Mouse Genetics and Transgenics A Practical Approach

, by Jackson, Ian J.; Abbott, Catherine M.

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ISBN: 9780199637089 | 0199637083
Cover: Paperback
Copyright: 3/9/2000

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A unique book that integrates knowledge from a wide range of expertise, specifically applied to the mouse, and addressed at a wide audience from those new to the field to experts who want an update on the state of the art. Mouse Genetics and Transgenics: APA covers all aspects of using themouse as a genetic model organism: care and husbandry; archiving stocks as frozen embryos or sperm; making new mutations by chemical mutagenesis; transgenesis; and gene targetting; mapping mutations and polygenic traits by cytogenetic, genetic, and physical means; and disseminating and researchinginformation via the Internet.

List of Contributors

xxi

Abbreviations

xxiii

Mouse care and husbandry

(26)

Colin M. Hetherington

Brendan Doe

Donald Hay

Introduction

(1)

Housing

(7)

Types of facilities

(1)

Conventional accommodation

(1)

Barrier accommodation or specified pathogen free

(1)

Germ-free (axenic) and gnotobiotic accommodation

(1)

Maintenance of pathogen-free animals

(1)

Breeding performance and production

(1)

Interpretation of data

(1)

Collaborative experiments

(1)

Health screening

(1)

Quarantine

(1)

Flexible film isolators

(1)

Individually ventilated cage (IVC) racks

(1)

Fumigation

(3)

Husbandry

(3)

Caging

(1)

Bedding

(1)

Diet

(1)

Water

(1)

Environmental control

(1)

Environmental enhancement

(1)

Animal identification

(5)

Ear punch

(1)

Toe clip

(1)

Ear tags

(1)

Tail and paw tattooing

(3)

Electronic tags

(2)

Record keeping

(1)

Breeding systems

(4)

Timed mating

(1)

Pseudopregnancy and vasectomy

(1)

Superovulation

(1)

Rederivation

(4)

Euthanasia

(1)

Transportation

(1)

Legislation

(3)

Acknowledgements

(1)

References

(1)

Further reading

(2)

Cryopreservation and rederivation of embryos and gametes

(34)

Peter H. Glenister

William F. Rall

Introduction

(1)

Proliferation of mouse models

(2)

Long-term maintenance of mouse models

(1)

Cryopreservation and banking of mouse germplasm: resources for future research

(1)

Principles of cryopreservation

(4)

Controlled freezing

(2)

Vitrification

(1)

Skills required for embryo and gamete cryopreservation

(1)

Special equipment required for cryopreservation

(1)

Cryopreservation and recovery of mouse embryos

(12)

Source of embryos and preferred developmental stages

(1)

Freezing embryos using propylene glycol as cryoprotectant

(3)

Recovery of embryos and live mice from embryos frozen according to Protocol 2

(1)

Freezing embryos using glycerol as cryoprotectant

(2)

Vitrification of embryos in vitrification solution VS3a

(2)

Recovery of embryos and live mice from embryos cryopreserved according to Protocols 4 and 5

(2)

Cryopreservation and recovery of mouse gametes

(7)

Cryopreservation of mouse metaphase II oocytes

(1)

Recovery of oocytes frozen using Protocol 7

(1)

Cryopreservation of mouse sperm

(2)

In vitro fertilization of mouse oocytes

(2)

Hints and tips

(2)

Embryo cryopreservation

(1)

Sperm cryopreservation and in vitro fertilization

(1)

Long-term storage of embryos and gametes

(2)

Expected overall survival of cryopreserved embryos and gametes

(2)

Genetic resource banks

(4)

Acknowledgements

(1)

References

(3)

Spatial analysis of gene expression

(26)

Stefan G. Nonchev

Mark K. Maconochie

Introduction

(1)

Dissection of post-implantation embryos

(1)

Whole-mount non-radioactive in situ hybridization

(9)

Precautions for RNA work

(1)

Theory of in situ hybridization

(1)

Generation of riboprobe

(2)

Fixation and pre-treatment of embryos

(1)

Hybridization and removal of non-specific hybrids

(1)

Immunodetection of signals

(2)

Troubleshooting

(1)

Reporter transgenes

(5)

General considerations

(1)

Introduction and uses of reporter genes

(1)

Detection of β-galactosidase activity

(1)

Detection of alkaline phosphatase activity

(1)

Use of the green fluorescent protein (GFP) in transgenesis

(2)

Multiple and combined detection systems

(6)

Whole-mount staining of early (8.0--12.5 dpc) embryos

(1)

Multiple detection on cryostat and paraffin sections

(5)

Whole-mount skeletal analysis

(4)

Acknowledgements

(1)

References

(2)

Mapping phenotypic trait loci

(34)

Benjamin A. Taylor

Introduction

(1)

Rationale for mapping

(1)

Genetic definition of trait locus

(1)

Identification of candidate genes

(1)

Genetic manipulation

(1)

Background information for mapping phenotypic trait loci of the mouse

(1)

Definitions

(1)

Mouse genome

(1)

Mapping basics

(1)

A backcross mapping experiment: a model for simple mapping experiments

(11)

Identifying the phenotypic variant

(1)

Choosing a tester strain

(2)

Mating mutant and tester stock to produce F1 progeny

(1)

Producing backcross progeny

(1)

Classifying progeny for the target locus

(1)

Extracting a DNA sample

(1)

A linkage testing plan

(2)

Genotyping a subset of backcross progeny for selected markers

(1)

Recording data

(1)

Scanning data for linkage

(1)

Finding markers that flank the target

(1)

Finding closer markers

(1)

Analysing the complete data set to determine gene order and distance

(1)

Reporting linkage data

(1)

Size of cross

(1)

Markers for fine mapping

100

(1)

Incomplete penetrance, phenocopies and reduced viability

100

(1)

Mapping by intercross

101

(1)

QTL mapping, including the use of derivitive strains

102

(10)

General nature of QTL mapping

102

(1)

QTL mapping using strain crosses

103

(1)

Strain selection

103

(1)

Backcross versus intercross

103

(1)

Number of progeny

104

(1)

Marker spacing

104

(1)

Selective genotyping

105

(1)

Significance thresholds

106

(1)

Confidence intervals

107

(1)

Fine mapping QTLs

107

(1)

Selective phenotyping

107

(1)

Progeny testing

108

(1)

Congenic strain construction

108

(1)

Advanced intercross populations

108

(1)

Derivative inbred strains for QTL mapping

109

(1)

Recombinant inbred strains

109

(2)

Congenic strains

111

(1)

Recombinant congenic strains

111

(1)

Consomic strains

112

(1)

Markers

112

(2)

DNA pooling

114

(7)

Acknowledgements

118

(1)

References

118

(3)

Mapping genomes

121

(22)

Paul Denny

Stephen D. M. Brown

Introduction

121

(1)

Applications of genetic and physical mapping

122

(2)

Genetic mapping

124

(7)

Types of genetic marker

124

(1)

Genotyping using silver-staining of SSCP gels

124

(2)

Genotyping using fluorescently-labelled dCTP incorporation into PCR products from SSLP markers, for analysis on ABI sequencers

126

(2)

Linking different maps together

128

(1)

Generating new genetic markers in specific genomic regions

129

(2)

Criteria for making the decision to construct physical maps

131

(1)

Physical mapping

131

(12)

Introduction to physical mapping

131

(1)

Primary contig generation

132

(2)

Clone identification using hybridization assay

134

(2)

Chromosome walking/gap filling

136

(1)

Isolating insert end sequences

136

(2)

Validation of clone contigs

138

(2)

Acknowledgements

140

(1)

References

140

(3)

Mouse cytogenetics and FISH

143

(1)

Introduction

143

(1)

Analysing mouse chromosomal rearrangements with G-banded chromosomes

144

(10)

Ellen C. Akeson

Muriel T. Davisson

Introduction

144

(1)

Metaphase chromosomes

144

(4)

Stimulation of peripheral mouse lymphyocytes by phytohaemagglutinin and lipopolysaccharide

148

(1)

Phytohaemagglutinin

148

(1)

Lipopolysaccharide

149

(1)

G-bands

149

(2)

Identifying and karyotyping mouse chromosomes

151

(1)

Recognizing aberrant chromosomes

152

(2)

Acknowledgement

153

(1)

References

153

(1)

Fluorescent in situ hybridization (FISH) to mouse chromosomes

154

(17)

Margaret Fox

Sue Povey

Introduction

154

(1)

FISH and chromosome identification

154

(1)

Repeat DNA

154

(1)

Mouse chromosome paints

155

(1)

P1 probes

155

(1)

Obtaining mouse chromosomes

155

(3)

Probes and labelling

158

(2)

DNA

158

(1)

Labelling by nick translation

158

(1)

Chromosome paints and direct labelling

159

(1)

FISH

160

(7)

Probe preparation

160

(2)

Hybridization

162

(5)

Analysis and microscopy

167

(4)

References

169

(2)

Electronic tools for accessing the mouse genome

171

(14)

Janan T. Eppig

Introduction

171

(1)

Databases of genomic information for the mouse

171

(4)

The Mouse Genome Database (MGD)

171

(4)

The MRC Mammalian Genetics Unit

175

(1)

Specific data sets for genetic, radiation hybrid and physical mapping

175

(3)

Genetic data

175

(1)

The Whitehead Institute/MIT map

175

(1)

EUCIB

175

(1)

Jackson Laboratory backcross

176

(1)

Copeland-Jenkins interspecific backcross

176

(1)

M. Seldin interspecific backcross

176

(1)

Radiation hybrid data

176

(1)

The Jackson Laboratory mouse radiation hybrid database

177

(1)

The EBI radiation hybrid database

177

(1)

Physical mapping data

177

(1)

Genome-wide physical map

177

(1)

X-Chromosome physical map

177

(1)

Gene expression data

178

(1)

The Gene Expression Database (GXD)

178

(1)

The mouse 3D atlas

178

(1)

Databases of transgenics, knock-outs and other induced mutations

179

(1)

The transgenic/targeted mutation database (TBASE)

179

(1)

Mouse Knockout and Mutation Database (MKMD)

179

(1)

Induced mutant resource (IMR)

179

(1)

Animal resources lists

180

(1)

International mouse strain resource (IMSR)

180

(1)

The Jackson Laboratory: JAX mice IMR, MMR, DNA resource

180

(1)

European Mouse Mutant Archive (EMMA)

181

(1)

mgi-list, an electronic bulletin board for the mouse community

181

(1)

Summary

181

(4)

References

182

(3)

Mutagenesis of the mouse germline

185

(32)

Monica J. Justice

Introduction

185

(1)

Mouse mutagenesis

185

(6)

Spontaneous mutations

185

(1)

Systems for assessing mutation rate

186

(1)

Reporter genes

186

(1)

Specific locus test

187

(1)

Dominant phenotype assays

188

(1)

Other assays

188

(1)

Developing a mouse mutant resource

188

(1)

Determining functional complexity of genomic regions

189

(1)

Human disease models

189

(1)

Allelic series

190

(1)

Unravelling biochemical or developmental pathways

190

(1)

High-efficiency mutagenesis with N-ethyl-N-nitrosourea

191

(10)

Mode of action

191

(1)

ENU: chemical properties, stability and half-life

191

(1)

Types of DNA lesion caused by ENU

191

(1)

Effects on protein products

192

(1)

Induction of mutations in the mouse germline

192

(1)

Doses and treatment protocols

192

(4)

Genetic screens to isolate mutations

196

(1)

Dominant mutations

196

(1)

Single-locus screens for recessive mutations

197

(1)

Three-generation breeding scheme for recessive mutations

197

(2)

Two-generation breeding scheme using deletions

199

(1)

Modifiers and sensitized pathways

200

(1)

Practical considerations for ENU mutagenesis

201

(8)

Breeding considerations

201

(1)

Male rotations

201

(2)

Gamete sampling for spermatogonial stem-cell mutagenesis

203

(3)

Strain background effects

206

(1)

Inbred strains to use for mutagenesis

206

(1)

F1 hybrids

207

(1)

Other observations

208

(1)

Rate of recovery to fertility

208

(1)

Mutation rates for different loci

208

(1)

Cancer susceptibility and lifespan

208

(1)

Other mutagens

209

(2)

Radiation mutagenesis

209

(1)

X-rays: treatment and mutations recovered

209

(1)

Other types of radiation

210

(1)

Chlorambucil

210

(1)

Future prospects

211

(6)

DNA repair

211

(1)

Sequence-based screening for lesions

211

(1)

The future of mutagenesis

211

(1)

References

212

(5)

Generation of transgenic mice from plasmids, BACs and YACs

217

(30)

Annette Hammes

Andreas Schedl

Introduction

217

(4)

Principles and general considerations

217

(1)

Difficulties and limitations

218

(1)

Construct design

219

(1)

Perspectives

220

(1)

Factors influencing the efficiency of transgenesis

220

(1)

Choice of mouse strains

221

(1)

DNA isolation

221

(7)

Plasmid DNA

221

(2)

YAC DNA

223

(3)

BAC DNA

226

(1)

Testing the DNA concentration and quality

227

(1)

The microinjection set-up

228

(4)

Location and design of the injection table

229

(1)

Microscope

230

(1)

Micromanipulators

230

(1)

The holding pipette

231

(1)

Microinjection needles

231

(1)

The microinjection experiment

232

(8)

Superovulation and isolation of fertilized oocytes

232

(2)

Microinjections

234

(1)

Timing of injections

234

(1)

Injections

234

(2)

Oviduct transfer

236

(1)

Pseudopregnant females

236

(1)

Preparation of the transfer pipette

237

(1)

Oviduct transfer

238

(2)

Analysis of transgenic founders

240

(7)

Tail tipping and ear punching

243

(1)

Isolation of genomic DNA from tail biopsies

243

(2)

Southern blot analysis

245

(1)

References

245

(2)

Directed mutagenesis in embryonic stem cells

247

(38)

Antonius Plagge

Gavin Kelsey

Nicholas D. Allen

Introduction

247

(2)

Basic elements of construct design

249

(5)

Replacement versus insertion

249

(1)

Regions of homology

250

(1)

The mutation

251

(1)

Components of the targeting cassette

251

(1)

Enrichment for targeted events

252

(1)

Screening strategies

253

(1)

Alternative approaches for construct design

254

(1)

The use of site-specific recombinases in targeting

254

(9)

Excision of heterologous DNA from a targeted locus

255

(1)

Excision from ES-cell clones with recombinase expression plasmids

256

(1)

Excision in mice using transgenic mice expressing recombinase

257

(1)

Oocyte microinjection of recombinase

257

(1)

Use of recombinases to generate conditional somatic knock-outs

257

(1)

Spatially restricted knock-outs using tissue specific promoters to drive recombinase expression

258

(1)

Temporally regulated knock-outs using inducible recombinases

259

(3)

Knocking-in: recombinase mediated integration into chromosomally positioned target sites

262

(1)

Subtle mutations without site-specific recombinases

263

(2)

Double replacement

264

(1)

`Hit-and-run'

265

(1)

Chromosome engineering in ES cells

265

(3)

Deletions, inversions and duplications

265

(3)

Translocations

268

(1)

Generating, analysing and maintaining knock-out mice

268

(17)

ES-cell culture and pluripotency

268

(1)

Analysis of ES-cell potency in chimeras with tetraploid embryos

269

(1)

Equipment for injection of ES cells into embryos

269

(2)

Host embryos

271

(1)

Blastocyst injection

272

(3)

Morula injection

275

(2)

Morula aggregation

277

(1)

Transfer of embryos to the uterus

278

(1)

Genetic background

279

(1)

Maintenance of mutations as co-isogenic and congenic lines and mutant analysis in a hybrid background

280

(1)

Chimera analysis

281

(1)

Acknowledgements

282

(1)

References

282

(3)

List of suppliers

285

(5)

Index

290

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Mouse Genetics and Transgenics A Practical Approach

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Mouse Genetics and Transgenics A Practical Approach

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