Integrative Systems Biology Lab

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Now showing 1 - 5 of 68
  • Presentation

    The role of the brain in the adaptation to climate change

    (SPRINGER, 2017-04-01) Schunter, Celia Marei; Ravasi, Timothy; Biological and Environmental Science and Engineering (BESE) Division; Bioscience Program; Integrative Systems Biology Lab; King Abdullah Univ Sci & Technol, Biol & Environm Sci & Engn Div, Thuwal 239556900, Saudi Arabia

    The increase of CO2 in the oceans, termed ocean acidification, is projected to have detrimental effects on marine organisms. The magnitude of the impact on the marine ecosystems will depend on species capacity to adapt. Recent studies show that the behaviour of reef fishes is impaired at projected CO2 levels; however, individual variation exists that might promote adaptation. Offspring of CO2-tolerant and CO2-sensitive parents were reared at nearfuture CO2 (754 uatm) or present-day control levels (414 uatm) and exposed to higher levels of CO2 at different life stages. We study the transcriptomes and proteomes in the brain of Acanthochromis polyacanthus (spiny damselfish), to evaluate short-term, longterm (one generation) and transgenerational molecular responses to more acidified oceans. Withingeneration CO2 exposure lead to an increased expression of genes involved in GABAergic neurotransmission as well as the potassium-chloride cotransporter 2 (kcc2). The reversal of the transmembrane gradient for HCO3- and Cl- with elevated levels of extracellular bicarbonate is the likely cause for the excitement of the neuronal transmission which in turn causes the behavioural impairment in fish at near-future high CO2 levels. We find a clear signature of the parental sensitivity to CO2 in the molecular phenotype of the offspring, mainly driven by circadian rhythm genes. Furthermore, expression patterns with prior parental CO2 acclimation largely differ to short-term or long-term exposures emphasizing the importance of transgenerational acclimation in exposure experiments.

  • Presentation

    Astrocyte- specific signatures in response to methamphet-amine exposure in vitro

    (SPRINGER, 2017-04-01) Marcondes, M. C.; Bortell, N.; Basova, L.; Semenova, S.; Fox, H. S.; Ravasi, Timothy; Marcondes, M. C.; Biological and Environmental Science and Engineering (BESE) Division; Bioscience Program; Integrative Systems Biology Lab; King Abdullah Univ Sci & Technol, Environm Epigenet Program, Thuwal 23955, Saudi Arabia; Scripps Res Inst, Dept Mol & Cellular Neurosci, La Jolla, CA 92037 USA; Univ Calif San Diego, Sch Med, Dept Psychiat, San Diego, CA 92103 USA; Univ Nebraska Med Ctr, Dept Expt Pharmacol, Omaha, NE 68182 USA
  • Dataset

    Viral ecogenomics across the Porifera

    (figshare, 2020) Pascelli, Cecília; Laffy, Patrick W; Botté, Emmanuelle; Kupresanin, Marija; Rattei, Thomas; Lurgi, Miguel; Ravasi, Timothy; Webster, Nicole S.; Biological and Environmental Science and Engineering (BESE) Division; Bioscience Program; Computational Bioscience Research Center (CBRC); Computer, Electrical and Mathematical Science and Engineering (CEMSE) Division; Economic & Technology Development; Innovation and Economic Development; Integrative Systems Biology Lab; Australian Institute of Marine Science PMB No.3, Townsville MC Townsville, Queensland 4810 Australia; AIMS@JCU Townsville, Queensland Australia; James Cook University Townsville Australia; Department of Microbiology and Ecosystem Science, Division of Computational Systems Biology, University of Vienna Vienna Austria; Biosciences Department, University of Swansea Swansea Wales; Australian Centre for Ecogenomics, University of Queensland, Brisbane, Australia

    Abstract Background Viruses directly affect the most important biological processes in the ocean via their regulation of prokaryotic and eukaryotic populations. Marine sponges form stable symbiotic partnerships with a wide diversity of microorganisms and this high symbiont complexity makes them an ideal model for studying viral ecology. Here, we used morphological and molecular approaches to illuminate the diversity and function of viruses inhabiting nine sponge species from the Great Barrier Reef and seven from the Red Sea. Results Viromic sequencing revealed host-specific and site-specific patterns in the viral assemblages, with all sponge species dominated by the bacteriophage order Caudovirales but also containing variable representation from the nucleocytoplasmic large DNA virus families Mimiviridae, Marseilleviridae, Phycodnaviridae, Ascoviridae, Iridoviridae, Asfarviridae and Poxviridae. Whilst core viral functions related to replication, infection and structure were largely consistent across the sponge viromes, functional profiles varied significantly between species and sites largely due to differential representation of putative auxiliary metabolic genes (AMGs) and accessory genes, including those associated with herbicide resistance, heavy metal resistance and nylon degradation. Furthermore, putative AMGs varied with the composition and abundance of the sponge-associated microbiome. For instance, genes associated with antimicrobial activity were enriched in low microbial abundance sponges, genes associated with nitrogen metabolism were enriched in high microbial abundance sponges and genes related to cellulose biosynthesis were enriched in species that host photosynthetic symbionts. Conclusions Our results highlight the diverse functional roles that viruses can play in marine sponges and are consistent with our current understanding of sponge ecology. Differential representation of putative viral AMGs and accessory genes across sponge species illustrate the diverse suite of beneficial roles viruses can play in the functional ecology of these complex reef holobionts. Video Abstract

  • Software

    Ecogenomics/BamM: Metagenomics-focused BAM file manipulation

    (Github, 2014-05-26) Robbins, Steven J.; Chan, Cheong Xin; Messer, Lauren F.; Singleton, Caitlin M.; Geers, Aileen U.; Ying, Hua; Baker, Alexander; Bell, Sara C.; Morrow, Kathleen M.; Ragan, Mark A.; Miller, David J.; Forêt, Sylvain; Ball, Eldon; Beeden, Roger; Bongaerts, Pim; Hoegh-Guldberg, Ove; Cooke, Ira; Leggat, Bill; Sprungala, Susan; Fitzgerald, Anna; Shang, Catherine; Lundgren, Petra; Fyffe, Theresa; Rubino, Francesco; van Oppen, Madeleine; Weynberg, Karen; Voolstra, Christian R.; Tyson, Gene W.; Bourne, David G.; Berumen, Michael L.; Aranda, Manuel; Ravasi, Timothy; Biological and Environmental Science and Engineering (BESE) Division; Bioscience Program; Integrative Systems Biology Lab; Marine Science Program; Red Sea Research Center (RSRC); Reef Genomics Lab; Australian Centre for Ecogenomics, The University of Queensland, Brisbane, Queensland, Australia.

    Metagenomics-focused BAM file manipulation

  • Software

    chancx/dinoflag-alt-splice: Modified scripts for recognising alternative splice-sites, tailored for dinoflagellate genomes

    (Github, 2019-06-12) Robbins, Steven J.; Chan, Cheong Xin; Messer, Lauren F.; Singleton, Caitlin M.; Geers, Aileen U.; Ying, Hua; Baker, Alexander; Bell, Sara C.; Morrow, Kathleen M.; Ragan, Mark A.; Miller, David J.; Forêt, Sylvain; Ball, Eldon; Beeden, Roger; Bongaerts, Pim; Hoegh-Guldberg, Ove; Cooke, Ira; Leggat, Bill; Sprungala, Susan; Fitzgerald, Anna; Shang, Catherine; Lundgren, Petra; Fyffe, Theresa; Rubino, Francesco; van Oppen, Madeleine; Weynberg, Karen; Voolstra, Christian R.; Tyson, Gene W.; Bourne, David G.; Berumen, Michael L.; Aranda, Manuel; Ravasi, Timothy; Biological and Environmental Science and Engineering (BESE) Division; Bioscience Program; Integrative Systems Biology Lab; Marine Science Program; Red Sea Research Center (RSRC); Reef Genomics Lab; Australian Centre for Ecogenomics, The University of Queensland, Brisbane, Queensland, Australia.

    Modified scripts for recognising alternative splice-sites, tailored for dinoflagellate genomes