Biology subjects

Powell, R.

Publications and source records attributed to Powell, R..

12 recordsLinked to original sources

bioRxiv2025

A human iPSC-derived motor neuron-myogenic cell coculture platform to evaluate neuromuscular junction innervation after axon injury and in Spinal Muscular Atrophy

Traumatic nerve injury is challenging as motor neurons with damaged axons repair slowly, which can lead to muscle degeneration, while in Spinal Muscular Atrophy (SMA), muscle innervation is reduced. While pro-regenerative or neuroprotective compounds have been identified, their specific ability to enhance or restore neuromuscular junction (NMJ) function in patients remains unclear due to a lack of in vitro human models that track axon growth, NMJ innervation and muscle function. We developed a human iPSC-derived motor neuron-myogenic coculture platform that enables real-time monitoring of axon growth NMJ innervation and axon regeneration and muscle activity following axonal injury, and for SMA-derived motor neurons. We identified spontaneous synchronized GCaMP6f muscle activity as a useful functional marker of NMJ formation. Using this platform, we show that blebbistatin, a pro-regenerative non-muscle myosin II (NMII) inhibitor differentially regulates growth cone dynamics in injured versus uninjured motor neurons, resulting in enhanced NMJ reinnervation. This highlights the therapeutic potential of developing pro-regenerative compounds to promote NMJ innervation. We also confirm that NMJ function is reduced in SMA type 0 (prenatal onset) and type I (pediatric onset) patient-derived motor neurons in the coculture. This human stem cell-based framework can be used, therefore, to evaluate pro-regenerative compounds for axon injury and neuroprotective one for neurodevelopmental and neurodegenerative disorders.

neuroscience↗

bioRxiv2025

Novel chromosome-length genome assemblies of three distinct subspecies of pine marten, sable, and yellow-throated marten (genus Martes, family Mustelidae)

The genus Martes consists of medium-sized carnivores within the family Mustelidae that are commonly known as martens, many of which exhibit extensive geographic variation and taxonomic uncertainty. Here, we report chromosome-length genome assemblies for three subspecies, each representing a different marten species: the Tobol sable (M. zibellina zibellina), the Ural pine marten (M. martes uralensis), and the Far East yellow-throated marten (M. flavigula aterrima). Using linked-read sequencing and Hi-C scaffolding, we generated assemblies with total lengths of 2.39-2.45 Gbp, N50 values of 137-145 Mbp, and high BUSCO scores (93.6-96.4%). We identified 19 chromosomal scaffolds for sable and pine marten, and 20 for yellow-throated marten, which agrees with the known karyotypes of these species (2n=38 and 2n=40, respectively). Annotation predicted ~20,000 protein-coding genes per genome, of which >90% were assigned functional names. Repeats encompass 36.9-40.4% of the assemblies, with a prevalence of LINEs and SINEs, and is conservative across the genus. Synteny analysis of our generated and available marten genome assemblies revealed assembly artifacts in previously published assemblies, which we confirmed through investigation of Hi-C contact maps. Among other rearrangements, we verified a sable-specific inversion on chromosome 11 using the published cytogenetic data. Our assemblies broaden the genomic resources available for Martes, extending coverage to geographically distant and taxonomically significant subspecies. Together, they provide a robust framework for assessing intraspecific genetic diversity, identifying signatures of hybridization, and refining the complex taxonomy of the genus. Beyond conservation and evolutionary applications, these references will facilitate comparative genomics across Mustelidae and other carnivorans.

genomics↗

bioRxiv2025

Cryptic splicing in synaptic and membrane excitability genes links TDP-43 loss to neuronal dysfunction

TDP-43 pathology is a defining pathological hallmark of multiple neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). A major feature of TDP-43 pathology is its nuclear depletion, leading to the aberrant inclusion of cryptic exons during RNA splicing. STMN2 and UNC13A have emerged as prominent TDP-43 splicing targets, but the broader impact of TDP-43-dependent cryptic splicing on neuronal function remains unclear. Here, we report new TDP-43 splicing targets critical for membrane excitability and synaptic function, including KALRN, RAP1GAP, SYT7 and KCNQ2. Using human stem cell-derived neurons, we show that TDP-43 reduction induces cryptic splicing and downregulation of these genes, resulting in impaired excitability and synaptic transmission. In postmortem brains from patients with FTD, these cryptic splicing events occur selectively in neurons with TDP-43 pathology. Importantly, suppressing individual cryptic splicing events using antisense oligonucleotides partially restores neuronal function, and combined targeting almost fully rescues the synaptic deficit caused by TDP-43 loss. Together, our findings provide evidence that cryptic splicing in these synaptic and membrane excitability genes is not only a downstream marker but instead a direct driver of neuronal dysfunction, establishing a mechanistic link between TDP-43 pathology and neurodegeneration in ALS and FTD.

neuroscience↗

bioRxiv2025

Caenorhabditis elegans Uses Canonical and Non-canonical Hippo signaling

Hippo signaling is a conserved regulator of tissue homeostasis across metazoans. The Ste20 family kinase Hippo/MST activates the NDR family kinase Warts/LATS to inhibit the transcriptional coactivator Yorkie/YAP/TAZ and its transcription factor partner Scalloped/TEAD. In Caenorhabditis elegans, cell lineages and organ sizes are largely invariant, and classical Hippo phenotypes such as tissue overgrowth are absent. Nevertheless, WTS-1, YAP-1, and the TEAD-like transcription factor EGL-44 form a conserved core module required for larval development past the L2 stage. Crucially, a direct role for Hippo signaling remains unestablished. To address this question, we generated a fluorescently tagged endogenous YAP-1 as a live biomarker of pathway activity. Upon WTS-1 loss, endogenous YAP-1 translocated from cytosol to nucleus in epithelium and intestine. Tissue-specific depletion revealed that intestinal, but not epithelial, WTS-1 is essential for progression past L2. The duplicated Hippo-related kinases CST-1 and CST-2 repressed YAP-1 nuclear localization in the epithelium but not intestine, indicating that intestinal WTS-1 functions without CST-1/2. The Ste20 kinase MIG-15, orthologous to Drosophila Misshapen and mammalian MAP4K4/6/7/8, was redundant with CST-1/2 for larval progression. Yet deficient MIG-15 uniquely increased YAP-1 abundance without driving nuclear localization. By contrast, the Ste20 kinase GCK-2, orthologous to Drosophila Happyhour and mammalian MAP4K1/2/3/5, had no detectable role. Our findings establish C. elegans as a model for Hippo signaling, with a canonical cascade active in the epithelium and noncanonical inputs controlling WTS-1 in the intestine. In this context, YAP-1/EGL-44 outputs are repurposed from growth control to non-proliferative developmental functions.

developmental biology↗

bioRxiv2025

Genomics of sable (Martes zibellina) x pine marten (Martes martes) hybridization

The sable (Martes zibellina) and pine marten (Martes martes) are two Palearctic mustelids with long-recognized hybrids (kidases), whose fertility was controversial for years. Early genetic studies confirmed hybrids beyond F1, but details remained unclear due to low-resolution methods. Both species were hunted for centuries, but anthropogenic pressures during the 20th-century caused severe bottlenecks in the sable followed by hunting bans and large-scale reintroduction programs across much of its range, including the sympatric zone, potentially affecting hybridization. We resequenced 30 individuals from most of the sables range and Eastern part of pine martens. Among samples, we found a broad spectrum of hybrid types with mosaic recombinant chromosomes that confirm hybrid fertility and indicate crossover is not suppressed in kidases. This necessitates re-evaluation of previous research, as we detected notable discrepancies between STR-based ancestry and whole-genome analysis. In pine martens, we revealed mitochondrial DNA introgression from sables, indicating displacement of native pine marten mitochondrial sequences. Pine marten heterozygosity is relatively low ([~]0.5-0.6 hetSNPs/kbp) while sable diversity ([~]1.5-1.8 hetSNPs/kbp) is unexpectedly high for a species with its demographic history, likely reflecting successful reintroduction programs. We dated species divergence at 1.52 (CI: 1.05-2.06) Mya and identified candidate genes associated with ecological, morphological, and dietary differences, as well as hybrid fertility issues. This study is the first to elucidate marten hybridization at the whole-genome level, opening new research directions for understanding hybridization among Holarctic martens, the genetic consequences of reintroduction programs, and comparative adaptomics.

genomics↗

bioRxiv2025

Localization of AP2α2, TRPV1 and PIEZO2 to the Large Dense Core Vesicles of Human Dorsal Root Ganglion Neurons

Dorsal Root Ganglia (DRG) consist of both peptidergic and non-peptidergic nociceptive neurons. CGRP, an inflammatory neuropeptide, is a classical marker of peptidergic nociceptors and CGRP is stored within the large dense core vesicles (LDCVs) of these neurons. In addition to storing large peptide neurotransmitters, LDCVs might also serve to transport key membrane proteins to the peripheral terminals. This immunohistochemical study investigated the localization of different membrane proteins to the LDCVs of human DRG neurons. Previously validated antibodies against the endocytotic subunit AP22, the heat-activated channel TRPV1 and the mechanosensitive channel PIEZO2 were used in conjunction with an antibody against CGRP on sections of intact human DRG isolated from de-identified human subjects. Immunohistochemical studies were also performed on human synovial tissue to examine peripheral terminals. High magnification confocal microscopy was used to determine the co-localization signal of these membrane proteins with CGRP. We observed a strong co-localization of AP22 with the CGRP containing LDCVs signifying its role in membrane recycling. Moreover, we also observed a strong colocalization of TRPV1 and PIEZO2 with CGRP suggesting that LDCV release controls the trafficking of these channels to the membrane. It is likely that during injury, bulk exocytosis of CGRP will concomitantly increase the surface expression of TRPV1 and PIEZO2 channels enhancing the responsiveness of these neurons to painful stimuli. This model suggests that neurons that co-localize TRPV1 and PIEZO2 to CGRP containing LDCVs are likely silent nociceptors.

neuroscience↗

bioRxiv2024

Chromosome-scale genome assembly and de novo annotation of Alopecurus aequalis.

Alopecurus aequalis is a winter annual or short-lived perennial bunchgrass which has in recent years emerged as the dominant agricultural weed of barley and wheat in certain regions of China and Japan, causing significant yield losses. Its robust tillering capacity and high fecundity, combined with the development of both target and non-target-site resistance to herbicides means it is a formidable challenge to food security. Here we report on a chromosome-scale assembly of A. aequalis with a genome size of 2.83 Gb. The genome contained 33,758 high-confidence protein-coding genes with functional annotation. Comparative genomics revealed that the genome structure of A. aequalis is more similar to Hordeum vulgare rather than the more closely related Alopecurus myosuroides and has undergone an expansion of cytochrome P450 genes, a gene family involved in non-target-site herbicide resistance.

plant biology↗

bioRxiv2024

Whole Genome 3D Blood Biopsy Profiling of Canine Cancers: Development and Validation of EpiSwitch Multi-Choice Array-Based Diagnostic Test.

Veterinary oncology has a critical need for an accurate, specific, and sensitive non-invasive (blood) biomarker assay to assess multiple canine oncological indications early to better inform therapeutic interventions. Extended from clinical applications in human oncology, here we report on a novel 3D genomics approach to identify systemic blood biomarkers for canine diffuse large B-cell lymphoma (DLBCL), T-zone lymphoma (TZL), hemangiosarcoma (HSA), histiocytic sarcoma, osteosarcoma, and canine malignant melanoma, in a single assay format that encompasses multiple classes and phenotypes of cancer. In the validation of the independent test cohort the 3D whole-genome profiling in peripheral blood demonstrated high sensitivity and specificity for lymphomas and sarcomas as a class, with accuracy >80%; and high sensitivity and specificity for individual indications, with accuracy >89%. This study demonstrates a 3D genomic approach can be used to develop a non-invasive, blood-based test for multiple choice diagnosis of canine oncological indications. The modular EpiSwitch(R) Specific Canine Blood (EpiSwitch SCB) test promises to help veterinary specialists to diagnose the disease, make more informed treatment decisions, better utilize alternative effective treatments, minimize or avoid unnecessarily toxicity, and efficiently manage costs and resources.

molecular biology↗

bioRxiv2024

Genetic barcodes for ash (Fraxinus) species and generation of new wide hybrids

Native ash tree species in Europe and North America are being devastated by ash dieback and the emerald ash borer, respectively. As worldwide ash species differ in their level of susceptibility to these threats, hybrid breeding may allow resistance to be transferred among species. However, we do not know the extent to which distantly related ash species can be crossed, and many ash species are difficult to identify from morphology alone leading to some mislabelling in living collections. Here, we develop a genetic barcode system for the identification of Fraxinus species based on three low-copy-number protein coding genes. We also conduct experimental crosses among ash species in different sections. Our barcodes are effective in identifying ash samples to sectional level and in some cases to species level, and can also identify hybrids. They highlight that F. mandshurica, F. platypoda and F. chiisanensis may be frequently mistaken for one another in living collections. We succeeded in generating ten wide hybrid plants: two of section Melioides (species: F. pennsylvanica) {square} section Fraxinus (species: F. excelsior) and eight of section Ornus (species unclear) {square} section Fraxinus (species: F. excelsior). One hybrid from each of our crosses has survived natural infection with the ash dieback pathogen in Ireland. We also discovered a hybrid between section Melioides (species: F. latifolia) {square} section Fraxinus (species: F. excelsior) formed spontaneously in the ash collection at Kew. Our findings facilitate the deployment of global ash species diversity in response to alien pests and pathogens. Societal impact statementThe world-wide diversity of ash trees includes genetic information encoding resistance to the ash dieback fungus and the emerald ash borer beetle, which are currently devastating ash populations in Europe and North America. In order to mobilise this genetic diversity in conventional breeding programmes we need to be able to accurately identify ash species from around the world, and cross them with one another. Here, we present a genetic barcoding system for ash species, and a series of hybridisation experiments between European ash and other species. Two of the hybrids show early promise against ash dieback.

plant biology↗

bioRxiv2022

Building a novel nuclear-organelle genomic framework for the fever tree (Cinchona pubescens Vahl) through short and long-read DNA data assemblies

BackgroundThe Andean Fever tree (Cinchona L.; Rubiaceae) is the iconic source of bioactive quinine alkaloids, which have been vital to treating malaria for centuries. C. pubescens Vahl, in particular, has been an essential source of income for several countries within its native range in north-western South America. However, an absence of available genomic resources is essential for placing the Cinchona species within the tree of life and setting the foundation for exploring the evolution and biosynthesis of quinine alkaloids. FindingsWe address this gap by providing the first highly contiguous and annotated nuclear and organelle genome assemblies for C. pubescens. Using a combination of [~]120 Gb of long sequencing reads derived from the Oxford Nanopore PromethION platform and 142 Gb of short-read Illumina data. Our nuclear genome assembly comprises 603 scaffolds comprising a total length of 904 Mb, and the completeness represents [~]85% of the genome size (1.1 Gb/1C). This draft genome sequence was complemented by annotating 72,305 CDSs using a combination of de novo and reference-based transcriptome assemblies. Completeness analysis revealed that our assembly is moderately complete, displaying 83% of the BUSCO gene set and a small fraction of genes (4.6%) classified as fragmented. Additionally, we report C. pubescens plastome with a length of [~]157 Kb and a GC content of 37.74%. We demonstrate the utility of these novel genomic resources by placing C. pubescens in the Gentianales order using additional plastid and nuclear datasets. ConclusionsOur study provides the first genomic resource for C. pubescens, thus opening new research avenues, including the provision of crucial genetic resources for analysis of alkaloid biosynthesis in the Fever tree.

bioinformatics↗

bioRxiv2021

3D genomic capture of regulatory immuno-genetic profiles in COVID-19 patients for prognosis of severe COVID disease outcome

Human infection with the SARS-CoV-2 virus leads to coronavirus disease (COVID-19). A striking characteristic of COVID-19 infection in humans is the highly variable host response and the diverse clinical outcomes, ranging from clinically asymptomatic to severe immune reactions leading to hospitalization and death. Here we used a 3D genomic approach to analyse blood samples at the time of COVID diagnosis, from a global cohort of 80 COVID-19 patients, with different degrees of clinical disease outcomes. Using 3D whole genome EpiSwitch(R) arrays to generate over 1 million data points per patient, we identified a distinct and measurable set of differences in genomic organization at immune-related loci that demonstrated prognostic power at baseline to stratify patients with mild forms of illness and those with severe forms that required hospitalization and intensive care unit (ICU) support. Further analysis revealed both well established and new COVID-related dysregulated pathways and loci, including innate and adaptive immunity; ACE2; olfactory, G{beta}{psi}, Ca2+ and nitric oxide (NO) signalling; prostaglandin E2 (PGE2), the acute inflammatory cytokine CCL3, and the T-cell derived chemotactic cytokine CCL5. We identified potential therapeutic agents for mitigation of severe disease outcome, with several already being tested independently, including mTOR inhibitors (rapamycin and tacrolimus) and general immunosuppressants (dexamethasone and hydrocortisone). Machine learning algorithms based on established EpiSwitch(R) methodology further identified a subset of 3D genomic changes that could be used as prognostic molecular biomarker leads for the development of a COVID-19 disease severity test.

biochemistry↗

bioRxiv2020

Physiological diversity enhanced by recurrent divergence and secondary gene flow within a grass species

O_LIC4 photosynthesis evolved multiple times independently in angiosperms, but most origins are relatively old so that the early events linked to photosynthetic diversification are blurred. The grass Alloteropsis semialata is an exception, as this single species encompasses C4 and non-C4 populations. C_LIO_LIUsing phylogenomics and population genomics, we infer the history of dispersal and secondary exchanges before, during, and after photosynthetic divergence in A. semialata. We further establish the genetic origins of polyploids in this species. C_LIO_LIOrganelle phylogenies indicate limited seed dispersal within the Central Zambezian region of Africa, where the species originated [~] 2-3 Ma. Outside this region, the species spread rapidly across the paleotropics to Australia. Comparison of nuclear and organelle phylogenies and analyses of whole genomes reveal extensive secondary gene flow. In particular, the genomic group corresponding to the C4 trait was swept into seeds from distinct geographic regions. Multiple segmental allopolyploidy events mediated additional secondary genetic exchanges between photosynthetic types. C_LIO_LILimited dispersal and isolation allowed lineage divergence, while episodic secondary exchanges led to the pollen-mediated, rapid spread of the derived C4 physiology. Overall, our study suggests that local adaptation followed by recurrent secondary gene flow promoted physiological diversification in this grass species. C_LI

evolutionary biology↗