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Results for “developmental biology”

Search indexed bioRxiv preprints in genomics, neuroscience, cell biology and bioinformatics. Read source abstracts and check manuscript versions; preprints are not peer reviewed.

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At least 541 records · Page 30Linked to original sources

bioRxiv2020

An Image-Based Data-Driven Analysis of Cellular Architecture in a Developing Tissue

Quantitative microscopy is becoming increasingly crucial in efforts to disentangle the complexity of organogenesis, yet adoption of the potent and ever-growing toolbox provided by modern data science has been slow, primarily because data-driven tools focus on "big data" whereas microscopy produces "rich data". We tackle this issue using a newly developed algorithm for point cloud-based morphometry to unpack the rich information encoded in high-resolution 3D image data into a straightforward numerical representation. This allowed us to employ machine learning for multi-modal data integration of cell morphology, intracellular organization, gene expression and annotated contextual knowledge that facilitates data exploration. We apply these techniques to construct and explore a quantitative atlas of cellular architecture for the zebrafish posterior lateral line primordium, an experimentally tractable model of complex self-organized organogenesis. In doing so, we are able to retrieve both previously established and novel biologically relevant patterns, demonstrating the potential of our data-driven approach.

developmental biology↗

bioRxiv2022

Early precision of radial patterning of the mouse cochlea is achieved by a linear BMP signaling gradient and is further refined by SOX2

Positional information encoded in signaling molecules is essential for early patterning in the prosensory domain of the developing cochlea. The cochlea contains an exquisite repeating pattern of sensory hair cells and supporting cells. This requires precision in the morphogen signals that set the initial radial compartment boundaries, but this has not been investigated. To measure gradient formation and morphogenetic precision in developing cochlea, we developed a quantitative image analysis procedure measuring SOX2 and pSMAD1/5/9 profiles in mouse embryos at embryonic day (E)12.5, E13.5, and E14.5. Intriguingly, we found that the pSMAD1/5/9 profile forms a linear gradient in the medial [~]75% of the PSD during E12.5 and E13.5. This is a surprising activity readout for a diffusive BMP4 ligand secreted from a tightly constrained lateral region1,2 since morphogens typically form exponential or power-law gradient shapes. This is meaningful for gradient interpretation because while linear profiles offer the theoretically highest information content and distributed precision for patterning, a linear morphogen gradient has not yet been observed. In addition to the information-optimized linear profile, we found that while pSMAD1/5/9 is stable during this timeframe, an accompanying gradient of SOX2 shifts dynamically. Third, we see through joint decoding maps of pSMAD1/5/9 and SOX2 that there is a high-fidelity mapping between signaling activity and position in the regions soon to become Kollikers organ and the organ of Corti, where radial patterns are more intricate than lateral regions. Mapping is ambiguous in the prosensory domain precursory to the outer sulcus, where cell fates are uniform. Altogether, this research provides new insights into the precision of early morphogenetic patterning cues in the radial cochlea prosensory domain. Summary ParagraphThe organ of Corti is the precisely patterned group of cells in the cochlea responsible for transforming sound energy into our perception of hearing. Morphogenetic signals encoding positional information are crucial for the early stages of patterning along the developing cochleas radial axis. SOX2 and pSMAD1/5/9 are transcription factors that together serve as an integrative readout of morphogen activity during E12.5 to E14.5 in the developing mouse cochlea. However, the role of spatiotemporal precision in these signals is unknown. Here we show that pSMAD1/5/9 forms a linear profile to establish a domain spanning reference frame of positional information and that SOX2 further refines precision. We found that the pSMAD1/5/9 signal retains its linear shape across at least 24 h of development while SOX2 dynamically shifts. The stable linear pSMAD1/5/9 profile provides a global reference point of radial positional information, while the SOX2 profile improves local precision with steep slopes. Furthermore, a linear profile from a diffusive ligand is unexpected, suggesting unidentified mechanisms of BMP regulation unique to this system. A version of the source-sink model for creating a linear morphogen profile modified from its original formulation3 is explored in this system, enabling a tight fit between the BMP model and pSMAD1/5/9 data. We expect the methods and results shown here to be a starting point for increased precision in cochlear morphogen activity measurements to enable further modeling and experimental inquiry. This combination of quantitative mechanistic explanation for how signals form, along with quantitative interpretations of their decoding properties, revealing why they form a certain way, together form a potent basis for biological discovery and may even be applied to the design of synthetic systems.

developmental biology↗

bioRxiv2023

An extra-genital cell population contributes to urethra closure during mouse penis development

Hypospadias, or incomplete closure of the urethra along the penis, is the second most common birth defect in the United States. We discovered a population of extra- genital mesenchymal cells that are essential for proper penile urethra closure in mouse embryos. This extra-genital population first appeared in the mesenchyme posterior to the hindlimb of the fetus after the onset of penis formation. These extra-genital cells, which transiently express a lineage marker Nr5a1, migrated centrally and colonized the penis bilateral to the urethra epithelium. Removal of the Nr5a1+ extra-genital cells, using a cell-type specific ablation model, resulted in severe hypospadias. The absence of extra-genital cells had the most significant impacts on another mesenchymal cells, the peri-urethra that were immediately adjacent to the Nr5a1+ extra-genital cells. Single cell mRNA sequencing revealed that the extra-genital cells extensively interact with the peri-urethra, particularly through Neuregulin 1, an epidermal Growth Factor (EGF) ligand. Disruption of Neuregulin 1 signaling in the ex-vivo slice culture system led to failure of urethra closure, recapitulating the phenotypes of extra-genital cell ablation. These results demonstrate that the Nr5a1+ extra-genital mesenchymal cells from outside of the fetal penis are indispensable for urethra closure through their interaction with the peri-urethra mesenchymal cells. This discovery provides a new entry point to understand the biology of penis formation and potential causes of hypospadias in humans.

developmental biology↗

bioRxiv2024

Long-range chemical signalling in vivo is regulated by mechanical signals

Biological processes are regulated by chemical and mechanical signals, yet the interaction between these signalling modalities remains poorly understood. Using the developing Xenopus laevis brain as a model system, we identified a critical crosstalk between tissue stiffness and long-range chemical signalling in vivo. Targeted knockdown of the mechanosensitive ion channel Piezo1 in retinal ganglion cells (RGCs) led to pathfinding errors in vivo. However, pathfinding errors were also observed in RGCs expressing Piezo1, when Piezo1 was downregulated in the surrounding brain tissue. Depleting Piezo1 in the brain parenchyma led to a decrease in the expression of the long-range chemical guidance cues Semaphorin3A (Sema3A) and Slit1, which instruct turning responses in distant cells. Furthermore, Piezo1 knockdown markedly reduced tissue stiffness. This tissue softening was independent of Sema3A depletion, and was caused by a decrease in the cell-cell adhesion proteins NCAM1 and N-Cadherin. Downregulating NCAM1 and N-Cadherin was sufficient to reduce tissue stiffness and Sema3A expression. Conversely, increasing environmental stiffness ex vivo resulted in enhanced tissue-level force generation and an increase in Slit1 and Sema3A expression. Moreover, stiffening soft brain regions in vivo induced ectopic Sema3A production via a Piezo1-dependent mechanism. Hence, tissue mechanics can locally modulate the availability of diffusive, long-range chemical signals, thus influencing cell function at sites distant from the mechanical cue. Such indirect regulatory mechanisms of cell function through mechanical signals are likely widespread across biological systems.

developmental biology↗

bioRxiv2024

Co-transcriptional splicing facilitates transcription of gigantic genes

Although introns are typically tens to thousands of nucleotides, there are notable exceptions. In flies as well as humans, a small number of genes contain introns that are more than 1000 times larger than typical introns, exceeding hundreds of kilobases (kb) to megabases (Mb). It remains unknown why gigantic introns exist and how cells overcome the challenges associated with their transcription and RNA processing. The Drosophila Y chromosome contains some of the largest genes identified to date: multiple genes exceed 4Mb, with introns accounting for over 99% of the gene span. Here we demonstrate that co-transcriptional splicing of these gigantic Y-linked genes is important to ensure successful transcription: perturbation of splicing led to the attenuation of transcription, leading to a failure to produce mature mRNA. Cytologically, defective splicing of the Y-linked gigantic genes resulted in disorganization of transcripts within the nucleus suggestive of entanglement of transcripts, likely resulting from unspliced long RNAs. We propose that co-transcriptional splicing maintains the length of nascent transcripts of gigantic genes under a critical threshold, preventing their entanglement and ensuring proper gene expression. Our study reveals a novel biological significance of co-transcriptional splicing.

developmental biology↗

bioRxiv2025

Benchmarking porcine pancreatic ductal organoids for drug screening applications

Primary human pancreatic ductal organoids (HPDO) have emerged as a model to study pancreas biology and disease. Yet, donor material availability, and a lack of extensive benchmarking limits the range of applications. To address this gap, we established porcine pancreatic ductal organoids (PPDO) as a system from an easily obtainable source to model pancreatic ductal/progenitor biology. We benchmarked PPDO to HPDO and primary porcine pancreas using single-cell RNA sequencing (scRNA-Seq). We observed no overt phenotypic differences in PPDO derived from distinct developmental stages, with a WNT signaling enriched population characterizing PPDO. PPDO exhibited differentiation potential towards mature ductal cells and limited potential towards endocrine lineages. We used PPDO as a platform to assess the safety of FDA-approved drugs and showed conserved toxicity of statins and -adrenergic receptor inhibitors between PPDO and HPDO cultures. Overall, our results highlight the PPDO as a model for mammalian duct/progenitor applications.

developmental biology↗

bioRxiv2021

Biological Action at a Distance: Correlated pattern formation in adjacent tessellation domains without communication

Tessellations emerge in many natural systems, and the constituent domains often contain regular patterns, raising the intriguing possibility that pattern formation within adjacent domains might be correlated by the geometry, without the direct exchange of information between parts comprising either domain. We confirm this paradoxical effect, by simulating pattern formation via reaction-diffusion in domains whose boundary shapes tessellate, and showing that correlations between adjacent patterns are strong compared to controls that self-organise in domains with equivalent sizes but unrelated shapes. The effect holds in systems with linear and non-linear diffusive terms, and for boundary shapes derived from regular and irregular tessellations. Based on the prediction that correlations between adjacent patterns should be bimodally distributed, we develop methods for testing whether a given set of domain boundaries constrained pattern formation within those domains. We then confirm such a prediction by analysing the development of subbarrel patterns, which are thought to emerge via reaction-diffusion, and whose enclosing borders form a Voronoi tessellation on the surface of the rodent somatosensory cortex. In more general terms, this result demonstrates how causal links can be established between the dynamical processes through which biological patterns emerge and the constraints that shape them.

developmental biology↗

bioRxiv2022

Differential expression of Nanog 3UTR and coding region mRNA components defines an embryonic stem cell niche

Differential expression of mRNA coding sequences (CDSs) and 3untranslated regions (UTRs) is widespread, yet whether these domains contribute independently to cellular function remains unclear. Here, using Nanog as a model, we find that Nanog mRNA domain usage is spatially organized in mouse and human pluripotent cells and in the blastocyst, with cells enriched in 3UTR transcripts marking colony borders and cells enriched for the Nanog CDS located interior. Functional perturbation reveals a marked asymmetry between mRNA domains. Loss of the Nanog 3UTR leads to defects in colony architecture, cell spreading and morphogenetic behavior, accompanied by decreased extracellular matrix modeling gene expression and ROCK dependent cytoskeletal organization. In contrast, deletion of the Nanog CDS primarily disrupts epithelial polarity-associated transcriptional programs and the expression of chromatin regulators, consistent with a dominant role for the Nanog protein in transcriptional and epigenetic control. These domain specific effects are not redundant but instead reflect separable regulatory activities encoded within a single transcript. Together, these findings demonstrate that distinct regions of a single mRNA can encode separable and asymmetric biological functions, revealing mRNA domain usage as a distinct regulatory layer through which genes can encode multiple biological outputs beyond protein coding capacity.

developmental biology↗

bioRxiv2023

Growth enhances colors, shapes and biological functions of Turing color patterns of Eucaryotes

Evidenced in zebrafishes skin and Mimulus petal, Turing-like mechanisms are suspected to be responsible for many periodic colour patterns of Eukaryotes. They are characterised by the mathematical relationships linking their cellular or molecular actors, the periodicity and the geometrical range of the patterns they produce: spots, stripes or mazes. Nevertheless, some periodic patterns such as leopard iconic rosettes required additional ingredients to explain their formation. Growth being the main candidate, we extensively explore its multiple facets, at the Eukaryotes scale. We show that far beyond the particular feline coat pattern, putative-growth Turing colour patterns are present in many diverse lineages of plants and animals and seem absent in Fungi and unicellular lineages. Using models, we show the many ways growth can induce new shapes and colours, and that putative-growth pattern locations correlates with tissue hot spots of growth, suggesting the latter as the underlying mechanism. By reverse reasoning, we show that growth effects could reveal crucial information about pattern formation. We show how putative growth patterns can contribute to influence organisms visibility, thereby improving camouflage or aposematism. Our results demonstrate the range of morphogenetic roles that tissue expansion can take, by interacting with a scale-sensitive mechanism, here Turing-like patterning. Considering this extensive overview of its biological importance, both qualitatively and quantitatively, links between growth and form might more than ever needed to be explored.

developmental biology↗

bioRxiv2023

Dynamical states of self-organized waves in a giant single-celled organism feeding on light

A hallmark of self-organisation in living systems is their capacity to stabilise their own dynamics, often appearing to anticipate and act upon potential outcomes. Caulerpa brachypus is a marine green alga consisting of differentiated organs resembling leaves, stems and roots. While an individual can exceed a metre in size, it is a single multinucleated giant cell. Thus Caulerpa presents the mystery of morphogenesis on macroscopic scales in the absence of cellularization. The experiments reported here reveal self-organised waves of greenness -- chloroplasts -- that propagate throughout the alga in anticipation of the day-night light cycle. Using dynamical systems analysis we show that these waves are coupled to a self-sustained oscillator, and demonstrate their entrainment to light. Under constant conditions light intensity affects the natural period and drives transition to temporal disorder. Moreover, we find distinct morphologies depending on light temporal patterns, suggesting waves of chlorophyll could link biological oscillators to metabolism and morphogenesis in this giant single-celled organism.

developmental biology↗

bioRxiv2026

Multipolar spindle assembly and mitotic slippage underlie symbiont-mediated asexual reproduction

Maternally inherited bacteria can profoundly impact animal biology. A notable example is the induction of thelytokous parthenogenesis: the asexual production of female offspring. Despite decades of symbiont-mediated parthenogenesis documented across diverse arthropods, the underlying cell biological mechanisms remain poorly understood. In some species of parasitic wasps, Wolbachia causes a chromosome segregation failure during the first mitotic division in unfertilized haploid embryos. This diplodizes the embryo and facilitates asexual reproduction of females. To elucidate the mechanism of mitotic failure and understand how the animal continues development, we compared meiosis and early embryonic mitoses of the parasitoid wasp, Trichogramma pretiosum, with and without their parthenogenesis-inducing Wolbachia symbiont. We show that meiosis in these animals is anastral, and embryos undergo de novo microtubule organizing center (MTOC) biogenesis prior to the first embryonic mitosis, regardless of Wolbachia. During the first mitosis, embryos with Wolbachia had increased numbers of MTOCs associated with the oocyte nucleus and formed multipolar spindles in a modified metaphase, after which chromosome segregation failed. A restitution nucleus formed, and mitotic slippage enabled the diploid nucleus to transition to interphase and replicate. Subsequent mitotic divisions inherited supernumerary MTOCs, but formed pseudo-bipolar spindles and segregated normally. These results demonstrate that Wolbachia-mediated parthenogenesis stems from altered MTOC biology, provide a structural basis for mitotic failure and the subsequent restitution. Symbiont-mediated parthenogenesis offers unique opportunities to uncover the cell biology of asexual reproduction and a fascinating model for understanding mitosis more broadly.

Developmental Biology↗

bioRxiv2020

Lineage recording of zebrafish embryogenesis reveals historical and ongoing lineage commitments

It has been challenging to characterize the lineage relationships among cells in vertebrates, which comprise a great number of cells. Fortunately, recent progress has been made by combining the CRISPR barcoding system with single-cell sequencing technologies to provide an unprecedented opportunity to track lineage at single-cell resolution. However, due to errors and/or dropouts introduced by amplification and sequencing, reconstruction of accurate lineage relationships in complex organisms remains a challenge. Thus, improvements in both experimental design and computational analysis are necessary for lineage inference. In this study, we employed single-cell Lineage tracing On Endogenous Scarring Sites (scLOESS), a lineage recording strategy based on the CRISPR-Cas9 system, to trace cell fate commitments for zebrafish larvae. With rigorous quality control, we demonstrated that lineage commitments of complex organisms could be inferred from a limited number of barcoding sites. Together with cell-type characterization, our method could homogenously recover lineage information. In combination with the cell-type and lineage information, we depicted the development histories for germ layers as well as cell types. Furthermore, when combined with trajectory analysis, our methods could capture and resolve the ongoing lineage commitment events to gain further biological insights into later development and differentiation in complex organisms.

developmental biology↗

bioRxiv2020

Epigenetic mechanisms mediating cell state transitions in chondrocytes.

Epigenetic modifications play critical roles in regulating cell lineage differentiation, but the epigenetic mechanisms guiding specific differentiation steps within a cell lineage have rarely been investigated. To decipher such mechanisms, we used the defined transition from proliferating (PC) into hypertrophic chondrocytes (HC) during endochondral ossification as a model. We established a map of activating and repressive histone modifications for each cell type. ChromHMM state transition analysis and Pareto-based integration of differential levels of mRNA and epigenetic marks revealed that differentiation associated gene repression is initiated by the addition of H3K27me3 to promoters still carrying substantial levels of activating marks. Moreover, the integrative analysis identified genes specifically expressed in cells undergoing the transition into hypertrophy. Investigation of enhancer profiles detected surprising differences in enhancer number, location, and transcription factor binding sites between the two closely related cell types. Furthermore, cell type-specific upregulation of gene expression was associated with a shift from low to high H3K27ac decoration. Pathway analysis identified PC-specific enhancers associated with chondrogenic genes, while HC-specific enhancers mainly control metabolic pathways linking epigenetic signature to biological functions.

developmental biology↗

bioRxiv2023

Endothelial Cell SMAD6 Balances ACVRL1/Alk1 Function to Regulate Adherens Junctions and Hepatic Vascular Development

BMP signaling is critical to blood vessel formation and function, but how pathway components regulate vascular development is not well-understood. Here we find that inhibitory SMAD6 functions in endothelial cells to negatively regulate ALK1/ACVRL1-mediated responses, and it is required to prevent vessel dysmorphogenesis and hemorrhage in the embryonic liver vasculature. Reduced Alk1 gene dosage rescued embryonic hepatic hemorrhage and microvascular capillarization induced by Smad6 deletion in endothelial cells in vivo. At the cellular level, co-depletion of Smad6 and Alk1 rescued the destabilized junctions and impaired barrier function of endothelial cells depleted for SMAD6 alone. At the mechanistic level, blockade of actomyosin contractility or increased PI3K signaling rescued endothelial junction defects induced by SMAD6 loss. Thus, SMAD6 normally modulates ALK1 function in endothelial cells to regulate PI3K signaling and contractility, and SMAD6 loss increases signaling through ALK1 that disrupts endothelial junctions. ALK1 loss-of-function also disrupts vascular development and function, indicating that balanced ALK1 signaling is crucial for proper vascular development and identifying ALK1 as a "Goldilocks" pathway in vascular biology regulated by SMAD6.

developmental biology↗

bioRxiv2024

3D Reconstruction of Neuronal Allometry and Neuromuscular Projections in Asexual Planarians Using Expansion Tiling Light Sheet Microscopy

The intricate coordination of the neural network in planarian growth and regeneration has remained largely unrevealed, partly due to the challenges of imaging the central nervous system (CNS) in three dimensions (3D) with high resolution and within a reasonable timeframe. To address this gap in systematic imaging of the CNS in planarians, we adopted high-resolution, nanoscale imaging by combining tissue expansion and tiling light-sheet microscopy, achieving up to 4-fold linear expansion. Using an automatic 3D cell segmentation pipeline, we quantitatively profiled neurons and muscle fibers at the single-cell level in over 400 wild-type planarians during homeostasis and regeneration. We validated previous observations of neuronal cell number changes and muscle fiber distribution. We found that the increase in neuron cell number tends to lag behind the rapid expansion of somatic cells during the later phase of homeostasis. By imaging the planarian with up to 120 nm resolution, we also observed distinct muscle distribution patterns at the anterior and posterior poles. Furthermore, we investigated the effects of {beta}-catenin RNAi on muscle fiber distribution at the posterior pole, consistent with changes in anterior-posterior polarity. The glial cells were observed to be close in contact with dorsal-ventral muscle fibers. Finally, we observed disruptions in neural-muscular networks in inr-1 RNAi planarians. These findings provide insights into the detailed structure and potential functions of the neural-muscular system in planarians and highlight the accessibility of our imaging tool in unraveling the biological functions underlying their diverse phenotypes and behaviors.

developmental biology↗

bioRxiv2026

Fat1 deletion enhances Fibro-Adipogenic Differentiation and Adipogenic expansion following injury in skeletal muscle

Skeletal muscles regenerate following injury, owing not only to myogenic stem cells, but also to non-myogenic cells such as fibro-adipogenic progenitors (FAPs). Quiescent in healthy muscles, FAPs transiently proliferate in response to tissue-damage, to support myogenic repair. Aside from their pro-myogenic role in healthy muscles, FAPs are also the origin of intramuscular fibro-adipose tissue that infiltrate muscles with chronic inflammation and degeneration in various muscle pathologies. Here, we investigate how the Fat1 Cadherin, previously identified as a regulator of embryonic muscle morphogenesis, influences FAP biology during damage-induced muscle regeneration. Fat1 expression is transiently induced in FAPs and myogenic cells after muscle damage. We found that mesenchyme-specific Fat1 ablation leads to increased fibro-adipogenic infiltrations following glycerol injury, while minimally affecting myogenic repair. Using an inducible Pdgfra-cre/ERT line, we further demonstrated that Fat1 restricts FAP adipogenic differentiation through both cell-autonomous and non-cell-autonomous mechanisms. These findings identify Fat1 as a novel regulator of FAP biology, essential for limiting FAP differentiation and the development of fibro-fatty infiltrations after muscle injury.

developmental biology↗

bioRxiv2021

Epigenetic clocks reveal a rejuvenation event during embryogenesis followed by aging

The notion that germline cells do not age goes back to the 19th century ideas of August Weismann. However, being in a metabolically active state, they accumulate damage and other age-related changes over time, i.e., they age. For new life to begin in the same young state, they must be rejuvenated in the offspring. Here, we developed a new multi-tissue epigenetic clock and applied it, together with other aging clocks, to track changes in biological age during mouse and human prenatal development. This analysis revealed a significant decrease in biological age, i.e. rejuvenation, during early stages of embryogenesis, followed by an increase in later stages. We further found that pluripotent stem cells do not age even after extensive passaging and that the examined epigenetic age dynamics is conserved across species. Overall, this study uncovers a natural rejuvenation event during embryogenesis and suggests that the minimal biological age (the ground zero) marks the beginning of organismal aging.

developmental biology↗

bioRxiv2024

Dynamical systems theory informed learning of cellular differentiation landscapes

AO_SCPLOWBSTRACTC_SCPLOWSuccessful development from a single cell to a complex, multicellular organism requires that cells differentiate in a coordinated and organized manner in response to a number of chemical morphogens. While the molecular underpinnings may be complex, the resulting phenomenon, in which a cell decides between one fate or another, is relatively simple. A body of work--rooted in dynamical systems theory--has formalized this notion of cellular decision making as flow in a Waddington-like landscape, in which cells evolve according to gradient-like dynamics within a potential that changes shape in response to a number of signals. We present a framework leveraging neural networks as universal function approximators to infer such a parameterized landscape from gene expression data. Inspired by the success of physics-informed machine learning in data-limited contexts, we enforce principled constraints motivated not by physical laws, but by this phenomenological understanding of differentiation. Our data-driven approach infers a governing landscape atop a manifold situated within expression space, thereby describing the dynamics of interest in a biologically meaningful context. The resulting system provides an intuitive, visualizable, and interpretable model of cellular differentiation dynamics.

developmental biology↗