Biology subjects

Gibson, M. C.

Publications and source records attributed to Gibson, M. C..

14 recordsLinked to original sources

bioRxiv2026

Comparative 3D analysis reveals species-specific patterns of coral polyp morphology and gastrovascular integration

Coral reefs are constructed by colonial cnidarians whose survival depends on the coordinated growth and physiological integration of thousands of interconnected polyps. While coral skeletons have been extensively studied, the internal three-dimensional organization of coral tissues remains poorly resolved, limiting our understanding of how reef-building corals function as integrated modular organisms. In this study, we established a contrast-enhanced X-ray tomography (XRT) workflow for decalcified coral tissues, enabling detailed visualization and quantitative comparison of internal polyp architecture across four reef-building species with distinct colony forms: Acropora cervicornis, Acropora millepora, Montipora capitata, and Pocillopora damicornis. Importantly, this methodology resolved previously inaccessible patterns of tissue organization and structural connectivity among neighboring polyps. The two Acropora species shared a conserved axial - radial organization but differed in mesenterial morphology, whereas M. capitata exhibited complex, entangled mesenterial networks that connected both neighboring and distant polyps. In contrast, P. damicornis displayed superficial connectivity restricted to the coenosarc. Together, these results suggest that internal tissue architecture is an evolutionarily flexible trait, shaped by ecological and developmental pressures rather than strictly by shared ancestry. Our XRT workflow thus provides a new comparative framework for understanding how corals function as integrated living colonies.

evolutionary biology↗

bioRxiv2026

Minicollagen expression dynamics reveal a transcriptional program for cnidogenesis in the sea anemone Nematostella vectensis

Cnidae are explosive harpoon-like organelles localized within stinging cells, or cnidocytes, of the phylum Cnidaria (jellyfish, hydroids, sea anemones, and corals). These unique Golgi-derived vesicular structures define the phylum and are prominent examples of an evolutionary cellular novelty. While recent studies have focused on the developmental specification and regulation of cnidocytes more broadly, less is understood about gene expression patterns, structural variations, and toxin repertoires within distinct cnidae subtypes. Here, we determine the transcriptional profile of two major cnidae subtypes in the sea anemone Nematostella vectensis, nematocytes and spirocytes, using the cnidae-specific structural family of proteins called minicollagens. We first define the in vivo expression patterns for three known and three uncharacterized minicollagen orthologs. We show that four minicollagens are broadly expressed throughout ectodermal cnidocytes in developing larvae and primary polyps while two others are restricted to tentacular cnidocytes. Leveraging whole adult scRNA-seq data and two novel transgenic reporter lines, we then demonstrate that the tentacle-restricted cnidocytes are developing spirocytes that are distinguished by expression of the minicollagen NvNcol5. To deepen our analysis of cnidocyte gene expression, we used a customized RNA-FACS-seq pipeline to determine global transcriptional differences between these two subtypes. This approach identified a suite of differentially expressed genes, illuminating spatial and temporal gene expression dynamics across both developing nematocytes and spirocytes. Altogether, our experiments provide fundamental and novel insights into the specialization of cnidarian stinging cells while establishing a rich set of resources for further investigation.

evolutionary biology↗

bioRxiv2026

Morphological, molecular, and functional evidence for a CNS-like oral nerve ring in the sea anemone Nematostella vectensis

The emergence of centralized nervous systems reflects a major inflection point in evolution, enabling animals to integrate diverse inputs and coordinate complex behaviors. Neural centralization is typically associated with Bilateria, whereas their sister group, Cnidaria (jellyfish, anemones, and corals), has long been thought to rely on diffuse nerve nets mediating simple reflexes. This view, reinforced by limited anatomical and molecular data, has left unresolved whether cnidarians can form localized centers for neural processing, a question sharpened by the growing recognition of their diverse behavioral repertoires. Here we show that the sea anemone Nematostella vectensis possesses an oral nerve ring composed of ganglion-like condensations, a hallmark of centralized organization. These neurons are enriched for excitatory, inhibitory, and modulatory receptors but lack sensory or ciliary markers, yielding a molecular profile most consistent with bilaterian interneurons. Genetic disruption of a conserved inhibitory receptor subunit predominantly expressed in the oral nerve ring delayed the initiation of swallowing in a novel feeding paradigm, demonstrating a potential role in behavioral regulation. Together, these findings provide converging anatomical, molecular, and functional evidence that cnidarians can assemble localized integrative centers, suggesting that key elements of neural centralization predated the cnidarian-bilaterian split.

evolutionary biology↗

bioRxiv2026

The Nematostella synaptonemal complex mediates divergent and sex-specific meiotic programs

Throughout eukaryotes, the synaptonemal complex (SC) is a supramolecular structure essential for meiotic chromosome dynamics and sexual reproduction. While metazoan SC proteins display significant sequence divergence, the lack of functional analyses beyond bilaterian models has obscured a mechanistic understanding of SC evolution. Here we report that the sea anemone Nematostella vectensis exhibits synapsis of homologous chromosomes in a classic zipper-like manner and expresses eight orthologs of ten known vertebrate SC proteins. Surprisingly, mutagenesis of the core SC components sycp1, syce2, and sycp3 resulted in divergent and sexually dimorphic phenotypes, indicating the functional diversification of these conserved factors. Combined, these findings challenge the assumption that the conservation of protein sequence or ultrastructure implies mechanistic homology.

evolutionary biology↗

bioRxiv2025

Basal Cell-Contact Dynamics Influence Tissue Packing in a Proliferating Mammalian Epithelium

Animal tissue morphology is determined by the shape, position, and proliferative capacity of individual epithelial cells. Nevertheless, it remains incompletely understood how the dynamic shape transformations implicit in mitotic proliferation influence tissue packing, particularly at the level of basal cell contacts. Here, we use an in silico vertex model to show that epithelial mitotic rounding necessitates a sequence of dynamic basal contact rearrangements, including basal diminution of the mitotic cell volume, transient multicellular rosette assembly, basal reinsertion of daughter cells, and neighbor reorganization. We then leverage a mammalian intestinal organoid model to confirm nearly identical basal cell-contact dynamics as those predicted in silico. Pharmacological inhibition of mitotic progression reveals that two events--basal diminution of the cell body and daughter cell reinsertion--independently drive distinct contact rearrangements. Together, our results uncover a previously underappreciated topological role for basal mitotic cell dynamics in shaping epithelial packing and morphogenesis.

developmental biology↗

bioRxiv2025

Clonal effects of the Ras oncogene revealed by somatic mutagenesis in a Drosophila cancer model

Somatic mutations of Ras, encoding a small GTPase, are detected in a wide range of human cancers. Tumor genome sequencing further reveals a cancer type-dependent mutational spectrum for the Ras gene, suggesting that tissue- and allele-specific effects underlie tumorigenic activity. Although biochemical studies have characterized the GTPase activity of several Ras variants in vitro, precisely how somatic mutations of the endogenous Ras locus differentially affect tissue growth and homeostasis remain elusive. Here we engineered the endogenous Drosophila Ras locus to create a spectrum of inducible oncogenic alleles and then compared their activities in vivo. In the developing wing primordium, somatic clones carrying the oncogenic mutation Ras G12V exhibited a weak activation of downstream MAPK signaling but did not disrupt tissue architecture. However, cell clones carrying the same Ras G12V allele in the adult midgut exhibited a growth advantage and progressively took over the tissue, resulting in intestinal barrier dysfunction. In contrast, cell clones expressing a distinct allele, Ras Q61H, formed aberrant cysts that disrupted epithelial architecture and triggered local cell death. Conversely, when we induced cell clones carrying Ras Q61H in the midgut, hyper-proliferating mutant cells rapidly expanded to occupy the entire tissue. Surprisingly, this population of rapidly expanding mutant cells was eventually eliminated from the midgut, restoring wild-type cells and normal barrier function. Thus, in the midgut, Ras G12V was ultimately more deleterious than Ras Q61H due to the regression of Ras Q61H mutant cells. These results establish a new model for somatic mutagenesis at the Ras locus and illuminate a mechanistic basis for the tissue-specific effects of oncogenic Ras variants. Further, this study provides direct evidence that allele-dependent clonal dynamics may play a critical role in the tissue-selectivity of Ras oncogenic mutations.

cancer biology↗

bioRxiv2023

Graded FGF activity patterns distinct cell types within the apical sensory organ of the sea anemone Nematostella vectensis

Bilaterian animals have evolved complex sensory organs comprised of distinct cell types that function coordinately to sense the environment. Each sensory unit has a defined architecture built from component cell types, including sensory cells, non-sensory support cells, and dedicated sensory neurons. Whether this characteristic cellular composition is present in the sensory organs of non-bilaterian animals is unknown. Here, we interrogate the cell type composition and gene regulatory networks controlling development of the larval apical sensory organ in the sea anemone Nematostella vectensis. Using single cell RNA sequencing and imaging approaches, we reveal two unique cell types in the Nematostella apical sensory organ, GABAergic sensory cells and a putative non-sensory support cell population. Further, we identify the paired-like (PRD) homeodomain gene prd146 as a specific sensory cell marker and show that Prd146+ sensory cells become post-mitotic after gastrulation. Genetic loss of function approaches show that Prd146 is essential for apical sensory organ development. Using a candidate gene knockdown approach, we place prd146 downstream of FGF signaling in the apical sensory organ gene regulatory network. Further, we demonstrate that an aboral FGF activity gradient coordinately regulates the specification of both sensory and support cells. Collectively, these experiments define the genetic basis for apical sensory organ development in a non-bilaterian animal and reveal an unanticipated degree of complexity in a prototypic sensory structure.

developmental biology↗

bioRxiv2023

Environmental and molecular regulation of asexual reproduction in the sea anemone Nematostella vectensis

Cnidarians exhibit incredible reproductive diversity, with most capable of sexual and asexual reproduction. Here we investigate factors that influence asexual reproduction in the burrowing sea anemone Nematostella vectensis, which can propagate asexually by transverse fission of the body column. By altering culture conditions, we demonstrate that the presence of a burrowing substrate strongly promotes transverse fission. In addition, we show that animal size does not affect fission rates, and that the plane of fission is fixed along the oral-aboral axis of the polyp. Homeobox transcription factors and components of the TGF{beta}, Notch, and FGF signaling pathways are differentially expressed in polyps undergoing physal pinching suggesting they are important regulators of transverse fission. Gene ontology analyses further suggest that during transverse fission the cell cycle is suppressed and that cell adhesion and patterning mechanisms are downregulated to promote separation of the body column. Finally, we demonstrate that the rate of asexual reproduction is sensitive to population density. Collectively, these experiments provide a foundation for mechanistic studies of asexual reproduction in Nematostella, with implications for understanding the reproductive and regenerative biology of other cnidarian species.

animal behavior and cognition↗

bioRxiv2021

The feedback regulator Nord controls Dpp/BMP signaling via extracellular interaction with Dally in the Drosophila wing

The Drosophila BMP 2/4 homologue Decapentaplegic (Dpp) acts as a morphogen to regulate diverse developmental processes, including wing morphogenesis. Transcriptional feedback regulation of this pathway ensures tightly controlled signaling outputs to generate the precise pattern of the adult wing. Nevertheless, few direct Dpp target genes have been explored and our understanding of feedback regulation remains incomplete. Here, we employ transcriptional profiling following dpp conditional knockout to identify nord, a novel Dpp/BMP feedback regulator. Nord mutants generated by CRISPR/Cas9 mutagenesis produce a smaller wing and display low penetrance venation defects. At the molecular level, nord encodes a heparin-binding protein and we show that its overexpression is sufficient to antagonize Dpp/BMP signaling. Further, we demonstrate that Nord physically and genetically interacts with the Dpp/BMP co-receptor Dally. In sum we propose that Nord acts with Dally to fine tune Dpp/BMP signaling, with implications for both developmental and disease models. Impact statementFunctional analyses of the Drosophila homologue of Neuron Derived Neurotrophic Factor reveal a new mode of extracellular heparan sulfate proteoglycan regulation required for proper morphogen action.

developmental biology↗

bioRxiv2020

Sea anemone genomes reveal ancestral metazoan chromosomal macrosynteny

Draft genome sequences of non-bilaterian species have provided important insights into the evolution of the metazoan gene repertoire. However, there is little information about the evolution of gene clusters, genome architectures and karyotypes during animal evolution. In this regard, slowly evolving anthozoan Cnidaria, the sister group of Bilateria, are particularly informative. Here we report chromosome-level genome assemblies of two related cnidarians, the sea anemones Nematostella vectensis and Scolanthus callimorphus. We find a robust set of 15 chromosomes with a clear one-to-one correspondence between the two species. Both sea anemone genomes show remarkable chromosomal conservation with other cnidarians, several bilaterians and the sponge Ephydatia muelleri, allowing us to reconstruct ancestral cnidarian and metazoan chromosomal blocks, consisting of at least 19 and 16 ancestral linkage groups, respectively. We show that, in contrast to Bilateria, the Hox and NK clusters of investigated cnidarians are largely disintegrated, despite the presence of staggered hox/gbx expression in Nematostella. This loss of microsynteny conservation may be facilitated by shorter distances between cis-regulatory sequences and their cognate transcriptional start sites. In line with that, we find no clear evidence for topologically associated domains, suggesting fundamental differences in long-range gene regulation compared to vertebrates. These data suggest that large sets of ancestral metazoan genes have been retained in ancestral linkage groups of some extant lineages, yet, higher order gene regulation with associated 3D architecture may have evolved only after the cnidarian-bilaterian split.

genomics↗

bioRxiv2020

Feeding-dependent tentacle development in the sea anemone Nematostella vectensis

In cnidarians, axial patterning is not restricted to embryonic development but continues throughout a prolonged life history filled with unpredictable environmental changes. How this developmental capacity copes with fluctuations of food availability and whether it recapitulates embryonic mechanisms remain poorly understood. To address these questions, we utilize the tentacles of the sea anemone Nematostella vectensis as a novel paradigm for developmental patterning across distinct life history stages. As a result of embryonic development, Nematostella polyps feature four primary tentacles, while adults have 16 or more. By analyzing over 1000 growing polyps, we find that tentacle progression is remarkably stereotyped and occurs in a feeding-dependent manner. Mechanistically, we show that discrete Fibroblast growth factor receptor b (Fgfrb)-positive ring muscles prefigure the sites of new tentacles in unfed polyps. In response to feeding, a Target of Rapamycin (TOR)-dependent mechanism controls the expansion of Fgfrb expression in oral tissues which defines tentacle primordia. Using a combination of genetic, cellular and molecular approaches, we demonstrate that FGFRb regionally enhances TOR signaling activity and promotes polarized growth, a spatial pattern that is restricted to polyp but not to embryonic tentacle primordia. These findings reveal an unexpected plasticity of tentacle development, and show that the crosstalk between TOR-mediated nutrient signaling and FGFRb pathway couples post-embryonic body patterning with food availability.

developmental biology↗

bioRxiv2020

Hedgehog signaling is required for endomesodermal patterning and germ cell development in Nematostella vectensis

Two distinct mechanisms for primordial germ cell (PGC) specification are observed within Bilatera: early determination by maternal factors or late induction by zygotic cues. Here we investigate the molecular basis for PGC specification in Nematostella, a representative pre-bilaterian animal where PGCs arise as paired endomesodermal cell clusters during early development. We first present evidence that the putative PGCs delaminate from the endomesoderm upon feeding, migrate into the gonad primordia, and mature into germ cells. We then show that the PGC clusters arise at the interface between hedgehog1 and patched domains in the developing mesenteries and use gene knockdown, knockout and inhibitor experiments to demonstrate that Hh signaling is required for both PGC specification and general endomesodermal patterning. These results provide evidence that the Nematostella germline is specified by inductive signals rather than maternal factors, and support the existence of zygotically-induced PGCs in the eumetazoan common ancestor.

developmental biology↗

bioRxiv2019

Wampa is a dynein subunit required for axonemal assembly and male fertility in Drosophila

Axonemal dyneins are motor proteins that form the inner and outer arms of the axoneme in cilia and flagella. Defects in dynein arms are the leading cause of primary ciliary dyskinesia (PCD), which is characterized by chronic respiratory infections, situs inversus, and sterility. Despite current understanding of pathological features associated with PCD, many of their causative genes still remain elusive. Here we analyze genetic requirements for wampa (wam), a previously uncharacterized component of the outer dynein arm that is essential for male fertility. In addition to a role in outer dynein arm formation, we uncovered additional requirements during spermatogenesis, including regulation of remodeling events for the mitochondria and the nucleus. Due to the conserved nature of axonemal dyneins and their essential role in both PCD and fertility, this study advances our understanding of the pathology of PCD, as well as the functional role of dyneins in axonemal formation and spermatogenesis.

developmental biology↗

bioRxiv2018

Electroporation of short hairpin RNAs for rapid and efficient gene knockdown in the starlet sea anemone, Nematostella vectensis

A mechanistic understanding of evolutionary developmental biology requires the development of novel techniques for the manipulation of gene function in phylogenetically diverse organismal systems. Recently, gene-specific knockdown by microinjection of short hairpin RNA (shRNA) has been applied in the sea anemone Nematostella vectensis, a cnidarian model organism. Due to the unusual architecture of the cnidarian microRNA processing pathway, the shRNA approach is unusually effective for sequence-specific knockdown of a gene of interest. However, the time- and labor-intensive process of microinjection limits access to this technique and its application in large scale experiments. To address this issue, here we present an electroporation protocol for shRNA delivery into Nematostella eggs. This method leverages the speed and simplicity of electroporation, enabling users to manipulate gene expression in hundreds of Nematostella eggs or embryos within minutes. We provide a detailed description of the experimental procedure, including reagents, electroporation conditions, preparation of Nematostella vectensis eggs, and follow-up care of experimental animals. Finally, we demonstrate the knockdown of several endogenous and exogenous genes with known phenotypes and discuss the potential applications of this method.

developmental biology↗