User:Yeem/BE.180/pset5

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Download the Matlab script.
Sample output from Matlab.
Sample output from Matlab.

This model assumes an evenly spaced lawn of bacteria that do not replicate, die off, or move. Four chemical gradients ("A" through "D") are established as shown in "external inputs".

  • To achieve the general pill shape of the design, cells are "activated" by chemical B and "repressed" by chemical "A". "B" diffuses radially outward from the center of the field, while two parallel lines of "A" run horizontally near the top and bottom. In the presence of "B", cells generate β protein, which forms a heterodimer with σ protein. σ is constantly produced by cells.
  • For the alternating color scheme, cells sense the concentration of vertically dispersed chemical "D" as indicated in "processes". According to the relative amount of chemical "D" in the cell, the βσ complex signals the production of red, blue, or green pigment. This can be accomplished by several band detectors keyed to different levels of "D".
  • Alternatively, using signaling agents, high levels of chemical "D" could signal red pigment production and also generation of signaling molecule π. These signaling molecules would elicit switch-like responses from neighboring cells: when π falls below a certain threshold, signal production switches to the φ molecule and blue pigment generation. When sufficienty far from the center line that chemical "D" is no longer present, signaling stops altogether and green pigment is produced as long as the cell is "active".
  • For the "hollowed out" rectangle within the design, high amounts of chemicals "C" and "D" signal the production of the Δ and γ proteins, which form a heterodimer that inactivates the βσ complex and prevents it from producing color. Chemicals "C" and "D" are placed as orthogonal lines, thus producing a squared-off rectangle shape.
  • Presence of chemical "A" results in production of α protein, which also inhibits βσ activity.

External inputs

Chemical "A" gradient.
Chemical "A" gradient.
Chemical "B" gradient.
Chemical "B" gradient.
Yellow: cells "activated" by B, "repressed" by A.
Yellow: cells "activated" by B, "repressed" by A.
Chemical "C" gradient.
Chemical "C" gradient.
Chemical "D" gradient.
Chemical "D" gradient.
Spectrum of colors dictated by D gradient.
Spectrum of colors dictated by D gradient.

Processes

Activation by B produces βσ heterodimer.
Activation by B produces βσ heterodimer.
Repression by α protein or Δγ heterodimer.
Repression by α protein or Δγ heterodimer.
Set_color activated by βσ heterodimer produces blue pigment.
Set_color activated by βσ heterodimer produces blue pigment.
Chemical Protein generated
A α
B β
C γ
D Δ


Concentration of D Color generated
+++++ red
++++ blue
+++ red
++ blue
+ red
- green


Δ-γ inhibition
Δ-γ inhibition
π-φ cell signalling alternative.
π-φ cell signalling alternative.
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