Biology subjects

Oates, A. C.

Publications and source records attributed to Oates, A. C..

12 recordsLinked to original sources

bioRxiv2026

Shield-4i: A Whole-mount Multiplexed Imaging Platform for Studying Multiscale Information Flow in 3D Multicellular Systems

Self-organization in multicellular systems emerges from reciprocal interactions across spatiotemporal scales. Understanding how subcellular organization, tissue remodeling and developmental outcome are coordinated, thus requires simultaneous profiling of biological processes spanning orders of magnitudes in space and time. Yet, a unified experimental and computational framework for capturing these multiscale properties across in vivo and stem cell-derived systems has been lacking. Here, we introduce Shield-4i, a high-throughput, versatile, and accessible method for automated in toto iterative immunofluorescence imaging of whole-mount structures at subcellular resolution. Through polyepoxide-mediated inter- and intramolecular crosslinking, Shield-4i preserves sample integrity during repeated SDS-based elution cycles. We benchmark this method in gastrulating zebrafish and post-implantation mouse embryos and demonstrate its applicability to stem cell-derived 3D gastruloids, achieving up to 30-plex measurements of proteins and their post-translational modifications across hundreds of samples. To enable scalable analysis, we developed a dedicated 3D workflow supporting OME-Zarr-based and FAIR-compliant data storage, standardized processing, and multiscale feature extraction. Applying this framework to investigate gastruloid self-organization, we quantify how cellular physicochemical state and signaling properties encode cell position along embryonic axes and connect molecular patterning and fate decisions to morphological symmetry breaking at the multicellular scale. Together, Shield-4i provides a high-content in toto spatial proteomics platform for dissecting multiscale information flow and self-organization in multicellular systems.

systems biology↗

bioRxiv2026

Real-Time Multi-Position and Multi-ROI Tracking with LiLiTTool for Smart Light-Sheet Microscopy in Growing Samples

Long-term live imaging of growing samples with light-sheet fluorescence microscopy provides unique insights into development, but morphogenesis often displaces features of interest outside the microscopes field of view (FOV), calling for automated methods to track these features and update the microscopes FOV in real time. Existing solutions, which typically rely on local or global intensity distributions, struggle to follow specific features robustly throughout morphogenesis, leading to truncated or incomplete datasets. Here, we present a light-sheet live tracking tool (LiLiTTool) that maintains user-defined regions of interest (ROI) within the FOV throughout extended imaging sessions. LiLiTTool uses Cotracker3, a state-of-the art deep learning-based motion predictor, augmented by sensor fusion with a trained object-detector. This enables robust compensation for drift, rotation, and deformation during morphogenesis, while meeting the timing constraints of live acquisition. We validated LiLiTool by integrating with the Viventis LS1 microscope, achieving sub-second processing and stable tracking of growing zebrafish embryos over many hours. LiLiTTool supports multi-ROI tracking in 3D, enabling simultaneous monitoring of multiple features within the same embryo and in multiple embryos during a single acquisition. LiLiTTool is modular and openly available on GitHub and as a napari plugin for post-acquisition tracking. By enabling precise, adaptive, and scalable real-time imaging, LiLiTTool advances smart microscopy approaches and provides the developmental biology community with a practical tool for capturing reliable spatio-temporal information in growing embryos or other morphogenetic systems.

developmental biology↗

bioRxiv2024

Unified Mass Imaging Maps the Lipidome of Vertebrate Development

Embryo development entails the formation of anatomical structures with distinct biochemical compositions. Compared with the wealth of knowledge on gene regulation, our understanding of metabolic programs operating during embryogenesis is limited. Mass spectrometry imaging (MSI) has the potential to map the distribution of metabolites across embryo development. Here, we established an analytical framework for the joint analysis of large MSI datasets that allows for the construction of multi-dimensional metabolomic atlases. Employing this framework, we mapped the 4D distribution of over a hundred lipids at quasi-single-cell resolution in Danio rerio embryos. We discovered metabolic trajectories that unfold in concert with morphogenesis and revealed spatially organized biochemical coordination overlooked by bulk measurements. Interestingly, lipid mapping revealed unexpected distributions of sphingolipid and triglyceride species, suggesting their involvement in pattern establishment and organ development. Our approach empowers a new generation of whole-organism metabolomic atlases and enables the discovery of spatially organized metabolic circuits.

systems biology↗

bioRxiv2024

Multiple Notch ligands in the synchronization of the segmentation clock

Notch signaling is a ubiquitous and versatile intercellular signaling system that drives collective behaviors and pattern formation in biological tissues. During embryonic development, Notch is involved in generation of collective biochemical oscillations that form the vertebrate body segments, and its failure results in embryonic defects. Notch ligands of the Delta family are key components of this collective rhythm, but it is unclear how different Delta ligands with distinct properties contribute to relaying information among cells. Motivated by the zebrafish segmentation clock, in this work we propose a theory describing interactions between biochemical oscillators, where Notch receptor is bound by both oscillatory and nonoscillatory Delta ligands. Based on previous in vitro binding studies, we first consider Notch activation by Delta dimers. This hypothesis is consistent with experimental observations in conditions of perturbed Notch signaling. Then we test an alternative hypothesis where Delta monomers directly bind and activate Notch, and show that this second model can also describe the experimental observations. We show that these two hypotheses assign different roles for a non-oscillatory ligand, as a binding partner or as a baseline signal. Finally, we discuss experiments to distinguish between the two scenarios. Broadly, this work highlights how a multiplicity of ligands may be harnessed by a signaling system to generate versatile responses.

developmental biology↗

bioRxiv2024

Single-cell transcriptional dynamics in a living vertebrate

The ability to quantify transcriptional dynamics in individual cells via live imaging has revolutionized our understanding of gene regulation. However, such measurements are lacking in the context of vertebrate embryos. We addressed this deficit by applying MS2-MCP mRNA labeling to the quantification of transcription in zebrafish, a model vertebrate. We developed a platform of transgenic organisms, light sheet fluorescence microscopy, and optimized image analysis that enables visualization and quantification of MS2 reporters. With these tools, we obtained single-cell, real-time measurements of transcriptional dynamics of the segmentation clock. Our measurements challenge the traditional view of smooth clock oscillations and instead suggest a model of discrete transcriptional bursts that are organized in space and time. Together, these results highlight how measuring single-cell transcriptional activity in the context of vertebrate organisms can reveal unexpected features of gene regulation and how this data can fuel the dialogue between theory and experiment.

developmental biology↗

bioRxiv2023

Clock driven waves of Tbx6 expression prefigure somite boundaries

The segmented body plan of vertebrates is established during embryogenesis by periodic and sequential formation of multi-cellular structures called somites. Somitogenesis is an example of patterning by a biological oscillator, the segmentation clock, which manifests as traveling waves of oscillating Hes/Her gene expression, reiterating during the formation of each1-3. How these waves are converted into the striped Mesp gene expression pattern that prefigures morphological somite boundaries4-8 remains unclear. Here, we image this conversion in real-time at single-cell resolution in zebrafish, using light-sheet microscopy of a novel reporter of Tbx6, a key activator of Mesp expression. We observe cellular oscillations and kinematic waves of Tbx6 expression that are driven by Hes/Her genes. Tbx6 waves arrest precisely in boundary cells that eventually express Mesp, thereby prefiguring the Mesp pattern, whereas Hes/Her waves do not. Although Hes/Her oscillations began before somitogenesis9-11, the first Tbx6 wave defines the boundary cells of the anterior-most somite, forming the head-trunk interface. Our findings imply that Tbx6 acts as a genetic clutch, converting Her/Hes pacemaker waves into Mesp stripes. We propose that this clock design shields the pacemaker from external perturbations, allowing flexible and robust patterning, making it of interest for organoids and tissue-engineering.

developmental biology↗

bioRxiv2023

OpenSIM: open source microscope add-on for structured illumination microscopy

Super-resolution techniques expand the abilities of researchers who have the knowledge and resources to either build or purchase a system. This excludes the part of the research community without these capabilities. Here we introduce the openSIM add-on to upgrade existing optical microscopes to Structured Illumination super-resolution Microscopes (SIM). The openSIM is an open-hardware system, designed and documented to be easily duplicated by other laboratories, making super-resolution modality accessible to facilitate innovative research. The add-on approach gives a performance improvement for pre-existing lab equipment without the need to build a completely new system.

bioengineering↗

bioRxiv2023

But, what are the cells doing? Image Analysis pipeline to follow single cells in the zebrafish embryo

Microscopy has rapidly evolved at pace with live markers, enabling ever higher spatiotemporal resolution of multicellular dynamics within larger fields of view. Consequently, we are now in the era of widespread production of terabyte (TB)-sized time-lapse movies of experimental model systems, including developing embryos and organoids. Working with these large datasets has presented a new set of hurdles, particularly due to the lack of standardized open-source pipelines for acquiring, handling and analyzing the data. Moreover, although long-term tracking of a cell throughout an entire process, for example vertebrate organogenesis, is key to revealing the underlying cellular dynamics, this has proven largely elusive. To specifically address the question "But, what are the cells doing?", we created an image analysis pipeline optimized to track single cells in light-sheet acquired datasets (1 TB sized time-lapse, 8h of imaging, 30 min gene expression cycle, cell movement speed (1{micro}m /1 minute), 200-400 {micro}m tissue depth). Our modular pipeline optimizes and connects the following: image acquisition parameters to improve tracking feasibility; hardware specifications; data handling and compression tools; pre-processing steps; state-of-the-art cell tracking tools (Mastodon, MaMuT) and a novel open-source/ python-based tool (Paleontologist) to analyze and visualize spatiotemporal dynamics of the tracked cells. Importantly, our pipeline is adaptable to a variety of experimental systems and accessible to researchers regardless of expertise in coding and image analysis. One-sentence SummaryUser-friendly cell-tracking pipeline that connects image acquisition in multicellular systems through to data analysis of cellular dynamics.

developmental biology↗

bioRxiv2022

Deconstructing body axis morphogenesis in zebrafish embryos using robot-assisted tissue micromanipulation

Microsurgical techniques, such as those used in the early 1900s by Mangold and Spemann, were not only foundational for experimental embryology, but are still in use today. Here, we build on these classic techniques by introducing a user-friendly robotic microsurgery platform that allows precise mechanical manipulation of soft tissues in zebrafish embryos. As a proof of principle, we investigated the contribution of different embryonic tissues to vertebrate anteroposterior (AP) axis elongation and segmentation. Using our platform, we reproducibly targeted precise regions of tail explants, and quantified the response in real-time by following notochord and presomitic mesoderm (PSM) morphogenesis and segmentation clock dynamics. We find an extension force generated through the posterior notochord, independent of notochord cell vacuolation, that is strong enough to buckle the structure. Our data suggest that this force generates a unidirectional notochord extension towards the tailbud because PSM tissue around the posterior notochord does not let it slide anteriorly. These results complement existing biomechanical models of axis elongation, revealing a critical coupling between the posterior notochord, the tailbud, and the PSM, and show that somite patterning is robust against structural perturbations.

biophysics↗

bioRxiv2021

Cell-autonomous generation of the wave pattern within the vertebrate segmentation clock

Rhythmic and sequential segmentation of the growing vertebrate body relies on the segmentation clock, a multi-cellular oscillating genetic network. The clock is visible as tissue-level kinematic waves of gene expression that travel through the pre-somitic mesoderm (PSM) and arrest at the position of each forming segment. Here we test how this hallmark wave pattern is driven by culturing single maturing PSM cells. We compare their cell-autonomous oscillatory and arrest dynamics to those we observe in the embryo at cellular resolution, finding similarity in the relative slowing of oscillations and arrest in concert with differentiation. This shows that cell-extrinsic signals are not required by the cells to instruct the developmental program underlying the wave pattern. We show that a cell-autonomous timing activity initiates during cell exit from the tailbud, then runs down in the anterior-ward cell flow in the PSM, thereby using elapsed time to provide positional information to the clock. Exogenous FGF lengthens the duration of the cell-intrinsic timer, indicating extrinsic factors in the embryo may regulate the segmentation clock via the timer. In sum, our work suggests that a noisy cell-autonomous, intrinsic timer drives the slowing and arrest of oscillations underlying the wave pattern, while extrinsic factors in the embryo tune this timers duration and precision. This is a new insight into the balance of cell-intrinsic and -extrinsic mechanisms driving tissue patterning in development.

developmental biology↗

bioRxiv2020

Somite deformations buffer imprecise segment lengths to ensure left-right symmetry

The body axis of vertebrate embryos is periodically segmented into bilaterally symmetric pairs of somites. The anteroposterior (AP) length of somites, their position and left-right symmetry are thought to be molecularly determined prior to somite morphogenesis. Here we discover that in zebrafish embryos, initial somite AP lengths and positions are imprecise and consequently many somite pairs form left-right asymmetrically. Strikingly, these imprecisions are not left unchecked and we find that AP lengths adjust within an hour after somite formation, thereby increasing morphological symmetry. We find that AP length adjustments result entirely from changes in somite shape without change in somite volume, with changes in AP length being compensated by corresponding changes in mediolateral length. The AP adjustment mechanism is facilitated by somite surface tension, which we show by comparing in vivo experiments and in vitro single-somite explant cultures with a mechanical model. Length adjustment is inhibited by perturbation of Integrin and Fibronectin, consistent with their involvement in surface tension. In contrast, the adjustment mechanism is unaffected by perturbations to the segmentation clock, thus revealing a distinct process that determines morphological segment lengths. We propose that tissue surface tension provides a general mechanism to adjust shapes and ensure precision and symmetry of tissues in developing embryos.

developmental biology↗

bioRxiv2020

Theory of genetic oscillations with external noisy regulation

We present a general theory of noisy genetic oscillators with externally regulated production rate. The observables that characterize the genetic oscillator are discussed, and it is shown how their statistics depend on the statistics of the external regulator. We show that these observables have generic features that are observed in two different experimental systems: the expression of the circadian clock genes in fibroblasts, and in the transient and oscillatory dynamics of the segmentation clock genes observed in cells disassociated from zebrafish embryos. Our work shows that genetic oscillations with diverse biological contexts can be understood in a common framework based on delayed negative feedback system, and slow regulator dynamics.

biophysics↗