Biology subjects

Webb, E. L.

Publications and source records attributed to Webb, E. L..

4 recordsLinked to original sources

bioRxiv2026

DISCO-LAMP: A Novel discontinuous LAMP assay for isothermal antigen detection

Proximity ligation assay (PLA), in which the ligation of two DNA probes is greatly accelerated by the associating target molecules, has emerged as a highly sensitive technique for protein detection. The detection of the ligated DNA typically relies on PCR, which requires temperature cycling. In this study, we report on a novel discontinuous (DISCO)-LAMP assay that enables the wash-free detection of PLA products via loop-mediated isothermal amplification (LAMP). Due to the exponential amplification nature of LAMP, a careful balance between efficient amplification of the ligated full-length DNA and minimal background amplification from the individual constituent probes is essential but often challenging to achieve. After extensive template/primer design and assay optimization, DISCO-LAMP assay achieved a detection limit of 1 fM for the ligated DNA probe while maintaining undetectable background amplification at 1 nM of each individual probe. DISCO-LAMP detected Shiga toxin 2 (Stx2) with a limit of detection (LoD) of 100 fM when functionalized with Stx2-binders, as well as both Wuhan-1 and Omicron spike protein when functionalized with DS16, a newly engineered DARPin targeting a conserved epitope on the SARS-CoV-2 Spike protein. We believe DISCO-LAMP represents a versatile and efficient LAMP-based PLA technology that is readily adaptable for sensing diverse targets.

bioengineering↗

bioRxiv2022

The clustering of spatially associated species unravels patterns in Bornean tree species distributions

Complex distribution data can be summarised by grouping species with similar or overlapping distributions to unravel patterns in species distributions and separate trends (e.g., of habitat loss) among spatially unique groups. However, such classifications are often heuristic, lacking the transparency, objectivity, and data-driven rigour of quantitative methods, which limits their interpretability and utility. Here, we develop and illustrate the clustering of spatially associated species, a methodological framework aimed at statistically classifying species using explicit measures of interspecific spatial association. We investigate several association indices and clustering algorithms and show how these methodological choices engender substantial variations in clustering outcome and performance. To facilitate robust decision making, we provide guidance on choosing methods appropriate to the study objective(s). As a case study, we apply the framework to model tree distributions in Borneo to evaluate the impact of land-cover change on separate species groupings. We identified 11 distinct clusters that unravelled ecologically meaningful patterns in Bornean tree distributions. These clusters then enabled us to quantify trends of habitat loss tied to each of those specific clusters, allowing us to discern particularly vulnerable species clusters and their distributions. This study demonstrates the advantages of adopting quantitatively derived clusters of spatially associated species and elucidates the potential of resultant clusters as a spatially explicit framework for investigating distribution-related questions in ecology, biogeography, and conservation. By adopting our methodological framework and publicly available codes, practitioners can leverage the ever-growing abundance of distribution data to better understand complex spatial patterns among species distributions and the disparate effects of global changes on biodiversity. Statement of authorshipSEHP and ELW conceived the idea and designed methodology. SEHP conducted all analyses and developed the methodological framework with key inputs from ELW, JWFS, and DZ. All authors contributed to the interpretation of the results. SEHP and ELW wrote the first draft of the manuscript. All authors provided feedback on the writing.

ecology↗

bioRxiv2022

Bacterial Microbiome of Foreskin Tissue: Impact of Short-course PrEP and Host Inflammation

As part of the CHAPS randomized clinical trial, we sequenced a segment of the bacterial 16S rRNA gene from foreskin tissue of 144 adolescents from South Africa and Uganda collected during surgical penile circumcision after receipt of 1 to 2 doses of placebo, emtricitabine with tenofovir disoproxil fumarate, or emtricitabine with tenofovir alafenamide. We found a large proportion of Corynebacterium in addition to other anaerobic species. Cutibacterium acnes was more abundant among participants from South Africa than Uganda, though this made no difference in surgical recovery. We did not find a difference in bacterial populations by treatment received nor bacterial taxa that were differentially abundant between participants who received placebo versus active drug. Using RNAseq libraries from foreskin tissue of the same participants, we found negative correlations between the relative abundance of bacterial taxa and the expression of genes downstream of the innate response to bacteria and regulation of the inflammatory response. When participants were divided into clusters based on bacterial community composition, two main clusters emerged which were distinguished by high and low bacterial diversity. Random forest classification showed higher expression of NFATC3 and SELENOS and lower expression of STAP1 and NLRP6 in the higher diversity group compared to the lower. Our results show no difference in the tissue microbiome of the foreskin with short-course PrEP but that bacterial taxa were largely inversely correlated with gene expression, consistent with non-inflammatory colonization. Author SummaryWe investigated the bacterial community of the foreskin of the penis. Previous studies found increased inflammation with certain anaerobic bacteria from swabs taken under the foreskin, but we found that higher relative abundances of the bacteria were correlated with lower expression of inflammatory genes. We did not find different bacteria in participants who received medicine to prevent HIV. Understanding the relationship between bacteria and inflammation in the penis will help us to understand how interventions like penile circumcision reduce the risk of acquiring sexually transmitted infections such as HIV.

microbiology↗

bioRxiv2019

Risk factors for asthma among schoolchildren who participated in a case-control study in urban Uganda

Data on asthma aetiology in Africa are scarce. We investigated the risk factors for asthma among schoolchildren (5-17years) in urban Uganda. We conducted a case-control study, enrolling 561 cases and 1,139 controls. Asthma was diagnosed by study clinicians.\n\nThe main risk factors for asthma were tertiary education for fathers [adjusted OR (95% CI); 2.49 (1.89-3.29)] and mothers [2.14 (1.64-2.78)]; area of residence at birth, with children born in a small town or in the city having an increased asthma risk compared to schoolchildren born in rural areas [2.00 (1.49-2.68)] and [2.82 (1.85-4.30)], respectively; fathers and mothers history of asthma; childrens own allergic conditions; atopy; and using gas/electricity for indoor cooking.\n\nAsthma was associated with a strong rural-town-city risk gradient, higher parental socio-economic status and urbanicity. This work provides the basis for future studies to identify specific environmental/lifestyle factors responsible for increasing asthma risk among children in urban areas in LMICs.

epidemiology↗