Index 273 Index A Acrylamide gel electrophoresis Trichomonas vaginalis, 231, 234 Agarose gel electrophoresis amplification detection, 3 HCV detection,

Transcription

1 Index 273 Index A Acrylamide gel electrophoresis Trichomonas vaginalis, 231, 234 Agarose gel electrophoresis amplification detection, 3 HCV detection, 167, 169, 170 Legionella species, 175, 177, 179, 180 LT-toxin gene, 106, 108, 109 LT-toxin gene amplification, 110 motif-dependent PCR detection, 119, 120, 122 PSA-positive cells, 218, 219, 222, 224 rodent parvoviruses, transgene integrants and homologous recombinants, transgenic plants, materials, 159 Amino acid sequence, BIV tat gene, 77 AMPLICOR MTB test processes, 203, 204 pulmonary tuberculosis diagnosis, clinical trials, 210, 213 cost impact, 210, 213 quality control, 209 results, 211 rapidity and reliability, 212, 213 sensitivity, 212 Amplifier molecules, bdna, 14, 15 Analytical flow cytometry prostate cancer, PSA-positive cells, Arbitrarily primed polymerase chain reaction (AP-PCR), genomic fingerprinting, 267 Automated sequencer, fluorescence PCR, MFS, B BDNA, amplifier molecules, 14, 15 BDNA technology, laboratory design, 10 Bisulfite-treated DNA PCR amplification principle, 157 transgenic plants, 158, 160, 161, 163 BIV nucleotide positions, 71 PCR diagnosis, serological surveys, 67 Western blot assays, 67, 68 BIV samples, pol PCR screening, 76 BIV tat gene, amino acid sequence, 77 Boar semen PRRSV detection, swine bioassay, 82 Bovine immunodeficiency-like virus, PCR diagnosis, Bovine immunodeficiency virus, PCR diagnosis,

2 274 Index Bovine lentivirus, PCR diagnosis, 67 Branched DNA signal amplification (bdna) description, principle, 15 C Cancer sequences AP-PCR fingerprinting, PCR fingerprinting, Cardenolide steroid, digoxigenin (DIG)-labeled DNA, 104 Causative mutation IVS protein assay, CDNA, plasmid clone, 193 CDNA-equalized reverse transcriptase PCR, CDNA probe hybrydization, differentially expressed genes, CDNA quantitation, cert-pcr assay, materials, 58, 59 CDNA synthesis causative mutation, 258, 260, 262 cert-pcr assay, 58, 60, 61, 64 colorectal cancer syndromes, 131, 133 PSA-positive cells, 218, 221, 223 transgenic plants, 158, 161 Centroid Linkage method, enterotoxigenic Escherichia coli (ETEC), 121 CERT-PCR assay cdna quantitation, 58, 59 cdna synthesis, 58, 60, 61, 64 inos, 63 PCR, 59, 62, 63 RNA extraction, 59, 60 RNA isolation, 58 templates, 62 tissue and cell lines, 57, 58 TNF and inos transcript quantitation, Chlamydia trachomatis, PCR, Classic PCR enzyme choice, 4 error sources, 5, 6, 49 primer annealing, 3, 4 primer selection, 3, 4 quantitative amplification, 5 variable optimization, 4 Clinical microbiology application, 1 17 history, 1 problems, 16 Cloning, transgenic plants, 159, 160, 162 Cocultivation techniques, virus isolation, 68 Colonoscopy, FAP, 129 Colorectal cancer syndromes, IVTT, Colorimetric detection digoxigenin (DIG)-labeled DNA, 104 LT-toxin gene, 106, 108, 109, 111 Competitive PCR, heteroduplex formation, 193 Competitive RT-PCR, mrna expression quantitation, Competitive templates, cert-pcr assay, methods, 62 Cosupression gene silencing, 153 RNA-RNA interactions, 153 Cytogenetic analysis, 127

3 Index 275 D Dendrogram, enterotoxigenic Escherichia coli (ETEC), 121 Densitometric analysis, HIV-1 mrna, 97 Differentially expressed genes, PCR detection and isolation, Digoxigenin (DIG)-labeled DNA cardenolide steroid, 104 colorimetric detection, 104, 218, 221, 223, 224 DNA extraction causative mutation, 257, 260, 262 colorectal cancer syndromes, 131, 132 hot start, 4, 5 Legionella species, PCR assays, Taq polymerase, 4 Toxoplasma gondii, transgene integrants and homologous recombinants, transgenic plants, 158, 160, 163 DNA extraction method one, PCR tests, 69, 70 DNA extraction method two, PCR tests, 69 71, 73 DNA fingerprinting ETEC, motif-dependent PCR detection, DNA sequence, exponential amplification, 1, 2 DNA template LT-toxin gene, 105, 107, 109 motif-dependent PCR detection, 117 E Electrophoresis, amplification detection, 3 Endoscopy, FAP, 129, 130 Enteropathogens, animal and human, 101 Enterotoxigenic Escherichia coli (ETEC) Centroid Linkage method, 121 dendrogram, 121 detection, DNA fingerprinting, types, 102 Env gene, PCR amplification, 74 Enzyme choice, Classic PCR, 4 Enzyme-linked immunoassay (ELISA), 104 Chlamydia trachomatis, 229, 230, 232 Escherichia coli, 101 identification, 115 Exponential amplification detection, 3 DNA sequence, 1, 2 principle, 1 4 F Familial adenomatous polyposis (FAP), 129, 130 Familial adenomatous polyposis mutations, IVS protein assay, FISH, 127 Flow cytometry, PSA-positive cells, Fluorescence PCR, automated sequencer, MFS, Fluorescent detection, LT-toxin gene, 107, 109, 111

4 276 Index Fluorescent (F) DNA fingerprinting, motif-dependent PCR detection, Fluorescent labeled amplicons, motif-dependent PCR detection, Fluorography, causative mutation, 258, 259, 261, 262 G Gel electrophoresis cancer sequences, causative mutation, 258, 259, 261, 262 Gene silencing, cosupression, 153 Genetic alterations, genomic fingerprinting, 267 Genome-amplification, strategy typing, 116 Genomic fingerprinting arbitrarily primed polymerase chain reaction (AP-PCR), 267 genetic alterations, 267 H HCV detection, RT-PCR, Heat-lable toxin coding gene, see LT-toxin gene Heat-stable toxin amino acid toxins, 102 ST-1a and ST-1b, 102 Hepatitis C virus, see HCV Hereditary nonpolyposis colorectal cancer, see HNPCC Heteroduplex analysis, 127 Heteroduplex formation, competitive PCR, 193 HIV-1 genome central region, enlargement, 90 HIV-1 mrna densitometric analysis, 97 hybridization signals, 97 pattern, 90 quantitative and discriminative detection, RNase mapping assay, sequential expression, 92 U1 cells, 96 vpr cdna probes, 91 HNPCC, IVTT, Homologous recombinants, PCR, Hot start DNA extraction, 4, 5 problems, 4, 6 HTLV-1, 92 Hybridization, Ross River virus, Hybridization signals, HIV-1 mrna, 97 I Improved nested pol PCR tests, 70, 72, 75 inos mrna, measurement, inos transcript quantitation, cert- PCR assay, In vitro synthesis, see IVS In vitro transcription/translation analysis, see IVTT IVS protein assay familial adenomatous polyposis mutations, HNPCC, 255 limitations, 254 strengths, 254 truncating genetic mutations,

5 Index 277 IVTT colorectal cancer syndromes advantages, interpretation, pathogenic mutations, 129 presymptomatic patient identification, 129 principles, 128 translation-terminating mutation identification, J Jembrana disease virus, PCR diagnosis, 67 L Laboratory design levels, 9, 10 nucleic acid amplification, 9, 10 Legionella species detection, PCR, Lelystad virus, see PRRSV Ligase chain reaction (LCR), description, 12 LT-toxin gene detection, nonisotopic PCR-based detection, M Marfan syndrome, see MFS MFS, analysis, 52, 53 diagnosis, illustrations, 53 one-step procedure, 50, 51, 53, 54 two-step procedure, 52, 53 Micromanipulator, 43 Microorganism detection identification, 6 8 RAPD, 8 ribosomal RNA PCR, 6, 8 nucleic acid amplification, 6 9 preparation, 8, 9 capture method, 9 lysis/extraction method, 9 optimal extraction method, 8, 9 Microorganism typing, aspects, 116 Molecular biology, history, 1 Motif-dependent PCR detection, DNA fingerprinting, 118 MRNA expression quantitation, competitive RT-PCR, Mullis, Kary, 1 Mutation identification, importance, 127 N Nested env PCR tests, serological methods, 69 virus isolation, 68, 69 Western blot assays, 68, 69 Nested PCR procedures, PRRSV detection, 83, 84, 86 Nested pol PCR tests, 70, 72 primer combinations, 73 serological methods, 69 virus isolation, 68, 69 Western blot assays, 68, 69 Nested RT-PCR, Ross River virus, Nonisotopic PCR-based detection, LT-toxin gene, Nucleic acid amplification alternative methods, application, 1 17, 9 11 contamination, 9, 10 detection, 3

6 278 Index laboratory design, 9, 10 microorganism detection, 6 9 PCR-problems, 5, 6 PCR-theory, 1 5 quality control, 11 technology improvements, 16, 17 Nucleotide positions, BIV, 71 O Oligonucleotides, annealing, 1, 2 Oligonucleotides primers PSA-positive cells, materials, 219 rodent parvoviruses PCR assays, 33 Optimal extraction method cost/benefit analysis, 9 description, 8, 9 Outer PCR procedures, PRRSV detection, 83, 84, 86 P Pathogenic mutations, IVTT, 129 PCR Southern analysis, 154, 155 time-saving benefit, 153, 154 virus detection, 145 PCR amplification cancer sequences, causative mutation, 258, 260, 261 Chlamydia trachomatis, 229, 231, 232, 234 colorectal cancer syndromes, 131, 133, 144 env gene, 74 Legionella species, 175, 177, 179 LT-toxin gene, 106, 107, 109 motif-dependent PCR detection, , 122 PCR assays, 32, PSA-positive cells, 218, 221, 223, 224 pulmonary tuberculosis diagnosis, materials, 205, 206 RT pol gene, 76 Toxoplasma gondii, 198, 199, 201 transgene integrants and homologous recombinants, transgenic plants, materials, 158, 159 Trichomonas vaginalis, 230, 233 PCR analysis, commercial kits, 11, 12 PCR-based methodology, schematic demonstration, 56 PCR diagnosis bovine immunodeficiency-like virus, bovine lentivirus, 67 PCR fingerprinting, cancer sequences, PCR primers, primer 45 and primer one, 77 PCR problems, 5, 6 PCR product detection, PRRSV detection, PCR tests DNA extraction-method one, 69, 70, 73 DNA extraction-method two, 69, 70, 71, 73 improved nested pol PCR, 72, 75 nested env PCR, nested pol PCR, 72 PCR amplification, 70 primer design, 72, PCR theory, 1 6 Plasmid clone, cdna, 193 Plasmid DNA, transgenic plants, methods, 162

7 Index 279 Pol PCR screening, BIV samples, 76 Polyacrylamide gel electrophoresis colorectal cancer syndromes, 132, 135, 141 Toxoplasma gondii, Polymerase chain reaction, see PCR Porcine reproductive and respiratory syndrome virus, see PRRSV Presymptomatic patient identification, IVTT, 129 Primer 45, PCR, 77 Primer 01, PCR, 77 Primer annealing, Classic PCR, 3, 4 Primer combinations, nested pol, 73 Primer design, PCR tests, methods, 72, Primers competitive TNF and inos mrna, 60 PRRSV detection, materials, 83, 86 Primer selection classic PCR, 3, 4 size, 3 temperature, 3 Primer sequences composition, 3, 4 tail, 3, 4 Probes, PRRSV detection, materials, 83, 86 Prostate cancer analytical flow cytometry, RT-PCR, PRRSV detection PCR analysis, boar semen, virus isolation, 82 PSA-positive cells analytical flow cytometry, analytical flow cytometry and RT-PCR, RT-PCR, PSTVd cdnas integration, PSTVdRNA RNA replication, 155, 156 PSTVdRNA RNA replication, PSTVd cdnas integration, 155, 156 PSTVd variants, viroid replication, 156 Pulmonary tuberculosis diagnosis AMPLICOR MTB test, Q QcRT-PCR construction standard, 189 construction strategy, 186 protocol, schematic diagrams, 188 Quantitative amplification, classic PCR, 5, 55, 57 Quantitative competitive PCR (qcpcr), internal standard, 185 Quantitative competitive RT-PCR, see qtrt-pcr R Random amplification of polymorphic DNA (RAPD), microorganism detection method, 8 Reverse transcriptase pol gene, PCR amplification, 76 RNA extraction causative mutation, 258, 260 cert-pcr assay, methods, 59, 60

8 280 Index colorectal cancer syndromes, HCV detection, HIV-1 mrna, 92, 93, 97 PRRSV detection, 83, 84 PSA-positive cells, 217, 220, 223 transgenic plants, 158, 160, 163 RNA isolation, cert-pcr assay, materials, 58 RNA probe synthesis, HIV-1 mrna, 92 94, 98 RNase mapping assay, Roche AMPLICOR Mycobacterium tuberculosis PCR test, see AMPLICOR MTB test Rodent parvoviruses detection, differentiation, 32 serologic detection, 31 Rodent parvoviruses PCR assays agarose gel electrophoresis, DNA extraction, oligonucleotides primers, 33 PCR analysis, 32, tissue collection, Ross River virus, nested RT-PCR, Ross River virus detection, singletube nested RT-PCR, RT-PCR disadvantages, 183, 184 HCV detection, HIV-1 mrna, 90, 92, 93, 97, 98 prostate cancer, PSA-positive cells, rapidity, 183 sensitivity, 183 RT pol gene, PCR amplification, 76 RT procedures, PRRSV detection, 83, 84, 86 RT reaction, cert-pcr assay, methods, 60, 61, 64 S Sanger dideoxy sequencing, amplification detection, 3 Selective ultraviolet radiation fractionation, see SURF Self-sustained sequence replication (3SR), description, 12, 13 Serological methods, nested pol and env PCR tests, 69 Serological surveys, BIV, 67 Serologic detection, rodent parvoviruses, 31 Serotyping, 115 Sigmoidoscopy, FAP, 129 Single-stranded conformation polymorphism (SSCP), 127 Single-tube nested RT-PCR Ross River virus detection, SIV-1, 92 Southern analysis, PCR, 154, 155 Southern blot, 127 differentially expressed genes, PSA-positive cells, 219, 222 Southern blot hybridization, Legionella species, Southern blot sequencing, amplification detection, 3 Spumaretroviruses, 92 SURF technique, advantages, 40 defined, 39 example, 44

9 Index 281 isolation vs elimination, 40 principles, 41 slide preparation, 43 tool modification, 40 Swine bioassay, boar semen, 82 T T7/SP6 polymerase expression vectors, HIV-1 mrna, 92 94, 98 Taq polymerase, DNA extraction, 4 Templates, HIV-1 mrna, methods, 90, 93, 97, 98 Tissue collection, PCR analysis, Tissue microdissection techniques, 39 TNF, measurement, TNF transcript quantitation, cert- PCR assay, Toxoplasma gondii, PCR detection, Toxoplasma infection pregnancy, 195, 196 prenatal diagnosis, 196, 197 Transgene integrants, PCR, Transgenic plants, PCR, Translation-terminating mutation identification, IVTT, Trichomonas vaginalis, PCR, Truncating genetic mutations, IVS protein assay, U U1 cells, HIV-1 mrna, 96 V Viroid replication PSTVd variants, 156 studies, 157, 162, 163 Virus detection, PCR, 145 Virus isolation BIV, 68 cocultivation techniques, 68 nested pol and env PCR tests, 68, 69 PRRSV detection, 82 Vpr cdna probes, HIV-1 mrna, 91 Vpr cdna template, 90 W Western blot assays BIV, 67, 68 nested env PCR tests, 68, 69 nested pol PCR tests, 68, 69