Biology subjects

Daly, A.

Publications and source records attributed to Daly, A..

6 recordsLinked to original sources

bioRxiv2025

Differential Cellular Mechanisms Underlie Language and Executive Decline in Amyotrophic Lateral Sclerosis

Cognitive manifestations, including impairment in language and executive functions, are seen in amyotrophic lateral sclerosis (ALS), but the mechanisms that underlie these deficits remain unclear. To address this, we mapped prefrontal cortex regions from ALS patients by integrating spatial and single-nucleus transcriptomics in a cognitively stratified patient cohort. We uncover that cognitive impairment in ALS is associated with distinct patterns of neuronal dysfunction and glial-vascular dysregulation that vary by region and cognitive subtype. Executive dysfunction is linked to reduced mitochondrial and synaptic activity in neurons localized to the deeper layers of the dorsolateral prefrontal cortex, whereas language-related deficits track with a more diffuse, pan-regional response involving both glial and vascular abnormalities. Our analyses also identify signatures in the prefrontal cortex that span both motor and cognitive phenotypes, including a multicellular gliosis response. The findings reveal that the clinical heterogeneity of ALS is driven by phenotype-specific molecular and cellular interactions in motor and non-motor regions of the brain.

genomics↗

bioRxiv2024

Autonomous control of extrusion bioprinting using convolutional neural networks

Extrusion bioprinting technology suffers from reproducibility challenges due to the open-loop nature of current hardware systems. Here, we present a novel AI-powered extrusion bioprinting platform with integrated real-time quality monitoring and automated error correction capabilities. To achieve this, we engineered a custom bioprinting system with an integrated camera for continuous process monitoring and trained convolutional neural networks (CNNs) to classify the extrusion process in real-time. The CNN models, including Xception and ResNet, were trained on a combination of real and synthetic data to classify extrusion quality (good, over, or under) across various printing scenarios, including single-line and infill patterns. Notably, transfer learning, utilizing synthetic data for initial training followed by refinement with real-world data enhanced classification accuracy, with the Xception model displaying 90% accuracy for single-line extrusion and 75% for infill extrusion. This intelligent monitoring system was then coupled with a closed-loop control system that dynamically adjusted extrusion parameters on-the-fly to correct errors. The platform successfully corrected both over- and under-extrusion errors for alginate and collagen bioinks with varying rheological properties, demonstrating adaptability to unseen materials. Importantly, extrusion errors were corrected within [~]10 seconds. This novel closed-loop bioprinting platform represents a significant advance over traditional open-loop systems.

bioengineering↗

bioRxiv2024

Single-cell transcriptomic landscape of the neuroimmune compartment in amyotrophic lateral sclerosis brain and spinal cord

Development of therapeutic approaches that target specific microglia responses in amyotrophic lateral sclerosis (ALS) is crucial due to the involvement of microglia in ALS progression. Our study identifies the predominant microglia subset in human ALS primary motor cortex and spinal cord as an undifferentiated phenotype with dysregulated respiratory electron transport. Moreover, we find that the interferon response microglia subset is enriched in donors with aggressive disease progression, while a previously described potentially protective microglia phenotype is depleted in ALS. Additionally, we observe an enrichment of non-microglial immune cell, mainly NK/T cells, in ALS central nervous system, primarily in the spinal cord. These findings pave the way for the development of microglia subset-specific therapeutic interventions to slow or even stop ALS progression.

neuroscience↗

bioRxiv2024

4D bioprinting shape-morphing tissues in granular support hydrogels: Sculpting structure and guiding maturation

During embryogenesis, organs undergo dynamic shape transformations that sculpt their final shape, composition, and function. Despite this, current organ bioprinting approaches typically employ bioinks that restrict cell-generated morphogenetic behaviours resulting in structurally static tissues. Here, we introduce a novel platform that enables the bioprinting of tissues that undergo programmable and predictable 4D shape-morphing driven by cell-generated forces. Our method utilises embedded bioprinting to deposit collagen-hyaluronic acid bioinks within yield-stress granular support hydrogels that can accommodate and regulate 4D shape-morphing through their viscoelastic properties. Importantly, we demonstrate precise control over 4D shape-morphing by modulating factors such as the initial print geometry, cell phenotype, bioink composition, and support hydrogel viscoelasticity. Further, we observed that shape-morphing actively sculpts cell and extracellular matrix alignment along the principal tissue axis through a stress-avoidance mechanism. To enable predictive design of 4D shape-morphing patterns, we developed a finite element model that accurately captures shape evolution at both the cellular and tissue levels. Finally, we show that programmed 4D shape-morphing enhances the structural and functional properties of iPSC-derived heart tissues. This ability to design, predict, and program 4D shape-morphing holds great potential for engineering organ rudiments that recapitulate morphogenetic processes to sculpt their final shape, composition, and function.

bioengineering↗

bioRxiv2024

Selective regulation of a defined subset of inflammatory and immunoregulatory genes by an NF-κB p50-IκBζ pathway

The five NF-{kappa}B family members and three nuclear I{kappa}B proteins play important biological roles, but the mechanisms by which distinct NF-{kappa}B and I{kappa}B proteins contribute to selective gene transcription remain poorly understood, especially at a genome-scale level. Using nascent transcript RNA-seq, we observed considerable overlap between p50-dependent and I{kappa}B{zeta}-dependent genes in Toll-like receptor 4 (TLR4)-activated macrophages. Key immunoregulatory genes, including Il6, Il1b, Nos2, Lcn2, and Batf, are among the p50-I{kappa}B{zeta} co-dependent genes. I{kappa}B{zeta} bound genomic sites occupied by NF-{kappa}B dimers at earlier time points. However, p50-I{kappa}B{zeta} co-dependence does not coincide with preferential binding of either p50 or I{kappa}B{zeta}, as both proteins and RelA co-occupy thousands of genomic sites. A common feature of p50-I{kappa}B{zeta} co-dependent genes is a nearby p50/RelA/I{kappa}B{zeta} co-bound site exhibiting p50-dependent binding of both RelA and I{kappa}B{zeta}. This result and others suggest that I{kappa}B{zeta} may act in concert with RelA:p50 heterodimers. Notably, the I{kappa}B{zeta}-dependent and p50-I{kappa}B{zeta}-co-dependent genes comprise a high percentage of genes that exhibit the greatest differential expression between TLR4-stimulated and tumor necrosis factor receptor (TNFR)-stimulated macrophages. Thus, our genome-centric analysis reveals a defined p50-I{kappa}B{zeta} pathway that selectively activates a set of key immunoregulatory genes and serves as an important contributor to the differential TNFR and TLR4 responses.

immunology↗

bioRxiv2022

Bioprinting in granular support hydrogels - characterizing the role of particle morphology and packing density

Despite significant advances in bioprinting technology, current hardware platforms lack the capability for process monitoring and quality control. This limitation hampers the translation of the technology into industrial GMP-compliant manufacturing settings. To address this, we developed a novel bioprinting platform integrating a high-resolution camera for in-situ monitoring of extrusion outcomes during embedded bioprinting. Leveraging classical computer vision and image analysis techniques, we then created a custom software module for assessing print quality. This module enables quantitative comparison of printer outputs to input CAD models, measuring area and positional accuracy. To showcase the platforms capabilities, we then investigated how the rheological properties of granular support hydrogels impact print quality during embedded bioprinting. Our results demonstrated that lower viscosity, faster thixotropy recovery, and smaller particle sizes significantly enhance print fidelity. This novel bioprinting platform, equipped with integrated process monitoring, holds great potential for establishing robust, reliable, and auditable biofabrication processes for industrial applications.

bioengineering↗