Biology subjects

Ryan, S.

Publications and source records attributed to Ryan, S..

At least 19 recordsLinked to original sources

bioRxiv2026

LIF is a pro-algesic mediator in human and mouse models of arthritis-related pain

Purpose: Emerging clinical and experimental data suggest that JAK inhibitors (JAKi) are effective in reducing pain in Rheumatoid Arthritis (RA). We recently showed that JAK/STAT signalling cytokines, specifically IL-6, LIF and IL-11, are present in the RA joint and can act directly on human induced pluripotent stem cell (iPSC) derived sensory neurons by increasing their STAT3 phosphorylation (pSTAT3) levels and expression of select pain-relevant genes. In this study, we determined that LIF is the most consequential cytokine out of the three, altering neuronal signalling, outgrowth and pain-like behaviours in in vitro and in vivo models of arthritis. Methods: Human iPSC-derived sensory neurons were stimulated with RA synovial fluid (SF) or with cytokine-treated RA synovial fibroblast conditioned media (CM) in the absence or presence of anti-cytokine antibodies. pSTAT3 and pSTAT1 levels, and gene expression patterns, were assessed by Western blot and RNA-sequencing (RNA-seq). The immortalised dorsal root ganglion (DRG)-derived cell line (HD 10.6) was assessed for LIF-induced JAK/STAT signalling in addition to neurite outgrowth assays as a functional readout of the sensory neurons. Lastly, mouse models were used to assess pain-related behaviours in vivo. Results: LIF was found to be consistently present in the SF from painful joints from individuals with inflammatory arthritis. Western blotting revealed that the addition of RA SF to iPSC-derived sensory neurons led to LIF-dependent induction of pSTAT3 and pSTAT1, while RNA-seq demonstrated that LIF alters the transcriptome of sensory neurons more prominently than IL-6 and IL-11, up-regulating signature genes related to peripheral neuron sensitization, such as TRPV1, NTRK1, BDNF, HRH1 and SCN10A. Similarly, cytokine-treated fibroblast conditioned media was shown to induce neuronal pSTAT3 and pSTAT1 and upregulate expression of BDNF, HRH1 and VGF in a LIF-dependent manner. Additionally, the immortalised dorsal root ganglion (DRG)-derived cell line (HD 10.6), which also exhibited LIF-induced pSTAT1 and pSTAT3, showed increased neurite outgrowth after axotomy when treated with LIF. Finally, in a mouse model of inflammatory arthritis, LIF was shown to be significantly increased in the affected joint. Furthermore, intraarticular injection of LIF into a healthy mouse knee resulted in increased responsiveness to painful pressure stimuli in that joint. Conclusions: Our data indicate that LIF may be a pro-algesic mediator and a possible therapeutic target to improve pain management in individuals living with inflammatory arthritis.

neuroscience↗

bioRxiv2026

IL-1α drives a tumor-stroma-neutrophil axis through inflammatory fibroblast activation in head and neck cancer

In head and neck squamous cell carcinoma (HNSCC), high tumor-associated neutrophil (TAN) density is a robust biomarker of poor prognosis. TANs predominantly localize to the stroma and their intratumoral density strongly correlates with adverse outcome. Here, we investigated how tumor-stroma communication regulates TAN recruitment, activation, and spatial organization. We identified interleukin-1 (IL-1), released by viable or necrotic tumor cells, as an upstream signal that induces an inflammatory cancer associated fibroblast (iCAF)-like transcriptional program in patient-derived mesenchymal stromal cells (MSCs) of the oral cavity. IL-1-stimulated MSCs secrete factors associated with neutrophil recruitment, survival, and function, together with mediators of extracellular matrix remodeling and angiogenesis. Notably, the IL-1-induced iCAF-like transcriptional program closely resembles CAF subsets in HNSCC that are associated with poor clinical outcome. Functionally, conditioned media from IL-1-stimulated MSCs promoted tumor growth and enhanced polymorphonuclear neutrophil survival, activation, trans-well migration and infiltration into spheroids, in vitro. In zebrafish xenografts, co-injection of IL-1-overexpressing tumor cells and MSCs markedly amplified neutrophil infiltration. TCGA analysis demonstrated robust correlations between the IL-1-induced MSC gene signature and neutrophil signatures across multiple TAN subsets in human HNSCC. Spatial analysis of HNSCC tissues showed that stromal regions adjacent to IL1A-positive tumor islets were enriched for CXCL8/CSF3 double-positive cells and exhibited increased TAN density, including higher frequencies of NE- and MPO-positive neutrophils. Collectively, these findings define an IL-1-dependent tumor-stroma signaling circuit that links tumor inflammation to stromal remodeling and neutrophil infiltration in HNSCC. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=180 SRC="FIGDIR/small/700440v1_ufig1.gif" ALT="Figure 1"> View larger version (47K): org.highwire.dtl.DTLVardef@f8d282org.highwire.dtl.DTLVardef@1c4575aorg.highwire.dtl.DTLVardef@1430cfcorg.highwire.dtl.DTLVardef@1098887_HPS_FORMAT_FIGEXP M_FIG Graphical abstract: IL-1 drives tumor-stroma communication and neutrophil recruitment in HNSCC. Here, we describe a mechanism in HNSCC that promotes high tumor-associated neutrophil (TAN) density, a biomarker associated with poor prognosis. Tumor-derived IL-1 activates stromal cells to adopt an inflammatory phenotype, resulting in the release of CXCL8, GM-CSF, and G-CSF to enhance neutrophil recruitment, activation, and survival. IL1A-positive tumor islets are surrounded by CXCL8/CSF3-rich stroma with elevated TAN densities in both tumor and stromal compartments. These TANs exhibit increased frequencies of MPO- and NE-positive cells, revealing a spatially organized inflammatory tumor microenvironment. Figure was created using BioRender. C_FIG

cancer biology↗

bioRxiv2025

The PPARβ/δ-induced mesenchymal stromal cell secretome has cytoprotective effects via ANGPTL4 in a pre-clinical model of acute lung inflammation

RationaleHuman bone marrow-derived mesenchymal stromal cells (hBM-MSCs) are known to exert immunomodulatory and pro-reparative effects in vivo. This makes hBM-MSCs an enticing therapeutic candidate for inflammatory diseases, such as acute respiratory distress syndrome (ARDS). The ARDS microenvironment is complex and contains an abundance of free fatty acids (FFAs); which are known to differentially impact MSC functionality. PPAR{beta}/{delta} is a ubiquitously expressed nuclear receptor that is activated in response to FFA-binding. PPAR{beta}/{delta} has been shown to impact the therapeutic efficacy of mouse MSCs. ObjectiveThis study sought to investigate the impact of PPAR{beta}/{delta}-modulation on human MSC functionality in vitro and in vivo. MethodshBM-MSCs were exposed to a synthetic PPAR{beta}/{delta} agonist/antagonist in the presence or absence of ARDS patient serum and the immunomodulatory and pro-reparative capacity of the MSC secretome was investigated using in vitro assays and a pre-clinical model of LPS-induced acute lung inflammation (ALI). ResultsOur results highlighted enhanced pro-reparative capacity of PPAR{beta}/{delta}-agonised hBM-MSCs secretome in CALU-3 lung epithelial cells, mediated by MSC derived angiopoietin-like 4 (ANGPTL4). PPAR{beta}/{delta}-induced ANGPTL4-high MSC secretome facilitated enhanced endothelial barrier integrity in the lungs of ALI mice. Therapeutic effects of PPAR{beta}/{delta}-agonised hBM-MSCs secretome were further enhanced by licensing MSCs with human ARDS patient serum. ARDS-licensed PPAR{beta}/{delta}-induced ANGPTL4-high MSC secretome had reduced clinical score and weight loss. The role ANGPL4 in these protective effects was confirmed using an anti-ANGPTL4 antibody. ConclusionThese findings conclude that the MSC secretome therapeutic effects can be enhanced both in vitro and in vivo through licensing strategies that upregulate the angiogenic factor ANGPTL4. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=145 SRC="FIGDIR/small/667170v2_ufig1.gif" ALT="Figure 1"> View larger version (44K): org.highwire.dtl.DTLVardef@a03b3dorg.highwire.dtl.DTLVardef@1915253org.highwire.dtl.DTLVardef@1b3fd4aorg.highwire.dtl.DTLVardef@1ba27ff_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2025

GPR17 modulates oligodendrocyte precursor cell maturation during development but has limited impact on myelin regeneration following demyelinating insults

Pharmacological enhancement of myelin regeneration is broadly recognized as the next frontier in therapeutic approaches for demyelinating diseases of the CNS such as multiple sclerosis. However, although several molecular targets for remyelination have been tested preclinically and in clinical trials, an efficacious and safe myelin repair treatment is yet to be developed. One promising molecular target to enhance myelin repair is the G protein-coupled receptor (GPCR) GPR17, which has been proposed to play a central role in the transition from early oligodendrocyte progenitor cells (OPC) into pre-myelinating oligodendrocytes. These findings are largely supported by studies using transgenic mice where GPR17 deletion results in developmental hypermyelination. Additionally, pharmacological modulation of GPR17 activity has been reported to enhance oligodendrocyte precursor cell (OPC) maturation and myelination. In our studies aimed to characterize and pharmacologically validate GPR17 as a viable target for drug development, we established by means of transcriptional profiling of GPR17 knockout versus wild type OPCs, that absence of this GPCR results in a gene signature revealing minor changes in myelin protein gene expression. Furthermore, blocking GPR17 receptor activity in OPC cultures using selective and potent antagonists or inverse agonists, results in limited enhancement of maturation and myelination in vitro. Importantly, remyelination in both the cuprizone and lysolecithin-induced demyelination models was not enhanced in the absence of GPR17. Our data demonstrate that GPR17 plays a minor role in OPC differentiation during development, and pharmacological modulation of its activity has a marginal effect on oligodendrocyte precursor maturation and myelin regeneration after injury.

neuroscience↗

bioRxiv2025

The MicroMap is a network visualisation resource for microbiome metabolism

The human microbiome plays a crucial role in metabolism and thereby influences health and disease. Constraint-based reconstruction and analysis (COBRA) has proven an attractive framework to generate mechanism-derived hypotheses along the nutrition-host-microbiome-disease axis within the computational systems biology community. Unlike for human, no large-scale visualisation resource for microbiome metabolism has been available to date. To address this gap, we created the MicroMap, a manually curated microbiome metabolic network visualisation, which captures the metabolic content of over a quarter million microbial genome-scale metabolic reconstructions. The MicroMap contains 5,064 unique reactions and 3,499 unique metabolites, including for 98 drugs. The MicroMap allows users to intuitively explore microbiome metabolism, inspect microbial metabolic capabilities, and visualise computational modelling results. Further, the MicroMap shall serve as an educational tool to make microbiome metabolism accessible to broader audiences beyond computational modellers. For example, we utilised the MicroMap to generate a comprehensive collection of 257,429 visualisations, corresponding to the entire scope of our current microbiome reconstruction resources, to enable users to visually compare and contrast the metabolic capabilities for diaerent microbes. The MicroMap seamlessly integrates with the Virtual Metabolic Human (VMH, www.vmh.life) and the COBRA Toolbox (opencobra.github.io), and is freely accessible at the MicroMap dataverse (https://dataverse.harvard.edu/dataverse/micromap), in addition to all the generated reconstruction visualisations.

systems biology↗

bioRxiv2024

Spatial characterizations of bacterial dynamics for food safety: Modeling for shared water processing environments

Bacterial dynamics occurring in shared water environments during food processing are typically modeled assuming a homogeneous mixing profile. However, given the tank configurations, and water recirculation and reuse specifications used in many facilities, uniform mixing is not always applicable. Towards this goal, we here developed a novel reaction-diffusion-advection model that captures temporal and spatial variations in the water tanks under dynamic conditions. We utilize the dynamics involved in poultry chilling as an example, as this process features a comprehensive interplay of bacteria, water chemistry and water flow dynamics, as well as determining bacteria levels on carcasses moving into final phases of the food production chain, thus directly influencing public health risk. Well-posedness, existence and uniqueness of positive steady-state solutions with global stability are proved, as well as an estimation of the time scale of convergence to the steady-state solution provided. Simulations are used to verify the analytical results incorporating parameters informed by experimental data from generic, non-pathogenic E. coli, and predictively estimate the time to equilibrium. We show that during a typical 8 h processing shift, the model reaches steady state within 2 h, applying this result to validate model simulations against commercial data. The calibrated model predicts a distribution of E. coli levels on post-chill carcasses with mean and standard deviation of 3.35 {+/-} 0.56 Log10 CFU/carcass, which closely compares to the experimentally observed distribution of 3.55 {+/-} 0.64 Log10 CFU/carcass in an industrial setting. Our results reinforce the key role of space in quantifying essential mechanisms that govern water chemistry and E. coli dynamics during poultry chilling. Our model is an important tool to improve decision making for pathogen control during poultry chilling, as well as a blueprint from which models for processing other commodities like fresh produce and pork can be established.

microbiology↗

bioRxiv2024

Blockade of rheumatoid arthritis synovial fluid-induced sensory neuron activation by JAK inhibitors

ObjectiveClinical studies suggest that compared to anti-TNF treatment, JAK inhibitors (JAKi) are superior in reducing pain in rheumatoid arthritis (RA). The underlying mechanisms for this observation are still unknown. Sensory neurons transmit noxious signals from inflamed joints to the central nervous system, where a pain percept is generated. We investigated whether JAKi exert direct effects on sensory neurons. MethodsIn-house and public RNA sequencing datasets of sensory neurons were analysed for relevant JAK/STAT and cytokine-receptor gene expression. Human induced pluripotent stem cell (IPSC)-derived sensory neurons were stimulated with serum and synovial fluid (SF) from individuals with RA, or with selected cytokines that were found in RA SF by Luminex. Phosphorylation of STAT3 (pSTAT3) was assessed by Western blot. Sensory neuron activation was examined by recording neuronal firing using multi-electrode array and measuring expression levels of pain-relevant genes with STAT3-binding sites. ResultsCell-free RA synovial fluid induced pSTAT3 in IPSC-derived sensory neurons, an effect which was completely blocked by the JAKi tofacitinib. Compared to paired serum, RA SF was enriched for the JAK/STAT cytokines IL-6, IL-11, LIF, IFN-alpha and IFN-beta, with their requisite receptors present on sensory neurons. Stimulation of IPSC- derived sensory neurons with these recombinant cytokines recapitulated pSTAT3 induction in these cells. Furthermore, IL-6+sIL-6R or LIF upregulated expression of pain-relevant genes which was blocked by tofacitinib. Finally, we provided evidence that LIF can induce neuronal sensitisation. ConclusionOur data indicate that JAKi can act directly on sensory neurons, providing a potential mechanistic explanation for their suggested superior analgesic properties.

immunology↗

bioRxiv2024

Walk This Way: Modeling Foraging Ant Dynamics in Multiple Food Source Environments

Foraging for resources is an essential process for the daily life of an ant colony. What makes this process so fascinating is the self-organization of ants into trails using chemical pheromone in the absence of direct communication. Here we present a stochastic lattice model that captures essential features of foraging ant dynamics inspired by recent agent-based models while forgoing more detailed interactions that may not be essential to trail formation. Nevertheless, our models results coincide with those presented in more sophisticated theoretical models and experiment. Furthermore, it captures the phenomenon of multiple trail formation in environments with multiple food sources. This latter phenomenon is not described well by other more detailed models. An additional feature of this approach is the ability to derive a corresponding macroscopic PDE from the stochastic lattice model which can be described via first principle interactions and is amenable to analysis. Linear stability analysis of this PDE reveals the key biophysical parameters that give rise to trail formation. We also highlight universal features of the modeling framework that this simple formation may allow it to be used to study complex systems beyond ants.

ecology↗

bioRxiv2023

Lipidome profiling of neutrophil-derived extracellular vesicles unveils their contribution to the ensemble of synovial fluid-derived extracellular vesicles during joint inflammation

The molecular signature of cell-derived extracellular vesicles (EVs) from synovial fluid (SF) offers valuable insights into the cells and molecular processes associated with joint disorders and can be exploited to define biomarkers. The signature of EVs is determined by cargo molecules and the lesser-studied lipid bilayer. We here investigated the lipidome of SF-EVs in inflamed joints derived from Rheumatoid Arthritis (RA) and Spondyloarthritis (SpA) patients, two autoimmune-driven joint diseases, and compared these signatures to the lipid profile of equine SF-EVs obtained during induced acute synovitis. Since neutrophils are primary SF-infiltrating cells during these inflammatory joint diseases, we also analyzed how inflammatory stimuli alter the lipidomic profile of human and equine neutrophil-derived EVs (nEVs) in vitro and how these signatures relate to the lipidome signatures of SF-EVs from inflamed joints. We identified neutrophil stimulation-intensity dependent changes in the lipidomic profile of nEVs with elevated presence of dihexosylceramide (lactosylceramide), phosphatidylserine, and phosphatidylethanolamine ether-linked lipid classes in human nEVs upon full neutrophil activation. In horses, levels of monohexosylceramide (glucosylceramide) increased instead of dihexosylceramide, indicating species-specific differences. The lipid profiles of RA and SpA SF-EVs were relatively similar and showed a relative resemblance with stimulated human nEVs. Similarly, the lipidome of equine synovitis-derived SF-EVs closer resembled the one of stimulated equine nEVs. Hence, lipidome profiling can provide insights into the contribution of nEVs to the heterogeneous pool of SF-EVs, deepening our understanding of inflammatory joint diseases and revealing molecular changes in joint homeostasis, which can lead to the development of more precise disease diagnosis and treatment strategies.

molecular biology↗

bioRxiv2023

Modeling identifies chromosome number, size, and non-homologous repulsion as novel determinants of meiotic pairing

During meiosis, pairing of homologous chromosomes (homologs) ensures the formation of haploid gametes from diploid precursor cells, a prerequisite for sexual reproduction. Pairing during meiotic prophase I facilitates crossover recombination and homolog segregation during the ensuing reductional cell division. Mechanisms that ensure stable homolog alignment in the presence of an excess of non-homologous chromosomes have remained elusive, but rapid chromosome movements during prophase I appear to play a role in the process. Apart from homolog attraction, provided by early intermediates of homologous recombination, dissociation of non-homologous associations also appears to contribute to homolog pairing, as suggested by the detection of stable non-homologous chromosome associations in pairing-defective mutants. Here, we have developed an agent-based model for homolog pairing derived from the dynamics of a naturally occurring chromosome ensemble. The model simulates unidirectional chromosome movements, as well as collision dynamics determined by attractive and repulsive forces arising from close-range physical interactions. In addition to homolog attraction, chromosome number and size as well as movement velocity and repulsive forces are identified as key factors in the kinetics and efficiency of homologous pairing. Dissociation of interactions between non-homologous chromosomes may contribute to pairing by crowding homologs into a limited nuclear area thus creating preconditions for close-range homolog attraction. Predictions from the model are readily compared to experimental data from budding yeast, parameters can be adjusted to other cellular systems and predictions from the model can be tested via experimental manipulation of the relevant chromosomal features. Author summaryPairing of homologous chromosomes (homologs) is a key feature of multiple cellular processes including gene expression control, chromosome break repair, and chromosome segregation. Homolog pairing during meiosis is shared among all sexually reproducing eukaryotes. Mechanistic determinants of homology-specific chromosome alignment are presently unknown. We have developed an agent-based model where contributions of the entire chromosome set to the pairing process is taken into account, comprising both homologous and non-homologous chromosomal encounters. Incorporating natural chromosome lengths, the model accurately recapitulates efficiency and kinetics of homolog pairing observed for wild-type and mutant meiosis in budding yeast, and can be adapted to nuclear dimensions and chromosome sets of other organisms.

biophysics↗

bioRxiv2022

A phenotypic screening platform for chronic pain therapeutics using all-optical electrophysiology

Chronic pain associated with osteoarthritis (OA) remains an intractable problem with few effective treatment options. New approaches are needed to model the disease biology and to drive discovery of therapeutics. Here, we present an in vitro model of OA pain, where dorsal root ganglion (DRG) sensory neurons were sensitized by a defined mixture of disease-relevant inflammatory mediators, here called Sensitizing PAin Reagent Composition or SPARC. OA-SPARC components showed synergistic or additive effects when applied in combination and induced pain phenotypes in vivo. To measure the effect of OA-SPARC on neural firing in a scalable format for drug discovery, we used a custom system for high throughput all-optical electrophysiology. This system enabled light-based membrane voltage recordings from hundreds of neurons in parallel with single cell resolution and a throughput of up to 500,000 neurons per day, with patch clamp-like single action potential resolution. A computational framework was developed to construct a multiparameter OA-SPARC neuronal phenotype and to quantitatively assess phenotype reversal by candidate pharmacology with different mechanisms of action. We screened ~3000 approved drugs and mechanistically focused compounds, yielding data from over 1.2 million individual neurons with detailed assessment of both functional OA-SPARC phenotype rescue and orthogonal "off-target" effects. Analysis of confirmed hits revealed diverse potential analgesic mechanisms including well-known ion channel modulators as well as less characterized mechanisms including MEK inhibitors and tyrosine kinase modulators, providing validation of the platform for pain drug discovery.

neuroscience↗

bioRxiv2021

Phyllosphere community assembly and response to drought stress on common tropical and temperate forage grasses

Grasslands represent a critical ecosystem important for global food production, soil carbon storage, and water regulation. Current intensification and expansion practices add to the degradation of grasslands and dramatically increase greenhouse gas emissions and pollution. Thus, new ways to sustain and improve their productivity are needed. Research efforts focus on the plant-leaf microbiome, or phyllosphere, because its microbial members impact ecosystem function by influencing pathogen resistance, plant hormone production, and nutrient availability through processes including nitrogen fixation. However, little is known about grassland phyllospheres and their response to environmental stress. In this study, globally dominant temperate and tropical forage grass species were grown in a greenhouse under current climate conditions and drought conditions that mimic future climate predictions to understand if (i) plant host taxa influence microbial community assembly, (ii) microbial communities respond to drought stress, and (iii) phyllosphere community changes correlate to changes in plant host traits and stress-response strategies. Community analysis using high resolution sequencing revealed Gammaproteobacteria as the dominant bacterial class, which increased under severe drought stress on both temperate and tropical grasses while overall bacterial community diversity declined. Bacterial community diversity, structure, and response to drought were significantly different between grass species. This community dependence on plant host species correlated with differences in grass species traits, which became more defined under drought stress conditions, suggesting symbiotic evolutionary relationships between plant hosts and their associated microbial community. Further understanding these strategies and the functions microbes provide to plants will help us utilize microbes to promote agricultural and ecosystem productivity in the future. IMPORTANCEGlobally important grassland ecosystems are at risk of degradation due to poor management practices compounded by predicted increases in severity and duration of drought over the next century. Finding new ways to support grassland productivity is critical to maintaining their ecological and agricultural benefits. Discerning how grassland microbial communities change in response to climate stress will help us understand how plant-microbe relationships may be useful to sustainably support grasslands in the future. In this study, phyllosphere community diversity and composition was significantly altered under drought conditions. The significance of our research is demonstrating how severe climate stress reduces bacterial community diversity, which previously was directly associated with decreased plant productivity. These findings guide future questions about functional plant-microbe interactions under stress conditions, greatly enhancing our understanding of how bacteria can increase food security by promoting grassland growth and resilience.

microbiology↗

bioRxiv2021

Disrupted microglial iron homeostasis in progressive multiple sclerosis

Multiple Sclerosis (MS) is a chronic autoimmune disease affecting the central nervous system (CNS). Despite therapies that reduce relapses, many patients eventually develop secondary progressive MS (SPMS), characterized by ongoing and irreversible neurodegeneration and worsening clinical symptoms. Microglia are the resident innate immune cells of the CNS. While the cellular and molecular determinants of disability progression in MS remain incompletely understood, they are thought to include non-resolving microglial activation and chronic oxidative injury. In this study, our aim was to better characterize microglia in SPMS tissues to identify disease-related changes at the single cell level. We performed single nucleus RNA-seq (snRNA-seq) on cryopreserved post-mortem brain cortex and identified disease associated changes in multiple cell types and in particular distinct SPMS-enriched microglia subsets. When compared to the cluster most enriched in healthy controls (i.e. homeostatic microglia), we found a number of SPMS-enriched clusters with transcriptional profiles reflecting increased oxidative stress and perturbed iron homeostasis. Using histology and RNA-scope, we confirmed the presence of iron accumulating, ferritin-light chain (FTL)-expressing microglia in situ. Among disease-enriched clusters, we found evidence for divergent responses to iron accumulation and identified the antioxidant enzyme GPX4 as a key fate determinant. These data help elucidate processes that occur in progressive MS brains, and highlight novel nodes for therapeutic intervention.

neuroscience↗

bioRxiv2019

Carry-over effects of temperature and pCO2 in multiple Olympia oyster populations

Predicting how populations will respond to ocean change across generations is critical to effective conservation of marine species. One emerging factor is the influence of parental exposures on offspring phenotype, known as intergenerational carryover effects. Parental exposure may deliver beneficial or detrimental characteristics to offspring that can influence larval recruitment patterns, thus shaping how populations and community structure respond to ocean change. Impacts of adult exposure to elevated winter temperature and pCO2 on reproduction and offspring viability were examined in the Olympia oyster (Ostrea lurida) using three populations of adult, hatchery-reared O. lurida, plus an additional cohort spawned from one of the populations. Oysters were sequentially exposed to elevated temperature (+4{degrees}C, at 10{degrees}C), followed by elevated pCO2 (+2204 {micro}atm, at 3045 {micro}atm) during winter months. Male gametes were more developed after elevated temperature exposure and less developed after high pCO2 exposure, but there was no impact on female gametes or sex ratios. Oysters previously exposed to elevated winter temperature released larvae earlier, regardless of pCO2 exposure. Those exposed to elevated winter temperature as a sole treatment released more larvae on a daily basis, but when also exposed to high pCO2 there was no effect. These combined results indicate that elevated winter temperature accelerates O. lurida spermatogenesis, resulting in earlier larval release and increased production, with elevated pCO2 exposure negating effects of elevated temperature. Altered recruitment patterns may therefore follow warmer winters due to precocious spawning, but these effects may be masked by coincidental high pCO2. Offspring were reared in common conditions for one year, then deployed for three months in four estuarine bays with distinct environmental conditions. Offspring of parents exposed to elevated pCO2 had higher survival rates in two of the four bays. This carryover effect demonstrates that parental conditions can have substantial ecologically relevant impacts that should be considered when predicting impacts of environmental change. Furthermore, Olympia oysters may be more resilient in certain environments when progenitors are pre-conditioned in stressful conditions. Combined with other recent studies, our work suggests that the Olympia may be more equipped than other oysters for the challenge of a changing ocean.

physiology↗

bioRxiv2019

Measuring vision using innate behaviours in mice with intact and impairedretina function

Measuring vision in rodents is a critical step for understanding vision, improving models of human disease, and developing therapies. Established behavioural tests for perceptual vision, such as the visual water task, rely on learning. The learning process, while effective for sighted animals, can be laborious and stressful in animals with impaired vision, requiring long periods of training. Current tests that that do not require training are based on sub-conscious, reflex responses (e.g. optokinetic nystagmus) that dont require involvement of visual cortex and higher order thalamic nuclei. A potential alternative for measuring vision relies on using visually guided innate defensive responses, such as escape or freeze, that involve cortical and thalamic circuits. In this study we address this possibility in mice with intact and degenerate retinas. We first develop automatic methods to detect behavioural responses based on high dimensional tracking and changepoint detection of behavioural time series. Using those methods, we show that visually guided innate responses can be elicited using parametisable stimuli, and applied to describing the limits of visual acuity in healthy animals and discriminating degrees of visual dysfunction in mouse models of retinal degeneration.

neuroscience↗

bioRxiv2018

Phenotypic and genotypic resistance to commonly used insecticides in Aedes aegypti among four cities in southern Ecuador

Insecticide resistance (IR) can undermine efforts to control vector species of public health importance. Aedes aegypti is the main vector of resurging diseases in the Americas such as yellow fever and dengue, as well as recently emerging chikungunya and Zika viruses, which have caused unprecedented epidemics in the region. Vector control remains the primary public health intervention to prevent outbreaks of Aedes transmitted diseases. In many high-risk regions, like southern Ecuador, we have limited information on IR in Ae. aegypti. In this study, IR status in Ae. aegypti was measured across four cities in El Oro Province in Ecuador using phenotypic assays and genetic screening for alleles associated with resistance to pyrethroid insecticides. Bottle bioassays showed significant inter-seasonal variation in resistance to deltamethrin, a pyrethroid insecticide commonly used by the Ministry of Health, and alpha cypermethrin, as well as differences in deltamethrin resistance between cities. There was also a significant difference in phenotypic response to the organophosphate, Malathion, between two of the cities during the second sampling season. Genotyping showed moderate to high frequencies of the V1016I and F1534C resistance alleles in all four cites. Frequency of resistance genotypes varied significantly between cities in the first sampling season, and not in the later seasons, suggesting a possible selective response to vector control activity. Overall, resistance levels were highest in Machala, a city where dengue is hyperendemic and where insecticide use has historically been more intense than in the other cities included in the study. Despite statistically significant evidence that resistance alleles conferred phenotypic resistance, there was not precise correspondence between these indicators. We found that 17.6% of F1534C and 45.6% of V1016I mutant mosquitoes were susceptible in the bottle bioassays. This study shows there is spatiotemporal variability in IR in southern Ecuador, and serves as an initial examination of the genotypic and phenotypic indicators of IR in this region, providing important information to guide the vector control interventions by the public health sector.

epidemiology↗

bioRxiv2017

Crosslinkers both drive and brake cytoskeletal remodeling and furrowing in cytokinesis

Cytokinesis and other cell shape changes are driven by the actomyosin contractile cytoskeleton. The molecular rearrangements that bring about contractility in non-muscle cells are currently debated. Specifically, both filament sliding by myosin motors, as well as cytoskeletal crosslinking by myosins and non-motor crosslinkers, are thought to promote contractility. Here, we examined how the abundance of motor and non-motor crosslinkers controls the speed of cytokinetic furrowing. We built a minimal model to simulate the contractile dynamics of the C. elegans zygote cytokinetic ring. This model predicted that intermediate levels of non-motor crosslinkers would allow maximal contraction speed, which we found to be the case for the scaffold protein anillin, in vivo. Our model also demonstrated a non-linear relationship between the abundance of motor ensembles and contraction speed. In vivo, thorough depletion of non-muscle myosin II delayed furrow initiation, slowed F-actin alignment, and reduced maximum contraction speed, but partial depletion allowed faster-than-expected kinetics. Thus, both motor and non-motor crosslinkers promote cytokinetic ring closure when present at low levels, but act as a brake when present at higher levels. Together, our findings extend the growing appreciation for the roles of crosslinkers, but reveal that they not only drive but also brake cytoskeletal remodeling.

cell biology↗

bioRxiv2017

Patterns of divergence across the geographic and genomic landscape of a butterfly hybrid zone associated with a climatic gradient

Hybrid zones are a valuable tool for studying the process of speciation and for identifying the genomic regions undergoing divergence and the ecological (extrinsic) and non-ecological (intrinsic) factors involved. Here, we explored the genomic and geographic landscape of divergence in a hybrid zone between Papilio glaucus and Papilio canadensis. Using a genome scan of 28,417 ddRAD SNPs, we identified genomic regions under possible selection and examined their distribution in the context of previously identified candidate genes for ecological adaptations. We showed that differentiation was genome-wide, including multiple candidate genes for ecological adaptations, particularly those involved in seasonal adaptation and host plant detoxification. The Z-chromosome and four autosomes showed a disproportionate amount of differentiation, suggesting genes on these chromosomes play a potential role in reproductive isolation. Cline analyses of significantly differentiated genomic SNPs, and of species diagnostic genetic markers, showed a high degree of geographic coincidence (81%) and concordance (80%) and were associated with the geographic distribution of a climate-mediated developmental threshold (length of the growing season). A relatively large proportion (1.3%) of the outliers for divergent selection were not associated with candidate genes for ecological adaptations and may reflect the presence of previously unrecognized intrinsic barriers between these species. These results suggest that exogenous (climate-mediated) and endogenous (unknown) clines may have become coupled and act together to reinforce reproductive isolation. This approach of assessing divergence across both the genomic and geographic landscape can provide insight about the interplay between the genetic architecture of reproductive isolation and endogenous and exogenous selection.

evolutionary biology↗