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[
WormBook,
2005]
Protein kinases are one of the largest and most influential of gene families: constituting some 2% of the proteome, they regulate almost all biochemical pathways and may phosphorylate up to 30% of the proteome. Bioinformatics and comparative genomics were used to determine the C. elegans kinome and put it in evolutionary and functional context. Kinases are deeply conserved in evolution, and the worm has family homologs for over 80% of the human kinome. Almost half of the 438 worm kinases are members of worm-specific or worm-expanded families. Such radiations include genes involved in spermatogenesis, chemosensation, Wnt signaling and FGF receptor-like kinases. The C. briggsae kinome is largely similar apart from the expanded classes, showing that such expansions are evolutionarily recent.
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[
WormBook,
2005]
Ion channels are the "transistors" (electronic switches) of the brain that generate and propagate electrical signals in the aqueous environment of the brain and nervous system. Potassium channels are particularly important because, not only do they shape dynamic electrical signaling, they also set the resting potentials of almost all animal cells. Without them, animal life as we know it would not exist, much less higher brain function. Until the completion of the C. elegans genome sequencing project the size and diversity of the potassium channel extended gene family was not fully appreciated. Sequence data eventually revealed a total of approximately 70 genes encoding potassium channels out of the more than 19,000 genes in the genome. This seemed to be an unexpectedly high number of genes encoding potassium channels for an animal with a small nervous system of only 302 neurons. However, it became clear that potassium channels are expressed in all cell types, not only neurons, and that many cells express a complex palette of multiple potassium channels. All types of potassium channels found in C. elegans are conserved in mammals. Clearly, C. elegans is "simple" only in having a limited number of cells dedicated to each organ system; it is certainly not simple with respect to its biochemistry and cell physiology.
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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.
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[
WormBook,
2006]
Contrary to textbook dogma, nematodes are not only highly diverse, but often also complex and biologically specialized metazoans. Just a few of the many fascinating adaptations are reviewed in this chapter, as a prelude to a quick tour through phylogenetic relationships within the phylum. Small Subunit rDNA sequences have confirmed several controversial prior hypotheses, as well as revealing some unexpected relationships, resulting in a recent proposal for revised classification. Three major lineages exist within the phylum: Chromadoria, Enoplia and Dorylaimia. The exact order of appearance of these lineages is not yet resolved, which also leaves room for uncertainty about the biology and morphology of the exclusive common ancestor of nematodes. Enoplia and Dorylaimia differ considerably in many respects from C. elegans, which is a member of Chromadoria. The latter group is extremely diverse in its own right, for example in ecological range, in properties of the cuticle and in structure of the pharynx. The formerly relatively widely accepted class Secernentea is deeply nested within Chromadoria, and has therefore recently been relegated to the rank and name of order Rhabditida. Within this order, closer relatives of C. elegans include strongylids, diplogasterids and bunonematids. Tylenchs, cephalobs and panagrolaimids are also members of Rhabditida, albeit probably more distantly related to C. elegans.
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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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[
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]
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.
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[
WormBook,
2006]
A distinctive feature of polarized epithelial cells is their specialized junctions, which contribute to cell integrity and provide platforms to orchestrate cell shape changes. The chapter discusses the composition and assembly of C. elegans cell-cell and cell-extracellular matrix junctions, proteins that anchor the cytoskeleton and mechanisms involved in establishing epithelial polarity. The focus remains cellular and does not properly deal with epithelial cells in the context of the developing embryo.
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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,
2005]
The most abundant synapses in the central nervous system of vertebrates are inhibitory synapses that use the neurotransmitter gamma-aminobutyric acid (GABA). GABA is also an important neurotransmitter in C. elegans; however, in contrast to vertebrates where GABA acts at synapses of the central nervous system, in nematodes GABA acts primarily at neuromuscular synapses. Specifically, GABA acts to relax the body muscles during locomotion and foraging and to contract the enteric muscles during defecation. The importance of this neurotransmitter for basic motor functions of the worm has facilitated the genetic analysis of proteins required for GABA function. Genetic screens have identified the GABA biosynthetic enzyme, the vesicular transporter, inhibitory and excitatory receptors, and a transcription factor required for the differentiation of GABA cell identity. The plasma membrane transporter and other GABA receptors have been identified by molecular criteria.