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Index
absolute temperature 9, 139, 180
acrosome (acrosomal vesicle) 228, 233
reaction 228
actin 9, 25, 244
cortical 36, 37, 38, 40–43, 243
cytoskeleton 12, 80, 243
density of 36
fiber 38, 39–49
filament (microfilament, F-actin) 7, 25, 26, 41, 43–49, 114, 205, 244
in actomyosin gel 245
in postfertilization 243
monomer (G-actin) 9, 84
myosin complex 157
network 128, 245
sol–gel transition in 245
activator
in reaction–diffusion systems 161, 181
transcriptional 65
active transport, see transport
active zone, see vertebrate limb
actomyosin gel 244, 247
adenosine triphosphate (ATP) 8, 13, 228
adherens junction, see cell junctions
adhesion molecule, see cell adhesion molecule
aggregate 29
embryo as 30
multicellular 29
spheroid 29
allantois 224
amphipathic molecules 39, 83
anaphase-promoting factor (APC) 63
angioblast 194
angiogenesis 196–197
animal cap (of frog blastula) 172
animal–vegetal axis (amphibian blastula) 177
anomalous diffusion, see diffusion
aorta 190, 194
apical ectodermal ridge (AER) 213, 216, 218
apical contraction, see cell
apical zone, see vertebrate limb
archenteron 117, 131, 189
area expansivity modulus 38
Aristotle 1
asters 25, 41
astral signal 41
distance between 42
distance from cortex 40, 41
mitotic spindle 40
astral signal 40, 41, 243
attractor, see fixed point
autocrine, see signaling
autoregulatory 65
loop of TGF- production 213
network of transcription factors 69, 110, 125, 165, 261
axes, embryonic
anteroposterior axis 118, 123, 178
dorsoventral axis 178
formation of primary axis 162, 177
reassigned in Xenopus 178
rostrocaudal axis 178
axon 16
bacteria 14
coasting 20
basal lamina 78, 80, 105, 110, 122, 213, 251
basin of attraction 57, 64, 69, 76, 116
Bateson, W. 163
beetle 260
Bell equation 88
Bell model 84–90
bending energy 101, see also Mittenthal–Mazo model
bending rigidity (bending stiffness) 39, 46
beetle 256
bifurcation 60
Hopf 59–63, 258
Turing 258
binary mixture of cells 91
binding affinity 67
blastocoel 27, 99, 110, 111, 112, 131
floor 224
fluid 100
internal cavity 110
wall 131
blastoderm
definition of 27
Drosophila 256
blastomere 28, 99, 128–130, 159
nuclei 53–57, 58
blastopore 131, 156, 178
rostral lip of 167, 178
blastula 24, 29, 30, 51, 178
formation 24, 27, 41, 43–49, 50, 51, 58, 224, see also cleavage
Drasdo–Forgacs model of 43
hollow 51, 58
manifestation of multicellularity 77, 92
mechanical properties 44
morphogenetic structure 43
Nieuwkoop center 182
polarized cells in 79
spherical 49
unstable 49
blood vessel formation, see vasculogenesis
body cavities 250
body plans 188, 189, 205
of metazoa 250
physical origin of 252–256
Boltzmann’s constant 9
bone 132, 134, 138, 143, 151, 188, 211
Bone Morphogenetic Protein (BMP) 125, see also morphogen
branching morphogenesis 205, see also salivary gland morphogenesis
Brownian motion 9, 11
Bussolino et al. model for vasculogenesis 199–203, 205
cadherin, see cell adhesion molecule
calcium ion Ca2+ 237, 238, see also fertilized egg
Ca2+ release induced by Ca2+
intracellular stores of 237, 238, 239
in signaling 239
saltatory 241
calcium ion channel 240
calcium ion oscillation in egg 240
calcium ion waves
in postfertilization egg 236–241, 242–247
reaction–diffusion (FDF) model for 239–241
saltatory 241
Cambrian explosion 250
canalization (canalizing selection) 263, 268
capillaries 190
cardiac looping 191, 193
cardiovascular system
development 190–203
cartilage 134, 150, 188, 211, 213
Cdc 2 58, 60, 63
cell 7
apical contraction of 114–115
compressibility of 45
contraction of 156, 157, 188
daughters (progeny) 57, 64
diploid 27
electical excitability 156, 188
eukaryotic 6, 15, 251
follicle 227
haploid 225
germ 224
migration of 201
nurse 227
pluripotent 51
prokaryotic 6
totipotent 51
unipotent 51
cell adhesion 30, 45, 78–80
covalent bond in 81
crosstalk in 152
heterophilic 79
homophilic 78, 79, 86
hydrogen bond in 81
in limb development 212, 217
in origination of body plans 255
ionic bond in 81
to substratum 78
substratum adhesion molecule (SAM) 78, 124
integrins 78, 80
steric hindrance in 81
van der Waals force in 81, 83
cell adhesion complex 78, 80
cell adhesion force 81
in Bell model 87
cell adhesion molecule (CAM) 46, 47, 77, 78, 95, 124
cadherin 77, 80, 83, 95, 97, 134, 150, 212
immunoglobulin superfamiliy 96
in cellular Potts model 152
N-CAM 77, 150
selectins 77, 103
cell aggregates (primitive) 250
cell cycle 25, 26, 254
and cell state
and cell surface tension 37
and surface contractions in egg 243
as component of two-oscillator pattern formation systems 160, 165
during cleavage 57–63
in Kaneko–Yomo model 73, 75
in sea urchin gastrulation 110
pattern formation 158
regulatory proteins in egg 227
time of 20, 46–47
cell detachment 134
cell division 24, 26, see also mitosis and meiosis
early 24
late 27
cell junction 78
adherens junction 78, 80, 125
desmosome 78
focal adhesion complex 78, 80
gap junction 78
hemidesmosome 78
tight junction 78
cell membrane, see membrane
cell migration as mechanism of pattern formation 157
cell relay (“bucket brigade”) mechanism 161, 173
cell repulsion 45
cell sheets 46, 78, 100, 251, see also epithelia
cell state
alternative 254
biochemical 52, 156
differentiated 8, 53
functional 53
cell surface 78, see also cell membrane
cell surface molecule 255, see also cell adhesion molecule
cell type 52
cellular automata 124, 126, 151
cellular Potts model (CPM) 151
for mesenchymal condensation 151–154
centromere 7, 25
centrosome 7, 25, 26
separate 25
spindle 25
channel, see protein channel
chaos 57
checkpoint 57–63
in cell cycle 57–63
Cheer et al. postfertilization mechanochemical model 245
chemical equilibrium 54
chemical wave 223, 234, see also calcium ion wave
chemoattractant, see also morphogen
gradient of 202
chemokinesis 157
chemotaxis 15, 135, 157, see also bacteria, coasting
chicken
cardiac looping 191, 199
egg 228
limb development 213
neural retina 70
somitic oscillator 163
symmetry breaking in primary axis 184
chromatid, see sister chromatids
chromatin 7, 25, 26
as DNA-protein complex 52
conformation of 52
closed 52
open 52
chromatin remodeling 65
chromosome 25, 26, 58
cilia 230
circulatory system 189, 190
cleavage 24, 27, 28, 30, 57, 60, 101–102
cell biology of 24–28
control of cell cycle during 57–63
holoblastic 28, 44
meroblastic 28
physical models of 38, 39–49
physical processes in 29–39
cleavage furrow 25
clefting (in glands) 204, 206, 210
clefting force 209, 210
clock and domino mechanisms 63
clock and wavefront mechanism, see pattern formation
cohesion energy (work of cohesion) 32, 103
cohesion of tissues 91, 93, 94, 95
collagen 133
thermodyamics of assembly 139
fibers 143
fibrils 143
fibrillogenesis 139
in ECM 139
community effect 70, see also Kaneko–Yomo model
compartment (in tissue) 80, 255
in mesenchyme 132
complex system 53
concentration gradient, see gradient of chemical or molecular cocentration
condensation, see mesenchymal condensation
conduction 16
connective tissues 138, 143, 213
irregular 143
regular 143
contact angle 32
contractile ring 25, 41, 43
molecular motors 25
convective flow 16, 230
convergence and extension, see convergent extension
convergent extension 100, 117–122, 189
as pattern formation 157
in gastrulation 109, 178, 184
in neural plate formation 124
Zajac–Jones–Glazier model of 119–122, 123
cornea 132, 142, 143
cortex, see membrane
cortical
actin 36, 37, 40–43
cytoplasm (amphibian egg) 177
granules 228, 234, 237
reaction 236–238, 239
rotation (amphibian egg) 177, 178
tension 34–38
determined by 36
measured 36
waves (on egg surface) 238
critical exponents 146
curvature 44
average 33, 46
in cleavage 44
local 39
radii of 33, 35, 36, 42, 209
definition 33
spontaneous 39, 46, 112
curvature energy (bending energy) 38–39, 46
cyclin 58, 63
cyclin-dependent kinase (Cdk) 63, see also Cdc2
cytokinesis 25
in cell division 25
cytoneme 133, 148
cytoplasm (cytosol) 12, 101
cytoplasmic streaming or flow 16, 243
cytoskeleton 7, 21
deformation 21
compression 34, 36, 153
elongation 21
in cell shape 48
shear 17, 22, 208
strain 22
de Gennes, P.-G. 3
delamination, see gastrulation
deoxyribonucleic acid (DNA) 24
as template 24
in nucleus 24
double helix 24
sequences of 65
synthesis (or S-phase) 25, 57
dephosphorylation 60
derivative 18, 54
definition of 18
ordinary 18
partial 18
dermamyotome, see somite
desmosome, see cell junction
determination (of cell type or fate) 51–52, 57, 64, 125
developmental
field 181
noise 271
program 249–250
systems 249
physical origin of
differential adhesion 78–80, 251 see also cell adhesion
as basis for pattern formation 155, 157
in body plan formation 255
in compartment formation 80
in Drosophila ovarian follicle development 94
in lumen formation 79, 80
in tissue engulfment 91
sorting-out in 69, 84, 155, 251, 255
physics of 92, 95–97
Steinberg–Phillips model 90–97
differential adhesion hypothesis (DAH) 91, 142, 150
differential equation 54
differentiation (of cell type) 51–52, 53, 63–76, 78, 117
and pattern formation 157, 159–162
control by transcription factors 65
in model of Hentschel et al. 215–216, 219
in morphogenesis 155
in neurulation 122
of cartilage in limb development 211–213, 215
of gametes 224–228
of muscle 69
regulation by Notch-Delta signaling 168–169, 187
diffusion 8–15
anomalous 12
facilitated 14
free 8–12, 251
in Bell model 85
in cell interior 8, 12–13
in cell membrane 84
in formation of body plans 252
in Kaneko–Yomo model 72
in lipid bilayer 84
in mesenchyme 133
in the presence of external forces 11, 13–14
of cells 14–15
of morphogens 156
diffusion coefficient 9, 10
of G-actin 10
diffusion current 14
diffusion time 10
digits (on limb) 211, 217
dimensional analysis 19
for surface tension 77, 97
for friction coefficient 96
diploblastic animals 99, 155
diploid organism 25, 57, 225, see also cell
dissipative system 54
Donnan ratio 236–238
dorsal aspect (of embryo) 90, 134–138
dorsal mesentery 224
drag force 16, 231, see also viscosity
Drasdo–Forgacs model 41, 43–49, 102
of cleavage and blastula formation 25, 41, 43–49
compared with Mittenthal–Mazo model 113, 126, 128
of gastrulation 111–113, 119, 156
drift velocity 14, 236
Drosophila melanogaster (fruit fly) 27, 174, 260, 261
segment polarity module 269, see also von Dassow et al.model for segment polarity
segmentation in 256–260, 264
dynamical system 53–57, 58, 63, 76
dynamical state 63
bistability 271
multistablity 64, see also Keller and Kaneko–Yomo models for cell differentiation
transitions 251
dynein, see molecular motor and protein
ectoderm 99, 109, 110, 156
limb 211, 213, see also apical ectodermal ridge
Ediacaran period 256
Einstein–Smoluchowski relation 17
in membrane potential 236
elastic
energy 107
material 21
modulus 21
pressure 245
elasticity 21
of cells 21
of extracellular matrix 30
of tissues 105, 107, 117, 251
electrical gradient, see gradient
electrical potential difference 14
electrochemical gradient, see gradient
embryogenesis 53
encounter complex 85, see also Bell model
endocrine cells, tissues, glands 135, 189
endocytosis 38
endoderm 99, 109, 172
endogenous 136
endothelium, endothelial cells 190, 200
ensemble average 9, 10
enthalpy 139
entropy 139
enzyme 58, see also protein
in Kaneko–Yomo model 72
protease 134
protein kinase 58, 60
epiblast 131, 224
epidermis 172
epigenetic 64
inheritance 64
state 64
system 264
epithelia 100
physical properties of 100–108
proliferation of 204
Mittenthal–Mazo model 104–108
epithelial–mesenchymal interaction 189, 204, 211, 215
epithelial-to-mesenchymal transformation 134, 190
equilibrium constant 85
Escherichia coli 63
eukaryotic cell, see cell
evolution 187, 261, 271
evolutionary experiments (in the model of Salazar-Ciudad et al.) 266
evolutionary innovation 261
evolvability 272
excitable medium 240, 244
chemical 101, 249, 254
electrical 51
mechanical 115, 116
mechanochemical 244
exocytosis 37, 38, 228, 234
exogastrulation, see sea urchin
exogenous 135
exoskeleton 189
extracellular component 46
extracellular effectors 119
extracellular gradients 156, 161, 165, 167, 168–169, 173
extracellular layer 44
extracellular matrix (ECM) 6, 7, 78, 81, 94, 100, 103, 189
and mesenchymal condensation 152
as communication medium 133
composition of 138–139
in epithelial–mesenchymal interactions 204
in gastrulation 110, 131
in haptotaxis 135, 225
in model of Hentschel et al. 217
in Kerszberg–Changeux model 125
in limb development 211–212, 220
in Lubkin–Li model 206
in mesenchymal morphogenesis 131–132
in model mesenchymal tissues 132, 138, 141, 200
in neural crest pathways 136–138, 139
in single-celled organisms 249
in tissue contraction 157, 167, 205
mineral in 81
networks and phase transitions in 134, 148
of egg vitelline membrane 228, 233
of fertilization membrane 234
percolating cluster of fibers in 148
proteoglycans of 138
receptors 83
secretion of 99, 110, 188
streaming in 138
viscoelastic properties of 133
extracellular portion of membrane proteins
extracellular signaling molecules 125
extracellular space 13, 29, 135, 161, 167
extracellular transport 46
extraembryonic membrane 27
facilitated diffusion, see diffusion
fate map 178
sea urchin 111
Xenopus 179
feather bud tracts 161, 190
feedback loops (in the model of von Dassow et al.)
negative 271
positive 271
feed-forward, see pattern formation, hierarchical inductive
fertilization 25, 177
envelope 110, 223, 231, 237
polyspermy 223
processes in 223
fertilized egg 4, 8, 237, see also zygote
biochemical oscillator in extracts of 57
Ca2+ waves in 236–241
cortex of 243
cytoskeleton in 12
diploid genome of 234
liquid drop model of 29
membrane resting potential 234–236
release of Ca2+ stores in 238–239
subdivision during cleavage 29
shape of 12
surface contraction waves in 242–247
mechanochemical model for 244–247
surface tension and division of 29–30
FGF receptors 213
FGFR1 213
FGFR2 213
FGFR3 213
fibroblast growth factor (FGF) 160, 213, see also morphogen
in limb development 216, 218
in somitogenesis 163
fibronectin 138
in cellular Potts model 152
in limb development 212, 216
in matrix-driven translocation 142
in mesenchymal condensation 150, 211
filamentous algae 250
filopodia 36, 37, 110, 131, 225
fire–diffuse–fire (FDF) model 239–241
first passage time 10, 11
fixed point (or node) 55
basin of attraction of 57
stable or attractor 55, 57, 60
unstable 55
fluid mosaic model 84
focal adhesion, see cell junction
follicle cell, see cell
fractals 197–199, 200, 250
free diffusion, see diffusion
friction 14
due to extracellular matrix 46
internal 16–17
frictional coefficient 14, 19
of tissues 96, 97
frictional motion 19, see also bacteria, coasting
frozen zone, see vertebrate limb
fruit fly, see Drosophila melanogaster
furrow 42
G1-phase, see interphase
G2-phase, see interphase
gametes 223, 227, 244
gametogenesis 224
gap junction 78, 133
gastrulation 24, 27, 78, 108–122
and convergent extension 100, 117–122
and evolutionary scenario 255
and Meinhardt reaction–diffusion model 181–184
and mesoderm induction 162
and Notch-Delta pathway 162, 168–169
definition of 69, 99
delamination in 109
epiboly in 109
epithelial to mesenchymal transformation during 134, 190
formation of Caudal gradient in 156
formation of mesenchyme in 111, 131, 132
hierarchical determination of cell specification during 272
in sea urchins 110–116, 117
Drasdo–Forgacs model 111–113, 119
model of Odell et al. 113–116, 119
ingression in 109
initiation of 58, 178
invagination in 109, 194
involution in 109
transport of mesenchymal cells during 142, 148
gel 12, 42, 146
gelation, gelation transition 145–147, see also sol–gel transition
gene 8, see also cell adhesion molecule, morphogen, transcription factor
constitutively active 64
developmentally regulated 52, 64
gap 260
homeobox 257, 260–261
housekeeping 52, 64
Hox 257
maternal 46
pair-rule 256, 260
segment-polarity 256
template-competent 52
transcribable 52
zygotic 46
gene expression 4, 8, 39, 64, 156, 167, 178
in animal cap cells 173, 178
asymmetric 191
axis-associated 178, 184
computational approaches to measurement 248
differential 2, 248
pair-rule 261
profile of 64
stripes in 258, 265
zygotic 239
gene–gene coupling constant (in model of Salazar-Ciudad et al.) 264
generic physical mechanisms 22, 188, 249
genetic networks 255, see also transcription factor
germ-band (of insect embryo) 268
intermediate 260
long 256, 261
short 256, 261
germ cell, see cell
germ layers 99, 155, 189 see also ectoderm, mesoderm, endoderm
germ-line cell 94, 224
germ plasm 224
germinal vesicle 227
Gibbs free energy 139
glycocalyx 46, 79, 81
glycolipids 83
glycoproteins, see proteins
glycosaminoglycans 138
heparin 150
hyaluronan 143, 211
in membrane proteins 81
in proteoglycans 81
gonads 224
gradient 156
electrical 14
electrochemical 14, 234–236
in evolutionary scenario 251, 252, 253, 256
in particle current 235
in sedimentation of yolk platelets 108, 254
of surface tension 40
velocity, at liquid–liquid interface 209
gradient of chemical or molecular concentration 13, 14, 15, 69, 157, 161, 168–169, 173, see also morphogen
as gate 164, 254
chemotactic, produced by egg 232
formation by emergent mechanism 254
generation by diffusion in tissues 174–176
in Kerszberg-Changeux model of neurulation 125, 156
induction of mesoderm by 171–173
of adhesive molecules (haptotactic) 135, 150, 157
of Dpp in the Drosophila wing disk 174, 176
of FGF8 in somitogenesis 164
of fibronectin in precartilage condensation 219
of gap gene products in the Drosophila embryo 257, 261
of maternal gene products in the Drosophila embryo 260, 261, 257
of TGF--like molecule in Niewukoop center 184
of VEGF-like molecule in vasculogenesis 201
grasshopper 260
segmentation in 257
gravity 108, 177, 253
gut (digestive tube, intestine) 172, 186, 224
haploid cell, see cell
haptotaxis 135, 157, 219, 225
He–Dembo model for cleavage 43
heart 179, 190
four-chambered 191, see also cardiac looping
heart muscle 191, 199
hemangioblast 194
hemidesmosome, see cell junction
Hensen’s node 131, 184, 186
Hentschel et al. model for limb development 213–215, 220
hindbrain 95
Holtfreter–Townes experiment 90
homologs of chromosome 225
homophilic, see cell adhesion
Hookean regime 21
Hooke’s law 21
Hopf bifurcation, see bifurcation
horseshoe crab 256, 258
human genes 52
humerus 211, 217
hyalin (protein) 233
hyaline layer (of egg) 30, 44, 46
hydrophilic 39, 82
hydrophobic 82
Hydra 90, 155
organizer in 178
hypoblast 131
ideal gas 16
imaginal disc 104, 173
immiscible liquids 34, 142
immunoglobulin superfamiliy, see cell adhesion molecule
in vitro systems 2, 58, 95, 133, 205–206
induction
of mesoderm 156, 162
of neural plate 122
of vertebral column 117
inertial motion 19, see also bacteria, coasting
inhibitor, see morphogen
inner cell mass 27
inositol trisphosphate (IP3) 239, 244
receptors 240
integrin, see cell adhesion molecule
interaction energy of cells 45
intercalation 111–113, 119
interfacial energy 30, 31, 103, 121
interfacial tension 30, 34, 210
in MDT 141
intermediate filament 7, 12
internal friction, see friction
interphase 26
DNA synthesis (S-phase) 25
time gap 1 (G1-phase) 25
time gap 2 (G2-phase) 25
intussusceptive growth 196
invagination 36, 37, 101, 109, 116, see also gastrulation
isologous diversification, see Kaneko–Yomo model
juxtacrine signaling, see signaling
Kaneko–Yomo model for cell differentiation- 52, 69–76
community effect in 70
isologous diversification 70, 254
Kartagener (immotile-cilia) syndrome 230
Keller model for cell differentiation 65–69, 254, see also autoregulatory network
Kerszberg–Changeux model for neurulation 125–126, 127, 156, see also neurulation
compared with Drasdo–Forgacs model 126
compared with Mittenthal–Mazo model 126
kidney 204
tubules 134, 152, 189
kinesin, see molecular motor and protein
kinetic energy 9
kinetochore 25, 26
tension 25
Lagrange multiplier 33
lamellipodia 36, 37
laminin 138
Lander et al. model of morphogen diffusion 174–176
Laplace pressure 33, 34, 36, 42
Laplace’s equation 33, 34, 35
lateral aspect (of embryo) 135
left–right asymmetry 160, 161, 162, 168–169, 191
Lewis model for somitic oscillator 164–168
ligand 83
limb 148, see also vertebrate limb
bud 148, 211
fore 148
hind 148
limit cycle 55
in Tyson–Novak model 59
in cell cycle 59
MPF cycle 59
phase of 63
linear stability analysis 55, 99, 128–130, 170, 171, 219
lipid bilayer, see membrane
lipid membrane, see membrane
liquid crystals 132
“liquid” tissues 94, 100, 105, 189, 206, 251, see also Steinberg–Phillips model and Mittenthal–Mazo model
lobules (of glands) 204, 211
loss angle 147, 151
in MDT 147
loss modulus 145, see also viscoelastic moduli
Lubkin–Li model, for salivary gland morphogenesis 205–210
lumen formation 79, 99, 100, 194, 251
lungs 189, 204
lymphocytes 84
matrix-driven translocation (MDT) 133, 139, 141, 142
M-phase, see mitosis
M-phase promoting factor (MPF) 58
mechanical wave 223
mechanochemical coupling 244
medial 135
Meinhardt model
for primary-axis formation 181–184, 185
for breaking of left–right symmetry 184, 185
meiosis or meiotic division 57–58, 226, 238, see also cell division
meiosis I 58, 225
meiosis II 58, 225
meiotic division, see meiosis
membrane of 7, 81–83
channel 83
composition of 81–83
cortex 42
energy of 38
lipid bilayer in 15, 82, 83
nanotube 36
plasma 13, 25, 29, 36, 38, 80–81, 82, 83, 114, 228, 233
semi-permeable 15
stretching of 45
tether 36
membrane potential 7, 14, 234, 235
membrane resting potential, see membrane potential
mesenchymal condensation 95, 133, 150–154, 189, 204, 211
mesenchymal-to-epithelial transformation 134, 152, 190
mesenchyme, see also tissue
phase separation in 148
primary (of sea urchin embryo) 110
mesoblast
limb 211
trilaminar embryo 131
mesoderm 109
extraembryonic 224
induction of 171–173
paraxial (presomitic, PSM) 162, 163, 164
somitic 117
metaphase 58
metazoa 7
as excitable media 251
body plans of 250
origin of 250–252
microarrays 248
microenvironment (of cells) 69, 81, 101, 138, 156, see also extracellular matrix and glycocalyx
microfilament 26, see also actin
microfingering flow 136–138
micropipette aspiration 36, 37
microspikes 36, 37
microtubule 7, 12, 26, 40, 243
and molecular motors 9
asters 25
centrosome 25
kinetochore 25
mitotic spindle 25
microtubule organizing center 25
microvilli 7, 36, 37
midblastula transition 27, 58, 63
migration, see cell migration
mitosis or mitotic division 25, 26, 58, see also cell division
oriented, as mechanism of pattern formation 157, 159
mitotic apparatus, see mitotic spindle
mitotic division, see mitosis
mitotic spindle (mitotic apparatus) 25, 40
Mittenthal–Mazo model for epithelial morphogenesis 104–108, 110–116, 117, 126
modules
biochemical 6
definition of 268
developmental 258, 266, 268–271, 272
genetic networks organized as 266
segment polarity of 258, 268–271, 272
tissue 162
molecular clock 27
molecular motor 8
dynein 25, 186, 230
LRD mutation of 186
kinesin 25
rotary 20, 230
translational 230
monocilia 186
Monte Carlo simulation 47–48, 112, 153
morphogen 125, 156
chordin 173
Derriere 182
FGF family 160, 173, 213
FGF8 163
Hedgehog 269
inhibitory 161, 173, 184, 213, 252
Lefty 184
Nodal 179, 184, 186
noggin 173
proto- 252
Sonic hedgehog (Shh) 125, 179, 186, 217
TGF- superfamily 160, 173
VEGF 197
Wingless 268, 269
Wnt-7A 217
Xnr 156, 161, 168–171
morphogenesis 156, 157, 189
cell movement in 46
morphogenetic field 125
motion 8
active 8
irregular 9, see also Brownian motion
passive 8
random 9, 10, see also Brownian motion
thermal 9
muscle 156, 211
contractility 188
differentiation 160
limb 211
origin in somites 162
N-CAM, see cell adhesion molecule
nanotubes 143
natural selection 1, 2, 7, 252, 263, 264
Navier–Stokes equation 18, 208
neo-Darwinism 261
neovacularization 196
Nernst–Planck equation 234–236
nerve 211
nerve cells 156, 188
neural crest
cephalic or cranial 136
compared with primordial germ cells 225
dispersal, migration, translocation 78, 134–138, 152, 189
epithelial–mesenchymal transformation 190
derivatives of 135
fluid properites of 136
trunk 135, 138
neural
folds 123, 189
groove 122–126
plate 122–126, 156, 160, 168–171, 194
tube 100, 122, 123, 136
neurulation 100, 122–126, 189
Kerszberg-Changeux model of 125–126, 127
neutrophil 38
Newton 1
law of gravity 1
first law 19
second law 19, 32, 33, 201, 207, 208
third law 230
Nieuwkoop organizer, see organizer
nodal flow 186
node, see fixed point
Notch–Delta signaling system 125, 160, 164–165, 168–169, 173, 255
in axial symmetry breaking in chicken 184
in model of Sherratt et al. 169
notochord 117, 136, 178, 189, 204
nuclear envelope 7, 25
in cell division 25
nucleoplasm 12
nurse cell, see cell
Odell et al., model for gastrulation 113–116, 119
compared with Drasdo–Forgacs model 113
oocyte 52, 58, 225
oogenesis 27, 58, 94, 159, 225–228
oogonia 225, see also germ-line cell
open system 54, 251
orbit 55
ordinary derivative 18
organ rudiment 189
organizer 180, 252
in Hydra 178
Nieuwkoop center 177, 180, 182
proto- 252, 254
Spemann–Mangold 173, 178, 180, 182
vegetal pole 173, 180
oscillating viscometer 146
oscillator, see also Tyson–Novak model and Lewis model
Bateson’s hypothesis 163
biochemical 57, 258, 260, 261
in formation of body plans 254
c-hairy1 163
somitic 164, 165
osmosis 15–16
osmotic pressure 7, 15, 16
in Cheer et al. model 245
oviduct 230
pancreas 190
paracrine, see signaling
parallel plate tensiometer 95
parasegments 258, 259, 268
partial derivative 18
particle current 14
pascal 17, 21
pattern formation, multicellular 108, 122, 158
by juxtacrine signaling 173
by mitosis 159
by paracrine signaling 172
by reaction–diffusion systems 173–174
cell autonomous 157, 159–160
clock and wavefront mechanism 157, 164, 167
in cell condensation 151
inductive 157
emergent 161, 177, 254
hierarchical 161, 252, 254
morphodynamic 177
morphogenetic 156, 157, 177
two-oscillator mechanism 160, 165, 254
percolation 134, 142–148, 197–199
spanning cluster 143
threshold 145
transition 145
periodic processes 27
phase plane 53
phase transition
liquid crystal 132
paramagnetic 180
percolation 145
phospholipids 82
phosphorylation 60
phyla 250
piston as viscous element 22
planar cell polarity, see polarity
plants 250
plasticity (of cell type) 254
Plato 1
plasma membrane 7, see also membrane
polar body 58, 227
polarity of cell
basolateral 44, 78, 194, 251
planar 113–116, 119, 122, 157
polycystic kidney disease 194
polyspermy 223, 234, see also fertilization
fast block to 234, 236
slow block to 234, 236–238
positional information 176
posterior growth (proliferative) zone
in arthropod segmentation 256, 258
in somitogenesis 163, 165
power law 145, 146, see also scale-free systems
for behavior of viscoelastic moduli 147
for viscosity 145
for Young's modulus 145
precartilage mesenchyme 211, see also mesenchyme
pregastrula 99
pressure force 208
primitive streak 131
primordial germ cell (PGC) 224
see also cell
prokaryotic cell, see cell
promoter (of gene) 65, 260
stripe-specific 261
pronucleus 233
protease, see enzyme
protein 8
see also enzyme, extracellular matrix, molecular motor, morphogen, and transcription factor
cytoskeletal 21
cytoplasmic 9, 12
homeodomain 256
glycoproteins 81, 228
integral membrane 83
transmembrane 21
protein channel 7, 83, 234
protein kinase, see enzyme
proteoglycan 138
proximodistal progression of limb development 211
pseudomorphism 263
pulmonary
artery 190
vein 190
radius and ulna 211, 217
random networks 143
rate constant 59–63
reaction–diffusion systems 161, 173–174, 181, 251, 252, 254, 261, see also pattern formation
diffusion-limited 241
in evolutionary scenario for insect segmentation 264
in model of Cheer et al. 245
in model of Hentschel et al. 217, 218, 219
in model of Lander et al. 175
in models of Meinhardt 181
random fluctuations in 186
reaction-limited 240, 241
receptor 83
FGF 213
IP3 240
Patched 269
VEGF 201
repressor, see transcription factor
ribonucleic acid (RNA)
mRNA or messenger RNA 69
transcript 52
robustness (of development) 222, 263, 264
in model of Salazar-Ciudad et al. 267
in model of von Dassow et al. 271
saddle points 42
salamander 137, 211
Salazar-Ciudad et al. model for evolution of development 264–267
salivary gland morphogenesis 190, 204–210, 211
epithelial theory of 205
mesenchymal theory of 206
Lubkin–Li model for, see Lubkin–Li model
scale-free systems 145, 146
scaling law 147
Schistocerca, see grasshopper
sclerotome, see somite
sea urchin 20, 27, 28
acrosome reaction 233
archenteron elongation in 111, 189
as radially symmetric 188
as triploblasts 99, 109, 117
cleavage in 40, 111
White–Borisy model 37, 40–43
Drasdo–Forgacs model 41, 43–49
exogastrulation 112
fertilization 223
fertilization wave 239
gastrulation in 110–116, 117
Drasdo–Forgacs model 111–113, 119
model of Odell et al. 113–116, 119
and Notch–Delta pathway 162, 168–169
hierarchical determination of cell specification 272
larva 110
jelly coat of egg 228
primary mesenchyme 110, 131, 135
secondary mesenchyme 131
size of egg 228
surface contraction waves 242–243
transitions between cell types 68
sedimentation (as a pattern-forming process) 108, 253, see also gravity
segment polarity module 258, 268–271, 272
segmentation 95, 162–168, 256–260, see also somite formation
clock 258
evolution of 257, 260–261
in long germ-band insects 256
in Drosophila 257
in short germ-band insects 256
molecular mechanisms of 256–260
physical mechanisms of 257, 260–261
selectin, see cell adhesion molecule
self-organization 101, 178, 191, 197, 200, 234, 251, 254
semi-permeable membrane, see membrane
separation of time scales 219
separatrix 57
shear 17, see also deformation
shear modulus 22
shear rate 17
shear stress 22
Sherratt et al. model for juxtacrine pattern formation 169–171
Sierpinski carpet 191, 199
signaling, signal transduction 69
autocrine 161
inside-out 83
juxtacrine 133, 160, 255, 83 see also Notch–Delta signaling system
outside-in 69, 83
paracrine 133, 160–161, see also morphogen
Wnt pathway 182
sister chromatids 25, 26, 58, 225
separation of 25, 26
situs inversus 186, 230
skeletal pattern
vertebral column 162
vertebrate limb 161
skeleton 211
soft matter 3, 248, see also viscoelastic material
sol–gel transition 145, 147, 245, see also gelation
solid blastula, see stereoblastula
somatopleure 191, 192
somite 135, 136, 162, 163
boundaries 161, 163, 167
dermamyotome 162
formation (somitogenesis) 160, 162–168
Lewis model for 164–168
intrasomitic space 136
number 162
sclerotome 162
somitic oscillator, see oscillator
Sonic hedgehog (Shh), see morphogen
sorting-out, see differential adhesion
Spemann–Mangold organizer, see organizer
sperm 52, 229, 243, 244, see also spermatozoon
capacitated 225
entry point of 177, 178, 239, 240, 243
flagellum of 228
locomotion of 228–232
motility of 228–232
viscous drag on 232
spermatocyte 225
spermatogenesis 58, 225–228
spermatogonia 225, see also germ-line cells
spermatozoon 228
spermiogenesis 228
S-phase, see DNA synthesis
spider 258
spinal cord 109, 117, 122
splanchnopleure 191, 192
spring, as elastic element 21
spring constant 21
standing waves (chemical) 260, see also reaction–diffusion systems
state space 53, 57
state variable 54
stationary state (steady state) 55
steady state, see stationary state
in the Keller model 68
Steinberg–Phillips model 90–97, see also differential adhesion hypothesis
stem cells 160
stereoblastula (solid blastula) 27
stiffness 21
stochastic force 46
Stokes' formula 18
storage modulus 146, see also viscoelastic moduli
strain, see deformation
strange attractor 56
stress 21
stripe pattern
in Drosophila syncytium 256
Engrailed 258
pair-rule gene product 258
pigment, in skin 161
precartilage condensations, in vertebrate limb 221
submandibular glands, see salivary gland morphogenesis
substrate adhesion molecule, (SAM) see cell adhesion
substratum 32
surface
concave 33
convex 33
surface energy 30, 31
surface density 32
liquid 32
solid 32
surface tension 29, 30–33, 251
anisotropic 36
apparent 30
definition of 30, 31, 32, 77, 103
gradient of 40
in tissue cohesivity 77, 95
isotropic 40
membrane–cytoskeleton adhesion 36
nondimensional 210
of cell 29, 36
of collagen solutions in MDT 142
of lipid membrane 36, 38
of liquid 29, 32
of spheroid 29
of tissue 91–95, 206
uniformity of 42
surface tension waves, see cortical waves
symmetry breaking 179
synapsis 225
syncytium in Drosophila embryo 256
syngamy 233
systems biology 249
tendons 132, 143
TGF- in limb development 213, see also morphogen
thermal energy 9
Thompson D. W. 249
tight junction, see cell junction
timelag or delay (in Lewis model) 156, 165
tissue
as liquid 91–95
cohesivity of 77, 95
engulfment of 91, 92, 155
epithelial 81, 94
epithelioid 81
mesenchymal or mesenchyme 81, 131
connective 81, 94
titration (as regulatory mechanism) 27
topology (of gene regulatory networks), see also pattern formation
in model of Salazar-Ciudad et al. 266
in model of von Dassow et al. 271
tracheal system (in insect) 189
tractional forces 134
trajectory 55
in phase plane 55
transcription 65
transcription factor 65
activator 65
Bicoid 260
caudal gene product 156
c-hairy1 163
Cubitus interruptus 269
Engrailed 258, 260, 268, 269
Even-skipped 258, 261
Foxp4 191
fushi tarazu gene product 258, 261
Giant 260
her1 and her7 gene products 165
Hox class 217, 257
Hunchback 260
Krüppel 260
network of transcription factors 65, see also autoregulatory network
repressor 63, 65
VegT 182
transdifferentiation 70
transmembrane protein, see protein
transport
active 16
diffusive along cytoskeleton 12, 13
intracellular 12–13
viscous 19
Tribolium, see beetle
triploblastic animal 99, 109, 162
trophoblast 27
tubes and tubules
branched 189
cardiogenic (heart-forming) 190, 191, 192, 193
epithelial 204
formation of, morphogenesis 101, 194, 196
by budding, sprouting 194
by cavitation 191
by cell hollowing 194
by cord hollowing 194
by wrapping 194
in primitive metazoans 256
kidney 194
networks 189, 190, 191
Turing, A. M. 156
Turing mechanism, see bifurcation and reaction–diffusion systems
tyrosine 58, 60
Tyson–Novak model 59–63
van de Waals forces, interactions, see cell adhesion
vascular system 189, see also circulatory system
vasculogenesis 160, 194, 195
network formation in 197
vector field 55
vegetal
plate (of sea urchin blastula) 110, 116
pole (of frog blastula) 108, 110, 112, 172
organizer 173
VEGF, see morphogen
vena cava 190
ventral aspect (of embryo) 135
vertebral column 99, 117
vertebrate limb 95, 148, 161, 190, see also skeletal pattern
core mechanism for development 214, 216–217
development 210, 212
active zone 216
apical zone 213, 216
frozen zone 216
Hentschel et al., model for 213–215
fore 148, 211
hind 148, 211
limb bud 132, 213
vimentin filaments 21
viscoelastic
behavior in gelation 146
forces 114
material 22, 98, 249
moduli, in MDT 146, 147
viscoelasticity 21
viscosity 13, 16–19, 231
definition of
of cytoplasm 7, 16–19, 247
of tissues 206, 210, 251
relation to loss modulus 146
viscous drag 16, see also viscosity
on sperm 228–232
viscous transport, see also transport
of cells 19
of spermatozoa 230
vitelline membrane 228, 233
von Dassow et al. model for segment polarity 268–271
water of hydration 34
wetting 32
complete 32
partial 25
White–Borisy model 37, 40–43
wiring diagram (for gene network) 65
work of adhesion 102–104, 120
Xenopus laevis 58
axis formation in 177–179
cardiac looping in 191
cortical contraction waves in zygote 243
egg 108, 228
fate maps 178
mesoderm induction in 161, 171–173
muscle differentiation 69
primordial germ cells 225
yolk 28, 108, 228
yolk sac 191, 224
Young’s equation 32, 34
Young’s modulus 21
relation to storage modulus 146
Zajac–Jones–Glazier model 119–122, 123, see also convergence and extension
zebrafish, somitogenesis in 165
zona pelucida 30, 228, 233
zygote 8, 24, 27, see also fertilized egg formation of 23
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