Fodor A et al. (1991) International C. elegans Meeting "PRECOCENES ARE NOT STRONG MUTAGENS BUT DECREASE THE LIFE SPAN OF CAENORHABDITIS REMANEI."

Fodor A, Timar T

[International C. elegans Meeting, 1991]

Some 7-alkoxy-2,2-dimethylchromenes (precocenes) adversely affect caenorhabditids. Some symptomps caused by them could partially be compensated by exogenous insect juvenile hormone analogue (JHA) methopren (Fodor et al., 1982, 1989; Fodor & Timar, 1989, Gen. Comp. Endocrinol.). Precocenes are suspected pro-mutagenes, which might be activated by epoxydases in some tissues and the JHA may act as a competitor. Whether precocenes could be used as selective agents for getting mutants resistant to free radicals, eleven biologically active analog were tested according to Szabad et al. (Mut. Res., 1981) by determining the frequency of mitotic recombination in untreated and P-- treated Drosophila melanoqaster. The results were practically negative but inconclusive, as the precocenes inactivated in the medium within a few hours. Just below its toxic concentration (at a dose of 150 ug/ml NGM medium), however, precocene II did significantly decrease the average life span of the amphimictic strain of C. remanei at 25 C from 8 days to 6. Whether the adverse effect on the life span can or cannot be compensated is under study.

H Pamjav et al. (1999) International C. elegans Meeting "Phylogenetic analysis of entomopathogenic nematode / bacterium symbiotic complexes by using PhastSystem PAGE PCR-RFLP of rDNA spacer sequences"

D Triga, A Fodor, H Pamjav, Z Buzas, E Szallas

[International C. elegans Meeting, 1999]

Entomopathogenic nematode (EPN)species belonging to the Steinernema and Heterorhabditis genera are closely related to C. elegans (Blaxter et al., 1998). They form an intimate symbiotic complex with bacteria Xenorhabdus spp. and Photorhabdus spp., respectively, which are closely related to E. coli . The symbiosis is developmentally regulated: there is a direct cell-cell contact between the gut cell of the (infective) dauerlarva and the primary phase variant of the symbiotic bacteria. The symbiosis is taxon specific. Individual Xenorhabdus species used as symbionts by each Steinernema species and individual strains of Photorhabdus luminescens used as symbionts by each Heterorhabditis strains belonging to different species. The phylogenetic relations between species and strains have been analysed by RFLP of the internally transcribed spacer region of the respective rRNA operon. The PCR-amplified DNAs were digested by different restriction enzymes and the restriction patterns obtained by PhastSystem PAGE were compared. On the basis of the comparative analysis of the ITS1 - ITS2 patterns nematodes could be identified at species level. Xenorhabdus species could also be identified on the basis of the comparative analysis of the spacer region of the 16S - 23S rRNA operon. P. luminescens strains, belonging to different subclusters (Szallas et al., 1997) could be separated on the basis of the RFLP pattern of the spacer region of the 16S - 23S rRNA operon. Adams, B.J. (1998). Species conception and the evolutionary paradigm in modern nematology. J. nematol. 30, 1-21. Adams, B.J., Burnell, A.M. @ Powers,T.O. (1998). A phylogenetic analysis of Heterorhabditis based on ITS 1 DNA sequence data. J. nematol. 30, 22-39. Blaxter,R. et al.(1998).Molecular evolutionary framework for Phylum nematoda. Nature 392,71-75. Szallas E., Koch, H., Fodor,A.,Szentirmai, A., Nealson,K.H. Stackebrandt, E.(1997).Phylogenetic evidence for taxonomic heterogeneity of P.luminescens. IJSB 47, 402-407.

Shmeleva N et al. (2000) East Coast Worm Meeting "Verification of gene prediction in the Caenorhabditis elegans genome"

Borodovsky M, Shmeleva N

[East Coast Worm Meeting, 2000]

Theoretical methods for gene finding in genomic DNA significantly accelerate analysis of experimental data by providing almost instant insight into their biological meaning. The danger of the error contamination of databases is increasing as more theoretically annotated genomes are becoming available and genes and proteins annotated by computer are used for subsequent annotation of new genomes. The complete C. elegans genome was annotated with an aid of computer program GeneFinder (P.Green and L. Hillier, unpublished). Assuming that the accuracy of GeneFinder is high we, nevertheless, attempted to get more precise evaluation of this method as a part of our project of creating experimentally verified training and test sets of genes in several eukaryotic genomes. This direction of our work has been started yet in 1996 in a project of using both GeneMark [1] and experimental verification of its prediction in finding exact exon-intron structure of C. elegans unc89 [2]. Another goal of our project has been improving the accuracy of the gene finding method GeneMark.hmm [3] that was demonstrated to be highly accurate for eukaryotic genome of Arabidopsis thaliana [4]. To assess the accuracy of gene prediction method we have generated a database of experimentally verified genes by matching genomic DNA with recently sequenced mRNA sequences available in GenBank. In C. elegans case this new set is used for comparison with original annotation (GeneFinder) as well as for training and testing of GeneMark.hmm. The results will be given in our presentation. [1] Borodovsky, M and McIninch, J. 1993. GeneMark: gene prediction of both DNA strands. Computers & Chemistry 17:123-133. [2] Benian, G., Tinley, T., Tang, X., and Borodovsky, M. 1996. The Caenorhabditis elegans gene unc-89, required for muscle M-line assembly, encoded a giant modular protein composed of Ig and signal transduction domains. Journal of Cell Biology 6: 835-848. [3] Lukashin A. and Borodovsky M. 1998, GeneMark.hmm: New solutions for gene finding, Nucl. Acids Res. 26, 1107-1115. [4] Pavy N., Rombauts S., Dehais P., Mathe C., Ramana D.V.V, Leroy P. and Rouze P. Evaluation of gen prediction software using a genomic data set: application to Arabidopsis thaliana sequences, Bioinformatics, 15, 887-899