Proteins labfax:
Gespeichert in:
| Format: | Buch |
|---|---|
| Sprache: | English |
| Veröffentlicht: |
San Diego [u.a.]
Academic Press
1996
|
| Schriftenreihe: | The labfax series
|
| Schlagworte: | |
| Online-Zugang: | Inhaltsverzeichnis |
| Beschreibung: | XXV, 318 S. Ill., graph. Darst. |
| ISBN: | 0125647107 |
Internformat
MARC
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| 245 | 1 | 0 | |a Proteins labfax |c ed. by N. C. Price |
| 264 | 1 | |a San Diego [u.a.] |b Academic Press |c 1996 | |
| 300 | |a XXV, 318 S. |b Ill., graph. Darst. | ||
| 336 | |b txt |2 rdacontent | ||
| 337 | |b n |2 rdamedia | ||
| 338 | |b nc |2 rdacarrier | ||
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| 999 | |a oai:aleph.bib-bvb.de:BVB01-007624164 | ||
Datensatz im Suchindex
| _version_ | 1804125855850430464 |
|---|---|
| adam_text | EDITED BY
N C PRICE
Department of Biological and Molecular Sciences,
University of Stirling,
Stirling FK9 4LA, UK
pios
SCIENTIFIC
PUBLISHERS
ACADEMIC PRESS
CONTENTS
Contributors xvii
Abbreviations xxi
Preface xxv
PURIFICATION
1 CHOICE OF ASSAY OR DETECTION METHOD 1
Introduction 1
Continuous versus discontinuous assays 2
Common techniques for the assay and detection of proteins (Table 1) 3
Photometric assays 2
Absorption 2
The coupled assay for fructose-1,6-bisphosphate aidolase (Figure 1) 4
Fluorescence 5
Turbidimetry 5
Radiometric assays 5
HPLC-based assays 6
Electrochemical assays 7
The oxygen electrode 7
The pH-stat (stationary pH) 7
Assays involving gel electrophoresis 8
Visualization of protein bands by protein staining 8
Visualization of protein bands by activity staining 8
Other electrophoresis-based assays 9
Immunological detection 9
Immunoblotting 9
Enzyme-linked immunosorbent assay 10
Radioimmunoassay and immunoradiometric assay 10
Conclusion 10
References 11
2 PREPARATION OF CELL EXTRACTS 13
Introduction 13
Disruption of cells and tissues 13
Choice of tissue 13
Disruption of tissue and separation of cells 14
Disruption of cells 14
Methods for disruption of cells (Table 1) 15
Protection of protein integrity 17
Control of pH 17
Control of temperature 17
Control of proteolysis • 17
Some inhibitors used to contol proteolysis (Table 2) 18
Protection of labile thiol groups 19
Control of mechanical stress 19
CONTENTS
Control o1 free radical formation 19
Control of the effects of dilution 19
Assays of proteins in unfractionated cell extracts 20
References 20
3 BUFFERS 21
Introduction 21
Factors determining the choice of buffer 21
Selected properties of commonly used buffers (Table 1) 22
Volatile buffer mixtures (Table 2) 24
Preparation of buffers 24
Metal ion buffers 25
References 26
4 THE DETERMINATION OF PROTEIN CONCENTRATION 27
Introduction 27
Principal methods for determination of protein (Table 1) 28
Recommendations 27
References 30
5, SALTING OUT: AMMONIUM SULFATE PRECIPITATION 31
Calculation of the amount of ammonium sulfate needed 31
Ammonium sulfate, grams to be added to 1 I of solution at S1% saturation, to take the saturation
to S2% (Table 1) 32
6 CHROMATOGRAPHIC PROCEDURES 33
Basic chromatographic theory 33
Progress of protein bands down an adsorption column under isocratic conditions (Figure 1) 34
Typical appearance of a chromatogram of a protein mixture on an ion exchange column (Figure 2) 34
Chromatographic materials 35
Ion-exchange chromatography 35
Ion exchanger types and nomenclature (Table 1) 36
Titration curves for a variety of proteins (Figure 3) 36
Buffers for ion exchange 37
Buffers for use in ion-exchange chromatography (Table 2) 38
Operation of an ion-exchange column 37
Chromatofocusing — general principles 39
Progress of a chromatofocusing column (Figure 4) 40
Operation of chromatofocusing 39
Hydrophobic chromatography 40
Sketch of the surface of a typical protein (Figure 5) 41
Hydrophobic interaction chromatography — practical aspects 41
Operation of a hydrophobic interaction column 42
Typical appearance of a chromatogram of a hydrophobic column (Figure 6) 43
Reverse-phase chromatography 42
Affinity chromatography 43
Affinity chromatography theory 43
Stages in affinity chromatography (Figure 7) 44
vi PROTEINS LABFAX
A selection of some commercially available group affinity adsorbents (Table 3) 45
Activation of the matrix 44
- Some activation chemistries for affinity chromatography and for protein immobilization (Table 4) 45
/Operation of affinity chromatography 45
Recombinant proteins 46
Some recombinant-fusion proteins designed for affinity purification (Table 5) 47
Affinity elution techniques 46
Principle of affinity elution from a cation exchanger (Figure 8) 47
Principle of affinity elution from an affinity adsorbent (Figure 9) 48
Dye—ligand chromatography 48
Selection of dye adsorbent 48
Batchwise screening of dye-ligand adsorbents (Figure 10) 49
Some dyes commonly used in dye-ligand chromatography (Table 6) 50
Two-adsorbent procedures — differential chromatography 50
Principle of differential tandem column chromatography (Figure 11) 51
Buffers for use in dye-ligand chromatography 50
Buffers for use in dye-ligand chromatography (Table 7) 52
Immobilized metal affinity chromatography 52
IMAC principles and practice 52
Buffer systems for IMAC (Table 8) 53
Gel filtration 53
Diagram to represent the separation of proteins on the basis of size by a gel filtration bead (Figure 12) 54
Gel filtration: operating conditions for separating proteins 53
Gel filtration to separate proteins from low molecular mass compounds 54
Media for gel filtration 55
Gel filtration media (Table 9) 55
Methods for concentrating proteins 56
Concentration by precipitation 56
Concentration by adsorption 56
Concentration by removal of water 57
Concentration by centrifugal force 57
Ultrafiltration to concentrate proteins (Figure 13) 58
Concentration by gas pressure 57
Concentration by water pressure 58
Concentration by osmotic pressure 58
Purification of small peptides from biological sources 58
Introduction 58
Practical considerations 59
Parameters affecting RP-HPLC seperation of peptides 60
Isolation of guinea-pig adrenocorticotrophin (ACTH) 61
Purification of guinea-pig ACTH from anterior pituitary extracts by sequential HPLC steps (Figure 14) 62
Conclusion 62
References 62
Further reading 64
7 COVALENT CHROMATOGRAPHY BY THIOL-DISULFIDE INTERCHANGE
USING SOLID-PHASE ALKYL 2-PYRIDYL DISULFIDES 65
Introduction 65
Covalent chromatography by thiol—disulfide interchange (TDCC) 65
Other applications of 2-pyridyl disulfides and the origins of TDCC 66
Sequential elution TDCC 66
Covalent affinity chromatography • 67
Covalent chromatography and salt-promoted thiophilic adsorption 67
Some examples of the applications of TDCC 67
Isolation of thiol-containing proteins 67
CONTENTS vii
Illustration of the range of thiol-containing proteins that have been isolated by covalent
* chromatography (Table 1) 68
Isolation and sequencing of thiol-containing peptides 67
Examples of the application of covalent chromatography in the isolation and sequencing of peptides
(Table 2) 68
Removal of prematurely terminated peptides in solid-phase peptide synthesis 68
Enzyme immobilization with associated purification 69
Thiol-specific covalent chromatography by methods other than thiol-disulfide interchange 69
Selectivity in covalent chromatography 69
References 70
8 CRITERIA OF PROTEIN PURITY 73
Introduction iy
Methods for assessing the purity of protein preparations (Table 1) 74
Detection of nonprotein contaminants 73
The quantification of nucleic acid contaminants in protein samples (Figure 1) 75
Detection of protein contaminants 73
Determination of purity 76
Specific activity measurement 76
Electrophoretic methods 76
The choice of electrophoretic method for the determination of protein purity (Table 2) 77
Some common problems encountered in electrophoresis and their remedy (Table 3) 78
The uses of capillary electrophoresis (Table 4) 79
CE can be used in a variety of modes (Figure 2) 80
Chromatographic techniques 78
Centrifugation methods 81
Mass spectrometry 81
Amino acid analysis and sequence analysis 82
Measurements of binding sites or active sites - 83
Summary 83
References 83
9 ELECTROPHORESIS METHODS 85
Introduction 85
Recipes for gels and buffers 85
One-dimensional polyacrylamide gel electrophoresis 85
Recipe for gel preparation using the SDS-PAGE discontinuous buffer system (Table 1) 86
Gel mixtures for a 5-20% SDS-PAGE gradient gel (Table 2) 86
Electrolytes used in IEF (Table 3) 87
Recipes for preparation of IEF gels (Table 4) 87
Two-dimensional gel electrophoresis 90
Recipes for first-dimensional IEF gel and second-dimensional SDS-PAGE gel (Table 5) 88
Immunoelectrophoresis 90
Reagents for immunoelectrophoresis (Table 6) 88
Sample preparation 91
Standard marker proteins used in either denaturing or IEF gels (Table 7) 89
Analysis of gels 91
In situ direct polypeptide detection methods in SDS gels without staining (Table 8) 90
Protein staining and detection methods used in IEF (Table 9) 91
Staining procedures for two-dimensional polyacrylamide gels (Table 10) 92
Staining procedures used after immunoelectrophoresis (Table 11) 92
In situ polypeptide detection methods in gels using fluorophore labeling (Table 12) 93
In situ detection of specific classes of proteins in gels (Table 13) - 93
viii PROTEINS LABFAX
Common blotting membranes (Table 14) 94
Blocking solutions to prevent nonspecific binding of the probe to the matric in protein blotting
(Table 15) 94
; Transfer buffers used in blotting (Table 16) 95
General protein stains for blot transfers (Table 17) 95
In situ detection of radioactive proteins in gels (Table 18) 95
Sensitivities of methods for radioisotope detection in polyacrylamide gels (Table 19) 96
Manufacturers and suppliers 96
References 97
10 INTEGRAL MEMBRANE PROTEINS 101
Introduction 101
Problems of solubilization, purification and assay of membrane proteins 101
Choice of detergent 101
General properties of a range of detergents used with membrane proteins (Table 1) 102
Methods of purification 101
Assay: use of reconstitution 105
Structural analysis of membrane proteins 105
References 106
Further reading 107
Liposomes and reconstitution methods 107
General 107
11 EXPRESSION SYSTEMS AND FUSION PROTEINS 109
Introduction 109
References for the production of fusion proteins (Table 1) 109
Proteins commonly used in gene fusion technology 110
Physical properties of the most common proteins used in gene fusion technology (Table 2) 110
Gene fusion vectors (Table 3) 111
Induction of expression 111
Conditions that influence induction of a recombinant fusion protein (Table 4) 112
Promoter and strain relationships (Table 5) 113
Proteolytic cleavage of fusion proteins 112
Properties of some of those proteases frequently used to liberate recombinant proteins from a
fusion partner (Table 6) 114
Purification of fusion proteins 112
Purification of fusion proteins (Table 7) 114
Detection of fusion proteins 113
Spectrophometric assays for fusion proteins (Table 8) 115
References 116
12 INCLUSION BODIES AND REFOLDING 119
Introduction 119
Origin of inclusion bodies and their advantage in the purification of recombinant proteins 119
Structure of inclusion bodies 119
Factors affecting inclusion body formation 120
When should the inclusion body route be chosen? 120
Methods for the isolation and solubilization of inclusion bodies 121
Recovery of proteins from inclusion bodies (Figure 1) 121
Methods for the isolation of inclusion bodies 122
CONTENTS ix
Solubilization 122
Renaturation of solubilized inclusion bodies 123
Refolding 123
Refolding strategies (Figure 2) 124
Disulfide bond formation 125
Proteins purified from inclusion bodies (Table 1) 126
Designing a procedure de novo for refolding and purification of an inclusion body protein 126
Generic purification approach for inclusion body protein when no or limited information on the
properties of the protein is available (Figure 3) 127
References 128
13 INDUSTRIAL SCALE PURIFICATION OF PROTEINS 131
Introduction 131
Scope 131
Process scale up 131
Developing a scale down process 132
Block diagrams and process flow sheeting 132
Block diagrams and process flow sheeting (Figure 1) 133
Selection of unit operations 133
Downstream processing technologies used in the industrial production of proteins (Figure 2) 134
Primary recovery 133
High-resolution purification steps 135
References 137
14 PEPTIDE SYNTHESIS 139
Introduction 139
General aspects of solid-phase peptide synthesis 140
Solid-phase supports, modes of synthesis and related apparatus 140
Materials for peptide synthesis supports (Table 1) 142
Peptide-resin linkage and protecting group strategy 141
Protection strategies in solid-phase peptide synthesis (Table 2) 144
Deprotection/scavenger mixtures suitable for the Fmoc strategy (Table 3) 144
Carboxyl activation and coupling: peptide bond formation 143
Active species and coupling reagents (Table 4) 145
Synthesis monitoring and control 146
Qualitative color tests on resins (Table 5) 147
Continuous flow monitoring systems (Table 6) 148
Other methods for monitoring peptide synthesis (Table 7) 149
Synthetic peptide analysis, purification and handling 146
Problems in handling and use of peptides (Table 8) 150
Synthetic peptides for antibody production 149
Prediction of immunogenic peptide sequences (Table 9) 151
Carriers for synthetic peptide immunogens (Table 10) 151
Conjugation methods to link peptide carriers (Table 11) 152
References 152
15 CRYSTALLIZATION PROCEDURES 155
Introduction * 155
Overview 155
Some of the factors which affect the crystallization of a protein (Table 1) 156
Methods for crystallizing proteins (Table 2) 157
PROTEINS LAFJFAX
Some specialist supplies and suppliers (Table 3) 158
Growth of large crystals 156
General scheme 157
A simple procedure for hanging drop crystallization 158
A simple procedure for crystallization by small-scale dialysis 159
Methods for buttons 159
Conclusion 159
References 159
Further reading 160
Sources of information on protein crystallization 160
PHYSICAL CHARACTERIZATION
16 SIZE DETERMINATION OF PROTEINS 161
A HYDRODYNAMIC METHODS 161
Introduction 161
Data from the analytical ultracentrifuge 161
Parameters measurable in the analytical ultracentrifuge (Table 1) 161
Complementary techniques 162
Complementary techniques (Table 2) 162
Theory 162
Sedimentation equilibrium 162
The diagnostic plot of In (c) versus r2 (Figure 1) 163
A plot of A^pp versus total solute loading concentration for two hypothetical systems, both with a
monomer molecular mass of 100 kDa (Figure 2) 164
Sedimentation velocity 164
Schematic diagram of the traces recorded with absorption optics in a typical sedimentation velocity
experiment (Figure 3) 165
Absorption optics traces for a sedimentation velocity experiment with a heterogeneous sample in
which the sedimentation coefficients of the two components differ sufficiently to give a
characteristic stepped boundary (Figure 4) 167
Advantages and disadvantages 167
The advantages and disadvantages of analytical centrifuge experiments (Table 3) 168
Essential additional information 167
Partial specific volume 167
Approximate partial specific volumes for common biological macromolecular constituents (Table 4) 168
Buffer density 169
Buffer viscosity 169
Instrumentation 169
Optics 169
Materials and methods 169
Sample preparation 169
Sedimentation equilibrium 170
Sedimentation velocity 171
Data analysis 171
Sedimentation equilibrium 171
Models embodied in Beckman Optima XL-A analysis software for equilibrium data (Table 5) 171
Sedimentation velocity • 172
Models embodied in Beckman Optima XL-A analysis software for velocity data (Table 6) 172
National analytical ultracentrifuge facilities 173
RASMB 174
CONTENTS xi
Examples of EPR spectra of transition metal ions (Figure 2) 221
Myperfine (electron-nuclear) interactions 222
) Some nuclei with magnetic moments (Table 2) 223
Types of EPR spectroscopy (Table 3) 224
Electron-electron interactions 222
Specialist EPR techniques 223
Sample requirements 225
Applications in the study of proteins 225
Measurements in whole-cell and tissue systems 225
Types of information obtained by EPR spectroscopy (Table 4) 226
Information on paramagnetic centers in proteins 225
Spin labels and spin probes 227
Examples of EPR spectra of free radicals (Figure 3) 228
Applications of spin labels to studies of proteins (Table 5) 229
Measurement of rates of motion 229
Interactions between paramagnetic centers and between macromolecules 230
References 230
21 PROTEIN STABILITY 233
Introduction 233
Measuring protein stability 233
Selecting a technique to monitor unfolding 233
Techniques used to monitor protein unfolding (Table 1) 234
Criteria for selecting a technique to monitor unfolding (Table 2) 235
Determining an unfolding curve 233
Urea and GdnHCI solutions (Table 3) 235
Equilibrium and reversibility 235
Data analysis 235
Urea denaturation of RNase T1 monitored by fluorescence (Figure 1) 236
Thermal denaturation of RNase T1 monitored by CD at 244 nm (Figure 2) 237
Regions of an unfolding curve (Table 4) 237
Methods used to measure ACj, (Table 5) 238
The conformational stability of globular proteins 238
References 238
22 COMPUTER ANALYSIS OF PROTEIN STRUCTURE 241
General biocomputing 241
Hardware and software requirements 241
World wide web 241
Gopher 241
Some key URLs (Table 1) 242
ftp 241
Telnet 242
Network news 242
How to access, view and and analyze protein 3D structures 242
Finding and transferring protein structures 242
A small section of a PDB file (Table 2) 243
Viewing proteins 243
RASMOL instructions (Table 3) 244
Mouse button and key combinations for RASMOL on PCs and UNIX (Table 4) 246
Structural analysis 245
A sample of a DSSP file (Table 5) 247
Making evolutionary comparisons 246
xiv PROTEINS LABFAX
A sample of an HSSP file (Table 6) 248
Assigning a protein to categories 249
Conformations! changes 249
How to retrieve and interpret protein sequences 249
Finding sequences 249
Protein databases (Table 7) 250
Comparing sequences 250
Some alternative ways of finding matching sequences (Table 8) 251
Multiple alignment 251
References 252
PROTEIN CHEMISTRY
23 PROTEIN CHEMISTRY METHODS, POST-TRANSLATIONAL
MODIFICATION, CONSENSUS SEQUENCES 253
Introduction 253
Consensus sequences and functional motifs (Table 1) 254
Co- and post-translational modifications in proteins (Table 2) 262
Post-translational modifications 269
Consensus sequences 269
One and three letter abbreviations for the amino acids (Table 3) 270
Computer analysis on the internet/WWW 269
Cleavage and hydrolysis of proteins and peptides 270
Hydrolysis of proteins for amino acid analysis 270
Protein hydrolysis methods (Table 4) 271
Elution order of amino acids and derivatives from ion-exchange analyzers (Table 5) 272
Enzymic and chemical cleavage of proteins 272
Digestion and cleavage of proteins and peptides (Table 6) 273
Identification and purification of modified peptides by HPLC 277
Prediction of peptide retention times on RP-HPLC 278
Altered retention of post-translationally modified peptides on RP-HPLC (Table 7) 279
Relative retention coefficients on RP-HPLC (Table 8) 280
Structure elucidation of modified peptides 280
N-terminal modifications of proteins 280
N-terminal modifications of proteins (Table 9) 281
Mass spectrometry 281
Interfering salts and buffers 282
Elution order of PTH-derivatives on HPLC (Table 10) 283
References 284
24 CHEMICAL MODIFICATION OF AMINO ACID SIDE-CHAINS 287
General aspects of the chemical modification of proteins 287
Characterization of site-specific modified proteins 287
Establishment of reaction stoichiometry 287
Correlation of the extent of modification with concomitant changes in biological activity 288
Identification of residue(s) modified 288
Comparison of the conformation of the modified protein to that of the native protein 289
Modification of specific amino acid residues 289
Cysteine 289
Reagents for the modification of cysteine in proteins (Table 1) 289
Cystine 290
Reagents for the modification of cystine in proteins (Table 2) 290
CONTENTS xv
Methionine 290
„ Reagents for the modification of methionine in proteins (Table 3) 290
Histidine 290
Reagents for the modification of histidine in proteins (Table 4) 291
Lysine 291
Reagents for the modification of lysine in proteins (Table 5) 291
Arginine 292
Reagents for the modification of arginine in proteins (Table 6) 292
Tryptophan 292
Reagents for the modification of tryptophan in proteins (Table 7) 292
Tyrosine 293
Reagents for the modification of tyrosine in proteins (Table 8) 293
Carboxyl groups 293
Reagents for the modification of carboxyl groups in proteins (Table 9) 293
References 293
25 AFFINITY-BASED COVALENT MODIFICATION 299
Introduction 299
Scope and general principles of the technique 299
Applications: an overview 299
Classical affinity labels 300
Quiescent affinity labels 301
Photoaffinity labels 301
Transition state affinity (K*s) labels 302
Mechanism-based irreversible inhibitors 302
Substrate-dependent nonaffinity labels 303
Substrate-derived site-specific reactivity probes 303
References 304
26 CROSS-UNKING REAGENTS FOR PROTEINS 307
Introduction 307
Reagents 307
Some amino group-directed homobifunctional cross-linking reagents (Table 1) 308
Some sulfhydryl group-directed homobifunctional cross-linking reagents (Table 2) 309
Some representative heterobifunctionai cross-linking reagents (Table 3) 310
Control of pH 308
Lysine-directed cross-linking reagents 310
Cysteine-directed cross-linking reagents 311
Other types of cross-linking reagent 311
Applications 311
Estimation of the native molecular mass of oligomeric proteins 312
Nearest neighbor analysis in oligomeric proteins 312
Studies on membrane proteins 313
Detection of conformational change 313
Detection of subunit association/dissociation 313
Conjugation of proteins 313
References 314
INDEX 315
xvi PROTEINS LABFAX
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| id | DE-604.BV011346530 |
| illustrated | Illustrated |
| indexdate | 2024-07-09T18:08:12Z |
| institution | BVB |
| isbn | 0125647107 |
| language | English |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-007624164 |
| oclc_num | 605155709 |
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| owner_facet | DE-20 DE-29 DE-91G DE-BY-TUM |
| physical | XXV, 318 S. Ill., graph. Darst. |
| publishDate | 1996 |
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| publisher | Academic Press |
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| series2 | The labfax series |
| spelling | Proteins labfax ed. by N. C. Price San Diego [u.a.] Academic Press 1996 XXV, 318 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier The labfax series Biochemische Methode (DE-588)4319880-6 gnd rswk-swf Proteine (DE-588)4076388-2 gnd rswk-swf Proteine (DE-588)4076388-2 s Biochemische Methode (DE-588)4319880-6 s DE-604 Price, Nicholas C. Sonstige oth HEBIS Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=007624164&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Proteins labfax Biochemische Methode (DE-588)4319880-6 gnd Proteine (DE-588)4076388-2 gnd |
| subject_GND | (DE-588)4319880-6 (DE-588)4076388-2 |
| title | Proteins labfax |
| title_auth | Proteins labfax |
| title_exact_search | Proteins labfax |
| title_full | Proteins labfax ed. by N. C. Price |
| title_fullStr | Proteins labfax ed. by N. C. Price |
| title_full_unstemmed | Proteins labfax ed. by N. C. Price |
| title_short | Proteins labfax |
| title_sort | proteins labfax |
| topic | Biochemische Methode (DE-588)4319880-6 gnd Proteine (DE-588)4076388-2 gnd |
| topic_facet | Biochemische Methode Proteine |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=007624164&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
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