Biology subjects

Andrews, H.

Publications and source records attributed to Andrews, H..

4 recordsLinked to original sources

bioRxiv2025

Vibrio harveyi plasmids as drivers of virulence in barramundi (Lates calcarifer)?

Vibrio species are an emerging public and animal health risk in marine environments and the opportunistic bacterial pathogen Vibrio harveyi is a major disease risk for tropical aquaculture. Current understanding of virulence in V. harveyi is limited by strain-specific variability and complex host-pathogen dynamics. This study sought to integrate genomic investigation, phenotypic characterisation and in vivo challenge trials in barramundi (Lates calcarifer) to increase our understanding of V. harveyi virulence. We identified two hypervirulent isolates, Vh-14 and Vh-15 that caused 100% mortality in fish within 48 hours, and that were phenotypically and genotypically distinct from other V. harveyi isolates. Virulent isolates contained multiple plasmids, including a 105,412 bp conjugative plasmid with type III secretion system genes originally identified in Yersinia pestis. The emergence of this hypervirulent plasmid-mediated patho-variant poses a potential threat to the sustainable production of marine finfish in Southeast Asia, the Mediterranean and Australia. In addition, we observed an effect of temperature on phenotypic indicators of virulence with an increase in activity at 28{degrees}C and 34{degrees}C compared to 22{degrees}C. This suggests that temperature fluctuations associated with climate change may act as a stressor on bacteria, increasing virulence gene secretion and host adaptation. Our results utilising a myriad of technologies and tools, highlights the importance of a holistic view to virulence characterisation.

microbiology↗

bioRxiv2023

Comparative genomics of Japanese encephalitis virus shows low rates of recombination and a suite of sites under episodic diversifying selection

Japanese encephalitis virus (JEV) is the dominant cause of viral encephalitis in the Asian region with 100,000 cases and 25,000 deaths reported annually. The genome is comprised of a single polyprotein that encodes three structural and seven non-structural proteins. We collated a dataset of 347 complete genomes from a number of public databases, and analysed the data for recombination, evolutionary selection and phylogenetic structure. There are low rates of recombination in JEV, subsequently recombination is not a major evolutionary force shaping JEV. We found a strong overall signal of purifying selection in the genome, which is the main force affecting the evolutionary dynamics in JEV. There are also a small number of genomic sites under episodic diversifying selection, especially in the envelope protein and non-structural proteins 3 and 5. Overall, these results support previous analyses of JEV evolutionary genomics and provide additional insight into the evolutionary processes shaping the distribution and adaptation of this important pathogenic arbovirus. Author SummaryThis comparative study of Japanese Encephalitis Virus is the largest genomic analysis of the virus to date. We undertake a suite of analyses to investigate phylogenetic relationships, rates of recombination and patterns of genomic selection. We show that recombination is not a significant driver of evolution in JEV, demonstrate support for previous phylogenetic reconstructions of the virus, and find a number of sites across the genome under episodic diversifying selection. These adaptive hotspots of evolution serve as key genomic points for the adaptive evolution of this important vector borne pathogen.

microbiology↗

bioRxiv2022

Why link diverse citizen science surveys? Widespread arboreal habits of a terrestrial amphibian revealed by mammalian tree surveys in Britain

Terrestrial anurans, with their typically short limbs, heavy-set bodies and absent claws or toe pads are incongruous tree climbers, but even occasional arboreal locomotion could offer substantial advantages for evading predators or accessing new shelter or food resources. Despite recent interest, arboreal behaviour remains rarely and unsystematically described for terrestrial amphibians in Europe, likely due to fundamental differences in survey methods and therefore a lack of field data. However, other taxa surveys specifically target trees and tree cavities. We undertook collaborations and large-scale data searches with citizen science projects surveying for arboreal mammals in Britain to investigate potential tree climbing by amphibians at a national scale. Remarkably, we found widespread arboreal usage by amphibians in England and Wales, with occupancy of hazel dormouse (Muscardinus avellenarius) nest boxes, tree cavities investigated as potential bat roosts and even a bird nest by common toads (Bufo bufo), but few additional records of frogs or newts. Toads are potentially attracted to tree cavities and arboreal nests because they provide safe and damp microenvironments which can support an abundance of invertebrate prey but the importance of such tree microhabitats for toad conservation remains unknown. Possible interactions with arboreal mammals are also unclear, but such mammals and even some birds may benefit from the occasional presence of toads if they feed on the mites and other arthropods that frequently infest their nests. We encourage expanding and linking of unrelated monitoring surveys and citizen science initiatives as valuable tools for investigating ecological traits and interactions.

ecology↗

bioRxiv2018

Whole Exome Sequencing in 20,197 Persons for Rare Variants in Alzheimer Disease

ObjectiveThe genetic bases of Alzheimers disease remain uncertain. An international effort to fully articulate genetic risks and protective factors is underway with the hope of identifying potential therapeutic targets and preventive strategies. The goal here was to identify and characterize the frequency and impact of rare and ultra-rare variants in Alzheimers disease using whole exome sequencing in 20,197 individuals.\n\nMethodsWe used a gene-based collapsing analysis of loss-of-function ultra-rare variants in a case-control study design with data from the Washington Heights-Inwood Columbia Aging Project, the Alzheimers Disease Sequencing Project and unrelated individuals from the Institute of Genomic Medicine at Columbia University.\n\nResultsWe identified 19 cases carrying extremely rare SORL1 loss-of-function variants among a collection of 6,965 cases and a single loss-of-function variant among 13,252 controls (p = 2.17 x 10-8; OR 36.2 [95%CI 5.8 - 1493.0]). Age-at-onset was seven years earlier for patients with SORL1 qualifying variant compared with non-carriers. No other gene attained a study-wide level of statistical significance, but multiple top-ranked genes, including GRID2IP, WDR76 and GRN, were among candidates for follow-up studies.\n\nInterpretationThis study implicates ultra-rare, loss-of-function variants in SORL1 as a significant genetic risk factor for Alzheimers disease and provides a comprehensive dataset comparing the burden of rare variation in nearly all human genes in Alzheimers disease cases and controls. This is the first investigation to establish a genome-wide statistically significant association between multiple extremely rare loss-of-function variants in SORL1 and Alzheimers disease in a large whole-exome study of unrelated cases and controls.

genetics↗