Biology subjects

Freeman, R.

Publications and source records attributed to Freeman, R..

At least 19 recordsLinked to original sources

bioRxiv2026

DAPHNE: A global database of pest herbivores and their natural enemies

Anticipating and managing the impact of herbivorous pests requires evidence-based knowledge about the interactions between pests and their natural enemies. Knowledge of species' ecologies and biological interactions are typically disseminated in unstructured text across hundreds of thousands of scientific articles spanning a rapidly growing scientific literature, but manually screening this literature is time-consuming and impractical at scale. Taxonomic and geographic coverage thus remains sparse, and structured data on interactions between individual species are lacking, particularly for invertebrates. Large language models (LLMs) have recently emerged as a novel and powerful text-mining tool for knowledge extraction and evidence synthesis in a wide range of scientific disciplines, including ecology and conservation. In this study, we use an open-weight, pre-trained LLM to analyse abstracts of a corpus of published material on biological pest control to obtain a global Database of Pest Herbivores and their Natural Enemies (DAPHNE). This method resulted in the extraction of 175,404 species interactions from 112,830 published pest control studies, containing16,755 unique animal taxa resolved at the species level. Interactions include herbivory (granivory, frugivory and gall-formation), predation, parasitism and hyperparasitism, and comprise a range of additional information, such as species' taxonomy, pest status, pest importance, natural enemy importance, provision of biocontrol, associated plants and industries, invasiveness and the vectoring of pathogens and diseases. Validation of the results shows that most data columns were extracted with high recall and precision (>90%) and comparison of DAPHNE with other sources shows a high degree of agreement, but also highlights that the dataset contains information that may have been missed by other sources. In addition to the identification of important crop pests and their natural enemies, DAPHNE may be used for a variety of use-cases, including the identification of invasive species and pathogen vectors, trophic network analysis and literature search and discovery.

ecology↗

bioRxiv2026

Confined T cell migration controls programmed cell death 1 expression

T cell immune checkpoint expression and dysfunction are attributed solely to molecular cues. We discover using microphysiological systems and in vivo models that transmigration through confined pores induces acute loss of programmed cell death 1 within minutes of surface immune checkpoint markers on CD8+ T cells through ubiquitin-mediated proteasomal degradation, corresponding with enhanced fitness and function. Such imprints and its underlying mechanism of programmed cell death 1 loss are conserved across species and applicable to human TIL and CAR T cells, and are correlative with disease outcomes in human melanoma. Our findings establish the diverse tissues landscapes that T cells traverse during immunosurveillance, and specifically transmigration, as a form of mechanical immune regulation, and reveal a mechano-modulatory strategy to improve the quality and persistence of engineered or patient-derived T cells for adoptive immunotherapy.

immunology↗

bioRxiv2025

Navigating methodological decisions: Balancing rigor and data volume of the Canadian Living Planet Index

The Living Planet Index -- a biodiversity indicator that assesses the relative change of aggregate vertebrate abundance data -- is an indicator used in global and national biodiversity monitoring frameworks. In Canada, the LPI has been modified (C-LPI) -- adopting differing methodological choices relative to the global LPI. However, there is no clear consensus on the most appropriate analytical methods, particularly as they pertain to the treatment of zeros, confidence intervals and uncertainty, time series length and number of data points required, modelling of short time series, removal of outliers, weighting species, and the impact of baseline year selection. Our analysis transparently explores multiple methodological options and the consequent C-LPI output for each of these decision points. Our research does not evaluate the superiority of a single approach but rather provides transparency and accountability in C-LPI reporting. We hope that this will further strengthen the utility of the C-LPI and provide decision makers with the necessary information to appropriately interpret patterns, evaluate progress towards biodiversity targets, and inform conservation action.

ecology↗

bioRxiv2025

Study of Protein-Protein Interactions in Septin Assembly: Multiple amphipathic helix domains cooperate in binding to the lipid membrane

Septins are a conserved family of cytoskeletal proteins known for sensing micron-scale membrane curvature via amphipathic helix (AH) domains. While cooperative interactions in septin assembly have been suggested, the molecular mechanisms governing membrane binding and assembly remain unclear. Building on prior findings, we use all-atom molecular dynamics simulations to examine how single and paired extended AH domains, derived from Cdc12, interact with lipid bilayers. A single membrane-bound AH adopts a curved conformation. In solution, a second AH peptide preferentially interacts with the bound peptide through conserved salt bridges, favoring an antiparallel arrangement. Simulations of covalently linked AH tandems confirm this configuration. Dual membrane-bound peptides induce lipid packing defects, reduce tail order, and exhibit slight membrane displacement, suggesting curved membranes may better accommodate multiple AH domains. Our findings advance the mechanistic understanding of septin-membrane interactions and highlight the role of cooperative AH domain binding in stabilizing higher-order structures.

biophysics↗

bioRxiv2025

A method for the detection and enrichment of endogenous cereblon substrates

C-Terminal cyclic imides are posttranslational modifications on proteins that are recognized and removed by the E3 ligase substrate adapter cereblon (CRBN). Despite the observation of these modifications across the proteome by mass spectrometry-based proteomics, an orthogonal and generalizable method to visualize the C-terminal cyclic imide would enhance detection, sensitivity, and throughput of endogenous CRBN substrate characterization. Here we develop an antibody-like reagent, termed "cerebody," for visualizing and enriching C-terminal cyclic imide-modified proteins. We describe the engineering of CRBN derivatives to produce cerebody and use it to identify CRBN substrates by Western blot and enrichment from whole cell and tissue lysates. CRBN substrates identified by cerebody enrichment are mapped, validated, and further characterized for dependence on the C-terminal cyclic imide modification. These methods will accelerate the characterization of endogenous CRBN substrates and their regulation.

biochemistry↗

bioRxiv2025

Halting predicted vertebrate declines requires tackling multiple drivers of biodiversity loss

Anthropogenic threats are reshaping Earths biodiversity at an unprecedented rate and scale1-3. Conservation policies often prioritise threats like habitat loss and exploitation based on their global prevalence. However, these assessments rarely quantify the impacts of individual or interacting threats, potential masking the true effects of the Anthropocene4-6. Here, we quantitatively analyse the trends of 3,129 vertebrate populations worldwide with documented exposure to specific and multiple threats. Populations impacted solely by habitat loss or exploitation, the most prevalent threats, do not show the fastest declines. Rather, populations exposed to disease, invasive species, pollution, and climate change decline more rapidly. However, habitat loss and exploitation - along with climate change - do act as additive interactive threats, amplifying population declines. Notably, these interactive threats contribute to population declines, more than temporal or spatial sources of variation. Finally, counterfactual scenarios show that to achieve global non-negative vertebrate population trends, we need to mitigate the effects of multiple threats. These findings underscore the urgency of addressing the compounding effects of multiple threats to halt biodiversity loss and suggest that the local-scale impacts of climate change may be more severe than previously recognized.

ecology↗

bioRxiv2024

Charge distribution and helical content tune the binding of septins amphipathic helix domain to lipid membranes

Septins are a class of cytoskeletal proteins that preferentially bind to domains of micron-scale curvature on the cell membrane. Studies have shown that amphipathic helix (AH) domains in septin oligomers are essential for septin curvature sensing. Yet, the underlying mechanochemical interactions that modulate this curvature sensing remain ambiguous. Here we use all-atom molecular dynamics alongside a metadynamics enhanced sampling approach to bridge the gap between time and length scales required to optimize and validate experimental design of amphipathic helices. Simulations revealed that the local charge on the termini of an 18-amino-acid AH peptide impacts its helical content and positioning within lipid membranes. These computational observations are confirmed with experiments measuring the binding of synthetic AH constructs with variable helical content and charged termini to lipid vesicles. Taken together, these results identify the helical content of amphipathic helices as a regulator of septin binding affinity to lipid membranes. Additionally, we examined an extended AH sequence including 8 amino acids upstream and downstream of the minimal 18-amino-acid-long AH domain to more closely mimic the native protein in simulations and experiments. Simulations and experiments show that the extended peptide sequence adopts a strong alpha-helical conformation when free in solution, giving rise to a higher affinity to lipid membranes than that of the shorter AH sequence. Together, these results provide insight into how the native septin proteins interact with membranes, and establish general design principles that can guide the interaction of future synthetic materials with lipid membranes in a programmable manner. STATEMENT OF SIGNIFICANCEUnderstanding how cells sense and react to their shape is necessary for numerous biological processes. Here we explore the interactions between amphipathic helices, a curvature sensing protein motif, and lipid membranes. Using molecular dynamics simulations, enhanced simulation sampling techniques, and experiments, we find that increasing the helical content of the amphipathic helix or adding charged capping sequences yields higher membrane binding affinity. Understanding these parameters for membrane-binding could enable us to interface and regulate native protein functions, as well as guide the design of synthetic curvature-sensing materials that can interact with and deform lipid membranes.

biophysics↗

bioRxiv2024

Cardiomyocyte PGC-1α enables physiological adaptations to endurance exercise through suppression of GDF15 and cardiac atrophy

Exercise training induces physiological cardiac hypertrophy, enhanced mitochondrial biogenesis and myocardial contractility. In skeletal muscle, the transcriptional coactivator PGC-1 is a key orchestrator of these responses. The heart expresses abundant and exercise-responsive PGC-1, but it is unclear whether cardiomyocyte PGC-1 is necessary for cardiac adaptation to endurance training. Here we demonstrate that cardiomyocyte PGC-1 is required for physiological cardiac hypertrophy during exercise training in mice. In the absence of cardiomyocyte PGC-1, voluntary wheel running does not improve exercise capacity and instead confers immune-fibrotic-atrophic heart failure after just 6 weeks of training. We identify cardiomyocyte PGC-1 as a negative regulator of stress-responsive senescence gene expression. The most enriched of these is the myomitokine GDF15. GDF15 is secreted locally but not systemically in PGC-1-deficient mouse hearts and reduces cardiomyocyte size. Cardiomyocyte-specific reduction of GDF15 expression preserves exercise tolerance and cardiac contractility in PGC-1-deficient mice during endurance training. Finally, we show that cardiomyocyte PPARGC1A expression correlates with cardiomyocyte number and negatively with GDF15 expression in human cardiomyopathies through single nucleus RNA sequencing. Our data implicate cardiomyocyte PGC-1 as a vital safeguard against stress-induced atrophy and local GDF15-induced dysfunction during exercise.

physiology↗

bioRxiv2023

Statistical Methods for Microrheology of Airway Mucus with Extreme Heterogeneity

The mucus lining of the human airway epithelium contains two gel-forming mucins, MUC5B and MUC5AC. During progression of cystic fibrosis (CF), mucus hyper-concentrates as its mucin ratio changes, coinciding with formation of insoluble, dense mucus flakes. We explore rheological heterogeneity of this pathology with reconstituted mucus matching three stages of CF progression and particle-tracking of 200 nm and 1 micron diameter beads. We introduce statistical data analysis methods specific to low signal-to-noise data within flakes. Each bead time series is decomposed into: (i) a fractional Brownian motion (fBm) classifier of the pure time-series signal; (ii) high-frequency static and dynamic noise; and (iii) low-frequency deterministic drift. Subsequent analysis focuses on the denoised fBm classifier ensemble from each mucus sample and bead diameter. Every ensemble fails a homogeneity test, compelling clustering methods to assess levels of heterogeneity. The first binary level detects beads within vs. outside flakes. A second binary level detects within-flake bead signals that can vs. cannot be disentangled from the experimental noise floor. We show all denoised ensembles, within- and outside-flakes, fail a homogeneity test, compelling additional clustering; next, all clusters with sufficient data fail a homogeneity test. These levels of heterogeneity are consistent with outcomes from a stochastic phase-separation process, and dictate applying the generalized Stokes-Einstein relation to each bead per cluster per sample, then frequency-domain averaging to assess rheological heterogeneity. Flakes exhibit a spectrum of gel-like and sol-like domains, outside-flake solutions a spectrum of sol-like domains, painting a rheological signature of the phase-separation process underlying flake-burdened mucus.

microbiology↗

bioRxiv2023

Nonequilibrium bending fluctuations reveal microtubule mechanics in-vivo and their regulation by glutamylation

Cells can be described as active composite materials. The mechanical properties of cells are controlled by complex polymer networks and are dynamically tuned for diverse cellular processes driven by force-generating motor proteins. Microtubules are the most rigid protein polymers in the cytoskeleton, and their material properties have been measured in vitro by active bending or by analyzing thermal bending fluctuations. Microtubule mechanics in living cells are extremely difficult to probe directly, while fluctuations are difficult to interpret because they are generated by active forces in a surrounding cytoplasm with poorly understood material properties. Here we introduce a method to measure the elastic properties of microtubules in living cells by making use of motor-generated forces that drive bending fluctuations. Bending dynamics are governed by three main factors: microtubule material properties, cytoskeletal active forces, and the response characteristics of the surrounding cytoplasm. We show theoretically that, when one factor can be independently determined, the other two can be derived from observed fluctuations. Using this method we discovered that polyglutamylation, a post-translational modification enriched on microtubule arrays that need to withstand large mechanical forces such as those in axons or cilia, increases microtubule stiffness in living cells. Our work provides a theoretical and experimental framework to study microtubule mechanics and their regulation by tubulin modifications and microtubule effectors in complex cellular environments. The approach can be extended to other large aspect ratio cellular structures such as the endoplasmic reticulum or the mitochondrial network.

biophysics↗

bioRxiv2023

How much data do we need? Reliability and data deficiency in global vertebrate biodiversity trends

Global biodiversity is facing a crisis, which must be solved through effective policies and on-the-ground conservation. But governments, NGOs, and scientists need reliable indicators to guide research, conservation actions, and policy decisions. Developing reliable indicators is challenging because the data underlying those tools is incomplete and biased. For example, the Living Planet Index tracks the changing status of global vertebrate biodiversity, but taxonomic, geographic and temporal gaps and biases are present in the aggregated data used to calculate trends. But without a basis for real-world comparison, there is no way to directly assess an indicators accuracy or reliability. Instead, a modelling approach can be used. We developed a model of trend reliability, using simulated datasets as stand-ins for the "real world", degraded samples as stand-ins for indicator datasets (e.g. the Living Planet Database), and a distance measure to quantify reliability by comparing sampled to unsampled trends. The model revealed that the proportion of species represented in the database is not always indicative of trend reliability. Important factors are the number and length of time series, as well as their mean growth rates and variance in their growth rates, both within and between time series. We found that many trends in the Living Planet Index need more data to be considered reliable, particularly trends across the global south. In general, bird trends are the most reliable, while reptile and amphibian trends are most in need of additional data. We simulated three different solutions for reducing data deficiency, and found that collating existing data (where available) is the most efficient way to improve trend reliability, and that revisiting previously-studied populations is a quick and efficient way to improve trend reliability until new long-term studies can be completed and made available.

ecology↗

bioRxiv2023

Biodiversity shows unique responses to land-use change across regional biomes

Biogeography has a critical influence on how ecological communities respond to threats and how effective conservation interventions are designed. For example, the resilience of ecological communities is linked to environmental and climatic features, and the nature of threats impacting ecosystems also varies geographically. Understanding community-level threat responses may be most accurate at fine spatial scales, however collecting detailed ecological data at such a high resolution would be prohibitively resource intensive. In this study, we aim to find the spatial scale that could best capture variation in community-level threat responses whilst keeping data collection requirements feasible. Using a database of biodiversity records with extensive global coverage, we modelled species richness and total abundance (the responses) across land-use types (reflecting threats), considering three different spatial scales: biomes, biogeographical realms, and regional biomes (the interaction between realm and biome). We then modelled data from three highly sampled biomes separately to ask how responses to threat differ between regional biomes and taxonomic group. We found strong support for regional biomes in explaining variation in species richness and total abundance compared to biomes or realms alone. Our biome case studies demonstrate that there is a high variation in magnitude and direction of threat responses across both regional biomes and taxonomic group, but all groups in tropical forest showed a consistently negative response, whilst many taxon-regional biome groups showed no clear response to threat in temperate forest and tropical grassland. Our results suggest that the taxon-regional biome unit has potential as a reasonable spatial and ecological scale for understanding how ecological communities respond to threats and designing effective conservation interventions to bend the curve on biodiversity loss.

ecology↗

bioRxiv2023

SCCA1/SERPINB3 promotes suppressive immune environment via STAT-dependent chemokine production, blunting the therapy-induced T cell responses

Radiotherapy is a commonly used cancer treatment; however, patients with high serum squamous cell carcinoma antigen (SCCA1/SERPINB3) are associated with resistance and poor prognosis. Despite being a strong clinical biomarker, the modulation of SERPINB3 in tumor immunity is poorly understood. We investigated the microenvironment of SERPINB3 high tumors through RNAseq of primary cervix tumors and found that SERPINB3 was positively correlated with CXCL1/8, S100A8/A9 and myeloid cell infiltration. Induction of SERPINB3 in vitro resulted in increased CXCL1/8 and S100A8/A9 production, and supernatants from SERPINB3-expressing cultures attracted monocytes and MDSCs. In murine tumors, the orthologue mSerpinB3a promoted MDSC, TAM, and M2 macrophage infiltration contributing to an immunosuppressive phenotype, which was further augmented upon radiation. Radiation-enhanced T cell response was muted in SERPINB3 tumors, whereas Treg expansion was observed. A STAT-dependent mechanism was implicated, whereby inhibiting STAT signaling with ruxolitinib abrogated suppressive chemokine production. Patients with elevated pre-treatment serum SCCA and high pSTAT3 had increased intratumoral CD11b+ myeloid cell compared to patients with low SCCA and pSTAT3 cohort that had overall improved cancer specific survival after radiotherapy. These findings provide a preclinical rationale for targeting STAT signaling in tumors with high SERPINB3 to counteract the immunosuppressive microenvironment and improve response to radiation.

cancer biology↗

bioRxiv2022

Recovering birds and mammals across Europe continue to be negatively impacted by threats but benefit from conservation measures

Even during ongoing global biodiversity losses and extinctions, numerous species have shown recoveries in terms of increased abundance and/or range extent. Understanding the mechanisms that contribute to, or limit, these recoveries is critical not just to ensure they continue, but to promote similar recoveries across broader ecosystems. Here, we explore the changes in abundance and range extent of selected 47 recovering species (24 mammals and 23 birds) in Europe using official data reported by EU Member States and supplemented using the Living Planet Index database. We investigate how the diversity of ongoing threats and conservation measures contribute to the likelihood and extent of recoveries. For birds, long-term recoveries were less likely among species impacted by a greater diversity of threats, although this may be mitigated by the diversity of conservation measures in place. Similarly, for mammals, populations with reported threats recovered less quickly while those with management actions in place recovered more quickly. To achieve the aims of the UN Decade on Restoration, we need to ensure, even for recovering species, that threats continue to be reduced and that conservation management actions are ongoing and effective.

ecology↗

bioRxiv2022

Past, present, and future of the Living Planet Index

As we enter the next phase of international policy commitments to halt biodiversity loss (e.g. Post-2020 Biodiversity Framework), biodiversity indicators will play an important role forming the robust basis upon which targeted, and time sensitive conservation actions are developed. Population trend indicators are perhaps the most powerful tool in biodiversity monitoring due to their responsiveness to changes over short timescales and their ability to aggregate species trends from global down to at a sub-national or even local scale. We consider how the project behind the foremost population level indicator - the Living Planet Index - has evolved over the last 25 years, its value to the field of biodiversity monitoring, and how its components have portrayed a compelling account of the changing status of global biodiversity through its application at policy, research and practice levels. We explore ways the project can develop to enhance our understanding of the state of biodiversity and share lessons learned to inform indicator development and mobilise action. O_TEXTBOXBox 1. The Living Planet Index Project The Living Planet Index project (the index, methodology, and database) and its secondary outputs (methods papers and R code, database and website, global index, and subset indices) have had wide-ranging applications within the fields of biodiversity monitoring and research, as well as across policy, education, and outreach. The Living Planet Index (LPI) is a biodiversity indicator which tracks trends in the relative abundance of wild vertebrate populations (where population is defined as to a single species in a defined location rather than the biological definition). Relative abundance captures how populations are changing over time on average in comparison to a reference point, or "baseline" (the LPI uses 1970). It is often described as analogous to a stock market index for species. The index is comprised of thousands of population time-series for vertebrate species from locations around the world; the trends from these populations are averaged to produce terrestrial, freshwater, and marine indices, which are further aggregated to a global LPI. The latest global LPI shows a decline of 68% between 1970 and 2016 globally 1. This is an average trend based on time-series data from 20,811 populations of 4,392 species of mammals, birds, reptiles, amphibians, and fish. The LPI database (LPD) can include population data for any species for which time-series population data could be found, regardless of threat status, or whether they show increasing or declining trends. These population time-series are sourced from scientific papers, online databases, government, and expert led published reports. They can be searched and downloaded from the project website (www.livingplanetindex.org). More technical information is available on the LPI stats website (http://stats.livingplanetindex.org/). C_TEXTBOX

ecology↗

bioRxiv2022

A user-friendly guide to using distance measures to compare time series in ecology.

O_LITime series are a critical component of ecological analysis, used to track changes in biotic and abiotic variables. Information can be extracted from the properties of time series for tasks such as classification, clustering, prediction, and anomaly detection. These common tasks in ecological research rely on the notion of (dis-) similarity which can be determined by using distance measures. A plethora of distance measures have been described in the scientific literature, but many of them have not been introduced to ecologists. Furthermore, little is known about how to select appropriate distance measures and the properties they focus on for time-series related tasks. C_LIO_LIHere we describe 16 potentially desirable properties of distance measures, test 42 distance measures for each property, and present an objective method to select appropriate distance measures for any task and ecological dataset. We then demonstrate our selection method by applying it to a set of real-world data on breeding bird populations in the UK. We also discuss ways to overcome some of the difficulties involved in using distance measures to compare time series. C_LIO_LIOur real-world population trends exhibit a common challenge for time series comparison: a high level of stochasticity. We demonstrate two different ways of overcoming this challenge, first by selecting distance measures with properties that make them well-suited to comparing noisy time series, and second by applying a smoothing algorithm before selecting appropriate distance measures. In both cases, the distance measures chosen through our selection method are not only fit-for-purpose but are consistent in their rankings of the population trends. C_LIO_LIThe results of our study should lead to an improved understanding of, and greater scope for, the use of distance measures for comparing time series within ecology, and allow for the answering of new ecological questions. C_LI

ecology↗

bioRxiv2022

Modeling predicts mechanisms altered by mutations of the SARS-CoV-2 delta and omicron variants

We apply our mechanistic, within-host, pre-immunity, respiratory tract infection model for unvaccinated, previously uninfected, and immune-compromised individuals. Starting from published cell infection and viral replication data for the SARS-CoV-2 alpha variant, we explore variability in outcomes of viral load and cell infection due to three plausible mechanisms altered by SARS-CoV-2 mutations of delta and omicron. We seek a mechanistic explanation of clinical test results: delta nasal infections express [~]3 orders-of-magnitude higher viral load than alpha, while omicron infections express an additional 1 to 2 orders-of-magnitude rise over delta. Model simulations reveal shortening of the eclipse phase (the time between cellular uptake of the virus and onset of infectious viral replication and shedding) alone can generate 3-5 orders-of-magnitude higher viral load within 2 days post initial infection. Higher viral replication rates by an infected cell can generate at most one order-of-magnitude rise in viral load, whereas higher cell infectability has minimal impact and lowers the viral load.

immunology↗

bioRxiv2022

Body mass and latitude as global predictors of vertebrate populations exposure to multiple threats

The interactive effects of multiple threats are one of the main causes of biodiversity loss, yet our understanding of what predisposes species to be impacted by multiple threats remains limited. Here we analyse a global dataset of over 7000 marine, freshwater, and terrestrial vertebrate populations, alongside trait, threat and geographical data, to identify the factors influencing the number of threats a species is subjected to at the population level. Out of a suite of predictors tested, we find that body mass and latitude both are broadly available for vertebrate species, and influence the number of threats a population is subjected to. Larger bodied species and those nearer the equator are typically affected by a higher number of threats. However, whilst this pattern broadly holds across ecosystems for most taxa, amphibians and reptiles show opposing trends. We suggest that latitude and body mass should be considered as key predictors to identify which vertebrate populations are likely to be impacted by multiple threats. These general predictors can help to better understand the impacts of the Anthropocene on global vertebrate biodiversity and design effective conservation policies.

ecology↗