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Davis, H.

Publications and source records attributed to Davis, H..

13 recordsLinked to original sources

Neurodegeneration-inducing macromolecules exit the brain via nanovascular conduits formed by reticular fibroblasts

Accumulation of proteins such as amyloid beta (Abeta), hyperphosphorylated tau and alpha-synuclein within the brain alters neural information processing and causes neurodegeneration(1-3), but how toxic solutes are cleared from the brain remains highly controversial(4,5). Proposed exit routes include efflux across endothelial cells into the blood(6,7), and movement to the pial surface via vasomotion-induced pumping along spaces within arteriolar smooth muscle(8) or via outflow along the perivascular space of ascending venules promoted by water flux through astrocytes (the glymphatic system(9)). From the pial surface of the brain, drainage may continue to dural lymphatics, along the outer sheaths of exiting cranial nerves and across the cribriform plate(10-14). We now report the presence, in mice and humans, of 2 micron diameter conduits that remove fluorescently labelled tau and Abeta from the brain. These conduits form a spatially-organised mesh within the walls of penetrating arterioles and pial arteries, and around the surface of ascending venules and deep cerebral and pial veins. They course through the pial and arachnoid layers to span the CSF space, wrapping the brain and cranial nerves. They are formed of reticular fibroblasts, which label for VE-cadherin(15) and PDGFRalpha(16), the lymphatic markers(17) podoplanin, VEGFR3 and Prox1, and reticular fibroblast extracellular matrix components collagen I and VI(16,18-20). Parenchymal tau drains from the brain at a similar rate via arteriolar conduits and via conduits around venules, arguing against preferential removal by a glymphatic mechanism. In Alzheimer's disease model mice, Abeta is seen traversing these lymph node-like conduits. Modulation of molecular transfer via this route may accelerate or delay cognitive decline, and slowed transfer from arteriolar to pial-arachnoid conduits may initiate cerebral amyloid angiopathy.

neuroscience↗

An Integrated Spatially Resolved Mechanistic Model of Hierarchical Auxin-Cytokinin-Ethylene Crosstalk Underlying Root Growth Inhibition in Arabidopsis

Decoding how plants integrate multiple hormone signals to coordinate growth requires tools capable of resolving pathway interactions at cellular resolution in living tissue. Here we present ACE (Auxin-Cytokinin-Ethylene) and ACE2, proof-of-concept single-locus reporters to simultaneously capture activity of multiple hormones. Deploying ACE alongside well-established reporters, exogenous hormone treatments, and reverse-genetic perturbations of hormone biosynthesis, signaling, and transport in three-day-old etiolated Arabidopsis seedlings, we dissect the spatiotemporal hierarchy governing primary root elongation and root apical meristem (RAM) size. We demonstrate that both ethylene- and cytokinin-triggered root growth inhibition involve a boost of TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS1 (TAA1)-mediated auxin biosynthesis and AUXIN RESISTANT1 (AUX1)-dependent auxin redistribution. Two spatially distinct auxin responses underlie the respective root growth effects: ethylene expands TAA1-dependent auxin biosynthesis from the root vasculature into the epidermis and promotes AUX1-mediated auxin import into the transition and elongation zones to inhibit cell elongation, while cytokinin confines ethylene-dependent TAA1-boosted activity to the vasculature and drives auxin accumulation in lateral root cap cells to reduce RAM size. Together, these data establish a reciprocal regulatory loop between these hormones, positioning ethylene as a convergence node in auxin-cytokinin crosstalk, and cytokinin as a modulator of the ethylene-auxin interaction. Critically, the changes in cross-activated reporter patterns described for different genetic backgrounds, alongside quantitative assessment of hormone-specific inhibition of the mutants growth, were consistent with the multi-hormone network established over two decades of research, and added cell-type-resolved spatial detail and a proposed hierarchy for the etiolated seedling root. Finally, a second-generation reporter, ACE2, overcomes key technical limitations of ACE, expanding the platforms capacity toward a higher-order multi-hormone monitoring system. These resources expand the Arabidopsis genetic toolkit and provide a generalizable framework instrumental for dissecting multi-hormone signaling hierarchies at the cellular level.

plant biology↗

Gene Flow Creates Fuzzy Species Boundaries in Fence Lizards

Species delimitation is a fundamental challenge in systematic biology, particularly for geographically variable taxa with hierarchical population structure and gene flow. Migration-aware coalescent models provide a powerful framework for investigating lineage divergence and accurately defining species boundaries. In this study, we combine statistical evaluations of gene flow with phylogenetic and population structure analyses to delimit species of fence lizards within the Sceloporus undulatus complex, a group characterized by extensive population subdivision, mitochondrial DNA introgression, and nuclear gene flow. We find that the undulatus complex exhibits uneven variation in genetic, morphological, and bioclimatic traits, resulting in variable distinctiveness among groups. In some cases, species boundaries are recognized by clear genetic discontinuities without gene flow. In others, shallow divergence, paraphyly, and gene flow produce leaky boundaries and fuzzy species limits. Mitochondrial introgression is extensive and concentrated at species boundaries, whereas nuclear gene flow occurs between only a few species and at much lower levels than within species. Neither within-species populations or species are substantially diverged across morphology or bioclimatic space, highlighting the limited utility of these traits for diagnosing species in this group. By integrating estimates of gene flow with phylogenetic and population structure analyses, this study provides a robust and biologically meaningful revised taxonomic framework for the undulatus complex that identifies independently evolving lineages as species.

evolutionary biology↗

A Direct DNA Extraction Workflow for Metabarcoding Fungal Bioaerosols from Adhesive Samplers

Monitoring fungal bioaerosols is essential for understanding their impacts on human health and crop productivity. However, current monitoring approaches rely on culture-dependent techniques, which underestimate the diversity of fungal exposures. Adhesive-coated films can effectively capture airborne particles but have been regarded as unsuitable for DNA downstream analysis, owing to the lack of standardised DNA extraction methods for the adhesive capture surface. Here, we present an optimised DNA extraction protocol for adhesive film, which we developed and validated to enable direct and culture-independent ITS2-based metabarcoding of fungal bioaerosols collected on a 96 well plate sealing film ( Sticky sampler). This validated approach was applied to field samples collected from four agricultural farms and from a domestic garden to evaluate seasonal and spatial changes in fungal bioaerosols. Our analysis uncovered pronounced site-specific contrasts linked to geography and land management, as well as clear seasonal shifts in garden fungal communities. This study demonstrates that adhesive samplers, combined with optimised DNA extraction, provide a practical and inexpensive tool for fungal bioaerosol research by resolving ecologically meaningful spatiotemporal dynamics of airborne fungi. This protocol opens new opportunities for highly scalable surveillance of environmental bioaerosols.

microbiology↗

A multivalent mRNA-LNP therapeutic vaccine with broad cross-genotype immunogenicity elicits clearance of HBV infected hepatocytes

Chronic hepatitis B remains a major global health challenge, affecting over 254 million individuals and causing over 1 million deaths annually. Despite current antiviral therapies effectively suppressing viral replication, functional cure rates are low due to HBV-induced immune dysfunction and exhaustion. Therefore, new therapeutic approaches to achieve immune control of HBV infection are needed. Following the systematic evaluation of multiple HBV mRNA antigen designs, we developed mRNA-1965, a trivalent therapeutic mRNA vaccine encoding nanoparticle-displayed PreS1 and PreS2 domains of HBsAg to bypass the immune interference caused by HBV subviral particles, along with mutant forms of HBV Core and Polymerase. In HBV naive mice, mRNA-1965 immunization induced dose-dependent HBV-neutralizing antibodies and Th1-skewed CD4+ and IFN{gamma}+ CD8+ T cell responses to all three encoded HBV antigens. In non-human primates, mRNA-1965 elicited broad antibody and T cell responses across multiple HBV genotypes. Furthermore, vaccination with mRNA-1965 achieved a strong neutralizing antibody response and complete clearance of serum and liver HBV biomarkers in in an AAV-HBV mouse model with [~]100 IU/mL baseline HBsAg. Notably, combining mRNA-1965 with immune stimulatory co-modalities targeting PD-L1 and OX40 further enhanced therapeutic efficacy in mice with [~]1000 IU/mL baseline HBsAg. Clearance of HBV in AAV-HBV mice was associated with T cell response to mRNA-encoded antigens and with activation and differentiation of Core-specific CD8+ T cells. These findings support the potential of mRNA-1965 to promote a functional cure for chronic hepatitis B by overcoming immune dysfunction and subsequently enabling robust, functional immunity.

immunology↗

A foundation model for microbial growth dynamics

Microbial growth dynamics contain rich information about microbial populations, which support applications from antibiotic testing to microbiome engineering. However, the high dimensionality of growth data and the scarcity of large, task-specific datasets have limited generalizable modeling analysis across systems. Here, we develop a foundation model for microbial growth dynamics. It is a large-scale, self-supervised representation model trained on [~]370,000 experimental and simulated growth curves spanning diverse microbial species, environmental conditions, and community contexts. The model learns lower-dimensional latent embeddings that capture essential dynamical features of raw growth data and enable accurate reconstruction of these data. The concise representations enhance predictive performance in diverse downstream applications. Using these embedding, we achieve few-shot learning for antibiotic classification and concentration prediction, accurate forecasting of simulated and experimental communities, and inference of total abundance from relative-abundance data. By extracting transferable representations from heterogeneous datasets, our model provides a general framework for analyzing and predicting microbial community dynamics from limited measurements.

synthetic biology↗

Identification of QTLs linked to partial resistance to foot and root rot caused by Fusarium avenaceum and Fusarium oxysporum in faba bean (Vicia faba)

Foot and root rot, caused by a complex of soil-borne fungal and oomycete pathogens, including several Fusarium spp., can cause serious yield losses in faba bean. Current control strategies rely largely on agronomic practices and limited varietal resistance. Identifying novel sources of genetic resistance is of great potential value for breeding elite varieties with improved foot rot resistance. A partially resistant Vicia faba accession ig124213 (NV490) was crossed with a moderately susceptible ig124301 (NV512) and a mapping population comprising 198 F3 families was developed. This was screened for resistance to a mixture of seven UK field isolates of Fusarium avenaceum and Fusarium oxysporum under glasshouse conditions. Several F3 families with moderate to high levels of resistance to both Fusarium species were identified, and a high-density linkage map of the V. faba genome including 6755 SNP-markers in seven linkage groups (LG) was generated using the Vfaba_v2 Axiom SNP array. Quantitative trait loci associated with improved resistance to Fusarium foot and root rot were identified, including one major QTL on LG4, corresponding to the chromosome 4 of V. faba. Key messageThe first QTL associated with partial resistance to Fusarium foot and root rot has been identified using a biparental mapping population of Vicia faba.

plant biology↗

A role for fibroblast and mural cell subsets in models of neuropathic pain.

Neuropathic pain is a particularly intractable type of chronic pain that can result from physical nerve damage due to surgery or entrapment. Here, we present data which suggest that a particular subclass of fibroblast and mural cells may be implicated in the sensory neuron dysfunction that is characteristic of this pain state. In a mouse model of traumatic painful neuropathy, we used cell sorting, nerve tissue clearing and RNA sequencing to study mesenchymal lineage cells. With cell sorting (n = 4 mouse nerves) and tissue clearing (n = 5), we show that fibroblasts and mural cells positive for the platelet-derived growth factor receptor beta (Pdgfrb) gene are increased in number for at least two months post-nerve damage. Moreover, single cell RNA sequencing data (n = 4) from our own lab and those of three other laboratories reveal that Pdgfrb+ cells express high levels of known and putative pro-algesic mediators. Bulk sequencing of sorted Pdgfrb+ fibroblasts (n = 10) and Pdgfrb+/Cd146+ mural cells (n = 11) further indicate that many of these mediators are upregulated in neuropathy. We go on to demonstrate that a human nerve pericyte line releases a selection of these pro-algesic mediators at protein level. Moreover, conditioned media from stimulated human pericytes induces intra-cellular changes in human induced pluripotent stem cell derived sensory neurons (n = 5 independent differentiations); these changes (phosphorylation of the transcription factor signal transducer and activator of transcription 3, STAT3) have been previously linked to sensory neuron activation. In summary, our data indicate that mesenchymal cell abnormalities should be considered when developing novel strategies to tackle neuropathic pain. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=108 SRC="FIGDIR/small/627455v2_ufig1.gif" ALT="Figure 1"> View larger version (23K): org.highwire.dtl.DTLVardef@186492corg.highwire.dtl.DTLVardef@12deb90org.highwire.dtl.DTLVardef@1c43b8aorg.highwire.dtl.DTLVardef@211952_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

Cell cycle plasticity underlies fractional resistance to palbociclib in ER+/HER2- breast tumor cells

The CDK4/6 inhibitor palbociclib blocks cell cycle progression in ER+/HER2- breast tumor cells. Although these drugs have significantly improved patient outcomes in metastatic breast cancers, a small percentage of tumor cells continues to divide in the presence of palbociclib--a phenomenon we refer to as fractional resistance. It is critical to understand the cellular mechanisms underlying fractional resistance because the precise percentage of resistant cells in patient tissue is a strong predictor of clinical outcome. Here, we hypothesize that fractional resistance arises from cell-to-cell differences in core cell cycle regulators that allow a subset of cells to escape CDK4/6 inhibitor therapy. We used multiplex, single-cell imaging to identify fractionally resistant tumor cells both in a cell culture model of ER+/HER2- breast cancer as well as live primary tumor cells resected from a patient. We found that tumor cells capable of proliferating in the presence of palbociclib showed both expected (e.g., CDK2, E2F1) and unexpected (e.g., Cdt1, p21, cyclin B1) shifts in core cell cycle regulators. Notably, resistant cells in both tumor models showed premature enrichment of the G1 regulators E2F1 and CDK2 protein and, unexpectedly, the G2/M regulator cyclin B1 just before cell cycle entry, suggesting that resistant cells may use noncanonical mechanisms to overcome CDK4/6 inhibition. Using computational data integration and trajectory inference approaches, we show how plasticity in cell cycle regulators gives rise to alternate cell cycle "paths" that allow individual ER+/HER2- tumor cells to escape palbociclib treatment. Understanding drivers of cell cycle plasticity, and how to eliminate resistant cell cycle paths, could lead to improved cancer therapies targeting fractionally resistant cells to improve patient outcomes.

cancer biology↗

Magneto-acoustic protein nanostructures for non-invasive imaging of tissue mechanics in vivo

Measuring cellular and tissue mechanics inside intact living organisms is essential for interrogating the roles of force in physiological and disease processes, and is a major goal in the field of mechanobiology. However, existing biosensors for 3D tissue mechanics, primarily based on fluorescent emissions and deformable materials, are limited for in vivo measurement due to the limited light penetration and poor material stability inside intact, living organisms. While magneto-motive ultrasound (MMUS), which uses superparamagnetic nanoparticles as imaging contrast agents, has emerged as a promising modality for real-time in vivo imaging of tissue mechanics, it has poor sensitivity and spatiotemporal resolution. To overcome these limitations, we introduce magneto-gas vesicles (MGVs), a unique class of protein nanostructures based on gas vesicles and magnetic nanoparticles that produces differential ultrasound signals in response to varying mechanical properties of surrounding tissues. These hybrid protein nanostructures significantly improve signal strength and detection sensitivity. Furthermore, MGVs enable non-invasive, long-term, and quantitative measurement of mechanical properties within 3D tissues and organs in vivo. We demonstrated the performance of MGV-based mechano-sensors in vitro, in fibrosis models of organoids, and in vivo in mouse liver fibrosis models.

biochemistry↗

BMP pathway antagonism by Grem1 regulates epithelial cell fate in intestinal regeneration

In the intestine, the homeostatic effect of Bone Morphogenetic Protein (BMP) on cell fate has predominantly been inferred through pathway inactivation. Here, we assessed the impact of autocrine Bmp4 expression on secretory cell fate. Ligand exposure reduced proliferation, expedited terminal differentiation, abrogated long-term secretory cell survival and prevented dedifferentiation. As stem cell plasticity is required for regenerative adaptive reprogramming, we spatiotemporally mapped and functionally explored BMPs role in epithelial restitution. Following ulceration, physiological attenuation of BMP signalling arose through upregulation of the secreted antagonist, Grem1, from topographically distinct populations of stromal cells. Concomitant expression supported functional compensation, following Grem1 deletion from tissue-resident fibroblasts. BMP pathway manipulation showed that antagonist-mediated BMP attenuation was obligatory, but functionally sub-maximal, as regeneration was impaired or enhanced by epithelial overexpression of Bmp4 or Grem1 respectively. Mechanistically, Bmp4 abrogated regenerative stem cell reprogramming, despite a convergent impact of YAP/TAZ on cell fate in remodelled wounds.

cell biology↗

Stabilising selection causes grossly altered but stable karyotypes in metastatic colorectal cancer

Aneuploidy, the loss and gain of whole and part chromosomes, is near-ubiquitous in cancer genomes and likely defines cancer cell biology. However, the temporal evolutionary dynamics that select for aneuploidy remain uncharacterised. Here we perform longitudinal genomic analysis of 755 samples from a total of 167 patients with colorectal-derived neoplastic lesions that represent distinct stages of tumour evolution through metastasis and treatment. Adenomas typically had few copy number alterations (CNAs) and most were subclonal, whereas cancers had many clonal CNAs, suggesting that progression goes through a CNA bottleneck. Individual CRC glands from the same tumour typically had very similar karyotypes, despite evidence of ongoing instability at the cell level in patient tumours, cell lines and organoids. CNAs in metastatic lesions sampled from liver and other organs, after chemotherapy or targeted therapies, and in late recurrences were typically similar to the primary tumour. Mathematical modelling and statistical inference indicated that these data are consistent with the action of negative selection on CNAs that traps cancer cell genomes on a fitness peak defined by the specific pattern of chromosomal aberrations. These data suggest that the initial progression of colorectal cancer requires the traversal of a rugged fitness landscape and subsequent CNA evolution, including metastatic dissemination and therapeutic resistance, is constrained by negative selection.

cancer biology↗

M-current downregulation leads to stellate ganglia sympathetic hyperactivity associated with hypertension

The activity of cardiac sympathetic nerves from the stellate ganglia is increased in many cardiovascular diseases contributing to the pathophysiology, however the mechanisms underlying this are unknown. Moreover, clinical studies show their surgical removal is an effective treatment, despite the biophysical properties of these neurons being largely unstudied. Here we demonstrate that stellate ganglia neurons from prehypertensive spontaneously hypertensive rats are hyperactive and describe in detail their electrophysiological phenotype guided by single cell RNA-sequencing, molecular biology and perforated patch-clamp to uncover the underlying mechanism. The expression of key transcripts was confirmed in human stellate ganglia. We further demonstrate the contribution of a plethora of ion channels to stellate ganglia neuronal firing, and show that hyperexcitability was curbed by M-current activators, non-selective sodium current blockers or inhibition of Nav1.1-1.3, Nav1.6 or INaP. These findings have implications for target discovery to reduce cardiac sympathetic activity without resorting to surgery.

neuroscience↗