Project description:To adapt to its changing dietary environment, the digestive tract is extensively remodeled from the embryo to the adult during vertebrate development. Xenopus laevis metamorphosis is an excellent model system for studying mammalian gastrointestinal development and is used to determine the genes and signaling programs essential for intestinal development and maturation. The metamorphosing intestine can be divided into four distinct developmental time points and these were analyzed with X. laevis microarrays. Due to the high level of conservation in developmental signaling programs and homology to mammalian genes, annotations and bioinformatics analysis were based on human orthologs. Clustering of the expression patterns revealed co-expressed genes involved in essential cell processes such as apoptosis and proliferation. The two largest clusters of genes have expression peaks and troughs at the climax of metamorphosis respectively. Novel conserved gene ontology categories regulated during this period include transcriptional activity, signal transduction, and metabolic processes. Interestingly, the induced genes associated with metamorphic climax correlated with the gene expression peaks observed around birth in the mouse intestine. Thus both mouse and amphibian, share similarities at the molecular levels for intestinal maturation and remodeling, which appears to be under the influence of increasing levels of circulating thyroid hormone. Moreover, our genome-wide analysis of the intestine during development identified larval/embryo- and adult-specific genes. Detailed analysis revealed 17 larval specific genes that may represent molecular markers for human colonic cancers, while many adult specific genes are associated with dietary enzymes. This global developmental expression study provides the first detailed molecular description of intestinal remodeling and maturation during postembryonic development, which should help improve our understanding of intestinal organogenesis and human diseases. This study significantly contributes towards our understanding of the dynamics of molecular regulation during development and tissue renewal, which is important for future basic and clinical research and for medicinal applications. Time series experiment through natural metamorphosis of intestine in Xenopus laevis. Biological replicates: 3 replicates for each stage of major change during amphibian metamorphosis (except in the climax where 2 bioogical replicates were used). Universal reference design was used instead of dye-swap design for 2-color hybridizations.

Project description:Larval settlement and metamorphosis is a vital transition period for marine invertebrates and can have far-reaching effects on the ecology and evolution of a species. To explore the molecular mechanisms of this critical process in a non-model organism, the tropical abalone Haliotis asinina, we employed cDNA microarray methods. By comparing gene expression profiles through mid to late larval development and metamorphosis, we identified 144 genes as likely candidates for a role in competence and/or metamorphosis. Gene characterization showed that ~60% of these were significantly similar to previously described genes from other taxa, while ~40% had no significant similarities to any known genes. A high 49.3% of genes were gastropod- or abalone-specific, but none appear to be Lophotrochozoan-specific, despite the fact that metamorphosis is thought to have had a separate origin in this group. Based on temporal expression profiles, the differentially expressed larval and postlarval genes can be clustered into 5 categories that reveal there are strikingly different transcriptional patterns occurring during this phase of development. Some classes of gene activation are contingent upon exogenous cues and correlate with the initiation of settlement and metamorphosis. Importantly, there is also extensive gene activity associated with the endogenous attainment of competence, which occurs prior to, and independent of, the exogenous induction of settlement. Our results show that as the haliotid veliger larva matures, it requires the coordinated regulation of temporally different batteries of genes involved in a wide range of physiological and developmental processes associated with colonisation of the benthos. Although the signalling pathways operating at metamorphosis may be conserved across the animal kingdom, it appears they are regulating the expression of novel genes specific to abalone, gastropods and molluscs during H. asinina metamorphosis. Keywords: timecourse; metamorphosis; marine ecology

Project description:Larval settlement and metamorphosis is a vital transition period for marine invertebrates and can have far-reaching effects on the ecology and evolution of a species. To explore the molecular mechanisms of this critical process in a non-model organism, the tropical abalone Haliotis asinina, we employed cDNA microarray methods. By comparing gene expression profiles through mid to late larval development and metamorphosis, we identified 144 genes as likely candidates for a role in competence and/or metamorphosis. Gene characterization showed that ~60% of these were significantly similar to previously described genes from other taxa, while ~40% had no significant similarities to any known genes. A high 49.3% of genes were gastropod- or abalone-specific, but none appear to be Lophotrochozoan-specific, despite the fact that metamorphosis is thought to have had a separate origin in this group. Based on temporal expression profiles, the differentially expressed larval and postlarval genes can be clustered into 5 categories that reveal there are strikingly different transcriptional patterns occurring during this phase of development. Some classes of gene activation are contingent upon exogenous cues and correlate with the initiation of settlement and metamorphosis. Importantly, there is also extensive gene activity associated with the endogenous attainment of competence, which occurs prior to, and independent of, the exogenous induction of settlement. Our results show that as the haliotid veliger larva matures, it requires the coordinated regulation of temporally different batteries of genes involved in a wide range of physiological and developmental processes associated with colonisation of the benthos. Although the signalling pathways operating at metamorphosis may be conserved across the animal kingdom, it appears they are regulating the expression of novel genes specific to abalone, gastropods and molluscs during H. asinina metamorphosis. Keywords: timecourse; metamorphosis; marine ecology Each microarray slide contained a different combination of 2 of the 9 developmental stages used in the experiment (66 hpf, 78 hpf, 90 hpf, 108 hpf, 120 hpf, 144 hpf, 12 hpi, 24 hpi, 48 hpi). Each developmental stage was subjected to 4 hybridisations â amounting to 4 technical replicates per stage - in a loop design (Churchill 2002; Oleksiak et al. 2002). This design led to raw data consisting of 72 measurements - 9 stages with 8 replicates (including 2 replicates per chip) - for each of 5541 spots.

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Studies on Xenopus laevis intestine reveal biological pathways underlying vertebrate gut adaptation from embryo to adult

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