Biology subjects

Caccavale, F.

Publications and source records attributed to Caccavale, F..

5 recordsLinked to original sources

bioRxiv2026

Minos transposon-mediated transgenesis in the sea urchin Paracentrotus lividus

In the multitude of suitable experimental systems used for functional studies in the field of developmental biology, the sea urchin plays a central role due to its amenability to various methods, including both transient and stable transgenesis. Among others, transposable elements represent powerful tools for generating stable transgenic specimens, and Minos transposon turned out to be an excellent genetic tool in marine organisms, despite its efficiency being host-dependent. This study provides new evidence for the activity of Minos transposable elements and their stable integration into the genome of the Mediterranean sea urchin Paracentrotus lividus. Using the Minos-based technology coupled with a fully-automated system used for the qPCR screening of the Minos transposon integration, we devised a new pipeline for performing transgenesis-based functional studies in P. lividus.

molecular biology↗

bioRxiv2026

Evolutionary landscapes of zygotic genome activation across animals

During early animal embryogenesis, gene expression control shifts from maternally deposited products to newly transcribed RNA through zygotic genome activation (ZGA). Although essential and universal, ZGA remains poorly understood outside a few model species. Here, we generated a transcriptomic atlas of early embryogenesis across 61 animal species from 13 phyla and used a unified computational framework to infer ZGA timing systematically. We find extensive variation in ZGA onset across animals, but show that the ratio between genome size and egg cytoplasmic volume, a proxy for the nuclear-to-cytoplasmic ratio, robustly predicts when genome activation begins. We also reveal that zygotic genes also differ from maternal transcripts in genomic architecture, function and evolutionary conservation, suggesting that ZGA follows a conserved molecular logic despite flexible transcriptomic outputs.

evolutionary biology↗

bioRxiv2025

Single Nucleus Profiling Highlights the All-Brain Echinoderm Nervous System

Metazoans comprise diverse tissues and cell types, each essential for the survival of the organism. Most of these cell types are established early in embryogenesis and persist into adulthood. However, in indirectly developing sea urchins, the continuity between embryonic and adult stages is thus interrupted by a planktonic larval stage that undergoes complete metamorphosis. In addition, while the gene regulatory networks governing distinct embryonic and larval cell lineages are well studied, the molecular and morphological identities of post-metamorphic sea urchin cell types remain poorly understood. Here, we reconstructed the cell type atlas of post-metamorphic Paracentrotus lividus juveniles using single-nucleus transcriptomics, shedding light on the conservation of genetic regulatory mechanisms in post-metamorphic cell types. We identified cell signatures corresponding to eight distinct cell type groups and analyzed at least twenty-nine neuronal cell families, including fifteen unique photoreceptor cell signatures. By combining single cell transcriptomics with spatial gene expression analysis and high-resolution electron microscopy, we identified homologues of vertebrate neuronal genes and photoreceptive opsins expressed throughout the sea urchin body. These findings provide evidence that the echinoderm body plan is not only predominantly head-like, but also exhibits an all-brain organization in an animal previously considered to have a primitive nervous system.

evolutionary biology↗

bioRxiv2024

Developmental toxicity of pre-production plastic pellets affects a large swathe of invertebrate taxa

Microplastics pose risks to marine organisms through ingestion, entanglement, and as carriers of toxic additives and environmental pollutants. Plastic pre-production pellet leachates have been shown to affect the development of sea urchins and, to some extent, mussels. The extent of those developmental effects on other animal phyla remains unknown. Here, we test the toxicity of environmental mixed nurdle samples and new PVC pellets for the embryonic development or asexual reproduction by regeneration of animals from all the major animal superphyla (Lophotrochozoa, Ecdysozoa, Deuterostomia and Cnidaria). Our results show diverse, concentration-dependent impacts in all the species sampled for new pellets, and for molluscs and deuterostomes for environmental samples. Embryo axial formation, cell specification and, specially, morphogenesis seem to be the main processes affected by plastic leachate exposure. Our study serves as a proof of principle for the potentially catastrophic effects that increasing plastic concentrations in the oceans and other ecosystems can have across animal populations from all major animal superphyla.

developmental biology↗

bioRxiv2020

Crosstalk between Nitric Oxide and Retinoic Acid pathways is essential for amphioxus pharynx development

During animal ontogenesis, body axis patterning is finely regulated by complex interactions between several signaling pathways. Nitric Oxide (NO) and Retinoic Acid (RA) are potent morphogens that play a pivotal role in vertebrate development. Their involvement in axial patterning of head and pharynx shows conserved features in the chordate phylum. Indeed, in the cephalochordate amphioxus NO and RA are crucial for the correct development of pharyngeal structures. Here we demonstrate the functional cooperation between NO and RA occurring in amphioxus embryogenesis. During neurulation, NO modulates RA production through the transcriptional regulation of Aldh1a.2 that irreversibly converts retinaldehyde into RA. On the other hand, RA regulates the transcription of Nos genes, probably through RA Response Elements found in their regulatory regions. The reciprocal regulation of NO and RA pathways results to be essential for the normal pharyngeal development in amphioxus and suggests that this regulatory crosstalk could be conserved in vertebrates.View Full Text

developmental biology↗