Biology Reference
In-Depth Information
is one of the main tasks in integrative bioinformatics. To trim down data to a manageable yet relevant size
and to analyze and identify new as well as altered versions of interaction patterns we have implemented
a new editor-controlled information system called VANESA (
http://vanesa.sf.net
)
.
VANESA provides new bioinformatics methods and visualization approaches to analyze dynamic
interacting networks. The idea of VANESA is to extend any molecular data based network by new
targets and interacting elements. Using VANESA we aim at developing sophisticated network structures
for the modeling and simulation of coordinated cell actions based on the quorum sensing system of the
bacteria
Aliivibrio salmonicida
.
Coordinated cell actions and basic cellular activities are controlled by cell signaling and communication
processes. The study of individual parts of cell signaling pathways has become a major objective in
bioinformatics. Bacterial cells are able to adapt their behavior to the environment and its conditions
[Schauder
et al.
, 2001]. In biology and medicine, investigating how cells perceive and respond to their
microenvironment adapting processes such as development, growth, tissue repair, virulence production
and other complex actions can lead to a better understanding of molecular interactions and the causes of
diseases [Visick
et al.
, 2005].
It is necessary to understand the gene-controlled cell differentiation processes to be able to modify the
metabolic behavior, which will be the elementary operation of synthetic biology. Until now methods
of biotechnology could not control the cell differentiation process, which is based on fundamental gene
regulation events. One aspect related to cell differentiation is cell-to-cell communication. Although
cell-to-cell communication is not stringently connected to cell differentiation, it plays an important
role in gene regulation processes.
Therefore it is necessary to study and to understand cell-to-cell
communication processes.
Based on the quorum sensing process of the organism
Aliivibrio salmonicida
our goal is to develop
sophisticated cell differentiation models. The exploration of the quorum sensing system includes many
different fields of studies. In addition to the actual experimental laboratory work, integrative bioinfor-
matics methods are necessary to extend the molecular knowledge. In systems biology and especially
in the case of cell-to-cell communication the path from an initial question to a proven answer consists
of many individual steps such as laboratory work, literature research, life-science database consulting,
modeling, simulation and visualization, among others.
In this paper we will present how to combine the aforementioned fields of studies to construct complex
Petri nets for the simulation of cell-to-cell communication processes. We will show how the quorum
sensing network of the bacteria
Aliivibrio salmonicida
has been reconstructed by VANESA, using
experimental data and literature. The main idea of VANESA is to offer a powerful network editor to
reconstruct biological systems. Presently none of the Petri net simulation software applications are able
to provide scientists with strong network editing function and network prediction tools. However, there
is an urgent need for a strong network editor with additional analysis functions to model experimental
results that can be expanded with database information. Since none of the Petri net simulation tools
offers such functionality, the software application VANESA was conceived.
Based on the project experimental data and the integrated databases we began our work by exploring
and reconstructing the quorum sensing system in VANESA. For the simulation processes of the cell-
to-cell communication processes we made use of the Petri net language. Therefore, we implemented
an additional software feature in VANESA, which allows the automatic transformation of the quorum
sensing network into the language of a Petri net.
Using VANESA and complex Petri net structures we now present new communication models for the
transmission and information flow within and across cells.
