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cell junction 78 axis 184
germ 224
adherens junction 78, 80, 125 chromatid, see sister chromatids
migration of 201
nurse 227 desmosome 78 chromatin 7, 25, 26
pluripotent 51 focal adhesion complex 78, 80 as DNA-protein complex 52
prokaryotic 6 gap junction 78 conformation of 52
totipotent 51 hemidesmosome 78 closed 52
unipotent 51 tight junction 78 open 52
cell adhesion 30, 45, 78--80 cell membrane, see membrane chromatin remodeling 65
covalent bond in 81 cell migration as mechanism of chromosome 25, 26, 58
crosstalk in 152 pattern formation 157 cilia 230
heterophilic 79 cell relay (˜˜bucket brigade”) circulatory system 189, 190
homophilic 78, 79, 86 mechanism 161, 173 cleavage 24, 27, 28, 30, 57, 60,
hydrogen bond in 81 cell repulsion 45 101--102
in limb development 212, 217 cell sheets 46, 78, 100, 251, see also cell biology of 24--28
in origination of body plans 255 epithelia control of cell cycle during
ionic bond in 81 cell state 57--63
to substratum 78 alternative 254 holoblastic 28, 44
substratum adhesion molecule biochemical 52, 156 meroblastic 28
(SAM) 78, 124 differentiated 8, 53 physical models of 38, 39--49
integrins 78, 80 functional 53 physical processes in 29--39
steric hindrance in 81 cell surface 78, see also cell cleavage furrow 25
van der Waals force in 81, 83 membrane clefting (in glands) 204, 206, 210
cell adhesion complex 78, 80 cell surface molecule 255, see also clefting force 209, 210
cell adhesion force 81 cell adhesion molecule clock and domino mechanisms 63
in Bell model 87 cell type 52 clock and wavefront mechanism, see
cell adhesion molecule (CAM) 46, 47, cellular automata 124, 126, 151 pattern formation
77, 78, 95, 124 cellular Potts model (CPM) 151 cohesion energy (work of cohesion)
cadherin 77, 80, 83, 95, 97, 134, for mesenchymal condensation 32, 103
150, 212 151--154 cohesion of tissues 91, 93, 94, 95
immunoglobulin superfamiliy centromere 7, 25 collagen 133
96 centrosome 7, 25, 26 thermodyamics of assembly 139
in cellular Potts model 152 separate 25 ¬bers 143
N-CAM 77, 150 spindle 25 ¬brils 143
selectins 77, 103 channel, see protein channel ¬brillogenesis 139
cell aggregates (primitive) 250 chaos 57 in ECM 139
INDEX 329


cytoneme 133, 148 control by transcription factors
community effect 70, see also
Kaneko--Yomo model cytoplasm (cytosol) 12, 101 65
cytoplasmic streaming or ¬‚ow 16, in model of Hentschel et al.
compartment (in tissue) 80, 255
in mesenchyme 132 243 215--216, 219
complex system 53 cytoskeleton 7, 21 in morphogenesis 155
concentration gradient, see gradient deformation 21 in neurulation 122
of chemical or molecular compression 34, 36, 153 of cartilage in limb development
cocentration elongation 21 211--213, 215
condensation, see mesenchymal in cell shape 48 of gametes 224--228
condensation shear 17, 22, 208 of muscle 69
conduction 16 strain 22 regulation by Notch-Delta
connective tissues 138, 143, 213 de Gennes, P.-G. 3 signaling 168--169, 187
irregular 143 delamination, see gastrulation diffusion 8--15
regular 143 deoxyribonucleic acid (DNA) 24 anomalous 12
contact angle 32 as template 24 facilitated 14
contractile ring 25, 41, 43 in nucleus 24 free 8--12, 251
molecular motors 25 double helix 24 in Bell model 85
convective ¬‚ow 16, 230 sequences of 65 in cell interior 8, 12--13
convergence and extension, see synthesis (or S-phase) 25, 57 in cell membrane 84
convergent extension dephosphorylation 60 in formation of body plans 252
convergent extension 100, 117--122, derivative 18, 54 in Kaneko--Yomo model 72
189 de¬nition of 18 in lipid bilayer 84
as pattern formation 157 ordinary 18 in mesenchyme 133
in gastrulation 109, 178, 184 partial 18 in the presence of external forces
in neural plate formation 124 dermamyotome, see somite 11, 13--14
Zajac--Jones--Glazier model of desmosome, see cell junction of cells 14--15
119--122, 123 determination (of cell type or fate) of morphogens 156
cornea 132, 142, 143 51--52, 57, 64, 125 diffusion coef¬cient 9, 10
cortex, see membrane developmental of G-actin 10
cortical ¬eld 181 diffusion current 14
actin 36, 37, 40--43 noise 271 diffusion time 10
cytoplasm (amphibian egg) 177 program 249--250 digits (on limb) 211, 217
granules 228, 234, 237 systems 249 dimensional analysis 19
reaction 236--238, 239 physical origin of for surface tension 77, 97
rotation (amphibian egg) 177, 178 differential adhesion 78--80, 251 for friction coef¬cient 96
tension 34--38 see also cell adhesion diploblastic animals 99, 155
determined by 36 as basis for pattern formation 155, diploid organism 25, 57, 225, see also
measured 36 157 cell
waves (on egg surface) 238 in body plan formation 255 dissipative system 54
critical exponents 146 in compartment formation 80 Donnan ratio 236--238
curvature 44 in Drosophila ovarian follicle dorsal aspect (of embryo) 90,
average 33, 46 development 94 134--138
in cleavage 44 in lumen formation 79, 80 dorsal mesentery 224
local 39 in tissue engulfment 91 drag force 16, 231, see also viscosity
radii of 33, 35, 36, 42, 209 sorting-out in 69, 84, 155, 251, 255 Drasdo--Forgacs model 41, 43--49,
de¬nition 33 physics of 92, 95--97 102
spontaneous 39, 46, 112 Steinberg--Phillips model 90--97 of cleavage and blastula formation
curvature energy (bending energy) differential adhesion hypothesis 25, 41, 43--49
38--39, 46 (DAH) 91, 142, 150 compared with Mittenthal--Mazo
cyclin 58, 63 differential equation 54 model 113, 126, 128
cyclin-dependent kinase (Cdk) 63, see differentiation (of cell type) 51--52, of gastrulation 111--113, 119, 156
also Cdc2 53, 63--76, 78, 117 drift velocity 14, 236
cytokinesis 25 and pattern formation 157, Drosophila melanogaster (fruit ¬‚y) 27,
in cell division 25 159--162 174, 260, 261
330 INDEX


segment polarity module 269, see state 64 in tissue contraction 157, 167, 205
also von Dassow et al. model system 264 mineral in 81
for segment polarity epithelia 100 networks and phase transitions in
segmentation in 256--260, 264 physical properties of 100--108 134, 148
dynamical system 53--57, 58, 63, 76 proliferation of 204 of egg vitelline membrane 228, 233
dynamical state 63 Mittenthal--Mazo model 104--108 of fertilization membrane 234
bistability 271 epithelial--mesenchymal interaction percolating cluster of ¬bers in 148
multistablity 64, see also Keller and 189, 204, 211, 215 proteoglycans of 138
Kaneko--Yomo models for cell epithelial-to-mesenchymal receptors 83
differentiation transformation 134, 190 secretion of 99, 110, 188
transitions 251 equilibrium constant 85 streaming in 138
dynein, see molecular motor and Escherichia coli 63 viscoelastic properties of 133
protein eukaryotic cell, see cell extracellular portion of membrane
evolution 187, 261, 271 proteins
ectoderm 99, 109, 110, 156 evolutionary experiments (in the extracellular signaling molecules 125
limb 211, 213, see also apical model of Salazar-Ciudad et al.) extracellular space 13, 29, 135, 161,
ectodermal ridge 266 167
Ediacaran period 256 evolutionary innovation 261 extracellular transport 46
Einstein--Smoluchowski relation 17 evolvability 272 extraembryonic membrane 27
in membrane potential 236 excitable medium 240, 244
elastic chemical 101, 249, 254 facilitated diffusion, see diffusion
energy 107 electrical 51 fate map 178
material 21 mechanical 115, 116 sea urchin 111
modulus 21 mechanochemical 244 Xenopus 179
pressure 245 exocytosis 37, 38, 228, 234 feather bud tracts 161, 190
elasticity 21 exogastrulation, see sea urchin feedback loops (in the model of von
of cells 21 exogenous 135 Dassow et al.)
of extracellular matrix 30 exoskeleton 189 negative 271
of tissues 105, 107, 117, 251 extracellular component 46 positive 271
electrical gradient, see gradient extracellular effectors 119 feed-forward, see pattern formation,
electrical potential difference 14 extracellular gradients 156, 161, 165, hierarchical inductive
electrochemical gradient, see 167, 168--169, 173 fertilization 25, 177
gradient extracellular layer 44 envelope 110, 223, 231, 237
embryogenesis 53 extracellular matrix (ECM) 6, 7, 78, polyspermy 223
encounter complex 85, see also Bell 81, 94, 100, 103, 189 processes in 223
model and mesenchymal condensation fertilized egg 4, 8, 237, see also zygote
endocrine cells, tissues, glands 135, 152 biochemical oscillator in extracts
189 as communication medium 133 of 57
2+ waves in 236--241
endocytosis 38 composition of 138--139 Ca
endoderm 99, 109, 172 in epithelial--mesenchymal cortex of 243
endogenous 136 interactions 204 cytoskeleton in 12
endothelium, endothelial cells 190, in gastrulation 110, 131 diploid genome of 234
200 in haptotaxis 135, 225 liquid drop model of 29
ensemble average 9, 10 in model of Hentschel et al. 217 membrane resting potential
enthalpy 139 in Kerszberg--Changeux model 125 234--236
release of Ca2+ stores in 238--239
entropy 139 in limb development 211--212, 220
enzyme 58, see also protein in Lubkin--Li model 206 subdivision during cleavage 29
in Kaneko--Yomo model 72 in mesenchymal morphogenesis shape of 12
protease 134 131--132 surface contraction waves in
protein kinase 58, 60 in model mesenchymal tissues 242--247
epiblast 131, 224 132, 138, 141, 200 mechanochemical model for
epidermis 172 in neural crest pathways 136--138, 244--247
epigenetic 64 139 surface tension and division of
inheritance 64 in single-celled organisms 249 29--30
INDEX 331


generic physical mechanisms 22,
FGF receptors 213 epiboly in 109
FGFR1 213 epithelial to mesenchymal 188, 249
FGFR2 213 transformation during 134, genetic networks 255, see also
FGFR3 213 190 transcription factor
¬broblast growth factor (FGF) 160, formation of Caudal gradient in germ-band (of insect embryo) 268
213, see also morphogen 156 intermediate 260
in limb development 216, 218 formation of mesenchyme in 111, long 256, 261
in somitogenesis 163 131, 132 short 256, 261
¬bronectin 138 hierarchical determination of cell germ cell, see cell
in cellular Potts model 152 speci¬cation during 272 germ layers 99, 155, 189 see also
in limb development 212, 216 in sea urchins 110--116, 117 ectoderm, mesoderm,
in matrix-driven translocation 142 Drasdo--Forgacs model 111--113, endoderm
in mesenchymal condensation 119 germ-line cell 94, 224
150, 211 model of Odell et al. 113--116, 119 germ plasm 224
¬lamentous algae 250 ingression in 109 germinal vesicle 227
¬lopodia 36, 37, 110, 131, 225 initiation of 58, 178 Gibbs free energy 139
¬re--diffuse--¬re (FDF) model 239--241 invagination in 109, 194 glycocalyx 46, 79, 81
¬rst passage time 10, 11 involution in 109 glycolipids 83
¬xed point (or node) 55 transport of mesenchymal cells glycoproteins, see proteins
basin of attraction of 57 during 142, 148 glycosaminoglycans 138
stable or attractor 55, 57, 60 gel 12, 42, 146 heparin 150
unstable 55 gelation, gelation transition 145--147, hyaluronan 143, 211
¬‚uid mosaic model 84 see also sol--gel transition in membrane proteins 81
focal adhesion, see cell junction gene 8, see also cell adhesion in proteoglycans 81
follicle cell, see cell molecule, morphogen, gonads 224
fractals 197--199, 200, 250 transcription factor gradient 156
free diffusion, see diffusion constitutively active 64 electrical 14
friction 14 developmentally regulated 52, electrochemical 14, 234--236
due to extracellular matrix 46 64 in evolutionary scenario 251, 252,
internal 16--17 gap 260 253, 256
frictional coef¬cient 14, 19 homeobox 257, 260--261 in particle current 235
of tissues 96, 97 housekeeping 52, 64 in sedimentation of yolk platelets
frictional motion 19, see also bacteria, Hox 257 108, 254
coasting maternal 46 of surface tension 40
frozen zone, see vertebrate limb pair-rule 256, 260 velocity, at liquid--liquid interface
fruit ¬‚y, see Drosophila melanogaster segment-polarity 256 209
furrow 42 template-competent 52 gradient of chemical or molecular
transcribable 52 concentration 13, 14, 15, 69,
G1-phase, see interphase zygotic 46 157, 161, 168--169, 173, see also
G2-phase, see interphase gene expression 4, 8, 39, 64, 156, 167, morphogen
gametes 223, 227, 244 178 as gate 164, 254
gametogenesis 224 in animal cap cells 173, 178 chemotactic, produced by egg 232
gap junction 78, 133 asymmetric 191 formation by emergent
gastrulation 24, 27, 78, 108--122 axis-associated 178, 184 mechanism 254
and convergent extension 100, computational approaches to generation by diffusion in tissues
117--122 measurement 248 174--176
and evolutionary scenario 255 differential 2, 248 in Kerszberg-Changeux model of
and Meinhardt reaction--diffusion pair-rule 261 neurulation 125, 156
model 181--184 pro¬le of 64 induction of mesoderm by
and mesoderm induction 162 stripes in 258, 265 171--173
and Notch-Delta pathway 162, zygotic 239 of adhesive molecules (haptotactic)
168--169 gene--gene coupling constant (in 135, 150, 157
de¬nition of 69, 99 model of Salazar-Ciudad et al.) of Dpp in the Drosophila wing disk
delamination in 109 264 174, 176
332 INDEX


of FGF8 in somitogenesis 164 in vitro systems 2, 58, 95, 133, kinetochore 25, 26
of ¬bronectin in precartilage 205--206 tension 25
condensation 219 induction
of gap gene products in the of mesoderm 156, 162 Lagrange multiplier 33
Drosophila embryo 257, 261 of neural plate 122 lamellipodia 36, 37
of maternal gene products in the of vertebral column 117 laminin 138
Drosophila embryo 260, 261, inertial motion 19, see also bacteria, Lander et al. model of morphogen
257 coasting diffusion 174--176
of TGF-β-like molecule in inhibitor, see morphogen Laplace pressure 33, 34, 36, 42
Niewukoop center 184 inner cell mass 27 Laplace™s equation 33, 34, 35
of VEGF-like molecule in inositol trisphosphate (IP3 ) 239, 244 lateral aspect (of embryo) 135
vasculogenesis 201 receptors 240 left--right asymmetry 160, 161, 162,
grasshopper 260 integrin, see cell adhesion molecule 168--169, 191
segmentation in 257 interaction energy of cells 45 Lewis model for somitic oscillator
gravity 108, 177, 253 intercalation 111--113, 119 164--168
gut (digestive tube, intestine) 172, interfacial energy 30, 31, 103, ligand 83
186, 224 121 limb 148, see also vertebrate limb
interfacial tension 30, 34, 210 bud 148, 211
haploid cell, see cell in MDT 141 fore 148
haptotaxis 135, 157, 219, 225 intermediate ¬lament 7, 12 hind 148
He--Dembo model for cleavage 43 internal friction, see friction limit cycle 55
heart 179, 190 interphase 26 in Tyson--Novak model 59
four-chambered 191, see also DNA synthesis (S-phase) 25 in cell cycle 59
cardiac looping time gap 1 (G1-phase) 25 MPF cycle 59
heart muscle 191, 199 time gap 2 (G2-phase) 25 phase of 63
hemangioblast 194 intussusceptive growth 196 linear stability analysis 55, 99,
hemidesmosome, see cell junction invagination 36, 37, 101, 109, 116, 128--130, 170, 171, 219
Hensen™s node 131, 184, 186 see also gastrulation lipid bilayer, see membrane
Hentschel et al. model for limb isologous diversi¬cation, see lipid membrane, see membrane
development 213--215, 220 Kaneko--Yomo model liquid crystals 132
hindbrain 95 ˜˜liquid” tissues 94, 100, 105, 189,
Holtfreter--Townes experiment juxtacrine signaling, see signaling 206, 251, see also
90 Steinberg--Phillips model and
homologs of chromosome 225 Kaneko--Yomo model for cell Mittenthal--Mazo model
homophilic, see cell adhesion differentiation- 52, 69--76 lobules (of glands) 204, 211
Hookean regime 21 community effect in 70 loss angle 147, 151
Hooke™s law 21 isologous diversi¬cation 70, 254 in MDT 147
Hopf bifurcation, see bifurcation Kartagener (immotile-cilia) syndrome loss modulus 145, see also viscoelastic
horseshoe crab 256, 258 230 moduli
human genes 52 Keller model for cell differentiation Lubkin--Li model, for salivary gland
humerus 211, 217 65--69, 254, see also morphogenesis 205--210
hyalin (protein) 233 autoregulatory network lumen formation 79, 99, 100, 194,
hyaline layer (of egg) 30, 44, 46 Kerszberg--Changeux model for 251
hydrophilic 39, 82 neurulation 125--126, 127, 156, lungs 189, 204
hydrophobic 82 see also neurulation lymphocytes 84
Hydra 90, 155 compared with Drasdo--Forgacs
organizer in 178 model 126 matrix-driven translocation (MDT)
hypoblast 131 compared with Mittenthal--Mazo 133, 139, 141, 142
model 126 M-phase, see mitosis
ideal gas 16 kidney 204 M-phase promoting factor (MPF)
imaginal disc 104, 173 tubules 134, 152, 189 58
immiscible liquids 34, 142 kinesin, see molecular motor and mechanical wave 223
immunoglobulin superfamiliy, see protein mechanochemical coupling 244
cell adhesion molecule kinetic energy 9 medial 135

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