Biology Reference
In-Depth Information
In order to simulate the quorum sensing network, initial parameters had to be assigned to the Petri
net. Particular for cell-cell-communication processes, where the lack of laboratory data is a common
problem, it is quite difficult to formulate a sophisticated system. For this reason, the Petri net simulation
was initiated with values from written sources and partially with data from laboratory experiments.
To give insight into the simulated system, it is briefly described which values are set up to model and
simulate the quorum sensing system under low and high population density.
The level of autoinducer (AI) outside the cell is set up to an abstract concentration of 30, the level of
AI inside the cell is set up to an abstract concentration of 10. To sense the real biological characteristics
and time response, each transition that fires a token to the enzymes that synthesize the AI has been
assigned a time delay parameter of 3. The cellular rhythm of the organism changes once a concentration
of autoinducers over 25 inside the cell is reached. Reaching an AI concentration value higher than 25, the
cascade inside the cell is activated and the system performs biological processes such as bioluminescense,
secretion, biofilm formation and motility. A lower concentration inhibits the aforementioned processes.
Some further characteristics of the simulated system are presented in the following charts. Chart 1
presents the AI C6-HSL level inside the cell in red, the C6-HSL level outside the cell in blue, the LuxU
concentration in purple and the AinR concentration in green. Because of the diffusion gradient the AI
diffuse into the cell until the AI levels inside and outside the cell are balanced. The intracellular circuitry
of the signal transduction is activated as soon as the AI concentration within the cell reaches the threshold
for the biological state change. Once the threshold is reached, the LuxU synthesis is increased and AinR
is activated.
Chart 1:
AI C6-HSL level inside the cell in red, the C6-HSL level outside the cell in blue, the LuxU concentration in purple
and the AinR concentration in green in the quorum sensing system. The
y
-axis represents the abstract concentration of the
elements. The
x
-axis represents the simulation steps to perform a fire state within the Petri net. (Colours are visible in the
online version of the article at
www.iospress.nl
.)
The second chart presents the AI 3-oxo-C6-HSL concentrations outside (blue) and inside the cell
(red). After the diffusion process the AI level is increasing equally inside and outside the cell. Beyond
the threshold level, the intracellular network switches into the “on” state. Additionally, the
lux
operon-
bioluminiscence (purple) is illustrated. The concentration level of the LuxR1 (blue)/LuxR2 (green)
varies within in the system. This behavior is related to the fact that the place LitR fires a token either to
LuxR1 or LuxR2 due to a stochastic distribution.
The third chart presents the different gene activation mechanisms by LuxR1/LuxR2 and LitR. The
secretion, the mobility, the biofilm formation and other operons (in blue) rise equally as soon as the
LitR place is active.
The concentration of the
lux
operon-bioluminiscence (in red) is lower than the
