Biology subjects

Harrison, K.

Publications and source records attributed to Harrison, K..

9 recordsLinked to original sources

bioRxiv2026

Pre-existing genome architecture partitions viral takeover in the smallest free-living eukaryote

Nuclear DNA viruses colonize host genomes already structured into complex spatial domains, yet whether established spatial boundaries dictate viral progression remains unresolved--in part because sequence composition and transcriptional output are intertwined in animal models. Here, we tracked productive lytic infection of the marine picoeukaryote Ostreococcus tauri by the giant double-stranded DNA prasinovirus OtV5, recording transcription, accessibility, and 3D contact dynamics across parallel time courses. Although total cellular transcript pools collapsed 18-fold by 10 h post-infection, the host transcriptional shutdown, decay of insulation, early chromatin opening, and viral DNA positioning were all bounded by architectural coordinates defined prior to viral arrival. Across two low-GC outlier domains, chromatin accessibility spiked rapidly, spatial insulation eroded, and loci exhibited relative upregulation by 6 hpi, with the smaller outlier region retaining elevated transcript levels per cell compared to the rest of the genome. Unexpectedly, viral DNA was preferentially depleted from these accessible outlier cores, contacting instead the standard-GC telomeric flanks situated immediately beyond the pre-existing spatial boundaries. Domain identity, rather than local accessibility or active host expression, thus governs viral positioning, demonstrating that pre-existing nuclear architecture partitions the physical and transcriptional takeover of the host cell.

evolutionary biology↗

bioRxiv2026

VECTR-Clasp: An open machine-learning and vector-based framework for objective quantification of motor dysfunction during hind-limb clasping in Cdkl5-deficient mice

Quantitative assessment of motor behaviour in rodents is central to the study of neurological disease, yet it remains constrained by manual categorical scoring systems that limit sensitivity, reproducibility, and the ability to detect subtle phenotypes. The hind-limb clasping assay, a standard test of motor dysfunction across many mouse models, is typically scored on an observer-defined categorical scale that may overlook meaningful movement features. We developed VECTR-Clasp, an open vector-based geometric framework that transforms standard pose-estimation output into continuous, body-relative kinematic measures. Combining DeepLabCut for markerless pose estimation with SimBA for automated clasping classification, our pipeline first reproduces conventional clasping detection at a level of agreement approaching that between trained human raters, and then extracts continuous geometric descriptors, including head directionality, total distance travelled, and swing count, that are inaccessible to categorical scoring. Applied to a mouse model of CDKL5 deficiency disorder, a rare neurodevelopmental condition in which motor impairment is a core clinical feature, this approach revealed previously uncharacterised motor microphenotypes: affected animals showed more constrained head direction, reduced overall movement, and fewer swings than wildtype controls. Critically, these differences were also present in affected animals that displayed no overt clasping. Together, these findings demonstrate that continuous geometric analysis of pose-estimation data uncovers motor phenotypes beyond the resolution of categorical scales, providing a more sensitive and reproducible framework for quantifying motor dysfunction. As it operates on standard pose-estimation output, the approach extends readily to other behavioural assays, disease models, and the evaluation of therapeutic interventions. Author SummaryMany neurological disorders impair movement, and researchers frequently study these deficits in mouse models. A widely used test lifts a mouse by the tail and records whether it retracts its hind limbs towards its body, a reflex associated with motor dysfunction. Traditionally, an observer watches the animal and assigns a categorical score. This approach depends on human judgement, varies between raters, and can miss subtle movement differences. We developed VECTR-Clasp, an open-source pipeline that validates machine-learning pose tracking to automate traditional clasping assessment and extends current methods using vector-based geometry. This quantifies the direction and extent of head and body movements, providing additional motor readouts. In a mouse model of CDKL5 deficiency disorder, a rare paediatric neurological disorder, VECTR-Clasp matched human scoring while revealing kinematic differences missed by standard assessment, including in animals appearing unaffected. This objective, sensitive framework could detect subtle motor changes and treatment responses across neurological diseases.

neuroscience↗

bioRxiv2025

De novo Cyclic Peptides Allow Visualisation of the Monomeric and Functional Amyloid Conformations of the Kinase RIPK3

Receptor Interacting Protein Kinase 3 (RIPK3) is a central regulator of necroptosis and a key mediator of inflammatory signaling. Its function is orchestrated through RIP Homotypic Interaction Motif (RHIM)-dependent interactions with other RHIM-containing adapter proteins, forming amyloid-structured necrosomes that trigger kinase activation and subsequently lead to immunogenic cell lysis. Necroptosis eliminates infected or damaged cells and provokes a strong inflammatory response. Dysregulated necroptosis is implicated in chronic inflammatory diseases and associated with ischaemic injury. Despite separate structural elucidation of the isolated RIPK3 kinase domain and the amyloid fibrils formed by the RIPK3 RHIM-containing region, visualizing full-length human RIPK3 in live cells remains challenging due to a lack of specific tools. To address this, we employed Random Non-standard Peptide Integrated Discovery (RaPID) mRNA display to identify cyclic peptides that bind the RHIM-containing region of RIPK3 during its assembly into amyloid fibrils. Three peptides were selected for characterisation and demonstrate utility in visualizing RIPK3 in human cells. These peptides represent promising tools for probing RIPK3 localisation and modulating its function.

biochemistry↗

bioRxiv2025

Insulated Outlier Chromosomes Drive Metabolic and Evolutionary Innovation in Minimal Eukaryotic Algae

Marine picoeukaryotes of the order Mamiellales, including Ostreococcus tauri, the smallest known free-living eukaryote, possess compact genomes yet maintain enigmatic "outlier chromosomes" characterised by lower GC content and hypervariability. To determine the structural and functional nature of these regions, we applied chromosome conformation capture to O. tauri and conducted comparative multi-omics analyses across the Mamiellales order, presenting the first analysis of three-dimensional genome organisation in marine picoeukaryotes. We reveal that outlier regions form structures resembling topologically associating domains, with sharp boundaries that spatially insulate them from the standard chromosomes. These compartments are defined by a distinctive chromatin state characterised by hypomethylation and transcriptional hyperactivity, and are frequently, though not universally, enriched in transposable elements. Crucially, species that lack transposable element enrichment in their outlier chromosomes nonetheless retain the transcriptional hyperactivity and distinct nucleotide composition of these regions, indicating that the functional identity of these compartments persists independently of transposon accumulation. The dynamic nature of these insulated domains is highlighted by the presence of structurally diverse giant polyketide synthase loci. We identify convergent genomic organisation in other chlorophytes, as well as phylogenetically distant stramenopiles. Our results suggest that such compartmentalisation of rapidly evolving, dynamic genomic regions represents a fundamental architectural principle of minimal eukaryotic genomes.

evolutionary biology↗

bioRxiv2024

A near-complete telomere-to-telomere genome assembly for Batrachochytrium dendrobatidis GPL JEL423 reveals a CBM18 gene family expansion and a M36 metalloprotease gene family contraction.

Batrachochytrium dendrobatidis (Bd) is responsible for mass extinctions and extirpations of amphibians, mainly driven by the Global Panzootic Lineage (BdGPL). BdGPL isolate JEL423 is a commonly used reference strain in studies exploring the evolution, epidemiology and pathogenicity of chytrid pathogens. These studies have been hampered by the fragmented, erroneous and incomplete B. dendrobatidis JEL423 genome assembly, which includes long stretches of ambiguous positions, and poorly resolved telomeric regions. Here we present and describe a substantially improved, near telomere-to-telomere genome assembly and gene annotation for B. dendrobatidis JEL423. Our new assembly is 24.5 Mb in length, [~]800 kb longer than the previously published assembly for this organism, comprising 18 nuclear scaffolds and 2 mitochondrial scaffolds and including an extra 839 kb of repetitive sequence. We discovered that the patterns of aneuploidy in B. dendrobatidis JEL423 have remained stable over approximately 5 years. We found that our updated assembly encodes fewer than half the number of M36 metalloprotease genes predicted in the previous assembly. In contrast, members of the crinkling and necrosis gene family were found in similar numbers to the previous assembly. We also identified a more extensive carbohydrate binding module 18 gene family than previously observed. We anticipate our findings, and the updated genome assembly will be a useful tool for further investigation of the genome evolution of the pathogenic chytrids. Author SummaryB. dendrobatidis is a fungus that has been implicated in the extinctions and declines of dozens of amphibians globally. Here we describe a new genome assembly for the commonly used B. dendrobatidis isolate JEL423, which is a substantial improvement from the previously used assembly. Compared with the previous assembly, we reveal that some gene families (such as carbohydrate binding module 18 genes) are more expanded than previously recognised, while others (such as the M36 metalloproteases) are more contracted than previously recognised. Our new genome assembly will be useful for future work exploring the pathogenicity, epidemiology and evolution of chytrid fungi.

genomics↗

bioRxiv2024

Cyanobacteria from marine oxygen deficient zones encode both form I and form II rubiscos

Cyanobacteria are highly abundant in the marine photic zone and primary drivers of the conversion of inorganic carbon to biomass. To date, all studied Cyanobacterial lineages encode carbon fixation machinery hinged upon form I rubisco enzymes within a CO2-concentrating carboxysome. Here, we report that the AMZ IB lineage of Prochlorococcus from global oxygen deficient zones (ODZs) harbor both form I and form II rubisco enzymes, the latter of which are typically non-carboxysomal and possess biochemical properties tuned towards low oxygen environments. Our analyses reveal that these cyanobacterial form II enzymes are functional in vitro and were likely acquired via lateral gene transfer from proteobacteria. Global metagenomic read recruitment demonstrates that Prochlorococcus with form II rubisco are essentially restricted to ODZs in the Eastern Tropical Pacific, suggesting that acquisition may confer an advantage specifically under low-O2 conditions. Populations of AMZ IB Prochlorococcus express both forms of rubisco in situ, with the highest form II rubisco expression at depths where both oxygen and light are particularly low, possibly as a mechanism to increase the efficiency of photoautotrophy under energy limitation. Our findings expand the diversity of carbon fixation configurations in the microbial world and may have implications for the overall capacity of ODZs to sequester carbon.

microbiology↗

bioRxiv2024

Prevalence of the Calvin-Benson-Bassham cycle in chemolithoautotrophic psychrophiles and the potential for cold-adapted Rubisco

The act of fixing inorganic carbon into the biosphere is largely facilitated by one enzyme, Rubisco. Beyond well-studied plants and cyanobacteria, many bacteria use Rubisco for chemolithoautotrophy in extreme environments on Earth. Here, we characterized the diversity of chemolithoautotrophic Rubiscos in subzero environments. First, we surveyed subzero environments and found that the Calvin-Benson-Bassham cycle was the most prevalent chemolithoautotrophic pathway. Second, we uncovered potential for chemolithoautotrophy in metagenomes from two distinct subzero, hypersaline Arctic environments: 40-kyr relic marine brines encased within permafrost (cryopeg brines) and first-year sea ice. Again, the Calvin-Benson-Bassham cycle was the dominant chemolithoautotrophic pathway in both environments, though with different Rubisco forms. From cryopeg brine, we reconstructed four metagenome-assembled genomes with the potential for chemolithoautotrophy, of which the sulfur-oxidizing genus Thiomicrorhabdus was most abundant. A broader survey of Thiomicrorhabdus genomes from diverse environments identified a core complement of three Rubisco forms (II, IAc, IAq) with distinct patterns of gain and loss. We developed a model framework and compared these different Rubisco forms across [CO2], [O2], and temperature. We found that form II outcompetes form I at low O2, but cold temperatures minimize this advantage. However, further inspection of form II from cold environments uncovered signals of thermal adaptation of key amino acids which resulted in a more exposed active site. These modifications suggest that these form II Rubisco proteins may have unique kinetics or thermal stability. This work can help address the limits of autotrophic functionality in extreme environments on Earth and other planetary bodies. ImportanceAutotrophy, or the fixation of inorganic carbon to biomass, is a key factor in lifes ability to thrive on Earth. Research on autotrophy has focused on plants and algae, but many bacteria are also autotrophic and can survive and thrive under more extreme conditions. These bacteria are a window to past autotrophy on Earth, as well as potential autotrophy in extreme environments elsewhere in the Universe. Our study focused on dark, cold, saline environments, which are likely to be found on Enceladus and Europa, as well as in the Martian subsurface. We found compelling evidence of cold adaptation in a key autotrophic enzyme, Rubisco, which could expand the known boundaries of autotrophy in rapidly disappearing icy environments on Earth. We also present a novel model framework that can be used to probe the limits of autotrophy not only on Earth but also on key astrobiological targets like Enceladus and Europa.

microbiology↗

bioRxiv2023

High pathogenicity avian influenza (H5N1) in Northern Gannets: Global spread, clinical signs, and demographic consequences

During 2021-22 High Pathogenicity Avian Influenza (HPAI) killed thousands of wild birds across Europe and North America, suggesting a change in infection dynamics and a shift to new hosts, including seabirds. Northern Gannets (Morus bassanus) appeared especially severely impacted, but limited understanding of how the virus spread across the metapopulation, or the demographic consequences of mass mortality limit our understanding of its severity. Accordingly, we collate information on HPAIV outbreaks across most North Atlantic gannet colonies and for the largest colony (Bass Rock, UK), provide impacts on population size, breeding success, adult survival, and preliminary results on serology. Unusually high numbers of dead gannets were first noted in Iceland during April 2022. Outbreaks in May occurred in many Scottish colonies, followed by colonies in Canada, Germany and Norway. By the end of June, outbreaks had occurred in five Canadian colonies and in the Channel Islands. Outbreaks in 12 UK and Ireland colonies appeared to follow a clockwise pattern with the last infected colonies recorded in late August/September. Unusually high mortality was recorded at 40 colonies (75% of global total colonies). Dead birds testing positive for HPAIV H5N1 were associated with 58% of these colonies. At Bass Rock, the number of occupied sites decreased by at least 71%, breeding success declined by [~]66% compared to the long-term UK mean and adult survival between 2021 and 2022 was 42% lower than the preceding 10-year average. Serological investigation detected antibodies specific to H5 in apparently healthy birds indicating that some gannets recover from HPAIV infection. Further, most of these recovered birds had black irises, suggestive of a phenotypic indicator of previous infection. Untangling the impacts of HPAIV infection from other key pressures faced by seabirds is key to establishing effective conservation strategies for threatened seabird populations, HPAIV being a novel and pandemic threat.

ecology↗

bioRxiv2018

CRISPR/Cas9-mediated mutagenesis of phytoene desaturase in diploid and octoploid strawberry

Gene editing using CRISPR/Cas9 is a simple and powerful tool for elucidating genetic controls and for crop improvement. We demonstrate use of CRISPR/Cas methodology in diploid Fragaria vesca ssp. vesca Hawaii 4 and octoploid F. x ananassa Calypso by targeting the visible endogenous marker gene PDS (phytoene desaturase). Agrobacterium-mediated transformation of leaf and petiole explants was used for efficient stable integration of constructs expressing plant codon-optimised Cas9 and single guide sequences under control of either the Arabidopsis U6-26 consensus promoter and terminator or Fragaria vesca U6III regulatory sequences. More than 80% ( Hawaii 4) and 50% ( Calypso) putative transgenic shoot lines exhibited mutant phenotypes. Of mutant shoot lines selected for molecular analysis, approximately 55% ( Calypso) and 75% ( Hawaii 4) included albino regenerants with bi-allelic target sequence variants. Our results indicate the PDS gene is functionally diploid in Calypso and clearly demonstrate that CRISPR/Cas9 can be used to edit single copy genes at high frequency within the genome of the diploid and the same target in octoploid strawberry.

molecular biology↗