Hall, Sarah E. et al. (2009) International Worm Meeting "Environmental programming of gene expression in C. elegans."

Russ, Carsten, Sengupta, Piali, Beverly, Matthew H., Hall, Sarah E., Nusbaum, Chad

[International Worm Meeting, 2009]

Environmental programming describes a phenomenon in which early environmental and developmental experience can affect adult health and behavior through long-lasting changes in gene expression. Increasing evidence suggests that affected genes are ''programmed'' by an environmental stimulus through changes in chromatin states. C. elegans makes an environmentally-regulated developmental decision in early larval stages to continue developing into a reproductive adult, or to enter the alternative dauer stage. When environmental conditions improve, animals exit the dauer stage and continue normal development. Although adults that have passed through or bypassed the dauer stage appear grossly identical, post-dauer adult worms have been reported to retain a cellular memory of their developmental decision. To identify the gene set whose expression may be regulated by a memory of passage through the dauer stage, we compared the transcription profiles of postdauer adult animals and control adult animals that bypassed the dauer stage. We found that the expression of 2,126 genes is predicted to be significantly up or down-regulated in postdauer as compared to control animals. Genes predicted to play roles in reproduction, sensory signal transduction, transcriptional regulation, RNAi, and chromatin remodeling were enriched in the affected gene set. In addition, we quantified altered reproductive and aging phenotypes in postdauer adults compared to controls. To determine whether chromatin remodeling plays a role in maintaining the altered gene expression patterns, we performed chromatin immunoprecipitation followed by Illumina Genome Analyzer sequencing (ChIP-Seq) of genomic regions using antibodies against the common histone modifications H3K4me3, H3K9me3, H3K27me3, and H4panAc. Analysis of the ChIP-Seq data in control and postdauer animals showed a direct correlation of gene expression levels and histone modification enrichments in gene regulatory regions for modifications associated with active transcription. However, we found that H3K9me3 and H3K27me3 modifications were independent of gene expression levels. Furthermore, genes whose expression was altered due to passage through the dauer stage exhibited predictable changes in histone enrichment profiles in postdauer animals. Preliminary evidence suggests that a subset of these gene expression changes are dependent on a chromatin remodeling factor and proteins implicated in RNAi, suggesting a RNAi-dependent transcriptional gene silencing mechanism of environmental programming. We expect that this work will allow us to understand how early environmental experiences affect adult phenotypes, and generate phenotypic diversity in an otherwise isogenic population.

Samuel, Buck S. et al. (2011) International Worm Meeting "WORMFOOD GENOMICS: E. COLI DETERMINANTS OF C. ELEGANS' FITNESS."

Carr, Chris, Rowedder, Holli, Plunkett, Guy, Melo, Justine, Durfee, Tim, Nusbaum, Chad, Glasner, Jeremy, Russ, Carsten, Ruvkun, Gary, Sykes, Sean, Samuel, Buck S., Young, Sarah

[International Worm Meeting, 2011]

Like other metazoans, C. elegans fitness (success) within its microbe-rich habitats depends on a tight balance of energy acquisition and expenditure. Thus, it is also highly tuned to microbial cues that allow it to separate potential food or friend from foe. Accordingly, some microbial signals have been postulated to influence fat storage in parallel to endogenous endocrine cues. Several studies also show that the E. coli-adapted N2-Bristol strain is especially sensitive to 'minor' differences in E. coli strains: faster growth rates, increased progeny delivery rates, and less fat retention is seen when worms consume HB101 compared to OP50. Perhaps due to this fitness benefit, worms also exhibit increased satiety and a behavioral preference for HB101. Thus, we have sought to identify the E. coli gene products that modulate C. elegans fitness. To this end, we have sequenced E. coli genomes routinely used in C. elegans cultivation: HB101 (2 isolates), OP50 (2 isolates) and HT115. Despite little variation among strain isolates, 350 and 412 genes are 'unique' to OP50 and HB101, respectively. Many are organized into clusters, and represent a range of gene functions: e.g., carbohydrate utilization (96), cell wall/LPS modification (42), amino acid metabolism (21), regulation (41), the Cascade system (6) and fatty acid metabolism (5). Phenotype microarrays were also used to confirm the metabolic defects. In order to systematically test the impact of these microbial gene products on C. elegans' fitness, we assembled nearly 200 single gene mutants with defined function in a 'neutral' and consistent genetic background (E. coli K12). We then used a number of assays to test a mutant's impact on N2 growth, broods, body size and fat storage. Our analyses indicate that both genes in core metabolism and transport/biosynthesis of conserved mediators of host interaction-autoinducers, biogenic amines, short-chain fatty acids and LPS-influence N2 fitness. Studies of these small molecules as sensory or nutritive cues to C. elegans directly or via regulation of E. coli metabolism are ongoing. However, results so far indicate that the microbial milieu of signals may be just as important of a determinant of C. elegans' fitness as the nutritional potential for supporting growth of a population within a given habitat.

Blaxter ML et al. (1998) European Worm Meeting "The phylogenetics of nematodes"

Blaxter ML, Vanfleteren JR, De Ley P, Thomas K, Dorris M, Frisse LM

[European Worm Meeting, 1998]

We are continuing in our quest to define the evolutionary history of the phylum Nematoda using molecular phylogenetic methods. The published analysis (Blaxter et al, Nature 392:71-75 (1998)) has now been complemented with over 100 additional sequenced taxa, arising from our work and that of others (Kampfer et al, Invert. Biol. 117:29-36 (1998) and Aleshin et al, Russ. J. Nematol. in press (1998)). Our analysis continues to support the division of the Nematoda into five major clades, and does not support the division of the phylum into two classes (Adenophorea and Secernentea). The origin of the Secernentea has been more closely defined as residing within the Chromadorida, although a separate chromadorid radiation is now evident. Caenorhabditis remains a close relative of the parasitic strongyles. We are extending the dataset using sequence data derived from fixed museum specimens. Formalin fixation preserves nematode structures very well, but is not good for DNA preservation. We have been able to extract PCR-amplifiable DNA from single 12-year fixed specimens of Strongyloides species using an amino acid titration method. Fragments up to 600 bp are recoverable and sequencable. For specimens preserved in alcohol, even at low temperatures, it has been much more difficult to obtain amplifiable DNAs, but we now have a rehydration-extraction method which works on larger samples. Current projects are focussing on the phylogenetics of the genus Strongyloides, parasites of vertebrate guts which have a facultative free-living generation. This group has turned out to be entertainingly complex, with the species divided into two distinct clades separated by freeliving and parasitic taxa from other genera. We find no correlation between host and parasite phylogenies, suggesting that horizontal transfer between hosts has been common in these parasites. We are examining in detail the coevolution of filarial nematodes and an endosymbiotic Wolbachia-like bacterium. In this case, we have strong evidence for vertical transmission of the endosymbiont within the filarial lineage. We are also providing a phylogenetic framework for comparative EST-based genome projects on additional filarial and other nematode species.