Biology subjects

Davidson, L. A.

Publications and source records attributed to Davidson, L. A..

8 recordsLinked to original sources

bioRxiv2025

Supracellular contractility in Xenopus laevis embryonic epithelia regulated by extracellular nucleotides and the purinergic G-protein coupled receptor P2Y2.

Extracellular signals regulate epithelial homeostasis, cell fate and pattern cell behaviors during embryogenesis, wound healing, regeneration, and disease progression. Previous studies in our group found cell lysate from intentionally wounded embryos triggers a strong but transient contraction in neighboring epithelia, whether contiguous to the wound site or in non-wounded embryos. We previously identified extracellular ATP (eATP) as a possible candidate. Here we test additional candidates and find several nucleotides including ADP, UTP, and UDP also trigger contractility. Through a temporal and spatial screen of lysate activity, an inhibitor screen, and morpholino knock-down of candidate receptors, we find contractility is mediated by a G-protein coupled purinergic receptor P2Y2 (P2RY2). Activated P2RY2 triggers F-actin assembly and myosin II contractility. Knockdown of P2RY2 or overexpression of mutant G-protein effectors abrogate epithelial contractility when epithelia are exposed to eATP or lysate. We demonstrate that the major contributors to epithelial contractility in lysate are extracellular nucleotide triphosphates ATP and UTP, which are sensed by P2RY2 and transduced through G-proteins to contract the epithelium. Summary StatementContractility of the Xenopus embryonic epithelium can be driven by extracellular nucleotides ATP or UTP and actuated by the G-protein coupled purinergic receptor P2Y2 (P2RY2). HighlightsO_LIExtracellular nucleotides ATP and UTP can trigger epithelial contractility. C_LIO_LIEpithelia contract in response to (ATP [~] UTP) > (ADP [~] UDP) > ADO (adenosine). C_LIO_LIThe purinergic G-protein coupled receptor P2Y2 is responsible for this contractile response by indirectly modulating actomyosin contractility. C_LI

cell biology↗

bioRxiv2024

The TissueTractor, a device for applying large strains to tissues and cells for simultaneous high-resolution live cell microscopy.

Mechanical strain substantially influences tissue shape and function in various contexts, from embryonic development to disease progression. Disruptions in these processes can result in congenital abnormalities and short-circuit mechanotransduction pathways. Manipulating strain in live tissues is crucial for understanding its impact on cellular and subcellular activities. Existing tools, such as optogenetic modulation of strain, are limited to small strain over limited distance and durations. Here, we introduce a high-strain stretcher system, the TissueTractor, designed for high-resolution spatiotemporal imaging of live tissues, enabling strain application varying from 0% to over 150%. This system is needed to unravel the intricate connections between mechanical forces and developmental processes. We demonstrated the stretcher with Xenopus laevis organotypic explants, human umbilical endothelial cells, and mouse neonatal cardiomyocytes to highlight the stretchers adaptability. These demonstrations underscore the potential of this stretcher to deepen our understanding of the mechanical cues governing tissue dynamics and morphogenesis. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=170 SRC="FIGDIR/small/600827v3_ufig1.gif" ALT="Figure 1"> View larger version (46K): org.highwire.dtl.DTLVardef@207163org.highwire.dtl.DTLVardef@1f424e7org.highwire.dtl.DTLVardef@1a2e9e1org.highwire.dtl.DTLVardef@a8d785_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2022

Myosin-dependent partitioning of junctional Prickle2 toward the anterior vertex during planar polarization of Xenopus neuroectoderm

Planar cell polarity (PCP) of tissues is established by mutually exclusive partitioning of transmembrane proteins Frizzled and Vangl with their respective binding partners, Dishevelled and Prickle. While the amplification and maintenance of this pattern have been well studied, it remains unclear how the anterior-biased protein localization is initiated. Moreover, PCP protein complexes are located at adherens junctions and their polarization requires the activity of non-muscle myosin II (NMII), but how NMII contributes to PCP is not fully understood. Here we analyze time-lapse images of mNeonGreen-tagged Prickle2 (Pk2) in mid-gastrula stage Xenopus presumptive neuroectoderm and demonstrate that Pk2 puncta move along bicellular apical junctions in a biased manner toward the anterior vertex, where the Vangl-Pk complexes are normally enriched. In addition, length changes of bicellular junction segments flanking each Pk2 punctum are often different from each other, and appear more dynamic near the vertices, suggesting that Pk2 movement is driven by intrinsic junction heterogeneity. Reducing NMII activity eliminates the anterior movement, and surprisingly, increases the displacement of Pk2 puncta. By assessing the correlation between Pk2 movement and the relative positioning of each Pk2 punctum along apical junctions, we uncovered that NMII activity is required for the anterior Pk2 movement by maintaining the elongation of posterior junction segment while inhibiting Pk2 movement toward both vertices flanking the junctions. Importantly, we found that the tight junction protein ZO-1 partitions alongside Pk2. Our findings provide the first evidence of biased partitioning of junctional PCP proteins toward the anterior vertex and support the hypothesis that NMII activity facilitates Pk2 polarization not via a direct transport but by regulating intrinsic dynamics of the bicellular junction.

cell biology↗

bioRxiv2021

scTenifoldKnk: a machine learning workflow performing virtual knockout experiments on single-cell gene regulatory networks

Bigger PictureO_LIGene knockout (KO) experiments, using genetically altered animals, are a proven powerful approach to elucidate the role of a gene in a biological process. However, systematic KO experiments targeting many genes are usually prohibitive due to limited experimental and animal resources. Here, we present scTenifoldKnk, an efficient virtual KO tool that allows the systematic deletion of many genes individually. scTenifoldKnk uses single-cell RNA sequencing (scRNAseq) data from wild-type (WT) samples to predict gene function in a cell type-specific manner. We show that predictions made by scTenifoldKnk recapitulate findings from real-animal KO experiments. scTenifoldKnk has proven to be a powerful and effective approach for elucidating gene function, prioritizing KO targets, predicting experimental outcomes before real-animal KO experiments are conducted. C_LI HighlightsO_LIscTenifoldKnk performs virtual KO experiments using scRNAseq data. C_LIO_LIscTenifoldKnk only requires data from WT samples; no data is needed from KO samples. C_LIO_LIPredictions made by scTenifoldKnk recapitulate findings from real-animal KO experiments. C_LI Data Science Maturity Level O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=14 SRC="FIGDIR/small/436484v2_ufig1.gif" ALT="Figure 1"> View larger version (8K): org.highwire.dtl.DTLVardef@157126aorg.highwire.dtl.DTLVardef@17a2e76org.highwire.dtl.DTLVardef@805c4dorg.highwire.dtl.DTLVardef@12bdc1b_HPS_FORMAT_FIGEXP M_FIG C_FIG eTOC blurbscTenifoldKnk is a machine learning workflow performing virtual KO experiments to predict gene function. It constructs gene regulatory networks using single-cell RNA sequencing data from wild-type samples and then computationally deletes target genes. Real-data applications demonstrate that scTenifoldKnk recapitulates findings of real-animal KO experiments and accurately predicts gene function in analyzed cells. SummaryGene knockout (KO) experiments are a proven, powerful approach for studying gene function. However, systematic KO experiments targeting a large number of genes are usually prohibitive due to the limit of experimental and animal resources. Here, we present scTenifoldKnk, an efficient virtual KO tool that enables systematic KO investigation of gene function using data from single-cell RNA sequencing (scRNAseq). In scTenifoldKnk analysis, a gene regulatory network (GRN) is first constructed from scRNAseq data of wild-type samples, and a target gene is then virtually deleted from the constructed GRN. Manifold alignment is used to align the resulting reduced GRN to the original GRN to identify differentially regulated genes, which are used to infer target gene functions in analyzed cells. We demonstrate that the scTenifoldKnk-based virtual KO analysis recapitulates the main findings of real-animal KO experiments and recovers the expected functions of genes in relevant cell types.

bioinformatics↗

bioRxiv2020

Furry is required for cell movements during gastrulation and functionally interacts with NDR1

Gastrulation is a key event in animal embryogenesis during which the germ layers precursors are rearranged and the embryonic axes are established. Cell polarization is essential during gastrulation driving asymmetric cell division, cell movements and cell shape changes. Furry (Fry) gene encodes an evolutionarily conserved protein with a wide variety of cellular functions mostly related to cell polarization and morphogenesis in invertebrates. However, little is known about its function in vertebrate development. Here we show that in Xenopus, Fry participates in the regulation of morphogenetic processes during gastrulation. Using morpholino knock-down, we demonstrate a role of Fry in blastopore closure and dorsal axis elongation. Loss of Fry function drastically affects the movement and morphological polarization of cells during gastrulation, in addition to dorsal mesoderm convergent extension, responsible for head-to-tail elongation. Finally, we demonstrate a functional interaction between Fry and NDR1 kinase, providing evidence of an evolutionarily conserved complex required for morphogenesis.

developmental biology↗

bioRxiv2019

Non-junctional Cadherin3 regulates cell migration and contact inhibition of locomotion via domain-dependent opposing regulations of Rac1.

Classical cadherins are well-known primary adhesion molecules responsible for physically connecting neighboring cells and signaling the cell-cell contact. Recent studies have suggested novel signaling roles for \"non-junctional\" cadherins (Niessen and Gottardi, 2008; Padmanabhan et al., 2017); however, the function of cadherin signaling independent of cell-cell contacts remains unknown. In this study, we used mesendoderm cells and tissues from gastrula stage Xenopus laevis embryos to demonstrate that extracellular and cytoplasmic cadherin domains regulate Rac1 in opposing directions in the absence of cell-cell contacts. Furthermore, we found that non-junctional cadherins regulate contact inhibition of locomotion (CIL) during gastrulation through alterations in the stability of the cytoskeleton. Live FRET imaging of Rac1 activity illustrated how non-junction cadherin3 (formerly C-cadherin) spatio-temporally regulates CIL. Our study provides novel insights into adhesion-independent signaling by cadherin3 and its role in regulating single and collective cell migration in vivo.

developmental biology↗

bioRxiv2019

Tissue mechanics drives epithelialization, goblet cell regeneration, and restoration of a mucociliated epidermis on the surface of embryonic aggregates.

Injury, surgery, and disease often disrupt tissues and it is the process of regeneration that aids the restoration of architecture and function. Regeneration can occur through multiple strategies including induction of stem cell expansion, transdifferentiation, or proliferation of differentiated cells. We have uncovered a case of regeneration that restores a mucociliated epithelium from mesenchymal cells. Following disruption of embryonic tissue architecture and assembly of a compact mesenchymal aggregate, regeneration first involves restoration of an epithelium, transitioning from mesenchymal cells at the surface of the aggregate. Cells establish apico-basal polarity within 5 hours and a mucociliated epithelium within 24. Regeneration coincides with nuclear translocation of the putative mechanotransducer YAP1 and a sharp increase in aggregate stiffness, and regeneration can be controlled by altering stiffness. We propose that regeneration of a mucociliated epithelium occurs in response to biophysical cues sensed by newly exposed cells on the surface of a disrupted mesenchymal tissue.

developmental biology↗

bioRxiv2018

Using a continuum model to decipher the mechanics of embryonic tissue spreading from time-lapse image sequences: An approximate Bayesian computation approach

Advanced imaging techniques generate large datasets capable of describing the structure and kinematics of tissue spreading in embryonic development, wound healing, and the progression of many diseases. These datasets can be integrated with mathematical models to infer biomechanical properties of the system, typically identifying an optimal set of parameters for an individual experiment. However, these methods offer little information on the robustness of the fit and are generally ill-suited for statistical tests of multiple experiments. To overcome this limitation and enable efficient use of large datasets in a rigorous experimental design, we use the approximate Bayesian computation rejection algorithm to construct probability density distributions that estimate model parameters for a defined theoretical model and set of experimental data. Here, we demonstrate this method with a 2D Eulerian continuum mechanical model of spreading embryonic tissue. The model is tightly integrated with quantitative image analysis of different sized embryonic tissue explants spreading on extracellular matrix (ECM) and is regulated by a small set of parameters including forces on the free edge, tissue stiffness, strength of cell-ECM adhesions, and active cell shape changes. We find statistically significant trends in key parameters that vary with initial size of the explant, e.g., for larger explants cell-ECM adhesion forces are weaker and free edge forces are stronger. Furthermore, we demonstrate that estimated parameters for one explant can be used to predict the behavior of other similarly sized explants. These predictive methods can be used to guide further experiments to better understand how collective cell migration is regulated during development.\n\nAuthor SummaryNew imaging tools and automated microscopes are able to produce terabytes of detailed images of protein activity and cell movements as tissues change shape and grow. Yet, efforts to infer useful quantitative information from these large datasets have been limited by the inability to integrate image analysis and computational models with rigorous statistical methods. In this paper, we describe a robust methodology for inferring mechanical processes that drive tissue spreading in embryonic development. Tissue spreading is critical during wound healing and the progression of many diseases including cancer. Direct measurement of biomechanical properties during spreading is not possible in many cases, but can be inferred through mathematical and statistical means. This approach identifies model parameters that are able to robustly predict results of new experiments. These methods can be integrated with more general studies of morphogenesis and to guide further experiments to better understand how tissue spreading is regulated during development and potentially control spreading during wound healing and cancer.

biophysics↗