Index
339
Cytoplasmic dorsalizing activity, GBP proteins
(impact), 31–32
Cytoskeleton, control, 127–128
Cytostatic factor (CSF)
activity, impact, 15
arrest dependence, 16
D
Dactylethra (genus name, usage), 4
Dand5
f ow-induced post-transcriptional
repression, 229
fow target, evolution, 229
identifcation, 226, 228
nodal-Dand5 module, high sequence
diversity, 230
repression, 236
Dand5 mRNA, post-transcriptional regulation,
228
Daudin, François Marie, 3–4
Xenopus description, 5
DaVinci, Leonardo, 233
Dawid, Igor, 9
Degradation-ensuring sequence motif (degon),
presence, 16
Deleted in AZoospermia-like (Dazl) family,
germ cell development, 33
De novo methylation, involvement, 179
Deoxyribonucleic acid (DNA)
overreplication, prevention, 18
packaging, 173–174
polymerase inhibitors, addition, 20
recovery, 179
re-replication, prevention, 18
segments, involvement, 314
SOM, metacluster linkage, 191
Deoxyribonucleic acid (DNA) methylation
barrier, 332
dynamics, 180–181
histone modif cations, repression/
modulation (contrast), 180–181
repression/crosstalk, histone modif cations
(usage), 181
Deoxyribonucleic acid (DNA) replication, 176
control, 17–18
DNA replication-coupled chromatin
assembly, impact, 178
feedback, 15
induction, Xenopus egg cytoplasm (impact), 13
initiation, control, 18–19
low-speed Xenopus egg extract, usage
(advantages), 17
ordering events, 18–20
origins/timing, 20
study, 13
De Robertis, Eddy, 263
Desmoid tumors, 304
Deuchar, Elizabeth, 3, 8
Developmental biology
Gurdon, impact, 8
researchers, impact, 8–9
Developmental cell signaling, mysteries, 238–239
Development/disease, genetic variation
(impact), 316–320
Dexter, John S., 77
Diabetes, 260, 268
Dickkopf (Dkk1)
experiments, loss, 69
induction, 57
Dickkopf (Dkk2) functions, 69
Dickkopf (DKK) protein family, binding, 66, 68
DIF-FRAC, 200
Diploid genome, impact, 302
Disease
insights, Xenopus functional neurobiology
(impact), 277
modeling, Xenopus genetic variability
(exploitation), 319–320
Disease ontology (DO) resources, 260
DKL1 genes, linkage, 147
Dlc/Notch/RBPG signaling, experimental
perturbation (consequences), 111
dll1STU/dll1 knock-down, impact, 95
Dominant-negative (DN) receptors,
introduction, 54–55
Dorsal blastomeres, β-catenin (nuclear
localization), 67
Dorsal center development, prevention, 91
Dorsal gene activation, β-catenin regulation
function, 31
Dorsal involuting marginal zone (DIMZ), 91
Dorsal midline (DML) development
hes/hey genes, impact, 96–97
notch pathway, core components, 92–94
Dorsal midline (DML) precursors, Notch
pathway differential expression, 98
Dorsal midline (DML) tissues, 98–99
Dorsal-ventral (D-V) axis
establishment, 90
patterning, notch (role), 91
Dorsal-ventral (D-V) patterning, signaling
components, 43, 44
Dorsal-ventral (D-V) tissues, origins (diagram), 46
Dorsal β-catenin, cytoplasmic activation, 31–32
Dorsal midline (DML)
germ layers development, notch pathway
(core components), 92–94
segregation, 91
Double strand break (DSB) repair, 305
Driesch, Hans, 43
Drosophila fruit f y
chordin, homologue, 47
mutant phenotype, discovery, 77
Trithorax/Polycobm group gene
identif cation, 178
usage, 43
Drosophila melanogaster, homeobox gene
screen, 235
dsBreaks, usage, 212, 214
D-V gradient, generation, 265
D-V histotypic cell differentiation, analysis, 45
D-V patterning, 268
Dynein Axonemal Particles (DynAPs), usage,
200
Dysmorphisms, description, 250
E
EAF 2 (transcriptional-level regulation), 71
Early blastula mesoderm/endoderm, 187
Early embryogenesis, notch signaling
functions, 77
Early gastrula mesoderm/endoderm, 187
Early-localizing mRNAs, 27
Early Xenopus embryogenesis, information
source, 302
Ectoderm
development, pluripotency-related
transcription factor (Pou5f ) homologues
(usage), 31
specif cation, 30–31
EGFP expression, 293
EGF receptor, deletion, 316
Egg constriction experiments, 25
Egg & Ego (Slack), 9
Egg storage histones, 178
Einsteck experiment, 52
Embryological experiments, Xenopus (usage), 210
Embryonic development, chromatin remodeling
(dynamics), 173
Embryonic manipulation-based approaches,
usage, 279
Embryos
antagonistic H3K4ME3/H3K27ME3 marks,
acquisition, 178–180
histone modifcation maps, 174
proxy-cancer phenotype, presence, 306
EMC1 variants, molecular connection, 71
Endoderm
commitment phase, 263
development, phases (timing), 261
endoderm-specifc transcription factor,
co-occupation, 178
formation, molecular basis, 261–263
gastrula-stage endoderm patterning, 263, 265
germ layer formation, conceptual phases, 262
induction phase, 263
maternal control, 29–30
maternal pre-pattern phase, 262–263
neurula-stage endoderm patterning,
265–266, 266
organ fate, induction, 266–271
organogenesis, temporal overview,
260–261, 261
patterning, 263–266
pharyngeal endoderm, thyroid
(relationship), 268
specifcation, gene regulatory networks
(usage), 187
Endodermal lineages, formation, 186
Endogenous ion channels, usage, 145–146
Entwicklungsmechanic, 126
ENU amplifcation, usage, 211
Ependymoglial cells, comparison, 290
Epidermal differentiation, hes/hey genes (role),
103–104
Epidermoid cysts, 304–305
Epigenetic poising mechanism, usage, 31
Epigenome
H3K9 methylation/H4K20me3 decoration,
180
Epigenome maps, 174, 176
Epithelial sodium channel (ENaC), beta subunit
(encoding), 146–147
Epithelium-to-mesenchyme transition (EMT),
125, 128, 302
anti-EMT compounds, range, 306
neural crest EMT/migration, 129–130
Erythropoiesis, GATA-1a/b function, 156
Esophageal atresia, 260
Esophagus, endoderm organ fate, 268
Eukaryotic mRNA isolation, 9
Eukaryotic transcription factor (TFIIIA),
isolation, 91
European Xenopus Resource Centre (EXRC),
transgenic line, 208
Exogenous DNA, carrying, 207
Exome sequencing, 236
Experimental embryology, 43–44, 126
studies, 51–54
Extracellular Chordin/Tolloid/Tsg/CV2/BMP
pathway, components, 44
339
Cytoplasmic dorsalizing activity, GBP proteins
(impact), 31–32
Cytoskeleton, control, 127–128
Cytostatic factor (CSF)
activity, impact, 15
arrest dependence, 16
D
Dactylethra (genus name, usage), 4
Dand5
f ow-induced post-transcriptional
repression, 229
fow target, evolution, 229
identifcation, 226, 228
nodal-Dand5 module, high sequence
diversity, 230
repression, 236
Dand5 mRNA, post-transcriptional regulation,
228
Daudin, François Marie, 3–4
Xenopus description, 5
DaVinci, Leonardo, 233
Dawid, Igor, 9
Degradation-ensuring sequence motif (degon),
presence, 16
Deleted in AZoospermia-like (Dazl) family,
germ cell development, 33
De novo methylation, involvement, 179
Deoxyribonucleic acid (DNA)
overreplication, prevention, 18
packaging, 173–174
polymerase inhibitors, addition, 20
recovery, 179
re-replication, prevention, 18
segments, involvement, 314
SOM, metacluster linkage, 191
Deoxyribonucleic acid (DNA) methylation
barrier, 332
dynamics, 180–181
histone modif cations, repression/
modulation (contrast), 180–181
repression/crosstalk, histone modif cations
(usage), 181
Deoxyribonucleic acid (DNA) replication, 176
control, 17–18
DNA replication-coupled chromatin
assembly, impact, 178
feedback, 15
induction, Xenopus egg cytoplasm (impact), 13
initiation, control, 18–19
low-speed Xenopus egg extract, usage
(advantages), 17
ordering events, 18–20
origins/timing, 20
study, 13
De Robertis, Eddy, 263
Desmoid tumors, 304
Deuchar, Elizabeth, 3, 8
Developmental biology
Gurdon, impact, 8
researchers, impact, 8–9
Developmental cell signaling, mysteries, 238–239
Development/disease, genetic variation
(impact), 316–320
Dexter, John S., 77
Diabetes, 260, 268
Dickkopf (Dkk1)
experiments, loss, 69
induction, 57
Dickkopf (Dkk2) functions, 69
Dickkopf (DKK) protein family, binding, 66, 68
DIF-FRAC, 200
Diploid genome, impact, 302
Disease
insights, Xenopus functional neurobiology
(impact), 277
modeling, Xenopus genetic variability
(exploitation), 319–320
Disease ontology (DO) resources, 260
DKL1 genes, linkage, 147
Dlc/Notch/RBPG signaling, experimental
perturbation (consequences), 111
dll1STU/dll1 knock-down, impact, 95
Dominant-negative (DN) receptors,
introduction, 54–55
Dorsal blastomeres, β-catenin (nuclear
localization), 67
Dorsal center development, prevention, 91
Dorsal gene activation, β-catenin regulation
function, 31
Dorsal involuting marginal zone (DIMZ), 91
Dorsal midline (DML) development
hes/hey genes, impact, 96–97
notch pathway, core components, 92–94
Dorsal midline (DML) precursors, Notch
pathway differential expression, 98
Dorsal midline (DML) tissues, 98–99
Dorsal-ventral (D-V) axis
establishment, 90
patterning, notch (role), 91
Dorsal-ventral (D-V) patterning, signaling
components, 43, 44
Dorsal-ventral (D-V) tissues, origins (diagram), 46
Dorsal β-catenin, cytoplasmic activation, 31–32
Dorsal midline (DML)
germ layers development, notch pathway
(core components), 92–94
segregation, 91
Double strand break (DSB) repair, 305
Driesch, Hans, 43
Drosophila fruit f y
chordin, homologue, 47
mutant phenotype, discovery, 77
Trithorax/Polycobm group gene
identif cation, 178
usage, 43
Drosophila melanogaster, homeobox gene
screen, 235
dsBreaks, usage, 212, 214
D-V gradient, generation, 265
D-V histotypic cell differentiation, analysis, 45
D-V patterning, 268
Dynein Axonemal Particles (DynAPs), usage,
200
Dysmorphisms, description, 250
E
EAF 2 (transcriptional-level regulation), 71
Early blastula mesoderm/endoderm, 187
Early embryogenesis, notch signaling
functions, 77
Early gastrula mesoderm/endoderm, 187
Early-localizing mRNAs, 27
Early Xenopus embryogenesis, information
source, 302
Ectoderm
development, pluripotency-related
transcription factor (Pou5f ) homologues
(usage), 31
specif cation, 30–31
EGFP expression, 293
EGF receptor, deletion, 316
Egg constriction experiments, 25
Egg & Ego (Slack), 9
Egg storage histones, 178
Einsteck experiment, 52
Embryological experiments, Xenopus (usage), 210
Embryonic development, chromatin remodeling
(dynamics), 173
Embryonic manipulation-based approaches,
usage, 279
Embryos
antagonistic H3K4ME3/H3K27ME3 marks,
acquisition, 178–180
histone modifcation maps, 174
proxy-cancer phenotype, presence, 306
EMC1 variants, molecular connection, 71
Endoderm
commitment phase, 263
development, phases (timing), 261
endoderm-specifc transcription factor,
co-occupation, 178
formation, molecular basis, 261–263
gastrula-stage endoderm patterning, 263, 265
germ layer formation, conceptual phases, 262
induction phase, 263
maternal control, 29–30
maternal pre-pattern phase, 262–263
neurula-stage endoderm patterning,
265–266, 266
organ fate, induction, 266–271
organogenesis, temporal overview,
260–261, 261
patterning, 263–266
pharyngeal endoderm, thyroid
(relationship), 268
specifcation, gene regulatory networks
(usage), 187
Endodermal lineages, formation, 186
Endogenous ion channels, usage, 145–146
Entwicklungsmechanic, 126
ENU amplifcation, usage, 211
Ependymoglial cells, comparison, 290
Epidermal differentiation, hes/hey genes (role),
103–104
Epidermoid cysts, 304–305
Epigenetic poising mechanism, usage, 31
Epigenome
H3K9 methylation/H4K20me3 decoration,
180
Epigenome maps, 174, 176
Epithelial sodium channel (ENaC), beta subunit
(encoding), 146–147
Epithelium-to-mesenchyme transition (EMT),
125, 128, 302
anti-EMT compounds, range, 306
neural crest EMT/migration, 129–130
Erythropoiesis, GATA-1a/b function, 156
Esophageal atresia, 260
Esophagus, endoderm organ fate, 268
Eukaryotic mRNA isolation, 9
Eukaryotic transcription factor (TFIIIA),
isolation, 91
European Xenopus Resource Centre (EXRC),
transgenic line, 208
Exogenous DNA, carrying, 207
Exome sequencing, 236
Experimental embryology, 43–44, 126
studies, 51–54
Extracellular Chordin/Tolloid/Tsg/CV2/BMP
pathway, components, 44