Index
343
Neurobiology
observations, Xenopus (usage), 278–279
present status, experimental approaches,
279, 281–282
Neurocristopathies, 250
Neurodevelopmental disorders (NDDs),
239–240, 281
Neurogenesis, 293–295
differentiation, hes/hey genes (role), 103–104
Neuronal circuit formation (assessment),
embryonic manipulation-based
approaches (usage), 279
Neurons, calcium-imaging, 285
Neurula patterning stages, 270
Neurula-stage endoderm patterning, 265–266,
266
New Head hypothesis, 126
NF35-NF43 early endoderm organ
morphogenesis, occurrence, 260–261
NFAT (calcium-sensitive transcription factor),
activation, 68
Nicotinic acetylcholine receptor (nAChR), multipass membrane-bound protein, 239–240
Niehrs, Christof, 263
Nieuwkoop center (NC), 90
Nieuwkoop, Pieter, 7, 59
Nitric oxide (NO) production, 249
nkx2.5-GFP insert, presence, 212
N-methyl-N-nitrosourea (NMU), usage, 302
nodal3 clusters, 163, 165
nodal5 clusters, 163, 165
Nodal antagonist (CerS), impact, 30
Nodal cascade, impact, 225–226
Nodal-Dand5 module, high sequence diversity,
230
Nodal-related genes, activation, 30
Nodal signaling
propagation, 225
spatiotemporal gradients, impact, 29
Non-canonical notch signaling, 78
Non-canonical Wnt/PCP signaling, 67
Non-canonical Wnt signaling, 68
canonical Wnt signaling, integration, 68
gene expression, regulation, 71
importance, 127
Non-histone chromatin state maps, 174
Non-involuting marginal zone (NIMZ), 91
contribution, 90–91
transcripts, accumulation, 904
Non-regenerative (NR-) mechanisms,
comparison, 289, 291
Non-regenerative (NR-) stages, 295
Sox2 reduction, 294
notch1 activity, regulation, 90
Notch1/RBPJ signaling, response (change), 95
Notch/genes/pathways, interplay, 111, 116
Notch Intracellular Domain (NICD), usage,
77, 237
Notch ligands, 99, 102
impact, 111
Notch pathway, 77–78
components, 81
components, impact, 99
core components, 106
genes, expression, 112–115
hes1-7/hey genes responsiveness,
experimental evidence, 83–87
involvement, 107
roles, 77, 107
Notch perturbation, time-dependent opposite
responses, 105
Notch receptors/ligands, early expression
patterns, 79
Notch signaling, 78
action, modes, 79
canonical notch signaling, 78
functions, 77
glycosylation, 237
immotile:motile cilia ratio establishment, 237
increase, 308
involvement, 116
non-canonical notch signaling, 78
pathway, 71
pathway, reactivation, 209
Notch targets, involvement, 95, 98
Notochord, appearance, 186
Nuclear pore complexes (NPCs), 238
Nuclear reprogramming
alternative methods, usage, 328
changes, 327–329
DNA methylation barrier, 332
histone modif cations/resistance, 332
methods, schematic, 328
process, molecular insights, 329–332
promotion, oocyte factors, 330–331
Xenopus laevis oocytes/eggs/egg extracts,
usage, 327
Nuclear reprogramming, inception, 325–327
Nuclear transport receptor (NTR), ARM
action, 238
Nuclear transport (NT), usage, 326
Nucleoplasmic extract (NPE)
creation, process, 19
development, 19
Nucleoporins, presence, 237–238
Nucleosome
dynamics/accessibility, histone variants/
linker histones (usage), 176–177
positions, importance, 173
Nucleus, canonical Wnt signaling, 66
Nup188, inner ring component, 238
O
OFF-memory, 180
Oken, Lorenz, 4
-Omics, neural crest development (insights),
127–131
Online Mendelian Inheritance in Man
(OMIM), 260
ON-memory, 180
Oocyte factors, 330–331
schematic model, 331
Oocytes
follicle-enclosed oocytes, receptor
presence, 143
histones, 178
mRNA localization, mechanisms, 27
RNA polymerases, presence, 9
Optical coherence tomography (OCT), 236
Ordinary differential equations (ODEs), usage,
69–70
Organ fate induction, combinatorial signals, 267
Origin recognition complex (ORC), 18
otx1 (endodermal identity), 34
Outbred lines, advantages, 316
P
Pancreas, endoderm organ fate, 268, 270
Pancreatic hypoplasia/agenesis, study, 270
PAPC (transcriptional-level regulation), 71
Pardue, Mary Lou, 9
Patient-derived CHD disease mechanisms,
discovery, 237–240
pCMBSS, water-transporting channel
sensitivity, 146
pDXTP (destination vector), usage, 209
Peacock, Bevill, 233
Peaker, Malcolm, 4
Pediatric Cardiac Genetic Consortium (PCGC),
exome sequencing, 236
Peptide-spectra matching, protein reference set
(obtaining), 199
Pericentriolar material (PCM), 238
Peripheral nervous system (PNS), morphophysiological information, 277
Perturbations, impact, 174
Perutz, Max, 4
Phantom sequences, providing, 199
Pharmacological properties, Xenopus oocytes
(usage), 143
Pharyngeal endoderm, thyroid (relationship), 268
Phloretin, water-transporting channel
sensitivity, 146
Phosphorylated Smad1/5/9 activity, D-V
gradient (generation), 265
Phospho-Smad1/5/8,usage, 47
PI3K/Akt signaling, increase, 133
PIF/harbinger-type transposons, distribution,
159
Pigmentation, melanocytes (impact), 131
Placode development, notch pathway role, 107
Platt, Julia, 126
Pluripotency
demonstration, 132
maintenance, 128
understanding, Xenopus (usage), 325
Pluripotency-related transcription factor
(Pou5f), homologues (usage), 31
Pluripotent embryonic cells, segregation, 260
Pluripotent stem cells (PSCs), 259
human PSC-derived endoderm, 270
human PSCs, differentiation, 260, 265, 268
induced pluripotent stem cells (iPSCs),
generation, 329
lines, generation, 327–328
Pole plasm, 26
Polycomb group genes, identif cation, 178
Polycomb Repression Complex 2 (PRC2),
transcription function, 176
Polymerase chain reaction (PCR)
amplifcation, usage, 211
screen, 225–226
usage, 198
Polymorphisms
impact, 314
simple sequence length polymorphism
(SSLP), 157
Polyploid organisms, whole genome sequences
(publications), 157
Polyubiquitination, 47
Positive autofeedback loop, 189
Posterior neural markers, induction, 56
Post-fertilization embryos (arrest), CSF
(impact), 16
Post-involuted mesendoderm, usage, 59
Post-translational modif cations, 202
Post-translational protein modif cation, 202
Precise integration into target chromosome
(PITCh) system, usage, 308
Pregnancy Diagnosis Center, 8
Xenopus source, 7
343
Neurobiology
observations, Xenopus (usage), 278–279
present status, experimental approaches,
279, 281–282
Neurocristopathies, 250
Neurodevelopmental disorders (NDDs),
239–240, 281
Neurogenesis, 293–295
differentiation, hes/hey genes (role), 103–104
Neuronal circuit formation (assessment),
embryonic manipulation-based
approaches (usage), 279
Neurons, calcium-imaging, 285
Neurula patterning stages, 270
Neurula-stage endoderm patterning, 265–266,
266
New Head hypothesis, 126
NF35-NF43 early endoderm organ
morphogenesis, occurrence, 260–261
NFAT (calcium-sensitive transcription factor),
activation, 68
Nicotinic acetylcholine receptor (nAChR), multipass membrane-bound protein, 239–240
Niehrs, Christof, 263
Nieuwkoop center (NC), 90
Nieuwkoop, Pieter, 7, 59
Nitric oxide (NO) production, 249
nkx2.5-GFP insert, presence, 212
N-methyl-N-nitrosourea (NMU), usage, 302
nodal3 clusters, 163, 165
nodal5 clusters, 163, 165
Nodal antagonist (CerS), impact, 30
Nodal cascade, impact, 225–226
Nodal-Dand5 module, high sequence diversity,
230
Nodal-related genes, activation, 30
Nodal signaling
propagation, 225
spatiotemporal gradients, impact, 29
Non-canonical notch signaling, 78
Non-canonical Wnt/PCP signaling, 67
Non-canonical Wnt signaling, 68
canonical Wnt signaling, integration, 68
gene expression, regulation, 71
importance, 127
Non-histone chromatin state maps, 174
Non-involuting marginal zone (NIMZ), 91
contribution, 90–91
transcripts, accumulation, 904
Non-regenerative (NR-) mechanisms,
comparison, 289, 291
Non-regenerative (NR-) stages, 295
Sox2 reduction, 294
notch1 activity, regulation, 90
Notch1/RBPJ signaling, response (change), 95
Notch/genes/pathways, interplay, 111, 116
Notch Intracellular Domain (NICD), usage,
77, 237
Notch ligands, 99, 102
impact, 111
Notch pathway, 77–78
components, 81
components, impact, 99
core components, 106
genes, expression, 112–115
hes1-7/hey genes responsiveness,
experimental evidence, 83–87
involvement, 107
roles, 77, 107
Notch perturbation, time-dependent opposite
responses, 105
Notch receptors/ligands, early expression
patterns, 79
Notch signaling, 78
action, modes, 79
canonical notch signaling, 78
functions, 77
glycosylation, 237
immotile:motile cilia ratio establishment, 237
increase, 308
involvement, 116
non-canonical notch signaling, 78
pathway, 71
pathway, reactivation, 209
Notch targets, involvement, 95, 98
Notochord, appearance, 186
Nuclear pore complexes (NPCs), 238
Nuclear reprogramming
alternative methods, usage, 328
changes, 327–329
DNA methylation barrier, 332
histone modif cations/resistance, 332
methods, schematic, 328
process, molecular insights, 329–332
promotion, oocyte factors, 330–331
Xenopus laevis oocytes/eggs/egg extracts,
usage, 327
Nuclear reprogramming, inception, 325–327
Nuclear transport receptor (NTR), ARM
action, 238
Nuclear transport (NT), usage, 326
Nucleoplasmic extract (NPE)
creation, process, 19
development, 19
Nucleoporins, presence, 237–238
Nucleosome
dynamics/accessibility, histone variants/
linker histones (usage), 176–177
positions, importance, 173
Nucleus, canonical Wnt signaling, 66
Nup188, inner ring component, 238
O
OFF-memory, 180
Oken, Lorenz, 4
-Omics, neural crest development (insights),
127–131
Online Mendelian Inheritance in Man
(OMIM), 260
ON-memory, 180
Oocyte factors, 330–331
schematic model, 331
Oocytes
follicle-enclosed oocytes, receptor
presence, 143
histones, 178
mRNA localization, mechanisms, 27
RNA polymerases, presence, 9
Optical coherence tomography (OCT), 236
Ordinary differential equations (ODEs), usage,
69–70
Organ fate induction, combinatorial signals, 267
Origin recognition complex (ORC), 18
otx1 (endodermal identity), 34
Outbred lines, advantages, 316
P
Pancreas, endoderm organ fate, 268, 270
Pancreatic hypoplasia/agenesis, study, 270
PAPC (transcriptional-level regulation), 71
Pardue, Mary Lou, 9
Patient-derived CHD disease mechanisms,
discovery, 237–240
pCMBSS, water-transporting channel
sensitivity, 146
pDXTP (destination vector), usage, 209
Peacock, Bevill, 233
Peaker, Malcolm, 4
Pediatric Cardiac Genetic Consortium (PCGC),
exome sequencing, 236
Peptide-spectra matching, protein reference set
(obtaining), 199
Pericentriolar material (PCM), 238
Peripheral nervous system (PNS), morphophysiological information, 277
Perturbations, impact, 174
Perutz, Max, 4
Phantom sequences, providing, 199
Pharmacological properties, Xenopus oocytes
(usage), 143
Pharyngeal endoderm, thyroid (relationship), 268
Phloretin, water-transporting channel
sensitivity, 146
Phosphorylated Smad1/5/9 activity, D-V
gradient (generation), 265
Phospho-Smad1/5/8,usage, 47
PI3K/Akt signaling, increase, 133
PIF/harbinger-type transposons, distribution,
159
Pigmentation, melanocytes (impact), 131
Placode development, notch pathway role, 107
Platt, Julia, 126
Pluripotency
demonstration, 132
maintenance, 128
understanding, Xenopus (usage), 325
Pluripotency-related transcription factor
(Pou5f), homologues (usage), 31
Pluripotent embryonic cells, segregation, 260
Pluripotent stem cells (PSCs), 259
human PSC-derived endoderm, 270
human PSCs, differentiation, 260, 265, 268
induced pluripotent stem cells (iPSCs),
generation, 329
lines, generation, 327–328
Pole plasm, 26
Polycomb group genes, identif cation, 178
Polycomb Repression Complex 2 (PRC2),
transcription function, 176
Polymerase chain reaction (PCR)
amplifcation, usage, 211
screen, 225–226
usage, 198
Polymorphisms
impact, 314
simple sequence length polymorphism
(SSLP), 157
Polyploid organisms, whole genome sequences
(publications), 157
Polyubiquitination, 47
Positive autofeedback loop, 189
Posterior neural markers, induction, 56
Post-fertilization embryos (arrest), CSF
(impact), 16
Post-involuted mesendoderm, usage, 59
Post-translational modif cations, 202
Post-translational protein modif cation, 202
Precise integration into target chromosome
(PITCh) system, usage, 308
Pregnancy Diagnosis Center, 8
Xenopus source, 7