Ralf J Sommer

..Using an in silico approach, we identified approximately 150 hits of P. pacificus collagen genes in the available EST, BAC-end, and fosmid-end sequences. However, 1:1 orthologs could only be identified for fewer than 20 collagen genes...

..I discuss redundancy as an evolutionary mechanism to explain developmental systems drift, a theory predicting conserved morphological structures to be generated by diverse molecular regulatory networks...

..These examples reveal a conserved and co-opted role of an endocrine signaling module involving the steroid hormone dafachronic acid. We will discuss how hormone signaling might facilitate life-history and morphological evolution...

..elegans, and we compare the seven available nematode genomes. One of the most striking findings is the unexpectedly high incidence of gene acquisition through horizontal gene transfer (HGT)...

..Genetic studies in some nematodes also shed light on the underlying mechanisms of evolutionary change...

..A group of vulva-defective mutants in Oscheius has been identified, with defects not seen in C. elegans...

..Furthermore, a synthesis of evo-devo with population genetics and evolutionary ecology is needed to meet future challenges...

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..I argue that continuity and hierarchy are separate but equally important issues of homology...

..How this beetle-association evolved and whether beetle-nematode coevolution occurred is still elusive. As a prerequisite to answering this question a robust phylogeny of beetle-associated Diplogastridae is needed...

..Evolutionary interpretations of differences in developmental, behavioral and ecological patterns require a phylogenetic framework of the genus Pristionchus...

..A Ppa-tra-1 morpholino phenocopies Ppa-tra-1 mutants and establishes the morpholino technology as a reverse genetic approach in P. pacificus...

..RNAi knock-down of mbd-2 in the two Caenorhabditis species results in varying percentages of lethality...

..Conservation of this small molecule ligand represents a fundamental link between dauer and infective larvae and might provide a general strategy for nematode parasitism...

..Thus, changes in the number, structure, and function of nematode hairy-like transcription factors are involved in the evolutionary alteration of this equivalence group...

..orientalis. Together, this study identifies P. pacificus as the most common Pristionchus nematode in field studies in Japan, identifies E. orientalis as an important host species, and provides the basis for the ecology of P. pacificus...

..elegans. Thus, intestinal peristalsis is critical to nematode health and contributes significantly to survival when fed Gram-positive bacteria...

..Bringing the nematode-bacterial interaction into the laboratory allows detailed functional studies, including the genetic manipulation of the interaction in both nematodes and bacteria...

..We discuss the potential effects of ecology on evolution of downstream effectors and upstream regulators on evolution of nematode innate immunity...

..We speculate that both genes were part of an ancestral DNA methylation system in nematodes and that gene loss and sequence divergence have abolished DNA methylation in C.elegans...

..Thus, comparative genomics analysis of three ecologically distinct nematodes offers a unique opportunity to investigate the association between genome structure and lifestyle...

..That EGL-4 homologs have been independently implicated for behavioral variations in other invertebrate models suggests that EGL-4 may act as a modulator for interspecies behavioral repertoires across large phylogenetic distances...

..Thus, despite similar lifestyle characteristics in the laboratory, the reproductive mode of hermaphroditism with rare facultative males can result in distinct genetic variability patterns in different ecological settings...

..We conclude that the genome annotation of C. elegans and other organisms can be greatly enhanced using modern machine learning technology...

..Thus, we describe the first specific developmental defect of a nematode pax-3 gene and our data reveal different regulatory networks for the specification of the vulva equivalence group...

..The mutation rates obtained for individual microsatellite markers provide guidelines for divergence time estimates that can be applied in P. pacificus next-generation sequencing approaches of wild isolates...

..Here, we use a transcriptomic approach to compare the dauer stage in the evolutionary model system Pristionchus pacificus with the dauer stage in C. elegans...

..Mutations in Cel-sem-4 and Cel-egl-17 cause similar defects. Thus, the molecular mechanisms of SM cell specification and migration are conserved between P. pacificus and C. elegans...

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..stercorosus to none, with Pelodera spp. being the most abundant group isolated. This study presents the first quantitative data on the Pristionchus spp. infection of beetles...

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..elegans and P. pacificus. Among 20 pathogenic strains with distinct virulence patterns against the two nematodes, we selected three B. cereus-like strains to investigate resistance and susceptibility immune responses in nematodes...

..We describe the initial evidence for the association of Pristionchus nematodes with beetles and provide a phylogeny based on sequence analysis of the small subunit ribosomal RNA gene...

..These results indicate that horizontal gene transfer-acquired genes undergo rapid evolutionary changes that affect all aspects of their molecular biology...

..The insect-to-nematode horizontal transfer is of special interest given that P. pacificus shows a tight association with insects...

..A comprehensive parts list of putative regulatory motifs was yet missing for this model system. In this study, we compile a set of putative regulatory motifs by combining evidence from conservation and expression data...

..pacificus contains operons and that downstream genes are trans-spliced to SL2. Surprisingly, the one operon analyzed so far in P. pacificus is not conserved in C. elegans, suggesting unexpected genomic plasticity...

..elegans. However, sequence comparison indicates that these genes may not be homologous to the fly Polycomb genes, suggesting that independent gene recruitment occurred during nematode evolution...

..Together, our results provide the first genetic evidence for a conserved function of PAX-3 in myogenesis between vertebrates and nematodes...

..We conclude that interception of the insect communication system might be a recurring strategy of Pristionchus nematodes but that different nematodes use distinct chemical cues for finding their beetle hosts...

..elegans hermaphrodite gonad; the arms fail to extend ventrally. Thus, this genetic analysis of gonad migration provides insight into the mechanisms underlying the generation of morphological novelty and organ shape...

..We use the mutant locus as a marker to develop transgenic technique by generating complex arrays and present flourescent-protein based transcriptional reporter constructs for P. pacificus...

..elegans paralogous Hox proteins can rescue Cel-mab-5. Experiments with chimeric, truncated and mutagenized Hox proteins suggest the specificity to be conferred by the N-terminal arm and helix I, but not helix II of the homeodomain...

..However, little is known about the functional activity and evolutionary longevity of genes acquired by horizontal gene transfer and the mechanisms favoring such processes...

..This study shows how hormonal signalling acts by coupling environmental change and genetic regulation and identifies dafachronic acid as a key hormone in nematode evolution...

..We conclude that Pristionchus olfaction is highly diverse among closely related species and is likely to be involved in shaping nematode-host interactions...

..Finally, some parasitic features evolved under free-living conditions. A recent study revealed a conserved endocrine mechanism controlling the formation of dauer and infective larvae in nematodes...

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..These results confirm developmental system drift as an important theory for the evolution of organ systems and they highlight the significance of protein modularity in signal transduction and the dynamics of signaling networks...

..Combined, these results provide the first catalog of the expressed genome of P. pacificus, refinement of its genome annotation, and the first comparison of related nematode models at the proteome level...

..pacificus. We apply focused centrality methods to identify neurons I1 and I2 as candidates for regulating predatory feeding and predict substantial divergence in the function of pharyngeal glands...

..pacificus to describe more thoroughly the molecular basis for these changes, as well as to better integrate our molecular knowledge with the biodiversity of Pristionchus species...

..The combination of mutation rate analysis with intraspecific divergence provides a powerful tool for the reconstruction of the natural history of P. pacificus, and we discuss the ecological implication of these findings...

..We therefore discuss intraspecific competition among genotypes as a previously unconsidered aspect of dauer formation...

..Investigation of Cel-vab-7 mutant animals showed a similar but weaker vulva defective phenotype to the one described for Ppa-vab-7...

..elegans. This study presents the first systematic comparison of phosphoproteomes and kinomes of two model nematodes and, as such, will be a useful resource for comparative studies of their signal transduction networks...

..Content will be continuously improved as we annotate the P.pacificus genome, and will be an indispensable resource for P.pacificus genomics...

..Individual ablation experiments in P. pacificus show significant differences in the effects of individual somatic tissues on germ line patterning in comparison to C. elegans...

..Thus, intrachromosomal rearrange ments occur frequently in nematodes, limiting the likelihood of identifying orthologous genes of P.pacificus and C.elegans based on positional information within the two genomes...

..Ultimately, it is the interplay of conservation and change of the specificity of genes and genetic networks that generates developmental novelty over evolutionary time...

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..This could indicate that Poikilolaimus species possess five bivalent chromosomes in their germ lines, in contrast to the hermaphroditic Caenorhabditis elegans or Pristionchus pacificus, which have six chromosomes...

..pacificus. This study provides the first molecular identification of the inductive vulva signal in a nematode other than Caenorhabditis...

..We show that nictation behaviour in P. pacificus nematodes serves as a host-finding behaviour. Our results suggest that nictation plays a role in the evolution of new life-history strategies, such as the evolution of parasitism...

..These results suggest that developmental mechanisms, some of which are redundantly involved in vulval fate specification of the genetic model organism Caenorhabditis elegans, can evolve without concomitant morphological change...

..This is the first study to show that the influence of the reproductive system on extending lifespan and innate immunity is conserved in evolution...

..It can also be used to examine the food choice of these nematodes when they are faced with a number of bacteria...

..The nematodes are then monitored for a few days and identified using simple morphological characteristics. This method is rapid, easy, and biased for Pristionchus species...

..Thus, P. pacificus is not only an established model system for evolutionary developmental biology, but also an emerging model system for the evolution of complex life-history traits...

..I then describe a genetic approach in the nematode Pristionchus pacificus that might identify those genetic and molecular processes that cause evolutionary changes of cell fate specification...

..pacificus genome. The integrated genome map thus provides a framework for positional cloning and the study of genome evolution in nematodes...

..pacificus. A mapping strategy using two selected markers per chromosome was devised and the efficiency of this approach was illustrated by the mapping of the Ppa-unc-1/Twitchin gene...

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..Additionally, it provides a platform for the Caenorhabditis elegans community to compare nematode genetic data in an evolutionary perspective...

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..Therefore, whereas the molecular mechanisms that generate vulval symmetry are conserved, the genetic control of vulva induction diversified during evolution...