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bioRxiv2025

A Porcine Model of Intervertebral Disc Injury Recapitulates Human Discogenic Pain via Notochordal Cell Loss and Pain-inducing Nucleus Pulposus Cell Emergence

Lower back pain (LBP) is one of the most common causes of disability, with up to 40% of LBP cases attributed to intervertebral disc (IVD) degeneration. While small animal models are widely used to study IVD and LBP, the small size of their IVDs limits translational and biological relevance. Large animal models more accurately emulate human disease; however, methods of measuring LBP are not well established. Pigs were also considered unfit for LBP research, due to notochordal cells (NCs) persistence through life, unlike humans. We developed a comprehensive porcine model with quantitative measure of discogenic pain via biobehavioral testing (BBT), MRI, and multi-omics tissue analysis of IVD and DRGs. MRI demonstrated the progression of IVD degeneration beginning at 4 weeks post-injury. BBTs showed the development of significant pain responses by week 4 post-injury, supported by transcriptomics of injury matched DRGs. Single cell transcriptomics, trajectory and cell-cell communication analyses suggest that, with injury, NCs are differentiating to nucleus pulposus cells (NPCs). Furthermore, NPCs showed upregulation of cellular stress, neural outgrowth, and inflammation pathway, consistent with pain-inducing distress signals found in human samples. This study establishes novel MRI and BBT-based methods for quantifying LBP in pigs and supports its translational relevance to human discogenic LBP. The identification of LBP-associated clusters mirrors our previous finding in humans. Moreover, the shift of NC to NPC phenotype further supports that the porcine model is relevant to human pathology, as the injury induced accelerated aging and loss of NCs with IVD degeneration and discogenic pain.

developmental biology↗

bioRxiv2025

Loss of MITF activity leads to emergent cell states from the melanocyte stem cell lineage

How embryonic cells generate large clones of cells in the adult represents a fundamental question in biology. Here using melanocyte stem cells (McSCs) in the zebrafish as a model we explore the function of the master melanocyte transcription factor (MITF) in safeguarding McSCs in embryonic development and their potential to pigment large clones in the adult. MITF is well known is for its role in the specification of melanoblasts from the neural crest (NC) and their differentiation into melanocytes, yet little is known about how this activity shapes the stem cell lineages. Here, we use live imaging coupled with single-cell transcriptomics and lineage tracing to show that MITF (mitfa in zebrafish) protects the melanocyte stem cell (McSC) fate in zebrafish. Utilizing a temperature sensitive mitfavc7 mutant, we show that loss of Mitfa activity leads to a surprising premature and aberrant expansion of McSC progeny at the niche during embryogenesis, coupled with novel emergent transcriptional cell states. Linage tracing of McSCs from the embryonic to juvenile stages reveals Mitfa activity is subsequently required in regeneration by Schwann cell-like and melanocyte stem cell progenitors that serve as a reservoir for fast-responding pigment progenitors. Thus, the impact of Mitfa loss on the melanocyte lineage is cell-state and stage-specific. The emergent cell states resulting from mitfa loss may have important implications for understanding how reduced MITF activity contributes to human genetic disease and melanoma.

developmental biology↗

bioRxiv2026

Comparison of immunohistochemistry methods in embryonic chicken corneal tissue

Immunohistochemistry (IHC) is widely used to assess protein expression in corneal tissue, yet staining outcomes are strongly influenced by tissue preparation methods and regional differences within the cornea. This study aimed to systematically compare three processing techniques including paraffin (wax) embedding, wax embedding with antigen retrieval (wax AR), and cryosectioning for IHC analysis in embryonic day 18 chicken corneal tissue. Markers representing key biological functions were evaluated, including progenitor activity (PAX6, P40), tissue architecture (actin), and immune surveillance (TAP1, CD68), across central and limbal regions. Cryosectioning consistently produced the most specific staining for nuclear and antigen-sensitive markers. PAX6 and P40 exhibited strong, nuclear-localized expression in the corneal epithelium only under cryo conditions, whereas wax-based methods resulted in reduced specificity and irregular signal distribution. TAP1-positive immune cells were detectable in the limbal stroma exclusively in cryosections, highlighting improved antigen preservation. In contrast, actin staining, was best preserved with wax AR, and provided superior structural clarity and expected expression patterns across corneal layers. CD68 showed minimal or inconsistent staining in corneal tissue across all methods despite positive control validation. These findings demonstrate that optimal IHC outcomes in corneal tissue are marker-dependent and influenced by preparation methods and regional tissue context. Cryosectioning is recommended for detecting nuclear and immune-related antigens, while wax AR is preferable for preserving tissue architecture. This study provides a practical framework for improving reproducibility and interpretation of corneal immunostaining in avian models. HighlightsO_LICryosectioning preserves nuclear and immunity antigens in cornea C_LIO_LIWax AR improves structural markers such as actin in corneal tissue C_LIO_LIStaining outcomes depend on marker and tissue preparation method C_LIO_LICryosectioning enables detection of limbal immune-associated cells (TAP1) C_LIO_LICD68 shows limited corneal expression despite positive control staining C_LI

developmental biology↗

bioRxiv2024

Engineering an fgfr4 knockout zebrafish to study its role in development and disease

Fibroblast growth factor receptor 4 (FGFR4) has a role in many biological processes, including lipid metabolism, tissue repair, and vertebrate development. In recent years, FGFR4 overexpression and activating mutations have been associated with numerous adult and pediatric cancers. As such, FGFR4 presents an opportunity for therapeutic targeting which is being pursued in clinical trials. To understand the role of FGFR4 signaling in disease and development, we generated and characterized three alleles of fgfr4 knockout zebrafish strains using CRISPR/Cas9. To generate fgfr4 knockout crispants, we injected single-cell wildtype zebrafish embryos with fgfr4 targeting guide RNA and Cas9 proteins, identified adult founders, and outcrossed to wildtype zebrafish to create an F1 generation. The generated mutations introduce a stop codon within the second Ig-like domain of Fgfr4, resulting in a truncated 215, 223, or 228 amino acid Fgfr4 protein compared to 922 amino acids in the full-length protein. All mutant strains exhibited significantly decreased fgfr4 mRNA expression during development, providing evidence for successful knockout of fgfr4 in mutant zebrafish. We found that, consistent with other Fgfr4 knockout animal models, the fgfr4 mutant fish developed normally; however, homozygous fgfr4 mutant zebrafish were significantly smaller than wildtype fish at three months post fertilization. These fgfr4 knockout zebrafish lines are a valuable tool to study the role of FGFR4 in vertebrate development and its viability as a potential therapeutic target in pediatric and adult cancers, as well as other diseases.

developmental biology↗

bioRxiv2025

Self-Organizing Assembloids Reveal Enteric Nervous System Dynamics in Gut Homeostasis and Regeneration

The enteric nervous system (ENS) is essential for intestinal health, exhibiting adaptability to environmental and physiological challenges. However, the mechanisms underlying ENS plasticity and resilience remain poorly understood. Organoid technology has revolutionized in vitro modeling by accurately replicating epithelial structures and enabling significant advancements in understanding gastrointestinal biology. However, traditional organoids are limited in their ability to study the ENS, as they lack the multicellular composition and functional architecture necessary to model complex interactions between neurons, glia, mesenchymal, smooth muscle, and epithelial cells. To address these limitations, we developed murine ENS-Rich Assembloids (ERAs) that self-organize to replicate the cellular diversity, including the epithelial structure, and functional architecture of native colonic tissue. These assembloids recreate neuron-glia interactions, reflect regenerative processes, and provide a novel platform for studying ENS dynamics under controlled conditions. Integrating findings from assembloids and an in vivo murine model, we demonstrate that inflammation induces coordinated reorganization of S100b+ glial cells, TUJ1+ neurons, PDGFRA+ mesenchymal cells, and epithelial cells, revealing conserved mechanisms of ENS plasticity. We identify pleiotrophin (PTN) signaling via Protein Tyrosine Phosphatase Receptor Type Z1 (PTPRZ1) as a key pathway facilitating neural elongation and enhancing neuron-glia interactions. Moreover, we show that activated neurons transfer lipids to glial cells, revealing a novel support mechanism during inflammation. These findings position enteric glia as protective hubs for neurons, fostering ENS adaptability and tissue regeneration. By building on the foundational success of organoid technology and addressing its limitations for studying the ENS, ENS-rich assembloids establish a transformative tool for investigating ENS responses in health, disease, and tissue repair.

developmental biology↗

bioRxiv2018

Drosophila anion exchanger 2 is required for proper ovary development and oogenesis

Understanding how cell fate decisions are regulated is a central question in stem cell biology. Recent studies have demonstrated that intracellular pH (pHi) dynamics contribute to this process. Indeed, the pHi of cells within a tissue is not simply a consequence of chemical reactions in the cytoplasm and other cellular activity, but is actively maintained at a specific setpoint in each cell type. We found previously that the pHi of cells in the follicle stem cell (FSC) lineage in the Drosophila ovary increases progressively during differentiation from an average of 6.8 in the FSCs, to 7.0 in newly produced daughter cells, to 7.3 in more differentiated cells. Two major regulators of pHi in this lineage are Drosophila sodium-proton exchanger 2 (dNhe2) and a previously uncharacterized gene, CG8177, that is homologous to mammalian anion exchanger 2 (AE2). Based on this homology, we named the gene ae2. Here, we generated null alleles of ae2 and found that homozygous mutant flies are viable but have severe defects in ovary development and adult oogenesis. Specifically, we find that ae2 null flies have smaller ovaries, reduced fertility, and impaired follicle formation. In addition, we find that the follicle formation defect can be suppressed by a decrease in dNhe2 copy number and enhanced by the overexpression of dNhe2, suggesting that this phenotype is due to the dysregulation of pHi. These findings support the emerging idea that pHi dynamics regulate cell fate decisions and our studies provide new genetic tools to investigate the mechanisms by which this occurs.

developmental biology↗

bioRxiv2020

Production of Hyaluronan by the Trophectoderm is a Prerequisite for Mouse Blastocyst Attachment

Embryo implantation requires execution of highly synchronized processes at the feto-maternal interface, initiated by blastocyst attachment to the endometrial epithelium. Hyaluronan is a major ECM component known to regulate adhesion-associated biological processes in various physiological settings. We hypothesized that hyaluronan may facilitate blastocyst attachment. In order to test our hypothesis, we characterized the blastocyst expression of hyaluronan synthesizing and degrading enzymes, as well as the expression of hyaluronan receptors during attachment. The functional impact of hyaluronan was challenged by the use of mouse transgenic blastocysts, in which genes encoding for hyaluronan synthesizing enzymes were deleted using lentiviral incorporation of Cas-9 endonuclease alongside specific short-guide RNAs into the embryonic trophectoderm. Embryos with transgenic trophectoderm were tested for their attachment in vitro, or assessed for implantation in vivo, upon transfer to foster dams. Deletion of the trophectoderm hyaluronan biosynthesis significantly reduced the number of blastocysts attached to human uterine epithelium cells in vitro. Reduced attachment was also observed in vivo, in pregnant mice carrying blastocysts with hyaluronan-depleted trophectoderm. In agreement, trophectoderm expression of osteopontin, was downregulated upon depletion of hyaluronan. MRI measurements revealed a decrease in uterine blood vessels permeability. Uterine expression of VEGF-A, PTGS-2 and uterine osteopontin, which constitute the immediate response to blastocyst attachment was also reduced. Furthermore, impaired implantation, associated with a decrease in hyaluronan synthesis in the mural trophectoderm, obtained upon tamoxifen treatment, has been recovered by LIF administration. These results demonstrate that estrogen-regulated hyaluronan-synthesis in the trophectoderm is indispensable for mouse blastocysts attachment to the uterine epithelium.

developmental biology↗

bioRxiv2026

DDR and TMEM132 genes control progenitor targeting and regenerative assembly of the planarian eye

How progenitors can faithfully self-assemble to build new organs in adulthood is a central unsolved problem in regeneration biology. The planarian eye is a model for uncovering principles of de novo organogenesis during regeneration. In this process, pluripotent adult stem cells specify into ovo+ migratory progenitors which target to the eye field due to Wnt and FGFRL signals produced from bodywall muscle, then differentiate into photoreceptor neurons (PRNs) and pigmented optic cup (OC) cells, followed by organization of these two cell types in an opposing pattern that completes eye organ maturation. We used scRNA-seq to characterize eye progenitor transcriptomes during regeneration, followed by FISH validation, and RNAi screening to identify regulators of eye regeneration. This uncovered a function for the discoidin domain receptor ddr-1 in preventing the premature terminal differentiation of migratory eye progenitors. DDRs encode collagen receptors, and bodywall muscle is the major source of collagen in planarians, suggesting eye progenitors likely interface with muscle ECM for their proper deployment in regeneration. We further identified a novel eye morphogenesis phenotype from knockdown of tmem132-1, causing failed heterotypic adhesion between eye cell types. TMEM132 factors are conserved cell-surface receptors that mediate adhesion and regulate migration, and human TMEM132 mutations are associated with several neurobehavioral diseases. Therefore, planarian tmem132-1 likely directly regulates the capture and assembly of migratory progenitors into mature eyes during regeneration. Together, these results define new steps in the eye regeneration pathway and suggest ancient roles for DDR and TMEM132 in progenitor migration and coordinated organ assembly.

developmental biology↗

bioRxiv2023

SH2 domain protein E (SHE) and ABL signaling regulate blood vessel size

Blood vessels in different vascular beds vary in lumen diameter, which is essential for their function and fluid flow along the vascular network. Molecular mechanisms involved in the formation of a vascular lumen of appropriate size, or tubulogenesis, are still only partially understood. Src homology 2 domain containing E (She) protein was previously identified in a screen for proteins that interact with Abelson (Abl)-kinase. However, its biological role has remained unknown. Here we demonstrate that She and Abl signaling regulate vascular lumen size in zebrafish embryos and human endothelial cell culture. Zebrafish she mutants displayed increased endothelial cell number and enlarged lumen size of the dorsal aorta (DA) and defects in blood flow. Vascular endothelial specific overexpression of she resulted in a reduced diameter of the DA lumen, which correlated with the reduced arterial cell number and lower endothelial cell proliferation. Chemical inhibition of Abl signaling in zebrafish embryos caused a similar reduction in the DA diameter and alleviated the she mutant phenotype, suggesting that She acts as a negative regulator of Abl signaling. Enlargement of the DA lumen in she mutants correlated with an increased endothelial expression of claudin 5a and 5b (cldn5a / cldn5b), which encode proteins enriched in tight junctions. Inhibition of cldn5a expression partially rescued the enlarged DA in she mutants, suggesting that She regulates DA lumen size, in part, by promoting cldn5a expression. SHE knockdown in human endothelial umbilical vein cells resulted in a similar increase in the diameter of vascular tubes, and also increased phosphorylation of a known ABL downstream effector CRKL. These results argue that SHE functions as an evolutionarily conserved inhibitor of ABL signaling and regulates lumen size during vascular tubulogenesis.

developmental biology↗

bioRxiv2025

FishFeats: streamlined quantification of multimodal labeling at the single-cell level in 3D tissues

SummaryCharacterizing the distribution of biological marker expression at the single cell level in whole tissues requires diverse image analysis steps, such as segmentation of cells and nuclei, detection of RNA transcripts (or other staining), or their integration (e.g., assigning nuclei and RNA dots to their corresponding cell). Several software programs or algorithms have been developed for each step independently, but integrating them into a comprehensive pipeline for the quantification of individual cells from 3D imaging samples remains a significant challenge. We developed FishFeats, an open-source and flexible Napari (Sofroniew et al. 2025) plugin, to perform all of these steps together within the same framework, taking advantage of available and efficient software applications. The primary core of our pipeline is to propose a user-friendly tool for users who do not have a computational background. FishFeats streamlines extracting quantitative information from multimodal 3D fluorescent microscopy images (smFISH expression in individual cells, immunohistochemical staining, cell morphologies, cell classification) to a unified "cell-by-cell" table for downstream analysis, without requiring any coding. Our second focus is to propose and ease manual correction of each step, as measurement accuracy can be very sensitive to small errors in the automatic process. Availability and implementationFishFeats is open source under the BSD-3 license, freely available on github: https://github.com/gletort/FishFeats. FishFeats is developed in python, as a Napari plugin for the user interface. Documentation is available in the github pages: https://gletort.github.io/FishFeats/.

developmental biology↗

bioRxiv2022

Patterned apoptosis modulates local growth and tissue shape in a fast-growing epithelium

What regulates organ size and shape remains one of the fundamental mysteries of modern biology. So far, research in this area has primarily focused on deciphering the regulation in time and space of growth and cell division, while the contribution of cell death has been much more neglected. This includes studies of the Drosophila wing imaginal disc, the prospective fly wing which undergoes massive growth during larval stage, and represents one of the best characterised systems for the study of growth and patterning. So far, it has been assumed that cell death was relatively neglectable in this tissue and as a result the pattern of growth was usually attributed to the distribution of cell division. Here, using systematic mapping and registration combined with quantitative assessment of clone size and disappearance, we show for the first time that cell death is not neglectable, and outline a persistent pattern of cell death and clone elimination in the disc. Local variation of cell death is associated with local variation of clone size, pointing to an impact of cell death on local growth which is not fully compensated by proliferation. Using morphometric analyses of adult wing shape and genetic perturbations, we provide evidence that patterned death affects locally and globally adult wing shape and size. This study describes a roadmap for accurate assessment of the contribution of cell death to tissue shape, and outlines for the first time an important instructive role of cell death in modulating quantitatively local growth and the morphogenesis of a fast-growing tissue.

developmental biology↗

bioRxiv2025

Small molecule influence on Caudal fin regeneration in Zebrafish: A proteomic based study

Dietary and addictive small molecules play a significant role in altering in vivo conditions. Due to their minuscule size, these molecules can seamlessly traverse tissues and cellular membranes, influencing key biological processes such as cellular growth, differentiation, and intracellular communication, which are crucial for tissue regeneration. The zebrafish (Danio rerio) serves as an excellent model for studying regenerative growth due to its remarkable ability to regrow amputated appendages. In this study, we systematically evaluated the effect of small molecules, including ethanol (0.5%), glucose (1%), and NaCl (0.2%), on zebrafish caudal fin regeneration over a 7-day period. Regenerative growth analysis indicated delayed fin regrowth across all treated groups, with ethanol exposure showing the most significant impairment. Behavioural assessments revealed significant stress-induced locomotor alterations in treated groups, with the ethanol-exposed group exhibiting the most pronounced reduction in total distance moved and velocity. Proteomic profiling using label-free quantification (LFQ) identified 113, 257, and 178 differentially expressed proteins in ethanol, glucose, and NaCl-treated groups, respectively. Subsequent validation using the iTRAQ labeling approach confirmed 16 commonly dysregulated proteins across all conditions, highlighting a shared molecular response associated with stress and repair mechanisms. Pathway enrichment analysis mapped differentially expressed proteins to various canonical signaling pathways, including GP6 signaling, mitochondrial dysfunction, RHO GTPase cycling, antigen processing, and metabolic regulation. Ingenuity Pathway Analysis (IPA) further revealed associations with disease and function networks specific to each treatment condition. Our findings provide valuable insights into how metabolic and ionic perturbations influence zebrafish fin regeneration at the molecular level, offering a deeper understanding of tissue repair mechanisms under stressed conditions.

developmental biology↗

bioRxiv2021

Differential Expression of α,β, and γ Protocadherin Isoforms During Differentiation, Aging, and Cancer

The cadherin family of cell surface glycoproteins plays a fundamental role in cell-cell recognition, thereby participating in diverse biological process such as embryonic morphogenesis and oncogenic transformation. The subset of clustered protocadherin (PCDH) genes generated from the , {beta}, and {gamma} loci, have been widely studied for their potential role in neuronal cell-cell recognition and neurogenesis, however their broader role in normal embryonic development and cancer has not been examined in detail. We utilized human embryonic stem (hES) cells to model early human development in vitro, comparing PCDH isoform transcription in diverse types of embryonic progenitors with normal adult-derived and cancer counterparts. Embryonic progenitors express genes from the and {beta} cluster at levels comparable to that seen in the CNS, while fetal and adult-derived cells express primarily from the {gamma} cluster. Replicative senescence left fibroblasts with markedly lower expression of all isoforms. We observe that an embryonic pattern of clustered protocadherin gene expression and associated CpG island methylation is commonly associated with cancer cell lines from diverse tissue types. The differential regulation of the , {beta}, and {gamma} loci coincide with alternate regions of DNA accessibility at CTCF binding sites and lamina-associated domains and CPL expression correlated with the expression of LMNA and LMNB1. These observations support a potential role for the differential regulation of genes within the clustered protocadherin locus in selective cell-cell adhesion during embryogenesis, regeneration, cancer and aging.

developmental biology↗

bioRxiv2017

Genome And Epigenome Engineering CRISPR Toolkit For Probing In Vivo cis-Regulatory Interactions In The Chicken Embryo

CRISPR-Cas9 genome engineering has revolutionised all aspects of biological research, with epigenome engineering transforming gene regulation studies. Here, we present a highly efficient toolkit enabling genome and epigenome engineering in the chicken embryo, and demonstrate its utility by probing gene regulatory interactions mediated by neural crest enhancers. First, we optimise efficient guide-RNA expression from novel chick U6-mini-vectors, provide a strategy for rapid somatic gene knockout and establish protocol for evaluation of mutational penetrance by targeted next generation sequencing. We show that CRISPR/Cas9-mediated disruption of transcription factors causes a reduction in their cognate enhancer-driven reporter activity. Next, we assess endogenous enhancer function using both enhancer deletion and nuclease-deficient Cas9 (dCas9) effector fusions to modulate enhancer chromatin landscape, thus providing the first report of epigenome engineering in a developing embryo. Finally, we use the synergistic activation mediator (SAM) system to activate an endogenous target promoter. The novel genome and epigenome engineering toolkit developed here enables manipulation of endogenous gene expression and enhancer activity in chicken embryos, facilitating high-resolution analysis of gene regulatory interactions in vivo.\n\nSummary StatementWe present an optimised toolkit for efficient genome and epigenome engineering using CRISPR in chicken embryos, with a particular focus on probing gene regulatory interactions during neural crest development.\n\nList of AbbreviationsGenome Engineering (GE), Epigenome Engineering (EGE), single guide RNA (sgRNA), Neural Crest (NC), Transcription Factor (TF), Next Generation Sequencing (NGS), somite stage (ss), Hamburger Hamilton (HH).

developmental biology↗

bioRxiv2019

The knockout of the HMG-Domain of the porcine SRY-gene by CRISPR/Cas RNP microinjection causes sex reversal in gene-edited pigs

1The sex-determining region on the Y chromosome (SRY) is thought to be the central genetic element of male sex development. Mutations within the SRY gene are associated with a male-to-female sex reversal syndrome in humans and other mammalian species such as mice and rabbits. However, the underlying mechanisms are largely unknown. To understand the biological function of the SRY gene, a site-directed mutational analysis is required to investigate associated phenotypic changes at the molecular, cellular and morphological level. In our study, we successfully generated a knockout of the porcine SRY gene by microinjection of two clustered regularly interspaced short palindromic repeats (CRISPR) - associated protein - 9 nuclease (Cas9) ribonucleoprotein (RNP) complexes targeting the centrally located "high mobility group" (HMG) domain of the SRY gene. Mutations within this region resulted in the development of complete external and internal female genitalia in genetically male pigs. The internal female genitalia including uteri, ovaries, and oviducts, revealed substantial size differences in 9-months old SRY-knockout pigs compared to age-matched female wild type controls. In contrast, a deletion within the 5 flanking region of the HMG domain was not associated with sex reversal. Results of this study demonstrates for the first time the central role of the HMG domain of the SRY gene in male sex determination in pigs. Moreover, quantitative analysis by digital PCR revealed evidence for a duplication of the porcine SRY locus. Our results pave the way towards the generation of boars exclusively producing phenotypically female offspring to avoid surgical castration without anesthesia in piglets. Moreover, the study establishes a large animal model that is much more similar to humans in regard of physiology and anatomy and pivotal for longitudinal studies.

developmental biology↗

bioRxiv2026

Smad1 and Smad5 differentially transduce BMP signaling during in vitro differentiation of mouse embryonic stem cells into dorsal interneurons

A central unresolved question in development biology is how systems of overwhelming complexity arise from relatively few families of growth factors. Compounding this issue, signaling pathways often show signal convergence, where many ligands interact with fewer receptors, which then signal through a single second messenger complex. Here we investigate this question in the context of bone morphogenetic protein (BMP) signaling and its role directing dorsal spinal cord development, focusing on two receptor-regulated (R) Smads, Smad1 and Smad5. Multiple models have been proposed for their mode of action from acting redundantly through combined signal strength, to having distinct activities that drive different fate outcomes. We sought to distinguish between these models by generating CRISPR-edited Smad1 and Smad5 null mouse embryonic stem cell (ESC) lines to dissect the cell fate of activities of individual R-Smads, with a resolution not possible in vivo. Using a directed differentiation protocol for dorsal interneurons (dI), together with bioinformatic analyses, we have defined the roles of the R-Smads at key decision points along the dI specification timeline. Together, these findings support a model in which Smad1 and Smad5 play largely distinct roles in dorsal spinal cord development. While both R-Smads can activate canonical BMP-responsive transcriptional targets, they asymmetrically contribute to cell fate specification. Smad1 plays a restricted role, while Smad5 has a dominant role, regulating dorsal progenitor transcriptional dynamics and reiteratively directing the dorsal-most dI fates.

developmental biology↗

bioRxiv2023

Cup is essential for oskar mRNA translational repression during early Drosophila oogenesis

The proper timing of mRNA translation is crucial across many biological systems for processes such as intercellular communication, body pattern formation, and morphogenesis. The main D. melanogaster posterior determinant, oskar, is maternally transcribed, but only translated when properly localized at the oocytes posterior cortex. Bruno 1 and Cup are two effector proteins known to participate in multiple aspects of oskar mRNA regulation. Current model describes a mechanism in which Bruno 1 is necessary for Cups recruitment to oskar mRNA, and Bruno 1 is indispensable for its translational repression. Here, we reveal that the Bruno 1-Cup interaction, as well as their interdependent influence on each others mRNA and protein expression, lead to precise oskar mRNA regulation during early oogenesis. We show that these factors stably associate with the oskar mRNA in vivo, but surprisingly, Bruno 1s stable association with oskar mRNA depends on Cup, while Bruno 1 is not necessary for Cup association to oskar mRNA. During early oogenesis, Cup, not Bruno 1, is the essential factor for oskar mRNA repression. Cup is a crucial P-body member that maintains proper P-body morphology during oogenesis, as well as it is necessary for oskar mRNAs association with P-bodies, thus driving the translational repression and stability of oskar mRNA. Our experimental results collectively suggest a regulatory mechanism where a feedback loop between Bruno 1 and Cup coordinates oskar mRNA regulation in the egg chamber allowing for proper development to occur.

developmental biology↗

bioRxiv2023

Turing pattern formation in reaction-cross-diffusion systems with a bilayer geometry

Conditions for self-organisation via Turings mechanism in biological systems represented by reaction-diffusion or reaction-cross-diffusion models have been extensively studied. Nonetheless, the impact of tissue stratification in such systems is under-explored, despite its ubiquity in the context of a thin epithelium overlying connective tissue, for instance the epidermis and underlying dermal mesenchyme of embryonic skin. In particular, each layer can be subject to extensively different biochemical reactions and transport processes, with chemotaxis - a special case of cross- diffusion - often present in the mesenchyme, contrasting the solely molecular transport typically found in the epidermal layer. We study Turing patterning conditions for a class of reaction-cross- diffusion systems in bilayered regions, with a thin upper layer and coupled by a linear transport law. In particular, the role of differential transport through the interface is explored together with the presence of asymmetry between the homogeneous equilibria of the two layers. A linear stability analysis is carried out around a spatially homogeneous equilibrium state in the asymptotic limit of weak and strong coupling strengths, where quantitative approximations of the bifurcation curve can be computed. Our theoretical findings, for an arbitrary number of reacting species, reveal quantitative Turing conditions, highlighting when the coupling mechanism between the layered regions can either trigger patterning or stabilize a homogeneous equilibrium regardless of the inde- pendent patterning state of each layer. We support our theoretical results through direct numerical simulations, and provide an open source code to explore such systems further.

developmental biology↗