Biology subjects

Stanley, E.

Publications and source records attributed to Stanley, E..

7 recordsLinked to original sources

bioRxiv2026

Superposition eyes of diurnal and nocturnal hawkmoths are imperfect spheres and lack acute zones.

Superposition compound eyes improve sensitivity by pooling light from multiple facets and are widespread among nocturnal insects, including moths and beetles. Optical theory predicts that superposition eyes must be nearly spherical to form coherent images and therefore lack highly pronounced acute zones with high spatial resolution. To examine this, we imaged eyes of six hawkmoths (Sphingidae) spanning diurnal and nocturnal activity with high-resolution microcomputed tomography. Our automated pipeline created detailed eye maps quantifying morphological parameters. We measured local eye curvature (radial distance), interommatidial angle ({Delta}{varphi}), facet size and crystalline cone skewness (tilt of cone axes relative to the local surface normal). All species show more curvature in the dorso-ventral plane with flattening in the antero-posterior plane. However, their eyes still retain near-spherical curvature globally, with diurnal species showing greater distortion. For facet parameters, spatial acuity is generally highest (lowest {Delta}{varphi}) near the eye center and decreases gradually toward the periphery. However, overall variation in spatial acuity is low and these eyes lack distinct acute zones. Facet size gradually changes from center to periphery, increasing in some species and decreasing in the others. Cone skewness is present in all six species (0{degrees}-10{degrees}), but in two diurnal species of hummingbird hawkmoths it increases markedly in the posterior region (15{degrees}-30{degrees}) possibly compensating for regional eye flatness. This paper provides foundational data of ommatidial and eye shape measurements and advances our assumptions about how superposition eyes function.

animal behavior and cognition↗

bioRxiv2026

Attenuated interferon signalling in alveolar epithelium limits resistance to Streptococcus pyogenes

The upper respiratory tract is a primary niche for Streptococcus pyogenes colonisation and disease. Lower respiratory tract infection (pneumonia) is the most common invasive S. pyogenes syndrome. Studies have not previously examined how epithelial cells, from the airway to the alveolus, respond to S. pyogenes infection. Here, we established a scalable human in vitro model by differentiating induced pluripotent stem cells (iPSCs) into mature pseudostratified airway epithelium or alveolar type 2 epithelial cells, cultured at air-liquid interface and infected with S. pyogenes (M1UK and M75 strains). Both strains attached to iPSC-derived lung epithelial cells, with significantly greater adherence to the airway epithelium by M75 compared to M1UK. Moreover, invasion by both S. pyogenes strains of alveolar epithelial cells was greater than for the airway epithelium. Dynamic S. pyogenes gene expression changes were evident between 6 and 24 hours after infection, which was influenced by the infected cell type; however, virulence genes were not significantly altered. While infection of the airway epithelium induced rapid and dynamic inflammatory signalling, the alveolar epithelium demonstrated augmented cell death and mounted a transcriptional pro-inflammatory and proliferative response that was uncoupled from cytokine secretion. The airway epithelium model exhibited consistently higher baseline type I interferon (IFN) signalling than the alveolar epithelium. Invasion by S. pyogenes and inflammation was significantly reduced in IFN-{beta}-treated alveolar epithelial cells. In summary, we have established the first model of S. pyogenes infection in physiologically relevant airway and alveolar epithelial cells. Our findings suggest that host responses to infection are influenced by lung compartment, the S. pyogenes strain type, and infection timepoint, highlighting context-specific pathways that could be leveraged therapeutically.

microbiology↗

bioRxiv2025

Spatial Transcriptomics Reveals that the Local Immune Response to Placental Guinea Pig

Cytomegalovirus infection can disrupt placental development and function either by directly infecting placental cells or by eliciting a pathogenic immune response. The relative contributions of these two mechanisms to adverse pregnancy outcomes remains poorly understood. In this study, we used spatial transcriptomics to quantify host and viral gene expression at the maternal-fetal interface at near single-cell resolution. Guinea pig cytomegalovirus (GPCMV) infection after mid-gestation causes focal infections at the base of the main placenta. Samples for spatial transcriptomics were collected from guinea pigs infected with GPCMV at 35 days gestation. Viral loads and the location of infected cells in placentas were assessed using virus-specific droplet digital PCR and in situ hybridization at 21 days post-infection. Representative placentas were sectioned onto Visium Spatial Gene Expression Slides and sequencing libraries were prepared from six infected and six uninfected tissue sections. Spatial transcriptomes from 33,687 55-{micro}m spots were generated and used in subsequent analyses. To assess how infection affected gene expression at the maternal-fetal interface, a combination of graph-based clustering and manual classification was used to assign spatial transcriptomes to clusters representative of different anatomic regions. Infection dysregulated more transcripts in the decidua and junctional zone than in the labyrinth or non-capillarized syncytium. Notably, infection downregulated transcripts involved in lipid metabolism and upregulated transcripts involved in antiviral defense and chemokine signaling. A second analysis compared the spatial transcriptomes of GPCMV-infected cells and their immediate microenvironment with similar regions in uninfected placentas. A transcriptional signature indicative of immune activation was clear in this comparison, and the local placental response to cytomegalovirus infection was driven by upregulated chemokine signaling. Thus, spatial transcriptomics revealed regional patterns of gene expression in the guinea pig placenta and illuminated how the host response to GPCMV may compromise placental function. Author SummaryThe placenta supports fetal development while also acting as an immune barrier against bloodborne pathogens. Cytomegalovirus (CMV), the most common viral cause of congenital infections and preventable neurologic disability in children, evades host defenses to infect the placenta. How CMV affects the placenta and fetal health remains poorly understood. Using a guinea pig model of CMV infection during pregnancy and spatial transcriptomics, a recently-developed method that enables gene expression to be studied at near-cellular resolution, this study compared normal and infected placentas. The effects of infection on directly infected cells and their immediate environment and indirect effects that occur at more distant sites were revealed. This information may inform the development of therapies to improve placental function after CMV infection.

immunology↗

bioRxiv2025

Application of spatial transcriptomics across organoids: a high-resolution spatial whole-transcriptome benchmarking dataset

Stem cell-derived organoids hold promise to model tissue-specific disease. To enable this, it is crucial to assess how transcriptional signatures, cellular organisation and composition of organoids compare to in vivo counterparts. However, technologies which elucidate regional molecular identity, like spatial transcriptomics, have been challenging to apply to organoids. This study presents the first systematic profiling of multiple stem cell derived organoid models (brain, heart muscle, heart valve, kidney, lung, cartilage, and haematopoietic) with Stereo-seq, a full transcriptome, spatial transcriptomics assay using on-chip in situ RNA capture at subcellular resolution. It describes optimisation of this assay to characterise organoids, use of multiple organoid samples on a single chip, assess differences in RNA capture efficiency compared to reference tissues and its limitations. This study introduces a bespoke analysis method that partitions samples into regions and further characterises them. These findings inform future works to characterise organoids using spatial transcriptomics, providing insights in optimising RNA capture of multiple organoids across a chip and novel methods for regional analysis.

bioinformatics↗

bioRxiv2025

Macrophages Mediate Antiviral Immunity and Repair of Type 2 Alveolar Epithelial Cells in a Human Stem Cell Model

The lung alveoli are constantly exposed to inhaled pathogens and inorganic hazards, relying on robust defence mechanisms to maintain homeostasis. Alveolar macrophages and type 2 alveolar epithelial cells (AT2s) collaborate to orchestrate protection. Compromised defence can dysregulate immunity and repair, leading to acute and chronic respiratory diseases. To better understand these processes and drive therapeutic discovery, human model systems that capture key cell interactions are essential. Here, we develop the first induced pluripotent stem cell (iPSC)-derived platform that integrates AT2 cells and macrophages in an air-liquid interface culture. Coculture enhanced AT2-specific gene expression and lipid synthesis, while macrophages actively phagocytosed AT2-derived surfactant. iPSC-derived AT2s supported macrophage survival by producing M-CSF and coculture promoted an alveolar macrophage-like phenotype. Additionally, during respiratory infection macrophages played a crucial role in modulating proinflammatory signalling, enhancing antiviral immunity, and restricting viral replication. Furthermore, we identify a role for iPSC-derived macrophages in epithelial repair, with VEGF signalling to macrophages increasing epithelial permeability. We present an iPSC-derived air-interface platform to study AT2-macrophage interactions in homeostasis, infection, and repair, providing insights into their potential roles in the initiation and progression of respiratory diseases.

cell biology↗

bioRxiv2022

Insights into the evolution of dermal armour: osteoderms in a mammal, the spiny mouse, Acomys.

Osteoderms are bony plates which develop in the dermis of the skin of vertebrates, most commonly found in fishes and reptiles. They have evolved independently at least eight times in reptiles suggesting the presence of a gene regulatory network which is readily activated and inactivated. The absence of osteoderms in birds and mammals, except for the one example of armadillos, has prevented a comparative molecular approach to their evolution. However, following CT scanning, we have discovered that in two genera of Deomyinae, the spiny mouse Acomys and the brush-furred mouse, Lophuromys there are osteoderms present in the skin of their tails. We have studied osteoderm development within the dermis of the tail in Acomys cahirinus to show that they begin development before birth in the proximal part of the tail skin and they do not complete differentiation throughout the tail until 6 weeks after birth. This has allowed us to study the cellular differentiation of the osteoderms with histology and immunocytochemistry and perform RNA sequencing to identify the gene networks involved in their differentiation. There is a widespread down-regulation of keratin genes and an up-regulation of osteoblast genes and a finely balanced expression of signaling pathways as the osteoderms differentiate. Future comparisons with reptilian osteoderms may allow us to understand how these structures have evolved, why they are so rare in mammals and how they are position-specific.

evolutionary biology↗

bioRxiv2020

Single cell resolution of SARS-CoV-2 tropism, antiviral responses, and susceptibility to therapies in primary human airway epithelium

The human airway epithelium is the initial site of SARS-CoV-2 infection. We used flow cytometry and single cell RNA-sequencing to understand how the heterogeneity of this diverse cell population contributes to elements of viral tropism and pathogenesis, antiviral immunity, and treatment response to remdesivir. We found that, while a variety of epithelial cell types are susceptible to infection, ciliated cells are the predominant cell target of SARS-CoV-2. The host protease TMPRSS2 was required for infection of these cells. Importantly, remdesivir treatment effectively inhibited viral replication across cell types, and blunted hyperinflammatory responses. Induction of interferon responses within infected cells was rare and there was significant heterogeneity in the antiviral gene signatures, varying with the burden of infection in each cell. We also found that heavily infected secretory cells expressed abundant IL-6, a potential mediator of COVID-19 pathogenesis.

microbiology↗