344
Index
Pre-placodal ectoderm (PPE), formation, 105
Prepattern genes, balanced expression, 99
Pre-placodal ectoderm (PPE)
appearance, 186
development, Hes genes (role), 107
formation, 105
Primary ciliary dyskinesia (PCD), 226
Primary neurogenesis, 99, 102
Hes1-7 genes, involvement, 102
Primordial germ cell (PGC)
formation, maternal control, 32–34
induction, 32–33
specifcation, germ plasm mRNAs (study), 33
Progenitor-restricted TFs, molecular
mechanisms, 266
Pro-infammatory (TH1) cells, cytokine
production, 314
Proliferating cell nuclear antigen-interacting
protein (PIP) box, usage, 18
Proliferating cell nuclear antigen (PCNA),
interaction, 18
Proneural genes, impact, 99
Pro-neural soxb1 expression, repressing,
128–129
Protein expression
developmental atlas, 201–202
encoding, 201
Proteins
degradation, impact, 15–16
post-translational sequence editing, 199
recruitment steps, 18
Proteoglycans, importance, 69
Proteomics
cell biology, relationship, 200
high-resolution proteomic analyses, 197–200
single-cell proteomics, 202–203
protocadherin 8 (pcdh8), repression, 111, 116
Proxy-cancer phenotype, presence, 306
Pseudogenes, cluster feature, 163
Pseudo-stratifed epithelial structure, recovery,
2932
pTransgenesis, usage, 208–209
R
Rabbit globin gene, eukaryotic mRNA
isolation, 9
Rana catesbiana studies, 290
Rana pipiens eggs
enucleated eggs, endoderm cells
(differentiation), 326
nuclei, usage, 14
Rana pipiens sperm nuclei, usage, 14
ranid species, study, 278
RAPGEF5, blocking, 239
RAR (receptor construct), usage, 54–55
RBPJ (DNA-binding protein), participation/
mediation, 78
Reactive oxygen species (ROSs), role, 291
Receptors (biophysics/pharmacological
properties), Xenopus oocytes (usage), 143
Recombinant DNA technologies, invention, 9
Red blood cells (RBCs), inf ltration, 291
Regenerative (R-) mechanisms, comparison,
289, 291
Regenerative (R-) stages, 294, 295
Regional neural inducers, model (Mangold), 53
Region-specifc microsurgeries, performing, 52
Regulative development, 25
Regulatory substrate, 173–174
Repetitive elements, heterochromatin marks, 180
Replication
dynamics (study), Xenopus egg extracts
(usage), 20
licensing, 17–18
origin f ring, 20
replication-coupled chromatin assembly
dynamics, 178
timing, concept (development), 20
Repression, histone modifcations (usage), 181
Reprogramming. See Nuclear reprogramming
feld (establishment), SCNT experiments
(usage), 326
gene expression patterns, change, 330
Respiratory progenitor induction, regulation,
269
Restriction enzyme-mediate integration
(REMI), 207–208
Retinal hyperproliferation, 304
Retinal pigmented epithelial (RPE) cells,
accumulation, 238
Retinoic acid (RA)
biosynthesis, 314
signaling, 54–55, 270
Reverse genetics, dsBreaks (usage), 212, 214
Reverse transcription (RT) reagents, usage, 203
Rhodopsin, multi-pass membrane-bound
protein, 239–240
RhoGEF TRIO, 212–213
Ribonucleic acid (RNA). See Messenger RNA
RNA-based SOM, generation, 191
RNA-binding proteins, identif cation, 200
RNAi, usage, 246, 305
RNA SOM metacluster linkage, 191
Ribosomal DNA (rDNA), separation, 9
Ribosome profling (RIBO-seq), 200
Right half embryo, sagittal cut, 48
Roeder, Bob, 9
Roux, Wilhelm, 43, 126
R-stage/NR-stage, transcriptomic/proteomic
level (biological process regulation), 296
RT-qPCR, usage, 163
rtTA expression, control, 209
RXR (receptor construct), usage, 54–55
S
Sanger method, usage, 157
Scaffolds
BAC location, 159
mapping, 157
Sclerostin (SOST), binding, 66, 68
Secreted frizzled-related protein (sFRP), Wnt
binding ability (loss), 45
Secreted ligand activation, 32
Selenoproteins, sequence, 199
Self-organizing map (SOM)
application, 190–191
linked SOM method, 191
metaclusters, presence, 191
RNA-based SOM, generation, 191
Sensory left-right organizer (sLRO) cells, prefow stages, 227
Sex chromosomes, W-specif c/Z-specif c
regions, 161
Sex-determining gene (DM-W ), female
specif city, 161
sfrp1 expression, conf nement, 70
Shapiro, Hillel, 7
Shared molecular pathways, 239–240
shRNA, usage, 209
Siamois clusters, 165
siamois gene cluster, sia expansion, 165
Signaling molecules, dynamic temporal
expression, 59
Signaling pathways
directions/questions, 71
importance, 132–133
usage, 54–58
Wnt/beta-catenin (β-catenin) signaling
pathway, 56–57
Signal integration, 57–58
Signal transduction (mediation), NICD (usage), 77
Simple sequence length polymorphism (SSLP),
157
Single-cell proteomics, 202–203
push, 203
Single-nucleotide polymorphism (SNP),
313–314
array analysis, usage, 236
Single-stranded DNA, replication, 17
Skpl-cullin-F-box protein (CCF) ubiquitin
ligase, impact, 19
Skull bones, growth, 250
Slack, Jonathan, 9
Sleeping Beauty, usage, 211–212
Slome, David, 7
Smad4-dependent Tgfβ signaling,
inhibitor, 31
Smit, Pierre Jacques (Xenopus tadpole
illustration), 5
snai1 expression, regulation, 129
snai2 expression
induction, 127
repression, 129
Snail family transcription factors, importance,
130
Sodium channels, identif cation, 146–147
Somatic cell nuclear transfer (SCNT), 325
experiments, impact, 326
Somite, appearance, 186
Somitogenesis, 107, 111, 116
notch/genes/pathways, interplay, 112, 116
notch ligands/hes genes, involvement, 111
notch pathway genes, expression, 112–115
Somitomeres
segmental prepattern, 111
whorls, formation, 111
Southern blotting, usage, 181
Sox2 protein
expression, 293
reduction, 294
Sox17, 263
Spatial exclusion, 189
subcircuits, 190
Spemann, Hans
egg constriction experiments, 25, 26
Spemann-Mangold experiment, 43, 48
Spemann organizer
formation, 186
inductive signals, 46
molecules, search, 44–45
neural induction, 47
relocalization, self-regulation, 47–48
S phase, M phase (transitions), 17
Spinal cord injury (SCI), 289
comparative cellular response (R-stage/
NR-stage), 292–293
early cellular response, 291
intermediate cellular response, 291, 293
late cellular response, 293
R-stage/NR-stage spinal cord, histological
differences, 291
Index
Pre-placodal ectoderm (PPE), formation, 105
Prepattern genes, balanced expression, 99
Pre-placodal ectoderm (PPE)
appearance, 186
development, Hes genes (role), 107
formation, 105
Primary ciliary dyskinesia (PCD), 226
Primary neurogenesis, 99, 102
Hes1-7 genes, involvement, 102
Primordial germ cell (PGC)
formation, maternal control, 32–34
induction, 32–33
specifcation, germ plasm mRNAs (study), 33
Progenitor-restricted TFs, molecular
mechanisms, 266
Pro-infammatory (TH1) cells, cytokine
production, 314
Proliferating cell nuclear antigen-interacting
protein (PIP) box, usage, 18
Proliferating cell nuclear antigen (PCNA),
interaction, 18
Proneural genes, impact, 99
Pro-neural soxb1 expression, repressing,
128–129
Protein expression
developmental atlas, 201–202
encoding, 201
Proteins
degradation, impact, 15–16
post-translational sequence editing, 199
recruitment steps, 18
Proteoglycans, importance, 69
Proteomics
cell biology, relationship, 200
high-resolution proteomic analyses, 197–200
single-cell proteomics, 202–203
protocadherin 8 (pcdh8), repression, 111, 116
Proxy-cancer phenotype, presence, 306
Pseudogenes, cluster feature, 163
Pseudo-stratifed epithelial structure, recovery,
2932
pTransgenesis, usage, 208–209
R
Rabbit globin gene, eukaryotic mRNA
isolation, 9
Rana catesbiana studies, 290
Rana pipiens eggs
enucleated eggs, endoderm cells
(differentiation), 326
nuclei, usage, 14
Rana pipiens sperm nuclei, usage, 14
ranid species, study, 278
RAPGEF5, blocking, 239
RAR (receptor construct), usage, 54–55
RBPJ (DNA-binding protein), participation/
mediation, 78
Reactive oxygen species (ROSs), role, 291
Receptors (biophysics/pharmacological
properties), Xenopus oocytes (usage), 143
Recombinant DNA technologies, invention, 9
Red blood cells (RBCs), inf ltration, 291
Regenerative (R-) mechanisms, comparison,
289, 291
Regenerative (R-) stages, 294, 295
Regional neural inducers, model (Mangold), 53
Region-specifc microsurgeries, performing, 52
Regulative development, 25
Regulatory substrate, 173–174
Repetitive elements, heterochromatin marks, 180
Replication
dynamics (study), Xenopus egg extracts
(usage), 20
licensing, 17–18
origin f ring, 20
replication-coupled chromatin assembly
dynamics, 178
timing, concept (development), 20
Repression, histone modifcations (usage), 181
Reprogramming. See Nuclear reprogramming
feld (establishment), SCNT experiments
(usage), 326
gene expression patterns, change, 330
Respiratory progenitor induction, regulation,
269
Restriction enzyme-mediate integration
(REMI), 207–208
Retinal hyperproliferation, 304
Retinal pigmented epithelial (RPE) cells,
accumulation, 238
Retinoic acid (RA)
biosynthesis, 314
signaling, 54–55, 270
Reverse genetics, dsBreaks (usage), 212, 214
Reverse transcription (RT) reagents, usage, 203
Rhodopsin, multi-pass membrane-bound
protein, 239–240
RhoGEF TRIO, 212–213
Ribonucleic acid (RNA). See Messenger RNA
RNA-based SOM, generation, 191
RNA-binding proteins, identif cation, 200
RNAi, usage, 246, 305
RNA SOM metacluster linkage, 191
Ribosomal DNA (rDNA), separation, 9
Ribosome profling (RIBO-seq), 200
Right half embryo, sagittal cut, 48
Roeder, Bob, 9
Roux, Wilhelm, 43, 126
R-stage/NR-stage, transcriptomic/proteomic
level (biological process regulation), 296
RT-qPCR, usage, 163
rtTA expression, control, 209
RXR (receptor construct), usage, 54–55
S
Sanger method, usage, 157
Scaffolds
BAC location, 159
mapping, 157
Sclerostin (SOST), binding, 66, 68
Secreted frizzled-related protein (sFRP), Wnt
binding ability (loss), 45
Secreted ligand activation, 32
Selenoproteins, sequence, 199
Self-organizing map (SOM)
application, 190–191
linked SOM method, 191
metaclusters, presence, 191
RNA-based SOM, generation, 191
Sensory left-right organizer (sLRO) cells, prefow stages, 227
Sex chromosomes, W-specif c/Z-specif c
regions, 161
Sex-determining gene (DM-W ), female
specif city, 161
sfrp1 expression, conf nement, 70
Shapiro, Hillel, 7
Shared molecular pathways, 239–240
shRNA, usage, 209
Siamois clusters, 165
siamois gene cluster, sia expansion, 165
Signaling molecules, dynamic temporal
expression, 59
Signaling pathways
directions/questions, 71
importance, 132–133
usage, 54–58
Wnt/beta-catenin (β-catenin) signaling
pathway, 56–57
Signal integration, 57–58
Signal transduction (mediation), NICD (usage), 77
Simple sequence length polymorphism (SSLP),
157
Single-cell proteomics, 202–203
push, 203
Single-nucleotide polymorphism (SNP),
313–314
array analysis, usage, 236
Single-stranded DNA, replication, 17
Skpl-cullin-F-box protein (CCF) ubiquitin
ligase, impact, 19
Skull bones, growth, 250
Slack, Jonathan, 9
Sleeping Beauty, usage, 211–212
Slome, David, 7
Smad4-dependent Tgfβ signaling,
inhibitor, 31
Smit, Pierre Jacques (Xenopus tadpole
illustration), 5
snai1 expression, regulation, 129
snai2 expression
induction, 127
repression, 129
Snail family transcription factors, importance,
130
Sodium channels, identif cation, 146–147
Somatic cell nuclear transfer (SCNT), 325
experiments, impact, 326
Somite, appearance, 186
Somitogenesis, 107, 111, 116
notch/genes/pathways, interplay, 112, 116
notch ligands/hes genes, involvement, 111
notch pathway genes, expression, 112–115
Somitomeres
segmental prepattern, 111
whorls, formation, 111
Southern blotting, usage, 181
Sox2 protein
expression, 293
reduction, 294
Sox17, 263
Spatial exclusion, 189
subcircuits, 190
Spemann, Hans
egg constriction experiments, 25, 26
Spemann-Mangold experiment, 43, 48
Spemann organizer
formation, 186
inductive signals, 46
molecules, search, 44–45
neural induction, 47
relocalization, self-regulation, 47–48
S phase, M phase (transitions), 17
Spinal cord injury (SCI), 289
comparative cellular response (R-stage/
NR-stage), 292–293
early cellular response, 291
intermediate cellular response, 291, 293
late cellular response, 293
R-stage/NR-stage spinal cord, histological
differences, 291