Biology subjects

Reynolds, S.

Publications and source records attributed to Reynolds, S..

16 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

Environmental Drivers and Distribution of Pathogenic Vibrio Species in the Teign Estuary, UK

Climate-driven increases in sea surface temperature have been associated with the expansion of Vibrio species and a corresponding rise in vibriosis cases in both human populations and aquaculture systems. Coastal waters across the south of England are increasingly becoming suitable for the growth and establishment of both human- and aquaculture-associated Vibrio species, potentially increasing vulnerability to the types of infections and disease outbreaks already reported elsewhere in the world. In this study, we report the presence of a diverse and well-established Vibrio community within the Teign Estuary, (Southwest, UK), including the human-pathogenic species V. parahaemolyticus, V. cholerae (non-O1/non-O139), V. alginolyticus, and V. diabolicus, as well as the important aquaculture pathogens V. jasicida, V. aestuarianus, and V. anguillarum. We identified V. diabolicus, a species that was indistinguishable from V. alginolyticus using conventional biochemical identification methods and could only be accurately resolved by whole-genome sequencing and developed novel PCR targets to differentiate these species in the lab. Using the insect infection model Galleria mellonella, we demonstrate that environmental isolates of V. cholerae (non-O1/non-O139), V. parahaemolyticus, and V. alginolyticus possess virulence potential. We also investigated the effects of sewage effluent on the growth of Vibrio isolates from the Teign Estuary and found that sewage can preferentially promote the growth of Vibrio species. Furthermore, several Vibrio isolates were multidrug resistant and carried antimicrobial resistance genes, highlighting the potential role of environmental Vibrio populations in the Teign Estuary as reservoirs of antimicrobial resistance. Together, these findings demonstrate how rising sea surface temperatures and sewage pollution may influence the emergence, persistence, and public health and aquaculture significance of Vibrio species in UK coastal waters.

microbiology↗

bioRxiv2026

Opportunities and pitfalls in preclinical cerebral blood flow mapping using arterial spin labelling MRI: insights from multicentre data

Cerebral blood flow (CBF) is a quantitative metric for mapping perfusion. While the prototypical MRI approach arterial spin labelling (ASL) is well-validated in humans, the reproducibility of rodent ASL mapping remains poor, limiting translational impact. To address this gap, we used both newly acquired and analysis of previously published data to illustrate biological and physical sources of variation in CBF measured with ASL. Via a meta-analysis, we quantified the variation in CBF reported from the cortex of healthy rodents. A total of 23 mouse studies (343 data points) and 5 rat studies (41 data points) met the inclusion criteria. We demonstrate that reported CBF values exhibit a broad variability (50-400 ml/100g/min) driven primarily by experimental confounds rather than physiological differences. Our meta-analysis explores which factors cause variance in perfusion rates measured. Our experimental data highlight biological factors, particularly the choice of anaesthesia (e.g., isoflurane vs. medetomidine) and strain variations, that alter baseline CBF. Our work, reflecting both state-of-the-art and conventional practice in preclinical imaging, highlights the need to account for multiple sources of variability. Establishing community guidelines for rigorous ASL calibration and physiological monitoring will support improved study design and accelerate translational alignment between rodent and human perfusion measurements. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=172 SRC="FIGDIR/small/733736v1_ufig1.gif" ALT="Figure 1"> View larger version (47K): org.highwire.dtl.DTLVardef@1e94d5org.highwire.dtl.DTLVardef@1bd5718org.highwire.dtl.DTLVardef@1a0fafcorg.highwire.dtl.DTLVardef@1bde97d_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2025

Temperature and predation alter metabolic scaling without changing size-based structure community in freshwater macroinvertebrates

Body size is a key trait that influences ecological processes such as metabolism, abundance, and species interactions. While the metabolic theory of ecology (MTE) proposes a universal scaling of metabolic rate with body mass, recent evidence shows that this relationship is not fixed. Environmental factors like temperature and predation can alter the metabolic scaling exponent, potentially reshaping size distribution. However, most research has examined these patterns within individual species, leaving open questions about how environmental drivers affect scaling at the community level. To address this, we performed a mesocosm experiment manipulating both temperature and fish predator presence in freshwater macroinvertebrate communities. We found that metabolic scaling at the community level is highly responsive to environmental context: warming steepened the scaling exponent in predator-free tanks but flattened it when predators were present. This suggests that larger individuals reduce their baseline metabolic rates under predation risk, especially at higher temperatures. Interestingly, the slope of the community size distribution remained stable across treatments, indicating that shifts in metabolic scaling occurred independently of changes in size structure. Together, these findings highlight the environmental sensitivity of metabolic scaling and suggest that links between metabolism scaling and size distribution may be more complex than MTE predicts.

ecology↗

bioRxiv2023

mRNA Vaccines Encoding Influenza Virus Hemagglutinin (HA) Elicits Immunity in Mice from Influenza A Virus Challenge

Influenza viruses cause epidemics and can cause pandemics with substantial morbidity with some mortality every year. Seasonal influenza vaccines have incomplete effectiveness and elicit a narrow antibody response that often does not protect against mutations occurring in influenza viruses. Thus, various vaccine approaches have been investigated to improve safety and efficacy. Here, we evaluate an mRNA influenza vaccine encoding hemagglutinin (HA) proteins in a BALB/c mouse model. The results show that mRNA vaccination elicits neutralizing and serum antibodies to each influenza virus strain contained in the current quadrivalent vaccine that is designed to protect against four different influenza viruses including two influenza A viruses (IAV) and two influenza B (IBV), as well as several antigenically distinct influenza virus strains in both hemagglutination inhibition assay (HAI) and virus neutralization assays. The quadrivalent mRNA vaccines had antibody titers comparable to the antibodies elicited by the monovalent vaccines to each tested virus regardless of dosage following an mRNA booster vaccine. Mice vaccinated with mRNA encoding an H1 HA had decreased weight loss and decreased lung viral titers compared to mice not vaccinated with an mRNA encoding an H1 HA. Overall, this study demonstrates the efficacy of mRNA-based seasonal influenza vaccines are their potential to replace both the currently available split-inactivated, and live-attenuated seasonal influenza vaccines.

immunology↗

bioRxiv2022

Longitudinal brain studies in adult zebrafish by MRI

Zebrafish (Danio rerio) has been successfully used for decades in developmental studies and disease modelling. The remarkable intake of zebrafish as a model system is partly due to its transparency during the early weeks of its development, allowing in vivo imaging of cellular and molecular processes. However, this key advantage wears off when tissues become opaque as the animal reaches juvenile and adult stages, rendering access to tissues for live imaging and longitudinal studies difficult. Here we aimed to provide a novel approach to image and assess tissue integrity of adult zebrafish using Magnetic Resonance Imaging (MRI) on live zebrafish suitable for longitudinal studies. We built a 3D-printed life support chamber and designed a protocol-directed sedation regime to recover adult zebrafish post scanning in a 9.4T MRI scanner. Our life support chamber is cheap and easy to create using 3D printing, allowing other groups to copy our template for quick setup. Additionally, we optimised the delivery of contrast agent to enhance brain signals in order to refine current delivery, usually delivered by intravenous in rodents. We show here that immersion in gadolinium was a viable alternative to intraperitoneal injection to reduce T1 relaxation times. This could lead to improved image contrast in adult zebrafish disease models. In conclusion, we provide here a detailed methodology to allow longitudinal studies of brain tissue integrity of adult zebrafish, combining safe and efficient delivery of contrast agent and live MRI. This technique can be used to bridge the gap between in vivo studies and longitudinal brain analysis in adult zebrafish which can be applied to the ever-growing number of adult zebrafish models of ageing and neurodegenerative diseases.

neuroscience↗

bioRxiv2021

Sleep problems in preschoolers with autism spectrum disorders are associated with sensory sensitivities and thalamocortical overconnectivity

Projections between the thalamus and sensory cortices are established early in development and play an important role in sleep regulation as well as in relaying sensory information to cortex. Atypical thalamocortical functional connectivity frequently observed in children with autism spectrum disorders (ASD) might therefore be linked to sensory and sleep problems common in ASD. Here we investigated the relationship between auditory-thalamic functional connectivity measured during natural sleep fMRI, sleep problems, and sound sensitivities in 70 toddlers and preschoolers (1.5 to 5-year-olds) with ASD compared to a matched group of 46 typically developing (TD) children. In children with ASD, sleep problems and sensory sensitivities were positively correlated, and increased sleep latency was associated with overconnectivity between the thalamus and auditory cortex in a subsample with high quality MRI data (n=29). Additionally, auditory cortex BOLD signal amplitude was elevated in children with ASD, potentially reflecting reduced sensory gating or a lack of auditory habituation during natural sleep. These findings indicate that atypical thalamocortical functional connectivity can be detected early in development and may play a crucial role in sleep problems and sensory sensitivities in ASD.

neuroscience↗

bioRxiv2020

Differential vaginal Lactobacillus species metabolism of glucose, L and D-lactate by 13C-nuclear magnetic resonance spectroscopy

IntroductionCervicovaginal dysbiosis can lead to infection-associated spontaneous preterm birth. ObjectiveTo determine whether vaginal Lactobacillus species, L. crispatus and L. jensenii, differentially metabolise glucose, L- and/or D-lactate to propagate their survival/dominance. MethodsBacteria were incubated anaerobically for 24h at 37{degrees}C, with 13Cu-glucose, 13C3-D-lactate or 13C3-L-lactate (singularly or combined) for 24h. 13C-spectra were acquired using a 9.4T NMR spectrometer. ResultsL. crispatus and L. jensenii (n=6 each) metabolised 13C-glucose to 13C-lactate and 13C-acetate. L. jensenii converted more 13C3-D- or 13C3-L-lactate to 13C-acetate than L. crispatus, p<0.001. ConclusionConversion of glucose and lactate to acetate by L. jensenii compared to L. crispatus, suggests a possibly important pathomechanism of dysbiosis and infection-associated spontaneous preterm birth.

microbiology↗

bioRxiv2018

Mathematical Modeling Identifies the Role of Adaptive Immunity as a Key Controller of Respiratory Syncytial Virus (RSV) Titer in Cotton Rats

Respiratory syncytial virus (RSV) is a common virus that can have varying effects ranging from mild cold-like symptoms to mortality depending on the age and immune status of the individual. We combined mathematical modeling using ordinary differential equations (ODEs) with measurement of RSV infection kinetics in primary well differentiated human airway epithelial (HAE) cultures in vitro and in immunocompetent and immunosuppressed cotton rats to glean mechanistic details that underlie RSV infection kinetics in the lung. Quantitative analysis of viral titer kinetics in our mathematical model showed that the elimination of infected cells by the adaptive immune response generates unique RSV titer kinetic features including a faster time scale of viral titer clearance than viral production, and a monotonic decrease in the peak RSV titer with decreasing inoculum dose. Parameter estimation in the ODE model using a non-linear mixed effects approach revealed a very low rate (average single cell lifetime > 10 days) of cell lysis by RSV before the adaptive immune response is initiated. Our model predicted negligible changes in the RSV titer kinetics on earlier days (< 5 d.p.i) but a slower decay in RSV titer at later days (>5 d.p.i) in immunosuppressed cotton rats compared to that in non-suppressed cotton rats in silico. These predictions were in excellent agreement with the experimental results. Our combined approach quantified the importance of the adaptive immune response in suppressing RSV infection in cotton rats, which could be useful in testing RSV vaccine candidates.\n\nImportanceA major difficulty in developing vaccines against RSV infection is our rudimentary understanding of the mechanisms that underlie RSV infection. We addressed this challenge by developing a mechanistic computational model with predictive powers for describing RSV infection kinetics in cotton rats. The model was constructed synergistically with in vitro and in vivo measurements. The combined framework determined an important role for CD8+ T cells responses in reducing RSV titers in cotton rats. The framework can be used to design future experiments to elucidate mechanisms underlying RSV infection and test outcomes for potential vaccine candidates. In addition, estimation of the model parameters provides quantitative values for parameters of biological and clinical interest such as the replication rate of RSV, the death rate of infected cells, and the average number of new infections initiated by a single infected cell.

microbiology↗

bioRxiv2018

Mathematical Modeling Identifies the Role of Adaptive Immunity as a Key Controller of Respiratory Syncytial Virus (RSV) Titer in Cotton Rats

Respiratory syncytial virus (RSV) is a common virus that can have varying effects ranging from mild cold-like symptoms to mortality depending on the age and immune status of the individual. We combined mathematical modeling using ordinary differential equations (ODEs) with measurement of RSV infection kinetics in primary well differentiated human airway epithelial (HAE) cultures in vitro and in immunocompetent and immunosuppressed cotton rats to glean mechanistic details that underlie RSV infection kinetics in the lung. Quantitative analysis of viral titer kinetics in our mathematical model showed that the elimination of infected cells by the adaptive immune response generates unique RSV titer kinetic features including a faster time scale of viral titer clearance than viral production, and a monotonic decrease in the peak RSV titer with decreasing inoculum dose. Parameter estimation in the ODE model using a non-linear mixed effects approach revealed a very low rate (average single cell lifetime > 10 days) of cell lysis by RSV before the adaptive immune response is initiated. Our model predicted negligible changes in the RSV titer kinetics on earlier days (< 5 d.p.i) but a slower decay in RSV titer in immunosuppressed cotton rats compared to that in non-suppressed cotton rats at later days (>5 d.p.i) in silico. These predictions were in excellent agreement with the experimental results. Our combined approach quantified the importance of the adaptive immune response in suppressing RSV infection in cotton rats, which could be useful in testing RSV vaccine candidates.\n\nImportanceA major difficulty in developing vaccines against RSV infection is our rudimentary understanding of the mechanisms that underlie RSV infection. We addressed this challenge by developing a mechanistic computational model with predictive powers for describing RSV infection kinetics in cotton rats. The model was constructed synergistically with in vitro and in vivo measurements. The combined framework determined an important role for CD8+ T cells responses in reducing RSV titers in cotton rats. The framework can be used to design future experiments to elucidate mechanisms underlying RSV infection and test outcomes for potential vaccine candidates. In addition, estimation of the model parameters provides quantitative values for parameters of biological and clinical interest such as the replication rate of RSV, the death rate of infected cells, and the average number of new infections initiated by a single infected cell.

microbiology↗

bioRxiv2018

Conserved cell types with divergent features between human and mouse cortex

Elucidating the cellular architecture of the human neocortex is central to understanding our cognitive abilities and susceptibility to disease. Here we applied single nucleus RNA-sequencing to perform a comprehensive analysis of cell types in the middle temporal gyrus of human cerebral cortex. We identify a highly diverse set of excitatory and inhibitory neuronal types that are mostly sparse, with excitatory types being less layer-restricted than expected. Comparison to a similar mouse cortex single cell RNA-sequencing dataset revealed a surprisingly well-conserved cellular architecture that enables matching of homologous types and predictions of human cell type properties. Despite this general conservation, we also find extensive differences between homologous human and mouse cell types, including dramatic alterations in proportions, laminar distributions, gene expression, and morphology. These species-specific features emphasize the importance of directly studying human brain.

neuroscience↗

bioRxiv2017

CosMIC: A Consistent Metric for Spike Inference from Calcium Imaging

In recent years, the development of algorithms to detect neuronal spiking activity from two-photon calcium imaging data has received much attention. Meanwhile, few researchers have examined the metrics used to assess the similarity of detected spike trains with the ground truth. We highlight the limitations of the two most commonly used metrics, the spike train correlation and success rate, and propose an alternative, which we refer to as CosMIC. Rather than operating on the true and estimated spike trains directly, the proposed metric assesses the similarity of the pulse trains obtained from convolution of the spike trains with a smoothing pulse. The pulse width, which is derived from the statistics of the imaging data, reflects the temporal tolerance of the metric. The final metric score is the size of the commonalities of the pulse trains as a fraction of their average size. Viewed through the lens of set theory, CosMIC resembles a continuous Sorensen-Dice coefficient -- an index commonly used to assess the similarity of discrete, presence/absence data. We demonstrate the ability of the proposed metric to discriminate the precision and recall of spike train estimates. Unlike the spike train correlation, which appears to reward overestimation, the proposed metric score is maximised when the correct number of spikes have been detected. Furthermore, we show that CosMIC is more sensitive to the temporal precision of estimates than the success rate.

neuroscience↗

bioRxiv2017

Multiphoton minimal inertia scanning for fast acquisition of neural activity signals

Multi-photon laser scanning microscopy provides a powerful tool for monitoring the spatiotemporal dynamics of neural circuit activity. It is, however, intrinsically a point scanning technique. Standard raster scanning enables imaging at subcellular resolution; however, acquisition rates are limited by the size of the field of view to be scanned. Recently developed scanning strategies such as Travelling Salesman Scanning (TSS) have been developed to maximize cellular sampling rate by scanning only regions of interest in the field of view corresponding to locations of interest such as somata. However, such strategies are not optimized for the mechanical properties of galvanometric scanners. We describe here the Adaptive Spiral Scanning (SSA) algorithm, which fits a set of near-circular trajectories to the cellular distribution to avoid inertial drifts of galvanometer position. We compare its performance to raster scanning and TSS in terms of cellular sampling frequency and signal-to-noise ratio (SNR). Using surrogate neuron spatial position data, we show that SSA acquisition rates are an order of magnitude higher than those for raster scanning and generally exceed those achieved by TSS for neural densities comparable with those found in the cortex. We show that this result also holds true for in vitro hippocampal mouse brain slices bath loaded with the synthetic calcium dye Cal-520 AM. The ability of TSS to \"park\" the laser on each neuron along the scanning trajectory, however, enables higher SNR than SSA when all targets are precisely scanned. Raster scanning has the highest SNR but at a substantial cost in number of cells scanned. To understand the impact of sampling rate and SNR on functional calcium imaging, we used the Cramer-Rao Bound on evoked calcium traces recorded simultaneously with electrophysiology traces to calculate the lower bound estimate of the spike timing occurrence. The results show that TSS and SSA achieve comparable accuracy in spike time estimates compared to raster scanning despite their lower SNR. SSA is an easily implementable way for standard multi-photon laser scanning systems to gain temporal precision in the detection of action potentials while scanning hundreds of active cells.

neuroscience↗

bioRxiv2017

ABLE: an Activity-Based Level Set Segmentation Algorithm for Two-Photon Calcium Imaging Data

We present an algorithm for detecting the location of cells from two-photon calcium imaging data. In our framework, multiple coupled active contours evolve, guided by a model-based cost function, to identify cell boundaries. An active contour seeks to partition a local region into two subregions, a cell interior and ex-terior, in which all pixels have maximally similar time courses. This simple, local model allows contours to be evolved predominantly independently. When contours are sufficiently close, their evolution is coupled, in a manner that permits overlap. We illustrate the ability of the proposed method to demix overlapping cells on real data. The proposed framework is flexible, incorporating no prior information regarding a cells morphology or stereotypical temporal activity, which enables the detection of cells with diverse properties. We demonstrate algorithm performance on a challenging mouse in vitro dataset, containing synchronously spiking cells, and a manually labelled mouse in vivo dataset, on which ABLE achieves a 67.5% success rate.\n\nSignificance statementTwo-photon calcium imaging enables the study of brain activity during learning and behaviour at single-cell resolution. To decode neuronal spiking activity from the data, algorithms are first required to detect the location of cells in the video. It is still common for scientists to perform this task manually, as the heterogeneity in cell shape and frequency of cellular overlap impede automatic segmentation algorithms. We developed a versatile algorithm based on a popular image segmentation approach (the Level Set Method) and demonstrated its capability to overcome these challenges. We include no assumptions on cell shape or stereotypical temporal activity. This lends our framework the flexibility to be applied to new datasets with minimal adjustment.

neuroscience↗

bioRxiv2017

Pan-cancer analysis reveals complex tumor-specific alternative polyadenylation

Alternative polyadenylation (APA) of 3 untranslated regions (3 UTRs) has been implicated in cancer development. Earlier reports on APA in cancer primarily focused on 3 UTR length modifications, and the conventional wisdom is that tumor cells preferentially express transcripts with shorter 3 UTRs. Here, we analyzed the APA patterns of 114 genes, a select list of oncogenes and tumor suppressors, in 9,939 tumor and 729 normal tissue samples across 33 cancer types using RNA-Seq data from The Cancer Genome Atlas, and we found that the APA regulation machinery is much more complicated than what was previously thought. We report 77 cases (gene-cancer type pairs) of differential 3 UTR cleavage patterns between normal and tumor tissues, involving 33 genes in 13 cancer types. For 15 genes, the tumor-specific cleavage patterns are recurrent across multiple cancer types. While the cleavage patterns in certain genes indicate apparent trends of 3 UTR shortening in tumor samples, over half of the 77 cases imply 3 UTR length change trends in cancer that are more complex than simple shortening or lengthening. This work extends the current understanding of APA regulation in cancer, and demonstrates how large volumes of RNA-seq data generated for characterizing cancer cohorts can be mined to investigate this process.

genomics↗

bioRxiv2017

Imaging seminiferous tubules - a 9.4T MRI mouse model

Fertility problems affect many couples. Research into male fertility commonly uses mouse models due to their availability and similar spermatogenesis to humans. A common target is the seminiferous tubules, the site of spermatozoa production, typically studied using biopsies and histological analysis. High-field Magnetic Resonance (MR) may offer a non-invasive alternative to investigate testicular function in infertility models. Here, we assess seminiferous tubules structure in sacrificed mice to determine the usefulness of MR compared to histology. Twelve mice (11 aged 35-57 days, one >9 months) were sacrificed and MR imaged at 9.4T with a Rapid Acquisition with Relaxation Enhancement sequence. Testes were scanned in situ for all mice, and excised in a subset of mice (n=4). A second subset of mice (n=4) had their testes selected for histological analysis. Seminiferous tubule diameter was measured manually from MRI and histology images. Custom image analysis scripts were created for the automated segmentation of seminiferous tubules and calculation of tissue volumes. All ex vivo and in situ images of testes exhibited clear outlines of seminiferous tubules. Ratio of total testis volume to volume of seminiferous tubules did not differ significantly between ex vivo and in situ measurements, and were similar in mature and younger mice. Both total testis volume and seminiferous tubule volume were larger in the mature animal. While histological slices trended towards larger average seminiferous tubules diameter than MRI images, we found no significant differences between MRI and histological measurements. High-field MRI can be used in a mouse model to assess testicular structure in situ. All volumetric measurements compared favourably with histological data. In situ scans also clearly showed identifiable extra-testicular tissues, such as epididymis and prostate tissues. The potential to image tissues associated with sperm maturation as well as spermatogenesis emphasises how MR could be a useful technique in mouse models of fertility, however further work is required to optimize tissue segmentation and validate this method for use in longitudinal studies. This type of measurement could be extended to human fertility studies in the future.

physiology↗