Fiona J Thompson et al. (2002) European Worm Meeting "Genome analysis of the effect of the host immune response on Strongyloides ratti."

Fiona J Thompson, Brandi Chiapelli, Claire Murphy, Clare P Wilkes, Mark E Viney, Jim McCarter, Sandra Clifton

[European Worm Meeting, 2002]

The establishment, survival and fecundity of nematodes is dramatically affected by the host immune response. However the molecular and biochemical nature of these effects have yet to be fully explored. We propose to exploit the nematode genome sequencing projects and EST data to analyse these phenomena. To this end we have generated a number of cDNA libraries from different stages of Strongyloides ratti including those from parasitic adults which had been exposed to different degrees of immune pressure. To date 7,793 ESTs have been sequenced and the cluster analysis of these clones will be presented. In order to generate microarrays all unique clones are being amplifed by PCR and arrayed. These microarrays will be differentially probed with cDNA isolated from populations of worms from varying immune pressures. We aim to identify gene sets whose expression levels vary as a result of changes in the host immune response and as such may be the basis of the immune dependant changes in the fitness of nematode infections.

James P McCarter et al. (2001) International C. elegans Meeting "Genes from Other"

Michael Dante, James P McCarter, John C Martin, Deana Pape, Brandi Chiapelli, Todd N Wylie, Robert H Waterston, Sandra W Clifton

[International C. elegans Meeting, 2001]

To build upon knowledge gained from the genome of C. elegans , we have begun generating Expressed Sequence Tags (ESTs) from parasitic (and free-living) nematodes. This project will generate >225,000 5' ESTs from 14 species by 2003. Additionally, the Sanger Centre and Edinburgh Univ. will complete 80,000 ESTs from 7 species. Through these combined efforts, we anticipate the identification of >80,000 new nematode genes. At the GSC, approximately 35,000 ESTs have been generated to date including sequences from Ancylostoma caninum, Heterodera glycines, Meloidogyne incognita and javanica, Parastrongyloides trichosuri, Pristionchus pacificus, Strongyloides stercoralis and ratti, Trichinella spiralis, and Zeldia punctata . We will report on our progress in sequence analysis, including the creation of the NemaGene gene index for each species by EST clustering and consensus sequence generation, identification of common and rare transcripts, and identification of genes with orthologues in C. elegans and other nematodes. All sequences are publicly available at www.ncbi.nlm.nih.gov/dbEST. NemaGene sequences and project details are available at WWW.NEMATODE.NET. We would like to thank collaborators who have provided materials and ideas for this project including Prema Arasu, David Bird, Rick Davis, Warwick Grant, John Hawdon, Doug Jasmer, Andrew Kloek, Thomas Nutman, Charlie Opperman, Alan Scott, Ralf Sommer, and Mark Viney. This work is funded by NIH-AI-46593, NSF-0077503, and a Merck / Helen Hay Whitney Foundation fellowship.