Biology Reference
In-Depth Information
d.
The “Settings…” tab is located near the top of the Interface screen. Alter the
“Settings…” so that particles bounce off the walls.
e.
Click on the “Procedures" tab in NetLogo. You will see sections of the code with
the following form:
;;
COMMENT
;;
what does this do?
NetLogo Code
;;
END COMMENT
For each occurrence, delete the phrase
;; what does this do?
and replace
it with a clear description of what that part of the NetLogo code does. (This is
called
commenting
your code.)
f.
Alter the code so that there is a constant source of 25 particles in the center of
the environment (at the origin). Hint: use
create-particles
.
In the body, the growth cone responds via four mainmechanisms: contact-mediated
attraction or repulsion, chemotaxis (attraction up gradients of the cue) or chemorepul-
sion (repulsion down gradients in the cue) [
32
]. Contact-mediated responses depend
on the amount of guidance cue in the environment and the gradient of the guidance
cue. The guidance cues, governing the direction of axon growth, originate and then
diffuse out from the midline [
34
].
There are various guidance molecules that have been identified and divided into
different families, namely Ephrin, Semaphorin, Netrin, and Slit [
35
]. In an effort
to create a manageable initial model, we will focus on two types of guidance cues
(Netrin and Slit) and three types of neuronal receptors (DCC, UNC5, and Robo 1).
Netrin both attracts and repulses axons, depending on the type of receptor on the axon.
Axons expressing the DCC receptor are attracted to areas with higher levels of Netrin,
which acts as a chemoattractant, whereas axons expressing the UNC-5 receptor are
repelled from high concentrations of Netrin, which acts as a chemorepellent [
32
,
34
].
Axons expressing the Robo 1 receptor are repelled by Slit. For some axons, the Robo
1 receptor is upregulated once the axon has crossed the midline resulting in the axon
being unable to return to the other side [
36
]. In short, one chemical (Netrin) acts as
both a chemo-attractant and -repellant, the other (Slit) acts as a chemorepellant, with
both of these being dependent on the receptor(s) expressed by the neuron. A schematic
of the known responses of different growth-cone types is shown in Figure
4.5
.
Certainly the description above represents a significant simplification. Axons usu-
ally have more than one kind of receptor, and there are multiple guidance cues. For
example, one axon might express both DCC and Robo 1 receptors, and it will behave
according to a combined response to the multiple cues.
Exercise 4.25.
Open the NetLogo model
Diffusion2.nlogo
. Answer the following
questions after reading the code in the “Procedures" tab.
a.
What is the difference between diffusion in this model and the model in
Diffu-
sion1.nlogo
?
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