Biology subjects

Hunter, G. L.

Publications and source records attributed to Hunter, G. L..

6 recordsLinked to original sources

bioRxiv2026

Functional Data Clustering of Filopodia Dynamics

Notch signaling plays a significant role in tissue patterning. During patterning of the fruit fly dorsal thorax peripheral nervous system, basal filopodia extend the spatial range of cell-cell communication, yet it is still unclear how Notch is activated in long range signaling via filopodia interaction. Filopodia undergo dynamic length changes during their lifetime, which could supply the mechanical pulling force required for notch activation. However, their dynamics are often characterized using individual scalar values such as maximum length and extension rate which could obscure more intricate dynamics. Our hypothesis is that signaling filopodia exhibit distinct and recurrent temporal patterns which can be identified by a consideration of their complete lifetime trajectories. Our work analyzes 60 filopodia trajectories at the basal surface of the fly dorsal thorax during patterning. Length profiles were smoothed using cubic B-splines and clustered by first reducing them to their dominant functional principal component followed by the application of various clustering algorithms. We found that 94.29% of the overall trajectory variation is explained by the first four functional principal components which account for variations in maximal length, extension and retraction rate, duration of stationary phase and length fluctuation frequency. Five recurrent temporal profiles (dynamic extension modes) with varying trajectory shapes and physical attributes, were identified using trimmed K-means. These findings demonstrate that whereas the major source of structural variation in filopodia profiles remains the length, extension rate and retraction rate, nontrivial combinations of these create distinct dynamic modes of extension which provide new insight into their length profiles. Our work thus offers a quantitative framework for future research connecting filopodia dynamic extension modes to productive Notch activation.

developmental biology↗

bioRxiv2026

SOPSim: A cell vertex-based application for simulating sensory bristle patterning with dynamic filopodia

Repeating patterns, such as the bristles on the thorax of fruit flies developed from sensory organ precursor (SOP) cells, play important roles in the lives of flies as they are connected to the central nervous system and help detect environmental cues and threats. Notch signaling is known to regulate the formation of these patterns. Primarily, Notch signaling involves local communication between neighboring cells in direct contact (apical or junctional interaction). However, this short-range interaction alone cannot fully explain the complex biological patterns observed. Further studies have revealed long-range communication between cells through actin-based protrusions known as filopodia. The precise understanding of how the dynamics of filopodia, such as protrusion and retraction, lead to Notch-Delta activation remains unclear, which limits our ability to fully comprehend the mechanisms underlying cell fate decisions and the emergence of spatially organized patterns during tissue development and regeneration. In this study, we extend the modeling framework for Notch signaling by incorporating a filopodia dynamics model driven by myosin-mediated contraction. We address existing gaps by defining criteria under which any given pair of filopodia will physically intersect. We also introduce the local sensory area (LSA), a metric for quantifying local SOP spacing, and use experimental data to calibrate a Notch threshold that distinguishes SOP from epithelial cells. Through numerical simulations, we confirm that long-range communication via filopodia is essential for reproducing the refined patterns observed in vivo. Additionally, we explore how filopodia length, lifetime, and orientation influence the spatial organization of SOP cells. To this end, a Python library has been developed which allows users to perform simulations of Notch Delta signaling via a (1) Graphical User Interface/website, local to the user's computer, (2) via commands in the command line interface, or (3) by calling the simulation using a function via a Python API. This library allows users without computational expertise to easily specify a small number of input parameters and generate simulations of the model.

developmental biology↗

bioRxiv2026

Clustered cytoneme interactions contribute to peripheral nervous system patterning in Drosophila

The formation of patterned adult tissues requires precise spatiotemporal communication between the cells that comprise the tissue during development. The dorsal thoracic sensory bristles of the peripheral nervous system (PNS) of the fruit fly Drosophila melanogaster relies on the activity of cell protrusions called cytonemes. Experimental studies have identified several of the mechanisms that govern individual cytoneme dynamics in the patterning PNS, and theoretical studies have considered the effects of their collective activity. However less is understood about how cytonemes in the developing PNS interact with each other to achieve wild type tissue patterning. Here, using in vivo and ex vivo imaging strategies combined with fly genetics, we show that cytonemes form clusters along the basal surface and that association with clusters promotes the dynamics of individual cytonemes. Clusters are dynamic and transient organizations of cytonemes, and we show that when their movement is perturbed ex vivo through locally aligned nanofibers wildtype PNS patterning is disrupted. We show evidence that cytoneme interactions via clusters is supported by the cell adhesion molecule E-cadherin, as reducing E-cadherin expression leads to changes in cluster dynamics, ability to promote cytoneme length, and overall patterning of the PNS. Taken together, our results support a model in which complex cytoneme interactions promote the dynamics of individual cytonemes. We propose that the enhanced dynamics and stability provided by increased cell-cell interactions may support both the range and strength of local signaling events.

developmental biology↗

bioRxiv2025

Quantifying bristle cell organization in Drosophila melanogaster

Developing tissues reproduce nearly identical patterns from animal to animal, despite the process being stochastic at the cell level. A major challenge for researchers is the ability to quantify and classify complex cell and tissue spot patterns across wild type and perturbed conditions. Here, we use the organization of small sensory bristles on the fruit fly thorax as a model system to address this problem. A well-known and easily observable distinguishing feature of spot patterns is density. Beyond this, it is unclear how to quantitatively distinguish between patterns in a reproducible way. Our work evaluates the utility of the spatial clustering of spot patterns in quantifying their organization. We propose four clustering features, obtained using the density-based spatial clustering of applications with noise (DBSCAN) algorithm. Together with pattern density we assess how these features can quantify and distinguish between bristle patterns in a variety of wild-type and mutant flies to confirm known perturbations and discover new ones. Our results show that a combination of spot pattern density and the variance between the size of clusters is sufficient to distinguish between 70% of patterns from wild-type and mutant tissues.

developmental biology↗

bioRxiv2023

Myosin XV is a negative regulator of signaling filopodia during long-range lateral inhibition

The self-organization of cells during development is essential for the formation of healthy tissues, and requires the coordination of cell activities at local scales. Cytonemes, or signaling filopodia, are dynamic actin-based cellular protrusions that allow cells to engage in contact mediated signaling at a distance. While signaling filopodia have been shown to support several signaling paradigms during development, less is understood about how these protrusions are regulated. We investigated the role of the plus-end directed, unconventional MyTH4-FERM myosins in regulating signaling filopodia during sensory bristle patterning on the dorsal thorax of the fruit fly Drosophila melanogaster. We found that Myosin XV is required for regulating signaling filopodia dynamics and, as a consequence, lateral inhibition more broadly throughout the patterning epithelium. We found that Myosin XV is required for limiting the length and number of signaling filopodia generated by bristle precursor cells. Cells with additional and longer signaling filopodia due to loss of Myosin XV are not signaling competent, due to altered levels of Delta ligand and Notch receptor along their lengths. We conclude that Myosin XV acts to negatively regulate signaling filopodia, as well as promote the ability of signaling filopodia to engage in long-range Notch signaling. Since Myosin XV is present across several vertebrate and invertebrate systems, this may have significance for other long-range signaling mechanisms.

developmental biology↗

bioRxiv2023

Scabrous is distributed via signaling filopodia to modulate Notch response during bristle patterning in Drosophila

During development, tissues must be patterned correctly in order to support tissue function and shape. The sensory bristles of the peripheral nervous system on the thorax of Drosophila melanogaster self-organize from an unpatterned epithelial tissue to a regular spot pattern during pupal stages. Wild type patterning requires Notch-mediated lateral inhibition. Scabrous is a protein that can bind to and modify Notch receptor activity. Scabrous can be secreted, but it is also known to be localized to basal signaling filopodia, or cytonemes, that play a role in long-range Notch signaling. Consistent with previous work, we show that Scabrous is primarily distributed basally, within the range of signaling filopodia extension. We show that signaling filopodia are required for the distribution of Scabrous protein during sensory bristle patterning stages. We show that the Notch response of epithelial cells is sensitive to the level of Scabrous protein being expressed by the sensory bristle precursor cell. Our findings at the cell-level suggest a model for how epithelial cells engaged in lateral inhibition at a distance are sensitive local levels of Scabrous protein.

developmental biology↗