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ONLINE

Weinheim : Wiley-VCH ; 2007

Chichester : John Wiley [distributor], 2007

1 online zdroj (xxiv, 454 stran) : ilustrace

ISBN 9783527610921

ISBN 3527610928

ISBN 9783527610938 (elektronická kniha)

ISBN 9783527314874 (vázáno)

Tištěné vydání Flow cytometry with plant cells. Weinheim : Wiley-VCH ; Chichester : John Wiley [distributor], 2007 ISBN 9783527314874 ISBN 3527314873

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Flow Cytometry with Plant Cells; Contents; Preface; List of Contributors; 1 Cytometry and Cytometers: Development and Growth; 2 Principles of Flow Cytometry; 3 Flow Cytometry with Plants: an Overview; 4 Nuclear DNA Content Measurement; 5 Flow Cytometry and Ploidy: Applications in Plant Systematics, Ecology and Evolutionary Biology; 6 Reproduction Mode Screening; 7 Genome Size and its Uses: the Impact of Flow Cytometry; 8 DNA Base Composition of Plant Genomes; 9 Detection and Viability Assessment of Plant Pathogenic Microorganisms using Flow Cytometry

Targeted at beginners as well as experienced users, this handy reference explains the benefits and uses of flow cytometery in the study of plants and their genomes. Following a brief introduction that highlights general considerations when analyzing plant cells by flow cytometric methods, the book goes on to discuss examples of application in plant genetics, genomic analysis, cell cycle analysis, marine organism analysis and breeding studies. With its list of general reading and a glossary of terms, this first reference on FCM in plants fills a real gap by providing first-hand practical hints.

Popsáno podle tištěné verze

001479507

Contents // Preface XVII // List of Contributors XXI // 1 Cytometry and Cytometers: Development and Growth 1 // Howard M. Shapiro // Overview 1 // 1.1 Origins 1 // 1.2 From Absorption to Fluorescence, from Imaging to Flow 2 // 1.2.1 Early Microspectrophotometry and Image Cytometry 3 // 1.2.2 Fluorescence Microscopy and the Fluorescent Antibody Technique 3 // 1.2.3 Computers Meet Cytometers: The Birth of Analytical Flow Cytometry 4 // 1.2.4 The Development of Cell Sorting 7 // 1.3 The Growth of Multiparameter Flow Cytometry 8 // 1.4 Bench-tops and Behemoths: Convergent Evolution 11 // 1.5 Image Cytometry. New Beginnings? 14 // References 15 // 2 Principles of Flow Cytometry 19 // J. Paul Robinson and Gerald Grégori // Overview 19 // 2.1 Introduction 19 // 2.2 A Brief History of Flow Cytometry 20 // 2.3 Components of a Flow Cytometer 21 // 2.3.1 Fluidics 22 // 2.3.2 Optics 25 // 2.3.3 Electronic Systems 27 // 2.4 Flow Cytometric Informatics 30 // 2.5 Spectral Compensation 33 // 2.6 Cell Sorting 34 // 2.7 Calibration Issues 37 // 2.8 Conclusions 37 References 3 9 // 3 Flow Cytometry with Plants: an Overview 41 // Jaroslav Doležel, Johann Greilhuber, and Jan Suda // Overview 41 // 3.1 Introduction 42 // 3.2 Fluorescence is a Fundamental Parameter 43 // 3.3 Pushing Plants through the Flow Cytometer 44 // 3.3.1 Difficulties with Plants and their Cells 44 // 3.3.2 Protoplasts are somewhat “Easier” than Intact Cells 45 // 3.3.3 Going for Organelles 46 // 3.4 Application of Flow Cytometry in Plants 47 // 3.4.1 Microspores and Pollen 47 // 3.4.2 Protoplasts 47 // 3.4.2.1 Physiological Processes 48 // 3.4.2.2 Secondary Metabolites 48 // 3.4.2.3 Gene Expression 48 // 3.4.2.4 Somatic Hybrids 49 // 3.4.2.5 DNA Transfection 49 // 3.4.3 Cell Nuclei 49 // 3.4.3.1 Ploidy Levels 50 // 3.4.3.2 Aneuploidy 51 // 3.4.3.3 ? Chromosomes 52 // 3.4.3.4 Sex Chromosomes 52 //

3.4.3.5 Cell Cycle and Endopolyploidy 52 // 3.4.3.6 Reproductive Pathways 53 // 3.4.3.7 Nuclear Genome Size 54 // 3.4.3.8 DNA Base Content 55 // 3.4.3.9 Chromatin Composition 56 // 3.4.3.10 Sorting of Nuclei 56 // 3.4.4 Mitotic Chromosomes 57 // 3.4.5 Chloroplasts 57 // 3.4.6 Mitochondria 58 // 3.4.7 Plant Pathogens 58 // 3.4.8 Aquatic Flow Cytometry 59 // 3.5 A Flow Cytometer in Every Laboratory? 59 // 3.6 Conclusions and Future Trends 60 References 61 // 4 Nuclear DNA Content Measurement 67 // Johann Greilhuber, Eva M. Temsch, and Joao ?. M. Loureiro // Overview 67 // 4.1 Introduction 67 // 4.2 Nuclear DNA Content: Words, Concepts and Symbols 69 // Contents // 4.2.1 Replication-Division Phases 69 // 4.2.2 Alternation of Nuclear Phases 70 // 4.2.3 Generative Polyploidy Levels 70 // 4.2.4 Somatic Polyploidy 71 // 4.3 Units for Presenting DNA Amounts and their Conversion Factors 72 // 4.4 Sample Preparation for Flow Cytometric DNA Measurement 74 // 4.4.1 Selection of the Tissue 74 // 4.4.2 Reagents and Solutions 75 // 4.4.2.1 Isolation Buffers and DNA Staining 76 // 4.5 Standardization 80 // 4.5.1 Types of Standardization 80 // 4.5.2 Requirement of Internal Standardization - a Practical Test 82 // 4.5.3 Choice of the Appropriate Standard Species 83 // 4.5.3.1 Biological Similarity 83 // 4.5.3.2 Genome Size 84 // 4.5.3.3 Nature of the Standard 84 // 4.5.3.4 Availability 84 // 4.5.3.5 Cytological Homogeneity 85 // 4.5.3.6 Accessibility 85 // 4.5.3.7 Reliability of C-Values 85 // 4.5.4 Studies on Plant Standards 86 // 4.5.5 Suggested Standards 88 // 4.6 Fluorescence Inhibitors and Coatings of Debris 89 // 4.6.1 What are Fluorescence Inhibitors and Coatings of Debris? 89 // 4.6.2 Experiments with Tannic Acid 92 // 4.6.3 A Flow-cytometric Test for Inhibitors 95 // 4.7 Quality Control and Data Presentation 95 // 4.8 Future Directions 98 References 99 //

5 Flow Cytometry and Ploidy: Applications in Plant Systematics, Ecology and Evolutionary Biology 103 // Jan Suda, Paul Kron, Brian C. Husband, and Pavel Trávníček // Overview 103 // 5.1 Introduction 103 // 5.2 Practical Considerations 104 // 5.2.1 Relative DNA Content, Ploidy and Flow Cytometry 104 // 5.2.2 General Guidelines for Ploidy-level Studies 105 // 5.2.3 Use of Alternative Tissues 108 // 5.2.3.1 Preserved or Dormant Tissue 108 // 5.2.3.2 Pollen 111 // 5.2.4 Other Considerations/Pitfalls 113 // 5.2.4.1 Holokinetic Chromosomes (Agmatoploidy) 113 // 5.2.4.2 DNA Content Variation within Individuals 113 // Vili Contents // 5.3 Applications in Plant Systematics 114 // 5.3.1 Systematics of Heteroploid Taxa 114 // 5.3.1.1 Detecting Rare Cytotypes 117 // 5.3.1.2 Phylogenetic Inference 117 // 5.3.2 Systematics of Homoploid Taxa 118 // 5.4 Applications in Plant Ecology and Evolutionary Biology 119 // 5.4.1 Spatial Patterns of Ploidy Variation 119 // 5.4.1.1 Invasion Biology 119 // 5.4.2 Evolutionary Dynamics of Populations with Ploidy Variation 120 // 5.4.3 Ploidy Level Frequencies at Different Life Stages (Temporal Variation) 121 // 5.4.4 Reproductive Pathways 122 // 5.4.4.1 Unreduced Gametes and Polyploidy 122 // 5.4.4.2 Asexual Seed Production 124 // 5.4.4.3 Hybridization 124 // 5.4.5 Trophic Level Interactions and Polyploidy 125 // 5.5 Future Directions 126 References 128 // 6 Reproduction Mode Screening 131 // Fritz Matzk // Overview 131 // 6.1 Introduction 131 // 6.2 Analyses of the Mode of Reproduction 134 // 6.2.1 Traditional Techniques 134 // 6.2.2 Ploidy Analyses of Progenies Originating from Selling or Crossing 139 // 6.2.2.1 Identification of ??, Biv and Mi Individuals after Selling or Intraploidy Pollinations 139 // 6.2.2.2 Crossing of Parents with Different Ploidy or with Dominant Markers 140 //

6.2.3 Flow Cytometric Analyses of the Relative DNA Content of Microspores or Male Gametes 141 // 6.2.4 The Ploidy Variation of Embryo and Endosperm Depending on the Reproductive Mode 142 // 6.3 A Recent Innovative Method: the Flow Cytometric Seed Screen 142 // 6.3.1 Advantages and Limitations of the FCSS 143 // 6.3.2 Applications of the FCSS 146 // 6.3.2.1 Botanical Studies 146 // 6.3.2.2 Evolutionary Studies 147 // 6.3.2.3 Genetical Analyses of Apomixis 147 // 6.3.3 Methodological Implications 147 // 6.4 Flow Cytometry with Mature Seeds for other Purposes 149 // 6.5 Conclusions 150 References 151 // 7 Genome Size and its Uses: the Impact of Flow Cytometry 153 // Ilia J. Leitch and Michael D. Bennett // Overview 153 Introduction 153 // Why is Genome Size Important? 154 // What is Known about Genome Size in Plants? 155 // Angiosperms 156 // Gymnosperms 157 // Pteridophytes 158 // Bryophytes 158 // Algae 158 // The Extent of Genome Size Variation across Plant Taxa 159 Understanding the Consequences of Genome Size Variation: Ecological and Evolutionary Implications 160 Influence of Genome Size on Developmental Lifestyle and Life Strategy 161 // Ecological Implications of Genome Size Variation 163 Implications of Genome Size Variation on Plants’ Responses to Environmental Change 166 // Genome Size and Plant Response to Pollution 166 Genome Size and Threat of Extinction 166 // Consequences of Genome Size Variation for Survival in a Changing World 167 // Methods of Estimating Genome Size in Plants and the Impact of Flow Cytometry 168 // The Development of Flow Cytometry for Genome Size Estimation // in Angiosperms 169 // Choice of Fluorochromes 169 // Internal Standardization 169 // The Need for Cytological Data 170 // Awareness of the Possible Interference of DNA Staining 170 // Potential for the Application of Flow Cytometry to Other Plant // Groups 171 //

Gymnosperms 171 // Pteridophytes 172 // Bryophytes 172 // Recent Developments and the Future of Flow Cytometry in Genome Size Research 172 References 174 // DNA Base Composition of Plant Genomes 177 // Armin Meister and Martin Barow // Overview 177 // Introduction 177 // Analysis of Base Composition by Flow Cytometry 178 // Fluorescence of Base-Specific Dyes: Theoretical Considerations 180 // Base Composition of Plant Species Determined by Flow Cytometry and its Relation to Genome Size and Taxonomy 185 // Comparison of Flow Cytometric Results with Base Composition Determined by other Physico-Chemical Methods 204 // Possible Sources of Error in Determination of Base Composition by Flow Cytometry 205 // Conclusions 211 // References 213 // 9 Detection and Viability Assessment of Plant Pathogenic Microorganisms using Flow Cytometry 217 // Jan H. W. Bergervoet, Jan M. van der Wolf, and Jemen Peters // Overview 217 // Introduction 217 // Viability Assessment 218 // Viability Tests for Spores and Bacteria 219 // Immunodetection 222 // Microsphere Immuno Assay 224 // Detection of Plant Pathogenic Bacteria and Viruses 225 // Paramagnetic Microsphere Immuno Assay 226 // Conclusions and Future Prospects 227 // References 229 // 10 Protoplast Analysis using Flow Cytometry and Sorting 231 // David W. Galbraith // Overview 231 // Introduction 231 // Protoplast Preparation 231 // Adaptation of Flow Cytometric Instrumentation for Analysis of Protoplasts 233 // Parametric Analyses Available for Protoplasts using Flow Cytometry 234 // Results of Protoplast Analyses using Flow Cytometry and Sorting 237 // Protoplast Size 237 // Protoplast Light Scattering Properties 238 // Protoplast Protein Content 239 // Protoplast Viability and Physiology 239 // Protoplast Cell Biology 243 // Construction of Somatic Hybrids 244 // The Cell Cycle 244 //

Walled Plant Cells: Special Cases for Flow Analysis and Sorting 246 // Prospects 247 // References 248 // 11 Flow Cytometry of Chloroplasts 251 // Erhard Pfündel and Armin Meister // Overview 251 // 11.1 I ntroduction 251 // 11.1.1 The Chloroplast 252 // 11.2 Chloroplast Signals in Flow Cytometry 255 // 11.2.1 Autofluorescence 255 // 11.2.2 Light Scattering 259 // 11.3 Progress of Research 259 // 11.3.1 Chloroplasts from C3 Plants 260 // 11.3.2 Chloroplasts from C4 Plants 261 // 11.4 Conclusion 263 References 264 // 12 DNA Flow Cytometry in Non-vascular Plants 267 // Hermann Voglmayr // Overview 267 // 12.1 Introduction 267 // 12.2 Nuclear DNA Content and Genome Size Analysis 271 // 12.2.1 General Methodological Considerations 272 // 12.2.1.1 Isolation and Fixation of Nuclei 272 // 12.2.1.2 Standardization 274 // 12.2.1.3 Fluorochromes for Estimation of Nuclear DNA Content 275 // 12.2.1.4 Secondary Metabolites as DNA Staining Inhibitors 276 // 12.2.2 DNA Content and Genome Size Studies 276 // 12.2.2.1 Algae 277 // 12.2.2.2 Bryophytes 280 // 12.3 Future Perspectives 283 // 12.4 Conclusion 284 References 285 // 13 Phytoplankton and their Analysis by Flow Cytometry 287 // George B, J, Dabelaar, Raffaella Casotti, Glen A. Tarran, and Isabelle C. Biegala // Overview 287 // 13.1 Introduction 288 // 13.2 Plankton and their Importance 288 // 13.2.1 Particles in Surface Water 288 // 13.2.2 Phytoplankton 289 // 13.2.3 Distributions in the Aquatic Environment 289 // 13.3 Considerations for using Flow Cytometry 291 // 13.3.1 Analytical Approach 291 // 13.3.2 Limitations and Pitfalls of using Biomedical Instruments 292 // 13.3.3 Instrument Modification and Specialized Cytometers 293 // XII // Contents // 13.3.4 Sizing and Discrimination of Cells 295 // 13.3.5 More Information per Particle: From Single Properties to (Silico-) Imaging 297 //

13.4 Sampling: How, Where and When 301 // 13.4.1 Sample Preparation 301 // 13.4.2 Critical Scales and Sampling Frequency 302 // 13.4.3 Platforms for Aquatic Flow Cytometry 303 // 13.5 Monitoring Applications 305 // 13.5.1 Species Screening: Cultures 305 // 13.5.2 Phytoplankton Species Biodiversity 307 // 13.5.3 Harmful Algal Blooms 308 // 13.6 Ecological Applications 308 // 13.6.1 Population-related Processes 308 // 13.6.2 Cell-related Processes and Functioning 311 // 13.6.3 Plankton Abundance Patterns in the Sea: Indicators of Change 314 // 13.7 Marine Optics and Flow Cytometry 314 // 13.8 Future Perspectives 315 References 319 // 14 Cell Cycle Analysis in Plants 323 // Martin Pfosser, Zoltán Magyar, and Laszlo Bögre // Overview 323 // 14.1 Introduction 323 // 14.2 Univariate Cell Cycle Analysis in Plant Cells 325 // 14.3 BrdUrd Incorporation to Determine Cycling Populations 326 // 14.4 Cell Cycle Synchronization Methods: Analysis of Cell Cycle Transitions in Cultured Plant Cells 327 // 14.5 Plant Protoplasts to Study the Cell Cycle 335 // 14.6 Root Meristems for Cell Cycle Synchronization 335 // 14.7 Study of Cell Cycle Regulation by using Synchronized Cell Cultures and Flow Cytometry 336 // 14.8 Cell Cycle and Plant Development 338 // 14.9 Flow Cytometry of Dissected Tissues in Developmental Time Series 339 // 14.10 Cell Type-specific Characterization of Nuclear DNA Content by Flow Cytometry 339 // 14.11 Other Methods and Imaging Technologies to Monitor Cell Cycle Parameters and Cell Division Kinetics in Developing Organs 340 // 14.12 Concluding Remarks 342 References 343 // 15 Endopolyploidy in Plants and its Analysis by Flow Cytometry 349 // Martin Barow and Gabriele Jovtchev // Overview 349 // 15.1 Introduction 349 // 15.2 Methods to Analyze Endopolyploidy 351 // 15.2.1 Microscopy 351 // 15.2.1.1 Chromosome Counts 351 //

15.2.1.2 Feulgen Microdensitometry, Fluorescence Microscopy, Image Analysis 352 // 15.2.2 Flow Cytometry 352 // 15.2.2.1 Evaluation of Histograms 353 // 15.2.2.2 Quantification of the Degree of Endopolyploidy 354 // 15.3 Occurrence of Endopolyploidy 355 // 15.3.1 Endopolyploidy in Species 356 // 15.3.2 Endopolyploidy in Ecotypes and Varieties 356 // 15.3.3 Endopolyploidy in Different Life Strategies 357 // 15.3.4 Endopolyploidy in Organs 359 // 15.4 Factors Modifying the Degree of Endopolyploidization 362 // 15.4.1 Genome Size and Endopolyploidy 362 // 15.4.2 Environmental Factors 363 // 15.4.3 Symbionts and Parasites 364 // 15.4.4 Phytohormones 365 // 15.5 Dynamics of Endopolyploidization 366 // 15.6 Endopolyploidy and Plant Breeding 367 // 15.6.1 Endopolyploidy in Crop Plants 367 // 15.6.2 In vitro Culture and Plant Regeneration 368 // 15.7 Conclusions 369 References 370 // 16 Chromosome Analysis and Sorting 373 // Jaroslav Doležel, Marie Kubaláková, Pavla Suchánková, Pavlína Kovárová, Jan Bartoš, and Hana Šimková // Overview 373 // 16.1 Introduction 374 // 16.2 How Does it Work? 375 // 16.3 How it All Began 377 // 16.4 Development of Flow Cytogenetics in Plants 379 // 16.4.1 Preparation of Suspensions of Intact Chromosomes 379 // 16.4.1.1 Biological Systems for Chromosome Isolation 379 // 16.4.1.2 Cell Cycle Synchronization and Metaphase Accumulation 383 // 16.4.1.3 Preparation of Chromosome Suspensions 383 // 16.4.2 Chromosome Analysis 385 // 16.4.2.1 Bivariate Analysis of AT and GC Content 385 // 16.4.2.2 Fluorescent Labeling of Repetitive DNA 386 // 16.4.2.3 The Use of Cytogenetic Stocks 386 // 16.4.2.4 Assignment of Chromosomes to Peaks on Flow Karyotypes 386 // 16.4.3 Chromosome Sorting 387 // 16.4.3.1 Estimating the Purity in Sorted Fractions 389 // 16.4.3.2 Improving the Sort Purity 389 // 16.4.3.3 Two-step Sorting 389 //

16.4.3.4 Purities and Sort Rates Achieved 390 // 16.5 Applications of Flow Cytogenetics 390 // 16.5.1 Flow Karyotyping 390 // 16.5.2 Chromosome Sorting 392 // 16.5.2.1 Physical Mapping and Integration of Genetic and Physical Maps 392 // 16.5.2.2 Cytogenetic Mapping 392 // 16.5.2.3 Analysis of Chromosome Structure 396 // 16.5.2.4 Targeted Isolation of Molecular Markers 396 // 16.5.2.5 Recombinant DNA Libraries 396 // 16.6 Conclusions and Future Prospects 398 // References 400 // 17 Analysis of Plant Gene Expression Using Flow Cytometry and Sorting 405 // David W. Galbraith // Overview 405 // 17.1 Introduction 405 // 17.2 Methods, Technologies, and Results 406 // 17.2.1 Current Methods for Global Analysis of Gene Expression 406 // 17.2.1.1 Methods Based on Hybridization 407 // 17.2.1.2 Methods Based on Sequencing 408 // 17.2.1.3 Emerging Sequencing Technologies 409 // 17.2.1.4 Other-omics Disciplines and Technologies 410 // 17.2.2 Using Flow Cytometry to Monitor Gene Expression and Cellular States 411 // 17.2.2.1 Transgenic Markers Suitable for Flow Cytometry and Sorting 411 // 17.2.2.2 Subcellular Targeting as a Means for Transgenic Analysis 412 // 17.2.3 Using Flow Sorting to Measure Gene Expression and Define Cellular States 414 // 17.2.3.1 Protoplast and Cell Sorting Based on Endogenous Properties 414 // 17.2.3.2 Protoplast Sorting Based on Transgenic Markers 416 // 17.2.3.3 Sorting of Nuclei Based on Transgenic Markers 417 // 17.3 Prospects 418 // 17.3.1 Combining Flow and Image Cytometry 418 // 17.3.2 Use of Protoplasts for Confirmatory Studies 418 // 17.3.3 Analysing Noise in Gene Expression 419 References 421 // 18 FLOWer: A Plant DNA Flow Cytometry Database 423 // Joŕo Loureiro, Jan Suda, Jaroslav Doležel, and Conceiqŕo Santos // Overview 423 // 18.1 Introduction 423 // 18.2 Taxonomic Representation in DNA Content Studies 425 //

18.3 Nuclear Isolation and Staining Buffers 427 // 18.4 Standardization and Standards 430 // 18.5 Fluorochromes 433 // 18.6 Quality Measures of Nuclear DNA Content Analyses 434 // 18.7 The Uses of DNA Flow Cytometry in Plants 435 // 18.8 Instrumentation 435 // 18.9 Where Are the Results Published? 436 // 18.10 Conclusion 437 References 438 // Index 439

(OCoLC)181345358