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221 results for “sea urchin”
Effects of paternal temperature on larval performance in purple sea urchin
The data is used to support the manuscript “Leach, T. S., Hofmann, G. E. (2023). Marine heatwave temperatures enhance larval performance but are meditated by paternal thermal history and inter-individual differences in the purple sea urchin, Strongylocentrotus purpuratus. Frontiers in Physiology. DOI: 10.3389/fphys.2023.1230590”
SBC LTER: Effect of algal diet on consumption, growth, and gonad weight of the purple sea urchin (Strongylocentrotus pupuratus)
Data are for an experiment evaluating the effects of algal diet on consumption, growth, and gonad weight of an important kelp forest grazer, the purple sea urchin, Strongylocentrotus pupuratus over a 13 week period (November 2010 - February 2011). Four co-occurring species of macroalgae known to be part of its diet were offered: two kelps Macrocystis pyrifera and Pterygophora californica, and the red algae Chondracanthus corymbiferus and Rhodymenia californica. During 9 consectutive trials in a controlled laboratory setting, we measured consumption, test (exoskeleton) growth, jaw growth, change in whole body wet weight and gonad weight of urchins fed one of five experimental diets. The algae chosen represent a large proportion (> 75%) of the algal biomass in Santa Barbara Channel reefs (California, USA). Changes in the availability of these four species of macroalgae could have large implications for the performance of purple sea urchins and consequently, for the structure of subtidal reef communities. These data are presented in a paper describing the effects of five southern California macroalgal diets on the consumption, growth and gonad weight of the purple sea urchin: Matthew C. Foster, M., Byrnes, J. E. K., D. C. Reed. 2015. Effects of five southern California macroalgal diets on consumption, growth and gonad weight in the purple sea urchin, Strongylocentrotus purpuratus. PeerJ. DOI: 10.7717/peerj.719
Segmentation of membrane of mouse, sea urchin and human oocytes from transmitted light images
<p>This dataset has been presented in our paper "An interpretable and versatile machine learning approach for oocyte phenotyping", in bioRxiv.</p> <p>It contains images acquired in transmitted light with different settings of mouse and human oocytes and sea urchin eggs, with the corresponding ground-truth of the membrane segmentation. Mouse oocyte images were taken before and during oocyte maturation (meiosis I). Some human oocyte images were taken during oocyte maturation (meiosis I), and some are M-II oocytes just after fertilization. Sea urchin images contains both fertilized and unfertilized eggs.</p> <p> </p>
Supplementary material for "Increased sensitivity of marine invertebrates to metal toxicity in the past two decades linked to Climate Change and Ocean Acidification: revelations from a natural population of sea urchins in the Mediterranean Sea." by "Davide Sartori, Guido Scatena, Cristina Vrinceanu, Andrea Gaion".
<p>Satellite observations of environmental factors and effect concentration 50 for copper to sea urchin, from 2003 to 2022.</p>
Analysis of the P. lividus sea urchin genome highlights contrasting trends of genomic and regulatory evolution in deuterostomes
<p><br> Supplementary datasets accompanying paper: </p> <p>stage_peaks_anc_sel.xlsx : ATAC peaks with classification, conservation and binding sites<br> Pliv.mfuzz.enrichGO.txt : GO enrichment in MFuzz cluster<br> Pliv_genes_master_filt.xlsx : Gene models with corresponding information<br> bindetect_results_anf.txt : results of TOBIAS<br> hits_pprx_cl0_ord3vrr+Et_red.fa : alignment of homeobox sequences<br> Pliv_aH2p.gn.gtf.gz : annotation in GTF format<br> Pliv_PqN3S_sm.fa.gz : genome of P. livius <br> ansr_*_network.tsv.gz : Stage specific networks from ANANSE analysis<br> ATAC_pks_normcov.tsv : Coverage of unified peaks for ATAC-seq<br> Cttg_pks_normcov.tsv : Coverage of unified peaks for Cut-and-tag H3K27Ac data<br> lncRNA_stgSpe_fpkm.tsv : Expression levels (FPKM) for predicted lncRNAs for available RNA-seq samples <br> Split_Urchin_FPKMs.clean.txt.gz : Expression levels for unified ATAc-seq peaks following direct and reverse orientation</p> <p> </p> <p> </p> <p> </p> <p> </p>
Data to support "delta13C and delta15N values from a mesocosm experiment showing sea urchins mediate the availability of kelp detritus to benthic consumers"
The purple sea urchin Strongylocentrotus purpuratus is an important herbivore and detritivore in southern California giant kelp (Macrocystis pyrifera) forests that grow on shallow rocky reefs (~3-20m depth) off southern California, including Santa Barbara where this study was done. To investigate the shredder activity of purple urchins, we assembled communities of common detritivores and suspension feeders from local reefs in mesocosms. Three species of brittle stars (Ophiopteris papillosa, Ophioplocus esmarki, and Ophiothrix spiculata), one vermetid gastropod (Thylacodes squamigerus), two barnacles (Chthamalus sp. and Megabalanus californicus), one polychaete worm (Chaetopterus sp.), and three sea cucumbers (Cucumaria piperata, Pachythyone rubra, and Cucumaria salma) were collected from the seafloor of local kelp forests at 5-15m depth in the Santa Barbara Channel. Ten of each species were placed in each of six 50 L (51x38x27 cm) flow-through unfiltered seawater tanks, each containing two concrete bricks for hard substrate on top of 3 cm of sand. Because sea urchins are highly mobile, capable of bulldozing other occupants, we isolated them above the experimental communities on plastic mesh (1cm). Mesh dividers were secured horizontally across each mesocosm 16 cm above the bottom. Ten individuals of each consumer species, along with 2-3 blades, totaling 47.3 g (±1.2 SE), of isotopically labeled kelp (see below) were placed on the floor of each tank, below the divider. On top of the mesh divider, we placed an additional 229.8 g (±6.1 SE) of enriched kelp blades, and in half of the tanks, 10 adult urchins (total mass 343.3 g ±1.3 SE) per tank. The kelp below the mesh ensured that the detritivores had direct access to degrading kelp detritus regardless of the urchin treatment, similar to the situation in the kelp forest, allowing us to more clearly ascertain the degree to which the detritivores were dependent on urchins for kelp detritus assimilation. The experiment wa
SBC LTER: Sea urchin foraging rates on giant kelp
These data describe the foraging rates of two sea urchin species (Strongylocentrotus purpuratus and Mesocentrotus franciscanus) on giant kelp (Macrocystis pyrifera) in laboratory mesocosms. Data are contained in two tables: 1) a data file describing the foraging rates of sea urchins as a function of urchin biomass where biomass was varied by manipulating the number of urchins in a foraging trial, and 2) a data file describing the foraging rates of sea urchins as a function of urchin biomass where biomass was varied by manipulating the size of urchins in a foraging trial.
Ocean acidification induces distinct transcriptomic responses across life history stages of the sea urchin Heliocidaris erythrogramma
Ocean acidification (OA) from seawater uptake of rising carbon dioxide emissions impairs development in marine invertebrates, particularly in calcifying species. Plasticity in gene expression is thought to mediate many of these physiological effects, but how these responses change across life history stages remains unclear. The abbreviated lecithotrophic development of the sea urchin <i>Heliocidaris erythrogramma</i> provides a valuable opportunity to analyze gene expression responses across a wide range of life history stages, including the benthic, post-metamorphic juvenile. We measured the transcriptional response to OA in <i>H. erythrogramma</i> at three stages of the life cycle (embryo, larva, and juvenile) in a controlled breeding design. The results reveal a broad range of strikingly stage-specific impacts of OA on transcription, including changes in the number and identity of affected genes; the magnitude, sign, and variance of their expression response; and the developmental trajectory of expression. The impact of OA on transcription was notably modest in relation to gene expression changes during unperturbed development and dwarfed by genetic contributions from parentage. The latter result suggests that natural populations may provide an extensive genetic reservoir of resilience to OA. Taken together, these results highlight the complexity of the molecular response to OA, its substantial life history stage specificity, and the importance of contextualizing the transcriptional response to pH stress in light of normal development and standing genetic variation to better understand the capacity for marine invertebrates to adapt to OA.
Supplementary data for calcium-vesicles perform active diffusion in the sea urchin embryo during larval biomineralization
<p><strong>Supplementary datasets for the paper Calcium-vesicles perform active diffusion in the sea urchin embryo during larval biomineralization.</strong></p> <p>Two deskewed and deconvolved lattice light-sheet datasets (100 frames each) from the live-cell experiments are available, a control embryo dataset (01-07-2016_TimeLapse4_DMSO_21hrs_Calcein_FM464) and a VEGFR inhibited dataset (24-06-2016_Timelapse1_Axtinib_150_19hrs_Calcein_FM464). These datasets were used for collecting size and motion statistics. The control embryo dataset is available in raw microscope output without deskew or deconvolution applied (Raw_01-07-2016_TimeLapse4_DMSO_21hrs_Calcein_FM464).</p> <p>Four confocal datasets from the cytoskeletal remodeling experiments are also included, phalloidin stained images, control (Phalloidin PMC DMSO 5 zoom4s) and VEGFR inhibited (Phalloidin PMC Axt 18 zoom4); and myosinIIP stained images, control (Myosin PMC 30h DMSO new slid 4a zoom4) and VEGFR inhibited (Phalloidin PMC Axt 18 zoom4).</p> <p>Source code and instructions for the analysis tools used for both the lattice light-sheet and confocal data is available at: <a href="https://git-bioimage.coe.drexel.edu/opensource/llsm-calcium-vesicles-lever">https://git-bioimage.coe.drexel.edu/opensource/llsm-calcium-vesicles-lever</a></p> <p>Code for the deconvolution and deskew algorithms is available from the Janelia research center at: <a href="https://www.janelia.org/open-science/lattice-light-deconvolution-software-cudadeconv">https://www.janelia.org/open-science/lattice-light-deconvolution-software-cudadeconv</a></p> <p> </p> <p> </p>
Micro-CT data from the skeleton of the sea urchin Cidaris rugosa at four different resolutions
<p>The sponge-like biomineralised calcite materials found in echinoderm skeletons are of interest in terms of both structure formation and biological function. Despite their crystalline atomic structure, they exhibit curved interfaces that have been related to known triply-periodic minimal surfaces. Here, we investigate the endoskeleton of the sea urchin <em>Cidaris rugosa</em> that has long been known to form a microstructure related to the Primitive surface. Using X-ray tomography, we find that the endoskeleton is organised as a composite material consisting of domains of bicontinuous microstructures with different structural properties. We describe, for the first time, the co-occurrence of ordered Primitive and Diamond structures and of a disordered structure within a single skeletal plate. We show that these structures can be distinguished by structural properties including solid volume fraction, trabeculae width, and to a lesser extent, interface area and mean curvature. In doing so, we present a robust method that extracts interface areas and curvature integrals from voxelized datasets using the Steiner polynomial for parallel body volumes. We discuss these very large scale bicontinuous structures in the context of their function, formation, and evolution.</p>
Data from: Artificial light at night and warming impact grazing rates and gonad index of the sea urchin Centrostephanus rodgersii
<p>Artificial light at night (ALAN) is a growing threat to coastal habitats, and is likely to exacerbate the impacts of other stressors. Kelp forests are dominant habitats on temperate reefs but are declining due to ocean warming and overgrazing. We tested the independent and interactive effects of ALAN (dark vs ALAN) and warming (ambient vs warm) on grazing rates and gonad index of the sea urchin <em>Centrostephanus rodgersii. </em>Within these treatments, urchins were fed either 'fresh' kelp or 'treated' kelp. Treated kelp (<em>Ecklonia radiata</em>) was exposed to the same light and temperature combinations as urchins. We assessed photosynthetic yield, carbon and nitrogen content and C:N ratio of treated kelp to help identify potential drivers behind any effects on urchins. Grazing increased with warming and ALAN for urchins fed fresh kelp, and increased with warming for urchins fed treated kelp. Gonad index was higher in ALAN/ambient and dark/warm treatments compared to dark/ambient treatments for urchins fed fresh kelp. Kelp carbon content was higher in ALAN/ambient treatments than ALAN/warm treatments at one time point. This indicates ocean warming and ALAN may increase urchin grazing pressure on rocky reefs, an important finding for management strategies.</p>
Selection shapes the genomic landscape of introgressed ancestry in a pair of sympatric sea urchin species
<p>A growing number of recent studies have demonstrated that introgression is common across the tree of life. However, we still have a limited understanding of the fate and fitness consequence of introgressed variation at the whole-genome scale across diverse taxonomic groups. Here, we implemented a phylogenetic hidden Markov model to identify and characterize introgressed genomic regions in a pair of well-diverged, non-sister sea urchin species: <em>Strongylocentrotus</em> <em>pallidus</em> and <em>S. droebachiensis</em>. Despite the old age of introgression, a sizable fraction of the genome (1% - 5%) exhibited introgressed ancestry, including numerous genes showing signals of historical positive selection that may represent cases of adaptive introgression. One striking result was the overrepresentation of hyalin genes in the identified introgressed regions despite observing considerable overall evidence of selection against introgression. There was a negative correlation between introgression and chromosome gene density, and two chromosomes were observed with considerably reduced introgression. Relative to the non-introgressed genome-wide background, introgressed regions had significantly reduced nucleotide divergence (<em>d</em><sub>XY</sub>) and overlapped fewer protein-coding genes, coding bases, and genes with a history of positive selection. Additionally, genes residing within introgressed regions showed slower rates of evolution (<em>d</em><sub>N</sub>, <em>d</em><sub>S</sub>, <em>d</em><sub>N</sub>/<em>d</em><sub>S</sub>) than random samples of genes without introgressed ancestry. Overall, our findings are consistent with widespread selection against introgressed ancestry across the genome and suggest that slowly evolving, low-divergence genomic regions are more likely to move between species and avoid negative selection following hybridization and introgression.</p>
Sea urchin transport data
<p>These data sets are from a series of transport trials conducted on the sea urchin <em>Strongylocentrotus droebachiensis</em></p>
Figure 1 in Egg Morphology of Five Species of Sea Urchins from Saipan, CNMI
Figure 1. The scanning electron microscope images showing general morphology of eggs along with a close-up image of egg outer membrane surface for each species. (a): Echinometra mathaei (scale bar=30.0 µm), (b): close up view of Echinometra mathaei (scale bar=4.0 µm), (c): Parasalenia poehlii (scale bar=40.0 µm), (d): close up view of Parasalenia poehlii (scale bar=5.0 µm), (e): Eucidaris metularia (scale bar=20.0 µm), (f): close up view of Eucidaris metularia (scale bar=5.0 µm), (g): Colobocentrotus mertensii (scale bar=30.0 µm), (h): close up view of Colobocentrotus mertensii (scale bar=5.0 µm), (i): Mespilia globulus (scale bar=50.0 µm), (j): close up view of Mespilia globulus (scale bar=5.0 µm).
Fig. 3 in Phylogeography of Long-spined Sea Urchin Across the Indo-Malay Archipelago.
Fig. 3. Diadema setosum. Minimum-spanning network of COI gene haplotypes. Area of circle proportional to haplotype frequency in total sample; length of branch proportional to number of mutations (scale bar: one mutational step) except alternative links between haplotypes, where number of mutational steps is represented by a series of perpendicular dashes. A few such links between distant haplotypes were omitted for better readability. White: haplotype sampled from Group-1 D. setosum; hachured white: Group-2; black: Sub-group-3a; grey: Sub-group-3b.
Fig. 2 in Phylogeography of Long-spined Sea Urchin Across the Indo-Malay Archipelago.
Fig. 2. Phylogeographic structure of Diadema setosum in the Indo-Malay archipelago. A: Multidimensional scaling plot based on the matrix of pairwise ФST (T92+G model; Arlequin). Ellipses delineate groups of samples designated by hierarchical clustering. Abbreviations for samples as in table 1. B: Pairwise estimates of genetic differentiation plotted against the logarithm of geographic distance [ln(gD), gD in km]. Black circles (●) intra-group comparisons; open circles (○) (resp. triangles): inter-group comparisons involving Group 1 (resp. Group 2).
Fig. 1 in Phylogeography of Long-spined Sea Urchin Across the Indo-Malay Archipelago.
Fig. 1. Diadema setosum sampling locations. Colours refer to the results of MDS analysis (see RESULTS). Bold dotted lines indicate inferred geographic barriers. SoM Strait of Malacca; Mak. Str. Makassar Strait; other abbreviations as in table 1. Table 1. Diadema setosum sampling details and GenBank accession numbers by sample. N sample size
Fig. 4. Syndesmis aonikenki n in Two new species of Syndesmis (Platyhelminthes, Rhabdocoela, Umagillidae) from the sea urchin Pseudechinus magellanicus (Echinodermata, Echinoidea) in the Southwestern Atlantic Ocean
Fig. 4. Syndesmis aonikenki n. sp. A, B, whole mount preparations. C, sagittal section of the body. Abbreviations: ed, ejaculatory duct; eg, egg; f, filament; fg, filament glands; i, intestine; ma, male atrium; ov, ovary; sr, seminal receptacle; st, stylet; u, uterus; va, vagina; vit, vitellaria.
Fig. 3 in Two new species of Syndesmis (Platyhelminthes, Rhabdocoela, Umagillidae) from the sea urchin Pseudechinus magellanicus (Echinodermata, Echinoidea) in the Southwestern Atlantic Ocean
Fig. 3. Schematic reconstruction of Syndesmis aonikenki n. sp. in dorso-ventral view. Abbreviations: eg, egg; f, filament; fg, filament glands; ov, ovary; st, stylet; t, testes; vit, vitellaria.
Fig. 1 in Two new species of Syndesmis (Platyhelminthes, Rhabdocoela, Umagillidae) from the sea urchin Pseudechinus magellanicus (Echinodermata, Echinoidea) in the Southwestern Atlantic Ocean
Fig. 1. Schematic reconstruction of Syndesmis selknami n. sp. in dorso-ventral view. Abbreviations: eg, egg; f, filament; fg, filament glands; ov, ovary; st, stylet; t, testes; vit, vitellaria.
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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.