X
346
Index
Wnt/beta-catenin (β-catenin) signaling
pathway, 56
Wnt/BMP/FGF signals, posteriorization,
270–271
Wnt/calcium signaling, 68
Wnt genes, co-discovery, 65
Wnt interactions, directions/questions, 71
Wnt pathways
genes, identif cation, 44
head formation, 56–57
Wnt/PCP/JNK signaling, 68
WNT-PCP pathway/signaling, control, 247, 249
WNT proteins, cell specif cation, 246
Wnt receptor function, 66
Wnt signaling, 29, 65
canonical Wnt signaling, 66, 68
cardiac organogenesis, 69
context-specifc Wnt signaling, 70
embryonic signaling/regulatory
environment, integration, 71
integrated signaling, 69
levels, functional manipulation, 56
modeling, 69–70
pathways, 67
pathways, characterization, 65–69
potentiation, 32
requirement, 105
W-specifc regions, 161, 162
Wylie, Chris, 29
Xelaev1801880tm, identif cation, 199
Xenopus. See Transgenic Xenopus
acquisition, importance, 7
analysis techniques, examples, 280–281
blastula stage endoderm patterning, 264
behavioral performance, 277–278
blastula ectodermal explants, usage, 47
blastula, regional specifcation (model), 26
blastula-stage embryo, fate map
(production), 8–9
cancer modeling, application potential,
305–307
cell-fate reprogramming Xenopus NT
embryos, eff ciency, 332
cell lineages, isolation, 330
clutches (genetic variation), experimental
outcome (schematic representation), 317
clutch variability/experimental design, 317
congenital heart disease, study (future), 240
craniofacial development/disorders, 245
CRISPR mutants, presence, 212
description, 3–4, 6
developmental biology researchers,
involvement, 8–9
digestive/respiratory system development/
disease, modeling, 259
dorsal midline (development), notch
pathway (core components), 92–94
dorsal-ventral patterning, signaling
components, 44
D-V tissues, origins (diagram), 46
early development, histone modif cations
(acquisition/dynamics), 178–180
early embryos (cell lineages), maternal
mRNAs (relationship), 25
egg constriction experiments, 25
egg cytoplasm, DNA replication induction,
13–14
embryonic manipulations, 278–279
endoderm germ layer formation, conceptual
phases, 262
endoderm organogenesis, temporal
overview, 260–261, 261
endoderm patterning, 69
explants, usage, 68
follicle-enclosed oocytes,
electrophysiological characterization,
144
functional neurobiology, 277
gene editing, future, 308
gene-specifc studies, 250, 251
genes study, novel roles (discovery),
237–238
genetically altered Xenopus (creation),
targeted nucleases (usage), 212–214
genetically engineered Xenopus models, 303
genetics/gene editing, 210–214
genetic variability, exploitation, 319–320
hes4-7/hey genes, early expression patterns, 80
hes/hey genes, cross-regulation, 88–89
high-resolution proteomic analyses,
development, 197
history, 3
images, 5
in vitro preparations, applicable
stimulation/recording techniques, 283
laboratory animal, usage (increase), 6–8
laboratory populations, genetic diversity,
316–317
large-scale genomic/genetic resource
development, 211
lines, availability, 315
literature, 9–10
mass spectrometry, usage, 198
maternal inheritance, demonstration, 9
mesendodermal GRN, FFL usage, 190
mesoderm/endoderm specif cation, gene
regulatory networks (usage), 187
metamorphosis, 209
midbrain/hindbrain boundary (MHB)
establishment, hes genes (impact), 110
model, 16, 71–72, 225
model system, success, 65
Nasco laboratory-bred colony, 316
naturally occurring tumors, 302
neural border/descendants, hes genes (role),
108–109
neural border/descendants, notch pathway
(core components), 106
neural crest development, 127–131
neural systems, examples, 280–281
neurogenesis/epidermal differentiation,
hes/hey genes (role), 103–104
oocytes, RNA polymerases (presence), 9
oocytes, test system importance, 29
ORFeome, incompatibility, 208
organ fate induction, combinatorial signals,
267
organizer, 43
organizer, historical background, 43–44
pathways, connection, 237
patient-derived CHD disease mechanisms,
discovery, 237–240
physiological studies, 279
proteomics, 203
rDNA, eukaryotic gene isolation, 9
research, advances, 69–70
research tool, 301–302
respiratory progenitor induction, regulation,
269
RNA-based SOM, generation, 191
sensory-motor capacity, 277–278
simple motor behaviors, 284
somitogenesis, notch pathway gene
(expression), 112–115
source (Pregnancy Diagnosis Center), 7
species, phylogenetic relationships,
160–161
Spemann organizer molecules, search,
44–45
stage NF20 Xenopus embryo, schematic, 266
system, strengths, 202
tracheoesophageal separation, regulation,
269
tract tracing, 278–279
tumor formation/regulation, study, 301
twinned embryos, result, 26
usage, 9, 278–279, 316–320, 325
vegetally localized mRNAs, 28
vertebrate cardiogenesis, studies, 235
wild-caught colony, population, 316
Xenopus BMP4, expression, 45
Xenopus, CHD/HTX (studying)
approaches, 236–237
morphological/developmental benef ts, 236
Xenopus development
localized mRNAs, roles, 27
maternal gene function, analysis, 28–29
overview, 186
Xenopus dorsal midline development
hes/hey genes, impact, 96–97
notch pathway, core components, 92–94
Xenopus egg extracts
cell division control/DNA replication,
study, 13
low-speed Xenopus egg extracts,
advantages, 17
preparation, 19
single-molecule approaches, usage, 20
system, development, 91
tractable system, providing, 19–20
usage, 15–16, 327
utility, increase, 19
Xenopus embryogenesis
control, gene regulatory networks (usage),
185
early Xenopus embryogenesis, information
source, 302
notch signaling, 78
past observations, 186–190
Xenopus embryos
32-cell stage, lineage tracing, 46
cell lineage, predictability, 45–46
early development, schematic, 261
gene regulatory networks (GRNs), usage,
188–190
histone modifcation maps, 174
Xenopus genome
evolution, 155
history, 155–156
sequences, usage (studies), 161–165
sequencing, 157–161, 198
Xenopus germ layers development
hes/hey genes, impact, 96–97
notch pathway, core components, 92–94
Xenopus laevis (XLA)
allotetraploidy, 155
chromosomes, 164
collection, 201
data (peptide-spectra matching), protein
reference set (obtaining), 199
346
Index
Wnt/beta-catenin (β-catenin) signaling
pathway, 56
Wnt/BMP/FGF signals, posteriorization,
270–271
Wnt/calcium signaling, 68
Wnt genes, co-discovery, 65
Wnt interactions, directions/questions, 71
Wnt pathways
genes, identif cation, 44
head formation, 56–57
Wnt/PCP/JNK signaling, 68
WNT-PCP pathway/signaling, control, 247, 249
WNT proteins, cell specif cation, 246
Wnt receptor function, 66
Wnt signaling, 29, 65
canonical Wnt signaling, 66, 68
cardiac organogenesis, 69
context-specifc Wnt signaling, 70
embryonic signaling/regulatory
environment, integration, 71
integrated signaling, 69
levels, functional manipulation, 56
modeling, 69–70
pathways, 67
pathways, characterization, 65–69
potentiation, 32
requirement, 105
W-specifc regions, 161, 162
Wylie, Chris, 29
Xelaev1801880tm, identif cation, 199
Xenopus. See Transgenic Xenopus
acquisition, importance, 7
analysis techniques, examples, 280–281
blastula stage endoderm patterning, 264
behavioral performance, 277–278
blastula ectodermal explants, usage, 47
blastula, regional specifcation (model), 26
blastula-stage embryo, fate map
(production), 8–9
cancer modeling, application potential,
305–307
cell-fate reprogramming Xenopus NT
embryos, eff ciency, 332
cell lineages, isolation, 330
clutches (genetic variation), experimental
outcome (schematic representation), 317
clutch variability/experimental design, 317
congenital heart disease, study (future), 240
craniofacial development/disorders, 245
CRISPR mutants, presence, 212
description, 3–4, 6
developmental biology researchers,
involvement, 8–9
digestive/respiratory system development/
disease, modeling, 259
dorsal midline (development), notch
pathway (core components), 92–94
dorsal-ventral patterning, signaling
components, 44
D-V tissues, origins (diagram), 46
early development, histone modif cations
(acquisition/dynamics), 178–180
early embryos (cell lineages), maternal
mRNAs (relationship), 25
egg constriction experiments, 25
egg cytoplasm, DNA replication induction,
13–14
embryonic manipulations, 278–279
endoderm germ layer formation, conceptual
phases, 262
endoderm organogenesis, temporal
overview, 260–261, 261
endoderm patterning, 69
explants, usage, 68
follicle-enclosed oocytes,
electrophysiological characterization,
144
functional neurobiology, 277
gene editing, future, 308
gene-specifc studies, 250, 251
genes study, novel roles (discovery),
237–238
genetically altered Xenopus (creation),
targeted nucleases (usage), 212–214
genetically engineered Xenopus models, 303
genetics/gene editing, 210–214
genetic variability, exploitation, 319–320
hes4-7/hey genes, early expression patterns, 80
hes/hey genes, cross-regulation, 88–89
high-resolution proteomic analyses,
development, 197
history, 3
images, 5
in vitro preparations, applicable
stimulation/recording techniques, 283
laboratory animal, usage (increase), 6–8
laboratory populations, genetic diversity,
316–317
large-scale genomic/genetic resource
development, 211
lines, availability, 315
literature, 9–10
mass spectrometry, usage, 198
maternal inheritance, demonstration, 9
mesendodermal GRN, FFL usage, 190
mesoderm/endoderm specif cation, gene
regulatory networks (usage), 187
metamorphosis, 209
midbrain/hindbrain boundary (MHB)
establishment, hes genes (impact), 110
model, 16, 71–72, 225
model system, success, 65
Nasco laboratory-bred colony, 316
naturally occurring tumors, 302
neural border/descendants, hes genes (role),
108–109
neural border/descendants, notch pathway
(core components), 106
neural crest development, 127–131
neural systems, examples, 280–281
neurogenesis/epidermal differentiation,
hes/hey genes (role), 103–104
oocytes, RNA polymerases (presence), 9
oocytes, test system importance, 29
ORFeome, incompatibility, 208
organ fate induction, combinatorial signals,
267
organizer, 43
organizer, historical background, 43–44
pathways, connection, 237
patient-derived CHD disease mechanisms,
discovery, 237–240
physiological studies, 279
proteomics, 203
rDNA, eukaryotic gene isolation, 9
research, advances, 69–70
research tool, 301–302
respiratory progenitor induction, regulation,
269
RNA-based SOM, generation, 191
sensory-motor capacity, 277–278
simple motor behaviors, 284
somitogenesis, notch pathway gene
(expression), 112–115
source (Pregnancy Diagnosis Center), 7
species, phylogenetic relationships,
160–161
Spemann organizer molecules, search,
44–45
stage NF20 Xenopus embryo, schematic, 266
system, strengths, 202
tracheoesophageal separation, regulation,
269
tract tracing, 278–279
tumor formation/regulation, study, 301
twinned embryos, result, 26
usage, 9, 278–279, 316–320, 325
vegetally localized mRNAs, 28
vertebrate cardiogenesis, studies, 235
wild-caught colony, population, 316
Xenopus BMP4, expression, 45
Xenopus, CHD/HTX (studying)
approaches, 236–237
morphological/developmental benef ts, 236
Xenopus development
localized mRNAs, roles, 27
maternal gene function, analysis, 28–29
overview, 186
Xenopus dorsal midline development
hes/hey genes, impact, 96–97
notch pathway, core components, 92–94
Xenopus egg extracts
cell division control/DNA replication,
study, 13
low-speed Xenopus egg extracts,
advantages, 17
preparation, 19
single-molecule approaches, usage, 20
system, development, 91
tractable system, providing, 19–20
usage, 15–16, 327
utility, increase, 19
Xenopus embryogenesis
control, gene regulatory networks (usage),
185
early Xenopus embryogenesis, information
source, 302
notch signaling, 78
past observations, 186–190
Xenopus embryos
32-cell stage, lineage tracing, 46
cell lineage, predictability, 45–46
early development, schematic, 261
gene regulatory networks (GRNs), usage,
188–190
histone modifcation maps, 174
Xenopus genome
evolution, 155
history, 155–156
sequences, usage (studies), 161–165
sequencing, 157–161, 198
Xenopus germ layers development
hes/hey genes, impact, 96–97
notch pathway, core components, 92–94
Xenopus laevis (XLA)
allotetraploidy, 155
chromosomes, 164
collection, 201
data (peptide-spectra matching), protein
reference set (obtaining), 199