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positioning of organ primordia at the shoot apex known as
phyllotaxis. A mapping of experimentally determined PIN
protein polarity and abundance on realistic cellular
templates of the shoot apex and computation of the
resultant fluxes showed that the convergent PIN polari-
zation that accompanies the formation of new organ
primordia is sufficient to initiate patterned auxin maxima
[64]
. The use of different scenarios as to how auxin
concentrations might feedback on PIN polarization and
abundance revealed how auxin maxima could self-orga-
nize in spatial patterns at the shoot apex, forming regular
patterns of outgrowth
[65,66]
. Changes in parameters of
the implemented feedback could be tuned to resemble
existing phyllotactic patterns
[66]
. These findings bring to
the fore two equally important messages. First, the work
beautifully illustrates that feedback between auxin levels
and polar auxin transport molecules can generate patterns
de novo. Second, different assumptions on feedback, none
of which are completely supported by biochemical
mechanisms, yield self-organizing systems, which tells us
that models do not always provide insight into mecha-
nisms. Another issue that has been raised is that these
phyllotaxis models are essentially two-dimensional and
do not explicitly take into account the relation of auxin
maxima at the surface and the internal auxin transport
away from them in underlying tissues. A revised model
was proposed in which cells at the surface transport auxin
up the concentration gradient, whereas inner cells trans-
port auxin down the flux gradient
[67]
. Again, it has yet
to be determined whether the proposed switch function
between the two mechanisms can be underpinned by
biochemical mechanisms. Based on the observation that
PIN polarity and microtubule arrangement respond coor-
dinately to stresses and strains, a phyllotaxis model has
been proposed that posits cell wall strains as an inter-
mediate factor in the feedback mechanism between auxin
and PIN polarity
[68]
. Although the biochemical nature of
such a feedback remains to be clarified, the model is
attractive because it can unify the work on gene regula-
tory networks and shoot development summarized above
with a hitherto unconnected body of interesting observa-
tions indicating direct influence of cell wall composition
on organ outgrowth at the shoot apex
[69,70]
.
Finally, models for trichome patterning, which shares
many of the factors acting in root hair patterning
[27]
, have
been constructed which indicate that transcriptional control
of negative regulators and trapping of moving proteins
contribute to pattern formation
[71,72]
.
The above examples illustrate that important progress
has been made in the identification and analysis of regu-
latory subnetworks in shoot development. However, the
numerous connections between the various subnetworks
have not yet been sufficiently dealt with, and it is very
likely that
properties of the shoot system as a self-organizing unit. For
example, the sizes of central and peripheral zones, now
modeled mainly by focusing on the WUS
cytokinin
network, have profound influence on the pattern of organ
initiation, currently modeled with a primary focus on auxin
distribution patterns. It is clear that genes that influence
meristem size and cytokinin signaling influence phyllotaxis
[73]
. In addition, PLT genes expressed in the shoot apex
control phyllotactic patterns, in part through regulation of
PIN levels in primordia but also through changes in the
shape and size of the meristem
[74]
. In addition, the
interplay between adaxial and abaxial (equivalent to dorsal
and ventral) polarity genes and the interaction between
STM and its homologs, along with primordium-expressed
genes, influence meristem maintenance. For a true under-
standing of shoot development all of these factors will have
to be taken into account, which will require multilevel
models that reconstitute shoot morphogenesis as well as the
observed expression domains of key regulators in all of the
subnetworks. Moreover, predictions of these models will
have to be tested rigorously in order to arrive at the proper
description of the most relevant interactions and compo-
nents. For this, classic genetic analysis will not be suffi-
cient, as it is more likely that models will vary in dynamic
responses to transient perturbations. In Arabidopsis, the
stage has been set for dynamic experiments that test
existing models with the development of methods for
sophisticated visualization and transient gene manipulation
within the shoot apex
[75
CLV
e
e
77]
.
e
DEVELOPMENT AND THE RESPONSE
TO ENVIRONMENTAL STRESS
Because plants are sessile organisms, they have evolved
different strategies from animals to deal with environ-
mental stimuli. Many of their responses involve modifying
their development. The aerial parts of plants grow toward
light and respond to complex cues when deciding to flower;
roots grow toward water and nutrients. Therefore, plant
developmental responses can be thought of as akin to
animal behavior.
Tissue-Specific Responses to Environment
Most of the initial work on responses to environmental
stimuli was performed at the level of whole plants or entire
organs. More recently the question has been asked, 'Are
there differential responses among different cell types to
environmental stimuli?' Put another way, the question
could be, 'Do cells respond to stimuli as individual entities
or as part of a coordinated response within the organism?'
Addressing this question requires the analysis of the
response to stimuli of individual cell types. One effort in
this direction involved growing plants on high levels of salt
these are key to some of the fundamental
