Biology subjects

Carney, R.

Publications and source records attributed to Carney, R..

8 recordsLinked to original sources

bioRxiv2026

RADIX: a deep learning framework that maps root barriers across species and reveals genetic and environmental contributions

Root anatomical barriers, including the suberized and lignified walls of the endodermis and exodermis, and cortical aerenchyma, regulate water and nutrient transport, gas exchange, and rhizosphere interaction. Their adaptive function places them as an important target for breeding environmentally resilient plant species. Quantifying these structures at high resolution is a manual bottleneck that limits experimental scale. We present RADIX (Root Anatomy Deep- learning Image segmentation across species and platforms), a framework that adapts a large self-supervised vision-transformer foundation encoder (DINOv3), pre-trained on billions of natural images, to root anatomy by fine-tuning its encoder with a dense-prediction-transformer decoder. Transferring these general-purpose vision encoders to a specialized biological domain with a high-quality annotated dataset is what allows RADIX to generalize across species and imaging platforms. We train and evaluate it on the first expert-annotated benchmark of root anatomical structures at scale, comprising 1,695 high-quality fluorescence images spanning 17 monocot and dicot species, six anatomical structures, and three imaging platforms. RADIX segments all six structures at inter-annotator-level accuracy and generalizes to unseen species, genotypes, growth conditions, and an imaging platform from an independent laboratory. A single unified model surpasses monocot- and dicot-specialist models without sacrificing in-group accuracy. Predicted masks yield aerenchyma and suberin/lignin measurements matching expert annotation at [~]1.2 s per image with a single GPU, reducing weeks of manual analysis to minutes. Applying RADIX across genotypes, microbial treatments, and growth systems, we show that these cell type features form a coordinated, multidimensional, and context-dependent system shaped by genetic and environmental factors.

plant biology↗

bioRxiv2026

Urban larval mosquito surveillance in Antananarivo, Madagascar: spatiotemporal heterogeneity and associated vector dynamics

Mosquito-borne diseases, such as malaria, remain an important public health problem globally, including on the island of Madagascar. Malaria vector control strategies are typically aimed at adult Anopheles mosquitoes in predominantly rural settings. However, very little information is available on larval populations of Anopheles and other vector genera, such as Aedes and Culex, in urban areas, where urbanization creates a multitude of potential larval habitats. Here, the objectives are to identify different types of existing larval habitats and the diversity of vector species in the capital city of Antananarivo, and to study the temporal dynamics and spatial distribution of mosquito vectors of public health interest. From 2022-2023, longitudinal larval surveillance was carried out across all six districts of Antananarivo and consisted of prospecting 2,856 potential larval habitats, of which 653 (23%) were found to contain Aedes, Culex, or Anopheles larvae. Anopheles larvae were reared and morphologically identified using taxonomic keys, and molecular identification by PCR and Sanger sequencing was used for Anopheles sibling species determination. A total of 27,418 larval specimens were collected from eight species: Culex quinquefasciatus (53%), Aedes albopictus (26%), Cx. pipiens (14%), Anopheles gambiae s.l. (3%, all molecularly identified as An. arabiensis), Cx. univittatus (1%), Cx. antennatus (1%), Cx. poicilipes (1%), and An. coustani (1%). Geospatial analysis reveals that 55% of larvae came from artificial larval habitats within the city, which harbor lower species diversity than natural larval habitats. Twenty-one different types of larval habitats were observed, and Cx. quinquefasciatus, a vector of West Nile virus, was present in all of them. Aedes albopictus, vector of arboviral pathogens, prefers artificial habitats such as tires and flower pots, whereas the common rural malaria vector, An. arabiensis preferred natural sites like brick pits and rice fields. An. coustani, often considered a livestock-associated rural vector, was found to thrive in brick pits, wells, ponds, and in aquatic agriculture. Notably, of the 1,270 Anopheles larvae collected, none were found in an artificial container. Culex quinquefasciatus, Cx. pipiens, and Ae. albopictus reached peak abundance in March during the rainy season, while malaria vectors An. arabiensis and An. coustani showed unexpected abundance peaks during the dry periods, in September and April. Two districts (arrondissements 2 and 5) showed higher abundance and diversity of mosquito vectors than the other districts. The data presented here reveal the spatiotemporal dynamics of malaria and arboviral mosquito vectors in urban Madagascar and highlight the heterogeneity of habitats across the urban ecosystem, with important practical implications for the surveillance and control of mosquito-borne diseases.

ecology↗

bioRxiv2026

A scutum-focused deep learning pipeline for species-level identification of Aedes aegypti and Aedes albopictus from citizen-science images

BackgroundMosquito-borne diseases transmitted by Aedes aegypti and Aedes albopictus -- including dengue, Zika, chikungunya, and yellow fever -- depend critically on rapid and accurate vector identification. Although deep learning has achieved high accuracy on curated laboratory images, performance degrades substantially when applied to community-submitted photographs that vary widely in quality, framing, and background. We sought to develop a robust pipeline for distinguishing these two morphologically similar vectors from real-world citizen-science images. MethodsWe compiled 2,112 mosquito images from the Global Mosquito Observation Database (GMOD) and assembled a multi-stage pipeline comprising: (i) a binary classifier to screen for mosquito presence; (ii) a YOLO-based object detector to localize specimens; (iii) an image-quality assessment module evaluating brightness, sharpness (Laplacian variance), contrast, and bounding-box ratio; (iv) Segment Anything Model (SAM) segmentation to isolate specimens from background clutter; and (v) a YOLO classifier trained on binary segmentation masks. To target the diagnostic characters used in conventional morphological taxonomy, we refined the pipeline to focus detection on the thoracic scutum -- the region bearing the lyre-shaped pale-scale pattern of Ae. aegypti and the median white stripe of Ae. albopictus. ResultsBaseline YOLO classification on raw images achieved 30.95% accuracy for Ae. aegypti and 78.4% for Ae. albopictus, reflecting strong class imbalance and background noise. Augmentation alone provided only modest gains. The presence/absence classifier reached 90.52% accuracy, and the object detector localized mosquitoes with near-perfect precision. Whole-body SAM-mask classification improved overall accuracy to 68.21%. Refining the pipeline to scutum-focused classification yielded preliminary accuracies of 87.5% and 83.3% for Ae. albopictus and Ae. aegypti, respectively. ConclusionsCommunity-sourced mosquito images, despite substantial noise and inconsistency, can support automated species-level vector surveillance when paired with a domain-informed, multi-stage deep-learning pipeline. Aligning machine attention with the morphological characters used by entomologists -- via scutum-focused detection -- delivers meaningful accuracy gains. This framework supports scalable citizen-science vector monitoring and lays the groundwork for integrating high-fidelity three-dimensional reference libraries to further strengthen real-world classifier performance.

bioinformatics↗

bioRxiv2025

Validation of Extracellular Vesicles in FACTORFIVEs EXOFECTA LyoBeads

ObjectiveThe objective of this project was to determine if extracellular vesicles (EVs) were present in FACTORFIVEs EXOFECTA LyoBeads to validate flash freezing and subsequent lyophilization as an effective EV preservation method. SummaryEVs were isolated from resuspended EXOFECTA LyoBeads using differential ultracentrifugation and subjected to further characterization techniques such as nanoparticle tracking analysis (NTA), single particle flow cytometry, and cryo-electron microscopy (cryo-EM). First, NTA revealed particles with size distributions and concentrations consistent with the expected characteristics of EVs, indicating successful isolation from samples. Secondly, flow cytometry was performed using antibodies targeting the canonical EV tetraspanins CD9, CD63, and CD81. Detection of these markers supported the presence of enriched EVs in the samples. Finally, cryo-EM was performed to confirm the existence of vesicular bodies and their morphology. Visualization of the samples revealed membrane-enclosed particles with a visible lipid bilayer, consistent with EVs. Overall, the results support EVs were in EXOFECTA LyoBeads, indicating EV retention in the final product after FACTORFIVEs method of flash freezing, stabilizing, and lyophilization.

molecular biology↗

bioRxiv2025

Neuron type-specific mRNA translation programs provide a gateway for memory consolidation.

Long-term memory consolidation is a dynamic process that requires a heterogeneous ensemble of neurons, each with a highly specialized molecular signature. Considerable effort has been devoted to identifying molecular changes that accompany the process of consolidation, but mostly hours or days after training, when memory consolidation is already complete. Studies have shown that protein synthesis is elevated during the early stages of consolidation, but how this increase impacts neuronal function remains unclear. We hypothesize that mRNAs translated during the early stages of consolidation could provide information on how diverse neurons involved in memory formation restructure their molecular signatures to support memory. Here, we generate a landscape of the translatome of three neuron types in the dorsal hippocampus during the first hour of contextual memory consolidation. Our results reveal that translation programs associated with consolidation are different among neurons, fueling the reconfiguration of specific biological processes. We further demonstrate the patterned translation of mRNAs in different neuron types during consolidation is explained by features hard-coded in the mRNA sequence, suggesting ubiquitous mechanisms controlling activity-induced neuronal translation. Altogether, our work uncovers previously unknown mechanisms controlling activity-induced translation in neurons and provides a large, readily available resource for scientists interested in the role of memory formation in health and disease.

neuroscience↗

bioRxiv2023

A regional One Health approach to the risk of invasion by Anopheles stephensi in Mauritius

BackgroundAnopheles stephensi is an invasive malaria vector in Africa that threatens to put an additional 126 million people at risk of malaria if it continues to spread. The island nation of Mauritius is highly connected to Asia and Africa and is at risk of introduction due to this connectivity. For early detection of An. stephensi, the Vector Biology and Control Division under the Ministry of Health in Mauritius, leveraged a well-established Aedes program, as An. stephensi is known to share Aedes habitats. These efforts triggered multisectoral coordination and cascading benefits of integrated vector and One Health approaches. MethodsBeginning June 2021, entomological surveys were conducted at points of entry (seaport, airport) and on ships transporting livestock in collaboration with the Civil Aviation Department, the Mauritian Port Authority and National Veterinary Services. A total of 39, 18, 723 mosquito larval surveys were respectively conducted in the seaport, airport and other localities in Mauritius while 20, two and 26 adult mosquito surveys were respectively conducted in the seaport, airport and twenty-six animal points. Alongside adult mosquito surveys, surveillance of vectors of veterinary importance (e.g.- licoides spp.) was also carried out in collaboration with National Parks and Conservation Service and land owners. ResultsA total of 8,428 adult mosquitoes were collected and 1,844 larval habitats were positive for mosquitoes. All collected mosquitoes were morphologically identified and 151 Anopheles and 339 Aedes mosquitoes were also molecularly characterized. Mosquito species detected were Aedes albopictus, Anopheles arabiensis, An. coustani, An. merus, Culex quinquefasciatus, Cx. thalassius and Lutzia tigripes. Anopheles stephensi was not detected. The One Health approach was shared with the French Agricultural Research Centre for International Development (CIRAD), strengthening collaboration between Mauritius and Reunion Island on vector surveillance at entry points and insecticide resistance monitoring. The Indian Ocean Commission (IOC) was also alerted to the risk of An. stephensi, leading to regional efforts supporting trainings and development of a response strategy to An. stephensi bringing together stakeholders from Comoros, Madagascar, Mauritius, Reunion Island and Seychelles. ConclusionsMauritius is a model system showing how existing public health entomology capabilities can be used to enhance vector surveillance and control and create multisectoral networks to respond to any emerging public and veterinary health vector-borne disease threat. Author summaryThe malaria mosquito, Anopheles stephensi, is invasive in Africa where it threatens to put an additional 126 million people at risk of malaria if it continues to spread throughout the continent. The island nation of Mauritius is highly connected to Asia and Africa through maritime trade and therefore may be at risk of An. stephensi introduction and establishment. Mauritius implemented a One Health approach, enhancing entomological surveillance at entry points and collaborating across sectors (e.g. veterinary services, sea and air port authorities, national parks and conservation, communities, etc.) conducted extensive integrated vector surveillance, inspecting 85,071 larval habitats, and analyzing 8,428 adult mosquitoes morphologically and molecularly. Although An. stephensi was not detected, the initiative catalyzed and strengthened multisectoral partnerships nationally and across the Indian Ocean region member states (Comoros, Madagascar, Mauritius, Reunion Island and Seychelles). Leveraging the threat of An. stephensi, Mauritius exemplifies utilizing existing capabilities to create multisectoral networks for effective vector surveillance and response.

ecology↗

bioRxiv2021

Engineered neuron-targeting, placental mesenchymal stromal cell-derived extracellular vesicles for in utero treatment of myelomeningocele

This study investigated the feasibility and efficiency of neuron-targeting hybrid placental mesenchymal stromal cell-derived extracellular vesicles (PMSC-EVs), engineered by membrane fusion with Targeted Axonal Import (TAxI) peptide modified, TrkB agonist 7,8-DHF-loaded liposomes for treatment of myelomeningocele (MMC) via intra-amniotic cavity administration. The prepared TAxI modified liposomes with 7,8-DHF were used to fuse with PMSC-EVs. Different fusion approaches were investigated and freeze-thaw-extrude method was found to be the optimal. The engineered PMSC-EVs had a uniform particle size and efficiently loaded 7,8-DHF. It also had typical markers of native EVs. Freeze-thaw-extrude process did not change the release profile of 7,8-DHF from engineered EVs compared to TAxI modified, 7,8-DHF loaded liposomes. The engineered EVs could elicit TrkB phosphorylation depending on the incorporation of 7,8-DHF while native EVs did not. The engineered EVs increased neurite outgrowth of apoptotic cortical neurons induced by staurosporine, suggesting that they exhibited neuroprotective function. In a rodent model of MMC, neuron-targeting, engineered EVs became an active targeting delivery system to MMC defect sites. Pups treated with engineered EVs had the lowest density of apoptotic cells and displayed a therapeutic outcome. The study suggests the potential use of engineered hybrid, active neuron-targeting EVs for the in utero treatment of MMC.

bioengineering↗

bioRxiv2020

E-cadherin promotes cell hyper-proliferation in breast cancer

The loss of the intercellular adhesion molecule E-cadherin is a hallmark of the epithelial- mesenchymal transition (EMT), during which tumor cells transition into an invasive phenotype. Accordingly, E-cadherin has long been considered a tumor suppressor gene. Using novel multi-compartment spheroids and multiple in vivo models, we show that E-cadherin promotes a hyper-proliferative phenotype in breast cancer cells via interaction with the transmembrane receptor EGFR. This interaction results in the activation of the MEK/ERK signaling pathway, leading to a significant increase in proliferation via the activation of transcription factors including c-Fos. Pharmacological inhibition of MEK activity in E-cadherin positive breast cancer cells significantly decreases both tumor growth and macro-metastasis in vivo. This work provides evidence for a novel role of E-cadherin in breast tumor growth and identifies a potential new target to treat hyper-proliferative E-cadherin-positive breast tumors.

cancer biology↗