Index
345
R-stage/NR-stage, transcriptomic/
proteomic level (biological process
regulation), 296
zebrafsh response, 295
Spinal cord injury (SCI), cellular response,
291, 293
R-stages/NR-stages, 293
Spinal cord regeneration
axon regeneration, 294
biological processes, identif cation,
294–296
neural stem/progenitor cells, role, 293–294
neurogenesis, 293–294
observations, 289–290
present status, 290–296
study, Xenopus laevis (model organism),
290–291
understanding, 289
S subgenomes
asymmetrical evolution, 159, 161
identifcation, 158–159, 160–161
Stage NF20 embryos, RNA-seq/ChIP-seq
analyses, 265
Stage NF20 Xenopus embryo, schematic, 266
Stage-specifc microsurgeries, performing, 52
Steinbeisser, Herbert, 45
Stomach, endoderm organ fate, 270
Structure-function mutagenesis, usage, 27
Subgenomes, evolution, 161
Surani, Azim, 45
Symmetrization, rotation, 25–26
Syndromic craniosynostosis, description, 251
T
T3 treatment, 294
Tadpole behavior, prof ling/quantif cation
ability, 281
Tailbud, dorsal half embryo, 48
Tail oscillations, motion recording, 285
Takahashi, Shuji, 163
Talin protein, information relay, 130
Targeted nucleases, usage, 212–214
Targeting induced local lesions in genomes
(TILLING), 211
screen, usage, 211
TATA-binding protein, pre-initiation complex
involvement, 331
TATA box, usage, 176
Taussig, Helen Brooke, 233
TAZ (Hippo signaling pathway component), 71
TBX20 mutations, presence, 235
tbxt (pan-mesodermal marker)
inhibition, 95
regulation, 188
Tbxt-expressing cells, change, 188
Tc1/mariner-type DNA transposons,
distribution, 159
TCF proteins, repressing, 31
Tdgf1.3, maternal supply, 30
Teleost lineage, WGD (occurrence), 163
Temperature-inducible hsp70 promoter, usage,
209
Temporal collinearity, def nition (ambiguity),
163
Tetracycline-inducible (TRE) promoter, usage,
209
TGFβ2 (transcriptional-level regulation), 71
Thyroid hormone (TH) levels, increase, 294
Thyroid, pharyngeal endoderm (relationship),
268
TILLING. See Targeting induced local lesions
in genomes
Tissue differentiation, 45–47
Wnt signaling, 65
Tissue remodeling, 296
Tissue-specifc promoters, usage, 209
TMEM16A (calcium-dependent chloride
channel ), 147
activation, 146
discovery, 144, 146
TMT-C+, usage, 197
TMT MS-3, usage, 197
Toll-like receptor (TLR) genes, impact, 314
Tolloid chordinase, 47
Tomlin, S.G., 8
Topologically associating domains (TADs), 173
Trachea, endoderm organ fate, 268
Tracheal-esophageal (T-E) f stula/esophageal
atresia, 260
Tracheal-esophageal (T-E) morphogenesis, 268
Tracheoesophageal separation, regulation, 269
Transcription activator-like effector nucleases
(TALENs), 301
apc TALEN mRNAs, targeted injection
(usage), 305
students, 212
systems, usage, 290
TALEN-mediated genome editing, 303
TALEN-mediated TSG disruption, 304–305
tumor model, generation, 305
Transcriptional reprogramming, usage, 330
Transcription factors (TFs)
binding, chromatin accessibility
(relationship), 177–178
binding, physical sites (identif cation), 190
CRMs, relationship, 188
docking, 185
expression, 268
importance, 132–133
neural crest cell transcription factors (NCCTFs), encoding, 105
regulation, Vegt/Vegt-induced Nodal
signals (usage), 30
target DNA sequence binding, 78
Transforming growth factor β (Tgfβ), encoding,
26–27, 30
Transgene construction, streamlining, 208–209
Transgenic strategies, dependence, 210
Transgenic Xenopus
generation, 207–209
pTransgenesis, usage, 208–209
technology development, 207–208
uses, 209–210
Transient receptor potential (TRP) cation
channels, 146
Transient receptor potential melastatin (TRPM)
family, 146–147
Transmembrane receptors, Fizzled family
receptors (binding), 65
Transposable elements, 314
localization, 180
Treacher Collins syndrome, 250
Treslin/TICRR, usage, 19
Trithorax group genes, identif cation, 178
Tumor dependencies (identif cation), GEXM
(usage), 305–306
Tumor-immune system interactions, 303
Tumor induction, 303
Tumor progression, in vivo monitoring tools,
307–308
Twinned embryos, result, 26
Twist1/Twist2 proteins (bHLH transcription
factors), mesodermal development role,
129–130
U
Ultraviolet (UV) irradiation, usage, 326
Undiluted cell lysates, making, 200
Unmethylated CpGs, capture, 174
UUCAC/UUUCU motifs, presence, 27
V
Vasointestinal peptide, 143
Vegetally localized mRNAs, 28
encoding, velo1 (usage), 33
vegt
endodermal identity establishment, 34
endoderm/mesoderm, maternal control, 29–30
locus, 175
mRNA, maternal role (assessment), 29–30
Vegt (maternal T-box transcription factor),
importance, 187
Velol1, usage, 33–34
Ventral BMP signaling, expression restriction,
268
Ventral genes, BMP4 signaling (impact), 45
Ventral half embryo, 48
Ventral mesenchyme, appearance, 186
Ventral mesoderm, formation, 188
Ventral-posterior GRN, 265
Ventral segments 3/4, progeny, 46
Ventral signaling center, 45
Ventx clusters, 165
Vertebrates
cardiogenesis, studies, 235
development, molecules/genes (roles), 127
embryonic development, regulatory network
diagrams (establishment), 185–186
embryonic development, Wnt signaling
(integrated understanding), 69
gastrulation, 68
neural crest, development/evolution, 125
notch signaling pathway, scheme, 79
somitogenesis, Clock/Wavefront hypothesis
(postulation), 107, 111
vg1 clusters, 163, 165
Vinculin protein, information relay, 130
Visual stimulus, learned associations, 281–282
Voltage sensor, 144
W
Waddington, C.H., 7, 132
Wagler, Johann Georg, 4
footnote, 6
Water-transporting channel sensitivity, 146
Wavefront hypothesis, postulation, 107, 111
Weissman, August, 126
Whole genome bisulfte sequencing, 174
Whole genome duplication (WGD), 155–156
usage, 162–163
Whole genome sequences, publications, 157
Whole genome sequencing (WGS), 157
Williams, Daniel Hale, 234
Wingless-type MMTV integration site (Wnt)
genes, cloning efforts, 27
Wnt11b, classif cation, 32
Wnt antagonists
expression, signaling, 263
overexpression, 32
345
R-stage/NR-stage, transcriptomic/
proteomic level (biological process
regulation), 296
zebrafsh response, 295
Spinal cord injury (SCI), cellular response,
291, 293
R-stages/NR-stages, 293
Spinal cord regeneration
axon regeneration, 294
biological processes, identif cation,
294–296
neural stem/progenitor cells, role, 293–294
neurogenesis, 293–294
observations, 289–290
present status, 290–296
study, Xenopus laevis (model organism),
290–291
understanding, 289
S subgenomes
asymmetrical evolution, 159, 161
identifcation, 158–159, 160–161
Stage NF20 embryos, RNA-seq/ChIP-seq
analyses, 265
Stage NF20 Xenopus embryo, schematic, 266
Stage-specifc microsurgeries, performing, 52
Steinbeisser, Herbert, 45
Stomach, endoderm organ fate, 270
Structure-function mutagenesis, usage, 27
Subgenomes, evolution, 161
Surani, Azim, 45
Symmetrization, rotation, 25–26
Syndromic craniosynostosis, description, 251
T
T3 treatment, 294
Tadpole behavior, prof ling/quantif cation
ability, 281
Tailbud, dorsal half embryo, 48
Tail oscillations, motion recording, 285
Takahashi, Shuji, 163
Talin protein, information relay, 130
Targeted nucleases, usage, 212–214
Targeting induced local lesions in genomes
(TILLING), 211
screen, usage, 211
TATA-binding protein, pre-initiation complex
involvement, 331
TATA box, usage, 176
Taussig, Helen Brooke, 233
TAZ (Hippo signaling pathway component), 71
TBX20 mutations, presence, 235
tbxt (pan-mesodermal marker)
inhibition, 95
regulation, 188
Tbxt-expressing cells, change, 188
Tc1/mariner-type DNA transposons,
distribution, 159
TCF proteins, repressing, 31
Tdgf1.3, maternal supply, 30
Teleost lineage, WGD (occurrence), 163
Temperature-inducible hsp70 promoter, usage,
209
Temporal collinearity, def nition (ambiguity),
163
Tetracycline-inducible (TRE) promoter, usage,
209
TGFβ2 (transcriptional-level regulation), 71
Thyroid hormone (TH) levels, increase, 294
Thyroid, pharyngeal endoderm (relationship),
268
TILLING. See Targeting induced local lesions
in genomes
Tissue differentiation, 45–47
Wnt signaling, 65
Tissue remodeling, 296
Tissue-specifc promoters, usage, 209
TMEM16A (calcium-dependent chloride
channel ), 147
activation, 146
discovery, 144, 146
TMT-C+, usage, 197
TMT MS-3, usage, 197
Toll-like receptor (TLR) genes, impact, 314
Tolloid chordinase, 47
Tomlin, S.G., 8
Topologically associating domains (TADs), 173
Trachea, endoderm organ fate, 268
Tracheal-esophageal (T-E) f stula/esophageal
atresia, 260
Tracheal-esophageal (T-E) morphogenesis, 268
Tracheoesophageal separation, regulation, 269
Transcription activator-like effector nucleases
(TALENs), 301
apc TALEN mRNAs, targeted injection
(usage), 305
students, 212
systems, usage, 290
TALEN-mediated genome editing, 303
TALEN-mediated TSG disruption, 304–305
tumor model, generation, 305
Transcriptional reprogramming, usage, 330
Transcription factors (TFs)
binding, chromatin accessibility
(relationship), 177–178
binding, physical sites (identif cation), 190
CRMs, relationship, 188
docking, 185
expression, 268
importance, 132–133
neural crest cell transcription factors (NCCTFs), encoding, 105
regulation, Vegt/Vegt-induced Nodal
signals (usage), 30
target DNA sequence binding, 78
Transforming growth factor β (Tgfβ), encoding,
26–27, 30
Transgene construction, streamlining, 208–209
Transgenic strategies, dependence, 210
Transgenic Xenopus
generation, 207–209
pTransgenesis, usage, 208–209
technology development, 207–208
uses, 209–210
Transient receptor potential (TRP) cation
channels, 146
Transient receptor potential melastatin (TRPM)
family, 146–147
Transmembrane receptors, Fizzled family
receptors (binding), 65
Transposable elements, 314
localization, 180
Treacher Collins syndrome, 250
Treslin/TICRR, usage, 19
Trithorax group genes, identif cation, 178
Tumor dependencies (identif cation), GEXM
(usage), 305–306
Tumor-immune system interactions, 303
Tumor induction, 303
Tumor progression, in vivo monitoring tools,
307–308
Twinned embryos, result, 26
Twist1/Twist2 proteins (bHLH transcription
factors), mesodermal development role,
129–130
U
Ultraviolet (UV) irradiation, usage, 326
Undiluted cell lysates, making, 200
Unmethylated CpGs, capture, 174
UUCAC/UUUCU motifs, presence, 27
V
Vasointestinal peptide, 143
Vegetally localized mRNAs, 28
encoding, velo1 (usage), 33
vegt
endodermal identity establishment, 34
endoderm/mesoderm, maternal control, 29–30
locus, 175
mRNA, maternal role (assessment), 29–30
Vegt (maternal T-box transcription factor),
importance, 187
Velol1, usage, 33–34
Ventral BMP signaling, expression restriction,
268
Ventral genes, BMP4 signaling (impact), 45
Ventral half embryo, 48
Ventral mesenchyme, appearance, 186
Ventral mesoderm, formation, 188
Ventral-posterior GRN, 265
Ventral segments 3/4, progeny, 46
Ventral signaling center, 45
Ventx clusters, 165
Vertebrates
cardiogenesis, studies, 235
development, molecules/genes (roles), 127
embryonic development, regulatory network
diagrams (establishment), 185–186
embryonic development, Wnt signaling
(integrated understanding), 69
gastrulation, 68
neural crest, development/evolution, 125
notch signaling pathway, scheme, 79
somitogenesis, Clock/Wavefront hypothesis
(postulation), 107, 111
vg1 clusters, 163, 165
Vinculin protein, information relay, 130
Visual stimulus, learned associations, 281–282
Voltage sensor, 144
W
Waddington, C.H., 7, 132
Wagler, Johann Georg, 4
footnote, 6
Water-transporting channel sensitivity, 146
Wavefront hypothesis, postulation, 107, 111
Weissman, August, 126
Whole genome bisulfte sequencing, 174
Whole genome duplication (WGD), 155–156
usage, 162–163
Whole genome sequences, publications, 157
Whole genome sequencing (WGS), 157
Williams, Daniel Hale, 234
Wingless-type MMTV integration site (Wnt)
genes, cloning efforts, 27
Wnt11b, classif cation, 32
Wnt antagonists
expression, signaling, 263
overexpression, 32