Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
221
datasets available to search
ShareScore release 0.9.0
Dataset results
221 results for “Sea Urchin”
Data for Sea urchin mass mortalities 40 years apart further threaten Caribbean coral reefs
Open the record for dataset details and reuse information.
Data from: The evolution of gametic compatibility and compatibility groups in the sea urchin Mesocentrotus franciscanus: an avenue for speciation in the sea
Open the record for dataset details and reuse information.
Population genomic analyses of the sea urchin Echinometra sp. EZ across an extreme environmental gradient
Open the record for dataset details and reuse information.
Divergence between sea urchins and their microbiota following speciation
Open the record for dataset details and reuse information.
Data from: Ocean acidification impacts spine integrity but not regenerative capacity of spines and tube feet in adult sea urchins
Open the record for dataset details and reuse information.
Data from: Calcification in sea urchin larvae is associated with low metabolic costs
Open the record for dataset details and reuse information.
Data from: Transcriptomics reveal transgenerational effects in purple sea urchin embryos: adult acclimation to upwelling conditions alters the response of their progeny to differential pCO2 levels
Open the record for dataset details and reuse information.
A chromosome-level genome assembly of the highly heterozygous sea urchin Echinometra sp. EZ reveals adaptation in the regulatory regions of stress response genes
Open the record for dataset details and reuse information.
Recent reconfiguration of an ancient developmental gene regulatory network in Heliocidaris Sea Urchins
Open the record for dataset details and reuse information.
Data from: Bioerosion by pit-forming, temperate-reef sea urchins: history, rates and broader implications
Open the record for dataset details and reuse information.
Data from: Geographic location and food availability offer differing levels of influence on the bacterial communities associated with larval sea urchins
Open the record for dataset details and reuse information.
Behavioral responses across a mosaic of ecosystem states restructure a sea otter-urchin trophic cascade
Open the record for dataset details and reuse information.
Extensive introgression among strongylocentrotid sea urchins revealed by phylogenomics
Open the record for dataset details and reuse information.
Data for: Tube feet regeneration and plasticity in the purple sea urchin (Strongylocentrotus purpuratus)
<p class="MsoBodyText">Sea urchins are key members of hydrodynamically intense habitats, such as open coast intertidal and shallow reefs. Secure attachment to the substrata, by means of tube feet and spines, is essential for survival. Previous studies suggest that environmental variables (i.e. hydrodynamics, substrate) can influence the morphology and adhesive performance of tube feet. Catastrophic failure of tube feet occurs often due to strong hydrodynamic forces. The time and ability of amputated tube feet to return to pre-amputation adhesive performance, and the interaction with environmental factors are unknown. To assess the dynamics of adhesive performance and re- generation of tube feet, we 1) evaluated phenotypic plasticity of disc surface area of two urchin populations inhabiting sites with different lithologies (field - in-situ conditions) and, 2) assessed regeneration of their functionality (tube foot length, time of disc first appearance, disc surface area, and tenacity) after amputation (laboratory - ex-situ conditions). Results showed that in the field, tube feet are plastic in their phenotype: sea urchins from the two sites differed in their disc surface area. Plasticity was also observed in the laboratory, where urchins regenerate tube feet that are shorter in length and have smaller discs compared to pre-amputation measurements. Thus, sea urchin tube feet recovering from amputation events in the intertidal may differ in their initial morphology and in the recovery period after amputation. Moreover, tube feet that were never amputated also decreased their disc area, suggesting that plasticity occurs on tube feet of urchins maintained in laboratory conditions. In shallow temperate reef systems, urchins are ecosystem engineers that affect the abundance and distribution of many other organisms. The plastic nature of morphological and adhesive abilities of sea urchin tube feet influences their ability to survive and dominate wave-battered habitats.</p>
Data from: Ocean warming and acidification alter the behavioural response to flow of the sea urchin Paracentrotus lividus
Ocean warming (OW) and acidification (OA) are intensively investigated as they pose major threats to marine organism. However, little effort is dedicated to another collateral climate change stressor, the increased frequency and intensity of storm events, here referred to as intensified hydrodynamics. A 2-month experiment was performed to identify how OW and OA (temperature: 21°C; pHT: 7.7, 7.4; control: 17°C-pHT7.9) affect the resistance to hydrodynamics in the sea urchin Paracentrotus lividus using an integrative approach that includes physiology, biomechanics and behaviour. Biomechanics was studied under both no-flow condition at the tube foot (TF) scale and flow condition at the individual scale. For the former, TF disk adhesive properties (attachment strength, tenacity) and TF stem mechanical properties (breaking force, extensibility, tensile strength, stiffness, toughness) were evaluated. For the latter, resistance to flow was addressed as the flow velocity at which individuals detached. Under near- and far-future OW and OA, individuals fully balanced their acid-base status, but skeletal growth was halved. TF adhesive properties were not affected by treatments. Compared to the control, mechanical properties were in general improved under pHT7.7 while in the extreme treatment (21°C-pHT7.4) breaking force was diminished. Three behavioural strategies were implemented by sea urchins and acted together to cope with flow: improving TF attachment, streamlining and escaping. Behavioural responses varied according to treatment and flow velocity. For instance, individuals at 21°C-pHT7.4 increased the density of attached TF at slow flows or, controlled TF detachment at fast flow to compensate for weakened TF mechanical properties. They also showed an absence of streamlining favouring an escaping behaviour as they ventured in a riskier faster movement at slow flows. At faster flows, the effects of OW and OA were detrimental causing earlier dislodgment. These plastic behaviours reflect a potential scope for acclimation in the field, where this species already experiences diel temperature and pH fluctuations.
Cellular bicarbonate accumulation and vesicular proton transport promote calcification in the sea urchin larva
The sea urchin embryo develops a calcitic endoskeleton through intracellular formation of amorphous calcium carbonate (ACC). Intracellular precipitation of ACC, requires HCO3-/CO32- concentrating as well as proton export mechanisms to promote calcification. These processes are of fundamental importance in biological mineralization, but remain largely unexplored. Here we demonstrate that the calcifying primary mesenchyme cells (PMCs) utilize Na+/H+- exchange (NHE) mechanisms to control cellular pH homeostasis during maintenance of the skeleton. During skeleton re-calcification, pHi of PMCs is increased accompanied by substantial elevations in intracellular [HCO3-] mediated by the Na+/HCO3-cotransporter Sp-Slc4a10. However, PMCs lower their pHi regulatory capacities associated with a reduction in NHE activity. Live-cell imaging using GFP reporter constructs in combination with intra-vesicular pH measurements demonstrated alkaline and acidic populations of vesicles in PMCs and extensive trafficking of large V-type H+-ATPase (VHA)-rich acidic vesicles in blastocoelar filopodial cells (BFCs). Pharmacological and gene expression analyses underline a central role of the VHA isoforms Sp-ATP6V0a1, Sp-ATP6V01_1 and Sp-ATPa1-4 for the process of skeleton re-calcification. These results highlight novel pH regulatory strategies in calcifying cells of a marine species with important implications for our understanding of the mineralization process in times of rapid changes in oceanic pH.
Data from: Characterization of the transcriptome and gene expression of four different tissues in the ecologically relevant sea urchin Arbacia lixula using RNA-seq
The sea urchin Arbacia lixula is a keystone species in Mediterranean ecosystems that drive landscape changes in littoral communities. However, genomic information available for the whole order Arbacioida is very limited. Using RNA-seq techniques, we have characterized the transcriptome of four different tissue types in A. lixula: the 'somatic' tissues (coelomocytes and digestive tissue) and the 'reproductive' tissues (ovary and testis), from two replicated cDNA libraries for each sample. Additionally, we performed a de novo assembly to build the 'reference' transcriptome, pooling reads of the four tissues, to analyse the differential expression (DE) in pairwise comparisons between tissues. The complete de novo assembly yielded 186 084 transcripts, with a sequence size limit of 100 nt, being 31% of them spliced isoforms. Approximately 21% of the transcripts had blast hits against proteins of metazoans (E < 10−5), being less than 2.2% functionally annotated. Between coelomocytes and digestive, 30 794 transcripts showed DE (~11.8% of them with blast hit), and 19 567 transcripts did so between testis and ovary (~28.5% of them with blast hit). Major GO-term categories upregulated in somatic tissues were those related to muscle contraction and energy generation in digestive, and lipid metabolism associated with immune response in coelomocytes. Between reproductive tissues, the major upregulated GO categories were related to energy generation in testis, and negative regulation of nucleotide metabolism in ovary. We particularly screened for a collection of target genes in each tissue because of their relevance for further studies on evolution and adaptation of echinoids.
Data from: Impacts of ocean acidification on sea urchin growth across the juvenile to mature adult life-stage transition is mitigated by warming
Understanding how growth trajectories of calcifying invertebrates are affected by changing climate requires acclimation experiments that follow development across life history transitions. In a long-term acclimation study, the effects of increased acidification and temperature on survival and growth of the tropical sea urchin Tripneustes gratilla from the early juvenile (5 mm test diameter- TD) through the developmental transition to the mature adult (60 mm TD) were investigated. Juveniles were reared in a combination of three temperature and three pH/pCO2 treatments, including treatments commensurate with global change projections. Elevated temperature and pCO2/pH both affected growth, but there was no interaction between these factors. The urchins grew more slowly at pH 7.6, but not at pH 7.8. Slow growth may be influenced by the inability to compensate coelomic fluid acid-base balance at pH 7.6. Growth was faster at +3 and +6 °C compared to that in ambient temperature. Acidification and warming had strong and interactive effects on reproductive potential. Warming increased the gonad index, but acidification decreased it. At pH 7.6 there were virtually no gonads in any urchins regardless of temperature. The T. gratilla were larger at maturity under combined near-future warming and acidification scenarios (+3 °C/pH 7.8). Although the juveniles grew and survived in near-future warming and acidification conditions, chronic exposure to these stressors from an early stage altered allocation to somatic and gonad growth. In the absence of phenotypic adjustment, the interactive effects of warming and acidification on the benthic life phases of sea urchins may compromise reproductive fitness and population maintenance as global climatic change unfolds.
Data from: Contemporary evolution of sea urchin gamete-recognition proteins: experimental evidence of density-dependent gamete performance predicts shifts in allele frequencies over time
Species whose reproductive strategies evolved at one density regime might be poorly adapted to other regimes. Field and laboratory experiments on the sea urchin Strongylocentrotus franciscanus examined the influences of the two most common sperm bindin alleles, which differ at two amino acid sites, on fertilization success. In the field experiment, the Arginine/Glycine (RG) genotype performed best at low densities and the Glycine/Arginine (GR) genotype at high densities. In the lab experiment, the RG genotype had a higher affinity with available eggs, whereas the GR genotype was less likely to induce polyspermy. These sea urchins can reach 200 years of age. The RG allele dominates in old sea urchins, whereas younger sea urchins have near equal RG and GR allele frequencies. A latitudinal cline in RG and GR genotypes is consistent with longer survival of sea urchins in the north and with predominance of RG genotypes in older individuals. The oldest sea urchins were likely conceived at low densities, before sea-urchin predators, like sea otters, were overharvested and sea urchin densities exploded off the west coast. Contemporary evolution of gamete-recognition proteins might allow species to adapt to shifts in abundances and reduces the risk of reproductive failure in altered populations.
Data from: Genetics of gene expression responses to temperature stress in a sea urchin gene network
Stress responses play an important role in shaping species distributions and robustness to climate change. We investigated how stress responses alter the contribution of additive genetic variation to gene expression during development of the purple sea urchin, Strongylocentrotus purpuratus, under increased temperatures that model realistic climate change scenarios. We first measured gene expression responses in the embryos by RNA-seq to characterize molecular signatures of mild, chronic temperature stress. We found that an increase from 12 °C to 18 °C caused widespread alterations in gene expression including in genes involved in protein folding, RNA processing, and development. To understand the quantitative genetic architecture of this response, we then focused on a well-characterized gene network involved in endomesoderm and ectoderm specification. Using a breeding design with wild-caught individuals, we measured genetic and gene-environment interaction effects on 72 genes within this network. We found genetic or maternal effects in 33 of these genes, and that the genetic effects were correlated in the network. 14 network genes also responded to higher temperatures, but we found no significant genotype-environment interactions in any of the genes. This absence may be due to an effective buffering of the temperature perturbations within the network. In support of this hypothesis, perturbations to regulatory genes did not affect the expression of the genes that they regulate. Together, these results provide novel insights into the relationship between environmental change and developmental evolution and suggest that climate change may not expose large amounts of cryptic genetic variation to selection in this species.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.