Biology subjects

Webb, C.

Publications and source records attributed to Webb, C..

12 recordsLinked to original sources

bioRxiv2026

COSMOS: integrated vector-pathogen metagenomics for mosquito-borne disease

By 2050, almost half of the global population will be at risk of mosquito-borne disease. Effective response requires monitoring both pathogen transmission and vector abundance, yet these are typically assessed using separate assays with limited taxonomic breadth. Here we present COSMOS (COmprehensive Sequencing for MOSquito-borne disease), a targeted metagenomics workflow designed to reconstruct pathogen genomes and mosquito community composition directly from mixed field-collected samples. Over three annual rounds of a major Australian surveillance program, we evaluated >120,000 mosquitoes in 219 traps, with 98.7% agreement with surveillance data across seven monitored arboviruses, and additional detections of Sindbis virus and the state's first detection of encephalitic Little Sussex virus. Of 137 viral detections, 101 yielded near-complete genomes (>90% coverage) at median 95x depth. Using an accompanying computational workflow, COSMOS quantified mosquito composition, matching entomological estimates of reported vector species (CCC 0.78-0.89). Joint analysis of virus and vector composition identified structured mosquito communities associated with spatial and temporal environmental variation, allowing the ecological context of arbovirus detections to be characterised. Detections during the Murray Valley encephalitis virus outbreak in 2023 were concentrated within a narrowly defined mosquito-community space corresponding to rural communities dominated by the inland S-AUS sub-lineage of Culex annulirostris. Integrated vector-pathogen metagenomics provides ecological and evolutionary context for arbovirus activity within a single scalable workflow for surveillance and outbreak response.

microbiology↗

bioRxiv2026

Differential sensitivity of k-mer based identification tools using closely related database sequences affects relative abundance estimation

Deep metagenomic sequencing is increasingly used for lineage profiling of complex biological mixtures, including applications such as wastewater virus surveillance and microbiome profiling. For profiling, sequence read sets are compared against a database of reference sequences to identify component genetic lineages, and estimate their relative abundance. However, there is currently a lack of clarity regarding the impact of two ubiquitous features of biological mixtures on compositional profiling: (1) population diversity, where reads contain genetic diversity not represented in the reference set, and (2) the presence of high sequence similarity between references, which causes ambiguity in read assignment. Here we show, using both simulated and real data, that performance of two commonly used tools for lineage profiling, KMA and Kallisto, is differently affected by sample-reference distance and the presence of highly similar competing reference sequences. Increasing sample-reference distance reduced read assignment for both tools, but more strongly for Kallisto, which led to directional bias in abundance estimates when distance differed between mixture components. In contrast, when sample-reference distance was low, Kallisto more specifically discriminated between highly similar competing references, whereas KMA was less able to partition reads accurately between them. This specificity-sensitivity trade-off was reflected in real datasets: KMA produced more accurate abundance estimates for mosquito COX1 mixtures, whereas Kallisto performed better for mixtures of closely related SARS-CoV-2 lineages, although neither tool fully resolved the most similar SARS-CoV-2 variants. Tool choice is therefore dependent on the degree of expected sample-reference distance and inter-reference distance within datasets.

bioinformatics↗

bioRxiv2026

Recombinant Echis disintegrins reveal distinct inhibitory profiles on platelet aggregation and endothelial cell migration

Disintegrins are snake venom toxins that bind integrins and modulate platelet aggregation and cell migration. Isolation from venom often yields insufficient quantities for comprehensive study, making recombinant expression essential for detailed toxin characterisation. Here, we produced and characterised four disintegrins from Echis coloratus and Echis ocellatus in Escherichia coli. These homologous proteins contain distinct integrin-binding motifs: EcDis_RGD, EoDis_RGD, EcDis_KGD, and EcDis_VGD. Functional activities were evaluated using human platelet aggregation and endothelial cell scratch wound-healing assays. RGD-containing disintegrins exhibited the strongest inhibition of platelet aggregation, with EcDis_RGD showing the highest potency. The EcDis_KGD disintegrin inhibited platelet aggregation less potently, whereas EcDis_VGD showed no detectable activity in our assays. In endothelial cells, EcDis_RGD disintegrin markedly impaired cell migration, while EoDis_RGD displayed weaker anti-migratory activity. Neither KGD- nor VGD-containing disintegrins significantly affected wound closure. EoDis_RGD exhibited similar antiplatelet activity to the native, venom-purified disintegrin ocellatusin, validating our recombinant expression strategy. However, the corresponding PII-SVMP preparation displayed reduced inhibitory activity, consistent with incomplete generation of fully mature disintegrins species. Our findings demonstrate the importance of both integrin-binding motif identity and surrounding sequence context in determining disintegrin function, and support further use of recombinant toxins in toxinology and as therapeutic lead molecules.

biochemistry↗

bioRxiv2026

Mapping the North American Terrestrial Carbon Cycle: A Process-based Reanalysis Using State Data Assimilation (SDA)

AbstractThe ability to accurately assess ecosystem C budgets across scales from individual sites to continents is essential for C accounting, management, and ultimately mitigating climate change. State data assimilation (SDA) provides a framework for harmonizing observations with models, while robustly accounting for and reducing multiple sources of uncertainty. In this study, we employed a hybrid SDA framework that combines process-based terrestrial biosphere modeling, hierarchical Bayesian inference, and machine learning to harmonize bottom-up and remotely-sensed data streams for 8,000 pre-selected 1km2 locations across North America within a hybrid structure. Combining bottom-up soils data (SoilGrids) with spectral (MODIS and Landsat) and microwave (SMAP) remote sensing helps constrain the major C and water stocks through space and time. Machine learning is used both to identify and correct systematic errors in the process model (SIPNET) and to interpolate the pre-selected locations onto a 1km grid, making it computationally feasible to generate annual ensemble maps of the North American carbon budget. Furthermore, the uncertainties for each variable were reduced compared to those from observations or models alone. Spatiotemporal analysis showed a slight decrease in aboveground biomass (AGB) across the western US, a loss of leaf area across the boreal, and a slight greening of the Alaskan tundra. The uncertainty trends suggest a significant reduction in the uncertainty about soil organic carbon (SOC), the largest C reservoir. Validation results show that we accurately estimate C pools, compared to the assimilated data streams and held-out observations of AGB from GEDI, ICESat-2, and the US FIA, and SOC from the ISCN network. Our ML-debiasing algorithm further improved the accuracy of major C pools (AGB, SOC). In general, our continental SDA framework will facilitate global C MRV (monitoring, reporting, and verification) by providing accurate and precise C-cycle estimates, along with their corresponding spatiotemporal uncertainties.

ecology↗

bioRxiv2025

Docking 14 million virtual isoquinuclidines against the mu and kappa opioid receptors reveals dual antagonists-inverse agonists with reduced withdrawal effects

Large library docking of tangible molecules has revealed potent ligands across many targets. While make-on-demand libraries now exceed 75 billion enumerated molecules, their synthetic routes are dominated by a few reaction types, reducing diversity and inevitably leaving many interesting bioactive-like chemotypes unexplored. Here, we investigate the large-scale enumeration and targeted docking of isoquinuclidines. These "natural-product-like" molecules are rare in the current libraries and are functionally congested, making them interesting as receptor probes. Using a modular, four-component reaction scheme, we built and docked a virtual library of over 14.6 million isoquinuclidines against both the {micro}- and{kappa} -opioid receptors (MOR and KOR, respectively). Synthesis and experimental testing of 18 prioritized compounds found nine ligands with low {micro}M affinities. Structure-based optimization revealed low- and sub- nM antagonists and inverse agonists targeting both receptors. Cryo-electron microscopy (cryoEM) structures illuminate the origins of activity on each target. In mouse behavioral studies, a potent member of the series with joint MOR-antagonist and KOR-inverse-agonist activity reversed morphine-induced analgesia, phenocopying the MOR-selective anti-overdose agent naloxone. Encouragingly, the new molecule induced less severe opioid-induced withdrawal symptoms compared to naloxone during withdrawal precipitation, and did not induce conditioned-place aversion, likely reflecting a reduction of dysphoria due to the compounds KOR-inverse agonism. The strengths and weaknesses of bespoke library docking, and of docking for opioid receptor polypharmacology, will be considered.

biophysics↗

bioRxiv2025

Populations of the Australian saltmarsh mosquito Aedes vigilax vary between panmixia and temporally stable local genetic structure

Pest management programs can operate more effectively when movement patterns of target species are known. As individual insects are difficult to track, genomic data can instead be used to infer movement patterns based on pest population structure and connectivity. These data can also provide critical information about cryptic taxa relevant to management. Here we present the first genomic investigation of Aedes vigilax, the Australian saltmarsh mosquito, a major arbovirus vector across Australasia. We used a ddRAD pool-seq approach and a draft genome assembly to investigate genetic variation in 60 Ae. vigilax pools from across Australia but with a focus on urban Newcastle and Sydney, NSW. There was strong genetic structure between samples from the west and east coasts of Australia, and additional structure that differentiated east coast populations. Within Newcastle and Sydney, contrasting patterns of genetic structure were evident. In Newcastle, there was no differentiation among subregions up to 60 km apart. In Sydney, samples from one urban subregion were differentiated from others < 3 km apart, and this structure was stable across sampling years. Heterozygosity and Tajimas D indicated no bottlenecks in Newcastle or Sydney populations, suggesting this structure represents a gene flow barrier. Nuclear differentiation patterns contrast with previous mtDNA data indicating two COI clades in the east coast, one of which was also present in Western Australia. The panmixia over 60 km across the Newcastle region corroborates previous field observations of high dispersal capacity in this mosquito. These findings indicate specific challenges that may hinder local suppression strategies for this species.

evolutionary biology↗

bioRxiv2024

A scoping review of evidence of naturally occurring Japanese encephalitis infection in vertebrate animals other than humans, ardeid birds and pigs

Japanese encephalitis virus (JEV) is the leading cause of human encephalitis in Asia. JEV is a vector-borne disease, mainly transmitted by Culex mosquitoes, with Ardeidae birds as maintenance hosts and pigs as amplifying hosts. Other vertebrate animal hosts have been suggested to play a role in the epidemiology of JEV. This scoping review followed PRISMA guidelines to identify species in which evidence of naturally occurring JEV infection was detected in vertebrates other than ardeid birds, pigs and people. Following systematic searches, 4372 records were screened, and data were extracted from 62 eligible studies. Direct evidence (virus, viral antigen or viral RNA) of JEV infection was identified in a variety of mammals and birds (not always identified to the species level), including bats, passerine birds (family Turdidae), livestock (cattle [Bos taurus] and a goat [Capra hircus]), carnivores (two meerkats [Suricata suricatta]), and one horse (Equus caballus). Bat families included Pteropodidae, Vespertilionidae, Rhinolophidae, Miniopteridae, Hipposideridae. Indirect evidence suggestive of JEV infection (antibodies) was detected in several mammalian and avian orders, as well as reported in two reptile species. However, a major limitation of the evidence of JEV infection identified in this review was diagnostic test accuracy, particularly for serological testing. Studies generally did not report diagnostic sensitivity or specificity. Although we hypothesise that bats and passerine birds could play an underappreciated role in JEV epidemiology, development of diagnostic tests to differentiate JEV from other orthoflaviviruses will be critical for effective surveillance in these, as well as the companion and livestock species that could be used to evaluate JEV control measures in currently endemic regions.

ecology↗

bioRxiv2022

Treatment history shapes the evolution of complex carbapenem-resistant phenotypes in Klebsiella spp.

Antibiotic resistance is driven by selection, but how a bacterial strains evolutionary history shapes drug-resistance remains an open question. Here we reconstruct the genetic and evolutionary mechanisms of carbapenem resistance in a clinical isolate of Klebsiella. A combination of short and long read sequencing, machine learning, genetic and enzymatic analyses established that this carbapenem-resistant strain carries no carbapenemase-encoding genes. Genetic reconstruction of the resistance phenotype confirmed that two distinct genetic loci are necessary for the strain to acquire carbapenem resistance. Experimental evolution of the carbapenem-resistant strains in growth conditions without the antibiotic revealed that both loci confer a significant cost, and are readily lost by de novo mutation resulting in the rapid evolution of a carbapenem-sensitive phenotype. Thus, historical contingency - a patients treatment history - can shape the evolution of antibiotic resistance and suggests that the strategic combinations of antibiotics could direct the evolution of low-fitness, drug-resistant genotypes.

microbiology↗

bioRxiv2022

Understanding spatiotemporal effects of food supplementation on host-parasite interactions using community-based science

O_LISupplemental feeding can increase the overall health of animals but also can have variable effects on how animals defend themselves against parasites. However, the spatiotemporal effects of food supplementation on host-parasite interactions remain poorly understood, likely because large-scale, coordinated efforts are difficult. C_LIO_LIHere, we introduce the Nest Parasite Community Science Project, which is a community-based science project that coordinates studies with bird nest box "stewards" from the public and scientific community. This project was established to understand broad ecological patterns between hosts and their parasites. C_LIO_LIThe goal of this study was to determine the effect of food supplementation on eastern bluebirds (Sialia sialis) and their nest parasite community across the geographic range of the bluebirds from 2018-2021. We received 646 nests from 68 stewards in 26 states in the eastern United States. Nest box stewards reported whether or not they fed their bluebirds mealworms or suet, then followed the nesting success of the birds (number of eggs laid and hatched, percent hatched, number and percent fledged). We then identified and quantified parasites in the nests. C_LIO_LIWe found that food supplementation increased fledgling numbers and proportional fledging success. The main nest parasite taxa were parasitic blow flies (Protocalliphora sialia), but a few nests contained fleas (Ceratophyllus idius, C. gallinae, Orchopeas leucopus) and mites (Dermanyssus spp. and Ornithonyssus spp.). Blow flies were primarily found at northern latitudes, where food supplementation affected blow fly abundance. However, the direction of this effect varied substantially in direction and magnitude across years. More stewards fed bluebirds at southern latitudes than at northern latitudes, which contradicted the findings of other community-based science projects. C_LIO_LIOverall, food supplementation of birds was associated with increased host fitness but did not appear to play a consistent role in defense against these parasites across all years. Our study demonstrates the importance of coordinated studies across years and locations to understand the effects of environmental heterogeneity, including human-based food supplementation, on host-parasite dynamics. Studies during a single year or considering only a single population might not provide the necessary data to develop management strategies for species. C_LI

ecology↗

bioRxiv2022

Enhanced production of antiviral dsRNA in the Chlamydomonas reinhardtii chloroplast via a novel convergent promoter expression system

Viral infection of farmed fish and shellfish represents a major issue within the aquaculture industry. One potential control strategy involves RNA interference of viral gene expression through the oral delivery of specific double-stranded RNA (dsRNA). In previous work we have shown that recombinant dsRNA can be produced in the chloroplast of the edible microalga, Chlamydomonas reinhardtii and used to control disease in shrimp. Here we report a significant improvement in antiviral dsRNA production and its use to protect shrimp against white spot syndrome virus (WSSV). A new strategy for dsRNA synthesis was developed that uses two convergent copies of the endogenous rrnS promoter to drive high level transcription of both strands of the WSSV gene element in the chloroplast. New vectors were designed that allow rapid Golden Gate-mediated assembly of a transformation plasmid in which the dual promoter-WSSV DNA cassette is targeted into the chloroplast genome, with selection based on the restoration of photosynthesis. PCR analysis of transformant lines confirmed the integration of the cassette and homoplasmy of the polyploid genome. Transcribed sense and antisense VP28-RNA were hypothesised to form an RNA duplex in the chloroplast stroma, and quantitative RT-PCR indicated that [~]100 g dsRNA is produced per litre of transgenic microalgae culture. This represents an [~]10,000-fold increase in dsRNA relative to previous reports using convergent psaA promoters. The engineered alga was assessed for its ability to prevent WSSV infection when fed to shrimp larvae prior to a challenge with the virus. Survival of shrimp fed with dsRNA-expressing C. reinhardtii was significantly enhanced (68.3%) relative to the negative control. The study suggests that this new dsRNA production platform is significantly more efficient than that reported previously, and merits further scale-up and downstream processing studies.

molecular biology↗

bioRxiv2022

A preliminary description of the ecological characteristics of wild waterbird Japanese encephalitis virus hosts in high risk landscapes in India

Wild reservoirs of Japanese encephalitis virus are under-studied globally, which presents critical knowledge gaps for JEV infection ecology despite decades of received wisdom regarding this high-impact mosquito-borne virus. As a result, ardeid birds, generally understood to be the primary reservoirs for JEV, as well as other waterbirds occupying landscapes at high risk for spillover to humans, are frequently ignored by current surveillance mechanisms and infrastructure. This is particularly true in India, which experiences a high annual burden of human outbreaks. Incorporating wild reservoirs into surveillance of human and livestock populations is therefore essential but will first require a data-driven approach to target individual host species. The current study sought to define a preliminary ecological profile of JEV hosts based on 1) species ecological traits, and 2) species presence and abundance adjusted for the biotic constraints of sympatry. Optimal host species tended to be generalists and demonstrate regionally-increasing populations. While ardeid bird species richness, abundance, and relative abundance did demonstrate the strongest and most consistent associations with the distribution of human JEV outbreaks, this study also identified several individual species among two other bird families in these landscapes, the Anatidae and the Rallidae, which also exhibited an optimal host profile and were strongly associated with the distribution of outbreaks. The findings from this work provide the first data-driven evidence base to inform wildlife sampling for the monitoring of JEV circulation in outbreak hotspots in India and thus identify good preliminary targets for the development of One Health wildlife JEV surveillance.

ecology↗

bioRxiv2019

Mechanistic characterization of RASGRP1 variants identifies an hnRNP K-regulated transcriptional enhancer contributing to SLE susceptibility

Systemic lupus erythematosus (SLE) is an autoimmune disease with a strong genetic component. We recently identified a novel SLE susceptibility locus near RASGRP1, which governs the ERK/MAPK kinase cascade and B-/T-cell differentiation and development. However, precise causal RASGRP1 functional variant(s) and their mechanisms of action in SLE pathogenesis remain undefined. Our goal was to fine-map this locus, prioritize genetic variants according to likely functionality, experimentally validate the contribution of three SNPs to SLE risk, and experimentally determine their biochemical mechanisms of action. We performed a meta-analysis across six Asian and European cohorts (9,529 cases; 22,462 controls), followed by in silico bioinformatic and epigenetic analyses to prioritize potentially functional SNPs. We experimentally validated the functional significance and mechanism of action of three SNPs in cultured T-cells. Meta-analysis identified 18 genome-wide significant (p<5x10-8) SNPs, mostly concentrated in two haplotype blocks, one intronic and the other intergenic. Epigenetic fine-mapping, allelic, eQTL and imbalance analyses predicted three transcriptional regulatory regions with four SNPs (rs7170151, rs11631591-rs7173565, and rs9920715) prioritized for functional validation. Luciferase reporter assays indicated significant allele-specific enhancer activity for intronic rs7170151 and rs11631591-rs7173565 in T-lymphoid (Jurkat) cells, but not in HEK293 cells. Following up with EMSA, mass spectrometry and ChIP-qPCR, we detected allele-dependent interactions between heterogeneous nuclear ribonucleoprotein K (hnRNP-K) and rs11631591. Furthermore, inhibition of hnRNP-K in Jurkat and primary T-cells downregulated RASGRP1 and ERK/MAPK signaling. Comprehensive association, bioinformatics, and epigenetic analyses yielded putative functional variants of RASGRP1, which were experimentally validated. Notably, intronic variant (rs11631591) is located in a cell type-specific enhancer sequence, where its risk allele binds to the hnRNP-K protein and modulates RASGRP1 expression in Jurkat and primary T-cells. As risk allele dosage of rs11631591 correlates with increased RASGRP1 expression and ERK activity, we suggest that this SNP may underlie SLE risk at this locus.

genetics↗