Biology subjects

Allen, H.

Publications and source records attributed to Allen, H..

8 recordsLinked to original sources

bioRxiv2026

Host identity and fungal source pools shape mycorrhizal assembly under carbon removal interventions in large-scale afforestation

1. Large-scale afforestation is central to global carbon dioxide removal (CDR) commitments. Soil inoculation and enhanced rock weathering (ERW) may increase tree biomass carbon stocks during woodland establishment. Both can alter soil fungal communities, but whether they change the root-colonising mycorrhizal fungi that support tree nutrition and growth is largely unknown. 2. In a fully-factorial field trial on former upland pasture in Wales (11.5 ha; ~25,000 saplings), we tested the effects of soil inoculation (addition of soil from nearby mature, donor forests) and ERW (basalt amendment) on root-associated ectomycorrhizal (EcM) and arbuscular mycorrhizal (AM) fungi, and tree growth in mixed-broadleaf and conifer plantations, two and four years after planting. To identify key colonisation sources, we also characterised mycorrhizal fungi in roots and soils of surrounding hedgerows, source tree nursery, non-forested control plots, donor woodlands and soil inoculum. 3. Soil inoculation caused a subtle shift in conifer EcM community composition (3% of variation) but had no detectable effect in broadleaves. Basalt amendment raised soil pH but did not change mycorrhizal composition, diversity, or colonisation. 4. Root-associated EcM communities were distinct from those detected in plantation soils and shared far more taxa with the tree nursery than with the donor inoculum (41-48% vs. 2-9% of plantation EcM taxa) whereas AM communities largely reflected fungi present in pre-existing pasture. 5. Host identity was the dominant factor structuring mycorrhizal communities, overshadowing both treatments, and was the strongest predictor of aboveground biomass. 6. Synthesis and applications: This field-scale evaluation shows early mycorrhizal assembly during woodland establishment is strongly structured by tree species identity and pre-existing fungal source pools, limiting the effect of inoculation at planting. Mycorrhizal management should therefore target the nursery stage and be tailored to individual tree species. Basalt amendment for ERW is unlikely to harm mycorrhizal communities during establishment. Because soil fungal communities did not reflect root symbiosis, our findings also stress that monitoring of belowground outcomes in CDR-focused planting should include root sampling rather than relying on soil DNA alone.

ecology↗

bioRxiv2026

An ancient retrotransposon provides species-specific tuning of IL-18 inflammatory signaling

Species differ markedly in how they regulate immune responses, yet the molecular basis of this variation remains incompletely understood. Here, we characterize an underexplored regulatory mechanism of the pro-inflammatory IL-18 pathway, centered on a truncated IL18R1 isoform with striking species-specific expression differences. This isoform, IL18R1-Short, derives from an ancient LINE2 retrotransposon insertion that provides an intronic polyadenylation signal, producing a receptor that lacks the intracellular signaling domain. Using RNA sequencing across nine mammals, we find that although this cis-regulatory element is broadly conserved, robust IL18R1-Short expression is species- and tissue-restricted: bats and mice express it at high levels, particularly in barrier tissues (lung, skin, intestine), whereas most other species, including humans, show little or no expression. Functionally, IL18R1-Short dampens IL-18-induced NF{kappa}B signaling in human, mouse, and bat systems, and knockdown of the mouse ortholog enhances IL-18-driven immune and inflammatory gene expression in mouse T cells. Together, these results identify IL18R1-Short as a transposable element-derived decoy receptor and highlight alternative transcription as a source of species-specific immune regulation.

evolutionary biology↗

bioRxiv2025

De novo genome assemblies of the dwarf honey bee subgenus Micrapis: Apis andreniformis and Apis florea

The Micrapis subgenus, which includes the black dwarf honey bee (Apis andreniformis) and the red dwarf honey bee (Apis florea), remains underrepresented in genomic studies despite its ecological significance. Here, we present high-quality de novo genome assemblies for both species, generated using a hybrid sequencing approach combining Oxford Nanopore Technologies (ONT) long reads with Illumina short reads. The final assemblies are highly contiguous, with contig N50 values of 5.0 Mb (A. andreniformis) and 4.3 Mb (A. florea), representing a major improvement over the previously published A. florea genome. Genome completeness assessments indicate high quality, with BUSCO scores exceeding 98.5% and k-mer analyses supporting base-level accuracy. Repeat annotation revealed a relatively low repetitive sequence content ([~]6%), consistent with other Apis species. Using RNA sequencing data, we annotated 12,232 genes for A. andreniformis and 12,597 genes for A. florea, with >97% completeness in predicted proteomes. These genome assemblies provide a valuable resource for comparative and functional genomic studies, offering new insights into the genetic basis of dwarf honey bee adaptations.

genomics↗

bioRxiv2025

First whole genome assembly of Python regius (ball python), a model of extreme physiological and metabolic plasticity

The study of nontraditional model organisms, particularly those exhibiting extreme phenotypes, offers unique insights into adaptive mechanisms of stress response and survival. Snakes, with their remarkable physiological, metabolic, and morphological adaptations, serve as powerful models for investigating these processes. Pythons are a unique model organism that have been studied for their extreme metabolic and physiological plasticity. To date, the Burmese python (Python bivittatus) is the only member of the Pythonidae family to have been sequenced. The low contiguity of this genome and rising challenges in obtaining Burmese pythons for study prompted us to sequence, assemble, and annotate the genome of the closely related ball python (Python regius). Using a hybrid sequencing approach, we generated a 1.45 Gb genome assembly with a contig N50 greater than 18 Mb and a BUSCO score of 98%, representing the highest quality genome to date for a member of the Pythonidae family. This assembly provides a valuable resource for studying snake-specific traits and evolutionary biology. Furthermore, it enables exploration of the molecular mechanisms underlying the remarkable cardiac and muscular adaptations in pythons, such as their ability to rapidly remodel organs following feeding and resist muscular atrophy during prolonged fasting. These insights have potential applications in human health, particularly in the development of therapies targeting cardiac hypertrophy and muscular atrophy.

genomics↗

bioRxiv2023

Mitochondrial dsRNA from B-ALL cells stimulates mesenchymal stromal cells to become cancer associated fibroblasts

Cancer associated fibroblasts (CAF) arising from bone marrow-derived mesenchymal stromal cells (MSC) are prominent in B-precursor acute lymphoblastic leukaemia (B-ALL). We have previously shown that CAF formation is triggered by exposure to reactive oxygen species-inducing chemotherapy and that CAF support chemoresistance by donating mitochondria to the cancer cells, through tunnelling nanotubes. In the present study, we show that exposure of MSC to ALL cell lines, PDX and primary cells or their conditioned media can also trigger CAF formation, in an oncogene-dependent manner. Using bulk RNA sequencing in cell lines, we show that the MSC to CAF transition is accompanied by a robust interferon pathway response and we have validated this finding in primary cells. Using confocal microscopy and flow cytometry, we identify the take up of leukaemia cell-derived mitochondrial dsRNA by MSC as a proximate trigger for the MSC to CAF transition. We show that degradation of dsRNA in ALL cell conditioned media by DMSO ablates the ability of the conditioned media to stimulate MSC to CAF transition. Since we find that only specific primary driver genetic subtypes of B-ALL possess the property to directly generate CAFs, we propose this phenomenon as the first mechanistic insight into the strong relationship between acute lymphoblastic leukaemia genetic subtype and survival outcomes. Key pointsX Exposure of MSC to B-precursor ALL cell lines triggers cancer-associated fibroblast formation in an oncogene-dependent manner The proximate trigger for CAF formation is ALL-derived mitochondrial double stranded RNA

cancer biology↗

bioRxiv2023

Regulation of interferon signaling by transposon exonization

SummaryInnate immune signaling is essential for clearing pathogens and damaged cells, and must be tightly regulated to avoid excessive inflammation or autoimmunity. Here, we found that the alternative splicing of exons derived from transposable elements is a key mechanism controlling immune signaling in human cells. By analyzing long-read transcriptome datasets, we identified numerous transposon exonization events predicted to generate functional protein variants of immune genes, including the type I interferon receptor IFNAR2. We demonstrated that the transposon-derived isoform of IFNAR2 is more highly expressed than the canonical isoform in almost all tissues, and functions as a decoy receptor that potently inhibits interferon signaling including in cells infected with SARS-CoV-2. Our findings uncover a primate-specific axis controlling interferon signaling and show how a transposon exonization event can be co-opted for immune regulation.

genomics↗

bioRxiv2021

Diversity of Antibiotic Resistance genes and Transfer Elements-Quantitative Monitoring (DARTE-QM): a method for detection of antimicrobial resistance in environmental samples

Effective monitoring of antibiotic resistance genes and their dissemination in environmental ecosystems has been hindered by the cost and efficiency of methods available for the task. We developed a method entitled the Diversity of Antibiotic Resistance genes and Transfer Elements-Quantitative Monitoring (DARTE-QM), a system implementing high-throughput sequencing to simultaneously sequence thousands of antibiotic resistant genes representing a full-spectrum of antibiotic resistance classes commonly seen in environmental systems. In this study, we demonstrated DARTE-QM by screening 662 antibiotic resistance genes within environmental samples originated from manure, soil, and animal feces, in addition to a mock-community used as a control to test performance. DARTE-QM offers a new approach to studying antibiotic resistance in environmental microbiomes, showing advantages in efficiency and the ability to scale for many samples. This method provides a means of data acquisition that will alleviate the obstacles that many researchers in this area currently face.

microbiology↗

bioRxiv2020

Accessory genome dynamics and structural variation of Shigella from persistent infections

Shigellosis is a diarrhoeal disease caused mainly by Shigella flexneri and Shigella sonnei. Infection from Shigella is thought to be largely self-limiting, with short- to medium- term and serotype-specific immunity provided following clearance. However, cases of men who have sex with men (MSM) associated shigellosis have been reported where Shigella of the same serotype were serially sampled from individuals between 1 to 1862 days apart, possibly due to persistent carriage or reinfection with the same serotype. Here, we investigate the accessory genome dynamics of MSM associated S. flexneri and S. sonnei isolates serially sampled from individual patients at various days apart. We find that pairs likely associated with persistent carriage infection and with smaller single nucleotide polymorphism (SNP) distance, demonstrated significantly less variation in accessory genome content than pairs likely associated with reinfection and with greater SNP-distance. We also observed evidence of antimicrobial resistance (AMR) acquisition during persistent Shigella infection, specifically the gain of extended spectrum beta-lactamase genes in two pairs associated with persistent carriage. Finally, we explored chromosomal structural variations and rearrangements in seven (5 chronic and 2 reinfection associated) pairs of S. flexneri 3a isolates from a MSM-associated epidemic sublineage, which revealed variations at several common regions across pairs. These variations were mediated by insertion sequence (IS) elements which facilitated plasticity of genetic material with a distinct predicted functional profile. This study provides insight on the variation of accessory genome dynamics and large structural genomic changes in Shigella during persistent infection. ImportanceShigella spp are Gram-negative bacteria that are the etiological agent of shigellosis, the second most common cause of diarrhoeal illness globally, particularly among children under the age of 5 in low-income countries. In high-income countries, an alternative transmission pathway of sexually transmissible disease among men who have sex with men (MSM) is emerging as the dominant presentation of the disease. Within MSM we have captured prolonged infection and/or recurrent infection with shigellae of the same serotype, challenging the belief that Shigella infection is short-lived, and confers homologous serotypic immunity. Using this recently-emerged transmission scenario we comprehensively characterise the genomic changes that occur over the course of individual infection with Shigella and uncover a distinct functional profile of variable genome regions in these globally important pathogens.

microbiology↗