Biology subjects

Weldon, C.

Publications and source records attributed to Weldon, C..

5 recordsLinked to original sources

bioRxiv2026

BioVault: A privacy-first data visitation platform for equitable global collaboration in biomedicine

Biomedical datasets representing diverse populations are essential for advancing precision medicine, yet remain siloed due to regulatory, sovereignty, and privacy constraints. Existing data-sharing solutions remain limited. Centralized repositories and Trusted Research Environments (TREs) require data migration into external infrastructure, introducing governance complexities, cost barriers, and constraints on accountable reuse. Secure computation frameworks from modern cryptography, and federated learning models demand deep domain expertise and substantial engineering effort, limiting their accessibility in resource-constrained environments. These barriers disproportionately impact under-resourced institutions, limiting equitable participation in global collaborations. Here, we introduce BioVault (https://www.biovault.net), an open-source platform for privacy-first biomedical collaboration through a peer-to-peer data visitation network, where analysis code travels to data rather than data being transferred to centralized systems. BioVault can be deployed as a desktop application or command-line interface, enabling out-of-the-box use for participants in diverse resource settings. BioVault supports both clinical and research workflows, and with built-in permissioning, audit trails, and local governance controls, it enables data holders and collaborators to retain oversight and control while participating in collaborative research. We demonstrate BioVaults utility in enabling two cross-border collaborations with under-resourced communities: a genome-wide association study of Type 2 Diabetes in Circassian and Chechen populations in Jordan, and allele frequency estimation across Caribbean cohorts. In both cases, analyses were executed locally without data export. We further demonstrate compatibility for user-defined secure, federated computation protocols built on state-of-the-art cryptographic tools (multiparty computation and homomorphic encryption), by lowering barriers to their deployment. Together, these results establish BioVault as a general-purpose framework for decentralized analytics that reduces the technical and financial constraints to biomedical collaboration - enabling diverse institutions to participate as equal partners in global discovery, while preserving privacy and data sovereignty.

genomics↗

bioRxiv2024

Lineage-specific trait variation generates widespread, contemporaneous coexistence and competitive exclusion dynamics in an invasive, multihost wildlife parasite

Invasive and highly virulent parasites are emerging worldwide, transported to new locations and into novel hosts by anthropogenic activities. Multiple introduction events lead to interactions amongst genetically dissimilar genotypes that can result in either competitive exclusion, coexistence, or cycling through a combination of the two. Here, we report how intra-lineage trait variation of the multihost amphibian parasite Batrachochytrium dendrobatidis drives contrasting outcomes of inter-lineage interactions on two continents, Europe and Africa. Through field surveys, competition experiments and mathematical modelling we show that interactions between the same two lineages in the two continents and in different hosts demonstrate both ends of the exclusion/coexistence continuum. Trait variation in one of the two predominating lineages, BdGPL, is responsible for these contrasting outcomes: In Europe, BdGPL is highly competitive and has constrained the distribution of the other, BdCAPE, to two locations. In Africa, BdGPL and BdCAPE can mutually invade host populations when the other lineage is already resident, potentially leading to coinfections and recombination. That these contrasting outcomes are prolonged and contemporaneous for the same two lineages shows that epidemiological models of invasive parasites need to account for trait variation both within and across lineages.

ecology↗

bioRxiv2021

A series of terribly unfortunate events: How environment and infection synergized to cause the Kihansi spray toad extinction

Outbreaks of emerging infectious diseases are trained by local biotic and abiotic factors, with host declines occurring when conditions favour the pathogen. Extinction of the Tanzanian Kihansi spray toad (Nectophrynoides asperginis) in 2004 was contemporaneous with the construction of a dam, implicating habitat modification in the loss of this species. However, high burdens of a globally emerging infection, Batrachochytrium dendrobatidis (Bd) were synchronously observed implicating infectious disease in this toads extinction. Here, by shotgun sequencing skin DNA from archived toad mortalities and assembling chytrid mitogenomes, we prove this outbreak was caused by the BdCAPE lineage and not the panzootic lineage BdGPL that is widely associated with global amphibian extinctions. Molecular dating showed an invasion of BdCAPE across Southern Africa overlapping with the timing of the extinction event. However, post-outbreak surveillance of conspecific species inhabiting this mountainous region showed widespread infection by BdCAPE yet no signs of amphibian ill-health or species decline. Our findings show that despite efforts to mitigate the environmental impact caused by dams construction, invasion of the pathogen ultimately led to the loss of the Kihansi spray toad; a synergism between emerging infectious disease and environmental change that likely heralds wider negative impacts on biodiversity in the Anthropocene.

ecology↗

bioRxiv2020

Discriminating lineages of Batrachochytrium dendrobatidis using quantitative PCR

The ability to detect and monitor infectious disease in a phylogenetically informative manner is critical for their management. Phylogenetically informative diagnostic tests enable patterns of pathogen introduction or changes in the distribution of genotypes to be measured, enabling research into the ecology of the pathogen. Batrachochytrium dendrobatidis (Bd), a causative agent of chytridiomycosis in amphibian populations, emerged worldwide in the 21st century and is composed of six lineages which are display varying levels of virulence in their hosts. Research into the distribution, ecology and pathogenicity of these lineages has been hampered by an inability to type lineage efficiently. Here, we describe a lineage-specific TaqMan qPCR assay that differentiates the two lineages of Bd most commonly associated with chytridiomycosis: BdGPL and BdCAPE. We demonstrate how this assay can be used for the surveillance of wild populations of amphibians in Southern Africa using skin swabs, tissue samples and cultured isolates.

ecology↗

bioRxiv2019

Disease driven extinction in the wild of the Kihansi spray toad (Nectophrynoides asperginis)

The Kihansi spray toad, Nectophrynoides asperginis, became extinct in the wild despite population monitoring and conservation management of its habitat in the Kihansi gorge, Tanzania. Anecdotal evidence has indicated human induced habitat modification, predators, pesticides and disease as possible causes of a rapid population decline and the species extirpation. Here, we systematically investigate the role of disease in the extinction event of the wild toad population. The amphibian chytrid fungus, Batrachochytrium dendrobatidis, was detected in spray toads that died during the extinction event and subsequently in other amphibian species in Kihansi Gorge and the adjacent Udagaji Gorge, but not in any toads collected prior to this. Following the population decline, the remnant spray toad population gradually disappeared over a nine-month period. We demonstrate how demographic and behavioral attributes predisposed the spray toads to chytridiomycosis, due to B. dendrobatidis infection, and how epidemic disease could have been exacerbated by altered environmental conditions in the spray wetlands. Our results show that chytridiomycosis was the proximate cause of extinction in the wild of N. asperginis. This represents the first known case of extinction by disease of an amphibian species in Africa. A captive breeding program in the US and Tanzania ensures the survival of the species and a reintroduction program is underway. However, we caution that chytridiomycosis remains an existing threat that requires a comprehensive mitigation strategy before the desired conservation outcome of an established population of repatriated toads can be achieved.

epidemiology↗