| Contributors | p. xi |
| Preface | p. xv |
| Manipulating Ciliary Protein-Encoding Genes in Tetrahymena thermophila | |
| Introduction | p. 2 |
| Designing the Targeting Fragment for Gene Disruption | p. 5 |
| Biolistic Transformation Protocol (Germline Gene Knockout) | p. 6 |
| Construction of Gene Knockout Heterokaryons | p. 10 |
| Disruption of Multiple Genes in the Germline | p. 14 |
| Somatic (Macronuclear) Gene Knockout | p. 16 |
| Phenotypic Rescue by Introduction of a Wild-type Gene into a Knockout Strain | p. 17 |
| References | p. 18 |
| Approaches for Functional Analysis of Flagellar Proteins in African Trypanosomes | |
| Introduction | p. 22 |
| Rationale | p. 23 |
| Methods | p. 24 |
| Materials | p. 48 |
| Summary and Outlook | p. 52 |
| References | p. 53 |
| Tools for Analyzing Intraflagellar Transport in Trypanosomes | |
| Introduction | p. 60 |
| Methodology | p. 63 |
| Perspectives | p. 76 |
| References | p. 78 |
| Schmidtea mediterranea: A Model System for Analysis of Motile Cilia | |
| Introduction | p. 82 |
| Materials and Methods | p. 84 |
| Discussion | p. 94 |
| Summary | p. 96 |
| References | p. 97 |
| Targeted Gene Silencing by RNA Interference in Chlamydomonas | |
| Introduction | p. 100 |
| Materials and Methods | p. 102 |
| Results and Discussion | p. 105 |
| Summary | p. 108 |
| References | p. 109 |
| Analysis of Cargo Transport by IFT and GFP Imaging of IFT in Chlamydomonas | |
| Introduction | p. 112 |
| Methods for GFP Imaging of IFT Proteins | p. 113 |
| IFT Cargo | p. 116 |
| References | p. 118 |
| Genetic and Phenotypic Analysis of Flagellar Assembly Mutants in Chlamydomonas reinhardtii | |
| Introduction | p. 122 |
| Isolation of Aflagellate Strains | p. 123 |
| Isolation of Conditional Flagellar Assembly (fla) Mutants | p. 124 |
| Characterizing Intraflagellar Transport in fla Mutants | p. 128 |
| Genetic Characterization | p. 132 |
| Characterization of Genetic Interactions | p. 139 |
| References | p. 141 |
| Recording and Analyzing IFT in Chlamydomonas Flagella | |
| Introduction | p. 146 |
| Methods | p. 146 |
| Summary | p. 154 |
| References | p. 155 |
| Total Internal Reflection Fluorescence (TIRF) Microscopy of Chlamydomonas Flagella | |
| Introduction | p. 158 |
| Rationale: A History of Flagellar Microscopy in Chlamydomonas | p. 159 |
| Materials and Methods: Technical Considerations of Chlamydomonas TIRF | p. 166 |
| Discussion: Future Prospects for Chlamydomonas TIRF | p. 170 |
| Summary | p. 174 |
| References | p. 174 |
| Purification of IFT Particle Proteins and Preparation of Recombinant Proteins for Structural and Functional Analysis | |
| Introduction | p. 180 |
| Isolating IFT Particle Proteins from Chlamydomonas Flagella | p. 181 |
| Recombinant IFT Particle Proteins | p. 191 |
| Summary and Concluding Remarks | p. 194 |
| References | p. 195 |
| Studying Cilia in Zebrafish | |
| Introduction | p. 198 |
| Summary | p. 215 |
| References | p. 215 |
| Analysis of IFT Kinesins in Developing Zebrafish Cone Photoreceptor Sensory Cilia | |
| Introduction | p. 220 |
| Comparison of Photoreceptor Model Systems | p. 222 |
| Zebrafish as a Model for Analysis of Photoreceptor IFT | p. 223 |
| Mutant Zebrafish | p. 223 |
| Antisense Morpholino Oligonucleotides | p. 225 |
| Transient Transgenesis Using Photoreceptor-Specific Promoters | p. 226 |
| Materials and Methods | p. 229 |
| Transmission Electron Microscopy | p. 231 |
| References | p. 232 |
| Analysis of Intraflagellar Transport in C. elegans Sensory Cilia | |
| Introduction | p. 236 |
| Rationale | p. 245 |
| Methods | p. 250 |
| Materials | p. 259 |
| Discussion | p. 260 |
| Summary | p. 262 |
| References | p. 262 |
| Functional Genomics of Intraflagellar Transport-Associated Proteins in C. elegans | |
| Introduction | p. 268 |
| Identification of Novel IFT-Associated and Ciliary Proteins | p. 279 |
| Characterization of Candidate and Known IFT-Associated Proteins | p. 281 |
| Conclusions | p. 298 |
| References | p. 299 |
| Generating Conditional Mutants to Analyze Ciliary Functions: The Use of Cre–Lox Technology to Disrupt Cilia in Specific Organs | |
| Introduction | p. 306 |
| The Design of a Conditional Targeted Allele | p. 307 |
| ES Clone Selection and Manipulation | p. 313 |
| The Cre Line | p. 315 |
| The Reporter | p. 316 |
| Practical Notes | p. 319 |
| Conditional Alleles in Cilia Biology | p. 320 |
| Methods | p. 321 |
| References | p. 328 |
| Imaging Intraflagellar Transport in Mammalian Primary Cilia | |
| Introduction | p. 332 |
| Rationale | p. 334 |
| Methods for Generation and Characterization of IFT/GFP Fusion Cell Lines | p. 335 |
| Live Imaging of Mammalian IFT | p. 339 |
| Outlook | p. 345 |
| References | p. 345 |
| Analysis of Hedgehog Signaling in Mouse Intraflagellar Transport Mutants | |
| Introduction | p. 348 |
| Rationale | p. 350 |
| Methods | p. 360 |
| Materials | p. 364 |
| Summary | p. 366 |
| References | p. 366 |
| Index | p. 371 |
| Volume in Series | p. 383 |
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