Biology subjects

Umulis, D. M.

Publications and source records attributed to Umulis, D. M..

12 recordsLinked to original sources

bioRxiv2025

Stochastic Modeling of BMP Heterodimer-Receptor Interactions Shows Emergence of Low-Pass Filtering Behavior

In developing tissues, signal transduction from morphogen gradients conveys positional information to cells, resulting in cell specification and differentiation. One such morphogen is bone morphogenetic protein (BMP), of the TGF-{beta} superfamily, whose signaling network is highly conserved across many species. In Danio rerio (zebrafish), this signaling pathway directs dorsoventral axis formation during early embryogenesis. Many of the molecules that play a role in this network are well-understood; however, the mechanisms through which they achieve noise attenuation and gradient robustness have not been fully defined. Specifically, the heterodimer-heterotetramer complex has been shown to be required for signal transduction[1], but current understanding and modeling of the BMP membrane receptors at this stage has not given any insight into evolutionary drivers of the requirement. In this study, we develop a stochastic model of receptor oligomerization with the published reports of binding kinetics of BMP ligand-receptor interactions to mechanistically assess zebrafish phenotype variability related to the distributions of noise and stochasticity. We can also analyze time-dependent signaling and frequency metrics that are not available in traditional, deterministic modeling. Fast Fourier Transform and cumulative energy spectral density visualization show that the heterodimer-heterotetramer complex may function as part of a low-pass filter mechanism in the dorsal-ventral axis formation process, specifically tuned to the noise of the system. Under dynamic conditions such as the mid-blastula transition (MBT), wherein the morphogen gradient rapidly changes shape, established metrics of noise and information transduction, such as coefficient of variation and mutual information, overlook important temporal effects that may be particularly relevant during development. As the BMP signaling pathway is highly conserved and has been implicated in human bone growth and wound healing, its study in simpler systems stands to accelerate our comprehension of BMP network structure and molecular mechanisms with potential application in regenerative medical studies.

developmental biology↗

bioRxiv2025

CalciumInsights: An Open-Source, Tissue-Agnostic Graphical Interface for High-Quality Analysis of Calcium Signals

Fluctuations and propagation of cytosolic calcium levels at both the cellular and tissue levels show complex patterns, referred to as calcium signatures, that regulate growth, organ development, damage responses, and survival. The quantitative analysis of calcium signatures at the cellular level is essential for identifying unique patterns that coordinate biological processes. However, a versatile framework applicable to multiple tissue types, allowing researchers to compare, measure, and validate diverse responses and recognize conserved patterns across model organisms, is missing. Here, we present a post-processing tool, CalciumInsights, which leverages the R packages Shiny and Golem. This tool has a graphical user interface and does not require software programming experience to perform calcium signal analysis. The open-source software has a modular framework with standardized functionalities that can be tailored for various research approaches. CalciumInsights provides descriptive statistical analysis through various metrics extracted from dynamic calcium transients and oscillations, such as peak amplitude, area under the curve, frequency, among others. The tool was evaluated with fluorescence imaging data from three model organisms: Danio rerio, Arabidopsis thaliana, and Drosophila melanogaster, demonstrating its ability to analyze diverse biological responses and models. Finally, the open-source nature of CalciumInsights enables community-driven improvements and developments for enabling new applications. Author SummaryThis manuscript introduces CalciumInsights, an open-source tool for calcium signature analysis. Designed to be a versatile tool that works with various tissue types and biological systems, CalciumInsights has an easy-to-use graphical user interface. Our program simplifies metrics extraction while maintaining the quality of the analysis by integrating several algorithms. CalciumInsights stands out for its user-friendliness, ease of use, and robust data exploration features, such as tunable filters for improved accuracy. These features promote inclusivity and lower barriers to scientific research by making calcium signature analysis accessible to users of all programming skill levels.

bioengineering↗

bioRxiv2025

Reactive Oxygen Species Counteract Wound Contraction and Promote Wound Healing

Reactive oxygen species (ROS) are second messengers that drive wound closure. However, the mechanism by which ROS regulate wound contraction to facilitate wound healing remains unclear. Here, we report that ROS counteract wound contraction by inhibiting the phosphorylation of myosin regulatory light chain. Acute ROS inhibition, through pharmacological perturbations, disturbs wound relaxation, delays wound closure, and impairs regrowth following amputation. Moreover, actomyosin inhibition relaxes tailfin contraction without impairing wound closure or regrowth. Over-contraction, on the other hand, impedes wound closure. Meanwhile, chronic depletion of epithelial ROS during embryonic development, achieved through morpholino-mediated knockdown of the duox gene, alters tissue stiffness, as measured using atomic force microscopy-based nanoindentation. Despite a reduced contraction force, the wound also appears to be over-contracted, with delayed healing and regrowth. An in silico linear elasticity simulation to calculate the second principal stress based on node-wise prescribed displacement recapitulated the contraction dynamics during acute and chronic ROS inhibition. Together, our results provide a novel understanding of how reactive oxygen species (ROS) facilitate wound closure, a process instrumental in restoring tissue integrity and maintaining homeostasis.

cell biology↗

bioRxiv2025

Digital Cousins: Simultaneous Optimization of One Model for BMP Signaling in Distant Relatives Reveals Essential Core

Spatially distributed, nonuniform morphogen gradients play a crucial role in tissue organization during development across the animal kingdom. The Bone Morphogenetic Protein (BMP) pathway, a well-studied morphogen involved in dorsal-ventral (D-V) axis patterning, has been extensively studied in zebrafish, Drosophila, and other organisms. Given that this pathway is highly conserved in both form and function, we sought to determine whether a core mathematical model that constrained topology and biophysical parameters could fully reproduce the observed dynamics of gradient formation in both Drosophila and zebrafish through changes in expression only. We used multi-objective optimization to simultaneously fit a single core model to Drosophila and zebrafish data and conditions. By exploring a single model with varied parameters, we identified both the homology and diversification of the BMP pathway. We find that a core model with only two parametric changes could simultaneously replicate the experimentally measured BMP gradients in both species. This approach, involving simulation and multispecies optimization, provides a rigorous method to identify the minimum parameter adjustments needed for the measurement and simulation of one species to have predictive power in another system. The process offers a framework for enhancing cross-species predictions and improving the utility of preclinical animal models. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=108 SRC="FIGDIR/small/640248v1_ufig1.gif" ALT="Figure 1"> View larger version (16K): org.highwire.dtl.DTLVardef@48bfddorg.highwire.dtl.DTLVardef@2c4964org.highwire.dtl.DTLVardef@1864d8eorg.highwire.dtl.DTLVardef@4db2b9_HPS_FORMAT_FIGEXP M_FIG C_FIG

systems biology↗

bioRxiv2025

Modeling Epithelial Morphogenesis and Cell Rearrangement during Zebrafish Epiboly: Tissue Deformation, Cell-Cell Coupling, and the Mechanical Response to Stress

Morphogenesis in early development involves complex and extreme deformations in response to intra- and intercellular forces. Zebrafish epiboly, the spreading of the blastoderm to cover and engulf the large yolk cell, is a key early event that sets the stage for the establishment of the body plan, but the way the forces driving expansion are generated and mediated is poorly understood. The enveloping layer (EVL), the thin squamous outer epithelium of the blastoderm, plays a central role. Forces generated in the yolk cell are transmitted through tight junctions to the marginal EVL cells, and then propagate through the rest of the EVL. To understand mechanisms of force generation and transduction during epiboly, we first need a mechanical model of the EVL capable of responding to such forces and undergoing the drastic deformation of epiboly. The expanding EVL more than doubles its surface area and experiences significant shear as it deforms from a thin cap at one pole to become a complete sphere, necessarily requiring extensive internal rearrangement. We constructed an agent-based model of the EVL and its response to exogenous forces using the center-based simulation framework, Tissue Forge. Our model captures the large viscoelastic deformation of the EVL by cell rearrangement, and incorporates algorithmic strategies to accommodate these dynamic changes while maintaining tissue cohesion. Features observed in living embryos, such as the straightening of the initially ragged leading edge, also emerge in the model. We identified two key components required for realistic epiboly in the model: first, a mechanism to enable tissue remodeling by cell rearrangement without tearing the tissue, and second, a negative feedback on the forces driving EVL expansion, to regulate and synchronize the advancement of the EVL margin. We discuss the implications of these findings for the behavior of living EVL and the mechanisms that drive epiboly.

developmental biology↗

bioRxiv2025

Local traveling waves of cytosolic calcium elicited by defense signals or wounding are propagated by distinct mechanisms

Cytosolic Ca2+ signatures with specific spatiotemporal patterns play crucial roles in plant responses to biotic and abiotic stresses. Perception of microbe- or damage-associated molecular patterns (MAMPs or DAMPs) initiates signaling cascades that represent the first layer of plant defense against pathogens known as pattern-triggered immunity (PTI). During PTI, MAMP/DAMP-induced cytosolic Ca2+ fluxes serve as essential messengers in the initiation and transmission of defense signals at the cellular, whole organ, and systemic levels. However, the specific patterns of these Ca2+ signatures in response to different pathogen cues, and the mechanisms that encode them, remain largely unexplored. In this study, we quantitatively assessed Ca2+ signatures at the single-cell level as well as the local traveling Ca2+ waves induced by global treatment of Arabidopsis cotyledons with MAMPs or DAMPs. We demonstrated that MAMPs induced distinct local spatiotemporal Ca2+ responses in epidermal pavement cells, with Ca2+ traveling waves consistently initiated from a subset of cells and spreading in an approximately radial pattern. These local traveling waves propagated at a slow but constant speed of approximately 1 {micro}m/s and spread to a limited number of neighboring cells. In contrast, wound-induced traveling waves displayed a diffusion-like decay pattern that moved rapidly away from the wounded cell but with diminishing speed over time and distance. Mathematical modeling supported a calcium-induced calcium release mechanism that could recapitulate the constant wave speed induced by MAMPs. These findings contribute to a deeper understanding of plant defense-related Ca2+ signaling mechanisms as well as how defense responses are spatially restricted within tissues. One Sentence SummaryA slow, local traveling wave of calcium is initiated from a subset of epidermal cells during plant immune signaling.

cell biology↗

bioRxiv2024

Optimal Performance Objectives in the Highly Conserved Bone Morphogenetic Protein Signaling Pathway

Throughout development, complex networks of cell signaling pathways drive cellular decision-making across different tissues and contexts. The transforming growth factor {beta} (TGF-{beta}) pathways, including the BMP/Smad pathway, play crucial roles in these cellular responses. However, as the Smad pathway is used reiteratively throughout the life cycle of all animals, its systems-level behavior varies from one context to another, despite the pathway connectivity remaining nearly constant. For instance, some cellular systems require a rapid response, while others require high noise filtering. In this paper, we examine how the BMP- Smad pathway balances trade-offs among three such systems-level behaviors, or "Performance Objectives (POs)": response speed, noise amplification, and the sensitivity of pathway output to receptor input. Using a Smad pathway model fit to human cell data, we show that varying non-conserved parameters (NCPs) such as protein concentrations, the Smad pathway can be tuned to emphasize any of the three POs and that the concentration of nuclear phosphatase has the greatest effect on tuning the POs. However, due to competition among the POs, the pathway cannot simultaneously optimize all three, but at best must balance trade-offs among the POs. We applied the multi-objective optimization concept of the Pareto Front, a widely used concept in economics to identify optimal trade-offs among various requirements. We show that the BMP pathway efficiently balances competing POs across species and is largely Pareto optimal. Our findings reveal that varying the concentration of NCPs allows the Smad signaling pathway to generate a diverse range of POs. This insight identifies how signaling pathways can be optimally tuned for each context.

systems 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↗

bioRxiv2022

Computational modeling of TGF-β2:TβRI:TβRII receptor complex assembly as mediated by the TGF-β co-receptor betaglycan

Transforming growth factor-{beta}1, -{beta}2, and -{beta}3 (TGF-{beta}1, -{beta}2, and -{beta}3) are secreted signaling ligands that play essential roles in tissue development, tissue maintenance, immune response, and wound healing. TGF-{beta} homodimers signal by assembling a heterotetrameric complex comprised of two type I receptor (T{beta}RI):type II receptor (T{beta}RII) pairs. TGF-{beta}1 and TGF-{beta}3 signal with high potency due to their high affinity for T{beta}RII, which engenders high affinity binding of T{beta}RI through a composite TGF-{beta}:T{beta}RII binding interface. However, TGF-{beta}2 binds T{beta}RII 200-500 more weakly than T{beta}RII and signals with lower potency compared to TGF-{beta}1 and -{beta}3. Remarkably, potency of TGF-{beta}2 is increased to that of TGF-{beta}1 and -{beta}3 in the presence of an additional membrane-bound co-receptor, known as betaglycan (BG), even though betaglycan does not directly participate in the signaling mechanism and is displaced as the signaling receptors, T{beta}RI and T{beta}RII, bind. To determine the role of betaglycan in the potentiation of TGF-{beta}2 signaling, we developed deterministic computational models with different modes of betaglycan binding and varying cooperativity between receptor subtypes. The models, which were developed using published kinetic rate constants for known quantities and optimization to determine unknown quantities, identified conditions for selective enhancement of TGF-{beta}2 signaling. The models provide support for additional receptor binding cooperativity that has been hypothesized, but not evaluated in the literature. The models further showed that betaglycan binding to TGF-{beta}2 ligand through two domains provides an effective mechanism for transfer to the signaling receptors that has been tuned to efficiently promote assembly of the TGF-{beta}2(T{beta}RII)2(T{beta}RI)2 signaling complex.

biophysics↗

bioRxiv2021

Quantitative imaging in whole-mount zebrafish embryos traces morphogen gradient maintenance and noise propagation in BMP signaling

Dorsoventral (DV) embryonic patterning relies on precisely controlled interpretation of morphogen signaling. In all vertebrates, DV axis specification is informed by gradients of Bone Morphogenetic Proteins (BMPs). We developed a 3D single-molecule mRNA quantification method in whole-mount zebrafish to quantify the inputs and outputs in this pathway. In combination with 3D computational modeling of zebrafish embryo development, data from this method revealed that Sizzled (Szl), shaped by BMP and Nodal signaling, kept a consistent inhibition level with Chordin (Chd) to maintain the BMP morphogen gradient. Intriguingly, BMP morphogen intrinsic expression is highly noisy at the ventral marginal layer in early zebrafish gastrula, where the gradient for DV patterning is established, which implies an unexpected role for noise in gradient shaping.

systems biology↗

bioRxiv2019

Mitofusin 2 regulates neutrophil adhesive migration via suppressing Rac activation

Neutrophils rely on glycolysis for energy production. How mitochondria regulate neutrophil function is not fully understood. Here, we report that mitochondrial outer membrane protein Mitofusin 2 (Mfn2) regulates neutrophil homeostasis in vivo. Mfn2-deficient neutrophils are released from the hematopoietic tissue and trapped in the vasculature in zebrafish embryos. Human neutrophil-like cells deficient with MFN2 fail to arrest on activated endothelium under sheer stress or perform chemotaxis. Deletion of Mfn2 results in a significant reduction of neutrophil infiltration to the inflamed peritoneal cavity in mice. Mfn2, but not Mfn1, -null mouse embryonic fibroblast cells have altered actin structure and are impaired in wound closure. MFN2-deficient neutrophil-like cells display heightened intracellular calcium levels and Rac activation after chemokine stimulation. Mechanistically, MFN2 maintains mitochondria-ER interaction. Restoring mitochondria-ER tether rescues the chemotaxis defect and Rac activation resulted from MFN2 depletion. Finally, inhibition of Rac restores chemotaxis in MFN2-deficient neutrophils. Altogether, we identified that MFN2 regulates neutrophil migration via suppressing Rac activation and uncovered a previously unrecognized role of MFN2 in regulating the actin cytoskeleton.

cell biology↗

bioRxiv2019

Evaluation of BMP-mediated patterning in zebrafish embryos using a growing finite difference embryo model

Bone Morphogenetic Proteins (BMPs) play an important role in dorsal-ventral (DV) patterning of the early zebrafish embryo. BMP signaling is regulated by a network of extracellular and intracellular factors that impact the range and signaling of BMP ligands. Recent advances in understanding the mechanism of pattern formation support a source-sink mechanism, however it is not clear how the source-sink mechanism shapes patterns in 3D, nor how sensitive the pattern is to biophysical rates and boundary conditions along both the anteroposterior (AP) and DV axes of the embryo. We propose a new three-dimensional growing Partial Differential Equation (PDE)-based model to simulate the BMP patterning process during the blastula stage. This model provides a starting point to elucidate how different mechanisms and components work together in 3D to create and maintain the BMP gradient in the embryo. We also show how the 3D model fits the BMP signaling gradient data at multiple time points along both axes. Furthermore, sensitivity analysis of the model suggests that the spatiotemporal patterns of Chordin and BMP ligand gene expression are dominant drivers of shape in 3D and more work is needed to quantify the spatiotemporal profiles of gene and protein expression to further refine the models.

systems biology↗