Biology subjects

Hunt, J. E.

Publications and source records attributed to Hunt, J. E..

4 recordsLinked to original sources

bioRxiv2025

An anthropoid/strepsirrhine divergence in ventral visual stream connectivity

The ventral visual stream has undergone extensive reorganisation within the primate lineage. While some work has examined restructuring of the ventral prefrontal cortical grey matter across primates, comparative studies of white matter connectivity are lacking primarily due to difficulties in data acquisition and processing. Here, we present a data-driven approach to the study of white matter connectivity using post-mortem diffusion MRI data. With this approach, we reconstruct anterior temporal-frontal and occipitotemporal-frontal connections across two anthropoids and one strepsirrhine: the rhesus macaque, the black-capped squirrel monkey, and the ring-tailed lemur. We find that the anthropoids exhibit more dorsal prefrontal innervation of these ventral visual connections. This study supports the hypothesis that anthropoid primates underwent extensive reorganisation of both grey and white matter during their emergence as visual foragers in a complex ecological niche. The data-driven techniques presented here enable further research on white matter connectivity in previously understudied species.

neuroscience↗

bioRxiv2025

Genomic and morphological characterisation of a novel iridovirus, bivalve iridovirus 1 (BiIV1), infecting the common cockle (Cerastoderma edule)

1High rates of mortality of the common cockle, Cerastoderma edule, have occurred in the Wash Estuary, UK since 2008. A previous study linked the mortalities to a novel genotype of Marteilia cocosarum, with a strong correlation between cockle moribundity and the presence of M. cocosarum. Here, we characterise a novel iridovirus, identified by chance during metagenomic sequencing of a gradient purification of Marteilia cells, with presence also correlated to cockle moribundity. The novel 179,695 bp iridovirus, bivalve iridovirus 1 (BiIV1), encodes 193 predicted open reading frames and has a 41% G+C content. BiIV1 clusters together with other aquatic invertebrate iridoviruses in phylogenetic analyses and has a similar genome size to other invertebrate iridoviruses. Comparative analysis revealed that BiIV1 has lost three genes that were previously thought to be common amongst all iridoviruses but has also gained genes, potentially from horizontal transfer from its bivalve mollusc host(s). Electron microscopy showed 158 nm icosahedral virions present in the haemocytes of cockles, typical of those observed in host tissues infected with viruses of the family Iridoviridae. Prevalence of BiIV1 in moribund cockles was higher than that in apparently healthy cockles at most sites in the Wash Estuary, with up to 100% PCR prevalence in moribund cockles. Our findings provide the first genome for a bivalve-infecting iridovirus and identify a second bivalve-associated iridovirus in publicly available genomic datasets, adding to the knowledge of invertebrate iridovirus genomics and diversity.

molecular biology↗

bioRxiv2025

Characterisation of Marteilia cocosarum in the Wash Estuary, UK, linked to mass mortalities of cockles (Cerastoderma edule), and its relationship to closely related species

Globally, Marteilia parasites have been associated with significant mass mortality events in populations of commercially important bivalve molluscs, frequently resulting in large-scale fishery collapses and substantial socio-economic impacts. The Wash Estuary, UK, supports several bivalve fisheries, and among these, common cockles Cerastoderma edule have suffered unusually high mortalities since 2008. We investigate potential causes of these mortalities, and confirm infection with Marteilia cocosarum, strongly associated with cockle moribundity, also confirming its presence in archived samples collected in 2009. Molecular and light microscopy screening of samples collected during mortality events in 2021, including healthy (buried) and moribund (weak, unable to bury) cockles, indicated high prevalence of M. cocosarum in moribund cockles (PCR incidence up to 95%) in contrast to healthy cockles (up to 42%), suggesting an association between cockle moribundity and Marteilia infection. Analysis of the full ribosomal RNA array identified consistently different nucleotides between M. cocosarum infections in The Wash (denoted as genotype WE) and those in Wales (denoted genotype BI). 83% of infections in The Wash could be identified as M. cocosarum WE and 12% as M. cocosarum BI, with both genotypes recovered from 5% of infected animals. Histopathologically, M. cocosarum WE infects the gill, mantle and connective tissues, identical to observations of M. cocosarum infecting Welsh cockles. Ongoing cockle mortalities in The Wash raise concerns regarding the sustainability of this resource ecologically and economically. Additional measures may be required to reduce the spread of this pathogen, noting that its distribution beyond The Wash and Wales is currently unknown.

molecular biology↗

bioRxiv2022

A novel mechanistic framework for precise sequence replacement using reverse transcriptase and diverse CRISPR-Cas systems

CRISPR/Cas systems coupled with reverse transcriptase (RT), such as the recently described Prime editing, allow for site-specific replacement of DNA sequences. Despite widespread testing of Prime editing, it is currently only compatible with type II CRISPR/Cas proteins such as Streptococcus pyogenes and Staphylococcus aureus Cas9. Enabling RT compatibility with other CRISPR/Cas domains, such as type V enzymes with orthogonal protospacer adjacent motif specificities and smaller protein size would expand the range of edits that can be made in therapeutic and industrial applications. We achieve this with a novel mode of DNA editing at CRISPR-targeted sites that reverse transcribes the edit into the target strand DNA (e.g., the complement of the PAM-containing strand), rather than the non-target strand DNA, as in Prime editing. We term this technology RNA encoded DNA replacement of alleles with CRISPR (hereafter, REDRAW). We show that REDRAW extends the utility of RT-mediated editing beyond type II to include multiple type V CRISPR domains. REDRAW features a broad (8-10 bases) targeting window, at which all types of substitutions, insertions and deletions are possible. REDRAW combines the advantages of type V CRISPR domains with the extensive range of genetic variation enabled by RT-mediated, templated sequence replacement strategies.

molecular biology↗