Biology subjects

Navajas Acedo, J.

Publications and source records attributed to Navajas Acedo, J..

5 recordsLinked to original sources

bioRxiv2026

FOCUS-3D: Robust, generalizable volumetric cell segmentation for three-dimensional fluorescence microscopy

Understanding how cells establish spatial organization within tissues is a fundamental question in life sciences. While modern three-dimensional fluorescence microscopy captures large-volume tissue architecture, extracting quantitative cellular insights from complex volumetric datasets remains a major barrier. Here, we introduce FOCUS-3D, a robust, broadly generalizable volumetric cell segmentation framework built on a large, diverse manually annotated cell resource and advanced AI designs. Integrating volumetric representation learning, multi-scale feature extraction, and query-based mask prediction, FOCUS-3D achieves state-of-the-art performance across diverse species, tissues, fluorescent reporters and imaging modalities. During zebrafish (Danio rerio) development, FOCUS-3D uncovers three successive phases of notochord morphogenesis. We disentangle early motility-driven rearrangements from later cell shape remodeling and tissue repacking, and further link these morphological states to spatial and developmental transcriptional programs across independent datasets.

bioinformatics↗

bioRxiv2026

Odor preference maps to cohesive transcriptional domains in the olfactory bulb

Animals classify odors along behaviorally relevant dimensions, yet how the olfactory bulb, the first stage of olfactory processing, is organized and how this organization relates to odor classification remains unclear. Here, we identify cohesive transcriptional domains within the larval zebrafish olfactory bulb whose differential functional recruitment reflects odor preference. Using a flow-based two-choice assay, we characterized behavioral preferences across chemically diverse odors. Mapping odor-evoked neuronal activity patterns revealed that similarly preferred odors converge onto shared spatial activation patterns in the olfactory bulb. Whole-mount multiplexed spatial transcriptomics revealed that projection neuron and interneuron subtypes form cohesive spatial domains. Mapping odor-activated neurons onto these domains identified preference-biased recruitment of specific neuronal subtypes. Targeted ablation of a TH+ interneuron population associated with attraction selectively impaired attraction while sparing aversion. Together, these findings reveal that the olfactory bulb is organized into spatially cohesive, transcriptionally defined domains and that selective recruitment of specific subtypes is linked to odor preference. Key findingsO_LIChemically diverse odorants elicit behaviors reflecting olfactory preference. C_LIO_LITranscriptionally defined neuronal subtypes form cohesive spatial domains in the olfactory bulb. C_LIO_LIOdorants of opposing preference recruit distinct transcriptional domains in the olfactory bulb. C_LIO_LIA TH+ interneuron population is selectively required for odor attraction but not aversion. C_LI

neuroscience↗

bioRxiv2025

Development of the zebrafish anterior lateral line system is influenced by underlying cranial neural crest

The mechanosensory lateral line system of aquatic vertebrates comprises a superficial network of distributed sensory organs, the neuromasts, which are arranged over the head and trunk and innervated by lateral line nerves to allow detection of changes in water flow and pressure. While the well-studied zebrafish posterior lateral line has emerged as a powerful model to study collective cell migration, far less is known about development of the anterior lateral line, which produces the supraorbital and infraorbital lines around the eye, as well as mandibular and opercular lines over the jaw and cheek. Here we show that normal development of the zebrafish anterior lateral line system from cranial placodes is dependent on another vertebrate-specific cell type, the cranial neural crest. We find that cranial neural crest and anterior lateral lines develop in close proximity, with absence of neural crest cells leading to major disruptions in the overlying anterior lateral line system. Specifically, in the absence of neural crest neither supraorbital nor infraorbital lateral lines fully extend, such that the most anterior cranial regions remain devoid of neuromasts, while supernumerary ectopic neuromasts form in the posterior supraorbital region. Both neural crest and cranial placodes contribute neurons to the lateral line ganglia that innervate the neuromasts and in the absence of neural crest these ganglia, as well as the lateral line afferent nerves, are disrupted. Finally, we establish that as ontogeny proceeds, the most anterior supraorbital neuromasts come to lie within neural crest-derived frontal and nasal bones in the developing cranium. These are the same anterior supraorbital neuromasts that are absent or mislocated in specimens lacking neural crest cells. Together, our results establish that cranial neural crest and cranial placode derivatives function in concert over the course of ontogeny to build the complex cranial lateral line system. HighlightsO_LIThe anterior lateral line and cranial neural crest develop in close proximity C_LIO_LIAbsence of neural crest disrupts anterior lateral line development C_LIO_LIAbsence of neural crest disrupts lateral line ganglion morphology and innervation C_LIO_LIEarly interactions of neural crest and placodes prefigure later anatomical interactions C_LI O_FIG O_LINKSMALLFIG WIDTH=196 HEIGHT=200 SRC="FIGDIR/small/637483v1_ufig1.gif" ALT="Figure 1"> View larger version (42K): org.highwire.dtl.DTLVardef@ce9c43org.highwire.dtl.DTLVardef@7511e5org.highwire.dtl.DTLVardef@1e9e208org.highwire.dtl.DTLVardef@1f6af7d_HPS_FORMAT_FIGEXP M_FIG C_FIG

developmental biology↗

bioRxiv2023

Persistence of the primary somatosensory system in zebrafish

The somatosensory system detects peripheral stimuli that are translated into behaviors necessary for survival. Fishes and amphibians possess two somatosensory systems in the trunk: the primary somatosensory system, formed by the Rohon-Beard neurons, and the secondary somatosensory system, formed by the neural crest cell-derived neurons of the Dorsal Root Ganglia. Rohon-Beard neurons have been characterized as a transient population that mostly disappears during the first days of life and is functionally replaced by the Dorsal Root Ganglia. Here, I comprehensively follow Rohon-Beard neurons in vivo and show that the entire repertoire remains present in zebrafish from 1-day post-fertilization until the juvenile stage, 15-days post-fertilization. These data indicate that zebrafish retain two complete somatosensory systems until at least up to a developmental stage when the animals display complex behavioral repertoires.

developmental biology↗

bioRxiv2019

Parallel control of mechanosensory hair cell orientation by the PCP and Wnt pathways

Cell polarity plays a crucial role during development of vertebrates and invertebrates. Planar Cell Polarity (PCP) is defined as the coordinated polarity of cells within a tissue axis and is essential for processes such as gastrulation, neural tube closure or hearing. Wnt ligands can be instructive or permissive during PCP-dependent processes, and Wnt pathway mutants are often classified as PCP mutants due to the complexity and the similarities between their phenotypes. Our studies of the zebrafish sensory lateral line reveal that disruptions of the PCP and Wnt pathways have differential effects on hair cell orientations. While mutations in PCP genes cause random orientations of hair cells, mutations in Wnt pathway members induce hair cells to adopt a concentric pattern. We show that PCP signaling is normal in hair cells of Wnt pathway mutants and that the concentric hair cell phenotype is due to altered organization of the surrounding support cells. Thus, the PCP and Wnt pathways work in parallel, as separate pathways to establish proper hair cell orientation. Our data suggest that coordinated support cell organization is established during the formation of lateral line primordia, much earlier than the appearance of hair cells. Together, these finding reveal that hair cell orientation defects are not solely explained by defects in PCP signaling and that some hair cell phenotypes warrant reevaluation.

developmental biology↗