Index. Bromdesoxyuridine (BrdU), 115 Buccal cell preparation, 142 smear, 142

Transcription

1 Index A Abort tissue preparation, 113 Absorption, 85 AcrocenM-FISH, 252 Acrocentric chromosomes directed multicolor FISH (acrom-/ acrocenm-fish), 252 Air-drying method, 114 Amniocytic fluid preparation, 113 Amniotic specimen, 123 Anti-centromere sera (CREST), 194 Applications of FISH, 4 APS-surface, 276 Archival cytogenetic slides, 137 Archival tissue, 147 Array-CGH, 8, 421 Array-slides, 427 Ataxia teleangiectasia (ATM), 231 Auto fluorescence, 76 B BAC-FISH, 58 Background, 76 Bacteria, 396 Bacterial artificial chromosomes (BACs) array, 428 clone, 262 probes, 53 B-agarase, 277 Bakers yeast Saccharomyces cerevisiae, 347 Banding cytogenetics-limitations, 421 Beam splitter, 87 Biotin/streptavidin FITC, 266 Black & white camera system, 89 Blood or bone marrow preparation without cultivation, 133 smear, 132 Breakpoints per metaphase (B/M), 232 Bromdesoxyuridine (BrdU), 115 Buccal cell preparation, 142 smear, 142 C Canada-balsam, 138 Carnoy s fixative, 114, 115 CCD-camera, 176 Cell cycle, 301 Centromere-specific multicolor-fish (cenm-fish/ CM-FISH), Centromeric, 30, 63 Charge coupled device (CCD), 76 Check incorporation of labels, 375 Chemical aging of FISH slides, 221 Chip-on chip experiments, 435 Chorion tissue preparation, 113 Chromatin modifications, 435 Chromosome aberrations, 3, 232 anomalies, 3 banding, 23 bar code, 244 enumeration probes, 305 microdissection, 36 mosaicism, 302 radiosensitivity, 239 spreading, 221 Chromosome-specific DNA libraries, 35 Chromosome-specific subctm probe process, 262 probe results, troubleshooting, 266 Cloned DNA libraries, 35 COBRA-FISH. See COmbined Binary RAtio labelling-fish Colcemide, 114,

2 448 Index Color-changing karyotyping (CCK), 217 COmbined Binary RAtio labelling-fish (COBRA-FISH), 176 Combined DAPI-banding and sequential G-banding and Zoo-FISH, 341 Comet assay, 15 Commercially available probes, 28 Comparative chromosome painting, 232 Comparative genome analysis (CGH), 8 Comparative genomic hybridization (CGH), 411 Complex aberrations, 238 Computer imaging, 75 Constitutional genomic aberration, 6 Contrast, 76 Copy number changes, 411, 423, 435 Copy number variations (CNV), 293, 435 COT DNA, 102 COT1 DNA, 99 COT isolation, 101 Cross-species chromosome painting, 324 Cryofixed tissue, 148, 151 Cultivation, 396 D DAPI-stained karyotype, 267 Database of genomic variants, 294 Degenerated oligonucleotide primers polymerase chain reaction (DOP-PCR), 411 Deletions, 270 Denaturation-buffer, 27, 64 Digital image analyses, 78 Digoxigenin/antidigoxigenin-rhodamine, 266 Direct labeling, 25 Direct PCR amplification, 35 DNA amplification, 281 fiber, 269 fragments, 279 methylation changes, 435 targets, 271 DNA-protein co-detection, 207 interaction, 194 DOP PCR, 35, 100 Down syndrome, 266 Drosophila melanogaster, 361 Dysmorphic child, 7 E EDTA-treated blood samples, 121 Electrophoresis, 277 Embedding procedure, 397 Emission, 85 Emitter, 86 Epigenetic changes, 435 Eukitt, 137 Eutherian orders, 324 Exciter, 86 Exposure time, 76 Expressed sequences, 288 Extended DNA fibers in plants, 380 F Fast hybridization kinetics, 67 Fermented and non fermented foods, 402 Filter cleaning, 95 Filter for fluorescence microscope, 77 Filter set, 89 Filters, microscope, FISH. See Fluorescence in situ hybridization FISH-applications in diagnostic microbiology, 396 in ecological microbiology, 396 in environmental microbiology, 396 in phylogenetic microbiology, 396 FISH-banding-human probes, 244 FISH-banding methods, 244 FISH-banding-murine probes, 244 Fixation and permeabilization of bacterial cells, 397 Flow-sorted chromosomes, 35 Fluorescence, 85 Fluorescence immunostaining, 194 Fluorescence in situ hybridization (FISH), 4, 23 analysis of fermented and non fermented foods, 397 in food microbiology, 396 on gametes, 161 on meiotic chromosomes, 164 in natural bacterial communities, 398 in plant chromosomes, 365 and process optimization, 397 and quality assurance, 397 on synaptonemal complexes, 166 of yeast chromosomes, 348 Fluorescence microscopy, 75 Fluorochromes, 65 Focusing, 78 Food microbiology, 396 Formalin-fixed/paraffin embedded tissue, 149 Formamide, 404

3 Index 449 G Gene and physical mapping, 194 Genome, 6 Genome-wide ACM-FISH probe process, probe results, 266 troubleshooting, 267 Genome-wide screening, 411 Genomic in situ hybridization (GISH), 348, 365 GTG-banding, 23 H Hair root cell preparation, 143 Hapten, 24 Heparinized treated blood samples, 116 Heterologous DNA, 361 High pressure mercury lamp, 77 Human chromosomes, 265 Human cytogenetics, 23 Human Genome Project, 9 Hybridization, 265, 266, 279 Hybridization-buffer, 27 Hypotonic solution, 115 I Image acquisition, 176 Imaging process, 78 Immunostaining, 198 Indirect labelling, 26 Individual radiosensitivity, 238 Inherited diseases, 5 Insect cells, 361 Insertion-deletion polymorphisms (INDEL), 293 In situ hybridization (ISH) techniques, 3 Interphase architecture, 313 cytogenetics, 131, 301 FISH studies, 147 Interphase FISH (I-FISH), 139, 141, 301 IPM-FISH, 244 K Kleihauer-Betke test, 121 Liquid samples, 400 Log 2 value, 428 Long-term culture, 118 M Magnification, 76 Malformations, 7 Mammalian species, 324 Maternal cell contamination, 121 Matrix CGH, 423 Meiosis analysis of, 157 aneuploidy, 157 anomalies in, 157 chromosomes, 201 chromosomes from plants, 379 Meiosis II (MII) oocytes FISH, 162 Mental retardation, 10 Mercury lamp, 89 Meristematic tissue, Metal halide lamps, 89 Metaphase FISH, 139 M-FISH consistent results, 183 MFISH filters, 92 M-FISH/SKY-restrictions, 243 Microdeletion syndromes, 10 Microdissected chromosomes, 35 Microdissection based comparative genomic hybridization (micro-cgh), 411 Microorganism, 395 Microscope, 75 Microscopic resolution, 76 Microwave-improved quick FISH, 57 Microwave treatment, 54 Mini- and microsatellites, 293 Mitotic metaphase plant cells, 378 Mosaicism, 7, 141, 302 Mounted formalin fixed/paraffin embedded tissue sections, 149 Multiband filter set, 88 Multicolor banding (mcb or m-band), 244 Multicolor fluorescence in situ hybridization, 175, 183 Multidirectional cross-species chromosome painting, 323 Multiplex-FISH (M-FISH), 176, 183 Multitude multicolor banding (mmcb), 246 L Lactobacillus helveticus, 403 Leukemia, 131 Limitations of banding cytogenetics, 421 N Nick translation, 29, 35 Nuclear extraction, 150 Numerical aperture, 76

4 450 Index O Oligonucleotide, 25 Oligonucleotides array, 422 Otto s solution, 142 Overlap, 271 P Paints, 35 Parental origin of chromosomes, 294 Pathogens, 397, 403 Peptide nucleic acids (PNAs), 61, 405 Peptides, 65 Peripheral blood preparation, 113 Permeabilization treatments, 405 Phenol/chloroform extraction, 280 Physical map, 287 Phytohemagglutinin, 114, 115 Pixel shift, 88 Plant molecular cytogenetics, 368 Plating on selective media, 395 PNA. See Peptide nucleic acids Polar body (PB) FISH, 162 Pollen mother cells, 379 Polymorphic rearrangements, 261 Polyploid species, 365 Prenatal cytogenetic diagnosis, 123 Prenatal FISH Quick Test, 127 Pretreatment of FISH slides, 222 Primed in situ (PRINS) hybridization, 23 Primers, 25 Probes, 61 Protein, 194 Proteinase K, 149 Q Quantification of FISH signals, 79 Quantitative FISH (QFISH), 79 R Radioactive in situ hybridization, 3 Radiosensitivity, 238 Random priming, 283 Rearrangements, 270 Recovery technique, 137 Released nuclei, 151 Removal of background, 101 Repetitive DNA sequences, 99 Restrictions of conventional chromosome banding techniques, 243 RNA-FISH techniques, 15 RNase treatment of FISH slide, 222 Rx-FISH, 245 S Scanning of array-slides, 428 Schneider cells, 362 Sequenase, 282 Sequential G-banding and Zoo-FISH, 326 Short term culture, 113 Signal amplification techniques, 6 Simultaneous DAPI-banding and Zoo-FISH, 341 Single-cell level, 301 Single nucleotide polymorphisms (SNP), 293 Skin fibroblasts preparation, 113 SKY. See Spectral karyotyping SKY-consistent results, 183 S1 laboratory, 58 Slide pretreatment, 29 Small supernumerary marker chromosomes (ssmc), 251 SNP arrays, 423 Sodiumacetate-treated blood samples, 121 Sodium chloride, 404 Sodium-thiocyanate, 149 Solid samples, 400 Spatial distribution of microbial population, 403 SpectraCube, 177 Spectral color banding (SCAN), 244 Spectral karyotyping (SKY), 176, 183 SpectraVysion TM probes, 184 Sperm FISH, 161 Sperm Head Decondensation, 162 Spreading of the chromosomes, 221 StarFISH probes, 184 Starter cultures, 402 Streptococcus thermophilus, 403 Stretching, 279 Stringency of protocols, 404 SubcenM-FISH, 252 Subcentromere-specific multicolor FISH (subcenm-fish), 252, 261 Sub-CTM-FISH, 262 Subtelomeric deletions, 10 Subtelomeric FISH probes chromosome-specific subctm, genome-wide ACM-FISH, 263 materials, 262 Suspension-FISH (S-FISH), 313 Synaptonemal complex (SC), 347 Synaptonemal complex (SC) protein, 194

5 Index 451 Synthetic oligodeoxynucleotide (ODN) probes, 67 T Taq DNA polymerase, 25 Telomere, 62, 261 Thermocycler, 33 Three-dimensional (3-D) analysis, 313 Transmission, 86 Triple-band filter set, 88 U Universal probe Eub338, 398 Unmasking the target DNA, 5 Unmounted formalin fixed/paraffin embedded tissues, 150 Urine cell preparation, 144 array-techniques, 443 cytogenetic associations, 443 cytogenetics, 441 diagnostic addresses, 445 FISH, 442 FISH-courses, 443 genetics and biology, 444 genetics and education, 444 genome browsers, 443 medical literature, 444 probes for FISH, 443 Whole chromosome or region-specific paint probes ( paints ), 35 Whole chromosome painting (wcp) probes, 231 X Xenon lamp, 89 V Vertebrate chromosomes, 261 W Wavelength, 85, 86 Weather conditions, 121 Websites Y YAC clones, 280 YAC-probes, 54 Yeast metaphase chromosomes, 347 Z Zoo-FISH, 232