Biology Reference
In-Depth Information
Chapter 17
Spatial Organization of Subcellular
Systems
Malte Schmick, Hern ´n E. Grecco and Philippe I.H. Bastiaens
Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Str. 11, 44227 Dortmund, Germany
Chapter Outline
Motivation
329
Causality From Variation and Perturbation Analysis
336
Dimensionality Effects in Biochemical Reactions
330
Model-Driven Experimentation and Experimentally Driven
Modeling
Towards a Systemic Understanding of Cellular Biology
330
337
Spatiotemporal Modeling of Cellular Processes
332
Conclusions
339
Spatiotemporal Quantification of Cellular Processes
334
References
340
In this chapter we describe how spatially organized
biochemical networks give rise to biological function on
the cellular scale. We will first introduce self-organized
reaction
computing and applying changes are therefore essential
functions of all living biological systems. On this time-
scale, each cell encapsulates the biochemical reactions
that evolved to perform these functions across the diffu-
sively linked intracellular compartments.
In such a well-mixed reaction vessel, the functional
possibilities are limited as all points perform the same
operation simultaneously and in synchrony. Slowing down
for example the diffusion of only one part of a reaction
network constitutes a bridging of time and length scales,
which introduces complexity to any system. Diffusion of
reactants and products transmits information about a local-
ized reaction beyond the area in which the reaction itself
occurred. While each point in space is equivalent to any
other, each senses a different environment and looks back
to a different history. These reactions are limited only by
the supply of energy and reactants, and thus
˚
ngstrom-
sized molecules can traverse meters (e.g., hormones such as
adrenaline can travel large distances in an organism) and
sub-second reactions can influence processes that occur at
much longer timescales (e.g., seasonal cycles, such as
mottling of fur). The richness of the involved reactions
limits the scope, flexibility and robustness of the higher-
order functions, such as a 'memory' of environmental
changes, and hence the success of the organism: simple
systems will be confined to simple functions, whereas
complex ones might be able to resolve the challenges
imposed by the ever-changing environment.
diffusion systems, because many of them are used
by living systems as platforms on which functionality is
added. We then describe spatial patterning in biological
systems, focusing on how intracellular compartmentaliza-
tion enables function. Finally, we discuss how new insight
into self-organization in reaction
e
diffusion systems can be
obtained by combining microscopy and computational
methods
[1]
.
e
MOTIVATION
Biological systems strive against entropy by consuming
energy and transforming it into order to reach a balance
between influx of energy and the energy necessary to
maintain a certain level of organization. This balance, in
which the system is apparently 'resting,' can be defined as
the state of the system. Take for example a mature
multicellular organism that does not grow or develop
although its cells keep dividing. A change in external
conditions disturbs the balance that the organism main-
tains, so the organism needs to change as well. This
adaptation requires the organism to sense and record the
environmental and internal history, while computing and
applying changes to its own conditions to re-acquire
proper balance,
i.e., a new state. Sensing, recording,
