Biology subjects

O'Neill, D.

Publications and source records attributed to O'Neill, D..

10 recordsLinked to original sources

bioRxiv2026

Genome-wide characterisation of the metallothionein gene family and their expression in response to copper in Pistia stratiotes (water lettuce).

Heavy metal contamination of aquatic environments poses persistent risks to ecosystems and human health. Aquatic macrophytes such as Pistia stratiotes are increasingly used for phytoremediation due to their capacity to accumulate contaminants without displaying symptoms of abiotic stress. However, the molecular mechanisms underlying their metal tolerance remain poorly understood. Metallothioneins (MTs) are cysteine-rich proteins involved in metal binding and detoxification in plants. In this study, genome-wide analysis was performed to identify and characterise candidate MT genes in P. stratiotes and to assess their transcriptional response to copper exposure. Six novel MT genes (PsMT2f, PsMT3a-d, and PsMT4) were identified and classified into MT2, MT3, and MT4 subfamilies based on conserved cysteine motifs and domain architecture. Quantitative real-time PCR showed differential and tissue-specific expression of MT genes in roots and leaves following exposure to copper for up to 4 h. These findings provide the first comprehensive characterisation of the MT gene family in P. stratiotes and demonstrate their potential role in copper tolerance, supporting the application of this species in the phytoremediation of metal-contaminated aquatic systems.

genetics↗

bioRxiv2026

Molecular identification of vertebrate blood meals in Culicoides biting midges reveals host-vector associations relevant to arbovirus transmission in Ireland

Understanding the vertebrate hosts exploited by Culicoides biting midges is fundamental to assessing the transmission risk of livestock arboviruses. Blood meal analysis provides direct evidence of host-vector interactions under natural conditions; however, molecular data on Culicoides host feeding are lacking in Ireland. This study aimed to identify the vertebrate blood meal hosts of Culicoides species of veterinary importance and establish host-vector associations relevant to arbovirus transmission. A total of 115 morphologically blood-fed Culicoides females collected from 13 sites across Ireland were analysed using a sequential molecular workflow. Species-specific real-time PCR assays were used to screen for vertebrate hosts, with positive detections confirmed by mitochondrial DNA sequencing. Blood-fed Culicoides were subsequently identified to species level using DNA barcoding, enabling direct linkage between vector species and their vertebrate hosts. Vertebrate DNA was detected in 50 specimens, with cattle and horses accounting for the majority of identified blood meals. Culicoides obsoletus accounted for most cattle (n = 12) and horse (n = 11) blood meals. Culicoides scoticus fed on cattle (n = 6), horses (n = 4) and sheep (n = 1), while C. dewulfi and C. chiopterus fed predominantly on cattle, with occasional horse blood meals. Four cattle blood meals were identified from C. punctatus. No cervid-derived blood meals were detected. This study provides the first molecular characterisation of Culicoides blood meal hosts in Ireland, confirming host-vector associations between major vector species and livestock hosts of veterinary importance. Although the number of successfully characterised blood meals was modest, reflecting the inherent difficulty of recovering recently blood-fed Culicoides from field collections, the findings establish an important baseline for Ireland. The sequential molecular workflow provides a practical framework for future blood meal investigations and will support improved understanding of host-vector interactions relevant to arbovirus surveillance and risk assessment.

molecular biology↗

bioRxiv2026

Repurposing drugs to treat Amoebic Gill Disease in Atlantic Salmon

Neoparameoba perurans causes Amoebic Gill Disease (AGD), a major parasitic disease of marine-phase Atlantic salmon and rainbow trout worldwide. Treatment options are limited to freshwater baths, which are costly at scale and exhibit only limited long-term efficacy. N. perurans contains an obligate eukaryotic symbiont, Perkinsela-like organism (PLO). PLO belongs to the class Kinetoplastida, which includes medically and veterinary important parasites such as Trypanosoma and Leishmania. As such, we hypothesised that trypanocidal drugs developed against other kinetoplastids might also affect N. perurans, potentially through disruption of its PLO symbiont, and used this hypothesis as a rationale for prioritising a focused panel of candidate compounds for screening. A holographic motility-based cytotoxicity assay was established to identify promising candidates in vitro, followed by controlled host tolerance testing and finally a field efficacy sea trial using naturally AGD-exposed site in the west of Ireland. Several compounds showed activity in vitro, especially miltefosine (EC50 1.84 uM, amoebicidal) and isometamidum (EC50 4.63 uM, amoebostatic). In vivo (two intramuscular injections, two weeks apart), miltefosine (Odds Ratio (OR) 0.62), isometamidum (OR 0.61) and benznidazole (OR 0.64) significantly improved gill score over four weeks, with miltefosine showing the largest effect size. Gill parasitaemia, measured via qPCR, was not reduced. Instead, two compounds increased apparent amoeba loads. This work support trypanocidal as potential AGD treatments in the field, although optimisation of dosing, delivery and mode of action requires further study.

microbiology↗

bioRxiv2025

Design and optimisation of rapid real-time PCR assays for the detection of key Culicoides species

In extensive surveillance programmes of Culicoides biting midges (Diptera: Ceratopogonidae), morphological identification can be time-consuming and difficult, while DNA barcoding, although highly accurate, may not be cost-effective or suitable for rapid analysis, as it requires individual specimen processing. To address these limitations, we developed a rapid screening method using real-time PCR assays with either SYBR Green or hydrolysis probe-based detection chemistries. Species-specific primers and, where necessary, hydrolysis probes were designed based on the updated sequences of the ITS2 region of seven Culicoides species. The specificity and efficiency of these assays were validated both in silico and through real-time PCR testing on target and non-target Culicoides species, tested individually and as mixed-species samples. The new real-time PCR assays detect vector species including C. obsoletus, C. scoticus, C. chiopterus, C. dewulfi, C. pulicaris, C. punctatus, and C. impunctatus in pools of individual specimens, with single-specimen sensitivity. The molecular techniques developed in this study provide a valuable tool for accurate and high-throughput Culicoides surveillance, which can be used for year-round monitoring of adult midges in traps and larvae in environmental samples, potentially revealing novel insights into the spatial and temporal turnover of Culicoides species. These methods can be applied to large-scale vector screening programmes involving pooled samples, addressing the limitations of previously described methods used in midge surveillance.

molecular biology↗

bioRxiv2025

Molecular characterisation of common Culicoides Biting Midges (Diptera: Ceratopogonidae) in Ireland

BackgroundBiting midges in the genus Culicoides (Diptera: Ceratopogonidae) act as vectors for several arboviruses, including Bluetongue virus (BTV) and Schmallenberg virus (SBV), which affect livestock health and productivity. In Ireland, limited genetic data are available regarding the diversity of Culicoides species. This study represents the first attempt to characterise Culicoides in this region using molecular techniques. MethodsAdult Culicoides samples were captured using Onderstepoort Veterinary Institute (OVI) traps across six locations in Ireland. Subsequent molecular analyses involved polymerase chain reaction (PCR) and sequencing of the cytochrome oxidase subunit 1 (CO1) and the internal transcriber spacer (ITS) barcoding regions to obtain species identities. Additionally, using both markers, we inferred the population genetic structure and potential colonisation pathways of Culicoides obsoletus sensu stricto (s. str.), the major vector species in Ireland. ResultsDNA barcoding facilitated identification of 177 specimens. Eight common Culicoides species were identified through DNA barcoding of CO1 and ITS gene regions. The presence of putative vectors of Bluetongue virus (BTV) and Schmallenberg virus (SBV) were also confirmed, including species in the subgenus Avaritia (C. obsoletus s. str., C. scoticus, C. chiopterus, and C. dewulfi) and subgenus Culicoides s. str. (C. pulicaris and C. punctatus). Phylogenetic analysis confirmed the relationship between these vector species and facilitated the placement of Culicoides sp. which could not be identified to species level through DNA barcoding. Haplotype network analysis of C. obsoletus showed that some haplotypes of these species are shared between Continental Europe, the UK, and Ireland, suggesting a possible incursion pathway for this vector. ConclusionDNA barcoding employing a combination of two barcodes, CO1 and ITS, proved effective in identifying Culicoides, especially species within the obsoletus complex, which are difficult to morphologically distinguish. Our findings also suggest that investigation of the population genetic structure of Culicoides spp. could be used to model the potential introduction routes of midge-borne pathogens into the country.

molecular biology↗

bioRxiv2024

Survival time and prognostic factors in dogs diagnosed with haemangiosarcoma in UK first opinion practice

AbstractVisceral haemangiosarcoma is considered clinically aggressive in dogs, with perceived poor prognosis often leading to euthanasia at presentation. This study aimed to determine survival times and prognostic factors in dogs with haemangiosarcoma under first-opinion care. Dogs diagnosed with haemangiosarcoma in first-opinion practice in 2019 were identified in VetCompass electronic health records (EHRs) and manually examined to capture variables potentially associated with survival. Median survival time (MST) from diagnosis was calculated for the whole population and based on the primary tumour location. Binary logistic regression was used to explore differences between dogs that died on the day of diagnosis and those that survived [≥]1 day. Cox proportional hazards modelling explored factors associated with time to death in dogs that survived [≥]1 day. Across all haemangiosarcoma cases (n=788), overall MST was 9.0 days (95%CI:5.0-15.0, range: 0-1789) and proportional 1-year survival was 12.0% (95%CI:9.7-15.0%). Dogs with splenic (MST=4.0 days, 95%CI 0.0-9.0) and cutaneous haemangiosarcoma (MST=119.0 days,95%CI:85.0-248.0) had MST greater than 0 days. Male sex and increasing tumour size were associated with increased hazard of death while cutaneous location and surgery were associated with reduced hazard of death. A very short survival time was identified for haemangiosarcoma under first-opinion care. Although survival time was longest for cutaneous cases, the actualised prognosis was poor overall for haemangiosarcoma. This study provides valuable information for contextualised care and dialogues with clients in first-opinion practice.

pathology↗

bioRxiv2024

Interoceptive Signals Bias Decision Making in Rhesus Macaques

Several influential theories have proposed that interoceptive signals, sent from the body to the brain, contribute to neural processes that coordinate complex behaviors. We altered the physiological state of the body using compounds that have minimal effect on the brain and evaluated their effect on decision-making in rhesus monkeys. We used glycopyrrolate, a non-specific muscarinic (parasympathetic) antagonist, and isoproterenol, a beta-1/2 (sympathetic) agonist, to create a sympathetic-dominated state in the periphery, that was indexed by increased heart rate. Rhesus monkeys were trained on two variants of an approach-avoidance conflict task. The tasks offered a choice between enduring mildly aversive stimuli in exchange for a steady flow of rewards, or cancelling the aversive stimuli, forgoing the rewards. The delay to interrupt the aversive stimuli was used as a measure of monkeys tolerance for contact with a hot but not painful stimulus or airflow directed at their muzzle. Both drugs reduced tolerance for the aversive stimuli. To determine whether the drug-induced autonomic state reduced the subjective value of the reward, we tested the effects of glycopyrrolate on a food preference task. Food preference was unaltered, suggesting that the sympathetic dominated state in the periphery selectively reduces tolerance for aversive stimuli without altering reward-seeking behaviors. As the drugs used are expected to have little or no direct effect on the brain, the observed biases in decision making are likely induced by interoceptive afferents that signal to the brain the physiological state of the body. Significance statementThe brain adjusts body physiology to the behavioral agenda of the organism through autonomic efferents; concomitantly interoceptive afferents carry signals that inform the brain about the physiological state of the body, closing a homeostatic regulatory loop. Persuasive theories proposed that interoceptive afferents contribute to higher cognitive functions, including emotion. Empirical evidence that these signals are sufficient to bias complex behavior has been limited by the difficulty of isolating interoceptive afferents from the rest of the homeostatic loop. Here we selectively manipulated the autonomic state of the body using drugs with limited penetrance of the brain in macaques performing decision-making tasks. Sympathetic-dominated peripheral states significantly altered decision making, suggesting that changes in interoceptive afferent signals are sufficient to bias behavior.

neuroscience↗

bioRxiv2023

DNA barcoding reveals an increased diversity within the genus Culex (Diptera: Culicidae) in Ireland

Arthropod populations are changing globally due to the combined impacts of climate change, land-use transformation, globalisation and trade. Changes in arthropod populations can potentially result in the decline and extinction of some native and/or endemic species, while other species that potentially pose threats may increase. Such dynamics lead to weakened ecosystem resilience, which can facilitate the establishment and spread of species with vector capabilities, such as mosquitoes. While many of the mosquito species present in Ireland possess vector capabilities, populations have not been nationally surveyed since 1991. At that time, species identification relied on morphological examination, a method that was even then recognised as inadequate for differentiating certain species within complexes. In this study, we present the first DNA barcoding investigation of Irish mosquito populations and reveal species and hidden diversity not previously recognised in Ireland. These include two potential new species/ecotypes, Culex torrentium and Culex pipiens form pipiens, which were recorded for the first time in Ireland. We demonstrate that barcoding with Cytochrome C Oxidase Subunit 1 (COI) based primers is suitable for the majority of species-level identifications. However, additional primer sets targeting the Internal Transcribed Spacer regions 1 and 2 (ITS1 and ITS2) were necessary to differentiate species within the Culex pipiens complex. The multi-locus approach employed in this study can enhance national surveillance efforts, especially in monitoring mosquitoes that may transmit vector-borne diseases, and in recognising increased species diversity from a biodiversity perspective.

ecology↗

bioRxiv2021

Primer biases in the molecular assessment of diet in multiple insectivorous mammals

Our understanding of trophic interactions of small insectivorous mammals has been drastically improved with the advent of DNA metabarcoding. The technique has continued to be optimised over the years, with primer choice repeatedly being a vital factor for dietary inferences. However, the majority of dietary studies examining the effect of primer choice often rely on in silico analyses or comparing single-niche species. Here we apply DNA metabarcoding to empirically compare the prey detection capabilities of two widely used primer sets when assessing the diets of a flying (lesser horseshoe bat; Rhinolophus hipposideros) and two ground dwelling insectivores (greater white-toothed shrew; Crocidura russula and pygmy shrew; Sorex minutus). Although R. hipposideros primarily rely on two prey orders (Lepidoptera and Diptera), the unique taxa detected by each primer shows that a combination of primers may be the best approach to fully describe bat trophic ecology. However, random forest classifier analysis suggest that one highly degenerate primer set detected the majority of both shrews diet despite higher levels of host amplification. The wide range of prey consumed by ground-dwelling insectivores can therefore be accurately documented from using a single broad-range primer set, which can decrease cost and labour. The results presented here show that dietary inferences will differ depending on the primer or primer combination used for insectivores occupying different niches (i.e. hunting in the air or ground) and demonstrate the importance of performing empirical pilot studies for novel study systems.

ecology↗

bioRxiv2019

Developing a rapid and highly efficient cowpea regeneration and transformation system using embryonic axis explants

Cowpea is one of the most important legume crops planted worldwide, especially in Sub-Saharan Africa and Asia. Despite decades of effort, genetic engineering of cowpea is still challenging due to inefficient in vitro shoot regeneration, Agrobacterium-mediated T-DNA delivery and transgenic selection. Here, we report a rapid and highly efficient cowpea transformation system using embryonic axis explants isolated from imbibed mature seeds. We found that removal of the shoot apical meristem by cutting through the middle of the epicotyl stimulated direct multiple shoot organogenesis from the cotyledonary node tissue. Furthermore, the application of a ternary transformation vector system using an optimized pVIR accessory plasmid provided high levels of Agrobacterium-mediated gene delivery. The utilization of spectinomycin as the selection agent enabled more efficient transgenic selection and plant recovery. Transgenic cowpea shoots developed exclusively from the cotyledonary nodes at high frequencies of 4.5 to 37% across a wide range of cowpea genotypes. We believe that the transformation principles established in this study could also be applied to other legumes to increase transformation efficiencies.

plant biology↗