WormBook is a comprehensive online review of C. elegans biology, containing over 100 original, peer-reviewed chapters on a wide range of topics related to the biology of C. elegans and related nematodes; as well as WormMethods, a collection of laboratory methods and protocols useful for nematode researchers. WormBook can be found on the web at http://www.wormbook.org

Contents

• A Transparent window into biology: A primer on Caenorhabditis elegans
  Ann K. Corsi, Bruce Wightman, and Martin Chalfie.
  • 1. Introduction
  • 2. C. elegans basics
  • 3. C. elegans genetics
  • 4. Why choose C. elegans?
  • 5. C. elegans tissues
  • 6. The C. elegans genome
  • 7. Caenorhabditis ecology and evolution
  • 8. Brief history of C. elegans research and key discoveries
  • 9. The C. elegans community
  • 10. Acknowledgements
  • 11. Literature cited
• Biochemistry
  • Ascaroside signaling in C. elegans
    Andreas H. Ludewig and Frank C. Schroeder.
  • Carbohydrates and glycosylation
    Patricia M. Berninsone.
  • Intermediary metabolism
    Bart P Braeckman, Koen Houthoofd, and Jacques R Vanfleteren.
• Cell biology
  • Basement membranes
    James M. Kramer.
    Created: September 1, 2005.
  • Cell-cycle regulation
    Sander van den Heuvel.
    Created: September 21, 2005.
  • Cell division
    Karen Oegema and Tony Hyman.
    Created: January 19, 2006.
  • Cell fusion
    Benjamin Podbilewicz.
    Created: January 6, 2006.
  • The C. elegans eggshell
    Kathryn K. Stein and Andy Golden.
  • Development, structure, and maintenance of C. elegans body wall muscle
    Kathrin Gieseler, Hiroshi Qadota, and Guy M. Benian.
  • Epithelial junctions, cytoskeleton, and polarity
    Gabriella Pásti and Michel Labouesse.
  • Membrane ion transport in non-excitable tissues
    Keith Nehrke.
  • C. elegans as a model for membrane traffic
    Ken Sato, Anne Norris, Miyuki Sato, and Barth D. Grant.
  • Sarcomere assembly in C. elegans muscle
    Donald G. Moerman and Benjamin D. Williams.
    Created: January 16, 2006.
  • Nematode sperm motility
    Harold E. Smith.
  • The cadherin superfamily
    Jonathan Pettitt.
    Created: December 29, 2005.
  • The cuticle
    Antony P. Page and Iain L. Johnstone.
    Created: May 3, 2007.
  • The sensory cilia of Caenorhabditis elegans
    Peter N. Inglis, Guangshuo Ou, Michel R. Leroux, and Jonathan M. Scholey.
  • Autophagy in C. elegans
    Alicia Meléndez and Beth Levine.
  • Tubulins in C. elegans
    Daryl D. Hurd.
• Developmental control mechanisms
  • Polarity establishment, asymmetric division and segregation of fate determinants in early C. elegans embryos
    Lesilee Rose and Pierre Gönczy.
  • Development and migration of the C. elegans Q neuroblasts and their descendants
    Teije C. Middelkoop and Hendrik C. Korswagen.
  • Embryological variation during nematode development
    Einhard Schierenberg.
    Created: January 2, 2006.
  • Epidermal morphogenesis
    Andrew D. Chisholm and Jeff Hardin.
    Created: December 1, 2005.
  • Gastrulation in C. elegans
    Jeremy Nance, Jen-Yi Lee, and Bob Goldstein.
    Created: September 26, 2005.
  • Notch signaling in the C. elegans embryo
    James R. Priess.
    Created: June 25, 2005.
  • Programmed cell death
    Barbara Conradt and Ding Xue.
    Created: October 6, 2005.
  • The C. elegans intestine
    James D. McGhee.
    Created: May 3, 2007.
  • The C. elegans pharynx: a model for organogenesis
    Susan E. Mango.
    Created: January 22, 2007.
  • Translational control of maternal RNAs
    Thomas C. Evans and Craig P. Hunter.
    Created: November 10, 2005.
• Disease models and drug discovery
  • C. elegans and volatile anesthetics
    P.G. Morgan, E.-B. Kayser, and M.M. Sedensky.
    Created: May 3, 2007.
  • Anthelmintic drugs and nematicides: studies in Caenorhabditis elegans
    Lindy Holden-Dye and Robert J. Walker.
  • Obesity and the regulation of fat metabolism
    Kaveh Ashrafi.
    Created: May 3, 2007.
• Nematode evolution and ecology
  • Introduction to nematode evolution and ecology
    David H.A. Fitch.
    Created: August 31, 2005.
  • A quick tour of nematode diversity and the backbone of nematode phylogeny
    Paul De Ley.
    Created: January 25, 2006.
  • Ecology of Caenorhabditis species
    Karin Kiontke and Walter Sudhaus.
    Created: January 9, 2006.
  • Evolution of development in nematodes related to C. elegans
    Ralf J. Sommer.
    Created: December 14, 2005.
  • Interactions with microbial pathogens
    Creg Darby.
    Created: September 6, 2005.
  • Natural variation and population genetics of Caenorhabditis elegans
    Antoine Barrière and Marie-Anne Félix.
    Created: December 26, 2005.
  • Nematode genome evolution
    Avril Coghlan.
    Created: September 7, 2005.
  • The phylogenetic relationships of Caenorhabditis and other rhabditids
    Karin Kiontke and David H. A. Fitch.
    Created: August 11, 2005.
  • Molecular evolution inferences from the C. elegans genome
    Asher D. Cutter.
• Genetics and genomics
  • Introduction to genetics and genomics
    Jonathan Hodgkin.
    Created: September 6, 2005.
  • Caenorhabditis nomenclature
    Mary Ann Tuli, Aric Daul, and Tim Schedl.
  • Complementation
    Karen Yook.
    Created: October 6, 2005.
  • Essential genes
    Kenneth Kemphues.
    Created: December 24, 2005.
  • Gene duplications and genetic redundancy in C. elegans
    Alison Woollard.
    Created: June 25, 2005.
  • Genetic enhancers
    Robert K. Herman and John Yochem.
    Created: September 16, 2005.
  • Genetic mosaics
    John Yochem and Robert K. Herman.
    Created: December 27, 2005.
  • Genetic suppression
    Jonathan Hodgkin.
    Created: December 27, 2005.
  • Karyotype, ploidy, and gene dosage
    Jonathan Hodgkin.
    Created: June 25, 2005.
  • C. elegans network biology: a beginning
    Fabio Piano, Kristin C. Gunsalus, David E. Hill, and Marc Vidal.
    Created: August 21, 2006.
  • C. elegans noncoding RNA genes
    Shawn L. Stricklin, Sam Griffiths-Jones, and Sean R. Eddy.
    Created: June 25, 2005.
  • Genomic classification of protein-coding gene families
    Erich M. Schwarz.
    Created: September 23, 2005.
  • Mitochondrial genetics
    Bernard Lemire.
    Created: September 14, 2005.
  • Overview of gene structure in C. elegans
    John Spieth, Daniel Lawson, Paul Davis, Gary Williams, and Kevin Howe.
  • Transposons in C. elegans
    Jean-Louis Bessereau.
    Created: January 18, 2006.
  • Genomics and biology of the nematode Caenorhabditis briggsae
    Bhagwati P. Gupta, Robert Johnsen, and Nansheng Chen.
    Created: May 3, 2007.
  • Oscheius tipulae
    Marie-Anne Félix.
    Created: August 16, 2006.
  • Pristionchus pacificus
    Ralf J. Sommer.
    Created: August 14, 2006.
  • The biology of Strongyloides spp.
    Mark E. Viney and James B. Lok.
  • The biology and genome of Heterorhabditis bacteriophora
    Todd Ciche.
    Created: May 3, 2007.
  • Biology and genome of Trichinella spiralis
    Makedonka Mitreva and Douglas P. Jasmer.
    Created: November 23, 2006.
• Molecular biology
  • Alternative splicing in C. elegans
    Alan M. Zahler.
    Created: September 26, 2005.
  • C. elegans microRNAs
    Monica C. Vella and Frank J. Slack.
    Created: September 21, 2005.
  • Replication and repair
    Ann Rose.
  • Endogenous RNAi pathways in C. elegans
    Allison C. Billi, Sylvia E. J. Fischer, and John K. Kim.
  • Mechanism and regulation of translation in C. elegans
    Robert E. Rhoads, Tzvetanka D. Dinkova, and Nadejda L. Korneeva.
    Created: January 28, 2006.
  • Operon and non-operon gene clusters in the C. elegans genome
    Thomas Blumenthal, Paul Davis, and Alfonso Garrido-Lecca.
  • RNA-binding proteins
    Min-Ho Lee and Tim Schedl.
    Created: April 18, 2006.
  • Roles of chromatin factors in C. elegans development
    Mingxue Cui and Min Han.
    Created: May 3, 2007.
  • Trans-splicing and operons in C. elegans
    Thomas Blumenthal.
  • Transcription mechanisms
    T. Keith Blackwell and Amy K. Walker.
    Created: September 5, 2006.
  • Transcriptional regulation of gene expression in C. elegans
    Valerie Reinke, Michael Krause, and Peter Okkema.
  • Ubiquitin-mediated pathways in C.elegans
    Edward T. Kipreos.
    Created: December 1, 2005.
  • Pre-mRNA splicing and its regulation in Caenorhabditis elegans
    Alan M. Zahler.
• Neurobiology and behavior
  • Egg-laying
    William R. Schafer.
    Created: December 14, 2005.
  • Male mating behavior
    Maureen M. Barr and L. Rene Garcia.
    Created: June 19, 2006.
  • Specification of the nervous system
    Oliver Hobert.
    Created: August 8, 2005.
  • Synaptogenesis
    Yishi Jin.
    Created: December 23, 2005.
  • The neuronal genome of Caenorhabditis elegans
    Oliver Hobert.
  • Potassium channels in C. elegans
    L. Salkoff, A.D. Wei, B. Baban, A. Butler, G. Fawcett, G. Ferreira, and C.M. Santi.
    Created: December 30, 2005.
  • Synaptic function
    Janet Richmond.
    Created: December 30, 2005.
  • Acetylcholine
    James B. Rand.
    Created: January 30, 2007.
  • Biogenic amine neurotransmitters in C. elegans
    Daniel L. Chase and Michael R. Koelle.
    Created: February 20, 2007.
  • GABA
    Erik M. Jorgensen.
    Created: August 31, 2005.
  • Ionotropic glutamate receptors: genetics, behavior and electrophysiology
    Penelope J. Brockie and Andres V. Maricq.
    Created: January 19, 2006.
  • Chemosensation in C. elegans
    Cornelia I. Bargmann.
    Created: October 25, 2006.
  • Mechanosensation
    Miriam B. Goodman.
    Created: January 6, 2006.
  • Ethanol
    Steven L. McIntire.
  • Neuropeptides
    Chris Li and Kyuhyung Kim.
  • Neurogenesis in the nematode Caenorhabditis elegans
    Oliver Hobert.
  • C. elegans feeding
    Leon Avery and Young-Jai You.
• Post-embryonic development
  • Dauer
    Patrick J. Hu.
  • Gene expression changes associated with aging in C. elegans
    Tamara R. Golden and Simon Melov.
    Created: February 12, 2007.
  • The measurement and analysis of age-related changes in Caenorhabditis elegans
    James J Collins, Cheng Huang, Stacie Hughes, and Kerry Kornfeld.
• Sex determination
  • Introduction to sex determination
    Robert K. Herman.
    Created: December 24, 2005.
  • Hermaphrodite cell-fate specification
    Michael A. Herman.
    Created: January 9, 2006.
  • Male development
    Scott W. Emmons.
    Created: November 10, 2005.
  • Sex determination in the germ line
    Ronald Ellis and Tim Schedl.
    Created: March 5, 2007.
  • Somatic sex determination
    David Zarkower.
    Created: February 10, 2006.
  • The evolution of nematode sex determination: C. elegans as a reference point for comparative biology
    Eric S. Haag.
    Created: December 29, 2005.
  • Morphogenesis of the vulva and the vulval-uterine connection
    Bhagwati P. Gupta, Wendy Hanna-Rose, and Paul W. Sternberg.
  • X-Chromosome dosage compensation
    Barbara J. Meyer.
    Created: June 25, 2005.
• Signal transduction
  • Introduction to signal transduction
    Iva Greenwald.
    Created: September 9, 2005.
  • Genomic overview of protein kinases
    Gerard Manning.
    Created: December 13, 2005.
  • Canonical RTK-Ras-ERK signaling and related alternative pathways
    Meera V. Sundaram.
  • Heterotrimeric G proteins in C. elegans
    Carol Bastiani and Jane Mendel.
    Created: October 13, 2006.
  • Neurotransmitter signaling through heterotrimeric G proteins: insights from studies in C. elegans
    Michael R. Koelle.
  • Homologs of the Hh signalling network in C. elegans
    Thomas R. Bürglin and Patricia E. Kuwabara.
    Created: January 28, 2006.
  • Insulin/insulin-like growth factor signaling in C. elegans
    Coleen T. Murphy and Patrick J. Hu.
  • Notch signaling: genetics and structure
    Iva Greenwald and Rhett Kovall.
  • Nuclear receptor signal transduction in C. elegans
    Adam Antebi.
  • Signaling in the innate immune response
    Dennis H. Kim and Jonathan J. Ewbank.
  • Small GTPases
    David J. Reiner and Erik A. Lundquist.
  • TGF-β signaling in C. elegans
    Tina L. Gumienny and Cathy Savage-Dunn.
  • The putative chemoreceptor families of C. elegans
    Hugh M. Robertson and James H. Thomas.
    Created: January 6, 2006.
  • Wnt signaling in C. elegans
    Hitoshi Sawa and Hendrik C. Korswagen.
  • Eph receptor signaling in C. elegans
    Michael A. Miller and Ian D. Chin-Sang.
• The germ line
  • Introduction to the germ line
    E. Jane Albert Hubbard and David Greenstein.
    Created: September 1, 2005.
  • Control of oocyte meiotic maturation and fertilization
    David Greenstein.
    Created: December 28, 2005.
  • Germline chromatin
    Christine E. Schaner and William G. Kelly.
    Created: January 24, 2006.
  • Germline genomics
    Valerie Reinke.
    Created: January 20, 2006.
  • Germline proliferation and its control
    Judith Kimble and Sarah L. Crittenden.
    Created: August 15, 2005.
  • Germline Survival and Apoptosis
    Anton Gartner, Peter R Boag, and T. Keith Blackwell.
  • Meiosis
    Kenneth J Hillers, Verena Jantsch, Enrique Martinez-Perez, and Judith L Yanowitz.
  • Specification of the germ line
    Susan Strome.
    Created: July 28, 2005.
  • Spermatogenesis
    S.W. L'Hernault.
    Created: February 20, 2006.
• WormHistory
  • Getting into the mind of a worm—a personal view
    John G. White.
  • History of research on C. elegans and other free-living nematodes as model organisms
    Victor Marc Nigon and Marie-Anne Félix.
• WormMethods
  • Behavior
    Anne C. Hart, ed.
    Created: July 3, 2006.
  • Assaying mechanosensation
    Martin Chalfie, Anne C. Hart, Catharine H. Rankin, and Miriam B. Goodman.
  • Keeping track of worm trackers
    Steven J. Husson, Wagner Steuer Costa, Cornelia Schmitt, and Alexander Gottschalk.
  • Microfluidics as a tool for C. elegans research
    Adriana San-Miguel and Hang Lu.
  • Methods for measuring pharyngeal behaviors
    David Raizen, Bo-mi Song, Nick Trojanowski, and Young-Jai You.
  • Biochemistry and molecular biology
    Albertha J. M. Walhout and Simon J. Boulton.
    Created: February 13, 2006.
  • Introduction and basics
    David Fay.
    Created: February 17, 2006.
  • Two-point mapping with genetic markers
    David Fay.
    Created: June 14, 2006.
  • Three-point mapping with genetic markers
    David Fay.
    Created: February 17, 2006.
  • Dominant mutations
    David Fay and Andy Spencer.
    Created: February 17, 2006.
  • Making compound mutants
    David Fay.
    Created: June 14, 2006.
  • Mapping with deficiencies and duplications
    David Fay.
    Created: June 14, 2006.
  • SNPs: Introduction and two-point mapping
    David Fay and Aaron Bender.
  • SNPs: Three-point mapping
    David Fay.
    Created: February 17, 2006.
  • Suppressor mutations
    David Fay and Wade Johnson.
    Created: February 17, 2006.
  • Synthetic and enhancer mutations
    David Fay.
    Created: February 17, 2006.
  • Classical genetic methods
    David S. Fay.
  • Genetic balancers
    Mark L. Edgley, David L. Baillie, Donald L. Riddle, and Ann M. Rose.
  • Genetic dissection of developmental pathways
    Linda S. Huang and Paul W. Sternberg.
    Created: June 14, 2006.
  • Maintenance of C. elegans
    Theresa Stiernagle.
    Created: February 11, 2006.
  • Nomarski images for learning the anatomy, with tips for mosaic analysis
    John Yochem.
    Created: January 24, 2006.
  • Profiling C. elegans gene expression with DNA microarrays
    Douglas S. Portman.
    Created: January 20, 2006.
  • Immunohistochemistry
    Janet S. Duerr.
    Created: June 19, 2006.
  • Protocols for large scale in situ hybridization on C. elegans larvae
    Tomoko Motohashi, Hiroaki Tabara, and Yuji Kohara.
    Created: July 24, 2006.
  • Reporter gene fusions
    Thomas Boulin, John F. Etchberger, and Oliver Hobert.
    Created: April 5, 2006.
  • RNA in situ hybridization of dissected gonads
    Min-Ho Lee and Tim Schedl.
    Created: June 14, 2006.
  • Single molecule fluorescent in situ hybridization (smFISH) of C. elegans worms and embryos
    Ni Ji and Alexander van Oudenaarden.
  • Methods in cell biology
    Shai Shaham, ed.
    Created: January 2, 2006.
  • Cell isolation and culture
    Sihui Zhang and Jeffrey R. Kuhn.
  • Mass spectrometry-based shotgun proteomic analysis of C. elegans protein complexes
    Bryan R. Fonslow, James J. Moresco, Patricia G. Tu, Antti P. Aalto, Amy E. Pasquinelli, Andrew G. Dillin, and John R. Yates III.
  • Isolation of C. elegans and related nematodes
    Antoine Barrière and Marie-Anne Félix.
  • Pristionchus pacificus protocols
    Andre Pires-daSilva.
  • Pristionchus pacificus genomics: from genetics to genome sequence
    Christoph Dieterich, Waltraud Roeseler, and Jagan Srinivasan.
    Created: August 14, 2006.
  • Strongyloides stercoralis: a model for translational research on parasitic nematode biology
    James B. Lok.
    Created: February 17, 2007.
  • Transgenesis in animal parasitic nematodes: Strongyloides spp. and Brugia spp.
    James B. Lok and Thomas R. Unnasch.
  • Neurophysiological methods in C. elegans: an introduction
    William R. Schafer.
    Created: June 2, 2006.
  • Caenorhabditis briggsae methods
    Scott E. Baird and Helen M. Chamberlin.
    Created: December 18, 2006.
  • Culture of embryonic C. elegans cells for electrophysiological and pharmacological analyses
    Laura Bianchi and Monica Driscoll.
    Created: September 30, 2006.
  • Electrophysiological recordings from the neuromuscular junction of C. elegans
    Janet E. Richmond.
    Created: October 6, 2006.
  • Electrophysiological recordings from the pharynx
    Alan Cook, Christopher J. Franks, and Lindy Holden-Dye.
    Created: May 17, 2006.
  • Heterologous expression of C. elegans ion channels in Xenopus oocytes
    Laura Bianchi and Monica Driscoll.
    Created: August 1, 2006.
  • Imaging the activity of neurons and muscles
    Rex A. Kerr.
    Created: June 2, 2006.
  • Reverse genetics
    Julie Ahringer, ed.
    Created: April 6, 2006.
  • C. elegans gene transformation by microparticle bombardment
    Peter J. Schweinsberg and Barth D. Grant.
  • Transformation and microinjection
    Thomas C. Evans, ed.
    Created: April 6, 2006.
  • A biologist's guide to statistical thinking and analysis
    David S. Fay and Ken Gerow.
  • Web resources for C. elegans studies
    Raymond Lee.
    Created: December 28, 2005.
  • An introduction to the UCSC Genome Browser
    Raymond Lee.
  • Transgenic solutions for the germline
    Christopher Merritt, Christopher M. Gallo, Dominique Rasoloson, and Geraldine Seydoux.
  • Modern techniques for the analysis of chromatin and nuclear organization in C. elegans
    Peter Askjaer, Sevinç Ercan, and Peter Meister.
  • Thermotaxis navigation behavior
    Miriam B. Goodman, Mason Klein, Samuel Lasse, Linjiao Luo, Ikue Mori, Aravi Samuel, Piali Sengupta, and Dong Wang.
  • Working with dauer larvae
    Xantha Karp.