More Resources

About C. elegans

C. elegans as Model Organism
Why study C. elegans? C. elegans general biology, e.g.: development, life cycle, chromosomes is introduced.
Dauer World
Introduction page for non-specialists who want to learn about C. elegans. It also introduces to the Riddle Lab which studies aging based on Dauer Larvae ( third-stage larvae- characterized by high life-endurance).
The Genes We Share
Hosted by HHMI. The genes we share with yeasts, flies, worms and mice: New clues to human health & disease.
C. elegans Project
Hosted by the Wellcome Trust Sanger Institute. It links to Caenorhabditis Genome Sequencing Projects.
Model Organisms Virtual Library
The WWW virtual library with information about "what is a model organism?", "general model organism resources", "comparative genomics of model and other organsisms" and also information about popular model organisms.
What Are Model Organisms?
Hosted by the Wellcome Trust. It describes what model organisms are and why study them. Examples are yeast, flies, worms, fish, mice, chickens and frogs.

C. elegans research

The Acembly/AceView genes
"AceView offers an integrated view of the human, nematode and Arabidopsis genes reconstructed by co-alignment of all publicly available mRNAs and ESTs on the genome sequence."
Bang Nembase
A very comprehensive website that covers materials from evolution/development through gene identification by expressed sequence tags to a variety of nematodes.
Caenorhabditis Genetics Center
Hosted at the University of Minnesota. This site contains links to Worm Breeder's Gazette (WBG), C. elegans bibliography, C. elegans nomenclature & C. elegans strain list etc.
The C. elegans Gene Knockout Consortium
Its mission is to facilitate genetic research of C. elegans through the production of deletion alleles at specified gene targets.
C.elegans Genome Browser
A ll about C. elegans genome. This is a good place to look up a gene or a chromosome and to compare them with other species.
C.elegans Server
C. elegans compendium: from recent research through papers, movies, worm literature sources to laboratories. It contains a good source of comprehensive (also for non-specialist) background information.
The Center for C. elegans Anatomy
It is a great place to find various lab techniques used in C. elegans research
ElegansNet
Provides various search engines (google, NCBI --) for searching information about C. elegans. It is a "Search Site for linking to Researchers, Research Topics, and Resources in Molecular, Cellular, System, and Organism Biology."
Genome Sequencing
This is a powerful site about C. elegans genome sequencing: history, methods and current projects worldwide (contains advanced data).
Interactome
A Map of the Interactome Network of the Metazoan C.elegans.
The Intronerator
A set of tools used for browsing cDNA alignments in the C. elegans genome. There are also links to websites including methods of DNA sequencing, introns, exons or cDNA pasting.
RNAi Database: results from RNAi phenotypic analysis of genes in C. elegans can be found.
Textpresso
An information retrieval and extraction system for biological literature - C. elegans version.
Worm Atlas
“A database of behavioral and structural anatomy of C. elegans”. This website provides lab methods such as cell identification. There is also a discussion forum.
WormBook
WormBook is the online text companion to WormBase, the C. elegans model organism database. WormBook contains original reviews on all aspects of C. elegans biology and up-to-date descriptions of technical procedures used to study this animal.
WORMBASE
The most comprehensive site for C. elegans research resources.
WORMATLAS
A database of behavioral and structural anatomy of Caenorhabditis elegans.

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C. elegans education

The Elegant Worm- Exploration
This site presents diverse research taking place on Vanderbilt campus. One of current projects is Miller’s "worm farm" which studies a mutant worm that can’t move backwards. The researchers try to investigate the genetic background of the process.

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Cell biology

The Abbalay Lab
The aim of this lab is to investigate the genetic basis of innate immunity. That means gaining insight into processes that make hosts either resistant or susceptible to bacteria. Researchers are trying to find differences and similarities between immune system in the worm and the vertabrate immune system.
The Alesandro Puoti Lab
This lab is investigating germ cell fates. They are interested in questions such as what factors trigger meiosis or mitosis in cell and what causes germ cells to differentiate either into oocytes or sperm.
Center for Cell Dynamics
Website focused on polarity in embryo development, especially during the first cell division. The research of interest includes determining how asymmetrical division works in the zygote.
The Colaiacovo Lab
This lab studies the synaptonemal complex- a structure found during meiosis. Assembly of this structure may be studied in C.elegans because its germ line cells account for more than a half of the cells in the worm.
The C. elegans Group
Study of DNA damage signaling, cell cycle and apoptosis in correlation with cancer tumor diagnostics. The objective is to find out what is required to initiate self-repair or self-destruction processes in cells.
The Goldstein Lab (movies)
This site presents movies from embryo to adult worm.
The Meyer Lab
The website is still under construction, but the lab investigates sex determination - in particular, what factors make a developing organism decide to become female or male. They are also interested in X chromosome compensation and segregation during division.
The Moerman Lab
The research focus is on muscle development in C. elegans, with emphasis on proteins that make up a sarcomere.
NASA's Space Biology Outreach Program
It is a special project conducted by NASA based on effects of spaceflight on C. elegans, with emphasis on tissue development, cell apoptosis, muscle physiology and gene expression.
The Rose Worm Lab
The Rose Lab tries to find patterns in meiotic distribution and cross-over occurrence. They are investigating questions such as why does crossing-over vary in frequency in different regions of chromosomes.
The Seydoux Lab
Researchers in the Seydoux lab study mechanisms that distinguish the formation of somatic cells from germ cells in C. elegans. One of the projects investigates molecular regulators responsible for germ cell fate, another focuses on protein degradation in determining embryonic polarity.
The Shaman Lab
This website provides a study of mechanisms and regulators of apoptosis in C. elegans. Research is based on genes that decide about cell fate. The second part of research is aimed at understanding the development and roles of glial cells (a poorly understood but common cell type in the human brain).
The Shedl Lab
Website on the role of genes in germ cell development. The focus is on the distal tip cell (DTC) (a structure that determines when germ cells should enter meiosis) and genes that are crucial for other stages of meiosis. Shedl Lab is also interested in molecular determinants of gender.
The Singson Lab
Researchers in this lab are studying mutations characteristic only for germ cells. They are trying to understand the processes occurring at fertilization and the genes that are involved.
The Starr Lab
The main interest of the lab is the positioning organelles in cell. The Starr Lab is trying to identify proteins that contribute to nuclear migration and understand its importance.
Wormland-Organogenesis
How does development from a single cell to a complicated organ occur? This includes investigations on cell-signaling in the formation of left-asymmetry as well as apoptosis regulation.

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Developmental Biology

The Ambros Lab at Dartmouth
One goal of Ambros research is to understand more about the genetic and molecular mechanisms that control C. elegans development. This is done by analyzing genes that affect the timing of the larval stages. Currently the special interest is small RNAs (microRNAs).
The Chin-Sang Lab
This is a study of regulatory molecules crucial for the development of C. elegans cells during morphogenesis. Research may be related in the future to the study of cancer.
The Chrisholm Lab Research in the Chrisholm lab focuses on tissue differentiation. The point is to investigate the processes that occurr while cells remodel their shape to acquire a new role in the body. That means understanding genetic regulators responsible for transcription.
The Chu Lab
The Chu Group investigates reasons for male infertility. Proteins that build up sperm chromatin may be important in this phenomenon and therefore researchers use molecular approach to study this process.
The Emmons Laboratory
Emmons lab is conducting investigations on cell fate specification, nervous system development, evolution and sexual behavior in C. elegans. They are trying to find answers for questions such as: how do genes determine behavior, how does genetic program evolve, and how do patterning genes determine properties of neurons.
The Herman Lab
This website presents study of genetic basics for animal development and behavior. That means scrutinizing genes important for development and identifying anatomical foci of these genes.
The Leroi Lab
The research of this laboratory is directed at understanding the evolutionary and developmental mechanisms that occur when a cell grows and divides. In particular, this lab is interested in the evolution of body size in nematodes.
The Lithgow Lab
The Lithgow lab focuses on the phenomenon of ageing using the worm. That involves finding aging genes and investigating factors that accelerate or inhibit ageing, such as antioxidants, hormones, DNA damages etc.
The Spence Lab
The aim of of the lab is to study sex determination and sexual differentiation. Since C. elegans can be either a hermaphrodite or male it provides a great opportunity for the Spence group to investigate the genetics underlying this process.
The Sternberg Lab
In this lab genetics is used to research cell development - differentiation, specialization and factors that trigger specific cell patterns. Additionally, the Sternberg group investigates mating behavior in order to identify genes responsible for neuronal functions.
The Virtual Embryo
This website presents developmental biology in context of embryonic induction: what processes need to occur so that a simple cell becomes specialized and what factors determine its fate.
The Ward Lab
The Ward Lab is a great resource for information about genetics, genomics and genes. It includes links to other labs and websites. The ongoing research is on sperm development and maturation.
The Wood Lab
The main focus of the lab is to examine mechanisms controlling embryo development.
Of special interest is the determination of cell polarity during the first cell division and the influence of genes used during embryogenesis to delineate body shape.

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Genetics

The Fire Lab
The Fire Lab studies how cells respond the introduction of foreign or unwanted genomic materials. One of the interesting experiments done was to inject foreign DNA or RNA into cells and it is not expressed (silencing effect). The major emphasis of the lab is now on the mechanism of RNAi.
The Fitch Lab
Main focus of the lab is to determine the role of genes in generating organism and population diversity through evolution. Currently there are three related research projects: male tail development (to study the processes influencing morphogenesis), evolution and systematics of nematode.
Genetic Nomenclature for Nematodes & Worm genetic nomenclature basics
The name of C. elegans genes follow specific rules of nomenclature. These sites explain this process.
The Genome of the Nematode C. elegans
This is a good starting place for learning about the C. elegans genome. It includes information about such topics as genes, clone-by-clone sequencing, lifecycles, RNAi, microarrays etc.
The Gronostajski Lab
Gronostajski Lab researches interactions between proteins, DNA, RNA transcription and metazoan development. In particular they study the Nuclear Factor I (NFI) and T-box families of site-specific DNA binding proteins. The NFI is expressed primarily during embryogenesis whereas in vertebrates it is also expressed in the adult.
The Hope Laboratory
Gene expression coordination during animal development is what this lab studies. Currently the Hope Lab employs GFP fusion proteins to better understand the organization of gene expression during development time.
NemaGENETAG
Because of similarities with the human genome, C. elegans may be used to study human pathologies. NemaGENETAG consortium is aiming to create a transposon library because transposons systems may be used for many genome manipulations, such as inserting new sequences.
The Plasterk Group
Their research concentrates on how the genome is protected from mutations and transposons phenomenon. It is not well understood how transposon regulation and mutator genes function and what their role in preventing mutations in the genome is.
The Roy Lab
This lab is interested in cell migration. Researchers are studying the mechanisms that lead a cell to its target and the genes that participate in this guidance.
The Vidal Lab
The goal of this lab is to approach C. elegans genome by studying several its aspects such as interactions between proteins, protein pathways characterization, cancer susceptibility genes or immunity mechanisms.

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Evolutionary biology

The Emmons Laboratory
Emmons lab is conducting investigations on cell fate specification, nervous system development, evolution and sexual behavior in C. elegans. They are trying to find answers for questions such as: how do genes determine behavior, how does a genetic program evolve, and how do patterning genes determine the properties of neurons.
The Fitch Lab
Main focus of the lab is to determine the role of genes in generating organism and population diversity through evolution. Currently there are three related research projects: male tail development (to study the processes influencing morphogenesis), evolution and systematics of nematode.
The Gronostajski Lab
Gronostajski Lab researches interactions between proteins, DNA, RNA transcription and metazoan development. In particular they study the Nuclear Factor I (NFI) and T-box families of site-specific DNA binding proteins. The NFI is expressed primarily during embryogenesis whereas in vertebrates it is also expressed in the adult.
The Leroi Lab
The research of this laboratory is directed at understanding the evolutionary and developmental mechanisms that occur when a cell grows and divides. In particular, this lab is interested in the evolution of body size in nematodes.

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Neuroscience

The Aroian Lab at San Diego
The research aim of this lab is how crystal proteins may protect plants from nematode and other animals that are trying to eat them. C. elegans is used as a model organism to understand what makes the worms either susceptible or resistant to these substances.
An interesting side of this research is that nematodes have an innate immune system in contrast to higher animals which have an adaptive immune system.
The Bessereau Lab
Study of neurotransmitters release and mechanisms governing adaptation to nicotinic agonists is presented on this website
The De bono Laboratory
Do genes influence behavior? Researchers from this lab are trying to determine the role of genes in the behavior of C. elegans. Sensory neurons in contact with noxious stimuli causes solitary behavior whereas positive environmental signals result in more social behavior.
The Jin Lab
Neural development studies in this lab concentrate on specialized neurons and synaptic connections between them. One of the projects examines genes responsible for expression of a phenotype which impairs the worm's ability to move smoothly - what are the properties of the locomotive neuron and its genetic program. Another study examines the remodeling of motor neurons during life which is quite unusual: the cell morphology stays the same but information is reversed.
The Kaplan Lab
Synapses play a crucial role in brain signaling and, consequently, in behavior. The focus of Kaplan Group is to investigate signaling in the worm brain in relation to synaptic diversity and how differences between the signals affect their functions. A current project examines two G proteins (Go and Gq) that antagonistically regulate neurotransmitter secretion in specific synapses.
The Nonet Lab -Dissecting Synapse Function and Development
Research in this lab concentrates primarily on synapses, in particular GTP-ase proteins that participate in synaptic transmission. By investigating two rab proteins, researchers are trying to find out that what their role is in secretion. Another aspect of this project is identifying genes that regulate these processes.
Martin Chalfie
C. elegans is used to research neuron development. The major questions that interest this lab are: what does it take to form a highly specialized neuronal cell and what are the molecular processes involved in mechanosensation (the formation of the various senses).
The Portman Lab
Members of Portman group define their objectives in these questions: how does the genome encode the information that generates a functional nervous system, how do genetic regulatory networks ensure that neurons of the right type are generated in the right place, at the right time and in the right number, and how do the resulting neuronal circuits integrate sensory information and generate coherent behavioral outputs.
The Schafer Lab
This neurological lab is investigating the development of sensory circuits indispensable not only for touch avoidance or chemotaxis but also for nicotine adaptation.
The Shen Lab
There are three stages to neural development: cell fate specification, axon guidance and synapse formation. The Shen Lab studies processes occurring during and after axon guidance, in particular synapse formation.
The Sengupta Lab
Research in this lab focuses on the olfactory and thermosensory neurons. The main areas of interest include the molecular basis that determines a cell's neuronal fate, acquisition of specialized functions and plasticity of sensory behaviors (changes in neuronal receptors in particular life stages or under specific conditions, such as food depravation).
The Wightman Lab
The gene fax-1 is responsible for the development of certain neurons. The Wightman Lab is studying mutations in this gene that, in humans, may cause blindness by disrupting photoreceptors cells in the retina.
The Worm Learning Lab
This website examines associative learning in C. elegans in the context of chemotactic movements. So far, researchers have found that worms can learn to distinguish between differnt ions. This type of analysis permits the study of genes necessary for learning.

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Research Protocols

Worm Culture

Dauer

• Dauer Pheromone Prep
• Making dauers with pheromone

Others

• Bacteria for worm food
• "Chunking" worms- easy strain maintenance
• Cleaning worms by floating on sucrose
• Cleaning worm stocks
• Cleaning Worm Stocks
• Cloning form low melt agarose
• Cool growth competent E. coli
• Culturing Worms
• Decontaminating worm population to remove fungi and bacteria
• Development of techniques for primary culture of C. elegans
• Development of techniques for primary culture of C. elegans embryonic neurons Laird Bloom
- Part 1
• Development of techniques for primary culture of C. elegans embryonic neurons
-Part 2
-Part 3
• ES cell culture
• Freezing worms
• Growing worms in liquid
• Liquid culture of worms #1
• Liquid culture of worms #2
• Liquid culture of worms in with fermentor
• Maintenance of lin2 strain C.elegans Worms
• N2 Development time at different temperatures #1
• N2 development times at different temperatures #2
• Preparation pf Petri plates
• Preparation of synchronized cultures (PDF)
• Preparation of Seeded NGM Plates For Worm Food
• Response to food
• Quick bleach cleaning of small numbers of worms
• Quick bleach decontamination of small numbers of C. elegans
• Synchronizing worm cultures
• Testing for Levasimole resistance

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Solutions

Buffer

• Buffers
• Embryo buffers

Media

• S-medium, S-basal and trace metal solution

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Mutagenesis

• C. elegans gene knockout protocol
• Chemical deletion mutagenesis
• DpnI mediated site-directed mutagenesis
• EMS mutagenesis
• ems mutagenesis
• Gene knockout with conventional mutagenesis
• Irradiation of worms in Y-building facility
• Making males by heat shock
• Transposon Insertion Mutagenesis

Mapping

• Mapping mutants using STS Polymorphisms
• Snip-SNP mapping with BSA
• Snip-SNP mapping with Polymorphisms
• SNP characteristics

Screening

• F2 mutant screen
• Oligos for screening of deletion libraries
• Rapid screen of transformants

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Injections

• Creating Transgenic C. elegans with Extrachromosomal Arrays
• Integrating extrachromosonal arrays
• Microinjecting worms
• Procedures for preparing pads and needles
• Transformation by injection into syncytial C.elegans germline

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Molecular & Biochemical Techniques

Blotting

• Western Blot Transfer and Detection
• Worm genomic southern blots
• Worm extracts and western blotting

Cell Culture

• Development of techniques form primary culture of embryonic neurons

DNA

• cDNA amplification
• Gel purification of DNA fragments
• Genomic DNA preparation
• Phenol extraction from low melt agarose
• Plasmid DNA prep
• Silica clean-up of DNA
• Worm genomic DNA prep
• “In gel-o” ligations
• Cosmid Preparation
• Cosmid Vectors Codes for C. elegans

RNA

• aRNA amplification
• Joe’s mRNA preparation
• Nematode genomic DNA isolation
• RNA isolation (TRIZO method)
• RNA preparation
• RNA synthesis (in vitro transcription)
• Total RNA preparation
• Yale RNA preparation

PCR

• PCR analysis of dead eggs from C. elegans
• Polymerase Chain Reaction
• Single Worm PCR #1
• Single Worm PCR #2
• Single egg PCR reactions

Proteins

• Affinity Purification of Antibodies to GST-fusion Proteins
• Bacillus thuringiensis (Bt) Toxin Purification
• Electrotransfer of proteins (electroblotting)
• Immunoprecipation
• Preparation of total SDS-soluble nematode proteins
• Preparation of GST-capping protein
• Protease inhibitors
• Purification of MBP Fusion Protein
• Purification of GST-Fusion Protein
• SDS- Page

Transforming Worms

• Integrating extrachromosanal array into C. elegans chromomosomes
• Large Scale Transformation by microparticle bombardments

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RNAi

• 96-well format RNAi in liquid culture
• Bacteria mediated RNAi protocol
• Double Stranded RNA interference (RNAi ) in C. elegans
• dsRNA preparation for RNAi by injection in C. elegans (PDF)
• Making RNAi primers
• Microinjection of RNA into C. elegans
• RNAi experiments
• RNA injection
• Silencing Genomes

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Staining

Antibody staining

• Antibody purification and Testing
• C. elegans P-granule antibody staining
• C. elegans Hermaphrodite or Embryo Antibody Staining: Seydoux and Dunn Method
• DCF staining
• Freeze- fracture for Immunofluorescence of Embryos
• How are antibodies produced?
With animation, it describes how lymphocytes process antigens to produce antibodies.
• Immunofluorescence of C. elegans Embryos
• Serotonin Antibody Straining
- Short version
- Long and detailed version
• Solutions for Anti-Serotonin protocol
• PAR1-staining
• Preabsorbing Antisera with C. elegans Acetone Powder
•What is an Antibody?
It describes the structure and functionality of antibody with a 2D illustration.

Fixation

• Electron Microscopy (EM) Fixation of C. elegans Embryos
• EM fixation of embryos
• Fixation
• Fixation and Permeabilization
• Fixation and staining parameters
• Standard Osmium/Glutheraldehyde Fixation
• Microwave fixes

Others

• Bacillus Thuringiensis Crystal Staining
• C. elegans: Whole Animal DAPI Staining
• Double dye filling
• Dye filling to stain amphid and phasmid neurons
• In situ hybridization
• Gonad dissections, fixation; DAPI staining, antibody staining, germline in situ hybridization
• Mms integration
• Nematode dye filling
• Phalloidin Staining
• RNA in situ hybridization of dissected gonads
• Staining C. elegans for B-galactosidase

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Microscopy

• Differential Interference Contrast (DIC) Microscopy
By Molecular Expressions Website Information: with information such as brief overview of DIC, basic concepts of DIC, comparison of DIC with phase contrast etc.
• Electron Microscopy (EM) Fixation of C. elegans Embryos
• EM fixation of embryos
• Electron Microscopy Techniques
Introduction to EM & how EM works. Information about EM for K-12, undergraduate and graduate students.
• Fluorescent dissecting stereo microscope
• Laser Ablation System
• Laser Scanning Confocal Microscopy
By Molecular Expressions Website Information : this contains detailed information such as basic concepts of LSCM, imaging mode, specimen preparation etc.
• Molecular Expressions Website Information
"This website is brought to you by the Optical Microscopy Division of the National High Magnetic Field Laboratory, a joint venture of The Florida State University, the University of Florida, and the Los Alamos National Laboratory." This is a comprehensive web site for optical microscopy.
• Multiphoton Fluorescence Microscopy
By Molecular Expressions Website Information: all about MPFE, e.g.: basic concepts, 2 photons and 3 photons, fluorescent excitation etc.
• Special Photo Techniques (SEM)
By Science Photo Library: brief introduction about SEM with some SEM images.
• Special Photon Techniques (TEM)
By Science Photo Library: brief introduction about TEM with some TEM images.
• Transmission Electron Microscopy
Ohio State - campus microscopy & imaging facility: a short description about TEM with sample images.

Other techniques

• Fermentor
• Gonad dissections
• Lethal phase determination
• Mms integration
• Quick and easy yeast transformation
• The Electropharyngeogram

Software/Plug-ins

Flash player ( ): play flash movies (files with .swf extension)
QT Player (): play quicktime movies (files with .mov extension)
Adobe Acrobat Reader (): open PDF documents (files with .pdf extension)
ImageJ: for image process and analyze, such as measure the size of an embryo.

Fun, games and quizzes

http://www.imbb.forth.gr/worms/
Here you can find not only research projects but also fun stuff: games, quizzes and images. The lab studies the mechanisms of mechanotransduction (how mechanical signals are interpreted by cells) and necrotic cell death (abnormal self-destruction).

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