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[
WormBook,
2006]
Many pathogens that can infect C. elegans have been described, including some that co-exist with the nematode in its natural environment. This chapter describes our current understanding of the different innate immune responses of C. elegans that follow infection. It focuses on the main signalling pathways that have been identified and highlights the inclusion of certain molecular cassettes in both immune and developmental functions.
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[
Genetics,
2019]
While <i>Caenorhabditis elegans</i> was originally regarded as a model for investigating determinate developmental programs, landmark studies have subsequently shown that the largely invariant pattern of development in the animal does not reflect irreversibility in rigidly fixed cell fates. Rather, cells at all stages of development, in both the soma and germline, have been shown to be capable of changing their fates through mutation or forced expression of fate-determining factors, as well as during the normal course of development. In this chapter, we review the basis for natural and induced cellular plasticity in <i>C. elegans</i> We describe the events that progressively restrict cellular differentiation during embryogenesis, starting with the multipotency-to-commitment transition (MCT) and subsequently through postembryonic development of the animal, and consider the range of molecular processes, including transcriptional and translational control systems, that contribute to cellular plasticity. These findings in the worm are discussed in the context of both classical and recent studies of cellular plasticity in vertebrate systems.
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[
WormBook,
2005]
Evolutionary innovation requires genetic raw materials upon which selection can act. The duplication of genes is of fundamental importance in providing such raw materials. Gene duplications are very widespread in C. elegans and appear to arise more frequently than in either Drosophila or yeast. It has been proposed that the rate of duplication of a gene is of the same order of magnitude as the rate of mutation per nucleotide site, emphasising the enormous potential that gene duplication has for generating substrates for evolutionary change. The fate of duplicated genes is discussed. Complete functional redundancy seems unstable in the long term. Most models require that equality amongst duplicated genes must be disrupted if they are to be preserved. There are various ways of achieving inequality, involving either the nonfunctionalization of one copy, or one copy acquiring some novel, beneficial function, or both copies becoming partially compromised so that both copies are required to provide the overall function that was previously provided by the single ancestral gene. Examples of C. elegans gene duplications that appear to have followed each of these pathways are considered.
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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,
2007]
Four biogenic amines: octopamine, tyramine, dopamine and serotonin act in C. elegans to modulate behavior in response to changing environmental cues. These neurotransmitters act at both neurons and muscles to affect egg laying, pharyngeal pumping, locomotion and learning. A variety of experimental approaches including genetic, imaging, biochemical and pharmacological analyses have been used to identify the enzymes and cells that make and release the amines and the cells and receptors that bind them. Dopamine and serotonin act through receptors and downstream signaling mechanisms similar to those that operate in the mammalian brain suggesting that C. elegans will provide a valuable model for understanding biogenic amine signaling in the brain.
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[
WormBook,
2006]
Most rapid excitatory synaptic signaling is mediated by glutamatergic neurotransmission. An important challenge in neurobiology is to understand the molecular architecture of functional glutamatergic synapses. By combining the techniques of genetics, molecular biology and electrophysiology in C. elegans we have the potential to identify and characterize the molecules that contribute to the function of glutamatergic synapses. In C. elegans both excitatory and inhibitory ionotropic glutamate receptors are linked to neural circuits and behavior. Genetic analysis has identified genes required for receptor expression, trafficking, localization, stabilization and function at synapses. Significantly, novel proteins required for glutamate receptor function have been discovered in the worm. These advances may also lead to a better understanding of glutamatergic signaling in vertebrates.
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[
WormBook,
2006]
There are two sexes in C. elegans, hermaphrodite and male. While there are many sex-specific differences between males and hermaphrodites that affect most tissues, the basic body plan and many of its structures are identical. However, most structures required for mating or reproduction are sexually dimorphic and are generated by sex-specific cell lineages. Thus to understand cell fate specification in hermaphrodites, one must consider how the body plan, which is specified during embryogenesis, influences the fates individual cells. One possible mechanism may involve the asymmetric distribution of POP-1 /Tcf, the sole C. elegans Tcf homolog, to anterior-posterior sister cells. Another mechanism that functions to specify cell fates along the anterior-posterior body axis in both hermaphrodites and males are the Hox genes. Since most of the cell fate specifications that occur in hermaphrodites also occur in males, the focus of this chapter will be on those that only occur in hermaphrodites. This will include the cell fate decisions that affect the HSN neurons, ventral hypodermal P cells, lateral hypodermal cells V5 , V6 , and T ; as well as the mesodermal M, Z1 , and Z4 cells and the intestinal cells. Both cell lineage-based and cell-signaling mechanisms of cell fate specification will be discussed. Only two direct targets of the sex determination pathway that influence cell fate specification to produce hermaphrodite-specific cell fates have been identified. Thus a major challenge will be to learn additional mechanisms by which the sex determination pathway interacts with signaling pathways and other cell fate specification genes to generate hermaphrodite-specific cell fates.
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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,
2005]
TGF-beta superfamily ligands play fundamental roles in the development and physiology of diverse animal species. Genetic and genomic analyses in the model organism Caenorhabditis elegans have contributed to the understanding of TGF-beta -related signal transduction mechanisms. In this chapter, I describe the currently characterized TGF-beta -related signals and signal transduction cassettes in C. elegans. Homology searches of the genome identify five TGF-beta -related genes, for which functions have been identified for three. Two of the TGF-beta -related genes,
daf-7 and
dbl-1 , function through conventional signaling pathways. These signaling pathways are comprised of ser/thr kinase receptors, Smads, and transcription co-factors. A third TGF-beta -related gene,
unc-129 , functions in axonal guidance using novel signaling mechanisms. Thus, TGF-beta -related signaling in C. elegans proceeds via both conserved and novel paradigms that can inform studies in other animal systems.
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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.