Biology subjects

Collins, L.

Publications and source records attributed to Collins, L..

15 recordsLinked to original sources

bioRxiv2026

Revealing parasitoid-pest interactions using multi-marker metabarcoding: a nationwide assessment of parasitism in cabbage stem flea beetle larvae

Management of insect pests of oilseed rape (Brassica napus L.) such as cabbage stem flea beetle (CSFB; Psylliodes chrysocephala L.) is increasingly challenging given a lack of effective permitted insecticides. Conservation biocontrol, including through naturally-occurring parasitoids of CSFB, is one of the first lines of defense and the baseline for integrated pest management (IPM) strategies, but we lack a comprehensive understanding of the parasitoids involved and how parasitism rates vary regionally. Such data have traditionally required rearing of parasitoids from their pest hosts, which is highly error-prone, laborious and overlooks instances of multiple parasitism and hyperparasitism. Using multi-marker DNA metabarcoding, including a novel host-exclusion parasitoid PCR primer pair, we assessed parasitism of 1,040 CSFB larvae from 13 counties in England, UK. We confidently identified seven parasitoids of CSFB larvae, with ten taxa present in unfiltered data. Parasitism rates differed between regions, with the north of England having significantly lower parasitism rates than southern regions. Our novel beetle parasitoid PCR primers demonstrate a high congruence with visual detections of parasitoids and a high rate of novel interaction detections. Ultimately, by determining both rates of parasitism and natural enemy identities, these data significantly extend our understanding of in-field CSFB parasitoid community dynamics. This information could guide the enhancement of farm management, especially using network science in decision support systems related to insecticide application, but also more broadly in the context of crop and habitat management for improved conservation biocontrol and IPM.

ecology↗

bioRxiv2026

Temporal dynamics of grooming reciprocity in crested macaques: do social bonds affect exchange?

Primates maintain cooperative relationships largely through grooming reciprocity, yet studies disagree on the timescales over which grooming is returned. Part of this disagreement stems from statistical issues: inconsistent definitions of a reciprocation window, combined with the exclusion of unreciprocated grooming, leave the debate unresolved. We still do not know if primates exchange grooming within the short windows predicted by biological market theory or over much longer timescales. Whilst survival analysis can identify reciprocation windows objectively by retaining unreciprocated grooming as censored data, previous studies have applied it inconsistently. This inconsistency leaves the true time frames over which primates reciprocate grooming somewhat blurred. Here, we use a statistical approach that addresses these problems to examine grooming reciprocity in crested macaques (Macaca nigra), a socially tolerant macaque species. We applied survival analysis to identify each group's short-term reciprocation window without imposing arbitrary cut offs, and Bayesian survival models to test whether social bond strength and eigenvector centrality predicted reciprocation latency. Short-term reciprocation occurred rarely (29% of events in one group and 5% in the other); most reciprocation occurred over longer timescales than previous research commonly assumes. Stronger bonds predicted faster reciprocation; this finding suggests that crested macaques express social investment in valued partners through how promptly they return grooming, meaning that the timing of exchange carries information about relationship value. Eigenvector centrality showed no credible effect, though our small sample size and dense groups prevent us from interpreting this outcome more robustly. Substantial variation between dyads remained unexplained, pointing to partnerspecific properties we have yet to identify. These findings caution against assuming that reciprocity operates over short windows. They show that social predictors, such as bond strength, remain essential to understanding when primates return grooming. This work provides a baseline for testing whether grooming is exchanged for other social commodities, and for comparing reciprocation timescales across macaque species that differ in social tolerance.

animal behavior and cognition↗

bioRxiv2026

Facility-Scale Workflows for Data Acquisition, Standardization, Machine Learning Analysis, and Reproducible Science

Scientific user facilities routinely generate large-scale microscopy datasets across diverse instruments and vendors, differing substantially in file formats, dimensionality, and resolution. Beyond these inconsistencies, datasets are frequently fragmented living across isolated instruments and constrained by security policies and uneven metadata practices. Consequently, tracking, standardizing, processing, and visualizing these datasets in a manner compatible with modern machine learning and autonomous experimentation workflows remains a major challenge. While existing initiatives address data archiving, standardization, or analysis individually, few provide integrated solutions that bridge instrument-level acquisition and scalable ML workflows within heterogeneous, security-constrained user facilities. Here, we establish a deployable, facility-scale infrastructure that bridges instrument-level data generation with cloud-based ML analytics while remaining compliant with institutional network constraints. Our framework integrates on-premises cloud computing, the in-house Pycroscopy ecosystem, and an open-source metadata management platform to transform heterogeneous microscopy datasets into standardized, ML-ready representations. We demonstrate this approach across distinct microscopy modalities through end-to-end workflows encompassing metadata capture, format harmonization, automated database ingestion, segmentation-based ML inference, and interactive visualization. By structurally separating acquisition from cloud-based analysis services, the framework enables scalable model deployment and iterative refinement without direct connectivity to instrument computers. Together, this work provides a reproducible blueprint for facility-scale data and AI infrastructure, enabling ML-ready analytics, metadata traceability, and future autonomous experimentation workflows in microscopy-driven research.

microbiology↗

bioRxiv2024

The Biochemical Effects of Carotenoids in Orange Carrots on the Colonic Proteome in a Mouse Model of Diet-induced Obesity

Carotenoids are naturally occurring pigments in plants and are responsible for the orange, yellow, and red color of fruits and vegetables. Carrots are one of the primary dietary sources of carotenoids. The biological activities of carotenoids in higher organisms are well documented in most tissues but not the large intestine. The gastrointestinal barrier acts as a line of defense against the systemic invasion of pathogenic bacteria, especially at the colonic level. Proteins involved in tight junction assembly between epithelial cells and mucus secretion from goblet cells are essential for maintaining intestinal barrier homeostasis. A high-fat diet can cause gut impairment by inducing barrier permeability, leading to low-grade chronic inflammation via metabolic endotoxemia. Our hypothesis for this study is that the dietary intake of carotenoid-rich foods can alleviate obesity-associated gut inflammation and strengthen the intestinal barrier function. Male C57BL/6J mice were randomized to one of four experimental diets for 20 weeks (n = 20 animals/group): Low-fat diet (LFD, 10% calories from fat), high-fat diet (HFD, 45% calories from fat), HFD with white carrot powder (HFD + WC), or HFD with orange carrot powder (HFD + OC). Colon tissues were harvested to analyze the biochemical effects of carotenoids in carrots. The distal sections were subjected to isobaric labeling-based quantitative proteomics in which tryptic peptides were labeled with tandem mass tags, followed by fractionation and LC-MS/MS analysis in an Orbitrap Eclipse Tribrid instrument. High-performance liquid chromatography results revealed that the HFD+WC pellets were carotenoid-deficient, and the HFD+OC pellets contained high concentrations of provitamin A carotenoids, specifically -carotene and {beta}-carotene. As a result of the quantitative proteomics, a total of 4410 differentially expressed proteins were identified. Intestinal barrier-associated proteins were highly upregulated in the HFD+OC group, particularly mucin-2 (MUC-2). Upon closer investigation into mucosal activity, other proteins related to MUC-2 functionality and tight junction management were upregulated by the HFD+OC dietary intervention. Collectively, our findings suggest that carotenoid-rich foods can prevent high-fat diet-induced intestinal barrier disruption by promoting colonic mucus synthesis and secretion in mammalian organisms. Data are available via ProteomeXchange with identifier PXD054150.

biochemistry↗

bioRxiv2024

Brain Age Prediction: Deep Models Need a Hand to Generalize

Predicting brain age from T1-weighted MRI is a promising marker for understanding brain aging and its associated conditions. While deep learning models have shown success in reducing the Mean Absolute Error (MAE) of predicted brain age, concerns about robust and accurate generalization in new data limit their clinical applicability. The large number of trainable parameters, combined with limited medical imaging training data, contribute to this challenge, often resulting in a generalization gap where there is a significant discrepancy between model performance on training data versus unseen data. In this study, we assess a deep model, SFCN-reg, based on the VGG-16 architecture, and address the generalization gap through comprehensive preprocessing, extensive data augmentation, and model regularization. Using training data from the UK Biobank, we demonstrate substantial improvements in model performance. Specifically, our approach reduces the generalization MAE by 44% (from 5.25 to 2.96 years) in the Alzheimers Disease Neuroimaging Initiative dataset and by 22% (from 4.35 to 3.40 years) in the Australian Imaging, Biomarker and Lifestyle dataset. Furthermore, we achieve a 29% reduction in scan-rescan error (from 0.86 to 0.61 years) while enhancing the models robustness to registration errors. Feature importance maps highlight anatomical regions used to predict age. These results highlight the critical role of high-quality preprocessing and robust training techniques in improving accuracy and narrowing the generalization gap, both necessary steps towards the clinical use of brain age prediction models. Our study makes valuable contributions to neuroimaging research by offering a potential pathway to improve the clinical applicability of deep learning models.

neuroscience↗

bioRxiv2022

Cholinergic and noradrenergic axonal activity is both strongly coordinated with behavioral state and heterogeneous across the dorsal cortex

Fluctuations in brain and behavioral state are supported by broadly projecting neuromodulatory systems. In this study, we use mesoscale two-photon calcium imaging to examine spontaneous activity of cholinergic and noradrenergic axons in awake mice in order to determine the interaction between arousal/movement state transitions and neuromodulatory activity across the dorsal cortex at distances separated by up to 4 mm. We confirm that GCaMP6s activity within axonal projections of both basal forebrain cholinergic and locus coeruleus noradrenergic neurons track arousal, indexed as pupil diameter, and changes in behavioral engagement, as reflected by bouts of whisker movement and/or locomotion. The broad coordination in activity between even distant axonal segments indicates that both of these systems can communicate, in part, through a global signal, especially in relation to changes in behavioral state. In addition to this broadly coordinated activity, we also find evidence that a subpopulation of both cholinergic and noradrenergic axons may exhibit heterogeneity in activity that appears to be independent of our measures of behavioral state. By monitoring the activity of cholinergic interneurons in the cortex we found that a subpopulation of these cells also exhibit state-dependent (arousal/movement) activity. These results demonstrate that cholinergic and noradrenergic systems provide a prominent and broadly synchronized signal related to behavioral state, and therefore may contribute to state-dependent cortical activity and excitability.

neuroscience↗

bioRxiv2022

Sex-bias in utero alters ovarian reserve but not uterine capacity in female offspring

Environmental stressors to which a foetus is exposed, affect a range of physiological functions in post-natal offspring. Such stressors include disproportionate steroid hormone concentrations in the uterine environment. We aimed to determine the in-utero effect of steroid hormones on reproductive potential of female offspring using a porcine model. Hypothesising that an in-utero sex bias will influence ovarian reserve and endometrial morphology in the breeding gilt. Reproductive tracts of pigs from female-biased litters (>65% female, n=15), non-biased litters (45-54.9% female, n=15), and male-biased litters (<35% females, n=9) were collected at slaughter (95-115 kg). Ovaries and uterine horns were processed for histological approaches and stained using H&E or IHC techniques. All measurements were conducted in QuPath (Bankhead et al, 2017). Variability of data within groups was analysed with a Levenes test, whilst data was analysed using linear models in R. In the ovarian reserve, there was a significant interaction between the birth weight and the sex ratio of a litter from which a pig originated (p=.015), with low-birth-weight pigs from male-biased litters having a higher number of primordial follicles and the opposite trend seen in pigs from female-biased litters. This was not reflected in recruited, nor atretic follicles. In the uterine horn sex bias held no effect on development as seen in this study. Birth weight held more effects on the gilts. A lower BW decreased the proportion of glands found in the endometrium (p=.045). BW was found to be far more variable in both male-biased and female-biased litters (p=.026). The variability of primordial follicles from male-biased litters was greater than non-and female-biased litters (p=.014). Similarly, endometrial stromal nuclei had a greater range in male- and female-biased litters than non-biased litters (p=.028). There was a greater effect on both ovarian reserve and uterine development of piglet BW than the litter bias. There seems a benefit of being androgenised on ovarian reserve whilst no effects were found for the morphology or endometrial gland proliferation of the uterine horns. However, a crucial finding was in the variability of the data. Both primordial follicles in the male-biased ovary, and stromal nuclei in the male- and female-biased uterine horns had a wider spread in numbers than non-biased litters. This could be inflating the variability of reproductive success seen in animals form male-biased litters by two means. Firstly, by a higher likelihood of insufficient primordial pools. Secondly, through a potential impact on stromal-derived growth factors or insufficient support of the underlying implantation structures, leading to an increased variability in uterine implantation capabilities, and thus survival of the embryo.

developmental biology↗

bioRxiv2022

Population dynamics of free-roaming dogs in Europe and implications for population control

Changes in free-roaming dog population size are important indicators of the effectiveness of dog population management. Assessing the effectiveness of different management methods also requires estimating the processes that change population size, such as the rates of recruitment into and removal from a population. This is one of the first studies to quantify the size, rates of recruitment and removal, and health and welfare status of free-roaming dog populations in Europe. We determined the size, dynamics, and health status of free-roaming dog populations in Pescara, Italy, and Lviv, Ukraine, over a 15-month study period. Both study populations had ongoing dog population management through catch-neuter-release and sheltering programmes. Average monthly apparent survival probability was 0.93 (95% CI 0.81-1.00) in Pescara and 0.93 (95% CI 0.84-0.99) in Lviv. An average of 7 dogs km-2 were observed in Pescara and 40 dogs km-2 in Lviv. Per capita entry probabilities varied between 0.09 and 0.20 in Pescara, and 0.12 and 0.42 in Lviv. In Lviv, detection probability was lower on weekdays (odds ratio: 0.74, 95% CI 0.53-0.96) and higher on market days (odds ratio: 2.58, 95% CI 1.28-4.14), and apparent survival probability was lower in males (odds ratio: 0.25, 95% CI 0.03-0.59). Few juveniles were observed in the study populations, indicating that recruitment may be occurring by movement between dog subpopulations (e.g. from local owned or neighbouring free-roaming dog populations), with important consequences for population control. This study provides important data for planning effective dog population management and for informing population and infectious disease modelling. The results emphasise the importance of dog population management efforts that encourage responsible ownership through reduced abandonment and cover the entire city to reduce the risk of dog movement between sections of the city hindering management efforts.

ecology↗

bioRxiv2021

A combination of two human neutralizing antibodies prevents SARS-CoV-2 infection in rhesus macaques

Human monoclonal antibody (mAb) treatments are promising for COVID-19 prevention, post-exposure prophylaxis, or therapy. However, the titer of neutralizing antibodies required for protection against SARS-CoV-2 infection remains poorly characterized. We previously described two potently neutralizing mAbs COV2-2130 and COV2-2381 targeting non-overlapping epitopes on the receptor-binding domain of SARS-CoV-2 spike protein. Here, we engineered the Fc-region of these mAbs with mutations to extend their persistence in humans and reduce interactions with Fc gamma receptors. Passive transfer of individual or combinations of the two antibodies (designated ADM03820) given prophylactically by intravenous or intramuscular route conferred virological protection in a non-human primate (NHP) model of SARS-CoV-2 infection, and ADM03820 potently neutralized SARS-CoV-2 variants of concern in vitro. We defined 6,000 as a protective serum neutralizing antibody titer in NHPs against infection for passively transferred human mAbs that acted by direct viral neutralization, which corresponded to a concentration of 20 g/mL of circulating mAb.

immunology↗

bioRxiv2021

Judgement Bias During Pregnancy In Domestic Pigs

In humans and rats, changes in mood and affect are known to occur during pregnancy, however it is unknown how gestation may influence mood in other non-human mammals. This study assessed changes in pigs judgment bias as a measure of affective state throughout gestation. Pigs were trained to complete a spatial judgement bias task with reference to positive and negative locations. We tested gilts before mating, and during early and late pregnancy, by assessing their responses to ambiguous probe locations. Pigs responded increasingly negatively to ambiguous probes as pregnancy progressed and there were consistent inter-individual differences in baseline optimism. This suggests that the pigs affective state may be altered during gestation, although as a non-pregnant control group was not tested, an effect of learning cannot be ruled out. These results suggest that judgement bias is altered during pregnancy in domestic pigs, consequently raising novel welfare considerations for captive multiparous species.

animal behavior and cognition↗

bioRxiv2021

Public attitudes towards free-roaming dogs and dog ownership practices in Bulgaria, Italy, and Ukraine

Overabundant, free-roaming dog populations are associated with risks to public health, livestock losses, wildlife conservation, and dog health and welfare. Dog population management is conducted to mitigate these issues. Assessing dog population management strategies is important to determine their effectiveness, efficiency, and long-term impact. It is essential to also determine how the behaviour and outlook of local communities may influence the efficacy of dog population management. This study aimed to determine public attitudes towards free-roaming dogs and their management and describe dog ownership practices in three European countries using an online questionnaire survey. This study found that most surveyed respondents wanted to see a reduction in free-roaming dog numbers, and felt that this should be achieved through sheltering, catch-neuter-release, and by controlling the breeding of owned dogs. This questionnaire also identified significant associations between public attitudes and dog ownership practices with gender, religious beliefs, age, education level, reason for dog ownership, previous experience with free-roaming dogs, and country of residence. Respondents who identified as: (i) being male, (ii) holding religious beliefs, (iii) owning dogs for practical reasons, (iv) being young, and (v) having no schooling or primary education had a lower probability of neutering and a higher probability of allowing dogs to roam. Respondents who identified as: (i) being female, (ii) feeling threatened by free-roaming dogs, (iii) being older, and (iv) having more education had a higher probability of answering that an increase in free-roaming dog numbers should be prevented. These findings can help to inform future dog population management interventions in these countries and highlight the importance of considering local public attitudes and dog ownership practices in the development of effective dog population management approaches. Including these social factors will ensure that both the community and organisations involved in dog population management work cohesively towards a shared goal.

ecology↗

bioRxiv2019

The fate of carbon in a mature forest under carbon dioxide enrichment

Atmospheric carbon dioxide enrichment (eCO2) can enhance plant carbon uptake and growth1,2,3,4,5, thereby providing an important negative feedback to climate change by slowing the rate of increase of the atmospheric CO2 concentration6. While evidence gathered from young aggrading forests has generally indicated a strong CO2 fertilization effect on biomass growth3,4,5, it is unclear whether mature forests respond to eCO2 in a similar way. In mature trees and forest stands7,8,9,10, photosynthetic uptake has been found to increase under eCO2 without any apparent accompanying growth response, leaving an open question about the fate of additional carbon fixed under eCO24, 5, 7,8,9,10,11. Here, using data from the first ecosystem-scale Free-Air CO2 Enrichment (FACE) experiment in a mature forest, we constructed a comprehensive ecosystem carbon budget to track the fate of carbon as the forest responds to four years of eCO2 exposure. We show that, although the eCO2 treatment of ambient +150 ppm (+38%) induced a 12% (+247 gCm-2yr-1) increase in carbon uptake through gross primary production, this additional carbon uptake did not lead to increased carbon sequestration at the ecosystem level. Instead, the majority of the extra carbon was emitted back into the atmosphere via several respiratory fluxes, with increased soil respiration alone contributing [~]50% of the total uptake surplus. Our results call into question the predominant thinking that the capacity of forests to act as carbon sinks will be generally enhanced under eCO2, and challenge the efficacy of climate mitigation strategies that rely on CO2 fertilization as a driver of increased carbon sinks in standing forests and afforestation projects.

ecology↗

bioRxiv2019

Distinct changes in morphometric networks in aging versus Alzheimer’s disease dementia

Brain gray matter (GM) morphometric changes are prevalent in both aging and Alzheimers disease (AD), though disentangling these two processes has proved challenging. Using independent component analysis, we derived morphometric networks from a large, multi-cohort dataset, and investigated how GM volume within these networks differs in young adulthood, old adulthood, and AD. Aging and AD contributed additive effects on GM loss in nearly all networks, except frontal lobe networks, where GM reductions were more specific to aging. While no networks show GM loss highly specific to AD, a higher degree of variability in the whole-brain pattern of GM volume characterized AD only. Preservation of the whole-brain GM pattern in cognitively normal older adults was related to better cognition and lower risk of developing cognitive impairment. These results suggest both aging and AD involve widespread atrophy, but that cognitive impairment is uniquely associated with disruption of morphometric organization.

neuroscience↗

bioRxiv2018

Design of a de novo aggregating antimicrobial peptide and bacterial conjugation delivery system

Traditional antibiotics are reaching obsolescence as a consequence of antibiotic resistance; therefore novel antibiotic approaches are needed. A recent non-traditional approach involves formation of protein aggregates as antimicrobials to disrupt bacterial homeostasis. Previous work on protein aggregates has focused on genome mining for aggregation-prone sequences in bacterial genomes rather than on rational design of aggregating antimicrobial peptides. Here, we use a synthetic biology approach to design an artificial gene encoding the first de novo aggregating antimicrobial peptide. This artificial gene, opaL (overexpressed protein aggregator Lipophilic), disrupts bacterial homeostasis by expressing extremely hydrophobic peptides. When this hydrophobic sequence is disrupted by acidic residues, consequent aggregation and antimicrobial effect decreases. Further, to deliver this artificial gene, we developed a probiotic approach using RK2, a broad host range conjugative plasmid, to transfer opaL from donor to recipient bacteria. We utilize RK2 to mobilize a shuttle plasmid carrying the opaL gene by adding the RK2 origin of transfer. We show that opaL is non-toxic to the donor, allowing for maintenance and transfer since its expression is under control of a promoter with a recipient-specific T7 RNA polymerase. Upon mating of donor and recipient Escherichia coli, we observe selective growth repression in T7 polymerase expressing recipients. This technique could be used to target desired pathogens by selecting pathogen-specific promoters to control opaL expression. This system provides a basis for the design and delivery of novel antimicrobial peptides.\n\nImportanceThe growing threat of antibiotic resistance necessitates new treatment options for bacterial infections that are recalcitrant to traditional antimicrobials. Existing methods usually involve small-molecule compounds which interfere with essential processes in bacterial cells. By contrast, protein aggregates operate by causing widespread disruption of bacterial homeostasis and may provide a new method for combating infections. We used rational design to create and test an aggregating de novo antimicrobial peptide, OpaL. In addition, we employed bacterial conjugation to deliver the opaL gene from donor bacteria to recipient bacteria while using a strain-specific promoter to ensure that OpaL was only expressed in targeted recipients. To the best of our knowledge, this represents the first design for a de novo peptide with aggregation-mediated antimicrobial activity. We envision that OpaLs design parameters could be used in developing a new class of antimicrobial peptides to help treat antibiotic resistant infections.

microbiology↗

bioRxiv2018

The relationship between brain atrophy and cognitive-behavioral symptoms in retired Canadian football players with multiple concussions

Multiple concussions, particularly in contact sports, have been associated with cognitive deficits, psychiatric impairment and neurodegenerative diseases like chronic traumatic encephalopathy. We used volumetric and deformation-based morphometric analyses to test the hypothesis that repeated concussions may be associated with smaller regional brain volumes, poorer cognitive performance and behavioural symptoms among former professional football players compared to healthy controls. This study included fifty-three retired Canadian Football League players, 25 age- and education-matched healthy controls, and controls from the Cambridge Centre for Aging and Neuroscience database for validation. Volumetric analyses revealed greater hippocampal atrophy than expected for age in former athletes with multiple concussions than controls and smaller left hippocampal volume was associated with poorer verbal memory performance. Deformation-based morphometric confirmed smaller bilateral hippocampal volume that were associated with poorer verbal memory performance in athletes. Repeated concussions may lead to greater regional atrophy than expected for age.

neuroscience↗