Biology subjects

Murphy, C. J.

Publications and source records attributed to Murphy, C. J..

4 recordsLinked to original sources

bioRxiv2026

MDA-MB-231 cell morphology influences chemotactic sensing of CXCL12 gradients in type 1 bovine collagen matrix

Chemotaxis plays a critical role in the metastatic progression of breast cancer. The chemokine CXCL12 is well recognized as an essential component of chemotactic migration in triple-negative breast cancer (TNBC) cells in vivo. The purpose of this study is to determine how the highly metastatic TNBC cell line, MDA-MB-231, migrates in response to well-defined CXCL12 gradients in vitro. Traditional 2D transwell migration assays were optimized to gauge the MDA-MB-231 cells responsiveness to various CXCL12 concentrations. The optimum chemoattractant concentrations were applied to a commercially available 3D chemotaxis assay as stable linearly diffused gradients. Cells were embedded in type 1 bovine collagen at two different collagen concentrations, and individual unlabeled cells were monitored for 24 hours using brightfield microscopy. Time-lapse videos were used to track cell movement and shape. Quantitative data analysis was performed using an automated tracking software to measure chemotactic parameters based on cell morphology. MDA-MB-231 cells were responsive to CXCL12 concentrations greater than 200 ng/mL in 2D and 3D systems. In 3D systems, significant directed migration was observed in denser collagen matrices. It was observed that in 3D matrices a range of cell morphologies was present. Therefore, chemotaxis was evaluated as a function of cell shape revealing some differences between sub cellular populations. Our findings show the cells shape influences the chemotactic sensing towards CXCL12 gradients.

cell biology↗

bioRxiv2025

Machine Learning Enables Rapid Assessment of Disease Vulnerability in a Threatened Cetacean Population

Cetaceans (whales and dolphins) are important ecosystem sentinels but face growing threats from major disease-related mortality events expected to intensify under climate change. Because both environmental factors (temperature, salinity) and demographics (age, sex) influence health and disease risk, understanding these relationships is essential for effective management. Direct health assessments are challenging in cetaceans, but skin lesions can indicate active infection and tooth-rake marks reflect social stressors that increase transmission risk. Yet, traditional photographic analysis of these indicators is inefficient, creating processing bottlenecks that limit timely evaluation of population health. To address this gap, we applied machine learning to rapidly assess lesions and rake marks in Tamanends bottlenose dolphins (Tursiops erebennus) photographed in the Chesapeake Bay, a known hotspot for disease-related die-offs. This represents the first analysis of environmental and demographic contributions to dolphin health in this region. We found significant negative relationships between lesion prevalence and both temperature and salinity for some lesion types. Adult males also showed higher rake mark coverage than adult females and calves. These patterns suggest dolphins in colder, fresher waters may face elevated disease risk, while adult males may be particularly vulnerable to behavioral stress and related health consequences. Our findings are consistent with prior studies, lending validity to our machine learning models, while also revealing novel patterns of calf and male vulnerability in this threatened population. More broadly, our approach demonstrates the potential of automated image analysis to enable timely, non-invasive health assessments across cetacean populations in an era of rapid global change.

ecology↗

bioRxiv2024

Automated Skin Lesion Detection and Prevalence Estimation in Tamanend's Bottlenose Dolphins

Anthropogenic global change is occurring at alarming rates, leading to increased urgency in the ability to monitor wildlife health in real time. Monitoring sentinel marine species, such as bottlenose dolphins, is particularly important due to extensive anthropogenic modifications to their habitats. The most common non-invasive method of monitoring cetacean health is documentation of skin lesions, often associated with poor health or disease, but the current methodology is inefficient and imprecise. Recent advancements in technology, such as machine learning, can provide researchers with more efficient ecological monitoring methods to address health questions at both the population and the individual levels. Our work develops a machine learning model to classify skin lesions on the understudied Tamanends bottlenose dolphins (Tursiops erebennus) of the Chesapeake Bay, using manual estimates of lesion presence in photographs. We assess the models performance and find that our best model performs with a high mean average precision (65.6%-86.8%), and generally increased accuracy with improved photo quality. We also demonstrate the models ability to address ecological questions across scales by generating model-based estimates of lesion prevalence and testing the effect of gregariousness on health status. At the population level, our model accurately estimates a prevalence of 72.1% spot and 27.3% fringe ring lesions, with a slight underprediction compared to manual estimates (82.2% and 32.1%). On the other hand, we find that individual-level analyses from the model predictions may be more sensitive to data quality, and thus, some individual scale questions may not be feasible to address if data quality is inconsistent. Manually, we do find that lesion presence in individuals suggests a positive relationship between lesion presence and gregariousness. This work demonstrates that object detection models on photographic data are reasonably successful, highly efficient, and provide initial estimates on the health status of understudied populations of bottlenose dolphins.

ecology↗

bioRxiv2021

Arap1 Loss Causes RPE Phagocytic Dysfunction and Subsequent Photoreceptor Death

PurposeArap1 is an Arf-directed GTPase-activating protein (GAP) shown to modulate actin cytoskeletal dynamics by regulating Arf and Rho family members. We have previously shown that Arap1-/- mice develop photoreceptor degeneration similar to the human condition retinitis pigmentosa (RP), corroborated by fundus examination, histopathology, and ERG analysis. However, Arap1 expression was not detected in photoreceptors, but in Muller Glia and retinal pigment epithelium (RPE), suggesting a non-cell-autonomous mechanism for degeneration. The aim of this study was to elucidate the role of retinal Arap1 in photoreceptor maintenance. MethodsAlbino Arap1-/- mice were generated via breeding pigmented Arap1-/- mice onto a Tyr-/- C57BL/6J background. Conditional knockout (cKO) mice were generated for Muller Glia/RPE, Muller Glia, and RPE via targeting Cralbp, Glast, and Vmd2 promoters, respectively, to drive Cre recombinase expression to knock out Arap1. Mice were analyzed by fundus photography, optical coherence tomography (OCT), histology, and immunohistochemistry. Arap1 binding partners were assayed by affinity purification mass spectrometry. ResultsVmd2-Cre Arap1tm1c/tm1c and Cralbp-Cre Arap1tm1c/tm1c mice, but not Glast-Cre Arap1tm1c/tm1c mice, recapitulated the photoreceptor degeneration phenotype originally observed in germline Arap1-/- mice. These findings were corroborated by fundus exam, OCT, and histological analysis. Mass spectrometry analysis of ARAP1 co-immunoprecipitation identified putative binding partners of ARAP1, revealing numerous interactants involved in phagocytosis, cytoskeletal composition, intracellular trafficking, and endocytosis. Quantification of rod outer segment (OS) phagocytosis in vivo demonstrated a clear phagocytic defect in Arap1-/- mice compared to Arap1+/+ littermate controls while cone phagocytosis was preserved. ConclusionsArap1 expression, specifically in RPE, is necessary for photoreceptor survival due to its indispensable function in RPE phagocytosis. We propose a model in which Arap1 regulates G-protein function for nonmuscle myosin II targeting during phagocytosis. This novel role of Arap1 is important for further understanding of both the diversity of its functions and the complex molecular regulation of RPE phagocytosis.

molecular biology↗