Dissecting the molecular anatomy of tissue: with ... 8 tables
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| Format: | Elektronisch E-Book |
|---|---|
| Sprache: | English |
| Veröffentlicht: |
Berlin [u.a.]
Springer
2005
|
| Schriftenreihe: | Principles and practice
|
| Schlagworte: | |
| Online-Zugang: | DE-355 Volltext Inhaltsverzeichnis |
| Beschreibung: | Literaturangaben |
| Beschreibung: | 1 Online-Ressource |
| ISBN: | 3540220062 9783540220060 9783540264828 |
| DOI: | 10.1007/b137665 |
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| 245 | 1 | 0 | |a Dissecting the molecular anatomy of tissue |b with ... 8 tables |c Michael R. Emmert-Buck ... (ed.) |
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Datensatz im Suchindex
| _version_ | 1809493931703926784 |
|---|---|
| adam_text |
MICHAEL R. EMMERT-BUCK
JOHN W. GILLESPIE
RODRIGO E CHUAQUI (EDS.)
DISSECTING THE MOLECULAR
ANATOMY OF TISSUE
WITH 43 FIGURES, 9 IN COLOR, AND 8 TABLES
UNIVERSITATS- UND LANDES
BIBLIOTHEK DARMSTADT
BIBLIOTHE
K BIOLOGI
E
^ SPRINGER
CONTENTS
I CLINICAL ISSUES AN
D TISSUE PROCESSING 1
1 MOLECULAR PATHOLOGY LABORATORY OF THE FUTURE
CHRISTOPHE
R
A.
MOSKALU
K
3
1.1 TH
E PAST 3
1.2 TH
E PRESEN
T 4
1.3 TH
E FUTUR
E 8
1.4 A SCENARI
O OF TH
E FUTUR
E OF TISSUE DIAGNOSTICS
:
A PROSTAT
E BIOPSY FOR ASSESSMEN
T OF CARCINOM
A 10
1.4.1 CURREN
T CLINICAL PROCEDURE
S 10
1.4.2 FUTUR
E CLINICAL PROCEDURE
S 11
1.5 SUMMAR
Y 14
REFERENCES 14
2 CLINICAL UTILITIES OF MICRODISSECTED SAMPLES
ISSAC
YI
KIM
, DAVI
D
K.
ORNSTEI
N
17
2.1 INTRODUCTIO
N 17
2.2 CURREN
T CLINICAL USES 17
2.2.1 DIAGNOSI
S 17
2.2.2 PROGNOSI
S ' 18
2.2.3 CYTOLOGY 19
2.2.4 DETECTIO
N OF VIRAL DNA 19
2.2.5 ASSESSMEN
T OF GENE COPY NUMBER
S 20
2.2.6 ANALYSIS OF CELL CYCLE PARAMETER
S 21
2.2.7 SLIDE CONTAMINATIO
N . . . . 22
2.3 FUTUR
E CLINICAL USES: ANALYSIS OF CELLULAR PROTEIN
S 22
2.4 CONCLUSION
S 23
REFERENCES 23
X CONTENTS
3 TISSUE PROCESSING
GALLYA GANNOT
, JOH
N
W.
GILLESPI
E
27
3.1 INTRODUCTIO
N
-C 27
3.2
-A
CLINICAL ASPECTS 28
3.3 \ SAMPLE ACQUISITIO
N AN
D INITIA
L TISSUE HANDLIN
G 28
3.4 \ TISSUE FIXATION AN
D SNAP-FREEZIN
G 29
3.5 \TISSUE EMBEDDIN
G 33
3.6 EVALUATION OF NEW METHOD
S FOR HANDLIN
G CLINICAL TISSUE
SPECIMENS
: PROSTAT
E CANCER AS A
N EXAMPLE OF TISSUE HANDLIN
G
FOR MOLECULAR ANALYSIS 34
3.6.1 NEW METHOD
S OF FIXATION/EMBEDDIN
G 34
3.6.2 NONFORMALI
N TISSUE FIXATIO
N 35
3.6.3 COMPARISO
N OF HISTOLOG
Y AN
D RECOVERY OF DNA, RNA,
AN
D PROTEIN
S 36
3.7 CONCLUSION
S AN
D FUTUR
E DIRECTION
S 40
REFERENCES 41
4 SAMPLE MANAGEMENT AND TRACKING
G.
STEVE
N BOVA
43
4.1 INTRODUCTIO
N . 43
4.2 TH
E TISSUE MICRODISSECTIO
N CORE LABORATORY
:
ORGANIZATIO
N AN
D BASIC DATA MANAGEMEN
T 43
4.3 INTEGRATE
D DATA MANAGEMEN
T FOR TH
E TISSUE-ORIENTE
D
BIOLOGICAL RESEARCH: THE LABMATRI
X SYSTEM 46
4.3.1 LABMATRI
X PRIMAR
Y MODULES 48
4.3.1.1 STUDY SUBJECTS 48
4.3.1.2 BIOMATERIALS 49
4.3.1.3 PROTOCOL
S 49
4.3.1.4 WORKFLOW-BASED DATA REVIEW:
FUNCTIONA
L GENOMI
C STATUS SUMMARIZATIO
N METHO
D 50
4.3.1.5 SCIENTIFIC QUER
Y BUILDER 50
4.3.1.6 EQUIPMEN
T AN
D SUPPLIES/CONTACTS" 51
4.3.1.7 IMAGES/CONFIGURATIO
N TOOLS 51
4.3.1.8 LABORATOR
Y ADMINISTRATO
R 51
4.3.2 ADDITIONA
L FEATURES OF LABMATRI
X PROTOTYP
E 52
4.3.2.1 INTERNA
L PROPRIETAR
Y AN
D PUBLIC REFERENCE DATABASE
S
AN
D COLLABORATIO
N FEATURES 52
4.3.2.2 DATA SECURIT
Y FEATURES AN
D REGULATORY COMPLIANC
E 52
4.3.2.3 INTEGRATIO
N WIT
H OTHE
R SCIENTIFIC TOOLS AN
D TECHNOLOGY 52
CONTENTS XI
II METHODS OF TISSUE MICROANALYSIS 55
5 TISSU
E MICROARRAY
S
STEPHE
N
M.
HEWIT
T
57
5.1 INTRODUCTIO
N 57
5.2 CONSTRUCTIO
N OF TISSUE MICROARRAY
S 57
5.3 TISSUE MICROARRAY
S AS A VALIDATION TOOL 58
5.4 IMMUNOHISTOCHEMISTR
Y AN
D TISSUE MICROARRAY
S 60
5.5 IN SITU HYBRIDIZATIO
N AN
D TISSUE MICROARRAY
S 63
5.6 IMAGE CAPTUR
E AN
D DATA ANALYSIS 64
REFERENCES . . . ? 66
III MOLECULAR ANALYSIS OF MICODISSECTED SAMPLES 67
6 METHOD
S OF MICRODISSECTIO
N AN
D NEW TECHNOLOGIE
S
MICHAE
L
A.
TANGREA
, JOH
N
W.
GILLESPIE
,
MICHAE
L
J.
FLAIG
, GALLYA GANNOT
, VLADIMI
R KNEZEVIC
,
MICHAE
L
R.
EMMERT-BUCK
, RODRIG
O
F.
CHUAQU
I
69
6.1 HISTORICA
L PERSPECTIVE 69
6.2 LASER-BASED DISSECTIO
N TECHNOLOGIES 71
6.2.1 LASER CAPTUR
E MICRODISSECTIO
N 71
6.2.2 PALM LASER MICRODISSECTIO
N
AN
D PRESSUR
E CATAPULTIN
G TECHNOLOGY 73
6.2.3 LEICA AS LMD 74
6.3 NOVEL TECHNIQUES 74
6.4 EXPRESSIO
N MICRODISSECTIO
N 75
6.4.1 FUTUR
E DIRECTION
S OF EXPRESSIO
N MICRODISSECTIO
N 81
6.5 LAYERED EXPRESSIO
N SCANNIN
G 84
6.5.1 OPE
N LAYERED EXPRESSIO
N SCANNIN
G SYSTEM 86
6.5.1.1 MULTIPLE NORTHER
N BLOTS 87
6.5.1.2 MULTIPLEX-IMMUNOBLOT
S : . 89
6.5.2 CLOSED LAYERED EXPRESSIO
N SCANNIN
G SYSTEM 90
6.5.3 OTHE
R PLATFORMS FOR TH
E LAYERED EXPRESSIO
N
SCANNIN
G TECHNIQUE 92
6.5.4 FUTUR
E DIRECTION
S 94
6.6 CONCLUSIO
N 96
REFERENCES 97
XII CONTENTS
7 STANDARD DIAGNOSTIC TECHNIQUES
SERGI
O GONZALE
Z
101
7.1 INTRODUCTIO
N 101
7.2 DIAGNOSTI
C HISTOPATHOLOG
Y 102
7.3 IMMUNOHISTOCHEMISTR
Y , 102
7.4 IN SITU HYBRIDIZATIO
N AN
D PCR-IN SIT
U HYBRIDIZATIO
N 107
7.5 MICRODISSECTIO
N 108
7.6 CLOSING REMARK
S 109
REFERENCES 109
8
DNA APPLICATIONS
PABL
O URIBE
, IGNACI
O
I.
WISTUB
A
IL
L
8.1 INTRODUCTIO
N IL
L
8.2 DNA EXTRACTIO
N , 112
8.3 DNA PCR AMPLIFICATION -11
2
8.4 MICROSATELLITE ANALYSIS 113
8.5 MUTATIO
N ANALYSIS 114
8.5.1 SINGLE-STRAN
D CONFORMATIO
N POLYMORPHIS
M 114
8.5.2 RESTRICTIO
N FRAGMEN
T LENGTH POLYMORPHIS
M 115
8.6 GENE METHYLATION ANALYSIS 116
8.7 CLONALITY ANALYSIS 117
8.7.1 OVERVIEW 117
8.7.2 MICROSATELLITE ANALYSIS . . . 118
8.7.3 GENE MUTATION
S 118
8.7.4 X-CHROMOSPM
E INACTIVATIO
N 118
8.7.5 GENOTYPIN
G ASSAY OF TH
E D310 REPEAT 120
8.8 SUMMAR
Y 120
REFERENCES 121
9 MRNA APPLICATIONS
FATI
H OZSOLAK
, VERONIC
A LUZZI
, MAR
K
A.
WATSO
N
125
9.1 INTRODUCTIO
N 125
9.2 TISSUE SELECTION FOR GENE EXPRESSIO
N ANALYSIS 126
9.3 RNA ISOLATIO
N 127
9.3.1 OVERVIEW 127
9.3.2 EXPECTED RESULTS 129
9.3.3 TROUBLESHOOTIN
G 130
9.4 TRANSCRIP
T AMPLIFICATION 131
9.4.1 OVERVIEW 131
9.4.2 EXPECTED RESULTS 132
CONTENTS XIII
9.4.3 TROUBLESHOOTIN
G 133
9.5 RT-PCR VALIDATION 135
9.5.1 OVERVIEW 135
9.5.2 PCR ASSAY DESIGN 135
9.5.3 QUANTIFICATIO
N 137
9.5.4 NORMALIZATIO
N CONTROL
S 138
9.5.5 EXPECTED RESULTS 140
9.5.6 TROUBLESHOOTIN
G 141
REFERENCES 143
10 PROTEOMIC APPLICATIONS
DAVI
D
H.
GEHO
, LANC
E
A.
LIOTTA
, EMANUE
L
F.
PETRICOI
N
. 145
10.1 INTRODUCTIO
N 145
10.2 LASER CAPTUR
E MICRODISSECTIO
N 148
10.3 PROTEI
N MICROARRAYS^ 149
10.4 MASS SPECTROMETR
Y IN TISSUE PROTEOMIC
S 153
10.5 CONCLUSION
S 157
REFERENCES 158
11 PROTOCOLS FOR TISSUE HANDLING AND MOLECULAR ANALYSIS
163
11.1 TISSUE PREPARATIO
N FOR PROSTAT
E PREPARE
D AS WHOLE-MOUN
T .
. 163
11.1.1 70% ETHANO
L FIXATION 163
11.1.2 EMBEDDIN
G 164
11.1.2.1 LOW-MELT POLYESTER EMBEDDIN
G " I. 164
11.1.2.2 PARAFFIN EMBEDDING
' 165
11.2 SLIDE PREPARATIO
N FOR MICRODISSECTIO
N
T
O PERFORM SUBSEQUEN
T DNA, RNA, AN
D PROTEI
N ANALYSIS .
. 166
11.2.1 SLIDE PREPARATIO
N FOR LASER CAPTUR
E MICRODISSECTIO
N 166
11.2.1.1 PARAFFIN-EMBEDDE
D SECTION
S AN
D FROZEN SECTIONS 167
11.2.1.2 LOW-MELT POLYESTER-EMBEDDE
D SECTION
S 167
11.2.2 SLIDE PREPARATIO
N FOR MANUA
L MICRODISSECTIO
N 168
11.2.2.1 PARAFFIN-EMBEDDE
D SECTION
S AN
D FROZEN SECTION
S 169
11.2.2.2 LOW-MELT POLYESTER-EMBEDDE
D SECTIONS 170
11.3 TECHNIQUES OF MICRODISSECTIO
N 170
11.3.1 LASER CAPTUR
E MICRODISSECTIO
N 170
11.3.2 IMMUNO-LASE
R CAPTUR
E MICRODISSECTIO
N 171
11.3.3 MANUA
L MICRODISSECTIO
N 172
11.4 PROCESSIN
G OF MICRODISSECTE
D TISSU
E FOR MOLECULAR ANALYSIS . . 173
11.4.1 DNA-BASED STUDIES 173
11.4.1.1 PROTOCO
L FROM PATHOGENETIC
S UNIT 173
11.4.1.2 DNA EXTRACTIO
N (PROTOCO
L FROM WISTUBA
) 175
XIV CONTENTS
11.4.2 RNA ISOLATIO
N 175
11.4.2.1 ISOLATIO
N OF TOTAL RNA FROM FROZEN MICRODISSECTE
D TISSUE .
. 175
11.4.2.2 PROTOCO
L FOR ISOLATIO
N OF RNA FROM FROZEN LCM TISSUE
(PROTOCO
L FROM WATSON) 177
11.4.2.3 PROTOCO
L FOR ISOLATIO
N OF RNA FROM FORMALIN-FIXED
,
PARAFFIN-EMBEDDE
D LCM TISSUE (PROTOCO
L FROM WATSON
) .
. 179
11.4.3 PROTEIN-BASE
D STUDIES 180
11.4.3.1 SAMPLE PREPARATIO
N FOR 2-D PAGE 180
11.4.3.2 IMMUNOBLO
T 181
11.5 DNA, RNA, AN
D PROTEI
N ANALYSIS 182
11.5.1 DNA ANALYSIS 182
11.5.1.1 CLONALITY
: X-CHROMOSOM
E INACTIVATIO
N 182
11.5.1.2 LOSS OF HETEROZYGOSIT
Y 185
11.5.1.3 DNA PCR AMPLIFICATION (PROTOCO
L FROM WISTUBA
) 190
11.5.1.4 ANALYSIS OF MICROSATELLITE MARKER
S (PROTOCO
L FROM WISTUBA
) . . 191
11.5.1.5 SINGLE-STRAN
D CONFORMATIONA
L POLYMORPHIS
M
J
(PROTOCO
L FROM WISTUBA
) 192
11.5.1.6 RESTRICTE
D FRAGMEN
T LENGTH POLYMORPHIS
M
(PROTOCO
L FROM WISTUBA
) 192
11.5.1.7 GENE METHYLATIO
N ANALYSIS (PROTOCO
L FROM WISTUBA
) 193
11.5.1.8 GENOTYPIN
G ASSAY OF TH
E D310 REPEAT
(PROTOCO
L FROM WISTUBA
) 193
11.5.1.9 IN SITU HYBRIDIZATIO
N PROTOCO
L FOR CYTOMEGALOVIRU
S
(PROTOCO
L FROM GONZALEZ) 194
11.5.2 RNA ANALYSIS 195
11.5.2.1 GENE-SPECIFIC RT-PCR 195
11.5.2.2 TARGETED DIFFERENTIAL DISPLAY 197
11.5.2.3 NONLSOTOPI
C IN SITU HYBRIDIZATIO
N PROTOCO
L
FOR MRNA DETECTIO
N (PROTOCOL FROM GONZALEZ) 201
11.5.2.4 PROTOCO
L FOR TRANSCRIP
T AMPLIFICATION (PROTOCO
L FROM WATSON) 202
11.5.2.5 PROTOCO
L FOR RT-PCR VALIDATION (PROTOCO
L FROM WATSON
) .
. 206
11.5.3 PROTEI
N ANALYSIS 209
11.5.3.1 2-D POLYACRYLAMID
E GEL ELECTROPHORESI
S 209
11.5.3.2 IMMUNOBLO
T 214
11.5.3.3 IMMUNOHISTOCHEMISTR
Y 216
11.6 LEGAL ISSUES
, INFORME
D CONSEN
T 220
SUBJECT INDEX
221
COLOR ILLUSTRATIONS
225 |
| adam_txt |
MICHAEL R. EMMERT-BUCK
JOHN W. GILLESPIE
RODRIGO E CHUAQUI (EDS.)
DISSECTING THE MOLECULAR
ANATOMY OF TISSUE
WITH 43 FIGURES, 9 IN COLOR, AND 8 TABLES
UNIVERSITATS- UND LANDES
BIBLIOTHEK DARMSTADT
BIBLIOTHE
K BIOLOGI
E
^ SPRINGER
CONTENTS
I CLINICAL ISSUES AN
D TISSUE PROCESSING 1
1 MOLECULAR PATHOLOGY LABORATORY OF THE FUTURE
CHRISTOPHE
R
A.
MOSKALU
K
3
1.1 TH
E PAST 3
1.2 TH
E PRESEN
T 4
1.3 TH
E FUTUR
E 8
1.4 A SCENARI
O OF TH
E FUTUR
E OF TISSUE DIAGNOSTICS
:
A PROSTAT
E BIOPSY FOR ASSESSMEN
T OF CARCINOM
A 10
1.4.1 CURREN
T CLINICAL PROCEDURE
S 10
1.4.2 FUTUR
E CLINICAL PROCEDURE
S 11
1.5 SUMMAR
Y 14
REFERENCES 14
2 CLINICAL UTILITIES OF MICRODISSECTED SAMPLES
ISSAC
YI
KIM
, DAVI
D
K.
ORNSTEI
N
17
2.1 INTRODUCTIO
N 17
2.2 CURREN
T CLINICAL USES 17
2.2.1 DIAGNOSI
S 17
2.2.2 PROGNOSI
S ' 18
2.2.3 CYTOLOGY 19
2.2.4 DETECTIO
N OF VIRAL DNA 19
2.2.5 ASSESSMEN
T OF GENE COPY NUMBER
S 20
2.2.6 ANALYSIS OF CELL CYCLE PARAMETER
S 21
2.2.7 SLIDE CONTAMINATIO
N . . . . 22
2.3 FUTUR
E CLINICAL USES: ANALYSIS OF CELLULAR PROTEIN
S 22
2.4 CONCLUSION
S 23
REFERENCES 23
X CONTENTS
3 TISSUE PROCESSING
GALLYA GANNOT
, JOH
N
W.
GILLESPI
E
27
3.1 INTRODUCTIO
N
-C 27
3.2
-A
CLINICAL ASPECTS 28
3.3 \ SAMPLE ACQUISITIO
N AN
D INITIA
L TISSUE HANDLIN
G 28
3.4 \ TISSUE FIXATION AN
D SNAP-FREEZIN
G 29
3.5 \TISSUE EMBEDDIN
G 33
3.6 EVALUATION OF NEW METHOD
S FOR HANDLIN
G CLINICAL TISSUE
SPECIMENS
: PROSTAT
E CANCER AS A
N EXAMPLE OF TISSUE HANDLIN
G
FOR MOLECULAR ANALYSIS 34
3.6.1 NEW METHOD
S OF FIXATION/EMBEDDIN
G 34
3.6.2 NONFORMALI
N TISSUE FIXATIO
N 35
3.6.3 COMPARISO
N OF HISTOLOG
Y AN
D RECOVERY OF DNA, RNA,
AN
D PROTEIN
S 36
3.7 CONCLUSION
S AN
D FUTUR
E DIRECTION
S 40
REFERENCES 41
4 SAMPLE MANAGEMENT AND TRACKING
G.
STEVE
N BOVA
43
4.1 INTRODUCTIO
N . 43
4.2 TH
E TISSUE MICRODISSECTIO
N CORE LABORATORY
:
ORGANIZATIO
N AN
D BASIC DATA MANAGEMEN
T 43
4.3 INTEGRATE
D DATA MANAGEMEN
T FOR TH
E TISSUE-ORIENTE
D
BIOLOGICAL RESEARCH: THE LABMATRI
X SYSTEM 46
4.3.1 LABMATRI
X PRIMAR
Y MODULES 48
4.3.1.1 STUDY SUBJECTS 48
4.3.1.2 BIOMATERIALS 49
4.3.1.3 PROTOCOL
S 49
4.3.1.4 WORKFLOW-BASED DATA REVIEW:
FUNCTIONA
L GENOMI
C STATUS SUMMARIZATIO
N METHO
D 50
4.3.1.5 SCIENTIFIC QUER
Y BUILDER 50
4.3.1.6 EQUIPMEN
T AN
D SUPPLIES/CONTACTS" 51
4.3.1.7 IMAGES/CONFIGURATIO
N TOOLS 51
4.3.1.8 LABORATOR
Y ADMINISTRATO
R 51
4.3.2 ADDITIONA
L FEATURES OF LABMATRI
X PROTOTYP
E 52
4.3.2.1 INTERNA
L PROPRIETAR
Y AN
D PUBLIC REFERENCE DATABASE
S
AN
D COLLABORATIO
N FEATURES 52
4.3.2.2 DATA SECURIT
Y FEATURES AN
D REGULATORY COMPLIANC
E 52
4.3.2.3 INTEGRATIO
N WIT
H OTHE
R SCIENTIFIC TOOLS AN
D TECHNOLOGY 52
CONTENTS XI
II METHODS OF TISSUE MICROANALYSIS 55
5 TISSU
E MICROARRAY
S
STEPHE
N
M.
HEWIT
T
57
5.1 INTRODUCTIO
N 57
5.2 CONSTRUCTIO
N OF TISSUE MICROARRAY
S 57
5.3 TISSUE MICROARRAY
S AS A VALIDATION TOOL 58
5.4 IMMUNOHISTOCHEMISTR
Y AN
D TISSUE MICROARRAY
S 60
5.5 IN SITU HYBRIDIZATIO
N AN
D TISSUE MICROARRAY
S 63
5.6 IMAGE CAPTUR
E AN
D DATA ANALYSIS 64
REFERENCES . . . ? 66
III MOLECULAR ANALYSIS OF MICODISSECTED SAMPLES 67
6 METHOD
S OF MICRODISSECTIO
N AN
D NEW TECHNOLOGIE
S
MICHAE
L
A.
TANGREA
, JOH
N
W.
GILLESPIE
,
MICHAE
L
J.
FLAIG
, GALLYA GANNOT
, VLADIMI
R KNEZEVIC
,
MICHAE
L
R.
EMMERT-BUCK
, RODRIG
O
F.
CHUAQU
I
69
6.1 HISTORICA
L PERSPECTIVE 69
6.2 LASER-BASED DISSECTIO
N TECHNOLOGIES 71
6.2.1 LASER CAPTUR
E MICRODISSECTIO
N 71
6.2.2 PALM LASER MICRODISSECTIO
N
AN
D PRESSUR
E CATAPULTIN
G TECHNOLOGY 73
6.2.3 LEICA AS LMD 74
6.3 NOVEL TECHNIQUES 74
6.4 EXPRESSIO
N MICRODISSECTIO
N 75
6.4.1 FUTUR
E DIRECTION
S OF EXPRESSIO
N MICRODISSECTIO
N 81
6.5 LAYERED EXPRESSIO
N SCANNIN
G 84
6.5.1 OPE
N LAYERED EXPRESSIO
N SCANNIN
G SYSTEM 86
6.5.1.1 MULTIPLE NORTHER
N BLOTS 87
6.5.1.2 MULTIPLEX-IMMUNOBLOT
S : . 89
6.5.2 CLOSED LAYERED EXPRESSIO
N SCANNIN
G SYSTEM 90
6.5.3 OTHE
R PLATFORMS FOR TH
E LAYERED EXPRESSIO
N
SCANNIN
G TECHNIQUE 92
6.5.4 FUTUR
E DIRECTION
S 94
6.6 CONCLUSIO
N 96
REFERENCES 97
XII CONTENTS
7 STANDARD DIAGNOSTIC TECHNIQUES
SERGI
O GONZALE
Z
101
7.1 INTRODUCTIO
N 101
7.2 DIAGNOSTI
C HISTOPATHOLOG
Y 102
7.3 IMMUNOHISTOCHEMISTR
Y , 102
7.4 IN SITU HYBRIDIZATIO
N AN
D PCR-IN SIT
U HYBRIDIZATIO
N 107
7.5 MICRODISSECTIO
N 108
7.6 CLOSING REMARK
S 109
REFERENCES 109
8
DNA APPLICATIONS
PABL
O URIBE
, IGNACI
O
I.
WISTUB
A
IL
L
8.1 INTRODUCTIO
N IL
L
8.2 DNA EXTRACTIO
N , 112
8.3 DNA PCR AMPLIFICATION -11
2
8.4 MICROSATELLITE ANALYSIS 113
8.5 MUTATIO
N ANALYSIS 114
8.5.1 SINGLE-STRAN
D CONFORMATIO
N POLYMORPHIS
M 114
8.5.2 RESTRICTIO
N FRAGMEN
T LENGTH POLYMORPHIS
M 115
8.6 GENE METHYLATION ANALYSIS 116
8.7 CLONALITY ANALYSIS 117
8.7.1 OVERVIEW 117
8.7.2 MICROSATELLITE ANALYSIS . . . 118
8.7.3 GENE MUTATION
S 118
8.7.4 X-CHROMOSPM
E INACTIVATIO
N 118
8.7.5 GENOTYPIN
G ASSAY OF TH
E D310 REPEAT 120
8.8 SUMMAR
Y 120
REFERENCES 121
9 MRNA APPLICATIONS
FATI
H OZSOLAK
, VERONIC
A LUZZI
, MAR
K
A.
WATSO
N
125
9.1 INTRODUCTIO
N 125
9.2 TISSUE SELECTION FOR GENE EXPRESSIO
N ANALYSIS 126
9.3 RNA ISOLATIO
N 127
9.3.1 OVERVIEW 127
9.3.2 EXPECTED RESULTS 129
9.3.3 TROUBLESHOOTIN
G 130
9.4 TRANSCRIP
T AMPLIFICATION 131
9.4.1 OVERVIEW 131
9.4.2 EXPECTED RESULTS 132
CONTENTS XIII
9.4.3 TROUBLESHOOTIN
G 133
9.5 RT-PCR VALIDATION 135
9.5.1 OVERVIEW 135
9.5.2 PCR ASSAY DESIGN 135
9.5.3 QUANTIFICATIO
N 137
9.5.4 NORMALIZATIO
N CONTROL
S 138
9.5.5 EXPECTED RESULTS 140
9.5.6 TROUBLESHOOTIN
G 141
REFERENCES 143
10 PROTEOMIC APPLICATIONS
DAVI
D
H.
GEHO
, LANC
E
A.
LIOTTA
, EMANUE
L
F.
PETRICOI
N
. 145
10.1 INTRODUCTIO
N 145
10.2 LASER CAPTUR
E MICRODISSECTIO
N 148
10.3 PROTEI
N MICROARRAYS^ 149
10.4 MASS SPECTROMETR
Y IN TISSUE PROTEOMIC
S 153
10.5 CONCLUSION
S 157
REFERENCES 158
11 PROTOCOLS FOR TISSUE HANDLING AND MOLECULAR ANALYSIS
163
11.1 TISSUE PREPARATIO
N FOR PROSTAT
E PREPARE
D AS WHOLE-MOUN
T .
. 163
11.1.1 70% ETHANO
L FIXATION 163
11.1.2 EMBEDDIN
G 164
11.1.2.1 LOW-MELT POLYESTER EMBEDDIN
G " I. 164
11.1.2.2 PARAFFIN EMBEDDING
' 165
11.2 SLIDE PREPARATIO
N FOR MICRODISSECTIO
N
T
O PERFORM SUBSEQUEN
T DNA, RNA, AN
D PROTEI
N ANALYSIS .
. 166
11.2.1 SLIDE PREPARATIO
N FOR LASER CAPTUR
E MICRODISSECTIO
N 166
11.2.1.1 PARAFFIN-EMBEDDE
D SECTION
S AN
D FROZEN SECTIONS 167
11.2.1.2 LOW-MELT POLYESTER-EMBEDDE
D SECTION
S 167
11.2.2 SLIDE PREPARATIO
N FOR MANUA
L MICRODISSECTIO
N 168
11.2.2.1 PARAFFIN-EMBEDDE
D SECTION
S AN
D FROZEN SECTION
S 169
11.2.2.2 LOW-MELT POLYESTER-EMBEDDE
D SECTIONS 170
11.3 TECHNIQUES OF MICRODISSECTIO
N 170
11.3.1 LASER CAPTUR
E MICRODISSECTIO
N 170
11.3.2 IMMUNO-LASE
R CAPTUR
E MICRODISSECTIO
N 171
11.3.3 MANUA
L MICRODISSECTIO
N 172
11.4 PROCESSIN
G OF MICRODISSECTE
D TISSU
E FOR MOLECULAR ANALYSIS . . 173
11.4.1 DNA-BASED STUDIES 173
11.4.1.1 PROTOCO
L FROM PATHOGENETIC
S UNIT 173
11.4.1.2 DNA EXTRACTIO
N (PROTOCO
L FROM WISTUBA
) 175
XIV CONTENTS
11.4.2 RNA ISOLATIO
N 175
11.4.2.1 ISOLATIO
N OF TOTAL RNA FROM FROZEN MICRODISSECTE
D TISSUE .
. 175
11.4.2.2 PROTOCO
L FOR ISOLATIO
N OF RNA FROM FROZEN LCM TISSUE
(PROTOCO
L FROM WATSON) 177
11.4.2.3 PROTOCO
L FOR ISOLATIO
N OF RNA FROM FORMALIN-FIXED
,
PARAFFIN-EMBEDDE
D LCM TISSUE (PROTOCO
L FROM WATSON
) .
. 179
11.4.3 PROTEIN-BASE
D STUDIES 180
11.4.3.1 SAMPLE PREPARATIO
N FOR 2-D PAGE 180
11.4.3.2 IMMUNOBLO
T 181
11.5 DNA, RNA, AN
D PROTEI
N ANALYSIS 182
11.5.1 DNA ANALYSIS 182
11.5.1.1 CLONALITY
: X-CHROMOSOM
E INACTIVATIO
N 182
11.5.1.2 LOSS OF HETEROZYGOSIT
Y 185
11.5.1.3 DNA PCR AMPLIFICATION (PROTOCO
L FROM WISTUBA
) 190
11.5.1.4 ANALYSIS OF MICROSATELLITE MARKER
S (PROTOCO
L FROM WISTUBA
) . . 191
11.5.1.5 SINGLE-STRAN
D CONFORMATIONA
L POLYMORPHIS
M
J
(PROTOCO
L FROM WISTUBA
) 192
11.5.1.6 RESTRICTE
D FRAGMEN
T LENGTH POLYMORPHIS
M
(PROTOCO
L FROM WISTUBA
) 192
11.5.1.7 GENE METHYLATIO
N ANALYSIS (PROTOCO
L FROM WISTUBA
) 193
11.5.1.8 GENOTYPIN
G ASSAY OF TH
E D310 REPEAT
(PROTOCO
L FROM WISTUBA
) 193
11.5.1.9 IN SITU HYBRIDIZATIO
N PROTOCO
L FOR CYTOMEGALOVIRU
S
(PROTOCO
L FROM GONZALEZ) 194
11.5.2 RNA ANALYSIS 195
11.5.2.1 GENE-SPECIFIC RT-PCR 195
11.5.2.2 TARGETED DIFFERENTIAL DISPLAY 197
11.5.2.3 NONLSOTOPI
C IN SITU HYBRIDIZATIO
N PROTOCO
L
FOR MRNA DETECTIO
N (PROTOCOL FROM GONZALEZ) 201
11.5.2.4 PROTOCO
L FOR TRANSCRIP
T AMPLIFICATION (PROTOCO
L FROM WATSON) 202
11.5.2.5 PROTOCO
L FOR RT-PCR VALIDATION (PROTOCO
L FROM WATSON
) .
. 206
11.5.3 PROTEI
N ANALYSIS 209
11.5.3.1 2-D POLYACRYLAMID
E GEL ELECTROPHORESI
S 209
11.5.3.2 IMMUNOBLO
T 214
11.5.3.3 IMMUNOHISTOCHEMISTR
Y 216
11.6 LEGAL ISSUES
, INFORME
D CONSEN
T 220
SUBJECT INDEX
221
COLOR ILLUSTRATIONS
225 |
| any_adam_object | 1 |
| any_adam_object_boolean | 1 |
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| bvnumber | BV022447832 |
| classification_rvk | XG 2103 |
| collection | ZDB-2-SBL |
| ctrlnum | (OCoLC)873420509 (DE-599)BVBBV022447832 |
| discipline | Medizin |
| discipline_str_mv | Medizin |
| doi_str_mv | 10.1007/b137665 |
| format | Electronic eBook |
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| id | DE-604.BV022447832 |
| illustrated | Not Illustrated |
| index_date | 2024-07-02T17:35:14Z |
| indexdate | 2024-09-07T00:11:28Z |
| institution | BVB |
| isbn | 3540220062 9783540220060 9783540264828 |
| language | English |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-015655773 |
| oclc_num | 873420509 |
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| series2 | Principles and practice |
| spelling | Dissecting the molecular anatomy of tissue with ... 8 tables Michael R. Emmert-Buck ... (ed.) Berlin [u.a.] Springer 2005 1 Online-Ressource txt rdacontent c rdamedia cr rdacarrier Principles and practice Literaturangaben Gewebe (DE-588)4020840-0 gnd rswk-swf Molekulare Diagnostik (DE-588)4589005-5 gnd rswk-swf Dissektion (DE-588)4303104-3 gnd rswk-swf Krebsforschung (DE-588)4165564-3 gnd rswk-swf (DE-588)4143413-4 Aufsatzsammlung gnd-content Krebsforschung (DE-588)4165564-3 s Molekulare Diagnostik (DE-588)4589005-5 s DE-604 Gewebe (DE-588)4020840-0 s Dissektion (DE-588)4303104-3 s Emmert-Buck, Michael R. Sonstige oth https://doi.org/10.1007/b137665 Verlag Volltext DNB Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=015655773&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Dissecting the molecular anatomy of tissue with ... 8 tables Gewebe (DE-588)4020840-0 gnd Molekulare Diagnostik (DE-588)4589005-5 gnd Dissektion (DE-588)4303104-3 gnd Krebsforschung (DE-588)4165564-3 gnd |
| subject_GND | (DE-588)4020840-0 (DE-588)4589005-5 (DE-588)4303104-3 (DE-588)4165564-3 (DE-588)4143413-4 |
| title | Dissecting the molecular anatomy of tissue with ... 8 tables |
| title_auth | Dissecting the molecular anatomy of tissue with ... 8 tables |
| title_exact_search | Dissecting the molecular anatomy of tissue with ... 8 tables |
| title_exact_search_txtP | Dissecting the molecular anatomy of tissue with ... 8 tables |
| title_full | Dissecting the molecular anatomy of tissue with ... 8 tables Michael R. Emmert-Buck ... (ed.) |
| title_fullStr | Dissecting the molecular anatomy of tissue with ... 8 tables Michael R. Emmert-Buck ... (ed.) |
| title_full_unstemmed | Dissecting the molecular anatomy of tissue with ... 8 tables Michael R. Emmert-Buck ... (ed.) |
| title_short | Dissecting the molecular anatomy of tissue |
| title_sort | dissecting the molecular anatomy of tissue with 8 tables |
| title_sub | with ... 8 tables |
| topic | Gewebe (DE-588)4020840-0 gnd Molekulare Diagnostik (DE-588)4589005-5 gnd Dissektion (DE-588)4303104-3 gnd Krebsforschung (DE-588)4165564-3 gnd |
| topic_facet | Gewebe Molekulare Diagnostik Dissektion Krebsforschung Aufsatzsammlung |
| url | https://doi.org/10.1007/b137665 http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=015655773&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| work_keys_str_mv | AT emmertbuckmichaelr dissectingthemolecularanatomyoftissuewith8tables |