Biology subjects

Harrop, T. W. R.

Publications and source records attributed to Harrop, T. W. R..

4 recordsLinked to original sources

bioRxiv2026

Heat-evolved strains of the coral symbiont Cladocopium proliferum have diverged in exon usage

Experimental evolution at 31{degrees}C produced strains of the coral symbiont Cladocopium proliferum (Symbiodiniaceae) that show increased thermal tolerance in culture, and some of them also raise the bleaching tolerance of coral. Here we investigated how exon usage and alternative splicing have diverged in the heat-evolved strains (SS3, SS5, SS8) from their wild-type cultures (WT10) by reanalysing published transcriptomes of the strains in symbiosis with Acropora kenti larvae at 27{degrees}C using limma, DEXSeq and rMATS. Exon usage separated the strains from an unselected wild-type strain, with 1,308 genes with differential exon usage for SS8, 4,931 for SS5 and 10,464 for SS3, and 59% to 72% of these genes showed no differential expression. SS8, the only strain that also raises the bleaching tolerance of coral larvae, was the closest to the wild type, while a shared set of 757 genes changed in all three heat-evolved strains together. Junction level splicing events (rMATS) did not follow this order (721, 687 and 847 events against WT10), and skipped exons were the most common type, followed by alternative 5' splice sites. Between SS8 and the non-protective strains, alternative 5' splice sites were the most common type (91 of 291 events against SS5 and 68 of 207 against SS3), and retained introns were nearly as common as skipped exons. No GO term was enriched in the shared set or the SS8 lists, but both held genes with a possible link to heat tolerance, among them a mitochondrial glutathione peroxidase in the shared set and a glutathione S-transferase in which SS8 differed from the non-protective strains. Future studies of heat-evolved symbionts should therefore include exon level and splicing analyses to resolve the fine scale differences between strains that gene level analyses miss.

evolutionary biology↗

bioRxiv2024

Rapid and cost-effective production of high-quality insect genome sequences

Insects are the most diverse group of animals on earth, with nearly 1 million species described to date, yet this variation is not reflected within the ranks of genomes currently available. In the current age of genetics, the generation of high-quality reference genomes is invaluable, often necessary and expensive. We prove that insect genomes do not need to come at a large cost. We demonstrate a cost-efficient method for producing high-quality insect genomes, with comparisons to current reference assemblies.

genomics↗

bioRxiv2022

The parthenogenesis mechanism and venom complement of the parasitoid wasp Microctonus hyperodae, a declining biocontrol agent.

A biocontrol system in New Zealand using the endoparasitoid Microctonus hyperodae is failing, despite once being one of the most successful examples of classical biocontrol worldwide. In this study, RNA-seq was used to characterise two key traits of M. hyperodae in this system, the venom complement, critical for the initial success of biocontrol, and the asexual reproduction, which influenced the decline. Full characterisation of M. hyperodae venom revealed 82 candidate venom transcripts with both signal peptides and significantly higher expression in venom. Among these were many involved in manipulating the host environment to source nutrition for the parasitoid egg, preventing a host immune response against the egg, as well as two components that may stimulate the hosts innate immune system. Notably lacking from this list was calreticulin, as it also had high expression in the ovaries. In-situ hybridisation revealed expression was localised to the follicle cells, which may result in the deposition of calreticulin into the egg exochorion. Investigating the asexual reproduction of M. hyperodae revealed core meiosis-specific genes had conserved expression patterns with the highest expression in the ovaries, suggesting M. hyperodae parthenogenesis involves meiosis and the potential for sexual reproduction may have been retained. Upregulation of genes involved in endoreduplication provides a potential mechanism for the restoration of diploidy in eggs after meiosis.

zoology↗

bioRxiv2019

Transcriptional analysis defines TCR and cytokine-stimulated MAIT cells as rapid polyfunctional effector T cells that can coordinate the immune response

MAIT cells are an abundant innate-like T cell population which can be activated via either their T cell receptor (TCR), which recognizes MR1-bound pyrimidine antigens derived from microbial riboflavin biosynthesis, or via cytokines, such as IL-12 and IL-18. In vivo, these two modes of activation may act in concert or independently depending upon the nature of the microbial or inflammatory stimuli. It is unknown, however, how the MAIT cell response differs to the different modes of activation. Here, we define the transcriptional and effector responses of human MAIT cells to TCR and cytokine stimulation. We report that MAIT cells rapidly respond to TCR stimulation through the production of multiple effector cytokines and chemokines, alteration of their cytotoxic granule content and transcription factor expression, and upregulation of co-stimulatory proteins CD40L and 4-1BB. In contrast, cytokine-mediated activation is slower and results in more limited production of cytokines, chemokines, and co-stimulatory proteins; differences in granule content and transcription factor expression are also evident. Therefore, we propose that in infections by riboflavin-synthesizing bacteria, MAIT cells play a key early role in effecting and coordinating the immune response, while in the absence of TCR stimulation (e.g. viral infection) their role is likely to differ.

immunology↗