Biology subjects

Harvey, C.

Publications and source records attributed to Harvey, C..

10 recordsLinked to original sources

bioRxiv2025

Identification of Amblyomma americanum antigens after vaccination with tick extracellular vesicles in white-tailed deer

Anti-tick vaccines represent a promising alternative to chemical acaricides for the management of ticks on wildlife; however little progress has been made to produce a vaccine effective in wild hosts that are critical for tick reproduction, such as the white-tailed deer (Odocoileus virginianus; WTD). To date, most tick antigens have been tested using laboratory models (i.e. rabbits); however, their expression in wild hosts has not been confirmed. We recently tested Amblyomma americanum salivary (SG) and midgut (MG) extracellular vesicles (EVs) as vaccine candidates in WTD, which resulted in on-host female tick mortality. Using a proteomic approach, we show that these SG- and MG-EVs contain a "core-cargo" enriched in chaperones, small GTPases, actin and actin-related proteins, and other proteins previously reported in small EVs. Label-free quantitative proteomics showed significant differences in protein cargo between MG and SG-EVs (333 proteins out of 516). Pre-vaccinated and day 57 post-injection serum samples from three vaccinated and one control WTD were used to immuno-precipitate antigenic proteins from SG- and MG-EV preparations. Proteomic analysis of immunoprecipitated proteins identified thirty antigens with potential for use in anti-tick vaccines, seven of which we have categorized as high priority. These proteins represent promising candidates for anti-tick vaccine design in WTD and other wildlife hosts.

immunology↗

bioRxiv2024

Evaluation of tick salivary and midgut extracellular vesicles as anti-tick vaccines in White-tailed deer (Odocoileus virginianus)

Current tick control measures are focused on the use of synthetic acaricides and personal protective measures. However, the emergence of acaricide resistance and the maintenance of tick populations in wildlife has precluded the efficient management of ticks. Thus, host-targeted, non-chemical control measures are needed to reliably reduce ticks parasitizing sylvatic reservoirs. This project aimed to evaluate extracellular vesicles (EVs) from Amblyomma americanum as vaccine candidates for white-tailed deer (Odocoileus virginianus; WTD). Salivary gland (SG) and midgut (MG) EVs were isolated by ultracentrifugation. Three deer were vaccinated with SG and MG EVs and received two boosters at days 28 and 50. Two control deer were injected with adjuvant and PBS only. On day 58, WTD were infested with 100 A. americanum nymphs, 50 females, and 50 males that were allowed to feed to repletion. On-host and off-host mortality, tick engorgement weight, nymph molting, time to oviposition, and egg hatchability were evaluated. Serum samples were recovered every seven days until the last day of tick drop off, and then at one year (Y1) and 1-year and 1-month (Y1M1). Vaccination resulted in seroconversion and significant increases in total IgG levels that remained significantly higher than controls and pre-vaccination levels at Y1 and Y1M1. No negative effects were observed in nymphs, but on-host mortality of female A. americanum was significantly higher in vaccinated animals. No effects were observed on reproductive parameters. These results indicate that proteins within female tick SG and MG vesicles are not good candidates for vaccine design against nymphs; however, the on-host adult mortality suggests that tick EVs harbor protective antigens against A. americanum females.

immunology↗

bioRxiv2024

predicTTE: An accessible and optimal tool for time-to-event prediction in neurological diseases

Time-to-event prediction is a key task for biological discovery, experimental medicine, and clinical care. This is particularly true for neurological diseases where development of reliable biomarkers is often limited by difficulty visualising and sampling relevant cell and molecular pathobiology. To date, much work has relied on Cox regression because of ease-of-use, despite evidence that this model includes incorrect assumptions. We have implemented a set of deep learning and spline models for time-to-event modelling within a fully customizable app and accompanying online portal, both of which can be used for any time-to-event analysis in any disease by a non-expert user. Our online portal includes capacity for end-users including patients, Neurology clinicians, and researchers, to access and perform predictions using a trained model, and to contribute new data for model improvement, all within a data-secure environment. We demonstrate a pipeline for use of our app with three use-cases including imputation of missing data, hyperparameter tuning, model training and independent validation. We show that predictions are optimal for use in downstream applications such as genetic discovery, biomarker interpretation, and personalised choice of medication. We demonstrate the efficiency of an ensemble configuration, including focused training of a deep learning model. We have optimised a pipeline for imputation of missing data in combination with time-to-event prediction models. Overall, we provide a powerful and accessible tool to develop, access and share time-to-event prediction models; all software and tutorials are available at www.predictte.org.

neuroscience↗

bioRxiv2023

Bird wings are shaped by thermoregulatory demand for heat dissipation

The tendency for animals in warmer climates to be longer-limbed (Allens Rule) is widely attributed to the demands of thermoregulation. However, the underlying mechanism remains unclear, because variation in limb-length can typically be driven by selection for both efficient heat retention and increased heat dissipation capacity. Using comparative phylogenetic models, we find that occurrence in warmer climates is associated with longer wing bones for 1,520 species of passerine birds. The highly vascularized musculature along these bones is only uncovered during flight, when the wings function as the primary site of heat exchange, cooling the organism by dissipating excess heat generated by muscular activity. Conversely, the musculature along the wing bones is insulated by feathering when at rest, playing a negligible role in heat retention, even in colder climates. Given this asymmetry in thermoregulatory roles, we can identify the positive relationship between temperature and wing bone length as a phenotypic gradient shaped by increased demand for heat dissipation in warmer climates. Our findings provide a clear illustration of the mechanism by which global warming can drive spatial and temporal trends in appendage length, and also highlight the role of heat dissipation in reshaping even the most critical features of vertebrate anatomy. Significance StatementAnimals tend to be longer-limbed in warmer climates, but it remains unclear whether this pattern is driven by selection for cold tolerance at low temperatures or efficient heat dissipation at high temperatures. We show that for 1,520 species of passerines, bird wing bones are relatively longer in warmer climates. The vascularized musculature along these bones primarily functions in heat exchange during flight, when the overwhelming thermoregulatory challenge is dissipating heat, suggesting longer wing-bone length is driven by heat dissipation demands. Our findings reveal the pervasive impacts of thermoregulatory demands on even the most important functional traits.

ecology↗

bioRxiv2022

Mitochondrial function determines severity but not risk of amyotrophic lateral sclerosis

Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease. Selective vulnerability of energy-intensive motor neurons (MNs) has fostered speculation that mitochondrial function is a determinant of ALS. Previously, the position of mitochondrial function in the pathogenic cascade leading to neurotoxicity has been unclear. We separated upstream genetic determinants of mitochondrial function, including genetic variation within the mitochondrial genome or autosomes; from downstream changeable factors including mitochondrial copy number (mtCN) and MN gene expression. We discovered that functionally validated mitochondrial haplotypes are a determinant of ALS survival but not ALS risk. Loss-of-function genetic variants within, and reduced MN expression of, ACADM and DNA2 lead to shorter ALS survival; both genes impact mitochondrial function. MtCN responds dynamically to the onset of ALS independent of mitochondrial haplotype, and is also significantly correlated with disease severity. We conclude that mitochondrial function impacts ALS progression but not risk; our findings have therapeutic implications.

genetics↗

bioRxiv2022

Low expression of EXOSC2 protects against clinical COVID-19 and impedes SARS-CoV-2 replication

New therapeutic targets are a valuable resource in the struggle to reduce the morbidity and mortality associated with the COVID-19 pandemic, caused by the SARS-CoV-2 virus. Genome-wide association studies (GWAS) have identified risk loci, but some loci are associated with co-morbidities and are not specific to host-virus interactions. Here, we identify and experimentally validate a link between reduced expression of EXOSC2 and reduced SARS-CoV-2 replication. EXOSC2 was one of 332 host proteins examined, all of which interact directly with SARS-CoV-2 proteins; EXOSC2 interacts with Nsp8 which forms part of the viral RNA polymerase. Lung-specific eQTLs were identified from GTEx (v7) for each of the 332 host proteins. Aggregating COVID-19 GWAS statistics for gene-specific eQTLs revealed an association between increased expression of EXOSC2 and higher risk of clinical COVID-19 which survived stringent multiple testing correction. EXOSC2 is a component of the RNA exosome and indeed, LC-MS/MS analysis of protein pulldowns demonstrated an interaction between the SARS-CoV-2 RNA polymerase and the majority of human RNA exosome components. CRISPR/Cas9 introduction of nonsense mutations within EXOSC2 in Calu-3 cells reduced EXOSC2 protein expression, impeded SARS-CoV-2 replication and upregulated oligoadenylate synthase (OAS) genes, which have been linked to a successful immune response against SARS-CoV-2. Reduced EXOSC2 expression did not reduce cellular viability. OAS gene expression changes occurred independent of infection and in the absence of significant upregulation of other interferon-stimulated genes (ISGs). Targeted depletion or functional inhibition of EXOSC2 may be a safe and effective strategy to protect at-risk individuals against clinical COVID-19.

genetics↗

bioRxiv2020

Genome-wide Identification of the Genetic Basis of Amyotrophic Lateral Sclerosis

Amyotrophic lateral sclerosis (ALS) is an archetypal complex disease centered on progressive death of motor neurons. Despite heritability estimates of 52%, GWAS studies have discovered only seven genome-wide significant hits, which are relevant to <10% of ALS patients. To increase the power of gene discovery, we integrated motor neuron functional genomics with ALS genetics in a hierarchical Bayesian model called RefMap. Comprehensive transcriptomic and epigenetic profiling of iPSC-derived motor neurons enabled RefMap to systematically fine-map genes and pathways associated with ALS. As a significant extension of the known genetic architecture of ALS, we identified a group of 690 candidate ALS genes, which is enriched with previously discovered risk genes. Extensive conservation, transcriptome and network analyses demonstrated the functional significance of these candidate genes in motor neurons and disease progression. In particular, we observed a genetic convergence on the distal axon, which supports the prevailing view of ALS as a distal axonopathy. Of the new ALS genes we discovered, we further characterized KANK1 that is enriched with coding and noncoding, common and rare ALS-associated genetic variation. Modelling patient mutations in human neurons reduced KANK1 expression and produced neurotoxicity with disruption of the distal axon. RefMap can be applied broadly to increase the discovery power in genetic association studies of human complex traits and diseases.

genomics↗

bioRxiv2020

Modeling robust and efficient coding in the mouse primary visual cortex using computational perturbations

Investigating how visual inputs are encoded in visual cortex is important for elucidating the roles of cell populations in circuit computations. We here use a recently developed, large-scale model of mouse primary visual cortex (V1) and perturb both single neurons as well as functional- and cell-type defined population of neurons to mimic equivalent optogenetic perturbations. First, perturbations were performed to study the functional roles of layer 2/3 excitatory neurons in inter-laminar interactions. We observed activity changes consistent with the canonical cortical model (Douglas and Martin 1991). Second, single neuron perturbations in layer 2/3 revealed a center-surround inhibition-dominated effect, consistent with recent experiments. Finally, perturbations of multiple excitatory layer 2/3 neurons during visual stimuli of varying contrasts indicated that the V1 model has both efficient and robust coding features. The circuit transitions from predominantly broad like-to-like inhibition at high contrasts to predominantly specific like-to-like excitation at low contrasts. These in silico results demonstrate how the circuit can shift from redundancy reduction to robust codes as a function of stimulus contrast.

neuroscience↗

bioRxiv2018

Dissection of yeast pleiotropic drug resistance regulation reveals links between cell cycle regulation and control of drug pump expression

Eukaryotes utilize a highly-conserved set of drug efflux transporters to confer pleiotropic drug resistance (PDR). Despite decades of effort interrogating this process, multiple aspects of the PDR process, in particular PDR regulation, remain mysterious. In order to interrogate the regulation of this critical process, we have developed a small-molecule responsive biosensor that couples PDR transcriptional induction to growth rate in Saccharomyces cerevisiae. We applied this system to genome-wide screens for potential PDR regulators using the homozygous diploid deletion collection. These screens identified and characterized a series of genes with significant but previously uncharacterized roles in the modulation of the yeast PDR in addition to recapitulating previously-known factors involved in PDR regulation. Furthermore, we demonstrate that disruptions of the mitotic spindle checkpoint assembly lead to elevated PDR response in response to exposure to certain compounds. These results not only establish our biosensor system as a viable tool to investigate PDR in high-throughput, but also uncovers novel control mechanisms governing PDR response and a previously uncharacterized link between this process and cell cycle regulation.\n\nSignificancePleiotropic drug resistance (PDR) is a conserved mechanism by which cells utilize membrane bound pumps to transport chemicals out of the cell. Here, we develop a growth-based biosensor system in yeast that enables high-throughput identification of factors that transcriptionally regulate PDR. Among the novel PDR regulators identified here, we show that spindle assembly checkpoint (SAC) proteins, which are important for cell cycle regulation, inhibit hyperactivation of PDR upon drug treatment. This result provides insights into PDR regulation, as well as potential targets for therapeutic intervention, particularly in chemoresistant cancers where the cell cycle regulation is often disrupted.

genetics↗

bioRxiv2017

Prefrontal cortex regulates amygdala response to threat in trait anxiety

BackgroundHighly co-morbid mood and anxiety disorders are associated with aberrant fronto-limbic signalling during emotional processing. Animal models suggest that hypoactive prefrontal cortex weakens top-down control of limbic structures, causing heightened limbic and behavioural reactivity to negative information. Here we tested for this causal mechanism in human trait anxiety. We reasoned that if dorsolateral prefrontal cortex controls amygdala response to affective information, then stimulation of that brain region should reduce the hyperactive amygdala threat responsivity seen in trait anxiety.\n\nMethodsUsing a within-subjects design, sixteen high-trait anxious females received active and sham transcranial direct current stimulation (tDCS) of the dorsolateral prefrontal cortex, in counterbalanced order, with sessions timed to be at least one month apart. Each session was followed immediately by a functional magnetic resonance imaging (fMRI) scan during which participants performed an attentional task with threat-related distractors.\n\nResultsAs predicted, compared to sham stimulation, active prefrontal cortex stimulation reduced amygdala threat reactivity and simultaneously increased activity in cortical regions associated with attentional control and improved task accuracy.\n\nConclusionsThese results demonstrate a causal role for impoverished frontal regulation of amygdaloid function in attentional capture by threat in trait anxiety. The finding that prefrontal stimulation reduces amygdala threat reactivity acutely indicates a neurocognitive mechanism that could contribute to tDCS treatment effects in affective disorders.

neuroscience↗