Lok JB (2007) WormBook "Strongyloides stercoralis: a model for translational research on parasitic nematode biology."

Lok JB

[WormBook, 2007]

Because of their free-living life cycle alternatives, Strongyloides and related nematode parasites may represent the best models for translating C. elegans science to the study of nematode parasitism. S. stercoralis, a significant pathogen of humans, can be maintained in laboratory dogs and gerbils. Biosafety precautions necessary for work with S. stercoralis, though unfamiliar to many C. elegans researchers, are straightforward and easily accomplished. Although specialized methods are necessary for large-scale culture of the free-living stages of S. stercoralis, small-scale cultures for experimental purposes may be undertaken using minor modifications of standard C. elegans methods. Similarly, the morphological similarities between C. elegans and the free-living stages of S. stercoralis allow investigational methods such as laser cell ablation and DNA transformation by gonadal microinjection to be easily adapted from C. elegans to S. stercoralis. Comparative studies employing these methods have yielded new insights into the neuronal control of the infective process in parasites and its similarity to regulation of dauer development in C. elegans. Furthermore, we have developed a practical method for transient transformation of S. stercoralis with vector constructs having various tissue- and cell-specific expression patterns and have assembled these into a modular vector kit for distribution to the community.

Horvitz HR (1981) "Neuronal cell lineages in the nematode Caenorhabditis elegans."

Horvitz HR

[1981]

A neuron can be characterized by its morphology, transmitter (s?), receptor(s) and the nature of its synaptic contacts (chemical or electrical; excitatory or inhibitory; number and distribution of synapses; identity of the cells to which it is presynaptic or postsynaptic). It is clear that according to such criteria nervous sytems consist of neurons of many distinct types. The origin of neuronal diversity is unknown. Both how such diversity is generated during development and how the relevant developmental programme is encoded in the genome remain to

Fredens J et al. (2014) Methods Mol Biol "Identification of novel protein functions and signaling mechanisms by genetics and quantitative phosphoproteomics in Caenorhabditis elegans."

Larsen MR, Moller-Jensen J, Fredens J, Engholm-Keller K, Faergeman NJ

[Methods Mol Biol, 2014]

Stable isotope labeling by amino acids combined with mass spectrometry is a widely used methodology for measuring relative changes in protein and phosphorylation levels at a global level. We have applied this method to the model organism Caenorhabditis elegans in combination with RNAi-mediated gene knockdown by feeding the nematode on pre-labeled lysine auxotroph Escherichia coli. In this chapter, we describe in details the generation of the E. coli strain, incorporation of heavy isotope-labeled lysine in C. elegans, and the procedure for a comprehensive global phosphoproteomic experiment.

Sander van den Heuvel (2005) WormBook "Cell-cycle regulation."

Sander Van Den Heuvel

[WormBook, 2005]

Cell-division control affects many aspects of development. Caenorhabditis elegans cell-cycle genes have been identified over the past decade, including at least two distinct Cyclin-Dependent Kinases (CDKs), their cyclin partners, positive and negative regulators, and downstream targets. The balance between CDK activation and inactivation determines whether cells proceed through G 1 into S phase, and from G 2 to M, through regulatory mechanisms that are conserved in more complex eukaryotes. The challenge is to expand our understanding of the basic cell cycle into a comprehensive regulatory network that incorporates environmental factors and coordinates cell division with growth, differentiation and tissue formation during development. Results from several studies indicate a critical role for CKI-1 , a CDK inhibitor of the Cip/Kip family, in the temporal control of cell division, potentially acting downstream of heterochronic genes and dauer regulatory pathways.

Neri C (2011) "Value of Invertebrate Genetics and Biology to Develop Neuroprotective and Preventive Medicine in Huntingtons Disease"

Neri C

[2011]

During the past decade, Drosophila and Caenorhabditis elegans genetics have emerged as powerful approaches for the study of cellular responses to neurodegenerative disease proteins. Such studies have provided new strategies and rationales for the development of neuroprotective drugs, such as the pharmacological manipulation of longevity modulator networks. This chapter will describe how and why these model systems may be used as efficient translational research tools for Huntington's disease (HD) in the discovery and development of neuroprotective drugs. Neurodegenerative diseases, including HD, constitute a large and clinically heterogeneous group of brain illnesses for which there are currently no neuroprotective drugs available. Although important methodologies have been developed by academic and industrial researchers to find therapies for these diseases, notably chemical screening tools, the large majority of the molecules so far evaluated in clinical trials have failed to show significant efficacy. In rodent models, the administration of neurotoxins may reproduce some features of the human diseases (von Bohlen Und Halbach, 2005), and this approach has been used extensively to search for new treatments with some success, such as the use of levodopa for symptomatic treatment of Parkinson's disease, although with significant side effects (Tse, 2006). However, neuroprotective treatments able to benefit large numbers of patients with minimal side effects have not yet been developed. Thus, to date research in the field of neurodegenerative disease pathogenesis has given limited benefit to patients, and drug discovery and development remain major challenges for industrial and preindustrial research and need to be improved. Drug development is an expensive and time-consuming process that works as a pipeline, with the proof of success being conclusive clinical trials. Although there is a need to improve clinical trial design to evaluate the effects of neuroprotective drugs, improvement may also be needed at the entry points of the pipeline and at critical points along the preclinical discovery process (Hung and Schwarzschild, 2007). With the advent of physiological genomics and network biology, the concepts and paradigms used to study neurodegenerative diseases are rapidly evolving (Feany, 2000; Lim et al., 2006b). Implementing these concepts and paradigms early into the drug development process may strongly enhance the translational infrastructure used to tackle neurodegenerative diseases. The aim of this chapter is to emphasize how and why invertebrate biology may allow new rationale(s) for drug discovery and development to be exploited for the development of new drugs for HD, notably in view of developing neuroprotective and preventive medicines. HD is a dominantly inherited disease caused by expanded polyglutamines (polyQs) in the huntingtin (htt) protein (Figure 6.1) and is clinically characterized by cortical and striatal degeneration accompanied by motor, cognitive, and neuropsychiatric symptoms (Walker, 2007). The toxic effects of polyQ-expanded htt forms and genetic modifiers of cytotoxicity are being studied in several cell systems and in model organisms, including yeast, nematodes, flies, and rodents (Levine et al., 2004; Rubinsztein, 2002; Sipione and Cattaneo, 2001). Thus, a large amount of knowledge is being accumulated on the roles of normal htt and the effects of polyQ-expanded htt at the neuronal cell level. There are also great efforts being made to collect detailed clinical data in a normalized manner (e.g., see http://www.euro-hd.net) and to characterize large cohorts of HD patients and presymptomatic individuals. Thus, HD has become a "model disease" to define the best ways to fight neuronal dysfunction and neurodegeneration in the brain and to improve drug discovery, which may foster the identification of a cure for this disease and perhaps other degenerative diseases.

Peredney CL et al. (2000) "Comparison of the toxicological effects of nitrate versus chloride metallic salts on Caenorhabditis elegans in soil."

Williams PL, Peredney CL

[2000]

There is growing interest in the use of bioindicators to assess metal toxicity in soil. The current ASTM Standard Guide for Conducting Laboratory Soil Toxicity Test with the lumbricid earthworm Eisenia fetida (E 1676-97) uses a common earthworm. The nematode Caenorhabditis elegans is a natural soil inhabitant with many characteristics that make an ideal alternate test organism. It has been used to assess metal toxicity in aquatic media, agar plates and in soil. Work is currently underway on the design of a C. elegans procedure for metals in soil. The objective of this study was to determine differences in LC50S between the chloride salt and the nitrate salt forms of cadmium, copper, lead, nickel, and zinc, in three types of soil: Cecil, Tifton, and ASTM artificial soil. Results indicated that the toxicological effect of the metallic salt varies and is dependent on the particular metal. For Cd and Pb the nitrate form is more toxic while Cu and Ni are more toxic in the chloride form. The composition of the soil also effected toxicity, with the metal being the least toxic in ASTM soil and more toxic in the Tifton soil. This strongly correlated with organic matter and clay content of the soil. It is important to determine the effects of carrier salt form and soil composition on metal toxicity, not only in order to standardize the protocol for C. elegans soil toxicity testing, but also in establishing acceptable exposure concentrations in the soil.

Min-Ho Lee et al. (2006) WormBook "RNA-binding proteins."

Tim Schedl, Min-Ho Lee

[WormBook, 2006]

The C. elegans genome encodes many RNA-binding proteins (RBPs) with diverse functions in development, indicative of extensive layers of post-transcriptional control of RNA metabolism. A number of C. elegans RBPs have been identified by forward or reverse genetics. They tend to display tissue-specific mutant phenotypes, which underscore their functional importance. In addition, several RBPs that bind regulatory sequences in the 3'' untranslated regions of mRNAs have been identified molecularly. Most C. elegans RBPs are conserved throughout evolution, suggesting that their study in C. elegans may uncover new conserved biological functions. In this review, we primarily discuss RBPs that are associated with well-characterized mutant phenotypes in the germ line, the early embryo, or in somatic tissues. We also discuss the identification of RNA targets of RBPs, which is an important first step to understand how an RBP controls C. elegans development. It is likely that most RBPs regulate multiple RNA targets. Once multiple RNA targets are identified, specific features that distinguish target from non-target RNAs and the type(s) of RNA metabolism that each RBP controls can be determined. Furthermore, one can determine whether the RBP regulates all targets by the same mechanism or different targets by distinct mechanisms. Such studies will provide insights into how RBPs exert coordinate control of their RNA targets, thereby affecting development in a concerted fashion.

Arpagaus M et al. (1992) "Nematode acetylcholinesterases. Several genes and molecular forms of their products."

Richier P, Berge J-B, Toutant J-P, Le Roy F, L'Hermite Y, Thierry-Mieg D, Arpagaus M

[1992]

In vertebrates, acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) are polymorphic enzymes presenting both globular and asymmetric forms. In invertebrates, only AChE has been characterized so far that presents a reduced molecular diversity. In insects for example the major molecular form of AChE is an amphiphilic dimeric form attached to the membrane through a glycolipid covalently linked at the C-terminus of each catalytic subunit. This AChE has a substrate specificity intermediate to those of mammalina AChE and BChE. A glycoplipid-anchored 7.5S from has also been observed in the trematode Schistosoma mansoni. Asymmetric forms have never been convincingly reported in invertebrates except in the more evolved animals such as Amphioxius. In the latter case also there is no BChE but AChE presents catalytic properties intermediate to those of vertebrate AChE and BChE. We are now interested in nematode AChE(s) for the following reasons: -several species are agricultural pest and it is important to get further informations on the target of potential nematicides; -it has been shown that at least three different genes code for AChE in Caenorhabditis elegans. It is therefore interesting to see whether the presence of multiple genes results in an increased molecular diversity, to define what are the structural characteristics of each gene product and finally to clone and sequence thee three genes for evolutionary relationships with the other members of the cholinesterase

Jean-Louis Bessereau (2006) WormBook "Transposons in C. elegans."

Jean-Louis BESSEREAU

[WormBook, 2006]

Transposons are discrete segments of DNA capable of moving through the genome of their host via an RNA intermediate in the case of class I retrotransposon or via a "cut-and-paste" mechanism for class II DNA transposons. Since transposons take advantage of their host''s cellular machinery to proliferate in the genome and enter new hosts, transposable elements can be viewed as parasitic or "selfish DNA". However, transposons may have been beneficial for their hosts as genome evolution drivers, thus providing an example of molecular mutualism. Interactions between transposon and C. elegans research were undoubtedly mutualistic, leading to the advent of needed genomic tools to drive C. elegans research while providing insights into the transposition field. Tc1, the first C. elegans transposon to be identified, turned out to be the founding member of a widespread family of mobile elements: the Tc1/ mariner superfamily. The investigation into transposition regulation in C. elegans has uncovered an unforeseen link between transposition, genome surveillance and RNA interference. Conversely, transposons were utilized soon after their identification to inactivate and clone genes, providing some of the first molecular identities of C. elegans genes. Recent results suggest that transposons might provide a means to engineer site-directed mutations into the C. elegans genome. This article describes the different transposons present in the C. elegans genome with a specific emphasis on the ones that proved to be mobile under laboratory conditions. Mechanisms and control of transposition are discussed briefly. Some tools based on the use of transposons for C. elegans research are presented at the end of this review.

Blumenthal TE et al. (1987) "Evolution and regulation of vitellogenin genes."

Zucker-Aprison E, Blumenthal TE

[1987]

Vitellogenins of many insects, vertebrates, nematodes and sea urchins are very similar in size and amino acid composition. We have determined the nucleotide sequences of the genes that encode vitellogenins in nematodes (C. elegans) and sea urchins (S. purpuratus), and compared the deduced amino acid sequences to the published sequences of two vertebrate vitellogenins (X. laevis and G. gallus). This comparison demonstrated unequivocally that the nematode and vertebrate proteins are encoded by distant members of a single gene family. The less extensive sequence data available for the sea urchin gene indicates that this, too, may be a member of this family of genes, as may the vitellogenin genes of locust. On the other hand, we were unable to detect any similarity between these genes and the D. melanogaster yolk protein genes. Thus it appears that while nematodes, vertebrates, sea urchins and at least some insects utilize the same family of genes to encode vitellogenins, Drosophila uses a different gene family. All of the vitellogenin genes are regulated in a tissue-specific manner. They are expressed in the intestine in nematodes, in the liver in vertebrates, in the fat body in insects, and in the intestine and gonad in sea urchins. Their production is limited to adult females in all species except sea urchins, in which they are expressed by adults of both sexes. In nematodes we have identified two heptameric sequence elements repeated multiple times in all eleven of the vitellogenin genes sequenced. One of these elements is also present in the vertebrate promoters and has recently been shown to be required for transcriptional activation. All of the 5' ends of the vitellogenin mRNAs of nematodes, vertebrates and locust can be folded into potentially-stable secondary structures. We present evidence that these structures have been strongly selected for and presumably perform some function in regulation of vitellogenin production.