Biology subjects

Jacobo, A.

Publications and source records attributed to Jacobo, A..

10 recordsLinked to original sources

bioRxiv2026

Vangl2 acts in distinct cell types to establish bidirectional hair-bundle polarity and maintains tissue-wide alignment in zebrafish neuromasts

The conserved core planar cell polarity (PCP) pathway orients cells and subcellular structures within an epithelium through asymmetric protein localization and intercellular communication. In vestibular organs and lateral-line neuromasts, mechanosensory hair cells are interspersed among support cells and form opposing hair-bundle orientations along a shared axis, enabling bidirectional sensitivity to head motion and water flow, respectively. In zebrafish neuromasts, Notch-mediated lateral inhibition gives rise to two hair-cell populations, distinguished by differential Emx2 expression, that orient their cell-intrinsic polarity machinery differently relative to a PCP-dependent tissue-wide axis. However, it remains unclear how PCP proteins are organized across hair cells and support cells to achieve both opposing hair-bundle orientations and tissue-wide alignment, and whether PCP signaling remains required after hair-bundle polarity is established. Combining quantitative spatial mapping of the core PCP protein Vangl2 with cell-type-specific and temporally controlled protein degradation, we show that hair cells and support cells make distinct yet coordinated contributions to the polarized Vangl2 organization within neuromasts and to bidirectional hair-bundle polarity. Support-cell Vangl2 facilitates tissue-wide alignment of hair bundles along the anteroposterior axis, whereas hair-cell Vangl2 is required to generate opposing hair-bundle orientations along this axis. Vangl2 degradation after hair bundles have formed disrupts their tissue-wide alignment, showing that planar polarity is actively maintained rather than fixed after establishment. Together, these findings reveal how Vangl2-dependent PCP signaling is distributed across distinct cell types within a heterogeneous epithelium to generate opposing polarity outcomes and remains necessary to preserve tissue-level planar organization.

developmental biology↗

bioRxiv2026

Notch-driven fate asymmetry dictates hair cell behavior via a fate-specific kinase

Cell-cell signaling and cell-fate decisions are essential for organ assembly, but how these molecular events translate into the physical properties and cell behaviors that drive development remains poorly understood. In the zebrafish lateral line, developing pairs of sensory hair cells undergo symmetry-breaking mediated by Notch signaling, leading to one cell becoming Notch-ON (receiver state) and its sibling becoming Notch-OFF (sender state). These cells then undergo coordinated movements that ensure that Notch-OFF cells are always positioned anterior to their Notch-ON sisters, and the Notch state of each sister ultimately determines the direction of hair bundle polarization. However, the cellular mechanisms and molecular programs that guide polarity-specific behaviors remain largely unknown. Here, using time-lapse imaging and a new 3D segmentation and tracking pipeline, we demonstrate that sister cells actively move in opposite directions - Notch-OFF cells migrate anteriorly while Notch-ON cells move posteriorly - enabling robust rotations when cells are initially mispositioned. Using single-cell RNA sequencing, we identify fate-dependent transcriptional programs and show that the differentially expressed kinase stk32a is required for proper navigation and hair bundle placement in Notch-ON cells. Strikingly, loss of stk32a reveals an underlying chiral bias in cell-pair rotations, suggesting the existence of an additional, previously unrecognized axis of symmetry breaking beyond the Notchmediated fate decision.

developmental biology↗

bioRxiv2025

Optogenetic interrogation of the lateral-line sensory system reveals mechanisms of pattern separation in the zebrafish brain

The ability of animals to interact with their environment hinges on the brains capacity to distinguish between patterns of sensory information and accurately attribute them to specific sensory organs. The mechanisms by which neuronal circuits discriminate and encode the source of sensory signals remain elusive. To address this, we utilized as a model the posterior lateral line system of larval zebrafish, which is used to detect water currents. This system comprises a series of mechanosensory organs called neuromasts, which are innervated by neurons from the posterior lateral line ganglion. By combining single-neuromast optogenetic stimulation with whole-brain calcium imaging, we developed a novel approach to investigate how inputs from neuromasts are processed. Upon stimulating individual neuromasts, we observed that neurons in the brain of the zebrafish show diverse selectivity properties despite a lack of topographic organization in second-order circuits. We further demonstrated that complex combinations of neuromast stimulation are represented by sparse ensembles of neurons within the medial octavolateralis nucleus (MON) and found that neuromast input can be integrated nonlinearly. Our approach offers an innovative method for spatiotemporally interrogating the zebrafish lateral line system and presents a valuable model for studying whole-brain sensory encoding.

neuroscience↗

bioRxiv2024

Ultrack: pushing the limits of cell tracking across biological scales

Tracking live cells across 2D, 3D, and multi-channel time-lapse recordings is crucial for understanding tissue-scale biological processes. Despite advancements in imaging technology, achieving accurate cell tracking remains challenging, particularly in complex and crowded tissues where cell segmentation is often ambiguous. We present Ultrack, a versatile and scalable cell-tracking method that tackles this challenge by considering candidate segmentations derived from multiple algorithms and parameter sets. Ultrack employs temporal consistency to select optimal segments, ensuring robust performance even under segmentation uncertainty. We validate our method on diverse datasets, including terabyte-scale developmental time-lapses of zebrafish, fruit fly, and nematode embryos, as well as multi-color and label-free cellular imaging. We show that Ultrack achieves state-of-the-art performance on the Cell Tracking Challenge and demonstrates superior accuracy in tracking densely packed embryonic cells over extended periods. Moreover, we propose an approach to tracking validation via dual-channel sparse labeling that enables high-fidelity ground truth generation, pushing the boundaries of long-term cell tracking assessment. Our method is freely available as a Python package with Fiji and napari plugins and can be deployed in a high-performance computing environment, facilitating widespread adoption by the research community.

developmental biology↗

bioRxiv2024

Robust virtual staining of landmark organelles

Correlative dynamic imaging of cellular landmarks, such as nuclei and nucleoli, cell membranes, nuclear envelope and lipid droplets is critical for systems cell biology and drug discovery, but challenging to achieve with molecular labels. Virtual staining of label-free images with deep neural networks is an emerging solution for correlative dynamic imaging. Multiplexed imaging of cellular landmarks from scattered light and subsequent demultiplexing with virtual staining leaves the light spectrum for imaging additional molecular reporters, photomanipulation, or other tasks. Current approaches for virtual staining of landmark organelles are fragile in the presence of nuisance variations in imaging, culture conditions, and cell types. We report training protocols for virtual staining of nuclei and membranes robust to variations in imaging parameters, cell states, and cell types. We describe a flexible and scalable convolutional architecture, UNeXt2, for supervised training and self-supervised pre-training. The strategies we report here enable robust virtual staining of nuclei and cell membranes in multiple cell types, including human cell lines, neuromasts of zebrafish and stem cell (iPSC)-derived neurons, across a range of imaging conditions. We assess the models by comparing the intensity, segmentations, and application-specific measurements obtained from virtually stained and experimentally stained nuclei and cell membranes. The models rescue missing labels, non-uniform expression of labels, and photobleaching. We share three pre-trained models (VSCyto3D, VSNeuromast, and VSCyto2D) and a PyTorch-based pipeline (VisCy) for training, inference, and deployment that leverages current community standards for image data and metadata.

bioinformatics↗

bioRxiv2024

Lipid-Based Transfection of ZebrafishEmbryos: A Robust Protocol for NucleicAcid Delivery in Zebrafish

Zebrafish, a widely used model organism in developmental and biomedical research, offers several advantages such as external fertilization, embryonic transparency, and genetic similarity to humans. However, traditional methods for introducing exogenous genetic material into zebrafish embryos, particularly microinjection, pose significant technical challenges and limit throughput. To address this, we developed a novel approach utilizing Lipofectamine LTX for the efficient delivery of nucleic acids into zebrafish embryos by lipid-based transfection. Our protocol bypasses the need for microinjection, offering a cost-effective, high-throughput, and user-friendly alternative. This protocol out-lines new strategies for gene delivery in zebrafish to enhance the efficiency and scope of genetic studies in this model system.

molecular biology↗

bioRxiv2023

Zebrahub - Multimodal Zebrafish Developmental Atlas Reveals the State Transition Dynamics of Late Vertebrate Pluripotent Axial Progenitors

Elucidating the developmental processes of organisms requires a comprehensive understanding of cellular lineages in the spatial, temporal, and molecular domains. In this study, we introduce Zebrahub, a dynamic atlas of zebrafish embryonic development that integrates single-cell sequencing time course data with lineage reconstructions facilitated by light-sheet microscopy. This atlas offers high-resolution and in-depth molecular insights into zebrafish development, achieved through the sequencing of individual embryos across ten developmental stages, complemented by trajectory reconstructions. Zebrahub also incorporates an interactive tool to navigate the complex cellular flows and lineages derived from light-sheet microscopy data, enabling in silico fate mapping experiments. To demonstrate the versatility of our multi-modal resource, we utilize Zebrahub to provide fresh insights into the pluripotency of Neuro-Mesodermal Progenitors (NMPs). Our publicly accessible web-based platform, Zebrahub, is a foundational resource for studying developmental processes at both transcriptional and spatiotemporal levels, providing researchers with an integrated approach to exploring and analyzing the complexities of cellular lineages during zebrafish embryogenesis.

developmental biology↗

bioRxiv2019

Symmetry breaking during morphogenesis of a mechanosensory organ

Actively regulated symmetry breaking, which is ubiquitous in biological cells, underlies phenomena such as directed cellular movement and morphological polarization. Here we investigate how an organ-level polarity pattern emerges through symmetry breaking at the cellular level during the formation of a mechanosensory organ. Combining theory, genetic perturbations, and in vivo imaging assisted by deep learning, we study the development and regeneration of the fluid-motion sensors in the zebrafishs lateral line. We find that two interacting symmetry-breaking events -- one mediated by biochemical signaling and the other by cellular mechanics -- give rise to a novel form of collective cell migration, which produces a mirror-symmetric polarity pattern in the receptor organ.

biophysics↗

bioRxiv2018

Notch-Mediated Polarity Decisions in Mechanosensory Hair Cells

The development of mechanosensory epithelia, such as those of the auditory and vestibular systems, results in the precise orientation of mechanosensory hair cells and consequently directional sensitivity. After division of a precursor cell in the zebrafishs lateral line, the daughter hair cells differentiate with opposite mechanical sensitivity. Through a combination of theoretical and experimental approaches, we show that Notch1a-mediated lateral inhibition produces a bistable switch that reliably gives rise to cell pairs of opposite polarity. Using our mathematical model of the process, we predict the outcome of several genetic and chemical alterations to the system, which we then confirm experimentally. We show that Notch1a downregulates the expression of Emx2, a transcription factor known to be involved in polarity specification, and acts in parallel with the planar-cell-polarity system to determine the orientation of hair bundles. By analyzing the effect of simultaneous genetic perturbations to Notch1a and Emx2 we infer that the generegulatory network determining cell polarity includes undiscovered polarity effectors.

developmental biology↗

bioRxiv2018

Connectomics of the zebrafish’s lateral-line neuromast reveals wiring and miswiring in a simple microcircuit

The lateral-line neuromast of the zebrafish displays a restricted, consistent pattern of innervation that facilitates the comparison of microcircuits across individuals, developmental stages, and genotypes. We used serial blockface scanning electron microscopy to determine from multiple specimens the neuromast connectome, or comprehensive set of connections between hair cells and afferent and efferent nerve fibers. This analysis delineated a complex but consistent wiring pattern with three striking characteristics: each nerve terminal is highly specific in receiving innervation from hair cells of a single directional sensitivity; the innervation is redundant; and the terminals manifest a hierarchy of dominance. Mutation of the canonical planar-cell-polarity gene vangl2, which decouples the asymmetric phenotypes of sibling hair-cell pairs, results in randomly positioned, randomly oriented sibling cells that nonetheless retain specific wiring. Because larvae that overexpress Notch exhibit uniformly oriented, uniformly innervating hair-cell siblings, wiring specificity is mediated by the Notch signaling pathway.

developmental biology↗