Biology subjects

Tyler, C. R.

Publications and source records attributed to Tyler, C. R..

10 recordsLinked to original sources

bioRxiv2026

Effects of gamebird release on the non-gamebird dietary diversity and composition of red foxes (Vulpes vulpes) in Southern England

The red fox, Vulpes vulpes, is abundant in England and can exert limiting effects on their avian and mammalian prey. Large-scale gamebird releases in the UK may be sustaining high predator numbers, leading to greater predation on other prey species, especially once gamebird stocks are depleted. However, little is known how gamebird release affects the broader diet of the red fox. Here we used DNA metabarcoding to assess the diet of foxes from 18 agricultural estates in Southern England, 10 of which released large numbers of gamebirds (red-legged partridges - Alectoris rufus, and common pheasants - Phasianus colchicus) and 8 which did not. Scats were collected over one year, allowing for seasonal investigation of the foxes' diet. We investigated the vertebrate species consumed and compared the non-gamebird dietary diversity and composition between release and non-release estates and across seasons. The field vole (Microtus agrestis) was found to be the most frequently predated species overall. Brown hares and field voles were detected more on release sites, while bank voles and dog faeces were detected more on non-release sites. We found little evidence that foxes predate ground nesting birds or other species of concern. The dietary diversity was significantly lower on estates that released gamebirds, and this difference was most notable during the post-shoot, spring months (February to April). On both estate types, diversity was highest in the summer months. The altered predatory behaviour due to gamebird release is likely to affect the populations of the non-game prey of the red fox and this should be considered when designing policies regarding gamebird management and biodiversity conservation. Alternative predation combined with predator control may be reducing predation pressure on non-game prey where gamebirds are released, but high fox density elsewhere likely results in higher predation pressure on a wide range of species.

ecology↗

bioRxiv2026

Biocontainment of phages inhibits bacterial clearance in micro niches

Phage therapy offers a promising solution to the antimicrobial resistance crisis. However, a major concern preventing the adoption of phage therapy is the potential for unintended consequences of phage release; both in regard to preventing the spread of phage resistance, and the proliferation of a non-endemic virus into the microbial ecosystem. Conditional replication (biocontainment) of phages through bioengineering may address these concerns, but the impact on bactericidal efficacy is unknown. Here, we created a biocontained T7 phage (T7{Delta}capsid) lacking the major structural capsid gene, gp10AB, that can only replicate on Escherichia coli strains expressing gp10AB in trans, and assessed its bactericidal efficacy compared with wild-type T7. Congruent with model predictions, T7{Delta}capsid was only able to clear a well-mixed culture of E. coli at a multiplicity of infection (MOI) of 10 or higher, whereas wild-type T7 prohibited growth at an MOI of 0.1. The reduction in efficacy was more evident in a complex structured environment within a microfluidic device, where phage success depends on its ability to penetrate a microbial niche via propagation. In this environment, T7{Delta}capsid was unable to propagate into the bacterial population and unlike wild-type T7, had no impact on the populations growth. This study shows that whilst biocontainment of phages may improve the biosafety of phage therapy, it comes at the cost of its propagation efficacy and niche penetration in relevant environments.

microbiology↗

bioRxiv2025

A high-quality reference genome and tissue expression atlas for the European lobster (Homarus gammarus)

The European lobster (Homarus gammarus) and its sister species, the American lobster (Homarus americanus), are notable for their remarkable immunity and longevity, with lifespans reaching up to 80 years in the wild. A reference genome is available for the American lobster, but not yet for the European lobster, despite its ecological significance, and importance to fisheries and aquaculture. Here, we present a high-quality genome assembly and annotation for the European lobster. The assembly spans 1.76 Gb, with a scaffold N50 of 1.82 Mb and a BUSCO completeness of 97.6%. As observed in the American lobster, the total assembly span is substantially smaller than genome size estimates derived from flow cytometry, performed using independently sampled European lobsters (3.18 - 3.42 Gb). This discrepancy may reflect the highly repetitive nature of decapod genomes, with 51.8% of the H. gammarus assembly consisting of repetitive elements. Leveraging a comprehensive multi-tissue RNA-seq dataset, we annotated 23,223 protein-coding genes and characterised gene expression across ten tissues to generate a tissue-level gene expression atlas, available at www.LobsterGeneX.com. Using single-copy orthologs, we estimated a divergence time of 26 Mya (95% HPD 22 - 30 Mya) between H. gammarus and H. americanus, corresponding to the Oligocene-Miocene boundary. We also identified Homarus-specific gene duplications with roles in immunity and longevity, including telomere maintenance. The reported genomic resources can facilitate future research into lobster biology, support sustainable fisheries and aquaculture management practices, and enable investigations of the evolutionary mechanisms underlying basic biological processes, notably immunity and longevity in Homarid lobsters. Significance StatementThe European lobster (Homarus gammarus) and the American lobster (Homarus americanus) are large benthic decapod crustaceans with significant seafood value, known for their remarkable longevity, with typical lifespans of 30-55 years in the wild and maximum lifespans of up to 80 years. Lobsters grow, reproduce and regenerate limbs throughout their life, and there are very few reports of tumours or age-related diseases. We generated and herein share a high-quality genome assembly and annotation for the European lobster alongside a tissue expression atlas, LobsterGeneX, which enables the visualisation of gene expression profiles across ten tissue types. Based on the genetic information generated, we also provide an estimated time for the divergence between H. gammarus and H. americanus (26 Mya) and identify duplication events for genes related to immunity and longevity. The European lobster reference genome will facilitate further research for investigations into local adaptation in lobster populations, genomic mixing in Homarid hybrids, and identification of genes of interest in aquaculture, ageing, regeneration, disease and cancer resistance.

genomics↗

bioRxiv2025

Optimised genome editing for precise DNA insertion and substitution using Prime Editors in zebrafish

CRISPR/Cas9-mediated genome editing has rapidly become a popular tool for studying gene functions and generating genetically modified organisms. However, using this system, stochastic integration of random insertions and deletions restricts precise genome manipulation. Advanced CRISPR/Cas9 technologies using Prime Editors (PEs), Cas9 proteins fused with reverse transcriptase, enable programmed integration of short DNA modifications into the genome. However, its application in precise genome editing in animal models is challenging. Here, we utilise a nickase-and a nuclease-based PE to perform programmed short DNA substitution and insertion in various loci in the zebrafish genome. Whereas nickase-based PE2 mediated a higher ratio of precise prime edits to the total edits, nuclease-based PEn was more efficient for short DNA modifications, achieving up to 27.3% precise insertion. To further evaluate our approach, we inserted a nuclear localisation signal into a reporter transgene to incorporate longer fragments by prime editing. These gene modifications were transmitted to the next generation. We show that PE-mediated prime editing can efficiently manipulate genome information in zebrafish without using exogenous donor DNA. Prime editing, CRISPR/Cas9, zebrafish, PE2, PEn

molecular biology↗

bioRxiv2023

In field use of water samples for genomic surveillance of ISKNV infecting tilapia fish in Lake Volta, Ghana

Viral outbreaks are a constant threat to aquaculture, limiting production for better global food security. A lack of diagnostic testing and monitoring in resource-limited areas hinders the capacity to respond rapidly to disease outbreaks and to prevent viral pathogens becoming endemic in fisheries productive waters. Recent developments in diagnostic testing for emerging viruses, however, offers a solution for rapid in situ monitoring of viral outbreaks. Genomic epidemiology has furthermore proven highly effective in detecting viral mutations involved in pathogenesis and assisting in resolving chains of transmission. Here, we demonstrate the application of an in-field epidemiological tool kit to track viral outbreaks in aquaculture on farms with reduced access to diagnostic labs, and with non-destructive sampling. Inspired by the "lab in a suitcase" approach used for genomic surveillance of human viral pathogens and wastewater monitoring of COVID19, we evaluated the feasibility of real-time genome sequencing surveillance of the fish pathogen, Infectious spleen and kidney necrosis virus (ISKNV) in Lake Volta. Viral fractions from water samples collected from cages holding Nile tilapia (Oreochromis niloticus) with suspected ongoing ISKNV infections were concentrated and used as a template for whole genome sequencing, using a previously developed tiled PCR method for ISKNV. Mutations in ISKNV in samples collected from the water surrounding the cages matched those collected from infected caged fish, illustrating that water samples can be used for detecting predominant ISKNV variants in an ongoing outbreak. This approach allows for the detection of ISKNV and tracking of the dynamics of variant frequencies, and may thus assist in guiding control measures for the rapid isolation and quarantine of infected farms and facilities.

genomics↗

bioRxiv2023

Comparative analysis of gonadal transcriptomes between turtle and alligator identifies common molecular cues activated during the temperature-sensitive period for sex determination

The mode of sex determination in vertebrates can be categorized as genotypic or environmental. In the case of genotypic sex determination (GSD), the sexual fate of an organism is determined by the chromosome composition with some having dominant genes, named sex-determining genes, that drive the sex phenotypes. By contrast, many reptiles exhibit environmental sex determination (ESD), whereby environmental stimuli drive sex determination, and most notably temperature. To date, temperature-dependent sex determination (TSD) has been found in most turtles, some lizards, and all crocodilians, but commonalities in the controlling processes are not well established. Recent innovative sequencing technology has enabled investigations into gonadal transcriptomic profiles during temperature-sensitive periods (TSP) in various TSD species which can help elucidate the controlling mechanisms. In this study, we conducted a time-course analysis of the gonadal transcriptome during the male-producing temperature (26L) of the Reeves turtle (Chinese three-keeled pond turtle) Mauremys reevesii. We then compared the transcriptome profiles for this turtle species during the TSP with that for the American alligator Alligator mississippiensis to identify conserved reptilian TSD-related genes. Our transcriptome-based findings provide an opportunity to retrieve the candidate molecular cues that are activated during TSP and compare these target responses between TSD and GSD turtle species, and between TSD species. Highlights- A time-course gonadal RNA-seq was conducted using Mauremys reevesii. - Sexual differentiation genes in males were activated at an earlier stage than the ones in females. - Turtle-alligator comparative analysis revealed novel candidate TSD genes.

developmental biology↗

bioRxiv2022

The Diversity and Ubiquity of Antibiotic Resistant Genes in Finfish Culture Ponds in Bangladesh

In Bangladesh, fish provide over 60% of animal-source food with 56.2% of this coming from aquaculture produced predominantly in rural freshwater ponds. Increasing demand for fish products is driving intensification and resulting in higher disease prevalence, posing a risk to food security. Biosecurity is often absent in rural aquaculture practices in Bangladesh and antibiotics are commonly used to treat and prevent disease outbreaks. Antibiotics are often administered incorrectly - a key factor associated with the development of antimicrobial resistance (AMR). AMR can be disseminated rapidly within microbial ecosystems via mobile genetic elements, posing a risk for humans and animals infected with AMR pathogens as treatments with antibiotics become ineffective. Early AMR detection and understanding of the spread of antimicrobial resistant genes (ARGs) in rural aquaculture practices is critical for both food security and human health protection. Here, we apply a metagenomic approach to assess the ARG composition in pond water from six finfish (tilapia and pangasius) farms in the Mymensingh division of North-central Bangladesh. We found microbial communities within the ponds had similar alpha and beta diversities, with multiple ARGs predicted to confer resistance to eighteen different classes of antimicrobials. The most common ARGs conferred resistance to aminoglycosides and sulphonamides and were present in taxa associated with both fish and human pathogens. This ARG diversity potentially confers resistance to a wide variety of antibiotic classes and questions the effectiveness of current and future treatment of diseases with antibiotics in earthen aquaculture ponds. The microbial and ARG compositions between fish ponds within each farm were similar, which may relate to parallels in farming practices creating similar microbial selection pressures and thus comparable microbial populations. Without a more controlled approach towards antibiotic usage, will inevitably further exacerbate the challenges in treating and preventing disease outbreaks as aquaculture production intensifies in Bangladesh. HighlightsO_LIARGs in Bangladesh rural fishponds indicate resistance to 18 different antibiotics C_LIO_LIThe most common AMR were to aminoglycosides and sulphonamides C_LIO_LIARGs were present in plasmids and taxa-associated pathogens C_LIO_LIFarming practices strongly influence microbial and ARG compositions C_LIO_LIIdentified ARGs question antibiotic treatment of disease in rural aquaculture C_LI

microbiology↗

bioRxiv2021

Relationships between pond water and tilapia skin microbiomes in aquaculture ponds in Malawi

Intensification of fish farming practices is being driven by the demand for increased food production to support a rapidly growing global human population, particularly in lower-middle income countries. Intensification of production, however, increases the risk of disease outbreaks and thus the likelihood for crop losses. The microbial communities that colonise the skin mucosal surface of fish are poorly understood, but are important in maintaining fish health and resistance against disease. This skin microbial community is susceptible to disruption through stressors associated with transport, handling and the environment of intensive practices, and this risks the propagation of disease-causing pathogens. In this study, we characterised the microbial assemblages found on tilapia skin -- the most widely farmed finfish globally -- and in the surrounding water of seven earthen aquaculture ponds from two pond systems in distinct geographic regions in Malawi. Metabarcoding approaches were used to sequence the prokaryotic and microeukaryotic communities. We found 92% of prokaryotic amplicon sequence variants were common to both skin and water samples. Differentially enriched and core taxa, however, differed between the skin and water samples. In tilapia skin, Cetobacterium, Paucibacter, Pseudomonas and Comamonadaceae were enriched, whereas, the cyanobacteria Cyanobium, Microcystis and/or Synechocystis, and the diatom Cyclotella, were most prevalent in pond water. Ponds that clustered together according to their water prokaryotic communities also had similar microeukaryotic communities indicating strong environmental influences on prokaryotic and microeukaryotic community structures. While strong site-specific clustering was observed in pond water, the grouping of tilapia skin prokaryotes by pond site was less distinct, suggesting fish microbiota have a greater buffering capacity against environmental influences. The characterised diversity, structure and variance of microbial communities associated with tilapia culture in Malawi provide the baseline for studies on how future intensification practices may lead to microbial dysbiosis and disease onset. HighlightsO_LIFish skin and pond water communities differ structurally, but share common taxa C_LIO_LIPond locations have a stronger influence on water versus fish skin microbiome community structure C_LIO_LISelected skin-associated taxa could be used to monitor dysbiotic events in aquaculture C_LIO_LITaxa with opportunistic pathogen potential were identified at low abundance C_LI

microbiology↗

bioRxiv2021

Human rare variant and zebrafish CRISPR/Cas9-mediated mutant analyses reveal novel functions for API5, HSPB7, and LMO2 in heart failure

The clinical heterogeneity of heart failure has challenged our understanding of the underlying genetic mechanisms of this disease. In this respect, large-scale patient DNA sequencing studies have become an invaluable strategy for identifying potential genetic contributing factors. The complex aetiology of heart failure, however, also means that in vivo models are vital to understand the links between genetic perturbations and functional impacts. Traditional approaches (e.g. genetically-modified mice) are optimal for assessing small numbers of proposed target genes, but less practical when multiple targets are identified. The zebrafish, in contrast, offers great potential for higher throughput in vivo gene functional assessment to aid target prioritisation and support definitive studies undertaken in mice. Here we used whole-exome sequencing and bioinformatics on human patient data to identify 3 genes (API5, HSPB7, and LMO2) suggestively associated with heart failure that were also predicted to play a broader role in disease aetiology. The role of these genes in cardiovascular system development and function was then further investigated using in vivo CRISPR/Cas9-mediated gene mutation analysis in zebrafish. We observed multiple impacts in F0 knockout zebrafish embryos (crispants) following effective somatic mutation, including reductions in ventricle size, pericardial oedema, and chamber malformation. In the case of lmo2, there was also a significant impact on cardiovascular function as well as an expected reduction in erythropoiesis. The data generated from both the human in silico and zebrafish in vivo assessments undertaken supports roles for API5, HSPB7, and LMO2 in human cardiovascular disease and identifies them as potential drug targets for further investigation. The data presented also supports the use of human in silico genetic variant analysis, in combination with zebrafish crispant phenotyping, as a powerful approach for assessing gene function as part of an integrated multi-level drug target validation strategy.

molecular biology↗

bioRxiv2021

Estrogen regulates early embryonic development of the olfactory sensory system via estrogen responsive glia

Estrogen is well-known to regulate development of sexual dimorphisms of the brain, however its role in the brain during early embryonic development prior to sex-differentiation is unclear. Using estrogen biosensor zebrafish models, we found that estrogen activity in the embryonic brain occurs specifically in a type of glia located within the OB, which we name estrogen-responsive olfactory bulb/EROB cells. With estrogen activity, EROB cells extend their ramified projections that overlay the OB outermost layer and tightly interact with olfactory sensory neurons (OSNs) at the olfactory glomeruli. Pharmacologically inhibiting estrogen activity and/or EROB cell ablation impedes olfactory glomerular development, including OSN pathfinding, topological organisation of olfactory glomeruli and inhibitory neurogenesis in the OB. Furthermore, activation of this estrogen/EROB-dependent mechanism decreases the intrinsic neuronal activity primarily in the OB, and this alteration of estrogen signalling disrupts olfaction-mediated behaviour. We propose that estrogen acts on glia to regulate development of functional OB circuits, thereby modulating the local intrinsic excitability in the OB and olfaction-mediated behaviour. Our data also suggest a possibility that the estrogen/EROB cascade may be an important site of action for environmental estrogens causative of neurodevelopmental impairments in animals and humans.

developmental biology↗