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[
WormBook,
2005]
Synaptogenesis is a process involving the formation of a neurotransmitter release site in the presynaptic neuron and a receptive field at the postsynaptic partners, and the precise alignment of pre- and post-synaptic specializations. In C. elegans synapses are found as en passant axonal swellings along the nerve processes. Genetic screens using a synaptic vesicle-associated GFP marker have identified key players in synaptic target recognition and organization of the presynaptic terminals. Importantly, the functions of most genes are evolutionarily conserved. Further studies using a combination of genetic modifier screens and reverse genetics have begun to reveal the underlying signaling pathways.
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[
WormBook,
2006]
Through genetic analyses, the function of genes is investigated by studying organisms where gene function is altered. In classical forward genetic screening, individuals are treated with mutagens to induce DNA lesions and mutants with a phenotype of interest are sought. After a mutant is found, the gene mutated is identified through standard molecular techniques. Detailed studies of the mutant phenotype coupled with molecular analyses of the gene allows elucidation of the gene's function. Forward genetics has been responsible for our understanding of many biological processes and is an excellent method for identifying genes that function in a particular process.In reverse genetics, the functional study of a gene starts with the gene sequence rather than a mutant phenotype. Using various techniques, a gene's function is altered and the effect on the development or behaviour of the organism is analysed. Reverse genetics is an important complement to forward genetics. For example, using reverse genetics, one can investigate the function of all genes in a gene family, something not easily done with forward genetics. Further, one can study the function of a gene found to be involved in a process of interest in another organism, but for which no forward genetic mutants have yet been identified. Finally, the vast majority of genes have not yet been mutated in most organisms and reverse genetics allows their study. The availability of complete genome sequences combined with reverse genetics can allow every gene to be studied.This chapter gives detailed protocols for the two main methods of perturbing gene function in C. elegans: RNA interference and the creation of deletion mutants. Either technique can be applied to the study of individual genes. With less than a day of actual work, RNAi creates a knockdown of gene function without altering the organism's DNA (see below). In contrast, with about a month of work, a deletion mutation permanently removes all gene function. Deciding which technique to use will depend on the nature of the experiment. The techniques can also be combined, where RNAi is used for rapid screening of loss of function phenotypes and then deletion mutants are made to study genes of particular interest. RNAi can also be carried out on a global scale, where knockdown of (nearly) every gene is tested for inducing a phenotype of interest. In this case, the reverse genetics technique of RNAi can be thought of as a forward genetic screening tool.
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[
WormBook,
2007]
Strongyloides is a genus of parasitic nematodes, which, unusually, has a free-living adult generation. Here we introduce the biology of this genus, especially the fascinating, but complex, life-cycle together with an overview of the taxonomy, morphology, genetics and genomics of this genus.
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[
WormBook,
2010]
The nervous system represents the most complex tissue of C. elegans both in terms of numbers (302 neurons and 56 glial cells = 37% of the somatic cells in a hermaphrodite) and diversity (118 morphologically distinct neuron classes). The lineage and morphology of each neuron type has been described in detail and neuronal fate markers exists for virtually all neurons in the form of fluorescent reporter genes. The ability to "phenotype" neurons at high resolution combined with the amenability of C. elegans to genetic mutant analysis make the C. elegans nervous system a prime model system to elucidate the nature of the gene regulatory programs that build a nervous system-a central question of developmental neurobiology. Discussing a number of regulatory genes involved in neuronal lineage determination and neuronal differentiation, I will try to carve out in this review a few general principles of neuronal development in C. elegans. These principles may be conserved across phylogeny.
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[
WormBook,
2005]
A genetic enhancer is a mutation in one gene that intensifies the phenotype caused by a mutation in another gene. The phenotype of the double mutant is much stronger than the summation of the single mutant phenotypes. The isolation of enhancers can lead to the identification of interacting genes, including genes that act redundantly with respect to each other. Examples in Caenorhabditis elegans of dominant enhancers are presented first, followed by a review of recessive enhancers of null mutations. In some of these cases, the interacting genes are related in structure and function, but in other cases, the interacting genes are nonhomologous. Recessive enhancers of non-null mutations can also be useful. A powerful advance for the identification of recessive enhancers is genome-wide screening based on RNA interference.
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[
WormBook,
2007]
It is now well established that cells modify chromatin to establish transcriptionally active or inactive chromosomal regions. Such regulation of the chromatin structure is essential for the proper development of organisms. C. elegans is a powerful organism for exploring the developmental role of chromatin factors and their regulation. This chapter presents an overview of recent studies on chromatin factors in C. elegans with a description of their key roles in a variety of cellular and developmental processes.
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[
WormBook,
2005]
C. elegans is a member of a group of nematodes called rhabditids, which encompasses a large number of ecologically and genetically diverse species. A new, preliminary phylogenetic analysis is presented for concatenated sequences of three nuclear genes for 48 rhabditid and diplogastrid species (including 10 Caenorhabditis species), as well as four species representing the outgroup. Although many relationships are well-resolved, more data are still needed to resolve some key relationships, particularly near the base of the rhabditid tree. There is high confidence for two major clades: (1) a clade comprising Mesorhabditis Parasitorhabditis, Pelodera, Teratorhabditis plus a few other species; (2) a large clade (Eurhabditis) comprising most of the remaining rhabditid genera, including Caenorhabditis and its sistergroup Protorhabditis-Prodontorhabditis-Diploscapter. Eurhabditis also contains the parasitic strongylids, the entomopathogenic Heterorhabditis, and the monophyletic group Oscheius which includes the satellite model organism O. tipulae. The relationships within Caenorhabditis are well resolved. The analysis also suggests that rhabditids include diplogastrids, to which the second satellite model organism Pristionchus pacificus belongs. Genetic disparity within Caenorhabditis is as great as that across vertebrates, suggesting Caenorhabditis lineages are quickly evolving, ancient, or both. The phylogenetic tree can be used to reconstruct evolutionary events within rhabditids. For instance, the reproductive mode changed multiple times from gonochorism to hermaphroditism, but only once from hermaphroditism to gonochorism. Complete retraction of the male tail tip, leading to a blunt, peloderan tail, evolved at least once. Reversions to unretracted tail tips occurred within both major rhabditid groups. The phylogeny also provides a guide to species which would be good candidates for future genome projects and comparative studies.
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[
WormBook,
2007]
Acetylcholine is the major excitatory neurotransmitter at nematode neuromuscular junctions, and more than a third of the cells in the C. elegans nervous system release acetylcholine. Through a combination of forward genetics, drug-resistance selections, and genomic analysis, mutants have been identified for all of the steps specifically required for cholinergic function. These include two enzymes, two transporters, and a bewildering assortment of receptors. Cholinergic transmission is involved, directly or indirectly, in many C. elegans behaviors, including locomotion, egg laying, feeding, and male mating.
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[
Genetics,
2022]
Light microscopes are the cell and developmental biologists' "best friend", providing a means to see structures and follow dynamics from the protein to the organism level. A huge advantage of C. elegans as a model organism is its transparency, which coupled with its small size means that nearly every biological process can be observed and measured with the appropriate probe and light microscope. Continuous improvement in microscope technologies along with novel genome editing techniques to create transgenic probes have facilitated the development and implementation of a dizzying array of methods for imaging worm embryos, larvae and adults. In this review we provide an overview of the molecular and cellular processes that can be visualized in living worms using light microscopy. A partial inventory of fluorescent probes and techniques successfully used in worms to image the dynamics of cells, organelles, DNA, and protein localization and activity is followed by a practical guide to choosing between various imaging modalities, including widefield, confocal, lightsheet, and structured illumination microscopy. Finally, we discuss the available tools and approaches, including machine learning, for quantitative image analysis tasks, such as colocalization, segmentation, object tracking, and lineage tracing. Hopefully, this review will inspire worm researchers who have not yet imaged their worms to begin, and push those who are imaging to go faster, finer, and longer.
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[
WormBook,
2006]
Studies in C. elegans have begun to reveal new components and new mechanisms associated with intracellular membrane traffic in a variety of cell types. The worm benefits from many of the advantages of yeast as a genetically tractable organism for these kinds of studies while offering the unique opportunity to probe how these pathways have been extended and modified in the context of a multicellular animal undergoing development to produce diverse cell types such as muscles, nerves, and polarized epithelia. This review summarizes recent work elucidating endocytic pathways, primarily in the worm germ line and coelomocytes, and also touches on diverse studies of secretion, especially in ectodermal cells of epithelial character.