“Welcome to the Modeling World” Why Modeling? Why MC?

We present a novel model of our synthetic Autoinducer-2
(AI-2) quorum sensing system in genetically engineered
Escherichia coli (E.coli) bacteria using the Membrane
Computing (MC) approach, which we implemented in
Mathematica (www.wolfram.com). Bacteria release chemical
signals that are used by the microbial population to monitor
cell population density in a process known as quorum
sensing. Through quorum sensing, bacteria are able to
coordinate individual and population behavior by altering
gene expression.
Membrane computing is a branch of Natural Computing
drawing inspiration from the compartmentalized biological
cell. MC is a parallel computing approach which processes
multisets of objects (agents) in a localized manner. MC has
introduced a powerful computing device for modeling some
of the functional and structural features of biological
membranes. Membranes are arranged in a hierarchal
manner, each associated with a distinct multiset of objects
and a unique set of interaction rules computed using a
compartmentalized version of Gillespieʼs algorithm.
Nowadays, many biologists use mathematical and
computational models as powerful tools to gain a deeper
understanding of biological systems. Given that molecular
biology experiments in vitro are very expensive and time
consuming, building models of biological processes as a
preliminary step helps to circumvent some of the
drawbacks of performing hypothesis testing in the wetlab.
This is why we feel that computational modelling is
important.
Emphasizing compartmentalization as a cornerstone
feature of cells, membrane computing (MC) is a powerful
approach for studying reactions in biological systems. MC
allows the user to focus on interactions at the level of an
individual cell, but also to observe the emergent properties
of entire cell populations. The MC approach seems to be
ideal for the construction of a quorum sensing model since
compartmentalization of the signal and the cascade
proteins are critical features of this process.

Contact Information:
University of Calgary
Afshin Esmaeili: a.esmaeili@ucalgary.ca iGEM 2009
Iman Yazdanbod: iyazdanb@ucalgary.ca
Sonja Georgijevic: sgeorgij@ucalgary.ca
Modelling
Thane Kubik: talkubik@ucalgary.ca Bacterial Chatter
Christian Jacob: cjacob@ucalgary.ca
with Mathematica
Or visit us at: http://2009.igem.org/Team:Calgary

2500 University Drive

Artistic Illustration NW, Calgary, AB, Canada
T2N 1N4
 Objects
Our Model:
Periplasmic
Space

Cytoplasmic Our MC Framework Future directions

Space In our model each bacterium is biological systems  in stochastic enables us to manipulate the We will implement SBML-
associated with two regions computations. system and observe its changed compatible file formats to save
Environment dynamics both on a
(periplasmic space and and exchange our
cellular level as well One of the strengths of
Simulation Visualization cytoplasmic space) and the
Results: as population level. this model is that the
experimental results.
objects involved are localized We are also planing to
AI-2 Signaling System: within these two regions based on Quorum sensing is a complicated
Emergent properties
results could be post this model online.
The process of producing, releasing, detecting, and responding their actual location in the of bacteria In addition, we intend
mechanism in its biological details,
populations can represented in various
to the signaling molecules in bacteria is referred to as quorum bacteria. 16 rules determine the to substitute Gillespie's
however its fundamental principles
sensing. In this quorum sensing system, AI-2 (autoinducer 2) is interactions between the objects. be identified in our ways such as matrixes, algorithm with swarm
are simple. This model provides a
Our incorporation of the Gillespie's model resulting from charts, and graphs. based approach. With
used as the inducer. This novel autoinducer was originally deeper understanding of how the
algorithm to the simulation brings features added such doing so, spatial
discovered in the quorum-sensing bacterium Vibrio harveyi. components of this signaling
us a step closer to real life as this as cell division and cell to cell dimensions will be introduced to
LuxS synthase is responsible for the production of AI-2. AI-2 is system interact, and how cell
algorithm is a proven approach for communication. The following the objects involved in the
bound to a periplasmic protein, called LuxP. LuxP  is  always  communication is affected by each
implementing randomness of figures present some results: simulation.
attached  to  another  membrane-bound  kinase protein, LuxQ, of the interactions. Our model
and the  LuxPQ  complex  mediates the signal transduction of
AI-2. At low cell density, in the absence of sufficient amounts of
AI-2 in the environment, this sensor acts as a kinase and
phosphorylates cytoplasmic protein LuxU. Phosphorylated LuxU
then acts as a kinase itself and adds a phosphate to DNA-binding
response regulator protein, LuxO. Lastly, the phosphorylated
LuxO would bind to a complex of transcription factor namely
sigma 54 and Pqrr4 promoter, which signals the expression of
GFP protein. GFP protein emits light and as a result, the bacteria
glow. At high cell density, AI-2 is accumulated in the environment
and eventually it enters the periplasmic space of bacteria and will
be detected by LuxPQ. Hence LuxPQ switches from being kinase
to being phosphatase. As a result, LuxPQ removes the
phosphate group from LuxU. LuxU acts as kinase, and thus it
cannot de-phosphorylate the LuxO. However, the housekeeping Left: AI-2 Binding to the LuxP-LuxQ Protein Middle: AI-2 Concentrations. On X-axis, time Right: Distributions of Applied Rules. For each
phosphotases slowly take away the phosphate off of LuxO, which Complex. Each column represents one of twenty steps are aligned, and on Y-axis number of AI-2 rule r0 to r16 the number of its application is
does not bind to Pqrr4; thus turning off the signal. Without the E.coli bacteria. The state of the modelled bacteria molecules are placed. This graph shows that the charted. Charts like this help to understand which
signal, the bacteria are no longer able to produce GFP and they over a period of 50 simulated time steps is depicted simulation is ran for 3000 time steps and started with rules, i.e. which interactions, are more or less
along the vertical axis. The color of each cell one cell (blue line) and other cells are generated over important within the simulated system or how
will turn dark by degradation of existing GFP.
indicates the binding degree between AI-2 and the time by divisions (red, green, and yellow lines). This changes in the rates of reactions affect the rule
LuxP-Q complex. The color spectrum spans from type of results provides information about distributions.
red (no binding) over white to blue (complete the general trend of change of concentrations in the
binding). As time progresses an increasing amount bacteria. demonstrates that   AI-2 concentration
of AI-2 is produced by LuxS and gets bound to changes logarithmically between divisions, and
LuxP-Q. suddenly drops at each division.