340
Index
Extracellular environment, active remodeling
(requirement), 130
Extracellular matrix (ECM)
components, presence, 296
degradation, 268
role, 291, 293
Extraocular motor nerves, extracellular
recordings, 285
Extreme anterior domain (EAD)
cells, impact, 247
craniofacial organizer function, 249
craniofacial signaling center, comparison, 249
expression, 248
identif cation, 249
LOF/GOF limitation, 245–246
F
F0 pkd1 knockout tadpole, 215
False discovery rate (FDR), 198
Familial adenomatous polyposis (FAP), 304
Fate map, 53
Feedforward loops (FFLs), subcircuits, 190
FERM-domain containing protein, impact, 57
Fetal alcohol spectrum disorder (FASD)
defects, polymorphisms (impact), 314
result, 316
Fetal growth restriction (FGR), induction, 319
FGF3/FGF8, transcription (activation), 58
FGF/MAPK/GSK3 phosphorylations, impact, 47
Fibroblast growth factor (FGF)
caudalizing factor, 56
gradients, cell specif cation, 246
ligands, ectopic expression, 55
pathway, role, 55
Fibroblast growth factor (FGF) signaling, 55–56
promotion, 128
requirement, 105
TF expression, 268
Fischberg, Michaïl, 7–8, 326
FISH analyses, usage, 158–159
Fish lines, 315
Flow-induced post-transcriptional repression, 229
Flow-induced symmetry, 226
Follicle-enclosed oocytes
presence, 147
receptor presence, 143
Follicle, native ion currents, 147
Force-felds, framework, 279
Forward genetic screens, usage, 210–211
Four-channel confocal image, merged image, 46
Foxal-4, 263
Foxd3 (forkhead box/winged helix transcription
factor), importance, 130
FOXG1 genes, linkage, 147
Foxh1, Tle recruitment, 177
Frizzled2 receptor (Fzd2), 239
Frizzled3 responsive element, identif cation, 71
Frizzled-like gene Frzb-1, impact, 57
Frog egg
fertilization, appearance, 26
post-fertilization, appearance, 26
Functional cDNA expression library screening,
usage, 57
Functional neurobiology, in vitro preparations
(usage), 282–285
G
Gain-of-function analysis, 186
Gain-of-function assays, usage, 67
Gain-of-function experiments, 102
complementing, 54–55
Gain of function (GOF), limitation, 245–246
Gain-of-function (GOF) mutation, 304
Gall, Joe, 9
Galnt11/GalNAc O-glycosylation, role, 237
Gap junctions, connexins (relationship), 146
Gardner's syndrome, 304
Gastrula
embryos, transplantation, 52–53
gastrula-stage endoderm patterning, 263, 265
mesoderm/endoderm, 187
stage endoderm patterning, 264
Gastrulating embryo, diagram, 91
Gastrulation, 265
assays, usage, 69
movements, impact, 52
Gastulation, gene regulatory networks (usage),
188
GATA-1a/b, erythropoiesis function, 156
Gata4-6, 263
Gaunt, Stephen, 45
Geminin protein, impact, 18
Gene cluster, formation, 163
Gene expression
chromatin accessibility, 176–178
reference, 163
regulation, 71
Gene regulatory network (GRN), 127, 261
component set, 129
constructs, 203–204
impact, 186–188
regulation, novel/non-canonical genes
(importance), 129
schematic representation, 247
status, 190–192
subcircuits, 188–190
usage, 185, 187, 188
Genes
batteries (expression), TF regulation, 185
clusters, cluster-specifc gene expansions, 164
editing, 210–214
gene-specifc studies, 251
hox genes, analyses, 162–163
models, ref nement, 203
near genes, heterochromatin marks, 180
organization, detail, 163, 165
structures, intron-exon-UTR annotation
(adjustment), 198
study, novel roles (discovery), 237–238
symbols (high-resolution proteomic
analyses), 199–200
Xenopus gene editing, future, 308
Genetically altered Xenopus (creation), targeted
nucleases (usage), 212–214
Genetically engineered cancer model organism,
Xenopus (research tool), 301–302
Genetically engineered Xenopus models
(GEXMs), 302, 303
clinically relevant GEXMs, generation,
303–304
usage, 305–307
Genetic research, diploid genome (impact), 302
Genetics, 210–214
reverse genetics, dsBreaks (usage), 212, 214
Genetic Xenopus tropicalis cancer model, TALENmediated TSG disruption, 304–305
Genomes
assembly scaffolds, 199
comparative genome analysis, 166
editing tools, advances, 207
human genome, natural polymorphisms,
313–314
notch signaling responsiveness, 82
Xenopus laevis genome, sequencing/
assembly, 157–158
zygotic genome activation (onset),
chromatin assembly (relationship), 177
Genome wide association screens (GWASs),
usage, 252
Genomic DNA, sequencing, 157
Genomic resources, improvement, 211
Germ cell development, Dazl family
involvement, 33
Germ layer
boundaries, refnement, 91, 95
patterning, maternal control, 29–32
segregation, notch targets (involvement),
95, 98
theory, 126
Germ layer development
hes/hey genes, impact, 96–97
notch pathway, core components, 92–94
Germ layer formation, 90–91, 95, 98
gene regulatory network, impact, 186–188
Germ layer induction
maternal control, 29–32
maternal secreted molecules, 30
Germ plasm
identif cation, 32–33
maternal germ plasm, assembly, 33–34
mRNAs, study, 33
presence, 26
Global transitions, genome-wide analyses, 174
Glycosylation, 237
Goldenhar syndrome, 250
Goosecoid, identif cation, 44–45
goosecoid-related homeobox genes, PCR
screen (usage), 225–226
GPCR proteins, impact, 57
Growth factor signaling pathways (revealing),
Xenopus experiments (usage), 259
gsc CRMs, input integration, 188
GSK3 (canonical signal transduction
component), 66
GTP binding, encoding, 116
Guanine nuclear exchange factor, identif cation,
238–239
Gunn, J.W.C., 3, 7
Gurdon, John, 7–9, 143, 325, 326
H
H2A.Z histone variant, presence, 176–177
H3K4ME3
DNA recovery, 179
increase, 180
mark, involvement, 176
H3K4 methylation, increase, 179
H3K27 acetylation mark, deposit, 176
Hamburger, Viktor, 7, 44
Haramoto, Yoshikazu, 163
Hardman, John Maurice, 234
Harland, Richard, 263
Hartwell, Leland (genetic experiments), 13
Hay, Elizabeth, 91
Head formation, Wnt pathway, 56–57
Head mesoderm, appearance, 186
Health (insights), Xenopus functional
neurobiology (impact), 277
Heasman, Janet, 29
Index
Extracellular environment, active remodeling
(requirement), 130
Extracellular matrix (ECM)
components, presence, 296
degradation, 268
role, 291, 293
Extraocular motor nerves, extracellular
recordings, 285
Extreme anterior domain (EAD)
cells, impact, 247
craniofacial organizer function, 249
craniofacial signaling center, comparison, 249
expression, 248
identif cation, 249
LOF/GOF limitation, 245–246
F
F0 pkd1 knockout tadpole, 215
False discovery rate (FDR), 198
Familial adenomatous polyposis (FAP), 304
Fate map, 53
Feedforward loops (FFLs), subcircuits, 190
FERM-domain containing protein, impact, 57
Fetal alcohol spectrum disorder (FASD)
defects, polymorphisms (impact), 314
result, 316
Fetal growth restriction (FGR), induction, 319
FGF3/FGF8, transcription (activation), 58
FGF/MAPK/GSK3 phosphorylations, impact, 47
Fibroblast growth factor (FGF)
caudalizing factor, 56
gradients, cell specif cation, 246
ligands, ectopic expression, 55
pathway, role, 55
Fibroblast growth factor (FGF) signaling, 55–56
promotion, 128
requirement, 105
TF expression, 268
Fischberg, Michaïl, 7–8, 326
FISH analyses, usage, 158–159
Fish lines, 315
Flow-induced post-transcriptional repression, 229
Flow-induced symmetry, 226
Follicle-enclosed oocytes
presence, 147
receptor presence, 143
Follicle, native ion currents, 147
Force-felds, framework, 279
Forward genetic screens, usage, 210–211
Four-channel confocal image, merged image, 46
Foxal-4, 263
Foxd3 (forkhead box/winged helix transcription
factor), importance, 130
FOXG1 genes, linkage, 147
Foxh1, Tle recruitment, 177
Frizzled2 receptor (Fzd2), 239
Frizzled3 responsive element, identif cation, 71
Frizzled-like gene Frzb-1, impact, 57
Frog egg
fertilization, appearance, 26
post-fertilization, appearance, 26
Functional cDNA expression library screening,
usage, 57
Functional neurobiology, in vitro preparations
(usage), 282–285
G
Gain-of-function analysis, 186
Gain-of-function assays, usage, 67
Gain-of-function experiments, 102
complementing, 54–55
Gain of function (GOF), limitation, 245–246
Gain-of-function (GOF) mutation, 304
Gall, Joe, 9
Galnt11/GalNAc O-glycosylation, role, 237
Gap junctions, connexins (relationship), 146
Gardner's syndrome, 304
Gastrula
embryos, transplantation, 52–53
gastrula-stage endoderm patterning, 263, 265
mesoderm/endoderm, 187
stage endoderm patterning, 264
Gastrulating embryo, diagram, 91
Gastrulation, 265
assays, usage, 69
movements, impact, 52
Gastulation, gene regulatory networks (usage),
188
GATA-1a/b, erythropoiesis function, 156
Gata4-6, 263
Gaunt, Stephen, 45
Geminin protein, impact, 18
Gene cluster, formation, 163
Gene expression
chromatin accessibility, 176–178
reference, 163
regulation, 71
Gene regulatory network (GRN), 127, 261
component set, 129
constructs, 203–204
impact, 186–188
regulation, novel/non-canonical genes
(importance), 129
schematic representation, 247
status, 190–192
subcircuits, 188–190
usage, 185, 187, 188
Genes
batteries (expression), TF regulation, 185
clusters, cluster-specifc gene expansions, 164
editing, 210–214
gene-specifc studies, 251
hox genes, analyses, 162–163
models, ref nement, 203
near genes, heterochromatin marks, 180
organization, detail, 163, 165
structures, intron-exon-UTR annotation
(adjustment), 198
study, novel roles (discovery), 237–238
symbols (high-resolution proteomic
analyses), 199–200
Xenopus gene editing, future, 308
Genetically altered Xenopus (creation), targeted
nucleases (usage), 212–214
Genetically engineered cancer model organism,
Xenopus (research tool), 301–302
Genetically engineered Xenopus models
(GEXMs), 302, 303
clinically relevant GEXMs, generation,
303–304
usage, 305–307
Genetic research, diploid genome (impact), 302
Genetics, 210–214
reverse genetics, dsBreaks (usage), 212, 214
Genetic Xenopus tropicalis cancer model, TALENmediated TSG disruption, 304–305
Genomes
assembly scaffolds, 199
comparative genome analysis, 166
editing tools, advances, 207
human genome, natural polymorphisms,
313–314
notch signaling responsiveness, 82
Xenopus laevis genome, sequencing/
assembly, 157–158
zygotic genome activation (onset),
chromatin assembly (relationship), 177
Genome wide association screens (GWASs),
usage, 252
Genomic DNA, sequencing, 157
Genomic resources, improvement, 211
Germ cell development, Dazl family
involvement, 33
Germ layer
boundaries, refnement, 91, 95
patterning, maternal control, 29–32
segregation, notch targets (involvement),
95, 98
theory, 126
Germ layer development
hes/hey genes, impact, 96–97
notch pathway, core components, 92–94
Germ layer formation, 90–91, 95, 98
gene regulatory network, impact, 186–188
Germ layer induction
maternal control, 29–32
maternal secreted molecules, 30
Germ plasm
identif cation, 32–33
maternal germ plasm, assembly, 33–34
mRNAs, study, 33
presence, 26
Global transitions, genome-wide analyses, 174
Glycosylation, 237
Goldenhar syndrome, 250
Goosecoid, identif cation, 44–45
goosecoid-related homeobox genes, PCR
screen (usage), 225–226
GPCR proteins, impact, 57
Growth factor signaling pathways (revealing),
Xenopus experiments (usage), 259
gsc CRMs, input integration, 188
GSK3 (canonical signal transduction
component), 66
GTP binding, encoding, 116
Guanine nuclear exchange factor, identif cation,
238–239
Gunn, J.W.C., 3, 7
Gurdon, John, 7–9, 143, 325, 326
H
H2A.Z histone variant, presence, 176–177
H3K4ME3
DNA recovery, 179
increase, 180
mark, involvement, 176
H3K4 methylation, increase, 179
H3K27 acetylation mark, deposit, 176
Hamburger, Viktor, 7, 44
Haramoto, Yoshikazu, 163
Hardman, John Maurice, 234
Harland, Richard, 263
Hartwell, Leland (genetic experiments), 13
Hay, Elizabeth, 91
Head formation, Wnt pathway, 56–57
Head mesoderm, appearance, 186
Health (insights), Xenopus functional
neurobiology (impact), 277
Heasman, Janet, 29