Biology subjects

Webster, A.

Publications and source records attributed to Webster, A..

8 recordsLinked to original sources

bioRxiv2026

Evidence from three taxonomically distinct species for a non-AhR mechanism of developmental neurotoxicity of an environmentally derived mixture of polycyclic aromatic hydrocarbons

Typical environmental exposures to the toxic class of chemicals known as polycyclic aromatic hydrocarbons (PAHs) involve complex mixtures; however, relatively few mechanistic toxicity studies have evaluated them as environmental mixtures, instead focusing on individual compounds or simple mixtures. In this study, we first derived Republic Sediment Extract (REPSE), a complex PAH mixture extracted from sediment at the Republic Creosoting site of the Elizabeth River in Norfolk, Virginia. After characterizing the PAH contents of REPSE, we evaluated its mechanisms of developmental neurotoxicity in three evolutionarily distinct taxa, leveraging the unique strengths of Atlantic killifish, zebrafish, and Caenorhabditis elegans as model species, with a focus on the Aryl hydrocarbon Receptor (AhR) pathway. Embryonic REPSE exposure caused induction of CYP1A in both fish species at sub-teratogenic concentrations, consistent with activation of the canonical AhR pathway. These sub-teratogenic exposures nevertheless induced neurotoxicity across both fish species, altering neurobehavioral phenotypes in fish, and induced dopaminergic neuronal damage in worms, again at non-teratogenic concentrations. To determine whether these effects were linked to canonical AhR response pathways, we examined killifish offspring from the pollution-adapted Republic Creosoting population, which exhibited characteristic recalcitrance to CYP1A induction, but remained susceptible to the neurobehavioral effects of REPSE. The induction of neuronal damage in worms provides orthogonal evidence for a non-AhR mechanism, because C. elegans AhR is not transcriptionally activated by PAHs as in vertebrates. Further probing of potential mechanisms underlying REPSE-induced neurotoxicity in worms revealed altered neuronal redox status (roGFP) and energy availability (ATP:ADP ratio). Collectively, our multispecies approach reveals conserved mechanisms of PAH mixture neurotoxicity, including effects that extend beyond canonical AhR signaling.

pharmacology and toxicology↗

bioRxiv2025

Whole-Proteome Screening and Multi-Modal Profiling of Antigen-Specific CD4+ T Cells at Single-Cell Resolution

Systematic whole-proteome screening and comprehensive profiling of antigen-specific CD4+ T cells are crucial for advancing our understanding of CD4+ T cell immunity, yet such efforts remain technically challenging. Here, we present a high-throughput platform that employs large-scale class II single-chain trimer libraries to detect antigen-specific CD4+ T cells, while simultaneously profiling their antigen specificity, TCR/{beta} sequences, MHC restriction, whole transcriptomes, and patient/timepoint origins at single-cell resolution. We benchmarked SCTs against conventional pMHCs and validated the SCT library-based approach in direct ex vivo identification of antigen-specific CD4+ T cells in healthy donors. We then applied the platform to screen the entire SARS-CoV-2 receptor-binding domain in a longitudinal patient cohort, identifying 2,188 antigen-specific CD4+ T cells and revealing key features that define antigen immunogenicity. Extending to cancer, we performed whole-proteome screening of HPV-16 E6/E7 for TCR repertoire profiling in a precancerous cohort, uncovering functional heterogeneity of HPV-specific TCRs. By integrating high-throughput antigen screening with high-dimensional, multi-modal cellular characterization, our approach offers an unprecedented window into CD4+ T cell immunity across diverse disease contexts and empowers the development of new therapies.

bioengineering↗

bioRxiv2025

APMAT analysis reveals the association between CD8 T cell receptors, cognate antigen, and T cell phenotype and persistence

Elucidating the relationships between a class I peptide antigen, a CD8 T cell receptor (TCR) specific to that antigen, and the T cell phenotype that emerges following antigen stimulation, remains a mostly unsolved problem, largely due to the lack of large data sets that can be mined to resolve such relationships. Here, we describe Antigen-TCR Pairing and Multiomic Analysis of T-cells (APMAT), an integrated experimental-computational framework designed for the high-throughput capture and analysis of CD8 T cells, with paired antigen, TCR sequence, and single-cell transcriptome. Starting with 951 putative antigens representing a comprehensive survey of the SARS-CoV-2 viral proteome, we utilize APMAT for the capture and single cell analysis of CD8 T cells from 62 HLA A*02:01 COVID-19 participants. We leverage this unique, comprehensive dataset to integrate with peptide antigen properties, TCR CDR3 sequences, and T cell phenotypes to show that distinct physicochemical features of the antigen-TCR pairs strongly associate with both T cell phenotype and T cell persistence. This analysis suggests that CD8+ T cell phenotype following antigen stimulation is at least partially deterministic, rather than the result of stochastic biological properties.

immunology↗

bioRxiv2023

Shifted levels of sleep and activity under darkness as mechanisms underlying ectoparasite resistance

Parasites harm host fitness and are pervasive agents of natural selection capable of driving the evolution of host resistance traits. Indeed, host resistance in natural populations typically shows ample genetic variation, which may be maintained when parasite resistance imposes fitness costs on the host in the absence of parasites. Previously we demonstrated significant evolutionary responses to artificial selection for increasing behavioral immunity to Gamasodes queenslandicus mites in replicate lines of Drosophila melanogaster. Here, we report transcriptional shifts in metabolic processes between selected and control fly lines based on RNA-seq analyses. We also show decreased starvation resistance and increased use of nutrient reserves in flies from mite-resistant lines. Additionally, resistant lines exhibited increased behavioral activity, reduced sleep, and elevated oxygen consumption under conditions of darkness. Using an independent panel of D. melanogaster genetic lines exhibiting variable sleep durations, we found a positive correlation between mite resistance and reduced sleep, providing additional support for a link between resistance and sleep. Experimentally restraining the activity of artificially selected mite-resistant flies during exposure to parasites under dark conditions reduced their resistance advantage relative to control flies. The results suggest that ectoparasite resistance in this system involves increased dark-condition activity and metabolic gene expression at the expense of nutrient reserves and starvation resistance. Significance statementParasites are potent agents of selection, yet resistance may often be constrained evolutionarily because of trade-offs involving other fitness-related traits. Using artificial selection, we show that resistance to ectoparasites directly increases metabolism and decreases starvation resistance, predominantly through altered sleep and activity patterns at night. These studies highlight that active-resting patterns of the host are a significant driving force in ectoparasite resistance, but may have a negative impact on fitness during periods of low food availability. Our strongly integrative work suggests that parasite pressure may influence the evolution of host sleep and activity patterns.

evolutionary biology↗

bioRxiv2022

Anthropogenic supply of nutrients in a wildlife reserve may compromise conservation success

In nutrient-poor wildlife reserves it has become common-place to provide supplemental mineral resources for wildlife. Yet, the impacts of anthropogenic mineral supplementation on community-wide wildlife nutrition, behaviour and subsequent impact on ecosystem processes remain poorly understood. Here, we examine the contribution of anthropogenic mineral lick provision to wildlife nutrient intake across a community of large mammals (>10kg) in the southern Kalahari Desert. Based on predicted daily nutrient requirements and a faecal nutrient assessment, large herbivores appear deficient in phosphorus (P), sodium (Na) and zinc (Zn). For these nutrients, anthropogenic salt and mineral licks constitute an important (>10%) source of nutrient intake helping to reduce or overcome requirement deficits. Larger-bodied species disproportionately consumed licks (p<0.01), acquiring more nutritional benefits. A comprehensive assessment of animal body condition indicated that in general large herbivores display good health. However, bulk grazers, hindgut fermenters and females were more likely to display signs of malnourishment. We discuss how provisioning of anthropogenic mineral licks may be inflating large herbivore populations beyond the long-term carrying capacity of the reserve, with subsequent impacts for ecosystem integrity and herbivore population instability. Based on results presented here, it is clear that anthropogenic provision of mineral licks should be considered carefully by wildlife managers aiming to conserve or restore natural processes in conservation and rewilding landscapes.

ecology↗

bioRxiv2022

An in vivo biomarker to characterize ototoxic compounds and novel protective therapeutics

There are no approved therapeutics for the prevention of hearing loss and vestibular dysfunction from drugs like aminoglycoside antibiotics. While the mechanisms underlying aminoglycoside ototoxicity remain unresolved, there is considerable evidence that aminoglycosides enter inner ear mechanosensory hair cells through the mechanoelectrical transduction (MET) channel. Inhibition of MET-dependent uptake with small molecules or modified aminoglycosides is a promising otoprotective strategy. To better characterize mammalian ototoxicity and aid in the translation of emerging therapeutics, a biomarker is needed. In the present study we propose that neonatal mice systemically injected with the aminoglycosides G418 conjugated to Texas Red (G418-TR) can be used as a histologic biomarker to characterize in vivo aminoglycoside toxicity. We demonstrate that postnatal day 5 mice, like older mice with functional hearing, show uptake and retention of G418-TR in cochlear hair cells following systemic injection. When we compare G418-TR uptake in other tissues, we find that kidney proximal tubule cells show similar retention. Using ORC-13661, an investigational hearing protection drug, we demonstrate in vivo inhibition of aminoglycoside uptake in mammalian hair cells. This work establishes how systemically administered fluorescently labeled ototoxins in the neonatal mouse can reveal important details about ototoxic drugs and protective therapeutics.

neuroscience↗

bioRxiv2020

Binding of guide piRNA triggers methylation of the unstructured N-terminal region of Aub leading to assembly of the piRNA amplification complex

Piwi proteins use guide piRNAs to repress selfish genomic elements, protecting the genomic integrity of gametes and ensuring the fertility of animal species. Efficient transposon repression depends on amplification of piRNA guides in the ping-pong cycle, which in Drosophila entails tight cooperation between two Piwi proteins, Aub and Ago3. Here we show that post-translational modification, symmetric dimethylarginine (sDMA), of Aub is essential for piRNA biogenesis, transposon silencing and fertility. Methylation is triggered by loading of a piRNA guide into Aub, which exposes its unstructured N-terminal region to the PRMT5 methylosome complex. Thus, sDMA modification is a signal that Aub is loaded with piRNA guide. Amplification of piRNA in the ping-pong cycle requires assembly of a tertiary complex scaffolded by Krimper, which simultaneously binds the N-terminal regions of Aub and Ago3. To promote generation of new piRNA, Krimp uses its two Tudor domains to bind Aub and Ago3 in opposite modification and piRNA-loading states. Our results reveal that post-translational modifications in unstructured regions of Piwi proteins and their binding by Tudor domains that are capable of discriminating between modification states is essential for piRNA biogenesis and silencing. HighlightsO_LIsDMA modification of Aub is essential for ping-pong cycle, transposon silencing and fertility. C_LIO_LIpiRNA loading triggers Aub sDMA modification by exposing its unstructured N terminal region to the methylosome complex. C_LIO_LIA single molecule of Krimp simultaneously binds piRNA-bound Aub and empty Ago3 to assemble ping-pong complex. C_LIO_LIThe distinct structure of two Tudor domains of Krimp ensures binding of Ago3 and Aub in opposite modification and piRNA-loading states. C_LI

biochemistry↗

bioRxiv2020

WNT and inflammatory signaling distinguish human Fallopian tube epithelial cell populations

A substantial fraction of ovarian/extra-uterine high-grade serous carcinomas (HGSCs) likely originate in the distal region of the Fallopian tubes epithelium (TE) before implanting/metastasizing to the ovary. Unfortunately, molecular and cellular mechanisms rendering preferential cancer susceptibility of the human distal TE remain insufficiently elucidated, largely due to limited primary human TE gene expression data. Here we report an in depth bioinformatic characterization of 34 primary TE cell mRNA-seq samples. These samples were prepared from the proximal and distal TE regions of 12 normal Fallopian tubes. TE cells were segregated based on their aldehyde dehydrogenase (ALDH) activity. As compared to the proximal TE, cells from the distal region form organoids with higher frequency and larger size during serial organoid formation assays. Consistent with enrichment for organoid-forming stem/progenitor cells, ALDH+ cells have greater WNT signaling activity. Comparative evaluation of proximal and distal TE cell populations shows heightened inflammatory signaling in distal differentiated (ALDH-) TE. Furthermore, comparisons of proximal and distal TE cell populations finds that the distal TE express gene sets characteristic of four HGSC molecular sub-types, and that distal ALDH+ cell populations exhibit greater enrichment than their ALDH-counterparts. Taken together, our study shows that increased organoid forming capacity, WNT and inflammatory signaling, and HGSC signatures underlie the differences between distal and proximal regions of the human TE. These findings provide the basis for further mechanistic studies of distal TE susceptibility to the malignant transformation.

cancer biology↗