Gene Cloning

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Index Entries which are simply page numbrs refer to the main text. Entries with g after the page number are in the glossary. A α globin, 103, 118 α helix, 445g α-1-antitrypsin, 373 β galactosidase, 55, 56, 96, 336, 337 β globin, 420, 424, 425, 429 β sheet, 445g β thalassemia, 420, 422, 425 16S rRNA, 242, 437 454 sequencing, 197–202 Ac elements, 157 Activator, 445g Active DNA transposons, 15 Adaptor, 106, 445g Adherence genes, 149 Aedes aegypti genetic manipulation of, 388–390 Affinity purification, 350–351 Agrobacterium tumefaciens use in construction of transgenic plants, 391–393 Alkaline phosphatase calf intestinal alkaline phosphatase (CIAP), 51–52 Allele, 445g Allele specific oligonucleotide, 427 Allele specific PCR amplification, 423 Alpha-globin see α-globin Alpha helix see α helix Alpha-1-antitrypsin see α-1-antitrypsin Alternative splicing, 12, 216 Alzheimer’s Disease, 372 Amelogenin, 414, 415 Amino terminus, 445g Amniocentesis, 426 ANDi, 384–388 Aneuploidy, 30, 445g Anneal, 445g Antibiotic resistance, 26 in selection for transformants, 37, 43–44 insertional inactivation with, 53–54 Antibody, 120, 342, 445g Antigen, 445g Antisense, 445g Arabidopsis thaliana, 20 knockouts in, 405–406 RNAi in, 288 Archaea, 242 Artemis, 213 ASO see allele specific oligonucleotide Autosome, 9 Auxotroph, 119, 269,283–284, 293, 299, 445g Avirulence (avr) gene, 157 B BAC see bacterial artificial chromosome BAC clones, 192 BAC library, 192 Bacterial artificial chromosome, 100–101, 102, 445g Bacteriophage, 445g Bacteriophage λ P L promoter, 256 cloning with, 97 expression vector, 96 genome, 26 in vitro packaging, 94, 95–96 in whole genome sequencing, 189 insertion vector, 95, 105 lysogenic pathway, 26 lytic pathway, 26 plating, 94 replacement vector, 95 size constraints on packaging, 97, 100 transfection, 95–96 vector for library construction, 26, 27, 93 Bacteriophage M13, 179–181 Baculovirus, 273 Beta-galactosidase, see β galactosidase Beta-globin see β globin Beta sheet see β sheet Beta-thalassemia see β thalassemia Biopharming, 373–374, 419, 445g Bioterrorism agents detecting, 438 BLAST, 226, 228 Blasticidin-S, 273 Blocks, 225 Blosum 62, 221, 222 BRCA1, 440 BRCA2, 441 Breast cancer, 422, 440 C Caenorhabditis elegans, 20, 156, 288–289 genome wide survey of gene function, 288–289, 367 Calcium phosphate mediated transfection, 272, 339
454 Gene Cloning Capillary electrophoresis, 185–186 Carboxyl terminus, 445g Carrier status, 422 CD4, 309 cDNA, 11, 103, 214,215, 323–326 445g cloning, 105–107 library see cDNA library rapid amplification of cDNA ends (RACE), 323–325 sequencing, 182–183 vectors for cloning, 105 cDNA library, 101–109, 167, 299 constructing, 103 differential screening, 132 screening, 118–123, 353 starting material, 102–103 vectors for cloning, 105 yeast one-hybrid screen, 351–353 Celera, 196–197 Centromere, 28, 445g cf-9 gene, 157–159, 172 CFTR gene, 226 Chimpanzee, 21, 23 Chinese hamser ovary cells see CHO cells CHO cells, 270 Chorionic villus sampling (CVS), 426 Chromatin, 340–341, 445g Chromosome, 7 aberration, 30 acrocentric, 28, 29 autosome, 9 centromere, 28 chromosomal location, 30 chromosome jumping, 161, 163, 445g chromosome walking, 163–166, 445g eukaryotic, physical characteristics, 28 G band, 28, 29 interband, 28 metacentric, 28, 29 number, 19 painting, 434–435 sex, 9 size, 28 sub-metacentric, 28, 29 Cladosporium fulvum, 157, 172 Cloning bacterial adherence genes, 149–152 bacterial genes with difficult phenotypes, 152–156 cDNA, 105–107 CF gene, 168–169 by complementation, 119–120 gene tagging, 142–159 genomic DNA, 36–45 genomic DNA libraries, 87–89 in cosmids, 99–100 map based, 159–167 PCR products, 74–76 plant resistance genes, 156–159 by signature tagged mutagenesis, 152–156 ClustalW, 233, 234 CODIS see Combined DNA Index System Codon, 446g Codon preference see codon usage Codon usage, 211, 212, 260, 446g Co-immunoprecipitation, 301–302 Colinearity, 21, 24 Combined DNA Index System, 416 Comparative biology, 22 Comparative genomics, 22 Competent cells, 43–44, 446g Complementary, 446g Complementary DNA see cDNA Complementation, 446g Concatemer, 97, 446g Consensus sequence, 233, 446g intron-exon boundary, 215 Conservative substitution, 220 Conserved domain, 230, 232, 446g Contig see contiguous sequence Contiguous sequence, 189–190, 446 Correlation score, 214 Cos site, 93, 94,99–100, 446g Cosmid, 98–100, 446g Cosmid library, 150–151 CpG island, 31–32, 215 Cre-loxP system, 404, 405 C-value paradox, 8 Cycle sequencing, 185–188 Cystic fibrosis, 142, 226, 422, 424–243 cloning of CF gene, 168–169, 172 diagnostic test, 431 mutations giving rise to, 425 cytocrome P450, 421 D Danio rerio, 20 Database combined DNA Index System, 415, 416 DNA sequence, 225 National DNA Database, 415, 416 primary sequence, 225 protein sequence, 225 secondary sequence, 225 DDBJ, 225 DEAE-dextran mediated transfection, 339 Deletion analysis example of use, 347–350 Denaturing high performance liquid chromatography, 433, 440
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Gene Cloning
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Published by: Taylor & Francis Grou
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vi Contents 3.14 Designing PCR Prim
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viii Contents 8.3 Identifying Eukar
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1 Introduction 1.1 The Beginning of
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Introduction 3 which also conveys a
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Introduction 5 thought, or the brin
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2 Genome Organization Learning outc
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Genome Organization 9 and not quite
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Genome Organization 11 both of whic
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Genome Organization 13 relative com
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Genome Organization 15 Box 2.2 Inte
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Genome Organization 17 Table 2.2 Hu
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Genome Organization 19 close to oth
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Genome Organization 21 individual g
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slower rate than junk DNA. (To be m
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Genome Organization 25 kb 0 2 4 6 8
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Genome Organization 27 cloning pred
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Genome Organization 29 (a) 1 2 3 4
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Genome Organization 31 interphase a
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Genome Organization 33 A2.3. Chromo
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3 Key Tools for Gene Cloning Learni
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Key Tools for Gene Cloning 37 repli
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Key Tools for Gene Cloning 39 Box 3
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Key Tools for Gene Cloning 41 (a) (
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Key Tools for Gene Cloning 43 then,
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Key Tools for Gene Cloning 45 Figur
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Key Tools for Gene Cloning 47 Clear
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Key Tools for Gene Cloning 49 that
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Key Tools for Gene Cloning 51 same
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3.9 More About Vectors Detecting su
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Key Tools for Gene Cloning 55 in th
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Key Tools for Gene Cloning 57 Q3.13
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Key Tools for Gene Cloning 59 alway
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Key Tools for Gene Cloning 61 Figur
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Key Tools for Gene Cloning 63 (a) C
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Key Tools for Gene Cloning 65 Box 3
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Key Tools for Gene Cloning 67 simpl
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Key Tools for Gene Cloning 69 (a) 5
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Key Tools for Gene Cloning 71 92 92
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Key Tools for Gene Cloning 73 polym
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Key Tools for Gene Cloning 75 (a) T
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Key Tools for Gene Cloning 77 DNA s
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Key Tools for Gene Cloning 79 Q3.7.
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Key Tools for Gene Cloning 81 A3.15
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Key Tools for Gene Cloning 83 A3.20
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86 Gene Cloning you extract DNA fro
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88 Gene Cloning Box 4.1 Preparation
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90 Gene Cloning which is 6.3 Mb, to
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92 Gene Cloning Also, if all the fr
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94 Gene Cloning (a) (b) Bacterial s
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96 Gene Cloning (a) Insertion vecto
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98 Gene Cloning The strictly define
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100 Gene Cloning BamHI Ap r Tet r p
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102 Gene Cloning parB Cm r parA rep
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104 Gene Cloning (a) TTTTT AAAAA TT
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106 Gene Cloning Box 4.3 Converting
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108 Gene Cloning of your gene is. A
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110 Gene Cloning A4.2. Extract chro
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112 Gene Cloning A4.8. See Section
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114 Gene Cloning Q4.15. What are th
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116 Gene Cloning dystrophin gene is
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118 Gene Cloning it is still a form
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120 Gene Cloning One obvious proble
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122 Gene Cloning The main difficult
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124 Gene Cloning (a) Labeled single
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126 Gene Cloning N terminus Phe Val
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128 Gene Cloning Box 5.3 Types of D
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130 Gene Cloning Box 5.4 Methods fo
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132 Gene Cloning the DNA probe. Bot
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134 Gene Cloning a b c d e f g h 1
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136 Gene Cloning S. cerevisiae, and
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138 Gene Cloning Q5.7. Would you ex
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140 Gene Cloning use your genomic c
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142 Gene Cloning diseases, where th
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144 Gene Cloning (a) Replicative Ta
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146 Gene Cloning where the transpos
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148 Gene Cloning DNA fragment in th
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150 Gene Cloning Bacteria transform
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152 Gene Cloning Wild-type gene Mut
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154 Gene Cloning molecule using PCR
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156 Gene Cloning digesting chromoso
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158 Gene Cloning + + Ac Avr Avr cf-
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160 Gene Cloning which are very clo
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162 Gene Cloning Box 6.3 Restrictio
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164 Gene Cloning Initial region clo
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166 Gene Cloning Box 6.4 Nonsense S
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168 Gene Cloning 6.10 Cloning of th
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170 Gene Cloning are two possible o
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172 Gene Cloning Isolation of the t
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174 Gene Cloning Two approaches wer
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176 Gene Cloning synthesize DNA de
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178 Gene Cloning Box 7.1 Denaturing
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180 Gene Cloning G A T C Figure 7.4
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182 Gene Cloning although other con
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184 Gene Cloning A large DNA fragme
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186 Gene Cloning chain reaction, fl
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188 Gene Cloning rounds of amplific
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190 Gene Cloning Contig 2 Clone 12
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192 Gene Cloning λ Clone Scaffold
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194 Gene Cloning Genomic DNA (a) Cl
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196 Gene Cloning therefore sequence
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198 Gene Cloning Tag sequence CGTGT
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200 Gene Cloning Genomic DNA (a) Ad
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202 Gene Cloning bases. The light s
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204 Gene Cloning A7.3. (a) The dide
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8 Bioinformatics Learning outcomes:
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Bioinformatics 209 Table 8.1 The ge
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Bioinformatics 211 5' accgcgcatggtg
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Bioinformatics 213 Correlation Scor
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Bioinformatics 215 AGG T R A G T C
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Bioinformatics 217 conjunction with
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Bioinformatics 219 (c) V S V K L Q
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Bioinformatics 221 Tiny P Small Ali
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Bioinformatics 223 Matrix: EBLOSUM6
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Bioinformatics 225 Box 8.2 DNA and
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Bioinformatics 227 (a) DB:ID Source
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Bioinformatics 229 (a) Sequences pr
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Bioinformatics 231 list is also of
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Bioinformatics 233 this relates to
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Bioinformatics 235 common functiona
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Bioinformatics 237 These two regula
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Bioinformatics 239 three-dimensiona
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Bioinformatics 241 Neisseria mening
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Bioinformatics 243 A8.1. The triple
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Bioinformatics 245 Q8.11. Which gro
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Bioinformatics 247 EMBL Nucleotide
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250 Gene Cloning What sorts of stud
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252 Gene Cloning 9.2 Requirements f
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254 Gene Cloning (a) The lac promot
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256 Gene Cloning lac: CCAGGCTTTACAC
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258 Gene Cloning phage (such as T7)
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260 Gene Cloning 9.4 Some Problems
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262 Gene Cloning Figure 9.6 Inclusi
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264 Gene Cloning Box 9.1 Translatio
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266 Gene Cloning Box 9.2 Signal Seq
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268 Gene Cloning Ribosome Cytosol P
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270 Gene Cloning Other yeast specie
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272 Gene Cloning (turned on by an i
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274 Gene Cloning 9.6 A Final Word A
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276 Gene Cloning study, as they wil
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10 Gene Cloning in the Functional A
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Gene Cloning in the Functional Anal
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316 Gene Cloning genomic sequences
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318 Gene Cloning the first exon of
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320 Gene Cloning Box 11.1 End Label
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322 Gene Cloning mRNA 5' 3' 3' 5' S
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324 Gene Cloning mRNA 5' 3' 3' 5' G
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326 Gene Cloning cloning step. RACE
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328 Gene Cloning Prepare RNA from c
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330 Gene Cloning Gene A condition 1
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332 Gene Cloning (a) (b) (c) Immobi
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334 Gene Cloning tat and one in whi
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336 Gene Cloning Box 11.3 Examples
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338 Gene Cloning (a) MCS for promot
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340 Gene Cloning important regulato
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342 Gene Cloning (a) F DP DPA DNA-t
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344 Gene Cloning DNA alone DNA-prot
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346 Gene Cloning [FNR] GA - + -90 -
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348 Gene Cloning (a) 1 2 3 4 5 Prom
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350 Gene Cloning bind the transcrip
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352 Gene Cloning Target sequence Ye
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354 Gene Cloning have been develope
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356 Gene Cloning detected by autora
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358 Gene Cloning vide a complete li
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360 Gene Cloning MS 503 750 1400 16
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362 Gene Cloning Q11.3. Why is it e
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364 Gene Cloning (transcriptomics o
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366 Gene Cloning Figure 12.1 Transg
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368 Gene Cloning Herbicide Non-tran
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370 Gene Cloning that has been used
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372 Gene Cloning tumors with high f
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374 Gene Cloning Transgene encoding
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376 Gene Cloning placed on the mark
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378 Gene Cloning Gene A: a gene whi
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380 Gene Cloning Isolate the gene o
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382 Gene Cloning Box 12.1 Recombina
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384 Gene Cloning damage to the DNA
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386 Gene Cloning Box 12.2 The Produ
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388 Gene Cloning as to whether the
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390 Gene Cloning transformed. The i
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392 Gene Cloning 1. Gene of interes
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394 Gene Cloning Showing that the D
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396 Gene Cloning complete plants by
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398 Gene Cloning 12.5 Knockout Mice
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400 Gene Cloning introduced back in
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