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Publication Analysis of mitogenomes from the family Keratoisididae reveals mitonuclear discordance and the presence of unknown open reading frames(Springer, 2025-02-13) Morrissey, Declan; Quattrini, Andrea M.; Allcock, A. Louise; Irish Research CouncilHistorically, evolutionary studies have not been able to resolve relationships within Octocorallia but recent advances in genomic techniques have allowed large numbers of Ultra Conserved Elements and exons, collectively referred to as conserved elements, to be extracted from the nuclear genome. Few studies have compared evolutionary histories generated with these conserved elements and with those inferred from complete mitogenomes. We examined the characteristics of 26 complete mitogenomes and constructed both mitochondrial and nuclear (1418 conserved elements) phylogenies of the family Keratoisididae, a prolific group of exclusively deep-sea corals. Relationships among most keratoisidid groups were well supported by the conserved element phylogeny while many were unresolved from mitogenomic inferences. In addition, some incongruences were observed. The position of keratoisidid groups F1 and I4, and the observed polyphyly of D2 in the nuclear inference phylogeny, provide evidence for mitonuclear discordance within the group. Multiple novel Open Reading Frames (ORFs) of unknown function were found in the mitogenome between cob and nad6. These ORFs ranged in size from 84 to 537 bp and were present in all examined mitogenomes except those assigned to keratoisidid group A1 which only has a 10 bp gap between coding regions. Further investigation is required to determine whether these ORFs are expressed and, if so, what function they have. The presence of mitonuclear discordance within the family indicates that phylogenies constructed with concatenated mitochondrial and nuclear markers may be inappropriate.Publication A decade to study deep-sea life.(Nature Research, 2020-11-25) Howell, Kerry L.; Hilário, Ana; Allcock, A. Louise; Bailey, David; Baker, Maria; Clark, Malcolm R.; Colaço, Ana; Copley, Jon; Cordes, Erik E.; Danovaro, Roberto; Dissanayake, Awantha; Escobar, Elva; Esquete, Patricia; Gallagher, Austin J.; Gates, Andrew R.; Gaudron, Sylvie M.; German, Christopher R.; Gjerde, Kristina M.; Higgs, Nicholas D.; Le Bris, Nadine; Levin, Lisa A.; Manea, Elisabetta; McClain, Craig; Menot, Lenaick; Mestre, Nelia C.; Metaxas, Anna; Milligan, Rosanna; Muthumbi, Agnes W. N.; Ramalho, Sofia P.; Ramirez-Llodra, Eva; Robson, Laura M.; Rogers, Alex D.; Sellanes, Javier; Sigwart, Julia D.; Sink, Kerry; Snelgrove, Paul V. R.; Stefanoudis, Paris V.; Sumida, Paulo Y; Taylor, Michelle L.; Thurber, Andrew R.; Vieira, Rui; Watanabe, Hiromi K.; Woodall, Lucy C.; Xavier, Joana R.; Narayanaswamy, Bhavani E.The United Nations Decade of Ocean Science for Sustainable Development presents an exceptional opportunity to effect positive change in ocean use. We outline what is required of the deep-sea research community to achieve these ambitious objectives.Publication Development of an ethogram for hutch-housed dairy calves and determination of factors influencing their behaviour(Elsevier, 2020-11-18) Ugwu, Nnenna; Love, Emma; Murrell, Jo; Whay, Helen; Knowles, Toby; Hockenhull, Jo; University of Bristol; Tertiary Education Trust Fund, NigeriaThe objectives of this study were to investigate the behaviour of hutch-housed dairy calves, develop an ethogram of general behaviour, and determine whether housing calves in different hutches, day, gender and time of day influenced the behaviour of dairy calves using the developed ethogram. Thirty-one apparently healthy Holstein Friesian calves (6 ± 1 week old) were recruited for this study. The ethogram was developed by directly observing the behaviour of ten female dairy calves housed in two group hutches for five days. Based on these observations, behaviour was then organized into three categories. The first category (I) comprised of postures, attentiveness and social interactive behaviour; the second category (II) comprised of event behaviour which were recorded each time they occurred while the last category (III) comprised of movement and activity behaviour whose duration were recorded. The ethogram was used to record the behaviour of 16 calves (4 males; 12 females) housed in groups of four using direct and video observations for two consecutive days to ascertain if there are behavioural differences between dairy calves housed in different hutches; between days and gender. Additionally, the ethogram was used to record the behaviour of an additional five dairy calves housed in a group hutch to determine the time of day effect. The behaviour of these five dairy calves were recorded hourly between the hours of 10:00 and 17:00 for two days using a combination of direct and video observations. Data were expressed as median frequency, duration or mean rank and significance was accepted at P ≤ 0.05. There were no significant differences in the behaviour of dairy calves housed in different hutches. Significant variations (P < 0.05) were observed in the response to observer, ear and mouth postures and ear flicking behaviour between the two days. Tongue position, ear flicking, tail wagging and walking behaviour were significantly higher (P < 0.05) in females than in males while body shaking and sniffing other calves were found to be significantly higher (P < 0.05) in males than in females. Time of day significantly (P < 0.05) influenced the location in the hutch, head, tail and standing posture; and the duration of standing, walking, and lying behaviour. While confirmation is needed, findings suggest the behaviour of dairy calves may be influenced by day, gender, and time of day and this should be considered when undertaking behavioural studies.Publication Microplastics in corals: An emergent threat(Elsevier, 2020-11-01) de Oliveira Soares, Marcelo; Matos, Eliana; Lucas, Caroline; Rizzo, Lucia; Allcock, A. Louise; Rossi, Sergio; JPI Oceans International Consortium/CONFAP; Conselho Nacional de Desenvolvimento Científico e Tecnológico – CNPq; Fundação Cearense de Apoio ao Desenvolvimento Científico e Tecnológico - FUNCAP; Science Foundation Ireland; Marine Institute; European Regional Development FundThis article seeks to present a summary of knowledge and thus improve awareness of microplastic impacts on corals. Recent research suggests that microplastics have a variety of species-specific impacts. Among them, a reduced growth, a substantial decrease of detoxifying and immunity enzymes, an increase in antioxidant enzyme activity, high production of mucus, reduction of fitness, and negative effects on coral-Symbiodiniaceae relationships have been highlighted in recent papers. In addition to this, tissue necrosis, lower fertilization success, alteration of metabolite profiles, energetic costs, decreased skeletal growth and calcification, and coral bleaching have been observed under significant concentrations of microplastics. Furthermore, impairment of feeding performance and food intake, changes in photosynthetic performance and increased exposure to contaminants, pathogens and other harmful compounds have also been found. In conclusion, microplastics may cause a plethora of impacts on corals in shallow, mesophotic, and deep-sea zones at different latitudes; underlining an emerging threat globally.Publication Animal life history is shaped by the pace of life and the distribution of age-specific mortality and reproduction(Nature Research (part of Springer Nature), 2019-07-08) Healy, Kevin; Ezard, Thomas H. G.; Jones, Owen R.; Salguero-Gómez, Roberto; Buckley, Yvonne M.; Science Foundation Ireland; Natural Environment Research Council; Australian Research Council; Danish Council for Independent ResearchAnimals exhibit an extraordinary diversity of life history strategies. These realized combinations of survival, development and reproduction are predicted to be constrained by physiological limitations and by trade-offs in resource allocation. However, our understanding of these patterns is restricted to a few taxonomic groups. Using demographic data from 121 species, ranging from humans to sponges, we test whether such trade-offs universally shape animal life history strategies. We show that, after accounting for body mass and phylogenetic relatedness, 71% of the variation in animal life history strategies can be explained by life history traits associated with the fast-slow continuum (pace of life) and with a second axis defined by the distribution of age-specific mortality hazards and the spread of reproduction. While we found that life history strategies are associated with metabolic rate and ecological modes of life, surprisingly similar life history strategies can be found across the phylogenetic and physiological diversity of animals.Publication Snake venom potency and yield are associated with prey‐evolution, predator metabolism and habitat structure(Wiley, 2019-01-07) Healy, Kevin; Carbone, Chris; Jackson, Andrew L.; Science Foundation Ireland; European Regional Development Fund; Higher Education Authority, Programme for Research at Third Level Institutions, Cycle 5 (PRTLI‐5); National University of Ireland, GalwaySnake venom is well known for its ability to incapacitate and kill prey. Yet, potency and the amount of venom available varies greatly across species, ranging from the seemingly harmless to those capable of killing vast numbers of potential prey. This variation is poorly understood, with comparative approaches confounded by the use of atypical prey species as models to measure venom potency. Here, we account for such confounding issues by incorporating the phylogenetic similarity between a snake's diet and the species used to measure its potency. In a comparative analysis of 102 species we show that snake venom potency is generally prey‐specific. We also show that venom yields are lower in species occupying three dimensional environments and increases with body size corresponding to metabolic rate, but faster than predicted from increases in prey size. These results underline the importance of physiological and environmental factors in the evolution of predator traits.Publication A gene regulatory network underlying the formation of pre-placodal ectoderm in Xenopus laevis(BioMed Central, 2018-06-16) Kumar Maharana, Santosh; Schlosser, Gerhard; Hardiman Research Scholarship, NUI Galway; Irish Research CouncilBackground: The neural plate border ectoderm gives rise to key developmental structures during embryogenesis, including the neural crest and the preplacodal ectoderm. Many sensory organs and ganglia of vertebrates develop from cranial placodes, which themselves arise from preplacodal ectoderm, defined by expression of transcription factor Six1 and its coactivator Eya1. Here we elucidate the gene regulatory network underlying the specification of the preplacodal ectoderm in Xenopus, and the functional interactions among transcription factors that give rise to this structure.Results: To elucidate the gene regulatory network upstream of preplacodal ectoderm formation, we use gain-and loss-of-function studies to explore the role of early ectodermal transcription factors for establishing the preplacodal ectoderm and adjacent ectodermal territories, and the role of Six1 and Eya1 in feedback regulation of these transcription factors. Our findings suggest that transcription factors with expression restricted to ventral (non-neural) ectoderm (AP2, Msx1, FoxI1, Vent2, Dlx3, GATA2) and those restricted to dorsal (neural) ectoderm (Pax3, Hairy2b, Zic1) are required for specification of both preplacodal ectoderm and neural crest in a context-dependent fashion and are cross-regulated by Eya1 and Six1.Conclusion: These findings allow us to elucidate a detailed gene regulatory network at the neural plate border upstream of preplacodal ectoderm formation based on functional interactions between ectodermal transcription factors. We propose a new model to explain the formation of immediately juxtaposed preplacodal ectoderm and neural crest territories at the neural plate border, uniting previous models.Publication Identification of novel cis-regulatory elements of Eya1 in Xenopus laevis using BAC recombineering(Nature Publishing Group, 2017-11-03) Maharana, Santosh Kumar; Pollet, Nicolas; Schlosser, Gerhard; |~|The multifunctional Eya1 protein plays important roles during the development of cranial sensory organs and ganglia, kidneys, hypaxial muscles and several other organs in vertebrates. Eya1 is encoded by a complex locus with candidate cis-regulatory elements distributed over a 329 kbp wide genomic region in Xenopus. Consequently, very little is currently known about how expression of Eya1 is controlled by upstream regulators. Here we use a library of Xenopus tropicalis genomic sequences in bacterial artificial chromosomes (BAC) to analyze the genomic region surrounding the Eya1 locus for enhancer activity. We used BAC recombineering to first create GFP reporter constructs, which were analysed for enhancer activity by injection into Xenopus laevis embryos. We then used a second round of BAC recombineering to create deletion constructs of these BAC reporters to localize enhancer activity more precisely. This double recombineering approach allowed us to probe a large genomic region for enhancer activity without assumptions on sequence conservation. Using this approach we were able to identify two novel cis-regulatory regions, which direct Eya1 expression to the somites, pharyngeal pouches, the preplacodal ectoderm (the common precursor region of many cranial sensory organs and ganglia), and other ectodermal domains.