The zebrafish: [Part C] Genetics, genomics and informatics
Gespeichert in:
| Format: | Buch |
|---|---|
| Sprache: | English |
| Veröffentlicht: |
San Diego [u.a.]
Acad. Press
2011
|
| Ausgabe: | 3. ed. |
| Schriftenreihe: | Methods in cell biology
104 |
| Online-Zugang: | Inhaltsverzeichnis |
| Beschreibung: | XX, 504 S., [16] Bl. Ill., graph. Darst. |
| ISBN: | 9780123748140 |
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| 245 | 1 | 0 | |a The zebrafish |n [Part C] |p Genetics, genomics and informatics |c ed. by H. William Detrich ... |
| 250 | |a 3. ed. | ||
| 264 | 1 | |a San Diego [u.a.] |b Acad. Press |c 2011 | |
| 300 | |a XX, 504 S., [16] Bl. |b Ill., graph. Darst. | ||
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Datensatz im Suchindex
| _version_ | 1804148585866985472 |
|---|---|
| adam_text | CONTENTS
Contributors
xiii
Preface
xix
Part
1.
Forward and Reverse Genetics
1.
Generating Conditional Mutations in Zebrafish Using Gene-trap Mutagenesis
3
Lisette
A. Maddison, Jianjun
Lu,
and Wenbiao Chen
I. Introduction
4
II. Rationale for Conditional Mutations
4
III. Rationale for Gene-trap Mutagenesis to Generate Conditional Mutations
S
IV. Rationale for Vector Design
5
V. Methods
7
VI. Discussion
19
VII.
Summary
20
Acknowledgments
20
References
21
2.
То/2
-mediated
Transgenesis, Gene
Trapping, Enhancer Trapping, and the
GaM-UAS System
23
Getnbu Abe, Maximilimno
L.
Suster,
and Koichi Kawakami
I. Introduction
24
II.
Transgenesis
by Using the Tol2 Transposable Element
26
Ш.
Γσ/2
-mediated
ВАС
Transgenesis
ЗО
IV. Gene Trapping and Enhancer Trapping with the Tol2 Transposon System
36
V. Gene Trapping and Enhancer Trapping with the GaMFF-UAS System
42
Acknowledgments
47
References
47
Contents
3. Engineering
Zinc
Finger Nucleases
for Targeted
Mutagenesis
of
Zebrafìsh
5
і
Jęffry
D.
Sander,
J.-R.
Joanna
Y eh,
Randall
T.
Peterson,
and J.
Keith Joung
I. Introduction
52
II. Methods and Resources for Engineering Zinc Finger Nucleases
52
III. Choice of Method to Engineer Zinc Finger Nucleases
54
Acknowledgments
56
References
56
4.
Retroviral-mediated Insertional Mutagenesis in Zebrafish
59
Adam Amsterdam, Gaurav Kumar Varshney, and Shawn Michael Burgess
I. Introduction
60
II. Mutagenesis
62
III. Cloning the Mutated Genes
65
IV. Retroviral-mediated Insertional Mutagenesis as a Reverse Genetic Tool
73
V. Future Directions
77
Acknowledgments
79
References
79
5.
Genetic Screens for Mutations Affecting Adult Traits and Parental-effect Genes
83
Francisco Peiegri and Mary
C. Mullins
I. Introduction
84
II. Strategies for Adult Trait and Parental-effect Screens
89
HI. Selection of Lines for Genetic Screens
101
IV. Recovery and Maintenance of Adult and Parental-effect Mutations
104
V. Mapping Adult and Parental-effect Mutations
108
VI. Solutions, Materials, and Protocols
112
VII.
Conclusions
117
Acknowledgments
117
References
117
6.
High-throughput Target-selected Gene Inactivation in Zebrafish
121
Ross
N.
W. Kettleborough, Ewart
de Bruijn, Freek
van
Eeden,
Edwin Cuppen
and Derek L.
Stemple
I. Introduction
122
И.
Mutagenesis and Library Creation
122
III. PCR
and Re-sequencing of Exons
124
IV. Analysis of Resequencing Data and Retrieval of Mutations
125
References
127
Contents
vii
7.
Genetic
Suppressor Screens in Haploids
129
Xiaoying
Bai,
Zhongan Yang, Hong Jiang, Shuo Lin, and Leonard I. Zon
I. Introduction and Rationale
130
H. Methods
—
an Example of Suppressor Screen in Moonshine Mutants
130
III, Conclusions and Prospective
135
Acknowledgments
136
References
136
8.
Transgenic Zebrafish Using Transposable Elements
137
Karl]. Clark, Mark D. Urban, KimberlyJ. Skuster, and Stephen C. Ekker
I. Introduction
138
II. Requesting and Assembling Tol2 System
141
III. Microinjection
144
IV. Quality Control
145
V. Select Injected Fish to Raise as Founder Generation FO
146
VI. Production of Fl Generation
146
VII.
Select the Best Substrain(s) Based on Observation of F2 Generation
147
VIII.
Discussion
147
Acknowledgments
147
References
147
9.
Spatiotemporal
Control of Embryonic Gene Expression Using Caged Morpholinos
151
llya A. Shestopalov and James K. Chen
I. Introduction
152
II. Design and Synthesis of cMOs
154
III. Synthesis of cFD
161
IV. Microinjection of Caged Reagents
162
V. Global Photoactivation of Caged Reagents
163
VI.
Titration
of cMO Dose for Optimum Dynamic Range
165
VII.
Localized Photoactivation of Caged Reagents
167
VIII.
Conclusion
169
Acknowledgments
171
References
171
Part
2. Transgenesis
10.
Advanced Zebrafish
Transgenesis
with Tol2 and Application for Cre/lox
Recombination Experiments
175
Christian Mosimann and Leonard I. Zon
I. Introduction
176
H.
Transgene
Design, Cloning, and To/2
Transgenesis 180
Ш.
Tol2
Transgene
Genetics
185
IV. CreERT2-Controlled lox Recombination Using 4-OHT
188
Contents
V. Discussion j
92
Conflict of interest statement
192
Acknowledgments
92
References
192
11.
Use of Phage PhiC31
Integrase
as a Tool for Zebrafish Genome Manipulation
195
James A. Lister
I. Introduction
196
II. Rationale I99
III. Materials and Methods
203
IV. Discussion
203
V. Summary
205
Acknowledgments
205
References
205
12.
Method for Somatic Cell Nuclear Transfer in Zebrafish
209
Katmika Siripattarapravat and Jose B.
Ghetti
I. Methods
210
II. Materials
216
References
217
Part
3.
The Zebrafish Genome and Mapping Technologies
13.
Single Nucleotide Polymorphism
(SNP)
Panels for Rapid Positional
Cloning in Zebrafish
221
Matthew D. Clark, Victor Guryev,
Ewart de
Bruijn, Isaac J. Nijman,
Masazumi
Tada,
Catherine Wilson,
Panos
Detoukas, John H. Postlethwait,
Edwin Cuppen and Derek L.
Stemple
I. Introduction
222
II. Extraction of Zebrafish Genomic
DNA 223
ΠΙ.
Afiymetrics Molecular Inversion Probe Panel
225
IV. Suggested Mapping Strategy
233
V. General Considerations
233
References
234
14.
Molecular Cytogenetic Methodologies and
а ВАС
Probe Panel Resource for
Genomic Analyses in the Zebrafish
237
Kimberly P. Dobrinski, Kim H. Brown, Jennifer L. Freeman and Charles Lee
I. Introduction
238
II. Cytogenetic Methods
240
ΠΙ.
Application of Cytogenetic Methods in Zebrafish Studies
247
IV. Methods for Array CGH
250
V. Application of Array CGH in Zebrafish Studies
254
VI. Summary
256
Acknowledgments
256
References
256
Contents
15.
Conserved Synteny and the Zebrafish Genome
259
Julian M.
Catchen, Ingo
Braasch and John H, Postlethwait
I. Introduction
260
П.
Rationale: Gene Duplication and Orthology Assignments
260
III. Methods
264
IV. Using the Synteny Database: A Case Study of Nerve Growth
Factor Receptors
272
V. Zebrafish, Conserved Syntenies, and the Teleost Genome Duplication
279
VI. Summary
280
Acknowledgments
281
References
281
16.
The
Zon
Laboratory Guide to Positional Cloning in Zebrafish
287
Yi Zhou and Leonard I. Zon
I. Introduction
288
II. Mapping Strains
289
III. Families and Genetic Markers
290
IV. Crosses for Line Maintenance and Mapping
291
V. Preparation of the
DNA 295
VI. Mapping Genes
296
VII.
General Flow
ofinformation
from the Zebrafish
Genome Sequence Assemblies
303
VIII.
Synteny between Human, Zebrafish,
Fugu,
and Tetraodon Genomes
304
IX. Proving a Candidate Gene is Responsible for the Mutant Phenotype
306
X. Morpholinos
307
XI. Future Technologies
307
References
308
Part
4.
Informatics and Comparative Genomics
17.
Data Extraction, Transformation, and Dissemination through ZFIN
313
Douglas G. Howe, Ken Frazer, David Fashena, Leyla Ruzicka, Yvonne Bradford,
Sridhar Ramachandran, Barbara J. Ruef,
Ceri
Van Slyke, Amy Singer and Monte Westerfield
I. Introduction
314
II. Extracting Data and Data How
314
III. Ensuring Accurate and Rapid Data Dissemination
319
IV. Submitting Data Directly to ZFIN
322
V. Conclusions
324
Acknowledgments
324
References
325
Contents
18. DNA Methylation
Profiling
in Zebrafish 327
Sltan-Fu Wu,
Haiying Zhang,
Saher
Sue
Hammoud, Magdalena
Potok,
Dam
d
Λ.
Six,
David A.Jones and
Bradky
R.
Caims
I. Introduction
328
II.
Rationale 332
III. Methods
332
VI. Discussion
336
Acknowledgments
336
References
337
19.
Chromatín Immunoprecípitation
in Adult Zebrafish Red Cells
341
Eirini Trotnpouki, Teresa
Venezia
Bowman, Anthony DiBiase, Yi Zhou and Leonard I. Zon
I. Introduction
342
И.
Adult Zebrafish Exsanguination
343
III.
Chromatín
Immunoprecipitation (Lee
et a/.,
2006) 343
IV. ChlP-seq Sample Preparation (Guenther
et aí.,
2008) 347
V. ChlP-seq Data Analysis
347
VI. Summary and Conclusions
348
VII.
Online tools
349
VIII.
Conflicts of Interest
350
Acknowledgments
350
References
350
20.
Discerning Different In vivo Roles of MicroRNAs by
Experimental Approaches in Zebrafish
353
Luke
Pase
and Graham J. Lieschke
I. Introduction
354
II. Using Zebrafish to Study the Function of miRNAS
366
III. Summary
373
Acknowledgments
374
References
374
21.
Sequencing-based Expression Profiling in Zebrafish
379
Jin Liang, Gabriel
Renaud
and Shawn M. Burgess
I. Introduction
380
II. Digital Gene Expression
382
III. Potential Issues in DGE
395
Acknowledgments
397
References
398
Contents
22. Chromatin
Modification
in Zebrafish Development 401
Jordi
Cayuso Mas, Emily
S. Noël
and
Elke
Α.
Ober
I. Chromatin Modifications
402
II. Chromatin Modifications in Development
408
Ш.
Functions of Chromatin Modifications inTissue Regeneration
421
IV. Outlook
422
Acknowledgments
423
References
423
Part
5.
Infrastructure
23.
Advances in Zebrafish Husbandry and Management
431
Christian Lawrence
I. Introduction
432
II. Breeding
432
Ш.
Larviculture
436
IV.
Aquaculture
Systems
439
V. Nutrition
440
VI. Health Management
442
VII.
Genetic Management
444
VIII.
Regulatory Compliance
445
IX. Education and Training
447
X. Summary
448
References
448
24.
Aquaculture
and Husbandry at the Zebrafish International Resource Center
453
Zoltán
M.
Varga
I. Introduction
454
И.
Methods
455
Ш.
Materials
475
Acknowledgments
477
References
477
Index
479
Volumes in Series
495
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| indexdate | 2024-07-10T00:09:29Z |
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| isbn | 9780123748140 |
| language | English |
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| spelling | The zebrafish [Part C] Genetics, genomics and informatics ed. by H. William Detrich ... 3. ed. San Diego [u.a.] Acad. Press 2011 XX, 504 S., [16] Bl. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Methods in cell biology 104 Methods in cell biology ... Detrich, H. William Sonstige (DE-588)1013514475 oth (DE-604)BV012446816 3 Methods in cell biology 104 (DE-604)BV002534878 104 Digitalisierung UB Regensburg application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=024559336&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | The zebrafish Methods in cell biology |
| title | The zebrafish |
| title_auth | The zebrafish |
| title_exact_search | The zebrafish |
| title_full | The zebrafish [Part C] Genetics, genomics and informatics ed. by H. William Detrich ... |
| title_fullStr | The zebrafish [Part C] Genetics, genomics and informatics ed. by H. William Detrich ... |
| title_full_unstemmed | The zebrafish [Part C] Genetics, genomics and informatics ed. by H. William Detrich ... |
| title_short | The zebrafish |
| title_sort | the zebrafish genetics genomics and informatics |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=024559336&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
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