Biology subjects

Buchan, A.

Publications and source records attributed to Buchan, A..

9 recordsLinked to original sources

bioRxiv2026

Dual MMP-9/12 Inhibition with AZD1236 Confers Neurovascular Protection and Reduces Post-Stroke Pain in Experimental Stroke Models.

Background: Stroke remains a leading cause of death and disability worldwide. Matrix metalloproteinases (MMPs), particularly MMP-9 and MMP-12, contribute to early blood-brain barrier (BBB) disruption, neuroinflammation, haemorrhagic transformation, and intracerebral haemorrhage (ICH). Intravenous thrombolysis is the only widely used pharmacological therapy for acute ischaemic stroke, but its utility is limited by narrow eligibility criteria and haemorrhagic risk. Inhibition of MMPs in the acute phase may offer a complementary neurovascular protective strategy. Methods: AZD1236, a selective dual MMP-9/-12 inhibitor, was evaluated in transient and permanent middle cerebral artery occlusion models and in a collagenase-induced ICH model in young, aged, obese, and female mice. Drug or vehicle was administered 2-6 hours after stroke onset. Outcomes included infarct or haematoma volume, BBB integrity, neurological function, and pain-related behaviours. Results: AZD1236 given within 2-4 hours after ischaemic or haemorrhagic insult significantly reduced infarct and haematoma volumes, improved short- and long-term neurological scores, and preserved BBB integrity, whereas treatment at 6 hours was largely ineffective. AZD1236 also attenuated the development of post-stroke mechanical allodynia and thermal hyperalgesia. Mechanistically, treatment reduced MMP-9 and MMP-12 activity, increased tight junction protein expression, and dampened inflammatory responses. Conclusions: Dual inhibition of MMP-9/-12 with AZD1236 confers robust neurovascular protection and mitigates post-stroke pain across clinically relevant models of ischaemic and haemorrhagic stroke. These findings provide a strong preclinical rationale for clinical evaluation of dual MMP-9/12 inhibition as an adjunctive neuroprotective strategy for acute stroke.

neuroscience↗

bioRxiv2026

Multimodal molecular profiling of the metabolic penumbra in hyperacute stroke

BackgroundThe ischemic penumbra, a metabolically compromised yet potentially salvageable region surrounding the ischemic core, is a prime target for acute stroke intervention. Yet an objective molecular definition of the penumbra, particularly during the earliest stages of ischemia, remains lacking. Methods and ResultsWe applied principal component analysis (PCA) followed by k-means clustering to high-resolution mass spectrometry imaging data covering multiple metabolic pathways to identify a metabolically defined penumbra in a mouse model of hyperacute stroke (45 min middle cerebral artery occlusion, MCAO). Targeted spatial metabolomic profiling by matrix-assisted laser desorption/ionization (MALDI) and desorption electrospray ionization (DESI) reveals a distinct penumbral metabolic profile, marked by relative preservation of high-energy phosphates, comparable lactate accumulation, and reduced succinate accumulation relative to the core. Spatial transcriptomics revealed selective induction of immediate-early genes, including Npas4, Fos and Junb, within the penumbra. Consistently, imaging mass cytometry shows enrichment of phospho-histone H3 (pHH3) within the penumbra, suggesting a chromatin-associated response potentially linked to immediate-early gene activation. ConclusionTogether, these findings provide a multimodal molecular atlas of the hyperacute metabolically defined penumbra and reveal molecular features that facilitates its identification and inform future therapeutic strategies.

neuroscience↗

bioRxiv2025

Prophage induction states drive structural and synergistic outcomes in marine bacterial biofilms

Microbes commonly live in biofilms, dense spatially structured assemblages where temperate phages can influence interactions amongst closely related strains. Yet, how these phage-host interactions impact biofilm architecture and ecological dynamics remains poorly understood, particularly in situations where antagonistic strains coexist in structured communities. In the marine Roseobacteraceae Sulfitobacter pontiacus, two genetically similar heteroimmune prophages, (termed A and D) establish lysogeny in their host. Depending on the host plasmid genotype, prophages are fixed in either high or low induction states, which consequently shape both biofilm structure and competitive outcomes. Using confocal scanning laser microscopy of fluorescently labeled lysogens, we investigated how prophage induction and phage genotype of phage-host coalitions influence monoculture and co-culture (competitive) S. pontiacus biofilms grown at a fluid-solid interface. Compared to their low induction counterparts, high-induction strains formed thicker and more voluminous monoculture biofilms, which primarily result from vertical protrusions arising from a basal monolayer. In co-culture experiments - mixing strains with reciprocal prophage genotypes that can mutually kill each other through phage-mediated allelopathy - we observed unexpected coexistence and synergistic biofilm enhancement rather than competitive exclusion. Reactive oxygen species (ROS) levels were significantly higher in co-cultures than monocultures and correlated with local cell density, suggesting that phage-mediated interactions generate hotspots of oxidative stress, which is expected to further promote prophage induction, creating a positive feedback loop that amplifies cell lysis and release of matrix components. These results suggest temperate phages can paradoxically stabilize and promote biofilm growth via mechanisms that combine antagonistic killing with cooperative matrix production, revealing how phage-mediated interactions can shape microbial community architecture in spatially structured environments. IMPORTANCEBacterial biofilms are ubiquitous in natural environments, yet understanding of how temperate bacteriophages shape biofilm development and microbial community dynamics remains limited. Here, we demonstrate that prophage induction state simultaneously drives antagonistic killing and cooperative biofilm enhancement in spatially structured microbial communities. Using Sulfitobacter pontiacus and its infecting temperate phages as a model system, we reveal that reciprocally antagonistic host-phage pairs, which can kill each other through phage-mediated allelopathy, form more robust biofilms when grown together rather than separately. These findings challenge traditional views of competition in dense microbial systems, highlighting the complex, multi-faceted roles that temperate phages play in microbial communities. Additionally, we propose that oxidative stress creates positive feedback loops that amplify prophage induction, promoting coexistence of host-phage pairs rather than driving competitive exclusion. These insights have broad implications for understanding microbial community assembly, maintenance of genetic diversity in biofilms, and evolutionary dynamics of host-phage interactions in structured environments.

microbiology↗

bioRxiv2025

Comparative genomics reveals multipartite genomes undergoing loss in the fungal endosymbiotic genus Mycetohabitans

Endosymbiotic bacteria extensively impact phenotypes of their eukaryotic hosts, while experiencing dramatic changes to their own genome as they become more host-restricted in lifestyle. Understanding the trajectory of such a genome has largely been done through study of animal-associated bacteria, especially insect endosymbionts. Yet, endofungal bacteria provide another natural experimental model for investigating how microbial genomes change when living inside of a host cell. Mycetohabitans spp. are culturable bacterial endosymbionts of the Mucoromycota fungus Rhizopus microsporus. To investigate the genome dynamics resulting from the endohyphal nature of this emerging model genus, we long-read sequenced and assembled new complete genomes to combine with previous assemblies, creating a global dataset of 28 complete Mycetohabitans genomes. All genomes were between 3.3 and 3.9 Mbp in size and were multipartite, structured into two conserved replicons with some strains having an additional plasmid. Based on evolutionary rate and gene content analysis of the different replicons, we termed the two major ones a chromosome and chromid. The differential presence of a third, mobilome-rich plasmid in some strains and the proliferation of transposable elements provide putative mechanisms for recombination or gene loss. The conservation of intact prophage and putative toxin-antitoxin systems, and extensive enrichment of secondary metabolite clusters in the Mycetohabitans genomes highlight the dynamic nature of this reducing genome. With fungal-bacterial symbioses becoming increasingly apparent phenomena, lessons learned from this symbiosis will inform our understanding of bacterial adaptation to novel hosts, and the process of microbe-microbe coevolution. SIGNIFICANCEGenomes change when organisms become closely associated, as bacterial partners undergo less opportunities for genetic exchange and become more reliant on their hosts. Our pangenome analysis of the endofungal genus Mycetohabitans shows a snapshot of evolution where the bacteria are moving from a facultative towards an obligate relationship with their host fungi. We find that Mycetohabitans genomes are marked by transposable elements, pseudogenes, a large biosynthetic repertoire, and novel bacteriophage. We provide a genomic resource to match publicly accessible strains for future work on endosymbiotic genetics and evolution.

genomics↗

bioRxiv2025

Seasonal Enhancement of the Viral Shunt Catalyzes a Subsurface Oxygen Maximum in the Sargasso Sea

Subsurface oxygen maxima (SOMs) occur directly beneath the mixed layer of stratified water columns across oligotrophic open ocean basins. SOMs occur seasonally and are hypothesized to result from elevated microbial net primary productivity (NPP). Here, we set out to identify mechanistic drivers of the SOM near the Bermuda Atlantic Time Series (BATS) site in the Sargasso Sea in October 2019. Coupled time-series analysis of metatranscriptomics, flow cytometry, and family-specific cyanophage quantification revealed elevated Prochlorococcus abundances, cyanophage abundances, and cyanophage-specific transcriptional activity in the SOM. These findings spurred us to analyze historical oxygen saturation profiles at BATS - identifying a repeated, seasonal cycle in SOM emergence associated with elevated virus-like particles and Prochlorococcus numbers. Returning to the 2019 study site, we found that transcriptional markers for increased dissolved organic matter uptake by copiotrophic bacteria were enriched in the SOM, consistent with enhanced catabolic activity due to the viral shunt. In addition, Prochlorococcus exhibited enrichment in ammonium transport transcripts at the SOM, consistent with increased responsiveness to remineralization activity by heterotrophs. Altogether, these findings suggest that enhanced viral lysis leads to locally elevated nutrient recycling and oxygen production, further reinforcing hypotheses that viruses may play a critical role in the emergence of SOMs in the oligotrophic ocean.

ecology↗

bioRxiv2024

Unlocking the genomic repertoire of a cultivated megaphage

Megaphages are bacteriophages (i.e., phages) with exceptionally large genomes that are ecosystem cosmopolitans, infect various bacterial hosts, and have been discovered across various metagenomic datasets globally. To date, almost all megaphages have evaded cultivation, with only phage G being in active culture for over 50 years. We examined with multiomics this five decades long cultivated history from nine different laboratories with five different lab variants to the modern era. In this work, we resolved the five complete phage G genomes, the particle proteome, de novo methylome, and used artificial intelligence (AI) to annotate the genome of phage G. Phage G is one of the largest phages with a size of >0.6 {micro}m, about half the width of the host cell, and a 499 kbp, non-permuted, linear genome that has, uniquely among known phages, two pairs of ends. Its closest known relative is Moose phage W30-1 which was metagenomically assembled without cultivation from a moose rumen sample. Phage G has >650 protein-coding open reading frames (ORFs), with >65% being hypothetical proteins with no known function, with the rest of the genome geared towards nucleic acid replication (e.g., helicases, polymerases, endonucleases) and are structural in nature (e.g., capsid, tail, portal, terminase). The genome encodes a 35 kbp stretch with 66 ORFs without any known functional homology, a cryptic genomic region that is roughly the size of phage lambda. Phage G has an expansive repertoire of auxiliary metabolic genes (AMGs) acquired from its bacterial host, including a phoH,ftsZ,UvsX/RecA-like, gyrA, gyrB,and DHFR. Furthermore, AMGs discovered in phage G could manipulate host sporulation (sspD, RsfA, spoK) and antiviral escape genes (e.g., anti-CBass nuclease and Anti-Pycsar protein). Phage proteomics found >15% of the protein ORFs were present in either the wild-type or mutant variants of phage G, including genes involved in replication (e.g.,UvsX/RecA-like), host sporulation, as well as structural genes (e.g., capsid, tail, portal). The methylome of phage G was localized to the cryptic region with limited functional homology, with supervised machine learning (i.e., HMMs) was unable to resolve this region, but was resolved with protein structural AI. This cryptic region was a hot spot for methylation at 32%, where many of the functions of the ORF are still unknown. Our study represents a doorway into the complexity of the genomic repertoire of the only cultivated megaphage, highlighting five decades of continuous cultivation for the first time.

microbiology↗

bioRxiv2022

Metabolic clearance rate modeling: A translational approach to quantifying cerebral metabolism using hyperpolarized pyruvate.

Hyperpolarized carbon-13 MRI is a promising technique for in vivo metabolic interrogation of alterations between health and disease. This study introduces a model-free formalism for quantifying the metabolic information in hyperpolarized imaging. This study investigated a novel model-free perfusion and metabolic clearance rate (MCR) model in pre-clinical stroke and in the healthy human brain. Simulations showed that the proposed model was robust to perturbations in T1, transmit B1, and kPL. A significant difference in ipsilateral vs contralateral pyruvate derived cerebral blood flow (CBF) was detected in rats (140 {+/-} 2 vs 89 {+/-} 6 mL/100g/min, p < 0.01, respectively) and pigs (139 {+/-} 12 vs 95 {+/-} 5 mL/100g/min, p = 0.04, respectively), along with an increase in fractional metabolism (26 {+/-} 5 vs 4 {+/-} 2 %, p < 0.01, respectively) in the rodent brain. In addition, a significant increase in ipsilateral vs contralateral MCR (0.034 {+/-} 0.007 vs 0.017 {+/-} 0.02 s-1, p = 0.03, respectively) and a decrease in mean transit time (MTT) (31 {+/-} 8 vs 60 {+/-} 2, p = 0.04, respectively) was observed in the porcine brain. In conclusion, MCR mapping is a simple and robust approach to the post-processing of hyperpolarized magnetic resonance imaging.

physiology↗

bioRxiv2020

Ecology of inorganic sulfur auxiliary metabolism in widespread bacteriophages

Microbial sulfur metabolism contributes to biogeochemical cycling on global scales. Sulfur metabolizing microbes are infected by phages that can encode auxiliary metabolic genes (AMGs) to alter sulfur metabolism within host cells but remain poorly characterized. Here we identified 191 phages derived from twelve environments that encoded 227 AMGs for oxidation of sulfur and thiosulfate (dsrA, dsrC/tusE, soxC, soxD and soxYZ). Evidence for retention of AMGs during niche-differentiation of diverse phage populations provided evidence that auxiliary metabolism imparts measurable fitness benefits to phages with ramifications for ecosystem biogeochemistry. Gene abundance and expression profiles of AMGs suggested significant contributions by phages to sulfur and thiosulfate oxidation in freshwater lakes and oceans, and a sensitive response to changing sulfur concentrations in hydrothermal environments. Overall, our study provides novel insights on the distribution, diversity and ecology of phage auxiliary metabolism associated with sulfur and reinforces the necessity of incorporating viral contributions into biogeochemical configurations.

microbiology↗

bioRxiv2019

Characterization of the interactive effects of labile and recalcitrant organic matter on microbial growth and metabolism

Geochemical models typically represent organic matter (OM) as consisting of multiple, independent pools of compounds, each accessed by microorganisms at different rates. However, recent findings indicate that organic compounds can interact within microbial metabolisms. The relevance of interactive effects within marine systems is debated and a mechanistic understanding of its complexities, including microbe-substrate relationships, is lacking. As a first step toward uncovering mediating processes, the interactive effects of distinct pools of OM on the growth and respiration of marine bacteria, individual strains and a simple, constructed community of Roseobacter lineage members were tested. Isolates were provided with natural organic matter (NOM) and different concentrations (1, 4, 40, 400 M-C) and forms of labile organic matter (acetate, casamino acids, tryptone, coumarate). The microbial response to the mixed substrate regimes was assessed using viable counts and respiration in two separate experiments. Two marine bacteria and a six-member constructed community were assayed with these experiments. Both synergistic and antagonistic growth responses were evident for all strains, but all were transient. The specific substrate conditions promoting a response, and the direction of that response, varied amongst species. These findings indicate that the substrate conditions that result in OM interactive effects are both transient and species-specific and thus influenced by both the composition and metabolic potential of a microbial community.

microbiology↗