Ethanol-treated Lytechinus variegatus (sea urchin) embryos
Ontology highlight
ABSTRACT:
ORGANISM(S): Lytechinus variegatus
PROVIDER: GSE207100 | GEO | 2022/06/28
REPOSITORIES: GEO
Similar Datasets
Project description:Ethanol-treated Lytechinus variegatus (sea urchin) embryos
| PRJNA853740 | ENA
Project description:Using scRNA-seq coupled with computational approaches, we studied transcriptional changes in cell states of sea urchin embryos during development to the larval stage. Eighteen closely spaced time points were taken during the first 24 hours of development of Lytechinus variegatus (Lv). Developmental trajectories were constructed using Waddington-OT, a computational approach to "stitch" together developmental timepoints. Skeletogenic and primordial germ cell trajectories diverged early in cleavage. Ectodermal progenitors were distinct from other lineages by sixth cleavage, though a small percentage of ectoderm cells briefly co-expressed endoderm markers indicating an early ecto-endoderm cell state, likely in cells originating from the equatorial region of the egg. Endomesoderm cells originated at 6th cleavage also and this state persisted for more than two cleavages, then diverged into distinct endoderm and mesoderm fates asynchronously, with some cells retaining an intermediate specification status until gastrulation. 79 of 80 genes (99%) examined, and included in published developmental gene regulatory networks (dGRNs), are present in the Lv-scRNA-seq dataset, and expressed in the correct lineages in which the dGRN circuits operate.
2021-09-24 | GSE184538 | GEO
Project description:The sea urchin embryo development toxicity test was used to investigate toxicity of the benthic substrate in Biscayne National Park (BISC). Twenty-five sites were selected based upon a high potential for anthropogenic stressor input (e. g., hydrocarbons, personal care products, nutrients, etc.) or proximity to coral reef habitats. We found that sediment interstitial water (porewater) was toxic to urchin embryos at 22 of 25 sites. Healthy sites included two coral reefs (Anniversary Reef and Marker 14 Reef) and Turkey Point Channel. Discrete areas of BISC have highly toxic sediments and the presence of sediment contaminants could negatively impact reproduction, growth and population density of benthic invertebrates, such as corals. Results of the sea urchin embryo development toxicity test can be used as a baseline assessment for monitoring improvements or degradation in ecosystem health and could be a valuable tool to investigate the suitability of degraded habitats for future reef restoration. Since the last comprehensive environmental assessment of BISC was performed in 1999, further investigation into the sources of toxicity at BISC is needed.
| S-EPMC9725154 | biostudies-literature
Project description:Sea urchins (echinoids) are common model organisms for research in developmental biology and for their transition from a bilateral larva into their post-metamorphic adult with pentaradial body symmetry. The adult also has a calcareous endoskeleton with a multimetameric pattern of continuously added elements, among them the namesake of this phylum, spines. Nearly all echinoids have both large primary spines, and an associated set of smaller secondary spines.We hypothesize that the secondary spines of the tropical variegated urchin species, Lytechinus variegatus, are morphologically and molecularly distinct structures from primary spines and not just small spines. To test this premise, we examined both spine types using light microscopy, micro-CT imaging, lectin labeling, transcriptomics, and fluorescent in situ hybridization (FISH). Our findings reveal basic similarities between the two types in mineral and cellular anatomy, but with clear differences in growth patterns, genes expressed, and in the location of gene expression within the two types of spines. In particular, secondary spines have non-overlapping, longitudinally concentrated growth bands that lead to a blunt and straight profile, and a distinct transcriptome involving the upregulation in many genes in comparison to the primary spines. Neural, ciliary, and extracellular matrix interacting factors are implicated in the differentially expressed gene (DEG) dataset, including two genes - ONECUT2 and an uncharacterized discoidin- and thrombospondin-containing protein - that show spine type- specific localizations in FISH, and may be of interest to ongoing work in urchin spine patterning.These results demonstrate that primary and secondary spines have overlapping but distinct molecular and biomineralized characteristics, suggesting unique developmental and regenerative mechanisms, and devotion to this spiny dermal phylum.
2024-05-15 | GSE267428 | GEO
Project description:Sea urchins have been a well-used model of fertilization and of the molecular biology of embryonic development. Our understanding of the molecular identity of adult tissues, on the other hand, has lagged significantly, a deficiency all too apparent with recent successes in mutational analyses in transgenerational studies. Here we focus on the developmental timing of gonadogenesis with particular reference to developmental features of when a juvenile reaches adulthood and begins to make eggs and sperm. We find a large variation in timing of reaching fertility in Lytechinus variegatus such that in 4.5 months, animals that have reached a mass/body ratio and making eggs or sperm. This is correlated with the external metric of opening of the gonadopore, indicative of gametogenesis. We identify a sac-like structure in juveniles that by both morphological and transcriptomic analysis appears to be an indeterminant gonad that transitions into an ovary or testis. We follow this development into adulthood and compare the transcriptomes of gonads and gametes to all 16 major tissues of the adult, revealing a broad definition of the tissue types, and displaying genes that are differentially enriched, and/or specifically expressed by each tissue. These datasets serve as a guide for gene selection in traditional CRISPR/Cas9 mutagenesis, for design of integrated transposase reporters, and for parsing out unique functions in tissues that in combination give this animal its unique attributes.
2025-09-01 | GSE300567 | GEO
Project description:Using scRNA-seq coupled with computational approaches, we studied transcriptional changes in cell states of sea urchin embryos during development to the larval stage. Eighteen closely spaced time points were taken during the first 24 h of development of Lytechinus variegatus (Lv). Developmental trajectories were constructed using Waddington-OT, a computational approach to 'stitch' together developmental time points. Skeletogenic and primordial germ cell trajectories diverged early in cleavage. Ectodermal progenitors were distinct from other lineages by the 6th cleavage, although a small percentage of ectoderm cells briefly co-expressed endoderm markers that indicated an early ecto-endoderm cell state, likely in cells originating from the equatorial region of the egg. Endomesoderm cells also originated at the 6th cleavage and this state persisted for more than two cleavages, then diverged into distinct endoderm and mesoderm fates asynchronously, with some cells retaining an intermediate specification status until gastrulation. Seventy-nine out of 80 genes (99%) examined, and included in published developmental gene regulatory networks (dGRNs), are present in the Lv-scRNA-seq dataset and are expressed in the correct lineages in which the dGRN circuits operate.
| S-EPMC8502253 | biostudies-literature
Project description:Animals of the phylum Echinodermata are characterized by a pentaradially symmetric endoskeleton in adults. Echinoids also have endoskeletal spines ranging in length from several millimeters (sand dollars e.g. Mellita quinquiesperforata of the order Clypeasteroida) to 30 cm (the black sea urchin, Diadema antillarum of the order Euechinoidea). Here we integrate an analysis of genetic, structural and molecular properties of spines from the variegated sea urchin, Lytechinus variegatus. Through genetic crosses we learned that white is dominant over red and green colors, and that pigmentation follows classic Mendelian genetics. The abundance of mRNAs encoding flavin mono-oxygenase variancts and polyketide synthase was predictive of the color of the adult and antibodies identified their histological location in the spine cells. By RNA in situ hybridization, candidate genes important for spine biomineralization and pigmentation were mapped onto the spine epithelia, and MicroCT scans of spines from different color morphs concluded that color morphs are entirely due to pigmentation and not to structural variations of the endoskeleton. By confocal microscopy we localized gene expression along and within the spines and learned that genes involved in pigment biosynthesis showed selective distribution along the spine. Spine epidermis is mitotically active and red spherule immunocytes are highly migratory within the spine. Overall the results provide a key foundation for examining the mechanisms of molecular diversity and patterning in the name sake of the phylum Echinodermata.
| S-EPMC11574130 | biostudies-literature
Project description:Sea urchins are emblematic marine animals with a rich fossil record and represent instrumental models for developmental biology. As echinoderms, sea urchins display several characteristics that set them apart from other deuterostomes such as their highly regulative embryonic development and their unique pentaradial adult body plan. To determine whether these characteristics are linked to particular genomic rearrangement or gene regulatory rewiring, we introduce a chromosome-scale genome assembly for sea urchin Paracentrotus lividus as well as extensive transcriptomic and epigenetic profiling during its embryonic development. We found that sea urchins show opposite modalities of genome evolution as compared to those of vertebrates: they retained ancestral chromosomal linkages that otherwise underwent mixing in vertebrates, while their intrachromosomal gene order has evolved much faster between sea urchin species that split 60 Myr ago than it did in vertebrates. We further assessed the conservation of the cis-regulatory program between sea urchins and chordates and identified conserved modules despite the developmental and body plan differences. We documented regulatory events underlying processes like zygotic genome activation and transition to larval stage in sea urchins. We also identified a burst of gene duplication in the echinoid lineage and showed that some of these expanded genes are involved in organismal novelties, such as Aristotle's lantern, tube feet, or in the specification of lineages through for instance the pmar1 and pop genes. Altogether, our results suggest that gene regulatory networks controlling development can be conserved despite extensive gene order rearrangement.
2023-02-09 | GSE202034 | GEO
Project description:Sea urchins lack proper eye organs but are photosensitive. In this study, we investigate an extraocular photoreceptor cell (PRC) system in developmental stages of the sea urchin Paracentrotus lividus.
2022-09-20 | GSE211842 | GEO
Project description:BackgroundGastrulation is a complex orchestration of movements by cells that are specified early in development. Until now, classical convergent extension was considered to be the main contributor to sea urchin archenteron extension, and the relative contributions of cell divisions were unknown. Active migration of cells along the axis of extension was also not considered as a major factor in invagination.ResultsCell transplantations plus live imaging were used to examine endoderm cell morphogenesis during gastrulation at high-resolution in the optically clear sea urchin embryo. The invagination sequence was imaged throughout gastrulation. One of the eight macromeres was replaced by a fluorescently labeled macromere at the 32 cell stage. At gastrulation those patches of fluorescent endoderm cell progeny initially about 4 cells wide, released a column of cells about 2 cells wide early in gastrulation and then often this column narrowed to one cell wide by the end of archenteron lengthening. The primary movement of the column of cells was in the direction of elongation of the archenteron with the narrowing (convergence) occurring as one of the two cells moved ahead of its neighbor. As the column narrowed, the labeled endoderm cells generally remained as a contiguous population of cells, rarely separated by intrusion of a lateral unlabeled cell. This longitudinal cell migration mechanism was assessed quantitatively and accounted for almost 90% of the elongation process. Much of the extension was the contribution of Veg2 endoderm with a minor contribution late in gastrulation by Veg1 endoderm cells. We also analyzed the contribution of cell divisions to elongation. Endoderm cells in Lytechinus variagatus were determined to go through approximately one cell doubling during gastrulation. That doubling occurs without a net increase in cell mass, but the question remained as to whether oriented divisions might contribute to archenteron elongation. We learned that indeed there was a biased orientation of cell divisions along the plane of archenteron elongation, but when the impact of that bias was analyzed quantitatively, it contributed a maximum 15% to the total elongation of the gut.ConclusionsThe major driver of archenteron elongation in the sea urchin, Lytechinus variagatus, is directed movement of Veg2 endoderm cells as a narrowing column along the plane of elongation. The narrowing occurs as cells in the column converge as they migrate, so that the combination of migration and the angular convergence provide the major component of the lengthening. A minor contributor to elongation is oriented cell divisions that contribute to the lengthening but no more than about 15%.
| S-EPMC5705275 | biostudies-literature