Biology subjects

Fleming, C.

Publications and source records attributed to Fleming, C..

11 recordsLinked to original sources

bioRxiv2026

Identification and inhibition of the Cyclin D Rb-docking interface that drives cell division

The animal cell division cycle is initiated by the cyclin-dependent kinases CDK4 and CDK6 in complex with D-type cyclins. Cyclin D-CDK4/6 complex formation is promoted by the assembly factors p21 and p27, which bind both subunits. p27 binds the hydrophobic patch on cyclin D that is similar to the patch used by other cell cycle cyclins to dock their substrates. This raised the question as to how cyclin D could find its substrates if its hydrophobic patch were already occupied? Here, we show that D-type cyclins use their A2 helix to dock the retinoblastoma protein Rb, a key substrate regulating cell cycle progression. The specific interface of cyclin Ds A2 helix is unique among cyclins and its mutation slows proliferation. Taken together, our work identifies a cyclin D-substrate docking mechanism that can be targeted by novel cancer therapeutics.

biochemistry↗

bioRxiv2025

The hyaluronan receptor CD44 drives COVID-19 severity through its regulation of neutrophil migration

The novel respiratory disease COVID-19 caused by the coronavirus SARS-CoV-2 continues to be a public health emergency worldwide, and there is a need for more effective therapy for patients. The relationship between the extracellular matrix and the host immune response to infection is severely understudied. Deposition of the polysaccharide hyaluronan (HA) into the lungs is associated with more severe COVID-19 disease outcomes. HA is a major component of the extracellular matrix in connective tissues and is abundant in many parts of the body, including cartilage, skin, brain, and vitreous body. CD44 is the primary receptor for HA and is found on almost all immune cells in the lung. Known functions of CD44 include mediation of immune cell migration, activation, and differentiation. We hypothesized that increased HA deposition during COVID-19 increases CD44-mediated immune cell infiltration into lungs and results in more severe pathology. Here, we report that in mice infected with a mouse-adapted strain of SARS-CoV-2, treatment with a combination of two anti-CD44 monoclonal antibodies confers a significant survival benefit and reduces weight loss and clinical score of the mice on Day 4 post infection. We show that anti-CD44 treatment decreases many key cytokines and chemokines in the bronchoalveolar lavage fluid on Day 4. With flow cytometry, we show that anti-CD44 reduces the numbers of neutrophils in infected lungs. We also show through immunofluorescence that treatment with anti-CD44 antibodies reduces colocalization of HA and CD45 in lung sections, indicating that HAs interaction with immune cells contributes to pathology. Our findings demonstrate that disruption of HA-receptor interactions is a way to prevent inflammatory pathology in pulmonary infection.

immunology↗

bioRxiv2025

Too few, too many, or just right? Optimizing sample sizes for population-level inferences in animal tracking projects

O_LISuccessful animal tracking projects depend on well-informed sampling strategies and robust methods to yield biologically meaningful inferences. Considering financial and logistical constraints, the reliability of research outputs is shaped by key decisions regarding study duration (how long should each individual be tracked?), sampling frequency (how often should new locations be collected?), and how many individuals should be tracked. To maximize their conservation value, studies must consider estimator precision and avoid biased inferences of key parameters related to movement behavior and space use, as this can lead to wasted resources and misguide management actions. C_LIO_LITo address these challenges, we propose a workflow for determining the optimal sample sizes for population-level home range area and speed estimates, explicitly addressing the trade-offs between sampling duration (T), sampling interval (reciprocal of frequency; {Delta}t), and population sample size (m). While a priori study design is considered best practice, this workflow can be applied at multiple stages, including concurrent with data collection, or as a post hoc evaluation. C_LIO_LIBy selecting robust methods that are sampling-insensitive, and by quantifying and propagating uncertainty through downstream analyses, we can determine whether our sample sizes (both at the individual- and population-level) are sufficient to yield robust population-level inferences. Furthermore, researchers can integrate additional logistical constraints such as fix success rate, location error, and potential device malfunctions, while also accounting for individual variation. We illustrate potential applications of this workflow through empirically-guided simulations. C_LIO_LITo facilitate its use and implementation, we incorporated this workflow into the user-friendly movedesign R Shiny application. This application enables researchers to easily test different sampling strategies, and as of version 0.3.3, integrates population-level analytical targets. This workflow has the potential to improve the rigor and reliability of animal tracking projects conducted under logistical and financial constraints, and thereby support more effective scientific research, wildlife management, and conservation efforts. It can also support grant or permit submissions by generating evidence-based recommendations for the number of biologgers needed or sampling effort required to achieve research objectives. C_LI

ecology↗

bioRxiv2025

Are your data too coarse for speed estimation? Diffusion rates as an alternative measure of animal movement

Estimates of speed and distance traveled are routine in ecological research to provide a link between behavior and energetics. Conventional straight-line displacement (SLD) methods return severely and differentially biased estimates with no ability to evaluate the accuracy of the estimate. Recent methodological advances have improved our ability to estimate these parameters using continuous-time speed and distance (CTSD) estimation. However, even with CTSD estimation, many datasets are too coarse, or the location error is too great to reliably measure speed or distance traveled. To address these limitations, we investigated the relationship between CTSD-estimated mean speed and diffusion rate, where diffusion rate is defined as the variance in displacements per time interval. We calculated CTSD mean speed and diffusion rate estimates using telemetry data (i.e., trajectory data) from over 100 white-tailed deer and simulated telemetry data generated from a known movement model. We examined the relationship between the two measures in both datasets and the effect of sampling frequency on the effective sample size and the estimation of the two parameters. We found that mean speed and diffusion rate were strongly and nonlinearly correlated, with a 1% increase in diffusion rate predicting a 0.40% increase in mean speed (99% CI: 0.38-0.42%) for our focal species. Diffusion rate estimates remained substantially more accurate and precise than speed across sampling interval regimes, even when speed estimation was not possible. Our findings demonstrate that diffusion rate outperforms mean speed as a measure of movement activity under marginal data conditions. Diffusion rate is a reliable measure of movement activity and can link behavior to energetics across a wider range of datasets while maintaining accuracy even when data quality is low. By using speed and diffusion together, researchers can rely on more robust insights into space use across a range of ecological contexts.

ecology↗

bioRxiv2025

Condensate screening identifies YM155 as β-catenin condensate inhibitor in colorectal cancer

{beta}-catenin is a transcriptional cofactor crucial in forming biomolecular condensates that drive WNT target gene transcription. Its pathological accumulation in the nucleus is a critical step in WNT-driven cancers, such as colorectal cancer. Disrupting {beta}-catenin condensates is a promising cancer treatment strategy, but no clinical applications currently exist. In this study, we developed a Nanobody Enabled Condensate Observation (NECO) screening platform to identify small molecules that modulate {beta}-catenin condensates. The platform revealed compounds that either enhanced or reduced {beta}-catenin transcriptional condensates. Among them, YM155 (sepantronium bromide) was identified as an inhibitor, disrupting essential weak interactions for condensate formation. This disruption effectively inhibits the proliferation of WNT-driven colorectal cancer organoids. These findings show that the NECO platform can identify small molecules that target {beta}-catenin condensates and suggest YM155 as a potential anti-cancer agent for colorectal cancer.

molecular biology↗

bioRxiv2024

The IL-33/ST2 signaling axis drives pathogenesis in acute SARS-CoV-2 infection

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), remains a significant threat to global public health. Immunopathological damage plays a role in driving pneumonia, acute respiratory distress syndrome (ARDS), and multiorgan failure in severe COVID-19. Therefore, dissecting the pulmonary immune response to SARS-CoV-2 infection is critical to understand disease pathogenesis and identify immune pathways targetable by therapeutic intervention. Considering that the type 2 cytokine IL-13 enhances COVID-19 disease severity, therapeutic targeting of upstream signals that drive type 2 immunity may confer further protection. In this study, we investigate the role of the IL-33/ST2 signaling axis, a potent inducer of type 2 immunity in the lung, in a mouse model of COVID-19. Upon infection with mouse-adapted SARS-CoV-2 MA10, ST2-/- mice had significantly improved weight loss and survival (69.2% vs 13.3% survival; P = 0.0005), as compared to wild-type mice. In a complementary pharmacologic approach, IL-33/ST2 signaling was inhibited using HpBARI_Hom2, a helminth derived protein that binds to mouse ST2 and blocks IL-33 signaling. In SARS-CoV-2 MA10 infection, HpBARI_Hom2-treated mice had significantly improved weight loss and survival (60% vs 10% survival; P = 0.0035), as compared to inert control-treated mice. These data demonstrate that loss of IL-33/ST2 signaling confers protection during acute SARS-CoV-2 MA10 infection, implicating the IL-33/ST2 signaling axis as an enhancer of COVID-19 disease severity. The protection conferred by pharmacologic blockade of IL-33/ST2 signaling was independent of viral control, as HpBARI_Hom2-treated mice had no reduction in viral titers. This finding suggests an immunopathogenic role for IL-33/ST2 signaling. One potential mechanism through which IL-33/ST2 signaling may drive severe disease is through enhancement of type 2 immune pathways including IL-5 production, as pulmonary IL-5 concentrations were found to depend on IL-33/ST2 signaling in acute SARS-CoV-2 MA10 infection.

immunology↗

bioRxiv2024

Home range spillover in habitats with impassable boundaries: Causes, biases, and corrections using autocorrelated kernel density estimation

O_LIAn animals home range plays a fundamental role in determining its resource use and overlap with conspecifics, competitors and predators, and is therefore a common focus of movement ecology studies. Autocorrelated kernel density estimation addresses many of the shortcomings of traditional home range estimators when animal tracking data is autocorrelated, but other challenges in home range estimation remain. C_LIO_LIOne such issue is known as spillover bias, in which home range estimates do not respect impassable movement boundaries (e.g., shorelines, fences), and occurs in all forms of kernel density estimation. While several approaches to addressing spillover bias are used when estimating home ranges, these approaches introduce bias throughout the remaining home range area, depending on the amount of spillover removed, or are otherwise inaccessible to most ecologists. Here, we introduce local corrections to home range kernels to mitigate spillover bias in (autocorrelated) kernel density estimation in the continuous time movement model (ctmm) package, and demonstrate their performance using simulations with known home range extents and distributions, and a real world case study. C_LIO_LISimulation results showed that local corrections minimised bias in bounded home range area estimates, and resulted in more accurate distributions when compared to commonly used post-hoc corrections, particularly at small-intermediate sample sizes. C_LIO_LIComparison of the impacts of local vs post-hoc corrections to bounded home ranges estimated from lake trout (Salvelinus namaycush) demonstrated that local corrections constrained bias within the remaining home range area, resulting in proportionally smaller home range areas compared to when post-hoc corrections are used. C_LI

ecology↗

bioRxiv2024

Modeling the transmission dynamics of African swine fever virus within commercial swine barns: Quantifying the contribution of multiple transmission pathways

Transmission of the African swine fever virus (ASFV) within commercial swine barns occurs through direct and indirect pathways. Identifying and quantifying the roles of ASFV dissemination within barns is crucial for the development of effective disease control strategies. We developed a stochastic transmission model to examine the ASFV dissemination dynamics through eight transmission routes within commercial swine barns. We consider seven transmission routes at three disease dynamics levels: within-pens, between-pens, and within-room transmission, along with the transfer of pigs between pens within the same room. We simulated ASFV spread within barns of various sizes and layouts from rooms with a median of 32 pens (IQR:28-40), where each pen housing a median of 34 pigs (IQR: 29-36). Our model enables the tracking of the viral load in each pen and the monitoring of the disease status at the pen level. Simulation results show that between-pen transmission pathways exhibited the highest contribution to ASFV spread, accounting for 71.4%, where within-pen and within-room pathways account for 20.1% and 8.5%, respectively. Among the direct transmission pathways, nose-to-nose contact between pens was the primary route of dissemination, comprising an average of 49%, while the fecal transmission between pens contributed 21%. On the other hand, aerosol transmission within pens had the lowest contribution, accounting for less than 1%. Furthermore, we show that the daily transfer of pigs between pens did not impact the spread of ASFV. The combination of passive surveillance of daily detection and active surveillance focused on mortality allowed the detection of ASFV within three Days, with peak detection occurring when mortality rates peaked. The model also allows us to pinpoint where the majority of infections and viral load are concentrated during the ASFV spread. This work significantly deepens our understanding of ASFV spread within commercial swine production farms in the U.S. and highlights the main transmission pathways that should be prioritized when implementing ASFV countermeasure actions at the room level.

ecology↗

bioRxiv2024

Modeling the impact of optimized airflow and sick pen management on the spread of infectious diseases in swine barns

The airborne spread of infectious livestock diseases plays a crucial role in the propagation of epidemics, particularly in populations confined to densely populated facilities, such as commercial swine barns. Therefore, quantitative assessments for the performance of barn ventilation systems may serve as an alternative biocontainment control strategy to reduce the spread of infectious pathogens. In this study, we present a framework to simulate airborne disease dissemination within swine barns and facilitate the strategic design of control actions, including optimization of ventilation and placement of sick animals (sick pen). This framework is based on a susceptible-infected-recovered (SIR) model that accounts for the between-pen disease spread within swine barns. A pen-to-pen contact network is used to construct a transmission matrix according to the transport of airborne respiratory pathogens across pens in the barns, via our Reynolds-averaged Navier-Stokes computational fluid dynamics (CFD) solver. By employing this CFD-augmented SIR model, we demonstrated that the location of the sick pen and the barn ventilation configuration played crucial roles in modifying disease dissemination dynamics at the barn level. In addition, we examined the effect of natural ventilation through different curtain adjustments. We observed that curtain adjustments either suppress the disease spread by an average of 56.5% or exacerbate the outbreak potential by an average of 5.7%, compared to the scenario where side curtains are not raised. Furthermore, we optimize the ventilation configuration via the selection and placement of ventilation fans through the integration of the CFD-augmented framework with the genetic algorithm to minimize the dissemination of swine disease within barns. Compared to regular barn ventilation settings, our optimized ventilation system significantly reduced disease spread by an average of 43.2%. Our study emphasizes the role of airborne transmission and a strategy for sick pen management in controlling the spread of within-barn disease.

bioengineering↗

bioRxiv2023

How resource abundance and stochasticity affect organisms' space-use requirements

The amount of space organisms use is thought to be tightly linked to the availability of resources within their habitats, such that organisms living in productive habitats generally require less space than those in resource-poor habitats. This hypothesis has widespread em-pirical support, but existing studies have focused primarily on responses to the mean amount of resources, while responses to the variance around the mean are still largely unknown. This is not a trivial oversight. Organisms adjust to variable environmental conditions, so failing to consider the effects of resource (un)predictability can result in a limited understanding of an organisms range size, which challenges ecological theory and applied conservation alike. In this study, we leverage the available literature to provide a unifying framework and hypotheses for the effect of mean and variance in resources on range sizes. Next, we use simulated movement data to demonstrate how the combined effects of mean and variance in resource abundance interact to shape predictable patterns in range size. Finally, we use real-world tracking data on a lowland tapir (Tapirus terrestris) from the Brazilian Cerrado to show how this framework can be applied to better understand the movement ecology of free-ranging animals.

ecology↗

bioRxiv2019

A report on the detection and management of a finding of PSTVd (Potato Spindle Tuber Viroid) in potato breeding material in Northern Ireland, UK.

Potato Spindle Tuber Viroid (PSTVd) is an infectious unencapsidated, small, circular, single-stranded RNA, that causes serious losses in infected potato plants. The pathogen has been detected in several European countries, including in England in the UK. In August 2016, the National Plant Protection Organisation of the Netherlands reported a finding of PSTVd in breeding material that originated in Northern Ireland, UK. A scheme of testing was carried out in Northern Ireland to identify the source of the infected breeding material. Trace-forward and trace-back tests identified 21 infected samples, of which 16 were from true seed samples, out of a total of 591 tested up to November 2016. The number of positive findings in true seed was further reduced to 4 after the samples were surface sterilized. Tests indicated that the infection probably entered the breeding station in Northern Ireland in the mid 1980s, with limited spread in the collection via contaminated breeding equipment. The instance of spread in the field could not be ruled out. Eradication efforts included removal and destruction of infected field stocks and neighbouring stocks, destruction of stored museum material by deep burial, and destruction of other field material by ploughing and exposing tubers to frost. The risk of potato genitor material for spreading PSTVd is discussed. The situation of PSTVd in Northern Ireland, UK is Transient, actionable, under eradication.

plant biology↗