Caenorhabditis Elegans

Contributors

Preface

Acknowledgments

PART I Genetics and Functional Genomics

Chapter 1: Mapping Mutations in C. elegans

I. Introduction

II. Mutant Origination

III. Mutations That Can Be Propagated as Homozygotes

IV. Mutations That Cannot Be Propagated as Homozygotes

V. Modifier Mutations

VI. SNP Mapping

VII. WGS and Beyond

Chapter 2: Specialized Chromosomes and Their Uses in Caenorhabditis elegans

I. Introduction

II. Chromosomal Rearrangements

III. Characterization of Chromosomal Rearrangements

IV. Engineered Constructs: Transgenic Arrays

Chapter 3: Genome Engineering by Transgene-Instructed Gene Conversion in C. elegans

I. Introduction

II. General Features of the MosTIC Technique and Experimental Outline

III. Methods

IV. Materials

V. Discussion: MosTIC Applications and Derivatives

VI. Summary

Chapter 4: RNAi Methods and Screening: RNAi Based High-Throughput Genetic Interaction Screening

I. Introduction: Large-Scale RNAi Screening in C. elegans

II. Methods

III. Materials

PART II Molecular Biology and Biochemistry

Chapter 5: Dissection of Genetic Pathways in C. elegans

I. Introduction

II. Strategies for Identifying Components in Pathways of Interest

III. Ordering Genes into Pathways

IV. Future Outlook

Chapter 6: Transgenesis in C. elegans

I. Introduction

II. Uses for Transgenes in C. elegans

III. Construction of Transgenes

IV. Obtaining Transgenic Animals

V. Perspectives: What Lies on the Horizon?

VI. Summary

Chapter 7: RNA Processing in C. elegans

I. Introduction

II. RNA Processing in Other Organisms

III. RNA Processing in C. elegans

Chapter 8: Analysis of microRNA Expression and Function

I. Introduction

II. Rationale, Methods, and Materials

III. Summary

Chapter 9: In situ Hybridization of Embryos with Antisense RNA Probes

I. Introduction

II. Rationale

III. Methods

IV. Animal Preparation and Fixation

V. Hybridization and Signal Development

VI. Materials

VII. Notes

VIII. Troubleshooting Guide

IX. Imaging of Stained Embryos

X. Summary

Chapter 10: Gene-Centered Regulatory Network Mapping

I. Introduction

II. Gene Regulatory Networks

III. Identifying Gene Regulatory Network Nodes

IV. Gene Regulatory Network Visualization and Analysis

V. Future Challenges

Chapter 11: Affinity Purification of Protein Complexes in C. elegans

I. Introduction

II. Generating Tools for Biochemistry

III. The Optimal Starting Material for Protein Purification

IV. Isolation of Nuclei from Embryos

V. Preparing Worm and Embryonic Extract

VI. Single-step Immunoprecipitation

VII. Tandem Affinity Purification Using a LAP Tag

VIII. Mass Spectrometry & Prioritization for Follow-up Experiments

IX. Summary

X. Solutions and Media

XI. Equipment

PART III Development

Chapter 12: Cell Identification and Cell Lineage Analysis

I. Introduction

II. Rationale

III. Resources

IV. Nomenclature and Conventions

V. Cell identification and Lineage Analysis

VI. Materials, Methods, and Protocols

VII. Discussion

Chapter 13: The Genetics and Cell Biology of Fertilization

I. General Introduction/Background

II. Finding Sterile Mutants

III. Maintaining Sterile Mutants

IV. Fecundity Analysis

V. Ovulation/Ovulation Rates

VI. Spermatogenesis

VII. Sperm Migratory Behavior/Tracking

VIII. Sperm Competition

IX. Oogenesis and Oocyte Maturation

X. Assessing Fertilization and Egg Activation in Egg-Sterile Mutants

XI. Eggshell Production

XII. Analysis of Fertilization-Specific Gene Products

XIII. Future Prospects/Issues

Chapter 14: Imaging Embryonic Morphogenesis in C. elegans

I. Introduction

II. Methods

III. Summary

Chapter 15: Molecular and Genetic Approaches for the Analysis of C. elegans Neuronal Development

I. Introduction

II. Strategies for In Vivo Labeling of Neurons and Compartments

III. Other Methods for Examining the Development of Neurons

IV. Functional Dissection of Signaling Pathways Controlling Neuronal Development

V. Examples of Neuronal Development

VI. Outlook

Chapter 16: Methods for Evaluating the Caenorhabditis elegans Dauer State: Standard Dauer-Formation Assay Using Synthetic Daumones and Proteomic Analysis of O-GlcNAc Modifications

I. Introduction

II. Rationale

III. Methods

IV. Materials

V. Discussion

VI. Summary

Appendix: Major Caenorhabditis elegans Web Resources

Index

Volumes in Series