The Mysterious World of the Human Genome

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The Mysterious World of the Human Genome Page 31

by Frank Ryan

Bernal, John Desmond 53–4, 83, 84, 90

  beta-globin 97–8, 107, 133–4, 141

  bidirectional transcripts 194

  Biological Journal of the Linnean Society 145

  Birkbeck college, Biomolecular Research Laboratory 83–4, 90–1

  Blair, Tony 124

  Blombos Cave, South Africa 227–8

  BNC2 (gene) 269

  Boivin, André 95

  Bonnet, Marie Louise 31–2

  Boule, Marcellin 262

  Bragg, Sir William Lawrence 51–2, 53, 54–5, 56, 64, 67, 68–9, 84, 86, 89

  Bragg, Sir William Henry 51, 52, 53–4, 68

  Bragg's Law 52, 89

  Branson, Herman 68

  BRCA 1 and BRCA 110, 188, 297

  Brenner, Sydney 96–7, 114, 115, 118, 185, 186, 294

  Briggs, Adrian 247

  British Museum 231

  Broad Institute 268

  Broca's area 254, 263

  Bronowski, Jacob 121

  The Ascent of Man 1

  The Identity of Man 1

  Brown, Wesley M. 214

  Caenorhabditis elegans (round worm) 114–15, 185, 186–7

  California Institute of Technology (Caltech) 41, 57, 67–8, 121

  Cambridge University 32–3, 48, 51–5, 56, 57, 58, 60, 62, 63, 64, 65, 68, 70, 75, 76, 78–9, 82, 86, 90, 91, 97, 114, 121, 222, 237 see also under individual laboratory or college name

  cancer 16

  bladder cancer 195

  bone cancer 195

  bowel cancer 141

  brain cancer 195

  breast cancer 110, 111, 141, 188, 195, 297, 300

  colon cancer 110, 111, 195

  genetic engineering and 295, 297, 300

  HERVs and 167, 170

  kidney cancer 141

  lncRNAs and 194–5, 294

  lung cancer 111, 195

  methylation patterns and 178–9

  mutations and 107, 109, 110–11, 141, 188

  ovarian cancer 90, 188, 297, 300

  prostate cancer 195

  research 128

  skin cancer 141

  somatic mutations and 141

  Cann, Rebecca L. 213–14

  Carbon-14 dating 236

  Carrel, Dr. Alexis 6

  Cartagena Protocol on Biosafety, 2000 299

  Cavalli, Sforza, Professor Luigi Luca 210, 211, 288

  Genes, Peoples and Languages 211

  Cavendish, Henry 51

  Cavendish Laboratory, Cambridge University 51–5, 57, 58, 60, 62, 63, 64, 65, 68, 78–9, 82, 86, 90, 114

  cave paintings 254–5

  CD+T helper lymphocyte 160

  CD4 160, 161

  Celera Genomics 123, 124, 125, 126, 127–8, 302, 303

  cell

  division (mitosis) 140–1, 186, 190–1

  DNA amount within 94–5, 113, 173

  eukaryotic 114

  germ cell 7, 8, 9, 10, 106, 107, 109, 162, 174, 198–9, 200, 205, 218, 283, 304

  nuclear genome within see nuclear genome

  pluripotent (“stem”) cells 115–16, 168, 172, 183, 194

  programmed cell death (apoptosis) 153, 185–9, 260

  regeneration and repair 260

  RNA, variation of amount within 94–5

  symbioses and 151, 152–4, 282

  totipotent 115

  viruses and 156–69

  zygote and see zygote

  CFTR (cystic fibrosis transmembrane regulator gene) 108

  Chargaff, Erwin 35, 79–81, 86, 92

  Chase, Martha 27–8, 34, 36, 53

  chemical bonds 65, 66–8, 71, 79, 81, 104

  Chetverikov, Sergei Sergeevich 140

  chloroplasts 151, 152

  chromosomes

  autosomes 107, 108, 114, 189, 212, 241

  Avery's discovery of DNA and 44

  bacterial transfer of DNA and 99–100

  chromosome 3 223

  chromosome 4 141, 142

  chromosome 6 179–82, 283–4

  chromosome 7 108, 165

  chromosome 8 223

  chromosome 19 223

  common male ancestor and 218–21

  Crick and Watson's discovery of structure of DNA and 55, 93, 98

  discovery of 8–9

  genotypes and 295

  haplotypes/haplogroups and 200–1, 204, 205, 206–7, 211–12, 218–19, 220, 222, 223, 224, 229, 239–40, 289–90

  homologous sexual recombination 9

  Hox genes and 116, 117

  lncRNAs (long non-coding RNAs) and 191–3

  Major Histocompatability Complex (MHC) and 179, 180–4, 269 283–4, 301

  meiosis 283

  MSRY (male specific region) of Y chromosome 218, 239–40

  mutation and 107, 108–9, 141–2, 200, 211, 241 see also mutations and Snips

  prokaryotes and 9–10

  retroviruses and 162, 163, 164, 165, 166, 167, 206–7, 222–3

  Schrödinger's What Is Life? and 39–40

  sequencing of entire human genome and 120, 122, 126, 127, 129, 132

  Snips and 200, 211, 241 see also SNPs (“single nucleotide polymorphisms”) (“snips”)

  VNTR and 286–7

  X-inactivation in female embryos 189–91

  Church, Dr. George M. 295

  chymotrypsin 22

  Cicero 147

  clades 201, 240

  Clinton, Bill 124

  Clovis culture 197–8, 207

  co-evolution 158, 160

  Coghlan, Andy 125

  Cold Spring Harbor Laboratory, New York 131, 274

  Collins, Francis 124, 127, 128

  color blindness 109, 190

  Columbia University 79, 93, 263

  Columnea plant 149–50

  “Complex I deficiency” 154–5

  Corey, Robert 68

  Corsica 289

  covalent bond 65–6, 67, 102, 176

  cranberry bog bacillus 19

  creative genomics 293–4

  creativity

  creative genomics 293–4

  Crick-Watson discovery of structure of DNA and 63–4, 69, 88, 90

  DNA and 3

  genomic 145, 175, 178, 282, 293, 304

  hybrid 266

  Neanderthal 270

  personality and scientific 20, 30–1

  Crichton, Michael: Jurassic Park 243

  Crick, Francis 34, 71, 74

  Avery's discovery of DNA and 53, 55

  background 52

  Brenner and see Brenner, Sydney

  Cavendish Laboratory and see Cavendish Laboratory, Cambridge

  character 54–5, 64–5

  Chargaff and 80–1, 86

  DNA extrapolation to proteins, investigates 93–4, 95–8, 114

  Franklin and 74, 76–8, 84, 85

  Gamow and 95–6

  Griffith and 78–9, 86, 97

  Pauling's paper on structure of DNA and 82–3, 85

  “perfect biological principle” and 79

  RNA Tie Club and 96, 97

  Schrödinger's inspires 40, 52, 52, 91, 93, 125

  second paper on genetic implications of the structure of DNA, 1953 88

  structure of DNA, investigation into and discovery of 34, 40, 53, 55, 59, 60, 54–6, 58, 61–5, 68, 69–70, 74, 76–91, 92, 93, 94, 99, 102, 103, 112

  Watson and 40, 55–6, 58, 60, 61–5, 69

  What Is Life? and 52–3

  “What Mad Pursuit” (ad-hoc seminar) 54–5

  Wilkins and 47, 75–6, 83

  Crick, Michael 62

  Crick, Odile 62

  cyanobacteria 151–2, 206, 282

  cystic fibrosis 108, 109, 300

  cytoplasm 94, 95, 131, 134, 152, 153, 165, 187, 203–4

  cytosine 17–18, 69, 77, 80, 81, 87, 94, 102, 142, 176, 177, 178, 181, 191, 199, 247

  “D” root (haplogroup) 201

  D4h3a (haplogroup) 202, 207

  Daily Telegraph 124, 281

  Dale, Sir Henry 33

  Danube River 230


  Darwin, Charles 7, 12, 14, 15, 31, 37, 41, 90, 130, 137–9, 144, 145, 146–7, 247–8, 281, 282, 283, 291, 298

  Darwinism 41–2, 144

  Dawkins, Richard: The Selfish Gene 146–7

  Dawson, M. H. 15–16

  deacetylase HDAC11 182

  Deichmann, Uti 24

  Delbruck, Max 26, 39, 41–2, 43, 44, 57–8, 63, 92, 96

  Denisovan man (Denisova hominins) 248, 276–8, 279, 288, 301

  Department of Agriculture, US. (USDA) 299

  Department of Energy, US. 122

  Derevianko, Anatoly 273, 275

  De Valera, Eamon 38–9

  developmental pathway 117–18

  Diamond, Jared 262

  disease 8, 10–11, 12–13, 20, 97–8, 106–11, 112, 120, 134–55, 160, 161, 164, 167, 169, 170, 175, 188, 190, 192, 195, 212–15, 242, 256, 261, 264, 269, 270, 271, 284, 289, 294–7, 298, 300–2 see also under individual disease name

  Dmanisi, Georgia 249

  DNA (deoxyribonucleic acid) 3

  anti-sense 105–6, 177, 194, 199

  cDNA (complementary DNA) 193

  coding triplets, search for 94–9

  codons 98–9, 106–7, 191

  constancy 25

  correspondence of number of genes to number of proteins 93, 130, 131–5

  discovered by Avery, 1944 14–35, 36

  discovery confirmed by Hershey and Chase's experiment with bacteriophage, 1951 27–8, 34, 36, 53

  epigenetics and see epigenetics

  exons and 132, 133, 134, 135, 142, 187, 190, 193

  extraction techniques 21–2, 25, 26, 28, 29, 226, 244, 246, 247, 250, 257, 258, 260, 268, 274, 276, 277

  extrapolation to proteins first explored 92–111, 112–23

  fingerprinting 285–7

  GACT (guanine, adenine, cytosine, thymine) bases 17–18, 77, 93, 94, 95

  genetics engineering/creative genomics and 292–304

  genomic level evolution and 172–85

  human ancestry and 197–291

  introns and 132, 133, 134, 135, 187, 190

  junk 164, 170

  mutations of see mutations

  natural selection and see natural selection

  number of protein-coding genes in human genome and 130–1, 135

  profiling 285

  promoter sequences 100, 113, 134, 141–2, 165, 169, 176–7, 183, 191, 193, 194, 207

  questions over the discovery of 24–9

  recombinant 294, 299

  RNA and see RNA

  sense strand 177, 186, 191, 194, 199

  sequencing of 120–3, 124–36, 167, 198, 202, 246–7, 258, 270–1, 278, 284–5, 287, 288–9, 302

  splicing 130–5, 87

  structure discovered by Crick and Watson, 1953 38–49, 50–8, 59–91, 92, 93, 95, 112, 113

  sugar—deoxyribose 94, 102

  symbiosis and see symbiosis

  tetranucleotide hypothesis and 18, 79, 80

  up-stream regulatory elements 134

  viruses and see viruses

  DNA-methyltransferase 176

  Dobzhansky, Theodosius 140

  Domagk, Dr. Gerhard 20

  Donohue, Jerry 86–7

  Douka, Dr. Katerina 226–38

  Down's syndrome 109

  Dubos, René Jules 5–7, 10, 14, 15, 16–17, 19–21, 22, 23, 29–30, 31, 32, 33, 34

  Dutton, Professor Gordon N. 145

  dystrophin 134–5

  East Africa 211, 212, 222

  Edge (website) 244

  Edqvist, Dr. Per-Henrik 167, 168

  Egbert (skeleton fossil) 231–3

  Egypt 244

  electron microscope, invention of 42

  electron spin resonance 234, 236

  Elmer, Perkin 126

  embryo/embryogenesis 2, 8, 37, 40, 109–10, 113–19, 120, 143, 164, 167–8, 172–3, 174, 178, 183, 189, 190–1, 194, 284, 294, 297, 304

  ENCODE “Encyclopedia of DNA coding elements” 171

  Environmental Protection Agency (EPA) 299

  enzymes 19, 22, 25, 26, 54, 93, 104, 117, 119, 143, 157, 158, 159, 160, 165, 182, 247

  EPAS1 (gene) 277–8

  epigenetics 116, 118–19, 120, 145, 157, 163, 164, 172, 173–84, 187, 189, 191, 192, 194, 236, 247, 282, 283, 285, 286, 293–4, 295, 296, 297, 301

  discovery of 96–106, 113–16

  epigenetic mark 182–3

  epigenetic silencing 163, 176–7, 183, 186, 189, 192

  epigenetic system 173–84

  epigenome and 175, 183, 295, 302

  evolutionary potential 175, 178, 182–3

  four epigenetic control systems 175–84

  genetic engineering and 293, 294, 295, 296, 297

  genomic creativity and 175, 178

  histone modification and 175, 180–3, 191

  Hox genes and see Hox genes

  imprinting 192

  lncRNAs and 192, 194

  LTRs and 164

  meiosis and 283

  methylation and 163, 175, 176–9, 180, 181, 182, 183, 191, 247

  mutation location and 285

  non-coding RNAs and 173–4, 175, 183–4, 185–96, 236, 266

  puberty and 118–19

  RNAi and 187–9

  tandem repeats and 286

  Escherichia coli—E. coli 99, 121

  Es Skhul cave site, Mount Carmel, Palestine 228, 234–5

  ESTs 302

  Ethelruda (fossil) 232, 233

  Ethiopia 220–1, 224

  eugenics 110, 297

  eukaryotes 9–10, 114, 135, 141

  Eurasia, human ancestry/migration patterns and 202–3, 214, 217, 228, 229, 230, 234, 235, 236, 237, 238, 239, 248, 249, 251, 256, 259, 261, 264–6, 269, 271, 272

  Europe: human ancestry/migration patterns and 143, 144, 197–8, 200–1, 202, 211, 212, 217–18, 224, 226, 227, 228, 229, 230, 236, 237, 238, 239–41, 249, 251, 253, 256, 258, 260, 261, 262, 264–5, 267, 269, 271–2, 277, 288, 289, 299–300, 301

  evolution

  continuing 301–2

  Darwin and theory of see Darwin, Charles

  genomic level 172–84

  see also under individual area of evolution

  evolutionary biologists 11–12, 37, 140, 198, 251

  exons 132, 133, 134, 135, 142, 176, 187, 190, 193, 194

  Feinbaum, Rhonda 185

  fingerprinting, DNA 285–7

  Finlayson, Clive 279

  Fire, Andrew Z. 186, 187

  Fisher, Ronald Aylmer 140

  Fisher, Simon 254

  Fleming, Alexander 19

  Flores, island of 248

  Food and Drug Administration (FDA), US 299

  454 Life Sciences 246

  Foxhall Road, Ipswich, Neanderthal hand axes found at 264

  FOXP2 (gene) 254, 260

  Francalacci, Paolo 219–20

  France 11, 165, 169

  GM crops and 300

  Homo sapiens ancestry and 230, 237, 238, 239, 255, 255, 263, 264

  Human Genome Project and 123, 124

  Frank, Albert Bernhard 147, 148

  Franklin, Rosalind 36, 47, 58

  background 70–2

  Biomolecular Research Laboratory, Birkbeck college, move to 83, 84, 90–1

  Biophysics Unit, King's College, role at 72–6

  character 71–2

  Crick and 74, 76

  death 90, 91

  discovery of structure of DNA, role in 47, 58, 70, 72–8, 82–5, 86, 88, 90

  Mering and 71–2

  Sayre and 74–6, 78

  science and everyday life, on separation of 36

  Watson and 43–4, 57, 60–1, 63, 70, 82–3, 84–5

  Wilkins and 47, 72–8, 82–5, 90

  French, Jennifer C. 237, 271

  fruit flies 8, 10, 25, 41, 93, 116, 126, 130, 290

  Galapagos islands 138

  Gamble, Clive 252

  Gamow, George 95–6, 97

  Garrod, Archibald E. 93

  gene

  defin
ition of 7–10

  expression 2, 8, 55, 93, 100, 113–14, 117, 120, 131, 134, 165, 166, 167, 168, 170, 173, 174, 175, 178, 188, 190 see also epigenetics

  therapy 108, 109, 110, 155, 175, 188, 294, 297

  genetic bottlenecks 221–2, 224, 301

  genetic engineering 293–300, 302

  genetics, birth of discipline 8

  genomic creativity (mutation, epigenetics, symbiosis and hybridization) 145, 175, 178, 282, 293, 304

  genotype 12, 295–6

  Gibraltar, Neanderthal remains in 251

  Gibraltar Museum 279

  Glasgow Caledonian University 145

  GM (genetically modified) 298–300

  Gold, Thomas 78–9

  Golding, William 262

  gonadotrophin-releasing hormone (GnRH) 119

  Gosling, Raymond 50, 72, 73, 76, 77, 78, 83, 86, 88, 90

  Gravettians 238

  Great Apes 165–6, 248, 281

  Griffith, Frederick 12–14, 15, 16

  Griffith, John 78–9, 86, 97

  guanine 17–18, 69, 80, 81, 87, 94, 102, 142, 177, 191

  Haemophilus influenza (bacterium) 126

  Haldane, John Burdon Sanderson 140

  Hamilton, Andrew 186

  haplotypes/haplogroups 200–9, 210–21, 223, 236, 239–40, 250, 268–9, 284, 288, 289

  Harvard Medical School 268, 276

  Harvard University 98, 268

  Healy, Bernadine 126–7

  Hedges, Professor Robert E. M. 231

  hemoglobin 52, 54–5, 57, 68, 69, 97–8, 107, 133–4, 278

  hemophilia 108, 190, 300

  heredity, principles of 7–15, 17, 18, 24, 25, 29, 33, 34, 36, 37–8, 61–2, 63, 64, 79, 81, 92, 93, 95, 106, 113, 120, 137–45, 153, 162, 178, 182, 184, 196, 204, 265, 283, 292

  Herriott, Roger 43

  Hershey, Alfred 27–8, 34, 36, 41–2, 43–4, 53, 96

  Herto, Ethiopia 220–1

  Higham, Thomas F. G. 231

  Highfield, Roger 124, 281

  histone modification 125, 175, 180–3, 191

  HIV-1 157, 159–60, 162, 223

  HLA-B (gene) 160

  Hodgkin, Dorothy 54

  Holloway, Ralph 263

  holobiont 148–9

  holobiontic genome 151, 153, 155, 159, 162, 164, 205, 222, 266

  hominids 244, 248

  hominins 228, 233, 234, 235, 244, 248, 249, 275–6, 277, 278

  Homo erectus 248–50, 251, 252, 259, 260, 277, 290

  Homo floresiensis 248

  Homo heidelbergensis 251, 252, 259–60, 278

  Hood, Leroy 121

  horizontal gene transfer 150–1, 299

  Horvitz, Robert 185

  Hotchkiss, Rollin 17, 26

  Howard Hughes Medical Institute 268

  Hox genes 116–18

  human endogenous retroviruses (HERVs) 162–70, 173, 212, 222–4, 236, 282, 288

  ERV3 166–7, 168

  HERV–FRD 166–7, 168–9

  HERV–Ks 162, 163, 166, 212, 222–4, 236, 288

  HERV–K106 223–4, 236, 288

  HERV–K113 212, 223, 236

 

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