Browsing by Author "Vize, Peter D."

Now showing 1 - 8 of 8
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    Coral spawning synchronicity: the role of ciradian genes in circalunar rhythms
    (2012) Brady, Aisling Kathleen; Vize, Peter D.
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    Temperature Modulation of Biological Clocks in a Reef-Building Coral
    (2018-01-25) Wuitchik, Daniel Michael; Vize, Peter D.; Yeaman, Sam; Cartar, Ralph; Antle, Michael
    Reef-building coral of the Great Barrier Reef demonstrate remarkably synchronized and precise timing of reproduction. They achieve this precision through sophisticated biological clock systems entrained by their local environment. This thesis explores how temperature and lunar light modulates the biological clocks of Acropora millepora by measuring transcriptomic changes with RNA-sequencing. Coral colonies were collected and maintained under artificial lunar light at the Heron Island Research Station under cool and warm temperature treatments corresponding to winter and summer averages at this locale. Individuals were sampled over a 24-hour period during a full lunar month to capture long-term daily profiles of gene expression. It was found that numerous biological clock genes were impacted by temperature and lunar light. Furthermore, temperature and lunar phase altered the expression of interesting hormonal pathways involved in reproductive behaviours. These data will help elucidate the mechanisms underlying the precise timing of reproduction in reef-building coral and the effect that different temperatures have on this process.
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    The Xenopus phenotype ontology: bridging model organism phenotype data to human health and development
    (2022-03-22) Fisher, Malcolm E.; Segerdell, Erik; Matentzoglu, Nicolas; Nenni, Mardi J.; Fortriede, Joshua D.; Chu, Stanley; Pells, Troy J.; Osumi-Sutherland, David; Chaturvedi, Praneet; James-Zorn, Christina; Sundararaj, Nivitha; Lotay, Vaneet S.; Ponferrada, Virgilio; Wang, Dong Z.; Kim, Eugene; Agalakov, Sergei; Arshinoff, Bradley I.; Karimi, Kamran; Vize, Peter D.; Zorn, Aaron M.
    Abstract Background Ontologies of precisely defined, controlled vocabularies are essential to curate the results of biological experiments such that the data are machine searchable, can be computationally analyzed, and are interoperable across the biomedical research continuum. There is also an increasing need for methods to interrelate phenotypic data easily and accurately from experiments in animal models with human development and disease. Results Here we present the Xenopus phenotype ontology (XPO) to annotate phenotypic data from experiments in Xenopus, one of the major vertebrate model organisms used to study gene function in development and disease. The XPO implements design patterns from the Unified Phenotype Ontology (uPheno), and the principles outlined by the Open Biological and Biomedical Ontologies (OBO Foundry) to maximize interoperability with other species and facilitate ongoing ontology management. Constructed in Web Ontology Language (OWL) the XPO combines the existing uPheno library of ontology design patterns with additional terms from the Xenopus Anatomy Ontology (XAO), the Phenotype and Trait Ontology (PATO) and the Gene Ontology (GO). The integration of these different ontologies into the XPO enables rich phenotypic curation, whilst the uPheno bridging axioms allows phenotypic data from Xenopus experiments to be related to phenotype data from other model organisms and human disease. Moreover, the simple post-composed uPheno design patterns facilitate ongoing XPO development as the generation of new terms and classes of terms can be substantially automated. Conclusions The XPO serves as an example of current best practices to help overcome many of the inherent challenges in harmonizing phenotype data between different species. The XPO currently consists of approximately 22,000 terms and is being used to curate phenotypes by Xenbase, the Xenopus Model Organism Knowledgebase, forming a standardized corpus of genotype–phenotype data that can be directly related to other uPheno compliant resources.
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    Transcriptome Dynamics Over a Lunar Cycle in Acropora humilis
    (2016-01-29) Oldach, Matthew J.; Vize, Peter D.; Muench, Douglas; Chua, Gordon; Brook, William
    The cycle of the moon serves as a cue for the reproduction of many species of corals, with many species spawning in the evening a few days following a full moon. Yet, little is known about the molecular mechanisms that allow corals to perceive moonlight and use this information for reproductive timing. To improve our understanding, short-read sequencing was used to assemble, de novo, the transcriptome of the coral Acropora humilis and identify differential patterns of gene expression in the month preceding spawning. Analysis revealed a number of biological processes that change over the lunar month including energy metabolism, skeletal deposition and translation. Furthermore, a number of circadian clock genes shift their expression over the lunar month suggesting a potential mechanism that corals may use detect moonlight and trigger a biochemical cascade that culminates in gamete release following the full moon.
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    Xenbase: gene expression and improved integration
    (Oxford University Press, 2010-01) Vize, Peter Bowes, Jeff B.; Snyder, Kevin A.; Segerdell, Erik; Jarabek, Chris J.; Azam, Kenan; Zorn, Aaron M.; Vize, Peter D.