591

Index

a alloimmunity 399 A/B axis 136 allopatric divergence 84 A/B polarity 137 allopatric populations 83, 86 Abd-B gene 373 allopatry 84 A-P axis 543 allopolyploid populations 90 A-P patterning 555 alveolar macrophages 280 aberrant DNA methylation 510 Alzheimer’s disease 524 abnormal karyotypes 510 amatoxins 36 accumulated molecular change 247 amber 166 acetylators 292 amber codon 57 acetylcholine 322 amber suppression 61 actagardin 53 amber suppression systems 61 actin 13 amino acids 214 actin cytoskeleton 369 aminoglycosides 275 action potential repolarization 433 amnioserosa 549 activation–inhibition dynamics 469 amniotes 472 activator–inhibitor couples 484, 486 amphibians 88, 253, 474, 509 actomyosin 14 amphiphilic molecules 218 adaptation 235 amphiphilic structure 37 adapter dimers 169 amplification 166 adaptive selection 153 amplification protocols 506 adaptive traits 488 ancient DNA 165 adenosine triphosphate 219, 242 ancient epigenome 180 admixture 173 anemia 294 ADP-ribosylation 437 aneuploid embryos 513 adrenal chromaffin cells 319 angiocrine support 581 adrenal medulla 328, 329 annelid worms 141 adverse events 286 annotated genome 95 aganglionic region 342 anterior-to-posterior gradient 543 aggregation factor 393 anterior–posterior axis 361 Agouti signaling protein 481 anteroposterior axis 475 allele 76, 177 anteroposterior gradient 469 allele-specific expression 507 anthropoids 233 allele-specific methylation 509 anti-codon 44 allelic composition 180 anti-retroviral therapy 280 allergenicity 525 antiapoptotic protein 402 allochronic mating 91 antibacterial agents 282 allogeneic transplantation 571 antibiotic activities 39 allografts 400 antibiotic production 42

Frontiers in Developmental Biology: Advances in Molecular Biology and Medicine First Edition. Edited by Robert A. Meyers. © 2019 Wiley-VCH Verlag GmbH & Co. KGaA. Published 2019 by Wiley-VCH Verlag GmbH & Co. KGaA. 592 Index

antibiotic-resistance 179 guidance 337 antibiotic resistance marker 51 axonal elongation 441 antibiotics 179 axonemal dynein 362 antibody affinity 55 AZD5847 295 antibody–antigen binding sites 230 anticancer activity 41 b antimicrobial activity 34, 42 backcross hybrids 82 antimycobacterial activity 285 backcrossing of hybrids 95 apical cell surfaces 373 bacteria 74, 110, 234 apical ectodermal ridge 147 bacterial conjugation 111 apoptosis 6, 10, 369, 399, 506 bacterial death 290 apoptotic degeneration 433 bacterial fermenters 62 3M-approach 286 bacterial gene regulation 234 apteria 475 bacterial genome 234, 236 arabidopsis 191 bacterial genotype 178 arabinogalactan 277 bacteriophage genomes 117 arabinotransferase 277 bacteriophage-mediated transduction 111 arachnids 145 bacteriophages 111 archaic hominins 175 bait molecules 169 archenteron 135 banana 195 argonaute protein 191 Bangladeshi regimen 296 aromatic rings 37 barbicels 472 artemin 327 barcode 169 arthropods 135, 141 barnase 46 artificial insemination 521 basal epithelial sheet 484 asconoid 388 base mismatches 173 assortative mating 78 base pairs 112 astrocyte differentiation 442 basic helix-loop-helix 10, 326, 479 astrocytes 430, 442 basic leucine zipper 10 astroglial marker genes 433 Bateson’s hypothesis 256 asymmetric body 367 Bcd protein 544 asymmetric cell division 420 beak size 259 asymmetric jaw 362 bedaquiline 274 asymmetry 361, 377 behavioral isolation 79 asynchrony 523 Belousov–Zhabotinski reaction 484 atherosclerosis 523 benthic zone 82 atrial natriuretic factor 41 Benzothiazinones 289 atypical protein kinase C 438 beta-hairpin loop 41 auditory tubes 259 biallelic expression 507 autapomorphies 75 bicoid protein 10 autism 432 bidentate metal chelation 56 autocrine signaling 10 bidirectional infection 92 autoimmune destruction 585 bilateria 361 autoimmunity 399 bilaterians 140 autonomic ganglia 322 bioavailability 62, 282 autonomic 317 biodiversity 73 autopod 147 biogeneric 139 autopolyploidy 90 biological evolution 109, 117 autoregulation 555 Biological Species Concept 74 auxin response factor 3, 194 biomineralization 402 auxotrophic host 43 biophysical probes 44, 50 average linkage 239 biosphere 217 axial skeleton 402 biosynthetic gene clusters 33, 35, 63 axis specification 542 biosynthetic logic 50, 60 Index 593 biosynthetic permissibility 53 Capicua 551 bird beak 259 carbohydrate-binding proteins 149 birds 472 carbohydrates 217 bisphenol A 11 5-carboxycytosine 503 Black Death 177 5-carboxylcytosine 437 blastocysts 24, 504 carcass analysis 525 blastoderm 412, 544 carcinogenesis 577 blastomere chirality 376 cardiac differentiation 580 blastomere clones 508 cardiac disease modeling 580 8-blastomere stage 364 cardiac muscle 322 blastomeres 8, 364, 508, 514, 522 cardiac outflow tract 336 blastula/gastrula 386 cardiomyocytes 21 blood flow 318 cartilage tissue 583 blood serum proteins 230 cartilaginous fishes 149 blood vessel networks 583 caspase 400 blood vessels 138, 330, 472, 581 cassettes 42 blunt-ending 167 catalysis 214 body axes 485 catalytic network 220 body axis 386, 407 catecholaminergic phenotype 329 body plan evolution 153 β-catenin 135, 372 body plan formation 417 cathepsin 403 body plan motifs 147 cell adhesion 12 body plans 132 cell chirality 373 bone 177, 402 cell communication system 407 bone cells 166 cell culture 410 bone marrow suppression 295 cell cycle 13, 554 bone morphogenetic protein 4, 319, 391, 469, 480 cell cycle coordination 513 bony plates 472 cell cycle progression 16 bortezomib 49 cell differentiation 6, 14, 132, 395, 500, 571 bottromycins 36 cell division 9, 137 boundary 146 cell ingression 135 brachyury 9, 398 cell junction 396 brain 19 cell lysis 290 brain fatty acid-binding protein 327 brain-derived neurotrophic factor 328 cell membrane 137 brainstem 317 cell migration 12, 141, 325 broad-spectrum antimicrobials 292 cell polarity 574 bronchitis 362 cell proliferation 11, 395 Buffalos 524 cell signals 377 burst-forming unit, erythroid 20 4-cell stage 365, 376 6-cell stage 366 c cell symmetry 252 c-Jun N-terminal kinase 444 cell wall biosynthesis 52 Cact protein 544 cell wall superpolymer 275 cadherin 132 cell-adhesion molecules 487 Cajal–Retzius cell zones 575 cell-adhesion protein 374 calcium carbonate 402 cell-cycle inhibitors 440 calcium oscillations 519 cell-replacement therapies 530 calcium phosphates 403 cell-surface molecules 136 calcium-binding proteins 322 cell-surface receptors 13, 395 camouflage 474 cell-to-cell transmission 574 cancer 446, 522, 584 cell-wall mycolic acid 293 canonical code 34 cell-wall peptidoglycan layer 295 canonical peptide chemical space 37 cellular defense mechanism 399 594 Index

cellular differentiation 21, 500 chromosome condensation 513 cellular mosaic 24 chromosome constitution 513 cellular reprogramming 529 chromosomes 83, 111, 237 cellularization 544, 553 chronological organization 252 cell–cell adhesion 135, 149, 393, 402 cichlid fish 85 cell–cell aggregation 393 cilia defects 362 cell–cell contact 133, 336, 544 ciliary ganglion 331 cell–matrix adhesion 402 ciliary structure 362 central canal 323 cis-regulatory elements 488 central nervous system 281, 318, 401, 549 cis-regulatory module 545 centriole 513 cis-regulatory mutations 488 centromere 252 cis-regulatory regions 433 centrosome 518 clade-specific mechanisms 147 cerebral cortex 339 clades 76, 177 cerebral organoids 20, 576 cladistic analysis 248 cervid species 526 cleavage 366, 420 cetyltrimethylammonium bromide 167 cleidocranial dysplasia 259 CG methylation 205 clinical antibiotics 52 character displacement 90 clock and wavefront model 470 Charles Darwin 73 clock-and-wavefront mechanism 146 chemical space 51 clockwise rotation 372 chemically assisted enucleation 517 clofazimine 296 chemotaxis 484 clonal enrichment 51 chick embryos 336, 485 cloning 22, 500 chimera 23 cloning efficiency 515 chimpanzee 232, 240 cloning technique 23 ChIP-seq 558 cnidaria 416 chloramphenicol acetyltransferase 46 cnidarians 136, 141 choanocytes 387 co-surfactants 218 choanoderm 387 coat color 179 choanoflagellate 134 cockroach 145 choline acetyltransferase 322 codon 234 cholinergic genes 333 coelenterates 387 cholinergic neurons 328, 333 Coffin–Siris syndrome 447 chondrichthyans 147 collagen 140, 391 chordates 135 collagen IV scaffold 140 chorioallantoic membrane 485 collective migration 336 chromatin 431, 501, 505 collencytes 391 chromatin accessibility 447 colony-forming unit 285 chromatin condensation 203 color macro-pattern 482 chromatin looping 449 color pattern 476 chromatin marks 432 coloration 474 chromatin regions 201 combinatorial regulation 10 chromatin remodeling 432, 447 commensalism 93 chromatin remodeling complexes 445 common ancestors 73 chromatin structure 20, 438 common ancestral sequence 132 chromatin-binding proteins 501 compartmentalization 14, 215, 419, 486 chromatophores 474 compartments 414, 471 chromodomains 446 compensatory mutations 45 chromosomal abnormalities 514 complement factor I 393 chromosomal damage 522 complementarity-determining region 56 chromosomal DNA 199 complementary parental strand 113 chromosomal genes 116 complementary promoter sequences 207 chromosomal rearrangement 254 concentration gradients 543 Index 595 conformational flexibility 118 cytoskeleton 13 congenital aganglionosis 342 cytotoxicity 284 conjugation 77, 116 conjugative plasmids 117 d conopeptides 36 D-V axis 543 conspecific sperm 80 Dachsous 372 constipation 343 Darwin’s theory of natural selection 107 contamination 166 Darwinian model 235 contamination rates 173 Darwinian theory 123 continence 317 Darwinian theory of evolution 107 continuum of speciation 75 deaminated cytosines 166 contour feathers 472 deamination 47 controller molecules 234 deazaflavin-dependent nitroreductase 293 convergent extension 13 decarboxylation 47 core peptide 35 deep-sea organisms 405 cortical rotation 419 degenerate oligonucleotide primers 52 corticogenesis 429 delamanid 274, 293 cotrimoxazole 296 Delta-Notch-dependent coordination 470 counterclockwise torsion 376 demography 173 covalent modifiers 46 demosponges 140, 387, 403 CpG islands 433, 502 demospongiae 387 cranial nerve 317 dendrites 323 CREB binding protein 438 dendritic branching 433, 441 CRM deletion 558 dendritic outgrowth 441 crocodiles 472 denisovans 176, 246 Cross-repression 545 dense dermis 479 crossing over 115 denticles 414 cryopreservation 520 deoxyribonucleic acid 107, 430 crystallographic experiments 44 derived features 247 ctenophores 141 dermal papilla 480 cultural evolution 122 dermal papillae cells 481 cumulus cells 523 dermal–epidermal recombination 485 cuticle melanization 488 dermis 472 cyanobacteria 37 dermomyotome 146, 478, 486 cyanobactin pathway 53 desaturated alpha carbon 37 cyanobactins 36, 57 desmosomes 11 cyclic AMP-responsive element-binding protein deuterostomia 402 1, 436 developing embryo 469 cyclization 59 developing organs 471 cyclodehydration 39 diabetes 280 cyclotides 36 DICER 449 cystic fibrosis 523 differentiation 390, 482 cytochrome P450 280 differentiation events 489 cytodifferentiation 11 differentiation profiles 527 cytokinesis 513, 543 differentiation programs 18 cytology 7 digestibility 525 cytoplasm 9, 511, 543 digital hormone model 484 cytoplasmic bridge 134 diploblastic 386 cytoplasmic incompatibility 92 diploblasts 135 cytoplasmic kinases 13 diploid DNA content (2C) and chromosome cytoplast 516 numbers 513 cytosine 112 diploid organisms 114 cytosine methylation 199, 206 directed evolution 44 cytoskeletal linking elements 135 directed evolution approaches 43 596 Index

directed evolution experiments 33, 37 drug metabolism capacity 582 directed mutagenesis 45 drug screening 571 directional dispersion 336 drug toxicity testing 580 directional torsion 366 drug-resistant TB 274 directly observed treatment short-course 277 drug-susceptibility testing 274 discovery phase 284 drug-susceptible tuberculosis 275 discriminator base pair 45 drug–comorbid disease interactions 282 disease modeling 571 drug–drug interactions 280 disruptive coloration 477 druggability 284 Disruptive patterns 477 DSB-induced small RNA 195 distributed enhancers 558 dynamical patterning modules 150 disulfide-constrained peptides loops 57 dysglycemia 279 divergence 82 dysregulation 260 divergent ecological selection 88 dystocia 520 division of labor 120 DNA acquisition 116 e DNA barcode 169 early bactericidal activity 278, 285 DNA fragments 167 early-cleavage stage embryos 519 DNA gyrase 114 early-stage embryos 134 DNA homeostasis 257 earth’s crust 217 DNA hybridization 238 Ecdysozoan 365 DNA inversion 114 ecological adaptation 82 DNA invertase 114 ecological contexts 471 DNA methylation 180, 198, 431 ecological selection 86 DNA methyltransferase 433, 502 ecomorphs 82 DNA microarray 505 ecosystem 108, 181 DNA polymerase 197 ectoderm 544, 548 DNA repair 258 ectodysplasin 480 DNA restriction–modification systems 111 ectodysplasin 480 DNA sequences 94, 108, 236 EDTA 166 DNA transformation 111 efflux pumps 42 DNA transposons 194 electron transport 50 DNA-binding factors 433 embryo 203, 370, 412, 542 DNA-dependent RNA polymerase 195 embryo splitting 525 DNA–DNA hybridization 236 embryo totipotency 504 donor genome 510 embryo transfer 510, 515 donor mitochondria 511 embryo-derived blastomeres 500 dopamine β-hydroxylase 322 embryogenesis 143, 362, 366, 372, 400, 429, 481, dormant bacilli 288 542, 572 dorsal carapace 472 embryology 7, 522 dorsal hair 476 embryonic blastomeres 510 dorsal root ganglia 319 embryonic carcinoma cells 510 dorsal–ventral axis 361 embryonic cell line 500 dosing frequency 282 embryonic compartments 482 double knockouts 206 embryonic development 18 double-helix model 111 embryonic gut 366, 368 double-stranded aDNA 167 embryonic mechanisms 487 down feathers 472 embryonic muscle progenitors 478 downregulation 203 embryonic neurogenesis 429, 439 Drosophila 138, 392, 542 embryonic stem (ES) cells 15, 20, 391, 442, 501, Drosophila E-cadherin 369 508, 571 Drosophila melanogaster 366 empirical MDR-TB treatment 279 drug development 62 enamel 259 drug efficacy and safety 584 encapsulation 215 Index 597 end-stage organ failure 585 epigenotypes 510 endangered species 526 epithelia 141 endopinacoderm 387 epithelial progenitor cells 334 endoplasmic reticulum 513 epithelial ridges 480 endosymbiont bacteria 92 epithelial to mesenchymal transition 321 endosymbiosis 120 epithelial–mesenchymal transformation 141 endothelial networks 582 epithelium 410 B receptor 338 ErbB receptors 325 endothelin-3 330 error-prone PCR 51 endothelin-converting enzyme 338 erythrophores 474 endothelin3b 483 Escherichia coli 111 engrailed 145, 486 esophagus 318, 335 enhanced protein stability 49 ethambutol 275 enhancer RNA 448 ethical issues 529 enhancers 444 ethical judgment of therapeutic cloning enteric nervous system 317 528 enteric neural crest-derived cell 336 eukaryotic organisms 25, 191 enteric neurogenesis 339 eukaryotic species 73 enterocolitis 343 eumelanic regions 476 entire genomes 42 eumelanin 474, 481 enucleated eggs 522 eumetazoans 135, 140 enucleated telophase zygotes 515 European Food Safety Administration enucleation 516 525 environmental conditions 81 evo-devo 252 environmental factors 197 evolution 73, 363 environmental mutagens 113 evolution genes 119 environmental stress 257 evolutionary biology 107 enzymatic processes 221 evolutionary closeness 233 enzyme cofactors 50 evolutionary fitness 119 enzyme inhibitors 41 evolutionary group 230 enzymes 111 evolutionary history 487 -B1 324 evolutionary pathway 122 epiblast 508 evolutionary rates 173 epiboly 135 evolutionary relationships 195 epidermal cells 473 exogenous DNA 165 epidermal ectoderm 319 exoskeleton 402 epidermal 398, 577 expression analyses 489 epidermal placodes 480 extensively drug-resistant TB 274 epidermal stem cells 20 extinct species 527 epidermis 472 extra-adrenal chromaffin cells 324 epifluorescence microscopy 517 extracellular matrix 11, 133, 395, 516, 574 epigenesis 252 extracellular signal-regulated kinase 444 epigenetic code 504 extracellular signals 139 epigenetic influence 254 extracellular space 36 epigenetic mark 436 extraembryonic fluid 363 epigenetic mechanisms 431 extrapulmonary disease 285 epigenetic modifications 504 epigenetic phenomena 505 f epigenetic regulation 49 facial skeleton 259 epigenetic reprogramming 509 familial dysautonomia 330 epigenetic signals 502 faropenem 296 epigenetic silencing 200 fatty acid bilayers 218 epigenetic therapy 439 fatty acid synthase 277 epigenetics 501 fatty acid vesicles 218 598 Index

fatty acids 218 g feather bud 480 G phase 543 feather row formation 485 G-protein 407 feathers 472 Galectin-8 149 fecal incontinence 343 gametes 80, 502 feedback loop 555 gametic isolation 80 ferric iron 391 gametogenesis 6, 194, 200, 521 fertility 284 gap genes 145, 545 fertilization 6, 77, 542, 543 gap junctions 11 fertilized embryos 504 gastric tissue 578 fetal growth regulation 506 gastrointestinal disorders 294 fetal kidney cells 583 gastrointestinal tract 338 fetal kidney progenitor cells 580 gastrulation 15, 135, 401, 544, 549 fibroblast growth factor 8, 146, 419, 480, 550 geminiviruses 197 fibroblasts 504 gene acquisition 117 fibronectin 141, 395 gene banks 526 gene clusters 387 field transplant experiments 95 gene content 529 fight-or-flight responses 317 gene dysfunction 259 filasterean 134, 135 gene dysregulation 521 fin-fold 148 gene expression 9, 252, 321, 377, 468, 527, 544 fin-to-limb transition 153 gene flow 73, 173 first-line anti-TB agents 280 gene flow barriers 95 first-line DST 278 gene interactions 555 Fisher model 89 gene manipulation techniques 41 Fisher’s “Dominance Theory” 256 gene mutations 577 fisher’s model 256 gene networks 420 fishes 88 gene promoters 504 five-digit configuration 247 gene regions 94 fixed mutation 120 gene regulation 432 flat fish 362 gene regulatory network 320, 546 flip-flop system 114 gene regulatory site 9 floating culture system 575 gene shuffling 51 fluroquinolones 275, 292 gene silencing 435 focal adhesions 13 gene transcription 252 follicles 473 gene trap locus 2, 507 forebrain 253, 435 gene-expression program 396 foregut 366 generation time 112 forkhead box protein 1, 323 genes 542 formulation feasibility 284 genetic “tool-kit” 471 5-formylcytosine 436, 503 genetic barriers 73 fossil records 363 genetic cascade 550 fossilized bone 166 genetic circuitry 25 four-cell embryos 24 genetic clusters 94 frameshift mutation 113 genetic code 33 Francis Crick’s “frozen accident” 33 genetic engineering 125, 529 French flag model 483, 551 genetic imprinting 506 Friedreich’s ataxia 441 genetic information 108 Frizzled 137, 407 genetic introgression 74 fruit flies 198 genetic language 117 functional polymers 215 genetic loci 512 fungi 132 genetic mapping 88, 489 fur 473 genetic mosaic embryos 374 fur hair 475 genetic mutation 41 Index 599 genetic oscillations 469 granulomas 278 genetic pathway 366 granulosa cells 510 genetic polymorphism 110 grapevine 198 genetic rearrangements 111 grasshopper 145 genetic repertoires 33, 54 Groucho 551 genetic screens 542 growth factors 583 genetic studies 79 growth lines 418 genetic tractability 52 guanosine triphosphatases 13 genetic variations 107 guard hair 476 genetic–epigenetic interactive pathway 255 gut epithelial organoids 577 genetically modified organism 125 gut mesenchyme 338 genetics 488 gut motility 341 genitalia rotation 373 genome projects 261 h genome scans 88 genome surveillance 196 H2-segment cells 375 genome wide association studies 88 hair 472 genome-wide screening 368 hair cells 166 genomes 10, 20, 108, 110 hair pigmentation 180 genomic change 239 haldane’s rule 81 genomic hybrid incompatibility 81 half-embryo 8 genomic imprinting 180, 505 half-maximal inhibitory concentration 284 genomic incompatibilities 81 halogenation 50 genotype-to-phenotype mapping 482 hammerhead ribozyme 220 genotypic clusters 76 handedness 364 genotyping 177 haploid genome 200 geochemical reactions 217 haploid organisms 113 geographic isolation 82, 108 haplotype frequencies 176 germ layers 134, 542 heart 330 germline 150 heart disease 580 germline chimeras 529 heat shock (stress) protein 249 germline stem cells 389 heat shock response 257 germline transmission 529 heat-responsive element 205 gestation 520 hedgehog 145, 546 gestation period 233, 336 helix-turn-helix proteins 409 gibbon 232 hematopoietic stem cells 20 glial cell line-derived neurotrophic factor 327 hemochorial placentation 233 glial fibrillary acidic protein 327, 439 hemoglobin 179, 231 gliogenic switch 450 hensen’s node 409 global methylation 503 hepatic biliary ductal system 579 glossopharyngeal nerve 332 hepatocyte transplantation 572 glucagon receptor 41 hepatogenesis 582 glucocorticoids 330 hepatotoxicity 279 glycocins 36 herceptin 49 gnathostomes 147 hereditary, and sensory autonomic neuropathy III golgi apparatus 513 330 gonads 10 heritable barriers 76 good clinical practice 285 heritable diseases 527 goosecoid 9 Hes1 gene 145 gorilla 231 heterochromatic DNA 194 GP130/neuropoietic receptor complex heterochromatin 194, 432 328 heterochromatinization 437 Gram-negative 41 heterocycles 37 Gram-positive bacteria 39 heterogeneity 74 600 Index

heterologous expressions 58 homophilic adhesion 136 heteroplasmy 511 horizontal gene transfer 111 heterospecific sperm 80 horizontal shunts 118 heterospecific tissue recombination 485 horizontal transfer 111 heterotaxy 362 horses 525 heterozygosity 256 housekeeping genes 119, 502, 554 hetsiRNA pathway 201 hox gene 142, 361, 545 hexactinellid 403 Hox proteins 139 Hexactinellida 387 human developmental biology 585 hexagonal pattern 485 human expansion 175 Hh protein 547 human family tree 173 high-diversity libraries 51 human immunodeficiency 197, 273 high-throughput genomics 95 human kidney model 579 high-throughput screening 282 human therapeutic cloning 528 HIGHRIF 1 study 291 human umbilical vein endothelial cells 376 HIGHRIF 2 study 291 Huntington’s disease 441 hindbrain 331, 414 hybrid gene 114 hindgut 333, 366 hybrid lethality 93 hindgut epithelium 374 hybrid sterility 81 hindgut rotation 373 hybrid vigor 512 HIPK2 341 hybridization 74, 169 Hirschsprung disease 338 hybridization probes 115 histone acetyltransferase 437 Hydra 370 histone chaperone 445 hydrogen bonds 218 histone chromatin mark 443 hydrophilic solutes 218 histone code 442 hydrops 520 histone complex 437 hydroxyapatite 402 histone deacetylase 435 5-hydroxymethylcytosine 436, 503 histone deacetylase inhibitor 505 5-hydroxytryptamine 339 histone demethylase 442 hyperacetylation 505 histone methylation 205, 510 hypermethylated 504 histone methyltransferase 441 hypermethylated regions 435 histone modifications 20, 49, 431 hypermethylation 205 histone octamer 432 hypoplasia 327 histone tails 439 hypostome 408, 410 histone variants 445 hypoxic granulomas 292 histone–DNA interactions 440 histones 504 i HIV protease inhibition 61 illegitimate recombinations 114 HIV-inhibition 41 imaginal disc cells 17 Hoffmann modulation 517 immediate early genes 449 Holozoa 131 immotile cilia 363 homeobox genes 415, 422, 486 immune reconstitution inflammatory syndrome homeobox protein 399 280 homeotic genes 252 immune rejection 571 homeotic selector genes 387, 414 immune responses 341 hominidae 233 immune system 9, 416 hominin lineages 173 immunedeficient mice 583 hominoid diversification 233 immunoglobulin 395 hominoid lineages 233 immunological reactivity 232 hominoids 232 immunological responses 62 homogametic sex 81 immunological tolerance 62 homogenization 83 immunostaining 503 homologous recombination 113, 524 impaired memory 436 Index 601 in paired-end sequencing 170 ion channels 330 in-situ hybridization 407 ionizing radiation 113 in-vitro fertilization 26, 519 iridophores 474 inbreeding 257 iris 330 incompatibilities 83 Iroquois gene 392 incompletely replicated DNA 522 islands of speciation 88 indels 172 isoniazid 275 index 169 isonicotinyl-NAD adduct 275 index of dissimilarity 232 isopeptide bonds 37 individualized regimens 278 induced pluripotent stem cell 571 j infected macrophage assay 294 JARID1B 443 infectious bacteria 34 JNK signaling 368 inferior mesenteric artery 329 jumping genes 250 inflammatory 62 Juxtacrine signaling 10 inner cell mass 503 inner mass cells 24 k inner submucosal plexus 340 Kartagener syndrome 362 insect larva 419 karyokinesis 543 insects 88 karyoplast 504 insertion sequence 115 Keller–Segel model 484 insertion targets 116 keratinization 473 insulin secretion 579 ketone functionality 47 insulin-like growth factor 2, 506 kidney cysts 14 integral-membrane proteins 132 kidney development 580 13, 140, 339, 395 kidneys 579 integrin-binding lasso peptides 54 KIF3B 363 integument 471 knockout animals 434 integumentary appendages 472 interbreeding natural populations 74 l gamma 280 lacrimal gland 317 intergenus heteroplasmy 511 β-lactam antibiotics 295 interindividual variation 255 β-lactamase inhibitor 295 intermediate progenitor 447 lamina propria 340, 578 intermediolateral cell column 317 lanthionine 37 internal mutations 195 lanthipeptides 36 International Chimpanzee Chromosome 22 lantibiotics 52 Consortium 261 large-bodied hominoids 238 interneurons 14 larval imaginal ring 375 interphase 515 larval tissue 372 interplanetary dust particles 217 lasso peptides 36 intersexual selection 88 latent TB infection 281 interstellar dust particle 217 latent tuberculosis infection 281 intestinal stem cells 577 lateral line 472 intra-peptide click reactions 61 law of large numbers 258 intra-tissue spaces 138 lead compounds 282 intracytoplasmic sperm injection 509 lead development 284 intragenomic DNA rearrangements 116 leader peptide 35 invariant TAG codon 56 lefty 363 inversus viscerum 362 legislation 528 invertebrates 363 legislative proposals 526 inverted repeat transcripts 191 lethal mutations 116 involucrin 246 leuconoid 389 involution 135 leucophores 474 602 Index

leukemia inhibition factor 20 mammary gland bioreactors 523 library 51 MAMS-TB-01 study 291 library preparation 167 mandatory labeling 526 -binding domain 399 MAP kinase pathway 551 ligase 220 mapping 170 limb bud 253 marker genes 391 limb skeletal patterning 149 master control genes 151, 253 limnetic zone 82 mate discrimination 93 linaridins 36 maternal information 367 lineage-associated genome 150 maternal spindle proteins 522 linear azol(in)e-containing peptides 36 maternal transmission 511 lipid membrane 214 maternal-to-zygotic transition 543 lipoarabinomannan 277 mathematical modeling 488 lipopolysaccharide 42 matrix-assisted laser desorption/ionization 54 liquid tissues 135 mechanical deformations 469 live-cell imaging 335 mechanical isolation 80 liver bud formation 581 mechanobiology 12 liver failure 579 megacolon 342 liver stem cells 579 megasclere 403 long germ mode 145 meiosis 14, 83, 203 long intergenic noncoding RNA 448 melanin 474 long interspersed nucleotide element 250 melanoblasts 479, 483 long noncoding RNA 194 melanocyte-stimulating hormone 481 long terminal repeat 202, 504 melanocytes 319, 333, 481, 474 long-term memory 367 melanophores 474, 483 loop region 54 melanosomes 481 looping structure 377 melting temperature 239 loose dermis 479 membrane permeabilization 52 loss-of-function 370 membrane transport 214 low-abundance variants 60 membranous systems 215 low-complexity reads 171 meristem 20 luciferase 406 meristem cells 196 lumbar ganglia 328 mersacidin 53 lumen 138 mesectoderm 548 lumen formation 150 mesencephalon 429 lungs 331 mesenchymal cells 338, 479 Lymnaea 363 mesenchymal condensation 149 lymphadenopathy 281 mesenchymal stem cell 12, 571 lymphoid enhancer factor 407 mesenchymal stem cell-like protein 391 Lysine-specific histone demethylase 1A 443 mesenchyme 147 mesentery 336 m mesoderm 408, 479, 544, 548 M-phase 543 mesodermal cell layer 386 macro-pattern 474 mesodermal tissue layer 140 macrocyclic peptides 58 mesohyl 387 macrocyclic structures 52 messenger RNA 24 macromutation 254 metabolic flux 42 Madin–Darby canine kidney 376 metabolic inactivation 42 magic traits 84 metagenomic sequencing 41 male gametes 200 metal-binding and redox-active amino acids 46 male genitalia 368, 374 metal-chelating functionalities 50 male sterility 362 metalloprotease 487 malignancy 577 metalloproteins 50 mammals 473 metamorphosis 372 Index 603 metanephric mesenchyme 580 mitochondrial genotypes 511 metaphase I 515 mitochondrial haplogroup 175 metaphase II 515 mitochondrial heteroplasmy 518 metaphase plate 514 mitochondrial respiratory chain 242 metaphase spindle complex 518 mitosis 17, 515 metazoa 131, 386 mitosis/meiosis switch 15 metazoan embryos 553 mitotic cyclin-dependent kinase 513 metazoan genomes 240 mitotic spindle 514 metazoans 236, 377 mixed ancestry 81 8-methoxyquinolones 292 mixedhybridancestry 86 methyl CpG-binding domain 435 model phenotypes 483 5′-methylated cytidine 503 modern evolutionary synthesis 235 5-methylcytosine 433 molecular assumption 231 methylation markers 201, 205 molecular clocks 232, 249 methylation pattern 502 molecular cloning 174, 393 methylation status 201 molecular evolution 108, 123 Metronidazole 292 molecular genetics 108 Michael addition 37 molecular gradients 146 micro-complement fixation 232 molecular interactions 134 micro-evolution 235 molecular noise 469 micro-manipulation 517 molecular–structural continuum 251 micro-manipulation experiments mollusca 153, 364 485 mollusks 141 micro-pattern 474 monocarboxylic acids 217 microarray data 506 monomers 215 microbiomes 121 mononucleotides 219 microbiota 341 morphogen gradient 397, 551 microcins 36 morphogen receptor gradient 9 microenvironment 12 morphogen receptors 469 microevolutionary change 150 morphogen signals 469 microinjection 518 morphogenesis 12, 132, 134, 369, 374, 377, 400, micromutation 254 484, 544 micronutrient deficiency 280 morphogenetic rearrangement 483 microphthalmia transcription factor 9 morphogenetic remodeling 393 microRNA 24, 321, 435 morphogenetic response 468, 471 microvidins 36 morphogenetic wave 480 mid-blastula transition 16, 553 morphogens 422, 469, 486, 488, 551 midgut 366 morphological diversity 471 milk composition 523 morphological evolution 488 milk production performances 525 morphological novelty 256 mineral skeleton 387 morphological traits 468 mini-organ technology 584 morphology 376 mini-organs 571 morphospace 150 minimum bactericidal concentration mortality 521 286 mosquito 198 minimum inhibitory concentration 275 motility disorder 343 miRNA expression 329 motor neurons 323 miRNA pathway 191 mouse embryonic skin 486 mirror image 373 mRNA 543 miscoding lesions 166 mRNA localization 545 mismatches 172 mule 525 mismatching genitals 80 multi-substrate efflux pump 288 mitochondrial DNA 174, 511 multicellular organisms 235 mitochondrial genome 174, 175 multicellularity 132 604 Index

multidrug-resistant TB 274 netrins 340 multifunctional enzymes 121 neural cell fate 439 multilayering 150 neural crest 318, 402 multiple endocrine neoplasia 2B 343 neural crest cells 440, 479 multipotency 571 neural outgrowth 441 Murchison meteorite 218 neural plate 319 murine brain 433 neural progenitor cell 435 murine embryonic stem cell 447 neural progenitors 430 murine myoblasts 376 neural stem cells 433, 442 muscularis mucosa 578 neural tube 322, 335, 469, 478, 479 mutagenesis 51, 111 neuroblastoma 331 mutagenesis screens 470 neuroblasts 327, 329, 549 mutagenicity 284 neuroectoderm 548 mutant mitochondria 512 neuroepigenetics 432 mutant mtDNA 511 neuroepithelial cell 429 mutation 253 neurogenesis 435, 439 mutation order speciation 86 neurogenin 2, 324 mutation rate 249 neuronal differentiation 341, 437 mutation screens 205 neuronal morphogenesis 439 mutations 81, 107 neuronal stem cell 445 mycobacteria cell wall 277, 289 neuronal tube 415 mycobacterial catalase-peroxidase 275 neuropeptides 330 mycobacterial membrane protein large 3, 289 324 Mycobacterium tuberculosis 273 neurotransmitter 322 Myo31DF expression 371 neurotrophin 327 Myo61F 372 neurturin 334 myocytes 388 neurulation 415, 429 myogenin 14 neutral mutation 235 myoglobin 234 New World apes 230 Myosin IC 372 next-generation compounds 286 Myosin ID 370 next-generation sequencing 94, 174, 505 Myosin II 368 nicotinamide adenine dinucleotide phosphate myotrophin 397 diaphorase 323 Nieuwkoop center 418 n nisin 37 nanostructures 489 nitric oxide 340 native chemical ligation 43 nitric oxide synthase 322 natural evolution 54 nitroimidazoles 292 natural patterns 468 nitroimidazoxazine 293 natural selection 86, 108, 173 nodal 363 NC specifier genes 320 nodal cassette 363 nDNA sequence 245 nodes 555 Neandertal DNA 165 non-Mendelian factors 254 Neanderthal 246 non-proteinogenic amino acids 34 Neanderthal genome 259 non-ribosomal peptide synthase 35 negative elongation factor 449 noncoding region 236 nematoda 153 noncoding RNA 432 neo-Darwinism 124 noncovalent modifiers 46 neocortex 429 nonhuman primates 527 nephron progenitors 580 nonsense suppression 44 nephrotoxicity 279 noradrenaline 322 nerve cord 549 Normarski differential interference 517 328 northern blot 407 nerves 472 notch 151, 341 Index 605

Notch/Delta signaling system 327 organizer 401 notochord 146, 415, 486, 522 organogenesis 14, 542, 544, 572 nuclear divisions 543 organogenetic processes 575 nuclear DNA 236 organoids 571 nuclear donor 507 origin of life 215 nuclear envelope disassembly 513 orthogonal aaRS/tRNA pairs 43 nuclear equivalence 8 orthogonal ribosomes 61 nuclear genes 242 oscillation 484 nuclear genomes 176 oscillatory mode 145 nuclear magnetic resonance 44 oscule region 399 nuclear pore complex 15 osteoderms 472 nuclear receptor corepressor complex 440 osteogenic differentiation 12 nuclear reprogramming 501, 505 otic ganglion 332 nuclear transfer 500 ototoxicity 279 nuclear–mitochondrial interactions 511 outer myenteric plexus 340 nucleic acids 214, 218 outside-in signaling 396 nucleobases 217, 218, 437 ovarian germ cells 14 nucleosomal histones 432, 505 over-all similarity 231 nucleosome core particle 432 oviedo convention 528 nucleosome remodeling deacetylase 435 oxazolidinones 294 nucleosome–DNA contacts 445 nucleosomes 20, 437 p nucleotide monomers 219 Père David’s deer 526 nucleotide sequences 108 pair-rule factors 548 nucleotide substitution 234 pair-rule genes 145, 422 nucleotides 112 pair-rule homologs 145 nucleus 9 pair-rule proteins 414 paired appendages 147 o paired-end reads 171 obesity 520 paleo-hominin genomes 168 Old World apes 230 paleo-human nucleosome map 180 oligodendrocytes 430 paleogenome 166 oligomers 220 pan-neuronal genes 325 oligopermeases 45 pancreatic tissues 578 one-cell cytoplasts 514 panning 55 one-cell embryos 512 paraganglia 328 one-cell stage embryos 519 paraHox cluster 415 ontogenetic mode 152 parapatric speciation 82 oocyte 514, 542 parapatry 85 oocyte activation 519 pararetrovirus genomes 195 oocytoplasm 518 parasegments 412 oogenesis 14, 252, 542 parasitic retrotransposons 502 operon 114 parasitic wasps 93 operon fusion 114 parasympathetic ganglia 331 optic cup 576 parasympathetic nervous system 317 optic neuritis 294 paravertebral ganglia 317 optic vesicle 576 parental pronuclei 516 orbitides 36 parthenogenetic activation 523 organ bud transplantation therapy 582 parturition 520 organ buds 571 passive demethylation 503 organ shortage 584 passive diffusion 221 organelles 374 patched 341 organic carbon 217 pathogenesis 121 organismal toxicity 61 pathogenic bacteria 62 606 Index

pattern blending 477 planar cell polarity 136, 470 pattern formation 10, 132, 386, 545 planetesimals 215 patterning 16 plant genomes 195 patterning strategies 471 plant taxa 88 patterns of methylation 181 plantar hair 475 PCR amplification 174 plantar surface 479 pediatric TB 281 plants 132 pelvic ganglia 331 plasma membrane 516 peptidic cofactors 220 plasmid stability 52 periderm 479 plasmids 110 peripatric speciation 84 plasticity 36 peripheral neuropathy 294 platelet-derived growth factor 10 peripheral tissues 322 pluripotency 509 permeability barrier 396 pluripotent 20 persister bacilli 278 pluripotent cells 509 persisters 278 pluripotent state 501 personalized therapy 584 pluripotent stem cells 20, 571, 578 PHABULOSA 193 point mutations 237, 254, 288 phage display 55 polarization 417 phage display selection 51 polarized cell division 377 phage reproduction 116 pollen grains 200 phallotoxins 36 pollen transfer 80 pharmaceutical protein production 523 pollinators 79 pharmacodynamics 284 polychlorobiphenyl 11 pharmacokinetic profile 299 polycomb group 17, 442 pharmacokinetics 62, 284 polycomb repressive complex 2, 203, 442 pharmacophores 37, 49 polycomb-mediated repression 434 phase II trials 285 polycomb/trithorax factors 548 phase III studies 286 polycystic kidney disease 580 phased siRNA 193 polyethylene glycol 62 phenotype 46 polygons 488 phenotypic diversity 488 polyketide synthase 35 phenotypic variations 107 polymerase chain reaction 45, 166 phenylethanolamine N-methyl transferase 329 polymerase II 191 pheomelanin 474 polymerization 219 phosphatase and tensin homolog 339 polymers 214 phosphorylation 437, 444 polymorphisms 76, 115 photomorphotropic protein 407 polypeptide backbone 50 photoperception 407 polyphenols 167 photoreception system 405 polyploid speciation 90 phylogenetic analysis using parsimony 246 polyploidization 89 phylogenetic magic bullet 251 polysaccharides 167 phylogenetic propinquity 245 polytheonamides 37 phylogenetic relationships 173 polyvinylpyrrolidone 167 phylogenetic studies 79 population divergence 94 physical space 51 population genetics 487 pigmentation 472 population genomic studies 176 pigments 474 Porifera 387 pinacocytes 391 positional cues 471 pituitary gland 10, 576 positional factors 471 placenta 512 positional molecules 486 placental abnormalities 521 positional signals 489 placental genes 521 positional–information model 253 plague victims 177 post-mitotic neurons 434 Index 607 post-ribosomal peptide synthesis 35 protein-coding genes 448 post-transcriptional mechanisms 198 protein-coding genome 554 post-transcriptional modification 321 protein-encoding genes 503 post-transcriptional RNA silencing 206 proteinase K 166 post-transcriptional silencing 202 proteins 111 post-translational modification 33, 432, 501 protein–protein interactions 49 posterior ganglia 329 proteome 45 posterior sex comb 17 proteusins 36 postganglionic neuron 317 protocadherins 134 postzygotic isolation 80 protocell 214 potato virus Y 198 protometazoans 132 pre-patterns 482 proton transfer chain 286 prebiotic earth 214 proximodistal axis 147 prebiotic environment 219 pseudo-polar body 514 preclinical optimization 62 pseudo-pronuclei 513 precursor miRNA 449 psychiatric disorders 279, 432 precursor peptides 34 pterylography 474 preganglionic neuron 317 pulmonary microangiopathy 280 pretomanid 293 pulmonary tuberculosis 273 prezygotic barriers 79 Pulmonata 363 prezygotic factor 77 pyrazinamidase 277 prezygotic isolation 77, 78 pyrazinamide 275 primer–template system 220 pyrrolysine 43 primitive features 247 primitive streak 141, 410 q primmorphs 389 QT-interval 293 primordia 368 quantitative structure–activity relationship 292 primordial axis 409 primordial germ cell 20, 509 r pro-caspase 400 racemization 47 proamniotic cavity 138 radiate accretive pattern 418 progeny 110 radiation cleavage 377 progesterone receptors 9 random mutagenesis 51 projection neurons 430 rare codons 45 prokaryotes 141 rate 231 prokaryotic organisms 123 ray-finned fishes 149 promoter mutant 291 re-differentiation 391 promoters 444 RE1-silencing transcription factor 436 pronuclear envelope 515 reaction–diffusion 469 pronuclei 543 reaction–diffusion hypothesis 146 proofreading devices 113 reactive oxygen species 296 prosencephalon 429 reading frame 113 prosimians 232 receptor agonists 41 protamine 246 receptor bacterium 117 protein biosynthesis 397 receptor genome 117 protein chemistry 44 receptor melanocortin-1 481 protein conformation 50 receptor protein-tyrosine phosphatase 395 protein distribution 374 receptor proteins 9 protein evolution 61 receptor tyrosine kinase 9, 395 protein folding 258 recessive mutations 81 protein sequencing 234 recessive state 258 protein stability 50 recognition element 45 protein synthesis 294 recognition sequence 39 protein therapeutics 34 recombination 91 608 Index

red deer 526 RiPP pharmacophores 57 reduced representation bisulfite sequencing 504 RNA 113 reference genome 170 RNA interference 20, 191 regenerative medicine 6, 24, 571 RNA oligomers 218 regulatory genes 252, 387 RNA polymerase 10, 41, 277 regulatory interactions 556 RNA polymerase II 553 regulatory molecules 14 RNA polymerase II complex 557 reinforcement 90 RNA silencing 191 release factor 1, 61 RNA World 214 renal organoids 579 RNA-binding protein 554 repetitive loci 201 RNA-dependent RNA polymerases 191 replication fork 112 RNA-induced silencing complexes 191, 449 replication states 277 RNA-polymerase 220 reproductive cloning 527 Robertsonian fusion 261 reproductive isolation 73, 108 rostrocaudal axis 322 reproductive isolation-by distance 83 runt-related transcription factor 1, 439 reptiles 472 reshuffling 118 s residue-specific incorporation 43 S-locus protein 11, 198 resistance mutations 42 S-phase 543 resistance, nodulation, and division 289 sacral ganglia 328 respiratory infections 520 sacral neural tube 331 restriction endonucleases 117 sactipeptides 36 restriction fragment length polymorphism 110 salivary epithelium 334 restriction–modification systems 119 salivary gland 330, 576 resuscitation-promoting factor 278 saturation mutagenesis 52 retina 14 scaffold proteins 138, 396 retinal 417 scales 472 retinitis pigmentosa 576 scarless’ cyclic peptide 59 retinoblastoma protein 14 Schwann cells 333, 479 retinoic acid 14, 254, 338, 399 sclerocytes 391, 403 retinoid X receptor 417 sclerotome 146, 324 retinoids 399 screening 60 retrotransposition 202 second-line anti-TB agents 281 retrotransposon sequences 198 second-line DST 278 retrotransposons 250 second-order selection 120 Rett syndrome 436 secondary crossover site 114 reverse transcriptase 196 secondary metabolite precursors 35 reverse transcriptase inhibitors 280 segment patterning 414 RG cells 429 segment-polarity 545 Rho-associated coiled-coil forming kinase 575 segmental plate 146 rhombencephalon 429 segmentation 142, 253, 387, 414, 544 ribonucleic acid 214, 431 segmentation genes 412 ribosomal RNA 242 selective pressure incorporation 43 ribosomal s6 kinase-2 444 selector genes 18, 414 ribosomally synthesized, post-translationally selenocysteine 43 modified peptide 34 self-activation 469 ribozymes 214 self-assembly 218 rifabutin 275 self-morphogenesis 574 rifampicin 274 self-organization 132 rifapentine 275 self-organizing strategies 484 RIFAQUIN trial 291 semaphorin 3A 324 RIFATOX trial 291 Sendai-virus 518 ring mutations 54 senescence 436 Index 609 sense codon 44 skink 472 sensory organs 361 small RNA 191 sequence comparison 245 Smaug 554 sequence fragments 169 snails 361 sequence similarity 246 snakes 362 sequencing 174 sodium dodecyl sulfate 167 sequencing cycles 169 solid-phase peptide synthesis 43 sequencing libraries 180 somatic cell nuclear transfer 504 sequencing library 169 somatic cells 199, 389, 430, 500 serine protease inhibitors 49 somatic nucleus 501 sertoli cells 510 somatic stem cells 389, 509, 571 serum–antiserum mixture 230 somatopleure 479 sex determination 553 somite boundaries 146 sexual conflict 78 somite formation 470 sexual dimorphism 88 somite polarity 485 sexual display 475 sonic hedgehog 339, 363, 447, 469 sexual reproduction 74 Southern hybridization 115 sexual selection 88 Sox10+ 339 sexually dichromatic taxa 89 spatial colinearity 412 sexually reproducing organisms 73 Spatzle ligand 543 shadow enhancers 558 speciation 82 short consensus repeat 393 speciation continuum 85 short germ-band mode 145 speciation genes 87 short interfering RNA 181 Spemann organizer 387 short interspersed nucleotide element 250 sperm 543 short interspersed nucleotide insertion 237 sperm-derived pronucleus 516 sibling species 85 spermatogenic cells 509 signal transduction 9 spicules 387 signal transduction pathways 9 spider silk proteins 524 signaling gradient 469 spina bifida 14 signaling molecules 469, 483 spinal cord 317 signaling pathways 255, 386 spindle formation 513 silenced loci 205 spines 472 silent spreading 258 spiral cleavage 364, 376 silicatein 391 splanchnic nerves 329, 331 silicon 391 splicing factor 448 similarity 247 split-intein circular ligation of peptides and protein single nucleotide alterations 110 59 single nucleotide polymorphism 248 sponges 140 single-copy DNA sequences 237 spontaneous local mutagenesis 113 single-nucleotide polymorphism 174 spontaneous mutation 110 single-pass transmembrane receptor 395 SQ109 289 single-stranded DNA 168 stem cell 12, 20, 389 sinistral activity 372 stem cell culture 572 sinistral mutant 364 stem/progenitor cell 21 sister chromatids 514 stem–loop structures 554 site-directed mutagenesis 51, 126 stem–loop RNAs 199 site-specific protein modification 44 sterilized environments 166 situs inversus 362 steroid hormones 9 Sjogren’s syndrome 577 stickleback 82 skeletal primordia 148 stings 472 skin discoloration 296 stomach 318 skin explant culture 480 stop codon 44 skin pattern 471 STREAM 279 610 Index

structure–activity relationships 52 TE silencing 204 stylopod 147 teeth 177 subclone 116 teleost 148 submucosa 578 telomerase 511 subventricular zone 429 telomerase reactivation 511 sudoterb 290 telomere erosion 510 sulfamethoxazole 296 telomere length 511 sulfilimine crosslinks 150 telomere length adjustment 511 SUMOylation 437 temporal colinearity 412 superior cervical ganglion 327 ten-eleven translocation 433 suppressor tRNA 45 tenascin 141 surrogate mothers 519 tephritid flies 90 survivorship 89 terminal system 545 sutezolid 294 test of reciprocity 232 sweat glands 322 testes 366 syconoid 388 testicular anlage 366 symbiotic associations 120 testis 14 sympathetic chain 329 tetraploid complementation 501 sympathetic ganglia 325 tetraploid embryo complementation 529 sympathetic nerve terminals 330 tetrapod limb 147 sympathetic neurons 326 tetrapods 147 sympathetic nervous system 317 tetraspanin 396 sympathoadrenal progenitors 329 therapeutic anti-HIV antibodies 56 sympatric speciation 82, 84 therapeutic cloning 527 sympatry 85 therapeutic margin 275 symplesiomorphic 247 therapeutic proteins 62 synapomorphic molecular states 248 thermal regulation 474 synaptogenesis 337 thiopeptides 36 syncytial blastoderm 143 third-line agents 275 syncytial embryo 551 thoracic cavity 331 syncytium 389 thoracic ganglia 328 synergistic activity 289, 290 thoracic spinal cord 322 synpolydactyly 257 thrombocytopenia 294 synthesis–diffusion–degradation 552 thymic aplasia 520 synthetic biology 41, 43 thyroid follicles 579 system bifurcations 469 thyroxin 254 systematic classification 107 tight junctions 11 systematics 230 tissue availability 78 tissue culture 196 t tissue deformations 470 TAG codon scanning 52 tissue dynamics 484 tail field 479 tissue elongation 150 target antigen 55 tissue engineering strategy 585 target genes 447 Tissue Expansion-Modulated Maternal Morphogen target organs 317 Scaling 552 target-based approach 282 tissue matrix 472 target-to-drug strategy 284 tissue/cell dynamics 489 targeted gene mutation 325 tobacco rattle virus 204 tautomeric forms 112 tolerability 295 taxic diversity 255 Toll signaling 549 TB prevalence 274 tooth eruption 260 TB reactivation 273 topoisomerase 2-beta 442 TB treatment regimens 299 tortoises 472 TB/HIV coinfection 280 totally drug-resistant TB 274 Index 611 totipotency 508 tyrosine phosphorylation 49 totipotent cells 24 tyrosine sulfation 56 totipotent embryonic state 500 toxic protein 51 u toxicology 284 uAA incorporation 61 toxicology studies 284 ubiquitination 437 trans-acting siRNA 193 uniform average rate 239 trans-differentiation 391, 448 uniparental disomy 506 transamination 47 unique morphological structures 250 transcript abundance 507 unnatural amino acid 34 transcription factors 143, 252, 320, 407, 414, 433, untranslated region 205, 449 543, 557 uracil 112 transcriptional enhancer 259 uracil-DNA glycosylase 166 transcriptional gene silencing 194 ureteric epithelium 580 transcriptional machinery 441 urogenital sinus 333 transectodermal cells 416 transfer RNA 242 v transforming growth factor-β 419 vagal region 335 transgene 204 vagus nerve 332 transgenerational silencing 200 vancomycin-resistant enterococci 62 transgenic reporter assays 558 vasoactive intestinal peptide 334 transgenic reporters 557 vegetative cell 200 translational machinery 45 vegetative nuclei 203 translational repression 545 ventral apterium 486 transmembrane domain 410 ventral dermal cells 479 transplantation 506 ventral hair 476 transporter speciation 85 ventral mesoderm 11 transposable element 191 ventral plastron 472 transposase 120 ventricular zone 429 transposition 115, 180 vernalization 203 transposons 250 vertebrate integument 472 treatment duration 291 vertebrate patterns 469 treatment regimens 278 vertebrate segmentation 238 tree of evolution 109 vertebrates 141, 370 tree of life 73 vertex model 374 trehalose monomycolate 289 vesicle formation 221 trimethoprim 296 veterinary medicine 39 triploblastic 386 vibrissae 473 triploblasts 135 vibrissae field 475 trophectoderm 503 vinculin 135 trunkamide 53 viral gene 238 tryptophan hydroxylase 2, 340 viral genomes 195 tubercle bacilli 285 viral infections 181 tuberculosis 273 viral siRNA 191 tumor cells 510 viral suppressors of RNA silencing tumor suppressor gene 577 191 Turing dynamics 470 virus immunity 197 Turing model 470 virus-mediated transduction 116 Turing patterning 470, 483 92, 110 Turing’s equations 470 visceral cells 369 Turing-type network 149 visual patterns 477 Twi transcription factors 549 vitamin C 436 tyrosine hydroxylase 322 vsiRNA-mediated defense 197 tyrosine kinase 327 vulnerability 284 612 Index

w Xenopus 11 whole genome in-solution capture xenotransplantation 501 169 whole-cell phenotypic screens 286 y whole-genome enrichment 168 yeast 141 wing pattern 79 Yersinia pestis 177 wing spot 488 wingless 145, 395, 546 z wingless morphogen 482 zebrafish 142, 336, 470, 484 wingless-int 575 zebrafish melanophores 376 within-appendage pattern 474 zebrafish mutant 377 within-hair patterning 481 Zelda 543 Wnt 137 zinc finger 10, 553 Wolbachia 92 zinc finger protein 57, 439 woolly mammoths 178 Zld protein 554 Wright’s model 256 zona pellucida 23, 133 zygote 80, 132, 417, 508 x zygotic genes 10, 419 X-chromosome inactivation 505 zygotic genome activation 553 X-linked genes 505 zygotic nucleus 543 xanthophores 474, 483