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WormBook
The Online Review of
C. elegans
Biology
Priess
James
Seydoux
Geraldine
2007
© 2007
Creative Commons Attribution License
Table of Contents
Book Information
Cell biology
Basement membranes
James M. Kramer
Created: September 1, 2005
1. Introduction
2. Collagen type IV
3. Laminins
4. Perlecan
5. Nidogen
6. Collagen type XVIII
7. SPARC/Osteonectin
8. Fibulin
9. Hemicentin
10. Integrins
11. References
Cell-cycle regulation
Sander van den Heuvel
Created: September 21, 2005
1. Overview
2. The paradigm of cell-cycle control
3. Regulators of the cell cycle
4. Cell-Cycle regulation in development
5. Acknowledgments
6. References
Cell division
Karen Oegema and Tony Hyman
Created: January 19, 2006
1. The
C. elegans
embryo as a system to study cell division
2. A timeline of events during the first mitotic division of the
C. elegans
embryo
3. Nuclear envelope structure and dynamics
4. Pronuclear migration
5. Centrosome assembly and duplication
6. Formation of mitotic chromosomes
7. Kinetochore assembly
8. Assembly of the mitotic spindle
9. Chromosome segregation
10. Cytokinesis
11. Acknowledgements
12. References
Cell fusion
Benjamin Podbilewicz
Created: January 6, 2006
1. Introduction
2. Cell biology of plasma membrane fusion
3. Genetics of cell fusion
4. eff-1 is necessary for most, but not all, cell fusion events in
C. elegans
5. Regulation of cell fusion
6. Open questions
7. Implications of cell fusion research beyond worms
8. Acknowledgements
9. References
Epithelial junctions and attachments
Michel Labouesse
Created: January 13, 2006
1. Introduction
2. Approaches to identify junctional and cytoskeletal components
3. Epithelial cytoskeleton
4. Apical junction components
5. Cell adhesion, microfilament anchorage and gate function
6. Assembly of apical junctions and establishment of epithelial polarity
7. Junction disassembly and cell fusion
8. Fibrous organelles: junctions with the extracellular matrix and mechanical coupling
9. Conclusions and future directions
10. Acknowledgements
11. References
Intracellular trafficking
Barth D. Grant and Miyuki Sato
Created: January 21, 2006
1. The endocytic pathway
2. The secretory pathway
3. General secretion
4. Polarized secretion
5. References
Sarcomere assembly in
C. elegans
muscle
Donald G. Moerman and Benjamin D. Williams
Created: January 16, 2006
1. Introduction
2. Muscle attachments
3. Dissection of muscle attachment assembly
4. Initiating a sarcomere leads to distinct assembly dependence pathways for dense bodies and M-lines
5. Distinguishing dense bodies from M-lines
6. Spacing of the components
7. Is sarcomere assembly in
C. elegans
a general model of sarcomere assembly?
8. Summary
9. Acknowledgements
10. References
Sperm motility and MSP
Harold Smith
Created: February 1, 2006
1. Spermatogenesis
2. Motility and fertilization
3. Motility and MSP
4. pH regulation
5. MSP assembly and structure
6. Reconstituted MSP polymerization system
7. Components that control MSP assembly
8. Evolution of the MSP gene family
9. Conclusion
10. References
The cadherin superfamily
Jonathan Pettitt
Created: December 29, 2005
1. The cadherin superfamily
2. The FAT-like cadherins: CDH-3 and CDH-4
3. FMI-1, a
C. elegans
FLAMINGO/STAN cadherin
4. CDH-11/Calsyntenin
5. CDH-9/DCad96Cb
6. Nematode-specific cadherins?
7. Conclusions and future prospects
8. References
The cuticle
Antony P. Page and Iain L. Johnstone
Created: May 3, 2007
1. Introduction
2. Function
3. Structure
4. Composition
5. Molting
6. Collagen biosynthetic pathway
7. Perspective
8. References
The sensory cilia of
Caenorhabditis elegans
Peter N. Inglis, Guangshuo Ou, Michel R. Leroux, and Jonathan M. Scholey
Created: November 27, 2006
1. General definition of cilia
2. Historical perspective
3.
C. elegans
cilia: distribution and architecture
4. Cilium biogenesis and intraflagellar transport (IFT)
5. Transcriptional regulation of cilium morphogenesis
6. The
C. elegans
ciliome
7. Understanding
C. elegans
ciliary functions through ciliary mutant analysis
8.
C. elegans
as a model system to study ciliopathies
9. Concluding remarks
10. Acknowledgements
11. References
Developmental control mechanisms
Asymmetric cell division and axis formation in the embryo
Pierre Gönczy and Lesilee S. Rose
Created: October 15, 2005
1. Introduction
2. The one-cell stage embryo: establishment of the anterior-posterior axis
3. The one-cell stage embryo: spindle positioning
4. The two-cell stage embryo: formation of the dorsal/ventral axis
5. The four-cell stage embryo: formation of the left/right axis
6. Evolutionarily conserved themes
7. Acknowledgements
8. References
Embryological variation during nematode development
Einhard Schierenberg
Created: January 2, 2006
1. Overview
2. Reproduction and diploidy
3. Polarity
4. Cleavage and germ line
5. Cell lineages
6. Cell cycles and maternal contribution
7. Cell-cell communication and cell specification
8. Gastrulation
9. Concluding remarks
10. Acknowledgements
11. References
Epidermal morphogenesis
Andrew D. Chisholm and Jeff Hardin
Created: December 1, 2005
1. Introduction
2. Formation and specification of epidermal cells
3. Movements of ventral neuroblasts
4. Intercalation of dorsal epidermal cells
5. Ventral enclosure
6. Embryonic elongation
7. Acknowledgements
8. References
Gastrulation in
C. elegans
Jeremy Nance, Jen-Yi Lee, and Bob Goldstein
Created: September 26, 2005
1. Summary of gastrulation events
2. Polarization of gastrulating cells
3. Mechanisms of cell ingression
4. Patterning cell ingressions
5. Future prospects
6. Acknowledgments
7. References
Notch signaling in the
C. elegans
embryo
James R. Priess
Created: June 25, 2005
1. Introduction
2. The first and second interactions in the AB lineage
3. Notch-dependent / Notch-independent gene regulation
4. The third AB Notch interaction: Formation of the bilaterally symmetrical head
5. The fourth AB Notch interaction: specification of the excretory cell
6. A combinatorial Notch code for AB specification
7. Intersection of the Notch pathway and the POP-1 polarity pathway
8. Notch interactions in later AB descendants
9. Notch interactions in P
1
descendants
10. Notch regulation of Notch signaling components
11. Perspectives
12. References
Programmed cell death
Barbara Conradt and Ding Xue
Created: October 6, 2005
1. Introduction
2. Killing phase
3. Specification phase
4. Execution phase
5. Conclusions
6. Acknowledgements
7. References
The
C. elegans
intestine
James D. McGhee
Created: May 3, 2007
1. Introduction
2. The intestinal cell lineage in time and space
3. Intestinal morphogenesis and patterning
4. Structure of an intestinal cell
5. Function: towards a molecular physiology of the intestine
6. Transcriptional control in the intestine
7. Future directions in the intestine
8. Acknowledgements
9. Bibliography
The
C. elegans
pharynx: a model for organogenesis
Susan E. Mango
Created: January 22, 2007
1. The pharynx as a model for organ development
2. Anatomy of the pharynx
3. Early control of pharyngeal development-the ABa lineage
4. Early control of pharyngeal development-the EMS lineage
5. The transition from maternal to zygotic control
6. The organ selector gene pha-4
7. Commitment to pharyngeal fate
8. Downstream of PHA-4: patterning the pharynx primordium
9. Temporal control during organogenesis
10. Cell-type regulation
11. Transcriptional strategies for organogenesis
12. Morphogenesis
13. Epithelium formation-the pharyngeal arcade cells
14. Is the pharynx a heart?
15. Conclusion
16. Acknowledgements
17. References
Translational control of maternal RNAs
Thomas C. Evans and Craig P. Hunter
Created: November 10, 2005
1. Introduction
2. Control of maternal mRNA translation begins in the hermaphrodite germ line
3. Control of maternal mRNAs in the embryo
4. Conclusions and perspectives
5. Acknowledgements
6. References
Disease models and drug discovery
C. elegans
and volatile anesthetics
P.G. Morgan, E.-B. Kayser, and M.M. Sedensky
Created: May 3, 2007
1. Introduction
2. Nematode response to volatile anesthetics
3. Radial dispersion, uncoordination/Presynaptic effects
4. Immobility/Neuronal effects
5. Immobility/Mitochondrial effects
6. Summary
7. References
Obesity and the regulation of fat metabolism
Kaveh Ashrafi
Created: May 3, 2007
1. Obesity: an overview
2.
C. elegans
fat
3. Metabolic pathways
4. Metabolic sensors and coordinated regulation of metabolic pathways
5. Development of fat storage capacity
6. Lipid uptake/transport
7. Neuroendocrine fat and feeding regulatory pathways
8. Perspectives
9. Acknowledgments
10. Bibliography
Nematode evolution and ecology
Introduction to nematode evolution and ecology
David H.A. Fitch
Created: August 31, 2005
1. A model system evolves
2. Nematode relationships to other animals
3. Acknowledgements
4. References
A quick tour of nematode diversity and the backbone of nematode phylogeny
Paul De Ley
Created: January 25, 2006
1. Nematodes are highly diverse, complex and specialized metazoans
2. Changing perspectives in nematode phylogeny and classification
3. The backbone of the nematode tree
4. Major features of Enoplea
5. Features and diversity of Chromadorea
6. Acknowledgements
7. References
Ecology of
Caenorhabditis
species
Karin Kiontke and Walter Sudhaus
Created: January 9, 2006
1. Introduction
2. Associations with other animals
3. Ecology of Caenorhabditis species
4. Ecology of the
Caenorhabditis
stem species and evolution of ecological features within
Caenorhabditis
5. List of 23
Caenorhabditis
species and their ecology
6. Acknowledgements
7. References
Evolution of development in nematodes related to
C. elegans
Ralf J. Sommer
Created: December 14, 2005
1. Introduction
2. Taxonomic overview
3. Developmental systems
4. Conclusion
5. Acknowledgments
6. References
Interactions with microbial pathogens
Creg Darby
Created: September 6, 2005
1. Introduction
2. Bacterial infections of the intestine
3. Bacterial infections of the cuticle
4. Bacteria with multiple or undetermined killing modes
5. Fungal infections
6. Toxin-mediated killing
7. Conclusions
8. Acknowledgements
9. References
Natural variation and population genetics of
Caenorhabditis elegans
Antoine Barrière and Marie-Anne Félix
Created: December 26, 2005
1. Molecular polymorphisms and population genetics
2. Phenotypic diversity
3. References
Nematode genome evolution
Avril Coghlan
Created: September 7, 2005
1. Introduction
2. Evolution of genome size
3. The evolution of chromosome number and structure
4. Evolution of gene content
5. The rate of evolution in nematodes
6. Summary
7. Acknowledgements
8. References
The phylogenetic relationships of
Caenorhabditis
and other rhabditids
Karin Kiontke and David H. A. Fitch
Created: August 11, 2005
1. Introduction
2. Rhabditid phylogeny
3. Examples of character evolution
4. Resources for comparative biology using rhabditids
5. Acknowledgments
6. References
Genetics and genomics
Introduction to genetics and genomics
Jonathan Hodgkin
Created: September 6, 2005
Complementation
Karen Yook
Created: October 6, 2005
1. A simple test for assigning a mutation to a genetic locus
2. When the complementation test is not so simple
3. Conclusion
4. Acknowledgements
5. References
Essential genes
Kenneth Kemphues
Created: December 24, 2005
1. Overview
2. Types of essential genes
3. Methods for identifying essential genes
4. Redundancy of essential genes
5. Pleiotropic essential gene phenotypes
6. Summary
7. References
Gene duplications and genetic redundancy in
C. elegans
Alison Woollard
Created: June 25, 2005
1. Gene duplications and genetic redundancy
2. Acknowledgements
3. References
Genetic enhancers
Robert K. Herman and John Yochem
Created: September 16, 2005
1. Overview
2. Dominant enhancers
3. Genetic redundancy
4. Enhancement of mutations in homologous genes
5. Enhancement of mutations in functionally redundant but nonhomologous genes
6. Recessive enhancers of non-null mutations
7. References
Genetic mosaics
John Yochem and Robert K. Herman
Created: December 27, 2005
1. Overview
2. How worm genetic mosaics are generated
3. A few examples of mosaic analysis in worms
4. Potential problems
5. The continued importance of mosaic analysis
6. References
Genetic suppression
Jonathan Hodgkin
Created: December 27, 2005
1. Introduction
2. Intragenic suppression by same site replacement
3. Intragenic suppression by compensatory second site mutation
4. Intragenic suppression by altered splicing
5. Intragenic suppression of dominant mutations by loss-of-function in cis
6. Extragenic suppression — overview
7. Informational suppression — overview
8. Nonsense suppression
9. Extragenic suppression by modified splicing
10. Suppression by loss of NMD (Nonsense Mediated Decay)
11. Extragenic suppression by non-specific physiological effects
12. Suppression by altered gene dosage
13. Bypass suppression
14. Extragenic suppression by interacting components
15. Suppression by removal of a toxic protein or protein complex
16. Suppression by modulators of activity
17. Suppression by epistasis
18. References
Karyotype, ploidy, and gene dosage
Jonathan Hodgkin
Created: June 25, 2005
1. Normal karyotype
2. Overview of chromosome organization
3. Abnormal karyotype
4. Tetraploids, triploids and haploids
5. Aneuploids
6. Chromosomal duplications
7. Chromosomal deficiencies
8. Dosage sensitive genes
9. References
C. elegans
network biology: a beginning
Fabio Piano, Kristin C. Gunsalus, David E. Hill, and Marc Vidal
Created: August 21, 2006
1. Introduction
2. Network components: transcriptome and ORFeome
3. Network connections: interactome
4. Network perturbations: phenome
5. Network dynamics: from transcriptome to localizome
6. Network modeling: "omic" data integration
7. Perspectives
8. Acknowledgments
9. References
C. elegans
noncoding RNA genes
Shawn L. Stricklin, Sam Griffiths-Jones, and Sean R. Eddy
Created: June 25, 2005
1. Introduction
2. Ribosomal RNAs
3. Transfer RNAs
4. Spliced leader RNAs
5. Small nucleolar RNAs (snoRNAs)
6. microRNAs (miRNAs)
7. Other known RNAs
8. ncRNA conservation
9. Prospects for novel ncRNAs
10. Acknowledgments
11. References
Genomic classification of protein-coding gene families
Erich M. Schwarz
Created: September 23, 2005
1. Introduction
2. Similarity, homology, and shared functions
3. Classifying proteins
4. Sorting proteins into homologs, orthologs and paralogs
5. Protein classes in
C. elegans
6. Evolutionary history
7. Functional classification
8. Acknowledgements
9. References
Mitochondrial genetics
Bernard Lemire
Created: September 14, 2005
1. Introduction
2. Mitochondrial DNA structure
3. mtDNA-encoded proteins
4. Mitochondrial DNA inheritance
5. Mitochondrial dynamics
6.mtDNA copy number
7. Role of mtDNA in development
8. mtDNA mutations
9. mtDNA and aging
10. Perspectives
11. Acknowledgements
12. References
Overview of gene structure
John Spieth and Daniel Lawson
Created: January 18, 2006
1. What is a gene?
2. Protein-coding genes
3. Pseudogenes
4. non-coding RNA genes
5. Genomic organization
6. Acknowledgements
7. References
Transposons in
C. elegans
Jean-Louis Bessereau
Created: January 18, 2006
1.
C. elegans
transposons, the catalog
2. Mechanisms of Tc1 and Tc3 transposition
3. Transposon insertion target
4. Repair of the excision site
5. Regulation of transposition
6. Transposon-based tools for
C. elegans
research
7. Acknowledgments
8. References
Genomics and biology of the nematode
Caenorhabditis briggsae
Bhagwati P. Gupta, Robert Johnsen, and Nansheng Chen
Created: May 3, 2007
1. Introduction
2. Overview of the
C. briggsae
genome
3. Evolutionary studies
4. Genetic approach to study functions of
C. briggsae
genes
5. Tools for genetic studies
6. Acknowledgements
7. Bibliography
Oscheius tipulae
Marie-Anne Félix
Created: August 16, 2006
1. Phylogenetic relationships
2. Natural populations
3. Basic biology in the laboratory
4. Genetics
5. Genome and molecular biology resources
6. Developmental biology
7. Acknowledgement
8. References
Pristionchus pacificus
Ralf J. Sommer
Created: August 14, 2006
1. Biology
2. Developmental biology
3. Phylogeny
4. Ecology
5. Genetics
6. Genomics
7. Acknowledgements
8. References
Strongyloides
spp.
Mark E. Viney and James B. Lok
Created: May 3, 2007
1.
Strongyloides
is a genus of parasitic nematodes
2.
Strongyloides
infection of humans
3.
Strongyloides
in the wild
4. Phylogeny, morphology and taxonomy
5. The life-cycle
6. Sex determination and genetics of the life-cycle
7. Controlling the life-cycle
8. Maintaining the life-cycle
9. The parasitic phase of the life-cycle
10. Genomics
11. Acknowledgments
12. References
The biology and genome of
Heterorhabditis bacteriophora
Todd Ciche
Created: May 3, 2007
1. Introduction
2. Discovery and diversity
3. Life-cycle
4. Parasitism
5. Symbiosis
6. Other biology of interest for
Heterorhabditis
7. Genetics and molecular biology of
H. bacteriophora
8. Status and future of the
H. bacteriophora
genome project
9. Conclusion
10. Acknowledgements
11. References
Biology and genome of
Trichinella spiralis
Makedonka Mitreva and Douglas P. Jasmer
Created: November 23, 2006
1. Introduction
2. Molecular and cellular interactions with the host
3. Use of molecular biology in
Trichinella
4. Previous genomic applications to study
Trichinella
5. Current genome sequencing project for
Trichinella
spiralis
6. Acknowledgements
7. References
Molecular biology
Alternative splicing in
C. elegans
Alan M. Zahler
Created: September 26, 2005
1. The Importance of alternative splicing
2. Splicing of precursors to messenger RNA
3. Models for alternative splicing regulation
4. Constitutive splicing factors in
C. elegans
5. Identification of alternatively spliced genes in
C. elegans
6. Some examples of alternatively spliced
C. elegans
genes
7. Regulation of alternative splicing in
C. elegans
8. Conclusions
9. Acknowledgements
10. References
C. elegans
microRNAs
Monica C. Vella and Frank J. Slack
Created: September 21, 2005
1. Introduction
2.
C. elegans
miRNAs
3. miRNAs versus siRNAs: distinct mechanisms of gene regulation?
4. Conclusions
5. References
DNA repair
Nigel O'Neil and Ann Rose
Created: January 13, 2006
1. Overview
2. Radiation sensitivity of
C. elegans
3. DNA damage checkpoints in the germ line
4. DNA mismatch repair
5. Homologous recombination repair
6. BRCA1 and BRCA2
7. The dog-1 and RecQ helicases
8. DNA damage repair and genomics
9. Summary
10. Acknowledgments
11. References
Mechanism and regulation of translation in
C. elegans
Robert E. Rhoads, Tzvetanka D. Dinkova, and Nadejda L. Korneeva
Created: January 28, 2006
1. Introduction
2. The Translational machinery
3. Structural features of mRNA that affect translational efficiency
4. Regulation of Translation
5. Acknowledgements
6. References
RNA-binding proteins
Min-Ho Lee and Tim Schedl
Created: April 18, 2006
1. Overview
2. RBPs function during germline and early embryo development
3. RBPs function in somatic development
4. RNA targets of RBPs
5. RNA binding specificity of RBPs
6. Closing remarks
7. Acknowledgements
8. References
Roles of chromatin factors in
C. elegans
development
Mingxue Cui and Min Han
Created: May 3, 2007
1. Introduction
2. Chromatin factors in
C. elegans
3. Chromatin factors regulate a number of cellular and developmental processes
4. Summary and future directions
5. Acknowledgements
6. References
Trans-splicing and operons
Thomas Blumenthal
Created: June 25, 2005
1. Trans-splicing
2. Trans-splicing precursors
3. Mechanism of trans-splicing
4. The role of snRNP proteins
5. Evolution and role of trans-splicing
6. Discovery of operons
7. Signals on the polycistronic pre-mRNA for SL2 trans-splicing
8. SL1-type operon
9. Function of operons
10. Evolution of operons in the nematodes
11. Acknowledgements
12. References
Transcription mechanisms
T. Keith Blackwell and Amy K. Walker
Created: September 5, 2006
1. mRNA transcription involves conserved mechanisms, and is regulated at many levels
2. Tools for studying transcription in
C. elegans
3. Global transcriptional repression in the early embryo
4. Analyses of GTF functions in
C. elegans
5. The many faces of Mediator
6. Chromatin regulation, an emerging field in
C. elegans
7. Conclusions
8. Acknowledgements
9. References
Transcriptional regulation
Peter G. Okkema and Michael Krause
Created: December 23, 2005
1. Introduction
2. Tools to study transcriptional regulation
3. Locating cis-acting regulatory elements
4. Simple promoters
5. Complex promoters
6. Trans-acting factors
7. Spatial specificity
8. Future
9. Acknowledgements
10. References
Ubiquitin-mediated pathways in
C.elegans
Edward T. Kipreos
Created: December 1, 2005
1. Overview of ubiquitin conjugation
2. 26S Proteasome
3. Ubiquitin
4. Ubiquitin-activating enzyme (E1)
5. Ubiquitin-conjugating enzymes (E2s)
6. Ubiquitin-protein ligases (E3s)
7. Acknowledgements
8. References
Neurobiology and behavior
Egg-laying
William R. Schafer
Created: December 14, 2005
1. A description of egg-laying behavior
2. Functional roles of egg-laying circuitry components
3. Perspectives
4. References
Male mating behavior
Maureen M. Barr and L. Rene Garcia
Created: June 19, 2006
1. Male mating behavior
2. Hermaphrodite signals for male mating
3. Response behavior
4. Turning behaviors
5. Vulva location
6. Spicule insertion
7. Ejaculation and plugging behavior
8. Concluding remarks
9. Acknowledgements
10. References
Specification of the nervous system
Oliver Hobert
Created: August 8, 2005
1. Overview
2. Neuronal vs. non-neuronal
3. Neuron lineage specification
4. Neuron class specification
5. Neuron subclass specification
6. Maintenance and plasticity of neuronal specification
7. Concepts in neuronal fate specification in
C. elegans
8. Perspectives
9. Acknowledgments
10. References
Synaptogenesis
Yishi Jin
Created: December 23, 2005
1. Introduction
2. Visualizing synapses in living animals
3. Genetic screens for synaptogenesis mutants
4. Presynaptic assembly
5. Synaptic target recognition
6. Synaptic ECM
7. Activity-dependence of synapse development
8. Perspectives
9. Acknowledgement
10. References
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
1. Introduction
2. The 6TM gene families
3. 2TM potassium channels
4. 4TM potassium channels
5. Usefulness of the information in
C. elegans
6. Acknowlegments
7. References
Synaptic function
Janet Richmond
Created: December 30, 2005
1. Overview
2. Exocytosis
3. Endocytosis
4. Summary
5. References
Acetylcholine
James B. Rand
Created: January 30, 2007
1. Introduction to cholinergic metabolism
2. Cholinergic pharmacology and drug-resistant mutants
3. Acetylcholine synthesis and vesicular loading
4. Choline transport
5. Acetylcholinesterases
6. ACh receptors - ligand gated sodium channels
7. Other ACh receptors
8. Cholinergic receptor-associated proteins and genes
9. ACh-mediated behaviors
10. Additional aspects of cholinergic biology
11. Acknowledgement
12. Bibliography
Biogenic amine neurotransmitters in
C. elegans
Daniel L. Chase and Michael R. Koelle
Created: February 20, 2007
1. Introduction
2. Octopamine
3. Tyramine
4. Dopamine
5. Serotonin
6. Acknowledgements
7. Bibliography
GABA
Erik M. Jorgensen
Created: August 31, 2005
1. History of GABA
2. GABA action
3. GABA neurons in nematodes
4. References
Ionotropic glutamate receptors: genetics, behavior and electrophysiology
Penelope J. Brockie and Andres V. Maricq
Created: January 19, 2006
1. Ionotropic glutamate receptors
2. Glutamate-gated chloride channels: distribution and function in
C. elegans
3. Distribution of iGluRs in the nervous system
4. Electrophysiological analysis of iGluRs in
C. elegans
5. The role of iGluRs in worm behavior
6. Mechanisms of iGluR localization, stabilization and function at the synapse
7. Glutamatergic signaling: what questions still remain?
8. Acknowledgements
9. References
Chemosensation in
C. elegans
Cornelia I. Bargmann
Created: October 25, 2006
1. Chemosensation and its regulation by ciliated sensory neurons
2. Signal transduction in chemosensation
3. Complex chemosensory behaviors
4. Concluding remarks
5. Bibliography
Mechanosensation
Miriam B. Goodman
Created: January 6, 2006
1. Introduction
2.
C. elegans
mechanoreceptor neurons
3. Neural circuits linking mechanosensation to locomotion
4. Molecules and mechanisms of mechanotransduction
5. Conclusions
6. Acknowledgements
7. References
Post-embryonic development
Gene expression changes associated with aging in
C. elegans
Tamara R. Golden and Simon Melov
Created: February 12, 2007
1. Aging, models and theories
2. Microarray experimental design and analysis
3. Published gene expression profiling relevant to
C. elegans
aging
4. What have we learned?
5. Future directions
6. References
Sex determination
Introduction to sex determination
Robert K. Herman
Created: December 24, 2005
Hermaphrodite cell-fate specification
Michael A. Herman
Created: January 9, 2006
1. Introduction
2. Basic body plan and role of
Hox
genes
3. HSN neuron
4. Epidermal cell fates
5. Somatic gonad
6. Intestine
7. Conclusions
8. Acknowledgements
9. References
Male development
Scott W. Emmons
Created: November 10, 2005
1. Male and hermaphrodite reproductive structures arise during postembryonic development
2. The major male mating structures form just before the last larval molt
3. Male and hermaphrodite embryogenesis are similar but some essential male cell fates are already established at hatching
4. Multiple pattern formation mechanisms specify cell fates in the tissues that generate the reproductive structures
5. Development of the male sensilla
6. The hindgut is highly differentiated to accommodate the spicules and the joining of the reproductive tract
7. Male-specific neuronal circuitry develops during L4
8. A complex male-specific program generates many new muscles for copulation
9. The cell lineage that gives rise to the asymmetric male gonad is a variation on that of the hermaphrodite
10. Acknowledgements
11. References
Sex determination in the germ line
Ronald Ellis and Tim Schedl
Created: March 5, 2007
1. Sex determination in germ cells
2. The soma acts through HER-1 to regulate the sexual fate of germ cells
3. In germ cells, the sex determination pathway acts through FOG-1 and FOG-3
4. Special regulatory modules promote hermaphrodite spermatogenesis
5. Regulation of
fem-3
translation is required for hermaphrodite oogenesis
6. Crucial questions for the future
7. Acknowledgements
8. References
Somatic sex determination
David Zarkower
Created: February 10, 2006
1. A global sex determination pathway controls sexual dimorphism
2. The balance of X-linked and autosomal signal elements controls xol-1
3. Sex determination and dosage compensation are coordinately regulated
4. HER-1 and TRA-2 provide cell non-autonomous control of sexual fate
5. High versus low tra-1 activity determines somatic cell sexual fates
6. TRA-1 links global and tissue-specific sexual regulation
7. Downstream sexual regulators: the interface between sex determination and sexual differentiation
8. Some aspects of sex determination may be evolutionarily conserved
9. Open questions
10. References
The evolution of nematode sex determination:
C. elegans
as a reference point for comparative biology
Eric S. Haag
Created: December 29, 2005
1. Introduction
2. Genetic and environmental sex determination in nematodes
3. Deep conservation and cooption in the evolution of nematode sex determination
4. Conservation of
C. elegans
pathway components:
C. briggsae
as the ruler
5. Two cases of species-specific genes
6. Comparative functional studies
7. Mating system evolution in
Caenorhabditis
8. Acknowledgements
9. References
Vulval development
Paul W. Sternberg
Created: June 25, 2005
1. Introduction
2. Generation of vulval precursor cells
3. Overview of VPC 1°-2°-3° pattern formation
4. Induction of the vulva by the anchor cell
5. Physiological inputs to vulval development
6. Negative regulation of induction
7. LIN-12-mediated lateral signaling
8. Coupling of LET-23 and LIN-12 signaling
9. Patterning of adult cell types
10. The vulval-uterine connection
11. Morphogenesis
12. Concluding remarks
13. Acknowledgments
14. References
X-Chromosome dosage compensation
Barbara J. Meyer
Created: June 25, 2005
1. Introduction
2. Genes encoding the dosage compensation machinery
3. Dosage compensation proteins assemble onto hermaphrodite X chromosomes to regulate gene expression and also function separately in chromosome segregation
4. Sex-specific targeting of the dosage compensation complex to hermaphrodite X chromosomes
5. The X:A signal controls dosage compensation by regulating xol-1
6. Recruitment of the dosage compensation complex for gene-specific versus chromosome-wide repression
7. Recruitment and spreading of the dosage compensation complex along hermaphrodite X chromosomes
8. Molecular identification of discrete X-recognition elements
9. Future endeavors
10. References
Signal transduction
Introduction to signal transduction
Iva Greenwald
Created: September 9, 2005
Genomic overview of protein kinases
Gerard Manning
Created: December 13, 2005
1. Introduction
2. The
C. elegans
kinome
3. Kinase evolution
4. Recent expansions and inventions in the worm kinome
5. The
C. briggsae
kinome
6. Phosphatases
7. References
A.Appendix A: Classification of worm kinases
RTK/Ras/MAPK signaling
Meera V. Sundaram
Created: February 11, 2006
1. Introduction
2. Overview of the core RTK/Ras/MAPK signal transduction pathway
3. Phenotypes of Ras pathway mutants
4. Screens used to identify Ras pathway components
5. Growth factors and RTKs that signal through Ras/MAPK
6. Regulators of LIN-3/EGF and EGL-17/FGF
7. Regulators and targets of LET-23/EGFR and EGL-15/FGFR
8. Regulators of Ras activity
9. Regulators of the Raf/MEK/ERK kinase cascade
10. Targets of MPK-1 ERK, and other factors influencing downstream responses
11. Interactions between the RTK/Ras/MAPK pathway and other signaling pathways
12. Conclusions and future prospects
14. References
Heterotrimeric G proteins in
C. elegans
Carol Bastiani and Jane Mendel
Created: October 13, 2006
1. Introduction
2. Gαs
3. Gαq
4. Regulators of EGL-30/G protein signaling network
5. Gαo
6. Gα12
7. GPAs
8. References
Homologs of the Hh signalling network in
C. elegans
Thomas R. Bürglin and Patricia E. Kuwabara
Created: January 28, 2006
1. Introduction
2. Hh pathway components in
C. elegans
3. Hh-r genes, the structure
4. Modification and function of Hh-r genes
5. SSD Proteins: PTC and PTC-related proteins
6. Role of PTC proteins in
C. elegans
7. Other SSD proteins provide clues to PTC and PTR function
8. Evolution
9. Summary
10. Acknowledgements
11. References
LIN-12/Notch signaling in
C. elegans
Iva Greenwald
Created: August 8, 2005
1. Introduction
2. Genetic identification and characterization of LIN-12 and GLP-1
3. Overview of signal transduction by LIN-12 and GLP-1
4. Identification and characterization of core components
5. Identification of modulators of
lin-12
and
glp-1
activity
6. Lateral specification and induction mediated by LIN-12 and GLP-1
7. Future prospects
8. Acknowledgements
9. References
Nuclear hormone receptors in
C. elegans
Adam Antebi
Created: January 3, 2006
1. Introduction
2. Structure and mechanism
3. Comparative phylogeny
4. Physiology
5. Sex determination
6. The molt cycle
7. Dauer formation
8. Xenobiotic response
9. Metabolic control
10. Neural development
11. Future directions
12. Acknowledgements
13. References
Signaling in the immune response
Jonathan J. Ewbank
Created: January 23, 2006
1. Introduction
2. The DBL-1 pathway
3. The DAF-2/DAF-16 pathway
4. The MAP kinase pathway
5. Role of Toll-like receptors
6. The ERK pathway
7. Recognition of infection through stress response
8. Perspectives
9. Acknowledgements
10. References
Small GTPases
Erik A. Lundquist
Created: January 17, 2006
1. Ras-superfamily GTPases in
C. elegans
2. Ras/Ral/Rap family GTPases
3. Summary and future directions
4. Acknowledgments
5. References
TGF-β signaling
Cathy Savage-Dunn
Created: September 9, 2005
1. Overview
2. Dauer pathway
3. Sma/Mab pathway
4. UNC-129
5. Acknowledgements
6. References
The putative chemoreceptor families of
C. elegans
Hugh M. Robertson and James H. Thomas
Created: January 6, 2006
1. Introduction
2. Summary of the chemoreceptor families
3. Gene expansions
4. Gene clusters
5. Function and expression patterns
6. Acknowledgements
7. References
Wnt signaling
David M. Eisenmann
Created: June 25, 2005
1. Introduction
2. Canonical and noncanonical Wnt signaling in flies and vertebrates
3. Wnt pathway components in
C. elegans
4. Canonical and noncanonical Wnt pathways in
C. elegans
5. Processes utilizing a canonical Wnt/BAR-1 pathway
6. Processes utilizing a noncanonical Wnt/WRM-1 pathway
7. Differences in noncanonical pathways
8. Other processes utilizing Wnt pathway components
9. Conclusion
10. Acknowledgements
11. References
The germ line
Introduction to the germ line
E. Jane Albert Hubbard and David Greenstein
Created: September 1, 2005
1. An unbroken chain: the germ line
2. Embryogenesis and early L1: germline specification
3. L1-L3: germline proliferation, survival and differentiation
4. Late larval and adult stages: germline proliferation and gametogenesis
5. Closing the circle: fertilization
Control of oocyte meiotic maturation and fertilization
David Greenstein
Created: December 28, 2005
1. Overview
2. Control of oocyte meiotic maturation
3. Control of ovulation
4. Control of fertilization
5. Conclusion
6. Acknowledgments
7. References
Germline chromatin
Christine E. Schaner and William G. Kelly
Created: January 24, 2006
1. General considerations
2. Histone modifications and chromatin structure
3. Embryonic germline chromatin
4. Post-embryonic germline chromatin
5. Completing the cycle: the zygote
6. Special circumstances: germline silencing of transgenes
7. Germline goals include genome protection
8. Future directions
9. References
Germline genomics
Valerie Reinke
Created: January 20, 2006
1. Regulatory mechanisms of germline gene expression
2. Gene expression profiling of the germ line
3. Chromosome bias for genes with germline-enriched expression
4. Integration of germline functional genomic data
5. Future directions
6. Useful links for germline genomics
7. References
Germline proliferation and its control
Judith Kimble and Sarah L. Crittenden
Created: August 15, 2005
1. Overview
2. Course of germline proliferation
3. Control of germline proliferation by Notch signaling and the somatic gonad
4. Control of the mitosis/meiosis decision
5. Other genes affecting germline proliferation
6. References
Specification of the germ line
Susan Strome
Created: July 28, 2005
1. Overview
2. pie-1 and transcriptional repression
3. The MES proteins and regulation of chromatin
4. P granules and regulation of RNA
5. mep-1 and avoiding germline specification
6. Summary and future directions
7. References
Spermatogenesis
S.W. L'Hernault
Created: February 20, 2006
1. Overview
2. Wild-type spermatogenesis
3. Identification of spermatogenesis defective mutants
4. Translational control during spermatogenesis
5. Mutants that affect sperm meiosis
6. Mutants affecting FB-MOs
7. Cytoskeletal mutants
8. Sex-specific aspects of spermiogenesis
9. Fertilization mutants
10. Post-fertilization mutants
11. Future prospects
12. Acknowledgements
13. References
WormMethods
Behavior
Anne C. Hart, ed
Created: July 3, 2006
1. Introduction
2. Mechanosensation
3. Osmotic avoidance
4. Chemosensation
5. Learning, adaptation and habituation
6. Thermal responses
7. Locomotion
8. Feeding
9. Egg-laying, males and mating
10. Assays of
C. elegans
reproductive behaviors
11. Defecation
12. Galvanotaxis
13. Circadian rhythms
14. References
Biochemistry and molecular biology
Albertha J. M. Walhout and Simon J. Boulton
Created: February 13, 2006
1. The yeast two-hybrid system
2. Tandem immuno-affinity purification
3. Acknowledgments
4. References
Introduction and basics
David Fay
Created: February 17, 2006
1. Fundamentals
2. A word about nomenclature
3. Types of mutations
4. Genetic shorthand
5. Feeding, growing, and maintaining worms
6. Worm chromosomes
7. Setting up crosses
8. The big picture
9. References
Two-point mapping with genetic markers
David Fay
Created: June 14, 2006
1. The basics
2. Calculating map distances
3. Other considerations
4. References
Three-point mapping with genetic markers
David Fay
Created: February 17, 2006
1. Basics
2. Saving recombinants
3. Some words of caution
4. Finding and picking recombinants
5. Exit strategies
Dominant mutations
David Fay and Andy Spencer
Created: February 17, 2006
1. Basics
2. Isolating dominant alleles
3. Mapping a dominant mutation
4. Different types of dominant mutations
5. Genetic tests for dominance classes
6. References
Making compound mutants
David Fay
Created: June 14, 2006
1. Background
2. Making double mutants
3. Using the power of counter-selection
4. Crossing mutants into reporter lines
Mapping with deficiencies and duplications
David Fay
Created: June 14, 2006
1. Basics
2. Setting up crosses with deficiencies
3. Mapping with duplications
4. References
SNPs: Introduction and two-point mapping
David Fay and Aaron Bender
Created: February 17, 2006
1. Basics
2. The SNP database
3. Using different types of SNPs
4. Two-point mapping with SNPs
5. Worm PCR protocol
6. References
SNPs: Three-point mapping
David Fay
Created: February 17, 2006
1. The basics
2. Examples of SNP mapping
3. General SNP mapping strategies
Suppressor mutations
David Fay and Wade Johnson
Created: February 17, 2006
1. Basics
2. Considerations and caveats
3. Suppressor identification strategies
4. Mapping suppressor mutations
Synthetic and enhancer mutations
David Fay
Created: February 17, 2006
1. Basics
2. Making mapping strains
3. Two-point mapping with genetic markers
4. Three-point mapping with genetic markers
5. Deficiency mapping
6. Using SNPs to map synthetic mutants
Genetic balancers
Mark L. Edgley, David L. Baillie, Donald L. Riddle, and Ann M. Rose
Created: April 6, 2006
1. Introduction
2. Types of balancers
3. Practical considerations of balancer use
4. The balancer map
5. A field guide to balancers
6. References
Genetic dissection of developmental pathways
Linda S. Huang and Paul W. Sternberg
Created: June 14, 2006
1. Introduction
2. Epistasis analysis
3. Epistasis analysis of switch regulation pathways
4. Extragenic suppressors
5. Prospects: use of new technologies for pathway analysis
6. Conclusion
7. Acknowledgements
8. References
Maintenance of
C. elegans
Theresa Stiernagle
Created: February 11, 2006
1. Introduction
2. Acquiring strains from the Caenorhabditis Genetics Center (CGC)
3. Preparation of growth media
4. Culturing
C. elegans
on petri plates
5. Growth of
C. elegans
in liquid medium
6. Cleaning contaminated
C. elegans
stocks
7. Freezing and recovery of
C. elegans
stocks
8. Acknowledgements
9. References
Nomarski images for learning the anatomy, with tips for mosaic analysis
John Yochem
Created: January 24, 2006
1. An overview
2. The tutorial
3. Acknowledgments
4. References
Profiling
C. elegans
gene expression with DNA microarrays
Douglas S. Portman
Created: January 20, 2006
1. Planning your experiment
2. Protocols
3. Following up
4. References
Immunohistochemistry
Janet S. Duerr
Created: June 19, 2006
1. Introduction
2. Protocols and procedures
3. References
Protocols for large scale
in situ
hybridization on
C. elegans
larvae
Tomoko Motohashi, Hiroaki Tabara, and Yuji Kohara
Created: July 24, 2006
1. Preparation of staged worms
2. Fixation
3. Hybridization and detection
4. Reagents
Reporter gene fusions
Thomas Boulin, John F. Etchberger, and Oliver Hobert
Created: April 5, 2006
1. General considerations
2. Protocols
3. References
RNA
in situ
hybridization of dissected gonads
Min-Ho Lee and Tim Schedl
Created: June 14, 2006
1. Introduction
2. General expression pattern
3. Materials
4. Procedure
5. Acknowledgements
6. References
Methods in cell biology
Shai Shaham, ed
Created: January 2, 2006
1. Introduction
2. Visualizing cells and their components
3. Protein-protein and protein-DNA interactions
4. Specific methods in
C. elegans
cell biology
5. Embryonic cell culture
6. References
Isolation of
C. elegans
and related nematodes
Antoine Barrière and Marie-Anne Félix
Created: July 17, 2006
1. Introduction
2. Isolation on an agar culture plate
3. Baermann funnel
4. Centrifugal flotation
5. Identifying
Caenorhabditis elegans
and other species
6. Typical time course and organization of an isolation experiment
7. Culture conditions
8. Freezing conditions
9. References
Pristionchus pacificus
genetic protocols
Andre Pires da Silva
Created: July 17, 2006
1. Introduction
2. Protocols
3. References
Pristionchus pacificus
genomics: from genetics to genome sequence
Christoph Dieterich, Waltraud Roeseler, and Jagan Srinivasan
Created: August 14, 2006
1. Introduction
2. Genomic resources for
P. pacificus
3. Genetic linkage map of
P. pacificus
4. Physical map of
P. pacificus
5. Bioinformatic resources for
P. pacificus
6. Acknowledgements
7. References
Strongyloides stercoralis
: a model for translational research on parasitic nematode biology
James B. Lok
Created: February 17, 2007
1. Introduction
2. Laboratory hosts for
S. stercoralis
3. Biosafety
4.
In vitro
cultivation of free-living stages
5. Transgenesis
6. Neuronal ablation
7. Future prospects
8. Afterword
9. Acknowledgments
10. References
Neurophysiological methods in
C. elegans
: an introduction
William R. Schafer
Created: June 2, 2006
1. Electrophysiology
2. Optical imaging
3.
In vitro
physiology
4. References
Caenorhabditis briggsae
methods
Scott E. Baird and Helen M. Chamberlin
Created: December 18, 2006
1. The
Caenorhabditis briggsae
model system
2. Natural history and population biology
3. Genetics
4. Reverse genetic methods
5. Online resources for
C. briggsae
genetics and genomics
6. References
Culture of embryonic
C. elegans
cells for electrophysiological and pharmacological analyses
Laura Bianchi and Monica Driscoll
Created: September 30, 2006
1. Introduction
2. A long-sought method for isolation and culture of embryonic
C. elegans
cells
3. The protocol
4. Cultured cells differentiate and behave
in vitro
as they do
in vivo
5. Electrophysiological techniques applicable to
C. elegans
cultured cells
6. Acknowledgments
7. References
Electrophysiological recordings from the neuromuscular junction of
C. elegans
Janet E. Richmond
Created: October 6, 2006
1. Introduction
2. Equipment
3. Materials
4. Dissection
5. Recording
6. References
Electrophysiological recordings from the pharynx
Alan Cook, Christopher J. Franks, and Lindy Holden-Dye
Created: May 17, 2006
1. Summary of available methods
2. Protocol 1. Extrapharyngeal recordings (EPGs)
3. Protocol 2. Intracellular recordings from the terminal bulb
4. Protocol 3. Patch clamp recordings from the pharynx
5. Acknowledgements
6. References
Heterologous expression of
C. elegans
ion channels in
Xenopus
oocytes
Laura Bianchi and Monica Driscoll
Created: August 1, 2006
1. Introduction
2. Basic characteristics of a
Xenopus
oocyte
3. cDNA cloning into the appropriate vectors
4.
In vitro
RNA synthesis
5. Oocyte procurement
6. Oocyte microinjection
7. Two-electrode-voltage clamp
8. Detecting proteins at the oocyte surface by fluorescent methods
9. Extracting proteins from
Xenopus
oocytes for immunoprecipitations and western blotting
10. Limitations of using
Xenopus
oocytes for expression of exogenous proteins
11. Concluding remarks
13. References
Imaging the activity of neurons and muscles
Rex A. Kerr
Created: June 2, 2006
1. Introduction
2. Background and theory
3. Protocols
4. References
Reverse genetics
Julie Ahringer, ed
Created: April 6, 2006
1. Introduction to reverse genetics in
C. elegans
2. Using RNAi to knockdown gene function
3. RNAi by injection
4. RNAi by soaking
5. RNAi feeding on agar plates
6. RNAi feeding in liquid culture (96 well format)
7. Construction and screening of deletion mutant libraries to generate
C. elegans
gene knockouts
8. References
Transformation and microinjection
Thomas C. Evans, ed
Created: April 6, 2006
1. Introduction
2. General considerations for DNA transformation
3. Microinjection
4. DNA transformation: Creating repetitive extrachromosomal arrays by microinjection
5. DNA transformation: Creating complex arrays by microinjection
6. Integration of extrachromosomal arrays
7. DNA transformation by gene bombardment
8. Future prospects: Targeted gene replacement
9. Acknowledgments
10. References
Web resources for
C. elegans
studies
Raymond Lee
Created: December 28, 2005
1. Introduction
2. Portal and knowledge environment
3. Literature search
4. Gene function
5. Sequence analysis-retrieval
6. Sequence analysis-search for homologous sequences
7. Genetics
8. Cell and anatomy
9. Concluding remark
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