Biology subjects

O'Toole, K.

Publications and source records attributed to O'Toole, K..

3 recordsLinked to original sources

bioRxiv2026

Leaf and root microbiome signatures of gray mangrove trees in the Red Sea

Mangroves persist under strong environmental constraints with support from microbes. Although microbial communities differ among mangrove compartments, their assembly mechanisms and compartment-specific functional signatures remain poorly resolved. Here, we combine peptide nucleic acid-clamping coupled with 16S rRNA gene amplicon sequencing and genome-resolved metagenomics to investigate the microbial communities associated with the leaves and roots of gray mangrove trees in the Red Sea. Our results suggest homogeneous selection and homogenizing dispersal as key processes of microbial community assembly in leaves. This phyllosphere hosts novel prokaryotic lineages, with some of its members probably synthesizing rhodopsins, plant polysaccharide-degrading enzymes, and gamma-aminobutyric acid, a metabolite that increase tolerance to salinity stress. Genomes affiliated with Desulfobacterales and Sedimenticolaceae taxa are abundant belowground, suggesting complementary sulfur- and nitrogen-cycling capacities similar as occur in other blue-carbon ecosystems. Comparison with root-derived genomes from cordgrass revealed a host-driven selection of Sedimenticolaceae species with convergent metabolic profiles. Overall, this study provides an integrative view about the microbial biology of gray mangrove trees, offering foundational insights into the diversity, ecology, and predictive functionality of their aboveground-belowground microbiomes.

microbiology↗

bioRxiv2024

Generation of morphologically distinct astrocyte subtypes from human iPSCs reveals a link between glial shape, function and reactivity

Astrocyte morphology in vivo is heterogeneous across different subtypes and dynamically changes in response to various stimuli. However, several questions on the mechanistic links between shape and function remain unanswered. Here, we developed an efficient protocol to generate pure populations of morphologically distinct human astrocytes in vitro, which we used for a systematic analysis of shape-function relationships. We performed a structural, molecular, and functional characterization of these populations and highlighted how their distinct morphologies mirror distinct functional and transcriptional patterns at the population level. We were also able to both correlate gene expression profiles of these morphologically distinct astrocyte subtypes with in vivo astrocytes in the human brain, and to validate our findings with primary isolated murine astrocytes in vitro. Moreover, we show that the observed morphological differences are correlated with changes in key cytoskeletal proteins, which offers a potential link to the observed functional differences. Finally, we demonstrated that different morphological subtypes of astrocytes have distinct reactivity responses to a common stimulus. This study offers a glimpse into the shape-function dynamics of human astrocytes, highlighting potential mechanistic links between cytoskeletal usage and astrocyte function, while also providing tools and datasets that will be useful for further studies into human glial biology in health and disease.

neuroscience↗

bioRxiv2022

Combining SLA 3D printing and soft lithography for fast, versatile, and accessible high-resolution fabrication of customised multiscale cell culture devices with complex designs

Cell culture devices, such as microwells and microfluidic chips, are designed to increase the complexity of cell-based models whilst retaining control over culture conditions and have become indispensable platforms for biological systems modelling. From microtopography, microwells, plating devices and microfluidic systems to larger constructs for specific applications such as live imaging chamber slides, a wide variety of culture devices with different geometries have become indispensable in biology laboratories. However, while their application in biological projects is increasing exponentially, due to a combination of the techniques and tools required for their manufacture, and the physical science background sometimes needed, the design and fabrication of such devices directly by biological labs remains a relatively high investment in terms of costs, use of facilities, needed collaborations and time. Whilst commercially available systems are available, these are also often costly, and importantly lack the potential for customisation by each single lab. This combination of factors still limits widespread application of microfabricated custom devices in most biological wet labs. Capitalising on recent important advancements in the fields of bioengineering and microfabrication, and taking advantage of low-cost, high-resolution desktop resin 3D printers combined with PDMS soft lithography, we have developed an optimised low-cost and highly reproducible microfabrication pipeline, capable of generating a wide variety of customisable devices for cell culture and tissue engineering in an easy, fast reproducible way for a fraction of the cost of conventional microfabrication or commercial alternatives. This protocol is designed specifically to be a resource for biological labs with little to none prior exposure to these fields technique and enables the manufacture of complex devices across the {micro}m to cm scale. We provide a ready-to-go pipeline for the efficient treatment of resin-based 3D printed constructs for PDMS curing, using a combination of curing steps, washes and surface treatments. Together with the extensive characterisation of the fabrication pipeline, we show the utilization of this system to a variety of applications and use cases relevant to biological experiments, ranging from micro topographies for cell alignments to complex multi-part hydrogel culturing systems. This methodology can be easily adopted by any wet lab, irrespective of prior expertise or resource availability and will enable the wide adoption of tailored microfabricated devices across many fields of biology.

bioengineering↗