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[
WormBook,
2005]
Mutations in many genes can result in a similar phenotype. Finding a number of mutants with the same phenotype tells you little about how many genes you are dealing with, and how mutable those genes are until you can assign those mutations to genetic loci. The genetic assay for gene assignment is called the complementation test. The simplicity and robustness of this test makes it a fundamental genetic tool for gene assignment. However, there are occasional unexpected outcomes from this test that bear explanation. This chapter reviews the complementation test and its various outcomes, highlighting relatively rare but nonetheless interesting exceptions such as intragenic complementation and non-allelic non-complementation.
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[
Methods Cell Biol,
1995]
This chapter is devoted to providing information on techniques applicable to studying transcription and translation in Caenorhabditis elegans. These techniques are constantly evolving and being passed among workers, each making improvements or adaptations. None of the techniques discussed below are original, but, rather, have emerged from a variety of sources over the years, making it difficult to trace their origin or give credit to the originators. Although each technique has been used successfully, for each there are alternative methods available in the literature that work equally well. In fact, depending on the available resources, you might find that an alternative technique suits your needs and facilities better than the one described below. For this reason, the procedures discussed below are usually accompanied by one or more references that will allow you to look at other, related methods. Where appropriate, there will also be a discussion of factors to consider when
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[
2010]
Over 30 years ago, Nobel laureate Sydney Brenner recognized that an intellectually straightforward strategy to delineate the basic principles in neurobiology is to utilize a model organism with a nervous system that is simple enough to lend itself to anatomical, cellular, genetic, and molecular analysis, yet be complex enough that lessons learned in that organism would give us insight into general principles of neural function. The humble organism he chose, the nematode Caenorhabditis elegans, is now one of the most thoroughly characterized metazoans, particularly in terms of its nervous system. One of Brenner's motivations in adapting C. elegans as a model organism was to understand the totality of the molecular and cellular basis for the control of animal behavior (Brener 1988). In this chapter, we review what is arguably the best-studied aspect of C. elegans behavior: response to chemical stimuli. The C. elegans neurobiology literature can be intimidating for the uninitiated; we attempt to limit the use of "worm jargon" in this review. For a more C. elegans-centric review, we refer you to other excellent sources (Bargmann 2006).
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[
Methods Cell Biol,
1995]
Complementary DNA libraries are useful tools for uncovering genes of interest in C. elegans and finding specific homologies to genes in other organisms (Waterston et al., 1992; McCombie et al., 1992). When working with existing cDNA libraries, be sure to carefully choose which libraries would be most beneficial to the type of research being done. Some libraries may be specific for genes that are present in lower copy numbers, whereas others may be of a more general nature. It is important to fully understand the source and construction of the library you will be working with. Once an appropriate library has been chosen, work may begin to isolate a specific cDNA and sequence it completely or to survey many cDNAs by single-pass DNA sequencing. Whatever the project, it is important to develop a specific strategy for both the sequencing and the organization of the clones being characterized. The strategies and procedures we have outlined in this chapter have proven effective for rapid and comprehensive cDNA characterization.
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[
WormBook,
2005]
C. elegans has emerged as a powerful genetic model organism in which to study synaptic function. Most synaptic proteins in the C. elegans genome are highly conserved and mutants can be readily generated by forward and reverse genetics. Most C. elegans synaptic protein mutants are viable affording an opportunity to study the functional consequences in vivo. Recent advances in electrophysiological approaches permit functional analysis of mutant synapses in situ. This has contributed to an already powerful arsenal of techniques available to study synaptic function in C. elegans. This review highlights C. elegans mutants affecting specific stages of the synaptic vesicle cycle, with emphasis on studies conducted at the neuromuscular junction.
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[
WormBook,
2005]
C. elegans presents a low level of molecular diversity, which may be explained by its selfing mode of reproduction. Recent work on the genetic structure of natural populations of C. elegans indeed suggests a low level of outcrossing, and little geographic differentiation because of migration. The level and pattern of molecular diversity among wild isolates of C. elegans are compared with those found after accumulation of spontaneous mutations in the laboratory. The last part of the chapter reviews phenotypic differences among wild isolates of C. elegans.
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[
WormBook,
2005]
This chapter reviews analytical tools currently in use for protein classification, and gives an overview of the C. elegans proteome. Computational analysis of proteins relies heavily on hidden Markov models of protein families. Proteins can also be classified by predicted secondary or tertiary structures, hydrophobic profiles, compositional biases, or size ranges. Strictly orthologous protein families remain difficult to identify, except by skilled human labor. The InterPro and NCBI KOG classifications encompass 79% of C. elegans protein-coding genes; in both classifications, a small number of protein families account for a disproportionately large number of genes. C. elegans protein-coding genes include at least ~12,000 orthologs of C. briggsae genes, and at least ~4,400 orthologs of non-nematode eukaryotic genes. Some metazoan proteins conserved in other nematodes are absent from C. elegans. Conversely, 9% of C. elegans protein-coding genes are conserved among all metazoa or eukaryotes, yet have no known functions.
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[
1977]
The workshop on nematodes presented current research from four laboratories on the development and physiology of C. elegans.
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[
WormBook,
2007]
The soil nematode Caenorhabditis briggsae is an attractive model system for studying evolution of both animal development and behavior. Being a close relative of C. elegans, C. briggsae is frequently used in comparative studies to infer species-specific function of the orthologous genes and also for studying the dynamics of chromosome evolution. The genome sequence of C. briggsae is valuable in reverse genetics and genome-wide comparative studies. This review discusses resources and tools, which are currently available, to facilitate study of C. briggsae in order to unravel mechanisms of gene function that confer morphological and behavioral diversity.
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[
WormBook,
2005]
A wide variety of bacterial pathogens, as well as several fungi, kill C. elegans or produce non-lethal disease symptoms. This allows the nematode to be used as a simple, tractable model host for infectious disease. Human pathogens that affect C. elegans include Gram-negative bacteria of genera Burkholderia, Pseudomonas, Salmonella, Serratia and Yersinia; Gram-positive bacteria Enterococcus, Staphylococcus and Streptococcus; and the fungus Cryptococcus neoformans. Microbes that are not pathogenic to mammals, such as the insect pathogen Bacillus thuringiensis and the nematode-specific Microbacterium nematophilum, are also studied with C. elegans. Many of the pathogens investigated colonize the C. elegans intestine, and pathology is usually quantified as decreased lifespan of the nematode. A few microbes adhere to the nematode cuticle, while others produce toxins that kill C. elegans without a requirement for whole, live pathogen cells to contact the worm. The rapid growth and short generation time of C. elegans permit extensive screens for mutant pathogens with diminished killing, and some of the factors identified in these screens have been shown to play roles in mammalian infections. Genetic screens for toxin-resistant C. elegans mutants have identified host pathways exploited by bacterial toxins.