/non-ceph)Strain # of cells Average width (microns)
Br upshift 1 hour (no ceph) 239 0.73+-0.05Br upshift 1 hour (ceph( 208 0.67+-0.04Br upshift 2 hours (no ceph) 552 0.85+-0.05Br upshift 2 hours (ceph) 70 0.83+-0.04Br upshift 3 hours (no ceph) 170 0.89+-0.04Br upshift 3 hours (ceph) 13 0.96+-0.1Br upshift 4 hours (no ceph) 335 0.90+-0.1Br upshift 4 hours (ceph) 0 N/ABr downshift 2 hours (no ceph) 1028 0.97+-0.05Br downshift 2 hours (ceph) 659 0.9+-0.07Br downshift 4 hours (no ceph) 1067 0.75+-0.07Br downshift 4 hours (ceph) 180 0.88+-0.09MG1655 upshift 1 hour (no ceph) 310 0.73+-0.04MG1655 upshift 1 hour (ceph) 295 0.70+-0.11MG1655 upshift 2 hours (no ceph) 489 0.69+-0.04MG1655 upshift 2 hours (ceph) 290 0.71+-0.03MG1655 downshift 2 hours (no ceph) 766 0.82+-0.07MG1655 downshift 2 hours (ceph) 532 0.78+-0.08MG1655 downshift 4 hours (no ceph) 740 0.75+-0.06MG1655 downshift 4 hours (ceph) 366 0.70+-0.10
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Growth curves for upshift
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Growth curves for downshift
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Br upshift 1 hour
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Br upshift 2 hours
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3hr and 4hr time points
I didn’t add these because there are so few cells that produce good data (they
are so long that the edge parameterization doesn’t work very
well).
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MG1655 upshift 1 hour
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MG1655 upshift 2 hours
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MG1655 downshift 2 hours
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MG1655 downshift 4 hours
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Contour level• Note that cell width is sensitive to contour level of
segmentation• The following slides show example galleries of images to
illustrate how the cells are segmented. If you zoom in, you can see the cell outline. I’ve tried to vary the contour level to fit each frame as much as possible.
• Note that it’s possible that the cells are in fact the same size, but that the contour levels are just different. I’m checking that out….
• Keep in mind that the cells are not drawn to scale. I’m trying to fix that but Matlab is retarded.
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Br Ala-Pro steady-state
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Br Ala-Pro steady-state
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Br Ala-Pro steady-state
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Br 2 hour upshift
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Br 2 hour upshift
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Br 2 hour upshift (zoom)
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MG1655 2 hour upshift
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MG1655 2 hour upshift
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MG1655 2 hour upshift (zoom)