An introduction to molecular biotechnology: molecular fundamentals, methods and applications in modern biotechnology
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| Format: | Book |
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| Language: | English German |
| Published: |
Weinheim
Wiley-VCH
2006
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| Subjects: | |
| Online Access: | Inhaltsverzeichnis |
| Physical Description: | LVI, 768 S. Ill. |
| ISBN: | 3527314121 9783527314126 |
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| 245 | 1 | 0 | |a An introduction to molecular biotechnology |b molecular fundamentals, methods and applications in modern biotechnology |c Ed. by Michael Wink |
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| adam_text | CONTENTS
PREFACE XXI
LIST OF CONTRIBUTORS XXIII
ABBREVIATIONS XXVII
COLOUR PLATES XXXVII
PART I FUNDAMENTALS OF CELLULAR AND MOLECULAR BIOLOGY
1 THE CELL AS THE BASIC UNIT OF LIFE 3
M. WINK
2 STRUCTURE AND FUNCTION OF CELLULAR MACROMOLECULES 7
M. WINK
2.1 INTRODUCTION 7
2.2 STRUCTURE AND FUNCTION OF SUGARS 9
2.3 STRUCTURE OF MEMBRANE LIPIDS 12
2.4 STRUCTURE AND FUNCTION OF PROTEINS 17
2.5 STRUCTURE OF NUCLEOTIDES AND NUCLEIC ACIDS (DNA AND RNA) 29
3 STRUCTURE AND FUNCTION OF A CELL 39
M. WINK
3.1 THE STRUCTURE OF A EUKARYOTIC CELL 40
3.1.1 THE STRUCTURE AND FUNCTION OF THE CYTOPLASMIC MEMBRANE 40
3.1.1.1 MEMBRANE PERMEABILITY 41
3.1.1.2 TRANSPORT PROCESSES ACROSS BIOMEMBRANES 43
3.1.1.3 RECEPTORS AND SIGNAL TRANSDUCTION AT BIOMEMBRANES 47
3.1.2 THE ENDOMEMBRANE SYSTEM IN A EUKARYOTIC CELL 52
3.1.3 MITOCHONDRIA AND CHLOROPLASTS 55
3.1.4 CYTOPLASM 62
3.1.5 CYTOSKELETON 65
3.1.6 CELL WALLS 68
AN INTRODUCTION TO MOLECULAR BIOTECHNOLOGY. EDITED BY M. WINK
COPYRIGHT 2006 WILEY-VCH VERLAG GMBH & CO. KGAA, WEINHEIM
ISBN: 3-527-31412-1
I
V
VI CONTENTS
3.2 THE STRUCTURE OF BACTERIA 69
3.3 THE STRUCTURE OF VIRUSES 70
3.4 THE DIFFERENTIATION OF CELLS 72
4 BIOSYNTHESIS AND FUNCTION OF MACROMOLECULES
(DNA, RNA, AND PROTEINS) 77
M. WINK
4.1 GENOMES, CHROMOSOMES, AND REPLICATION 77
4.1.1 GENOME SIZE 78
4.1.2 COMPOSITION AND FUNCTION OF CHROMOSOMES 83
4.1.3 MITOSIS AND MEIOSIS 86
A.I A REPLICATION 89
4.1.5 MUTATIONS AND REPAIR MECHANISMS 91
4.2 TRANSCRIPTION: FROM GENE TO PROTEIN 96
4.3 PROTEIN BIOSYNTHESIS (TRANSLATION) 102
5 DISTRIBUTING PROTEINS IN THE CELL (PROTEIN SORTING) 109
M. WINK
5.1 IMPORT AND EXPORT OF PROTEINS VIA THE NUCLEAR PORE 111
5.2 IMPORT OF PROTEINS IN MITOCHONDRIA AND CHLOROPLASTS 112
5.3 PROTEIN TRANSPORT IN THE ENDOPLASMIC RETICULUM 114
5.4 VESICLE TRANSPORT FROM THE ER VIA THE GOLGI APPARATUS
TO THE CYTOPLASMIC MEMBRANE 116
6 DIVERSITY OF ORGANISMS 121
M. WINK
6.1 PROKARYOTES 121
6.2 EUKARYOTES 122
FURTHER READING FOR CHAPTERS 1-6 326
PART II STANDARD METHODS IN MOLECULAR BIOTECHNOLOGY
7 ISOLATION AND PURIFICATION OF PROTEINS 131
T. WIELAND, S. LUTZ
7.1 INTRODUCTION 131
7.2 PRODUCING A PROTEIN EXTRACT 133
7.3 GEL ELECTROPHORETIC SEPARATION METHODS 134
7.3.1 PRINCIPLES OF ELECTROPHORESIS 134
7.3.2 NATIVE GEL ELECTROPHORESIS 134
7.3.3 DISCONTINUOUS SODIUM DODECYL SULFATE-POLYACRYLAMIDE GEL
ELECTROPHORESIS (SDS-PAGE) 135
7.3.4 TWO-DIMENSIONAL (2D) GEL ELECTROPHORESIS, ISOELECTRIC FOCUSSING
(IEF) 136
7.3.5 DETECTING PROTEINS IN GELS 137
7.4 METHODS OF PROTEIN PRECIPITATION 137
CONTENTS VII
7.5 COLUMN CHROMATOGRAPHY METHODS 238
7.5.1 GENERAL PRINCIPLES OF SEPARATION 138
7.5.1.1 SIZE EXCLUSION CHROMATOGRAPHY (GEL FILTRATION) 139
7.5.1.2 HYDROPHOBIE INTERACTION CHROMATOGRAPHY (HIC) 141
7.5.1.3 ION EXCHANGE CHROMATOGRAPHY 141
7.5.1.4 HYDROXYAPATITE CHROMATOGRAPHY 143
7.5.2 GROUP-SPECIFIC SEPARATION TECHNIQUES 143
7.5.2.1 CHROMATOGRAPHY ON PROTEIN A OR PROTEIN G 143
7.5.2.2 CHROMATOGRAPHY ON CIBACRON BLUE (BLUE GEL) 144
7.5.2.3 CHROMATOGRAPHY ON LECTINS 144
7.5.2.4 CHROMATOGRAPHY ON HEPARIN 145
7.5.3 PURIFICATION OF RECOMBINANT FUSION PROTEINS 145
7.5.3.1 CHROMATOGRAPHY ON CHELATING AGENTS 145
7.5.3.2 CHROMATOGRAPHY ON GLUTATHION-MATRICES 146
7.6 EXAMPLES 146
7.6.1 EXAMPLE 1: PURIFICATION OF NUCLEOSIDE DIPHOSPHATE KINASE
FROM THE CYTOSOL OF BOVINE RETINA ROD CELLS 146
7.6.2 EXAMPLE 2: PURIFICATION OF RECOMBINANT HIS
6
-RGS16 AFTER EXPRESSION
IN E. COLI 148
FURTHER READING 149
8 PEPTIDE AND PROTEIN ANALYSIS WITH ELECTROSPRAY TANDEM MASS
SPECTROMETRY 151
A. SCHLOSSER, W. D. LEHMANN
8.1 INTRODUCTION 151
8.2 PRINCIPLES OF MASS SPECTROMETRY 151
8.3 MASS PRECISION, RESOLUTION, AND ISOTOPE DISTRIBUTION 152
8.4 PRINCIPLES OF ELECTROSPRAY IONIZATION 153
8.5 TANDEM MASS SPECTROMETERS 154
8.5.1 MASS ANALYZERS 154
8.5.2 TRIPLE QUADRUPOLE 155
8.5.3 ION TRAP (PAUL TRAP) 156
8.5.4 Q-TOF 156
8.5.5 Q-FT-ICR 157
8.6 PEPTIDE SEQUENCING WITH MS/MS 157
8.7 IDENTIFYING PROTEINS WITH MS/MS-DATA AND PROTEIN DATABASES 158
8.7.1 DATABANK SEARCH WITH SEQUENCE DATA 158
8.7.2 DATABANK SEARCH WITH MS/MS RAW DATA 159
8.8 DETERMINING PROTEIN MOLECULAR MASS 160
8.9 ANALYSIS OF COVALENT PROTEIN MODIFICATION 162
FURTHER READING 364
9 ISOLATION OF DNA AND RNA 165
H. WEIHER, R. ZWACKA, I. HERR
9.1 INTRODUCTION 165
VIM CONTENTS
9.2 DNA ISOLATION 166
9.3 RNA ISOLATION 168
9.3.1 ENRICHMENT OF MESSENGER RNA (MRNA) 169
REFERENCES 169
10 CHROMATOGRAPHY AND ELECTROPHORESIS OF NUCLEIC ACIDS 171
H. WEIHER, R. ZWACKA, I. HERR
10.1 INTRODUCTION 171
10.2 CHROMATOGRAPHIE SEPARATION OF NUCLEIC ACIDS 171
10.3 ELECTROPHORESIS 172
10.3.1 AGAROSE GEL ELECTROPHORESIS: SUBMARINE ELECTROPHORESIS 173
10.3.2 PULSED FIELD AGAROSE GEL ELECTROPHORESIS 174
10.3.3 POLYACRYLAMIDE GEL ELECTROPHORESIS (PAGE) 174
FURTHER READING 174
11 HYBRIDIZATION OF NUCLEIC ACIDS 375
H. WEIHER, R. ZWACKA, I. HERR
11.1 THE SIGNIFICANCE OF BASE PAIRING 175
11.2 EXPERIMENTAL HYBRIDIZATION, KINETIC, AND THERMODYNAMIC
CONTROL 176
11.3 ANALYTICAL TECHNIQUES 176
11.3.1 CLONE DETECTION, SOUTHERN BLOTTING, NORTHERN BLOTTING,
AND GENE DIAGNOSIS 176
11.3.2 EXPRESSION SCREENING 178
11.3.3 IN SITU HYBRIDIZATION 179
FURTHER READING 180
12 THE USE OF ENZYMES IN THE MODIFICATION OF NUCLEIC ACIDS 181
I. HERR, H. WEIHER, R. ZWACKA
12.1 RESTRICTION ENZYMES (RESTRICTION ENDONUCLEASES) 181
12.2 LIGASES 183
12.3 METHYLASES 184
12.4 DNA POLYMERASES 185
12.5 NUCLEASES 186
12.6 T4 POLYNUCLEOTIDE KINASE 187
12.7 CALF INTESTINAL PHOSPHATASE 187
FURTHER READING 187
13 POLYMERASE CHAIN REACTION (PCR) 189
A. MOHR, H. WEIHER, I. HERR, R. ZWACKA
13.1 INTRODUCTION 189
13.2 TECHNIQUES 190
13.2.1 STANDARD PCR 190
13.2.2 RT-PCR 192
13.2.3 QUANTITATIVE/REAL TIME PCR 193
13.2.4 RAPID AMPLIFICATION OF CDNA ENDS (RACE) 194
CONTENTS IX
13.3 AREAS OF APPLICATION 395
13.3.1 GENOME ANALYSIS 295
13.3.2 CLONING TECHNOLOGY 195
13.3.3 EXPRESSION STUDIES 196
FURTHER READING 196
14 DNA SEQUENCING 197
R. ZWACKA, A. MOHR, I. HERR, H. WEIHER
14.1 INTRODUCTION 197
14.2 DNA SEQUENCING METHODS 198
14.2.1 CHEMICAL SEQUENCING METHOD (MAXAM-GILBERT METHOD) 198
14.2.2 ENZYMATIC SEQUENCING (SANGER-COULSON METHOD) 198
14.3 STRATEGIES FOR SEQUENCING THE HUMAN GENOME 200
14.4 THE PRACTICAL SIGNIFICANCE OF DNA SEQUENCING 201
FURTHER READING 201
15 CLONING PROCEDURES 203
T. WIELAND, S. LUTZ
15.1 INTRODUCTION 203
15.2 THE PRODUCTION OF RECOMBINANT VECTORS 204
15.2.1 THE INSERT 204
15.2.2 THE VECTOR 208
15.2.3 ESSENTIAL COMPONENTS OF VECTORS 208
15.2.3.1 THE BACTERIAL ORIGIN OF REPLICATION (ORI) 208
15.2.3.2 ANTIBIOTIC RESISTANCE 209
15.2.3.3 POLYLINKERS 209
15.2.4 CLONING USING RECOMBINATION SYSTEMS 209
15.2.5 FURTHER COMPONENTS OF VECTORS FOR PROKARYOTIC EXPRESSION
SYSTEMS 211
15.2.5.1 THE PROMOTER 211
15.2.5.2 THE RIBOSOME BINDING SITE 211
15.2.5.3 THE TERMINATION SEQUENCE 212
15.2.5.4 THE FUSION SEQUENCE 212
15.2.6 FURTHER COMPONENTS OF EUKARYOTIC EXPRESSION VECTORS 213
15.2.6.1 EUKARYOTIC EXPRESSION VECTORS: YEAST 213
15.2.6.2 EUKARYOTIC EXPRESSION VECTORS FOR MAMMAL CELLS 214
15.2.6.3 VIRAL EXPRESSION SYSTEMS FOR MAMMALIAN CELLS 218
15.2.7 NONVIRAL INTRODUCTION OF HETEROLOGOUS DNA TO HOST ORGANISMS
(TRANSFORMATION, TRANSFECTION) 220
15.2.7.1 TRANSFORMATION OF PROKARYOTES 220
15.2.7.2 TRANSFORMATION OF YEAST CELLS 221
15.2.7.3 TRANSFECTION OF MAMMAL CELLS 221
FURTHER READING 222
X CONTENTS
16 EXPRESSION OF RECOMBINANT PROTEINS 223
T. WIELAND, S. LUTZ
16.1 INTRODUCTION 223
16.2 EXPRESSION OF RECOMBINANT PROTEINS IN HOST ORGANISMS 224
16.2.1 EXPRESSION IN E. COLI 228
16.2.2 EXPRESSION IN YEASTS 230
16.2.3 EXPRESSION IN INSECT CELLS 232
16.2.3.1 EXPRESSION BASED ON RECOMBINANT BACULOVIRUSES 232
16.2.3.2 EXPRESSION OF PROTEINS IN STABLY TRANSFECTED INSECT CELLS 234
16.2.4 EXPRESSION OF PROTEINS IN MAMMALIAN CELLS 235
16.3 EXPRESSION IN CELL-FREE SYSTEMS 236
16.3.1 EXPRESSION OF PROTEINS IN RETICULOCYTE LYSATES 237
16.3.2 PROTEIN EXPRESSION USING E. COLI EXTRACTS 237
FURTHER READING 238
17 THE PATCH CLAMP METHOD 239
R. KRAFT, S. PATT
17.1 BIOLOGICAL MEMBRANES AND ION CHANNELS 239
17.2 PHYSICAL FOUNDATIONS OF THE PATCH CLAMP METHOD 240
17.3 PATCH CLAMP CONFIGURATIONS 241
17.4 HETEROLOGOUS EXPRESSION SYSTEMS AND SECTION PREPARATIONS 244
FURTHER READING 245
18 CELL CYCLE ANALYSIS 247
S. WOELFL, A. KITANOVIC
18.1 ANALYZING THE CELL CYCLE 247
18.2 EXPERIMENTAL ANALYSIS OF THE CELL CYCLE 249
18.2.1 PREPARING SYNCHRONIZED CELL CULTURES
OF SACCHAROMYCES CEREVISIAE 250
18.2.2 CENTRIFUGAL ELUTRIATION 250
18.2.3 CELL CYCLE ARREST USING THE ALPHA FACTOR 251
18.2.4 THE IDENTIFICATION OF CELL CYCLE STAGES 252
18.2.4.1 THE BUDDING INDEX 252
18.2.4.2 FLUORESCENT STAINING OF THE NUCLEUS 252
FURTHER READING 256
19 TECHNIQUES IN MICROSCOPY 257
C. FRICKER
19.1 LIGHT MICROSCOPY 257
19.2 PHASE CONTRAST LIGHT MICROSCOPY 257
19.3 DARKFIELD MICROSCOPY 259
19.4 POLARIZATION AND INTERFERENCE MICROSCOPY 259
19.5 FLUORESCENCE MICROSCOPY 260
19.6 CONFOCAL FLUORESCENCE MICROSCOPY 261
19.7 ELECTRON MICROSCOPY 262
FURTHER READING 264
CONTENTS XI
20 LASER APPLICATIONS 265
M. VOGEL, R. FINK
20.1 PRINCIPLES OF LASER TECHNOLOGY 265
20.2 PROPERTIES OF LASER RADIATION 267
20.3 TYPES OF LASERS AND THEIR SETUPS 268
20.4 APPLICATIONS 269
20.4.1 CONFOCAL AND MULTIPHOTON MICROSCOPY 269
20.4.2 OPTICAL TWEEZERS 270
20.4.3 LASER MICRODISSECTION 270
FURTHER READING 270
PART III KEY TOPICS
21 CENOMICS 273
M. FROHME, ST. WIEMANN
21.1 INTRODUCTION 273
21.2 TECHNOLOGICAL DEVELOPMENTS IN SEQUENCING 276
21.2.1 SEQUENCING TECHNOLOGY 276
21.2.2 BIOCHEMISTRY 276
21.2.3 EQUIPMENT 279
21.2.4 SOFTWARE AND INFORMATICS FOR SEQUENCING 280
21.3 GENOME SEQUENCING 281
21.3.1 MAPPING 281
21.3.1.1 RESTRICTION MAPPING AND RESTRICTION FINGERPRINTING 284
21.3.1.2 BAC-END SEQUENCING 285
21.3.1.3 GENETIC MAPPING 285
21.3.1.4 RADIATION HYBRID MAPPING 288
21.3.1.5 HAPPY MAPPING 289
21.3.1.6 MAPPING BY HYBRIDIZATION 290
21.3.1.7 STS, ESTS, SNPS, AND SEQUENCING LENGTH POLYMORPHISMS
(AFLPS, RAPD) 292
21.3.1.8 FISH, FIBRE FISH, OPTICAL MAPPING, AND CGH 295
21.3.2 TIME-LINE OF GENOME SEQUENCING 296
21.3.3 GENOME SEQUENCING STRATEGIES 296
21.3.3.1 CONVENTIONAL APPROACH: RANDOM SHOTGUN STRATEGY 296
21.3.3.2 THE WHOLE-GENOME SHOTGUN STRATEGY 300
21.3.3.3 SEQUENCING OF THE HUMAN GENOME 302
21.3.4 OUTLOOK FOR GENOME SEQUENCING 303
21.4 CDNA PROJECTS 304
21.4.1 CDNAS REPRESENT THE CELL S MRNA 304
21.4.2 PRODUCTION OF CDNA LIBRARIES 306
21.4.3 EST-PROJECTS FOR GENE IDENTIFICATION 310
21.4.3.1 WHAT IS AN EST? 310
21.4.3.2 IMAGE CONSORTIUM: CGAP 313
21.4.3.3 UNIGENE 314
XII CONTENTS
21.4.4 FULL-LENGTH PROJECT FOR THE PRODUCTION OF RESOURCES FOR
FUNCTIONAL
GENOMICS 316
FURTHER READING 318
22 FUNCTIONAL CENOMICS 321
M. FROHME, ST. WIEMCMN
22.1 INTRODUCTION 321
22.2 THE IDENTIFICATION AND ANALYSIS OF INDIVIDUAL GENES 324
22.2.1 POSITIONAL CLONING 325
22.2.2 GENE TRAP 328
22.2.3 DNA/RNA IN SITU HYBRIDIZATION 329
22.2.4 TISSUE ARRAYS 330
22.3 THE INVESTIGATION OF TRANSCRIPTIONAL ACTIVITY 331
22.3.1 SAGE (SERIAL ANALYSIS OF GENE EXPRESSION) 332
22.3.2 SUBTRACTIVE HYBRIDIZATION 334
22.3.3 RNA FINGERPRINTING 337
22.3.4 ARRAY-BASED TECHNIQUES 340
22.3.4.1 MACROARRAYS 343
22.3.4.2 MICROARRAYS 345
22.3.4.3 GLOBAL AND SPECIFIC ARRAYS 347
22.3.5 SPECIFICITY AND SENSITIVITY 349
22.4 CELL-BASED METHODS 350
22.4.1 GFP TECHNIQUES 350
22.4.2 ALTERNATIVES TO GFP 351
22.4.3 FLUORESCENCE RESONANCE ENERGY TRANSFER (FRET) 352
22.4.4 FLUORESCENCE RECOVERY AFTER PHOTOBLEACHING (FRAP) 354
22.4.5 CELL-BASED ASSAYS 355
22.4.5.1 ASSAY DESIGN 356
22.4.5.2 PIPETTING SYSTEMS 357
22.4.5.3 READING AND RECORDING OF DATA 358
22.4.5.4 DATA ANALYSIS 359
22.5 FUNCTIONAL ANALYSIS OF ENTIRE GENOMES 360
22.5.1 GENOTYPIC SCREENING IN YEAST 360
22.5.2 PHENOTYPIC SCREENING IN THE MOUSE 361
FURTHER READING 363
23 PROTEIN-PROTEIN AND PROTEIN-DNA INTERACTION 365
P. UETZ, E. POHL
23.1 PROTEIN-PROTEIN INTERACTIONS 366
23.1.1 CLASSIFICATION AND SPECIFICITY: PROTEIN DOMAINS 366
23.1.2 PROTEIN NETWORKS AND COMPLEXES 367
23.1.3 STRUCTURAL PROPERTIES OF INTERACTING PROTEINS 370
23.1.4 WHICH FORCES MEDIATE PROTEIN-PROTEIN INTERACTIONS? 371
23.1.4.1 THERMODYNAMICS 371
23.1.4.2 ENERGETICS 372
CONTENTS XIII
23.1.5 METHODS TO EXAMINE PROTEIN-PROTEIN INTERACTIONS 373
23.1.6 REGULATION OF PROTEIN-PROTEIN INTERACTIONS 374
23.1.7 THEORETICAL PREDICTION OF PROTEIN-PROTEIN INTERACTIONS 375
23.1.8 BIOTECHNOLOGICAL AND MEDICAL APPLICATIONS OF PROTEIN-PROTEIN
INTERACTIONS 376
23.2 PROTEIN-DNA INTERACTIONS 378
23.2.1 SEQUENCE-SPECIFIC DNA-BINDING 378
23.2.2 THERMODYNAMIC CONSIDERATIONS REGARDING PROTEIN-DNA
COMPLEXES 379
23.2.3 METHODS TO STUDY PROTEIN-DNA INTERACTIONS 379
23.2.4 MEDICAL RELEVANCE OF PROTEIN-DNA INTERACTIONS 384
23.2.5 BIOTECHNOLOGICAL APPLICATIONS OF PROTEIN-DNA INTERACTIONS 385
FURTHER READING 385
24 BIOINFORMATICS 387
B. BRORS, K. FELLENBERG
24.1 INTRODUCTION 387
24.2 DATA SOURCES 388
24.2.1 PRIMARY DATABANKS: EMBL/GENBANK/DDBJ, PIR, SWISSPROT 388
24.2.2 MOTIF DATABANKS: BLOCKS, PROSITE, PFAM, PRODOM, SMART 389
24.2.3 MOLECULAR STRUCTURE DATABANKS: PDB, SCOP 389
24.2.4 TRANSCRIPTOME DATABANKS: SAGE, ARRAYEXPRESS, GEO 390
24.2.5 REFERENCE DATABANKS: PUBMED, OMIM, GENECARDS 390
24.3 SEQUENCE ANALYSIS 391
24.3.1 KYTE-DOOLITTLE, HELICAL WHEEL, SIGNAL SEQUENCE ANALYSIS 391
24.3.2 PAIR ALIGNMENT 393
24.3.2.1 LOCAL/GLOBAL 394
24.3.2.2 OPTIMAL/ HEURISTIC 394
24.3.3 ALIGNMENT STATISTICS 394
24.3.4 MULTIPLE ALIGNMENT 395
24.3.5 PHYLOGENETIC ANALYSIS 396
24.4 GENE PREDICTION 398
24.4.1 NEURONAL NETWORKS OR HIDDEN MARKOV MODELS BASED
ON HEXANUCLEOTIDE COMPOSITION 399
24.4.2 COMPARISON WITH ESTS OR OTHER GENOMES (FUGU, MOUSE) 400
24.5 BIOINFORMATICS IN TRANSCRIPTOME AND PROTEOME ANALYSIS 402
24.5.1 PRE-PROCESSING, NORMALIZATION 402
24.5.2 CHARACTER SELECTION 404
24.5.3 SIMILARITY MEASURES: EUCLIDEAN DISTANCE, CORRELATION,
MANHATTAN DISTANCE, MAHALANOBIS DISTANCE, ENTROPY MEASURES 405
24.5.4 UNSUPERVISED LEARNING PROCEDURES: CLUSTERING, MAIN COMPONENT
ANALYSIS, MULTIDIMENSIONAL SCALING, CORRESPONDENCE ANALYSIS 406
24.5.5 SUPERVISED LEARNING PROCEDURES: LINEAR DISCRIMINANT ANALYSIS,
CHOICE TREES, SUPPORT VECTOR MACHINES, ARTIFICIAL NEURONAL
NETWORKS 407
XIV CONTENTS
24.6 SYSTEMS BIOLOGY 408
24.6.1 NETWORKS: BOOLEAN NETWORKS AND BAYESIAN NETWORKS 420
24.6.2 DETERMINISTIC DESCRIPTIONS: COMMON AND PARTIAL DIFFERENTIAL
EQUATIONS 410
24.6.3 NONDETERMINISTIC DESCRIPTION: STOCHASTICAL SIMULATION 411
FURTHER READING 411
25 DRUG RESEARCH 413
U. DENSCHLE, M. KOEGL, R. TOILE
25.1 INTRODUCTION 413
25.2 ACTIVE COMPOUNDS AND THEIR TARGETS 414
25.2.1 GENOMIC METHODS FOR THE IDENTIFICATION OF TARGETS 415
25.2.2 BIOINFORMATIC IDENTIFICATION OF TARGETS 416
25.2.3 COMPARATIVE GENOME ANALYSIS 417
25.2.4 EXPERIMENTAL TARGET IDENTIFICATION: IN VITRO METHOD 418
25.2.5 EXPERIMENTAL IDENTIFICATION OF TARGETS: MODEL ORGANISMS 418
25.2.6 EXPERIMENTAL TARGET IDENTIFICATION IN HUMANS 419
25.2.7 THE DIFFERENCE BETWEEN TARGET CANDIDATES AND GENUINE
TARGETS 420
25.2.8 BIOLOGICALS 422
25.2.9 DNA AND RNA IN NEW THERAPEUTIC APPROACHES 424
25.2.10 PATENT PROTECTION FOR TARGETS 424
25.2.11 COMPOUND LIBRARIES 425
25.2.12 HIGH-THROUGHPUT SCREENING 426
25.2.13 HIGH QUALITY PARAMOUNTS IN SCREENING ASSAYS 430
25.2.14 VIRTUAL LIGAND SCREENING 431
25.2.15 THE ACTIVITY OF AGENTS DESCRIBED IN TERMS OF EFFICIENCY
AND POTENCY 431
25.2.16 CHEMICAL OPTIMIZATION OF LEAD STRUCTURES 432
25.3 PRE-CLINICAL PHARMACOLOGY AND TOXICOLOGY 432
25.4 CLINICAL DEVELOPMENT 433
25.5 CLINICAL TESTING 434
FURTHER READING 435
26 DRUG TARGETING AND PRODRUGS 437
C. FRICKER
DRUG TARGETING 437
PASSIVE TARGETING BY EXPLOITING SPECIAL PHYSIOLOGICAL PROPERTIES
OF THE TARGET TISSUE 438
PHYSICAL TARGETING 439
ACTIVE TARGETING 440
CELLULAR CARRIER SYSTEMS 444
PRODRUGS 445
PRODRUGS TO IMPROVE DRUG SOLUBILITY 445
PRODRUGS TO INCREASE STABILITY 446
26
26
26
26
26
26
26
.1
.1.1
.1.2
.1.3
.1.4
.2
.2.1
26.2.2
CONTENTS XV
26.3 PENETRATION OF DRUGS THROUGH BIOLOGICAL MEMBRANES 446
26.4 PRODRUGS TO EXTEND DURATION OF EFFECT 448
26.5 PRODRUGS FOR THE TARGETED RELEASE OF A DRUG 449
26.6 PRODRUGS TO MINIMIZE SIDE EFFECTS 451
FURTHER READING 451
27 MOLECULAR DIAGNOSTICS IN MEDICINE 455
S. WOELFL, R. GESSNER
27.1 USES OF MOLECULAR DIAGNOSTICS 456
27.1.1 INTRODUCTION 456
27.1.2 MONOGENIC AND POLYGENIC DISEASES 456
27.1.3 INDIVIDUAL VARIABILITY IN THE GENOME: FORENSICS 459
27.1.4 INDIVIDUAL VARIABILITY IN THE GENOME: HLA TYPING 459
27.1.5 INDIVIDUAL VARIABILITY IN THE GENOME: PHARMACOGENOMICS 459
27.1.6 INDIVIDUAL VARIABILITY IN THE GENOME:
SUSCEPTIBILITY TO INFECTIOUS DISEASES 460
27.1.7 VIRAL DIAGNOSIS 460
27.1.8 MICROBIAL DIAGNOSIS AND RESISTANCE DIAGNOSIS 461
27.2 WHICH MOLECULAR VARIATIONS SHOULD BE DETECTED? 462
27.2.1 POINT MUTATIONS 462
27.2.2 INSERTIONS AND DELETIONS 464
27.2.3 NUCLEOTIDE REPEATS 464
27.2.4 DELETION OR DUPLICATION OF GENES 465
27.2.5 RECOMBINATION BETWEEN CHROMOSOMES 465
2/ .2.6 EPIGENIC CHANGES 466
27 .3 MOLECULAR DIAGNOSTIC METHODS 466
27.3.1 DNA/RNA PURIFICATION 467
27.3.2 DETERMINATION OF KNOWN SEQUENCE VARIATIONS 467
27.3.2.1 DIRECT LENGTH POLYMORPHISM 467
27.3.2.2 RFLP 467
27.3.2.3 ACRS 469
27.3.2.4 ARMS 469
27.3.2.5 MS-PCR 469
27.3.2.6 ALLELE-SPECIFIC HYBRIDIZATION 470
27.3.2.7 LCR 470
27.3.2.8 MINISEQUENCING 470
27.3.2.9 PYROSEQUENCING 472
27.3.2.10 QUANTITATIVE PCR 472
27.3.2.11 CHIP TECHNOLOGY 473
27.3.2.12 PRODUCTION AND MANUFACTURE OF MICROARRAYS 474
27.3.2.13 DETERMINATION OF UNKNOWN MUTATIONS 476
27.4 OUTLOOK 477
FURTHER READING 477
XVI CONTENTS
28 RECOMBINANT ANTIBODIES AND PHAGE DISPLAY 479
S. DUEBEL
28.1 INTRODUCTION 479
28.2 WHY RECOMBINANT ANTIBODIES? 481
28.2.1 RECOMBINANT ANTIBODIES ARE AVAILABLE IN VITRO WITHOUT
IMMUNIZATION 481
28.2.2 ANTIBODIES WITH NEW CHARACTERISTICS CAN BE CREATED 482
28.3 OBTAINING SPECIFIC RECOMBINANT ANTIBODIES 483
28.3.1 PREPARATION OF THE VARIETY OF ANTIBODY GENES 483
28.3.2 SELECTION SYSTEMS FOR RECOMBINANT ANTIBODIES 485
28.3.2.1 TRANSGENIC MICE 485
28.3.2.2 IN VITRO SELECTION SYSTEMS 486
28.4 PRODUCTION OF RECOMBINANT ANTIBODIES 489
28.4.1 RECOMBINANT PRODUCTION SYSTEMS 489
28.4.2 PURIFICATION OF RECOMBINANT ANTIBODIES AND THEIR FRAGMENTS 491
28.5 FORMATS FOR RECOMBINANT ANTIBODIES 491
28.5.1 MONOSPECIFIC ANTIBODY FRAGMENTS 493
28.5.1.1 FAB FRAGMENTS 493
28.5.1.2 FV FRAGMENTS 493
28.5.1.3 SINGLE CHAIN ANTIBODY FRAGMENTS (SCFV) 494
28.5.1.4 DISULPHIDE STABILIZED FV FRAGMENTS (DSFV) 494
28.5.1.5 V
H
AND CAMEL ANTIBODIES 495
28.5.2 MULTIVALENT ANTIBODY FRAGMENTS 495
28.5.2.1 BIFUNCTIONAL ANTIBODIES 496
28.5.2.2 BISPECIFIC ANTIBODIES 496
28.6 APPLICATIONS OF RECOMBINANT ANTIBODIES 499
28.6.1 CLINICAL APPLICATIONS 499
28.6.2 APPLICATIONS IN RESEARCH AND IN VITRO DIAGNOSTICS 500
28.6.2.1 RECOMBINANT ANTIBODIES IN LABORATORY DIAGNOSTICS 501
28.6.2.2 INTRACELLULAR ANTIBODIES 501
28.6.2.3 RECOMBINANT ANTIBODIES AS BINDING MOLECULES FOR ARRAYS 501
28.7 OUTLOOK 502
FURTHER READING 502
29 GENETICALLY MODIFIED MICE (TRANSGENIC AND KNOCKOUT)
AND THEIR IMPACT ON MEDICINE 511
R. SPRENGEL
29.1 OVERVIEW 511
29.2 TRANSGENIC MICE 514
29.2.1 RETROVIRAL INFECTION OF THE TRANSGENIC MOUSE 515
29.2.2 INJECTION INTO THE PRONUCLEUS FOR THE PRODUCTION OF TRANSGENIC
MICE 515
29.2.3 HOMOLOGOUS RECOMBINATION FOR THE PRODUCTION OF TRANSGENIC MICE
517
29.3 THE IMPACT OF GENETICALLY MODIFIED MICE IN BIOMEDICINE 521
FURTHER READING 522
CONTENTS XVII
30 GENE THERAPY: STRATEGIES AND VECTORS 523
I. HERR
30.1 INTRODUCTION 523
30.2 PRINCIPLES OF SOMATIC GENE THERAPY 525
30.3 GERM LINE THERAPY 527
30.4 SETBACKS IN GENE THERAPY 528
30.5 VECTORS FOR GENE THERAPY 530
30.5.1 RETROVIRAL VECTORS 531
30.5.2 ADENOVIRAL VECTORS 535
30.5.3 ADENO-ASSOCIATED VIRUS (AAV) 538
30.5.4 OTHER VIRAL VECTORS 540
30.6 SPECIFIC EXPRESSION 541
FURTHER READING 542
31 MODIFIED DNA, PNA, AND APPLICATIONS IN MEDICINE
AND BIOTECHNOLOGY 543
N. METZLER-NOLTE
31.1 INTRODUCTION 543
31.2 MODIFIED NUCLEIC ACIDS 544
31.2.1 PHOSPHORTHIOATE 545
31.2.2 METHYLPHOSPHONATE 547
31.2.3 PEPTIDE NUCLEIC ACIDS (PNA) 548
31.3 INTERACTIONS OF DNA ANALOGS WITH COMPLEMENTARY
DNA AND RNA 549
31.3.1 MELTING TEMPERATURE 549
31.3.2 MISMATCH SENSITIVITY 551
31.4 APPLICATIONS 552
31.4.1 ANTISENSE TECHNIQUE 552
31.4.2 OTHER APPLICATIONS FOR PNA 554
FURTHER READING 556
32 PLANT BIOTECHNOLOGY 557
R. HELL, H. HILLEBRAND
32.1 INTRODUCTION 557
32.1.1 THE GREEN GENETIC ENGINEERING -
A NEW METHOD ON THE WAY TO TRADITIONAL GOALS 557
32.1.2 SPECIAL ASPECTS OF PLANT BIOTECHNOLOGY 559
32.2 DEVELOPMENT OF TRANSGENIC PLANTS 559
32.2.1 TRANSFORMATION THROUGH DNA TRANSFER 560
32.2.1.1 AGROBACTERIUM AS A NATURAL TRANSFORMATION SYSTEM 560
32.2.1.2 BIOLISTIC METHOD: GENE GUN 563
32.2.1.3 OTHER PHYSICAL TRANSFORMATION SYSTEMS 565
32.2.1.4 PLASTID TRANSFORMATION 565
32.2.1.5 VIRAL SYSTEMS 567
32.3 SELECTION OF TRANSFORMED PLANT CELLS 568
XVIII CONTENTS
32.3.1 REQUIREMENTS FOR AN OPTIMAL SELECTION MARKER SYSTEM 568
32.3.2 NEGATIVE SELECTION MARKER SYSTEMS 570
32.3.3 POSITIVE SELECTION MARKER SYSTEM 571
32.3.4 COUNTER SELECTION 572
32.3.5 VISUAL MARKERS 573
32.3.6 SELECTION SYSTEMS GENETIC TECHNIQUES, SAFETY,
AND MARKER-FREE PLANTS 573
32.4 REGENERATION OF TRANSGENE PLANTS 575
32.4.1 REGENERATION PROCEDURES 575
32.4.2 COMPOUNDS OF REGENERATION MEDIA 576
32.5 PLANT ANALYSIS: IDENTIFICATION AND CHARACTERIZATION
OF GENETICALLY ENGINEERED PLANTS 577
32.5.1 DNA AND RNA VERIFICATION 577
32.5.2 PROTEIN ANALYSIS 579
32.5.3 GENETIC AND MOLECULAR MAPS 579
32.5.4 STABILITY OF TRANSGENE PLANTS 580
FURTHER READING 582
33 BIOCATALYSIS IN THE CHEMICAL INDUSTRY 583
SS. HAUER, M. BREUER
33.1 INTRODUCTION 583
33.2 BIOCONVERSION/ENZYMATIC PROCEDURES 590
33.3 DEVELOPMENT OF AN ENZYME FOR THE INDUSTRIAL BIOCATALYSIS 593
33.3.1 IDENTIFICATION OF NOVEL BIOCATALYSTS 593
33.3.2 IMPROVEMENT OF BIOCATALYSTS 594
33.3.3 PRODUCTION OF BIOCATALYSTS 596
33.3.4 OUTLOOK 596
33.3.5 CASE EXAMPLE 1: SCREENING FOR NEW NITRILASES 597
33.3.6 CASE EXAMPLE 2: USE OF KNOWN ENZYMES FOR NEW REACTIONS: LIPASES
FOR THE PRODUCTION OF OPTICALLY ACTIVE AMINES AND ALCOHOLS 598
33.3.7 CASE EXAMPLE 3: ENZYME OPTIMIZATION WITH RATIONAL AND EVOLUTIVE
METHODS 600
FERMENTATIVE PROCEDURES 603
IMPROVEMENT OF FERMENTATION PROCESSES 601
CLASSICAL STRAIN OPTIMIZATION 602
METABOLIC ENGINEERING 603
CASE EXAMPLE 4: PRODUCTION OF GLUTAMINE ACID WITH
CORYNEBACTERIUM GLUTAMICUM 604
MOLECULAR MECHANISM OF GLUTAMATE OVERPRODUCTION 605
CASE EXAMPLE 5: PRODUCTION OF LYSINE WITH
CORYNEBACTERIUM GLUTAMICUM 606
MOLECULAR MECHANISM OF LEUCINE BIOSYNTHESIS 607
DEREGULATION OF THE KEY ENZYME ASPARTATE KINASE 608
GENOMIC RESEARCH AND FUNCTIONAL GENOMICS 609
CASE EXAMPLE 6: FERMENTATIVE PENICILLIN PRODUCTION 610
33
33
33
33
33
33
.4
.4.1
.4.2
.4.3
.4.4
.4.4.1
33.4.5
33
33
33
33
.4.5.1
.4.5.2
.4.6
.4.7
CONTENTS XIX
33.4.8 CASE EXAMPLE 7: VITAMIN B2 PRODUCTION 620
33.4.8.1 RIBOFLAVIN BIOSYNTHESIS 611
33.4.8.2 CLASSICAL STRAIN DEVELOPMENT 611
FURTHER READING 612
PART IV BIOTECHNOLOGY IN INDUSTRY
34 INDUSTRIAL APPLICATION
(BIOTECH INDUSTRY, MARKETS AND OPPORTUNITIES) 615
J. SCHUELER
34.1 HISTORICAL OVERVIEW AND DEFINITIONS OF CONCEPTS 615
34.2 AREAS OF INDUSTRIAL APPLICATION OF MOLECULAR BIOTECHNOLOGY 617
34.2.1 RED BIOTECHNOLOGY 617
34.2.1.1 BIOPHARMACEUTICAL DRUG DEVELOPMENT 617
34.2.1.2 DRUG DELIVERY 620
34.2.1.3 CELL AND GENE THERAPY 621
34.2.1.4 TISSUE ENGINEERING AND REGENERATIVE MEDICINE 622
34.2.1.5 PHARMACOGENOMICS, PERSONALIZED MEDICINE,
AND SYSTEM BIOLOGY 623
34.2.1.6 SYSTEMS BIOLOGY 624
34.2.1.7 MOLECULAR DIAGNOSTICS 624
34.2.2 GREEN BIOTECHNOLOGY 625
34.2.2.1 TRANSGENIC PLANTS 626
34.2.2.2 GENOMIC APPROACHES IN GREEN BIOTECHNOLOGY 626
34.2.2.3 NOVEL FOOD AND FUNCTIONAL FOOD 627
34.2.2.4 LIVESTOCK BREEDING 627
34.2.3 GREY/WHITE BIOTECHNOLOGY 627
34.2.3.1 TECHNICAL ENZYMES 627
34.2.3.2 THE ENVIRONMENT 628
34.3 THE STATUS QUO OF THE BIOTECH INDUSTRY WORLDWIDE 628
34.3.1 GLOBAL OVERVIEW 628
34.3.2 USA 629
34.3.3 EUROPE 629
FURTHER READING 629
35 PATENTS IN THE PHARMACEUTICAL BIOTECHNOLOGY INDUSTRY:
LEGAL AND ETHICAL ISSUES 631
DAVID B. RESNIK
35.1 PATENT LAW 631
35.1.1 WHAT IS A PATENT? 631
35.1.2 HOW DOES ONE OBTAIN A PATENT? 633
35.1.3 WHAT IS THE PROPER SUBJECT MATTER FOR A PATENT? 634
35.1.4 TYPES OF PATENTS IN PHARMACEUTICAL BIOTECHNOLOGY 635
35.1.5 PATENT INFRINGEMENT 635
35.1.6 INTERNATIONAL PATENT LAW 636
XX CONTENTS
35.2 ETHICAL AND POLICY ISSUES IN BIOTECHNOLOGY PATENTS 637
35.2.1 NO PATENTS ON NATURE 637
35.2.2 THREATS TO HUMAN DIGNITY 638
35.2.3 ACCESS TO TECHNOLOGY 640
35.2.4 BENEFIT SHARING 642
35.3 CONCLUSION 644
FURTHER READING 644
36 DRUG APPROVAL IN THE EUROPEAN UNION AND UNITED STATES 647
GARY WALSH
36.1 INTRODUCTION 647
36.2 REGULATION WITHIN THE EUROPEAN UNION 648
36.2.1 THE EU REGULATORY FRAMEWORK 648
36.2.2 THE EMEA 649
36.2.3 NEW DRUG APPROVAL ROUTES 650
36.2.3.1 THE CENTRALIZED PROCEDURE 650
36.2.3.2 MUTUAL RECOGNITION 653
36.3 REGULATION IN THE USA 653
36.3.1 CDER AND CBER 654
36.3.2 THE APPROVALS PROCEDURE 655
36.4 INTERNATIONAL REGULATORY HARMONIZATION 657
FURTHER READING 658
37 THE EMERGENCE OF A BIOTECHNOLOGY INDUSTRY 659
C. KREMOSER
FURTHER READING 669
38 THE 101 OF FOUNDING A BIOTECH COMPANY 671
C. KREMOSER
38.1 THE FIRST STEPS TOWARDS YOUR OWN COMPANY 671
38.2 EMPLOYEES: RECRUITMENT, REMUNERATION, PARTICIPATION 677
39 MARKETING 683
C. KREMOSER
39.1 INTRODUCTION 683
39.2 WHAT TYPES OF DEALS ARE POSSIBLE? 685
39.2.1 WHAT MILESTONE OR LICENSE FEES ARE EFFECTIVELY PAID IN A BIOTECH/
PHARMA COOPERATION? 685
39.3 PUBLIC RELATIONS (PR) AND INVESTOR RELATIONS (IR) IN BIOTECH
COMPANIES 687
FURTHER READING 688
GLOSSARY 689
M. WINK
SUBJECT INDEX 733
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| isbn | 3527314121 9783527314126 |
| language | English German |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-013836773 |
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| spelling | An introduction to molecular biotechnology molecular fundamentals, methods and applications in modern biotechnology Ed. by Michael Wink Weinheim Wiley-VCH 2006 LVI, 768 S. Ill. txt rdacontent n rdamedia nc rdacarrier Biotechnologie - Lehrbuch Molekularbiologie - Lehrbuch Biotechnology Genetic Engineering Genetic engineering Molecular Biology Molecular biology Molekularbiologie (DE-588)4039983-7 gnd rswk-swf Biotechnologie (DE-588)4069491-4 gnd rswk-swf (DE-588)4123623-3 Lehrbuch gnd-content Molekularbiologie (DE-588)4039983-7 s DE-604 Biotechnologie (DE-588)4069491-4 s Wink, Michael 1951- Sonstige (DE-588)124618146 oth DNB Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=013836773&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | An introduction to molecular biotechnology molecular fundamentals, methods and applications in modern biotechnology Biotechnologie - Lehrbuch Molekularbiologie - Lehrbuch Biotechnology Genetic Engineering Genetic engineering Molecular Biology Molecular biology Molekularbiologie (DE-588)4039983-7 gnd Biotechnologie (DE-588)4069491-4 gnd |
| subject_GND | (DE-588)4039983-7 (DE-588)4069491-4 (DE-588)4123623-3 |
| title | An introduction to molecular biotechnology molecular fundamentals, methods and applications in modern biotechnology |
| title_auth | An introduction to molecular biotechnology molecular fundamentals, methods and applications in modern biotechnology |
| title_exact_search | An introduction to molecular biotechnology molecular fundamentals, methods and applications in modern biotechnology |
| title_full | An introduction to molecular biotechnology molecular fundamentals, methods and applications in modern biotechnology Ed. by Michael Wink |
| title_fullStr | An introduction to molecular biotechnology molecular fundamentals, methods and applications in modern biotechnology Ed. by Michael Wink |
| title_full_unstemmed | An introduction to molecular biotechnology molecular fundamentals, methods and applications in modern biotechnology Ed. by Michael Wink |
| title_short | An introduction to molecular biotechnology |
| title_sort | an introduction to molecular biotechnology molecular fundamentals methods and applications in modern biotechnology |
| title_sub | molecular fundamentals, methods and applications in modern biotechnology |
| topic | Biotechnologie - Lehrbuch Molekularbiologie - Lehrbuch Biotechnology Genetic Engineering Genetic engineering Molecular Biology Molecular biology Molekularbiologie (DE-588)4039983-7 gnd Biotechnologie (DE-588)4069491-4 gnd |
| topic_facet | Biotechnologie - Lehrbuch Molekularbiologie - Lehrbuch Biotechnology Genetic Engineering Genetic engineering Molecular Biology Molecular biology Molekularbiologie Biotechnologie Lehrbuch |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=013836773&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| work_keys_str_mv | AT winkmichael anintroductiontomolecularbiotechnologymolecularfundamentalsmethodsandapplicationsinmodernbiotechnology |