Favello A et al. (1995) Methods Cell Biol "Genomic DNA sequencing methods."

Wilson RK, Hillier L, Favello A

[Methods Cell Biol, 1995]

Sequence analysis of cosmids from C. elegans and other organisms currently is best done using the random or "shotgun" strategy (Wilson et al., 1994). After shearing by sonication, DNA is used to prepare M13 subclone libraries which provide good coverage and high-quality sequence data. The subclones are assembled and the data edited using software tools developed especially for C. elegans genomic sequencing. These same tools facilitate much of the subsequent work to complete both strands of the sequence and resolve any remaining ambiguities. Analysis of the finished sequence is then accomplished using several additional computer tools including Genefinder and ACeDB. Taken together, these methods and tools provide a powerful means for genome analysis in the nematode.

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.

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.