| 1. |
- Dylus, D.V., et al.
(author)
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Large-scale gene expression study in the ophiuroid Amphiura filiformis provides insights into evolution of gene regulatory networks
- 2016
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In: EvoDevo. - : Springer Science and Business Media LLC. - 2041-9139. ; 7:1
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Journal article (peer-reviewed)abstract
- © 2016 Dylus et al. Background: The evolutionary mechanisms involved in shaping complex gene regulatory networks (GRN) that encode for morphologically similar structures in distantly related animals remain elusive. In this context, echinoderm larval skeletons found in brittle stars and sea urchins provide an ideal system. Here, we characterize for the first time the development of the larval skeleton in the ophiuroid Amphiura filiformis and compare it systematically with its counterpart in sea urchin. Results: We show that ophiuroids and euechinoids, that split at least 480 Million years ago (Mya), have remarkable similarities in tempo and mode of skeletal development. Despite morphological and ontological similarities, our high-resolution study of the dynamics of genetic regulatory states in A. filiformis highlights numerous differences in the architecture of their underlying GRNs. Importantly, the A.filiformis pplx, the closest gene to the sea urchin double negative gate (DNG) repressor pmar1, fails to drive the skeletogenic program in sea urchin, showing important evolutionary differences in protein function. hesC, the second repressor of the DNG, is co-expressed with most of the genes that are repressed in sea urchin, indicating the absence of direct repression of tbr, ets1/2, and delta in A. filiformis. Furthermore, the absence of expression in later stages of brittle star skeleton development of key regulatory genes, such as foxb and dri, shows significantly different regulatory states. Conclusion: Our data fill up an important gap in the picture of larval mesoderm in echinoderms and allows us to explore the evolutionary implications relative to the recently established phylogeny of echinoderm classes. In light of recent studies on other echinoderms, our data highlight a high evolutionary plasticity of the same nodes throughout evolution of echinoderm skeletogenesis. Finally, gene duplication, protein function diversification, and cis-regulatory element evolution all contributed to shape the regulatory program for larval skeletogenesis in different branches of echinoderms.
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| 2. |
- Ramachandra, Rashmi, et al.
(author)
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A Potential Role for Chondroitin Sulfate/Dermatan Sulfate in Arm Regeneration in Amphiura filiformis.
- 2017
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In: Glycobiology. - : Oxford University Press (OUP). - 0959-6658 .- 1460-2423. ; 27:5, s. 438-449
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Journal article (peer-reviewed)abstract
- Glycosaminoglycans (GAGs), such as chondroitin sulfate (CS) and dermatan sulfate (DS) from various vertebrate and invertebrate sources are known to be involved in diverse cellular mechanisms during repair and regenerative processes. Recently, we have identified CS/DS as the major GAG in the brittlestar Amphiura filiformis, with high proportions of di- and tri-O-sulfated disaccharide units. As this echinoderm is known for its exceptional regeneration capacity, we aimed to explore the role of these GAG chains during A. filiformis arm regeneration. Analysis of CS/DS chains during the regeneration process revealed an increase in the proportion of the tri-O-sulfated disaccharides. Conversely, treatment of A. filiformis with sodium chlorate, a potent inhibitor of sulfation reactions in GAG biosynthesis, resulted in a significant reduction in arm growth rates with total inhibition at concentrations higher than 5 mM. Differentiation was less impacted by sodium chlorate exposure or even slightly increased at 1-2 mM. Based on the structural changes observed during arm regeneration we identified chondroitin synthase, chondroitin-4-O-sulfotransferase 2 and dermatan-4-O-sulfotransferase as candidate genes and sought to correlate their expression with the expression of the A. filiformis orthologue of bone morphogenetic factors, AfBMP2/4. Quantitative amplification by real-time PCR indicated increased expression of chondroitin synthase and chondroitin-4-O-sulfotransferase 2, with a corresponding increase in AfBMP2/4 during regeneration relative to nonregenerating controls. Our findings suggest that proper sulfation of GAGs is important for A. filiformis arm regeneration and that these molecules may participate in mechanisms controlling cell proliferation.
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| 3. |
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| 4. |
- Delroisse, J., et al.
(author)
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De novo transcriptome of the European brittle star Amphiura filiformis pluteus larvae
- 2015
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In: Marine Genomics. - : Elsevier. - 1874-7787. ; 23, s. 109-121
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Journal article (peer-reviewed)abstract
- Background: In non-classical model species, Next Generation Sequencing increases the ability to analyze the expression of transcripts/genes. In this study, paired-end Illumina HiSeq sequencing technology has been employed to describe a larval transcriptome generated from 64 h post-fertilization pluteus larvae of the brittle star Amphiura filiformis. We focused our analysis on the detection of actors involved in the opsin based light perception, respectively the opsins and the phototransduction actors. Methods & results: In this research, about 47 million high quality readswere generated and 86,572 total unigenes were predicted after de novo assembly. Of all the larval unigenes, 18% show significant matches with reference online databases. 46% of annotated larval unigenes were significantly similar to transcripts from the purple sea urchin. COG, GO and KEGG analyses were performed on predicted unigenes. Regarding the opsin-based photoreception process, even if possible actors of ciliary and rhabdomeric phototransduction cascadeswere detected, no ciliary or rhabdomeric opsinwas identified in these larvae. Additionally, partial non-visual RGR (retinal G protein coupled receptor) opsin mRNAs were identified,possibly indicating the presence of visual cycle reaction in early pluteus larvae. The eye morphogene Pax 6 was also identified in the pluteus transcriptome. Conclusions: Contrary to sea-urchin larvae, brittle star larvae appear to be characterized by an absence of visuallike opsins. These RNA-seq data also provide a useful resource for the echinoderm research community and researchers with an interest in larval biology. © 2015 Elsevier B.V.
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| 5. |
- Delroisse, Jérôme, et al.
(author)
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High opsin diversity in a non-visual infaunal brittlestar
- 2014
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In: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 15
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Journal article (peer-reviewed)abstract
- Background In metazoans, opsins are photosensitive proteins involved in both vision and non-visual photoreception. Echinoderms have no well-defined eyes but several opsin genes were found in the purple sea urchin (Strongylocentrotus purpuratus) genome. Molecular data are lacking for other echinoderm classes although many species are known to be light sensitive. Results In this study focused on the European brittle star Amphiura filiformis, we first highlighted a blue-green light sensitivity using a behavioural approach. We then identified 13 new putative opsin genes against eight bona fide opsin genes in the genome of S. purpuratus. Six opsins were included in the rhabdomeric opsin group (r-opsins). In addition, one putative ciliary opsin (c-opsin), showing high similarity with the c-opsin of S. purpuratus (Sp-opsin 1), one Go opsin similar to Sp-opsins 3.1 and 3.2, two basal-branch opsins similar to Sp-opsins 2 and 5, and two neuropsins similar to Sp-opsin 8, were identified. Finally, two sequences from one putative RGR opsin similar to Sp-opsin 7 were also detected. Adult arm transcriptome analysis pinpointed opsin mRNAs corresponding to one r-opsin, one neuropsin and the homologue of Sp-opsin 2. Opsin phylogeny was determined by maximum likelihood and Bayesian analyses. Using antibodies designed against c- and r-opsins from S. purpuratus, we detected putative photoreceptor cells mainly in spines and tube feet of A. filiformis, respectively. The r-opsin expression pattern is similar to the one reported in S. purpuratus with cells labelled at the tip and at the base of the tube feet. In addition, r-opsin positive cells were also identified in the radial nerve of the arm. C-opsins positive cells, expressed in pedicellariae, spines, tube feet and epidermis in S. purpuratus were observed at the level of the spine stroma in the brittle star. Conclusion Light perception in A. filiformis seems to be mediated by opsins (c- and r-) in, at least, spines, tube feet and in the radial nerve cord. Other non-visual opsin types could participate to the light perception process indicating a complex expression pattern of opsins in this infaunal brittle star.
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| 6. |
- Dupont, Samuel, 1971, et al.
(author)
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Impact of near-future ocean acidification on echinoderms.
- 2010
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In: Ecotoxicology. - : Springer Science and Business Media LLC. - 1573-3017 .- 0963-9292. ; 19:3, s. 449-462
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Research review (peer-reviewed)abstract
- As a consequence of increasing atmospheric CO(2), the world's oceans are warming and slowly becoming more acidic (ocean acidification, OA) and profound changes in marine ecosystems are certain. Calcification is one of the primary targets for studies of the impact of CO(2)-driven climate change in the oceans and one of the key marine groups most likely to be impacted by predicted climate change events are the echinoderms. Echinoderms are a vital component of the marine environment with representatives in virtually every ecosystem, where they are often keystone ecosystem engineers. This paper reviews and analyses what is known about the impact of near-future ocean acidification on echinoderms. A global analysis of the literature reveals that echinoderms are surprisingly robust to OA and that important differences in sensitivity to OA are observed between populations and species. However, this is modulated by parameters such as (1) exposure time with rare longer term experiments revealing negative impacts that are hidden in short or midterm ones; (2) bottlenecks in physiological processes and life-cycle such as stage-specific developmental phenomena that may drive the whole species responses; (3) ecological feedback transforming small scale sub lethal effects into important negative effects on fitness. We hypothesize that populations/species naturally exposed to variable environmental pH conditions may be pre-adapted to future OA highlighting the importance to understand and monitor environmental variations in order to be able to to predict sensitivity to future climate changes. More stress ecology research is needed at the frontier between ecotoxicology and ecology, going beyond standardized tests using model species in order to address multiple water quality factors (e.g. pH, temperature, toxicants) and organism health. However, available data allow us to conclude that near-future OA will have negative impact on echinoderm taxa with likely significant consequences at the ecosystem level.
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| 7. |
- Gräns, Albin, 1979, et al.
(author)
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Aerobic scope fails to explain the detrimental effects on growth resulting from warming and elevated CO2 in Atlantic halibut
- 2014
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In: Journal of Experimental Biology. - : The Company of Biologists. - 0022-0949 .- 1477-9145. ; 217:5, s. 711-717
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Journal article (peer-reviewed)abstract
- As a consequence of increasing atmospheric CO2, the world's oceans are becoming warmer and more acidic. Whilst the ecological effects of these changes are poorly understood, it has been suggested that fish performance including growth will be reduced mainly as a result of limitations in oxygen transport capacity. Contrary to the predictions given by the oxygen- and capacity-limited thermal tolerance hypothesis, we show that aerobic scope and cardiac performance of Atlantic halibut (Hippoglossus hippoglossus) increase following 14–16 weeks exposure to elevated temperatures and even more so in combination with CO2-acidified seawater. However, the increase does not translate into improved growth, demonstrating that oxygen uptake is not the limiting factor for growth performance at high temperatures. Instead, long-term exposure to CO2-acidified seawater reduces growth at temperatures that are frequently encountered by this species in nature, indicating that elevated atmospheric CO2 levels may have serious implications on fish populations in the future.
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| 8. |
- Hu, Marian Y., et al.
(author)
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Energy metabolism and regeneration impaired by seawater acidification in the infaunal brittlestar, Amphiura filiformis
- 2014
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In: Journal of Experimental Biology. - : The Company of Biologists. - 0022-0949 .- 1477-9145. ; 217:13, s. 2411-2421
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Journal article (peer-reviewed)abstract
- Seawater acidification due to anthropogenic release of CO2 as well as the potential leakage of pure CO2 from sub-seabed carbon capture storage sites (CCS) may impose a serious threat to marine organisms. Although infaunal organisms can be expected to be particularly impacted by decreases in seawater pH, due to naturally acidified conditions in benthic habitats, information regarding physiological and behavioral responses is still scarce. Determination of pO2 and pCO2 gradients within the burrows of the brittlestar Amphiura filiformis during environmental hypercapnia demonstrated that besides hypoxic conditions, increases of environmental pCO2 are additive to the already high pCO2 (up to 0.08 kPa) within the burrows. In response to up to 4 weeks exposure to pH 7.3 (0.3 kPa pCO2) and pH 7.0 (0.6 kPa pCO2), metabolic rates of A.filiformis were significantly reduced in pH 7.0 treatments accompanied by increased ammonium excretion rates. Gene expression analyses demonstrated significant reductions of acid-base (NBCe and AQP9) and metabolic (G6PDH, LDH) genes. Determination of extracellular acid-base status indicated an uncompensated acidosis in CO2 treated animals, which could explain depressed metabolic rates. Metabolic depression is associated with a retraction of filter feeding arms into sediment burrows. Regeneration of lost arm tissues following traumatic amputation is associated with significant increases in metabolic rate, and hypercapnic conditions (pH 7.0, 0.6 KPa) dramatically reduce the metabolic scope for regeneration reflected in 80% reductions in regeneration rate. Thus, the present work demonstrates that elevated seawater pCO2 significantly affects the environment and the physiology of infaunal organisms like A. filiformis.
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| 9. |
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Intrinsic gene expression during regeneration in arm explants of Amphiura filiformis
- 2012
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In: Journal of Experimental Marine Biology and Ecology. - : Elsevier BV. - 0022-0981. ; 413, s. 106-112
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Journal article (peer-reviewed)abstract
- The extensive regeneration ability of ophiuroids, particularly in relation to arm re-growth following amputation, is becoming increasingly recognized as a useful model system for understanding cellular differentiation and regeneration in a whole animal context. Amputated ophiuroid arms are referred to as explants. These are able to survive for several months in seawater and, when amputated at both ends (“double amputated”), can undergo partial regeneration at one end and wound healing at the other. As such, they present a simplified and controlled regenerating model system which can potentially provide clues as to the mechanism involved in the programming and polarity of cellular differentiation. In this first investigation of gene expression in an ophiuroid explant we used cDNA microarrays in the transcriptional profiling of the proximal, medial and distal sections of double amputated explants of the temperate brittle star Amphiura filiformis. The results demonstrated an active transcriptome with extensive differential gene expression focused at the original distal part of the arm explant where the regenerating blastema was located. The transcription profiles also revealed that expression patterns showed subtle differences in the levels of gene expression rather than the presence or absence of certain genes. The sections of arm under study were no longer attached to the whole animal and therefore reduced levels of activity of some transcripts e.g. ciboulot, a gene potentially involved in cell differentiation events such as neuronal development, suggest that transcript dosage and/or relative expression of certain gene combinations may play an important role in the progression of cellular differentiation events.
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