Biology subjects

Forster, R.

Publications and source records attributed to Forster, R..

8 recordsLinked to original sources

bioRxiv2026

The City Nature Challenge increases urban biodiversity knowledge and public engagement with blue spaces

Global biodiversity is declining at an unprecedented rate due to rapid environmental change and increasing human pressures. Ongoing urban expansion fragments natural systems, while urban design increasingly seeks to mitigate these impacts through the integration of blue-green infrastructure. Effective biodiversity monitoring is therefore essential to evaluate ecological conditions within these novel socio-ecological systems. Although urban biodiversity monitoring is challenged by its high landscape heterogeneity, dense human populations provide opportunities for large-scale data collection through public participation in citizen science. Using data from 25 City Nature Challenge (CNC) projects across the United Kingdom (2020-2025), we assessed the effects of the four-day bioblitz on species inventories, participation in biological recording, and spatial patterns of recording effort. CNC events doubled public participation in iNaturalist recording relative to baseline activity, leading to the documentation of numerous previously unrecorded species through increased observer effort and broader use of urban blue-green spaces. These results show that CNC events enhance urban biodiversity datasets by increasing the number of observers and reducing spatial and observer biases, providing a cost-effective tool for enriching urban biodiversity data. In addition to generating ecological data, CNC events could have public health benefits through increased exposure to urban blue-green spaces.

ecology↗

bioRxiv2025

Accessible AI Enhances Monitoring of Coral Seeding Devices in Reef Restoration

1. Coral seeding devices (CSDs) - tools designed to deliver sexually propagated corals to target locations - offer a promising means to increase coral abundance on degraded reefs. However, evaluating CSD effectiveness for coral reef restoration across wide areas and over many years is limited by the lack of robust and efficient monitoring approaches. Large-area reef imagery offers an attractive potential solution, but manual detection of CSDs within imagery is slow and limits the scalability of CSD monitoring. 2. We investigated whether machine learning classifiers could accurately detect CSDs in reef orthoimages and tested the performance of classifiers created following minimal manual annotation effort. Using freely available software, we first evaluated classifier performance in a single-site experiment using an orthoimage containing 989 CSDs deployed in Palau. We then also evaluated performance in a multi-site experiment using orthoimages containing a different CSD design deployed across seven sites in the central Great Barrier Reef, Australia. 3. In Experiment 1, classifiers trained on just 30 CSDs annotated within 10 minutes achieved mean recall and precision of 96.7% and 97.1% respectively, reducing manual annotation time by 95.6% whilst still detecting 98.8% of the number of devices found manually. Larger training sets yielded less reliable classifiers and required more manual effort. In Experiment 2, classifiers trained on 30 CSD annotations from one site performed excellently across seven orthoimages from multiple reefs, achieving mean recall and precision of 99.2% and 93.3%. 4. We present evidence that CSD classifiers can be highly effective across both single- and multi-site CSD deployments. In using a free and user-friendly software, we also demonstrate their accessibility to reef restoration practitioners. To facilitate wider uptake of CSD monitoring, we provide a step-by-step protocol for implementing CSD classifiers. By improving access to efficient, direct assessment of intervention outcomes, this method can play a vital role in guiding the enhancement of approaches aiming to restore coral reefs.

ecology↗

bioRxiv2024

Herpes Simplex Virus Assembly and Spread in murine skin after infection from the outside

Herpes simplex viruses (HSV) cause many skin diseases, particularly in immunocompromised patients. HSV-1 infection of murine skin recapitulates many aspects of human pathology. However, many protocols rely on mechanical or enzymatic skin disruption to induce lesions, although this can alter skin homeostasis and prime antiviral inflammation before inoculation. To investigate the initial events following HSV-1 primary skin infection before the onset of symptoms, we developed a novel murine ex vivo explant model using gentle depilation but no further scarification and infected keratinocytes from the outside with minimal tissue damage. Two-photon microscopy studies showed that HSV-1 spread exclusively in the epidermis. The infection centers increased in number and size over time and contained hundreds of infected keratinocytes. We investigated the HSV-1 spread at the cellular level, using reporter strains with fluorescently-tagged capsid protein VP26, and monitored the formation of nuclear capsid assembly sites, nuclear capsid egress, and the recruitment of the inner tegument protein pUL37GFP, the outer tegument protein VP11/12GFP, and the envelope protein gDGFP to cytoplasmic capsids. By electron microscopy, the skin appeared intact, and keratinocytes contained many nuclear capsids, primary virions in the nuclear envelope, cytosolic membrane-associated capsids, and enveloped virions. Our protocol provides a robust and reproducible approach to investigate the very early events of HSV-1 spread in the skin, to characterize the phenotypes of HSV-1 mutants in terminally differentiated skin tissues, and to evaluate potentially antiviral small molecules in a preclinical ex vivo infection model. IMPORTANCEThis study describes a novel murine ex vivo skin explant model to investigate early events in HSV-1 infection without causing significant tissue damage. To infect from the outside, via the apical keratinocytes, this method relies on gentle depilation, which maintains skin integrity. HSV-1 spread exclusively within the epidermis, with infection centers growing over time and involving hundreds of keratinocytes. Using advanced microscopy techniques, we tracked HSV-1 spread at the cellular level and intracellular assembly of all intermediate virus structures. This model offers a valuable tool for studying the initial stages of HSV-1 infection, assessing viral mutant phenotypes, and testing antiviral compounds in a more physiological context to provide critical insights into HSV-1 pathogenesis and therapeutic strategies.

microbiology↗

bioRxiv2024

Different CMV-specific effector T cell subtypes are associated with age, CMV serostatus, and increased systolic blood pressure

Cytomegalovirus (CMV) infection is one of the most common infections in humans, and CMV antigens are the major drivers of repetitive T-cell stimulation as a part of a well-adapted immune response in immunocompetent individuals. With higher age, the recurrent clonal expansion of CMV-specific T cells results in high frequencies of CMV-specific effector T cells. CMV seropositivity has also been linked to arterial stiffness and an increased risk of developing cardiovascular diseases (CVD). The RESIST Senior Individuals (SI) cohort is a population-based cohort with focus on the elderly, established to shed light on the age-related changes of the immune system and the accompanied reduced capability to fight infectious diseases. Here we investigated the frequency and phenotype of CMVpp65-specific CD8+ T cells in the circulation of individuals of different age groups by means of MHC-I tetramer staining and their associations with age and associated factors such as serostatus and blood pressure. In the SI cohort, the frequency of CMV-specific T cells within the CD8+ T cell fraction was increased with age, as previously reported. We add to previous knowledge by showing that this frequency is associated with the total percentage and absolute counts of CD8+ and CD4+CD8+ double-positive T cells within leukocytes. Systolic blood pressure (SBP) and history of CVD correlated with the frequency of CMV-specific CD8+ T cells. Focusing on CMV-specific T cell subtypes, we show here that the frequencies of TEM and CD27-expressing TEMRA cells were associated with higher age. TEM and CD27- TEMRA cell frequencies were increased in donors with high CMV-IgG titers. Furthermore, SBP significantly correlated with CMV-specific effector CD8+ T cells, which was mostly reflected by CD27- TEMRA cells. In conclusion, different effector T-cell subtypes were associated with age, serostatus and SBP, suggesting that it is not age per se that renders elderly CMV-positive individuals susceptible to CVD, but the immune response to CMV. Our study suggests that detailed immunophenotyping may identify individuals whose immune systems are strongly influenced by the response to CMV, leading to health consequences and impairing healthy aging.

immunology↗

bioRxiv2023

Mechanisms of SARS-CoV-2 Inactivation using UVC Laser Radiation

Severe acute respiratory syndrome coronavirus 2 (SARS-Cov-2) has had a tremendous impact on humanity. Prevention of transmission by disinfection of surfaces and aerosols through a chemical-free method is highly desirable. Ultraviolet C (UVC) light is uniquely positioned to achieve inactivation of pathogens. We report the inactivation of SARS-CoV-2 virus by UVC radiation and explore its mechanisms. A dose of 50mJ/cm2 using a UVC laser at 266nm achieved an inactivation efficiency of 99.89%, whilst infectious virions were undetectable at 75mJ/cm2 indicating >99.99% inactivation. Infection by SARS-CoV-2 involves viral entry mediated by the spike glycoprotein (S), and viral reproduction, reliant on translation of its genome. We demonstrate that UVC radiation damages ribonucleic acid (RNA) and provide in-depth characterisation of UVC-induced damage of the S protein. We find that UVC severely impacts SARS-CoV-2 spike proteins ability to bind human angiotensin-converting enzyme 2 (hACE2) and this correlates with loss of native protein conformation and aromatic amino acid integrity. This report has important implications for the design and development of rapid and effective disinfection systems against the SARS-CoV-2 virus and other pathogens.

microbiology↗

bioRxiv2020

Label-free and Multimodal Second Harmonic Generation Light Sheet Microscopy

Light sheet microscopy (LSM) has emerged as one of most profound three dimensional (3D) imaging tools in the life sciences over the last decade. However, LSM is currently performed with fluorescence detection on one- or multi-photon excitation. Label-free LSM imaging approaches have been rather limited. Second Harmonic Generation (SHG) imaging is a label-free technique that has enabled detailed investigation of collagenous structures, including its distribution and remodelling in cancers and respiratory tissue, and how these link to disease. SHG is generally regarded as having only forward- and back-scattering components, apparently precluding the orthogonal detection geometry used in Light Sheet Microscopy. In this work we demonstrate SHG imaging on a light sheet microscope (SHG-LSM) using a rotated Airy beam configuration that demonstrates a powerful new approach to direct, without any further processing or deconvolution, 3D imaging of harmonophores such as collagen in biological samples. We provide unambiguous identification of SHG signals on the LSM through its wavelength and polarisation sensitivity. In a multimodal LSM setup we demonstrate that SHG and two-photon signals can be acquired on multiple types of different biological samples. We further show that SHG-LSM is sensitive to changes in collagen synthesis within lung fibroblast 3D cell cultures. This work expands on the existing optical methods available for use with light sheet microscopy, adding a further label-free imaging technique which can be combined with other detection modalities to realise a powerful multi-modal microscope for 3D bioimaging.

biophysics↗

bioRxiv2020

Application of Airy beam Light sheet microscopy to examine early neurodevelopmental structures in 3D hiPSC-derived human cortical spheroids

BackgroundThe inability to observe relevant biological processes in vivo significantly restricts human neurodevelopmental research. Advances in appropriate in vitro model systems, including patient-specific human brain organoids and human Cortical Spheroids (hCSs) offer a pragmatic solution to this issue. In particular, hCSs are an accessible method of generating homogenous organoids of dorsal telencephalic fate, which recapitulate key aspects of human corticogenesis, including the formation of neural rosettes. These neurogeneic niches give rise to neural progenitors that subsequently differentiate into neurons. Atypical formation of these structures has been associated with neurodevelopmental disorders such as autism spectrum conditions, from studies of patient-specific human induced pluripotent stem cells grown as 2D cultures. Thus far however, conventional methods of tissue preparation in this field limit the ability to image these structures in three-dimensions within intact hSC or other 3D preparations. To overcome this limitation, we have sought to optimise a methodological approach to process hCSs to maximise the utility of a novel Airy-beam light sheet microscope (ALSM) to acquire high resolution volumetric images of internal structures within hCS representative of early developmental time points. ResultsConventional approaches to imaging hCS by confocal microscopy were limited in their ability to image effectively into intact spheroids. Conversely, volumetric acquisition by ALSM offered superior imaging through intact, non-clarified, in vitro tissues, in both speed and resolution as compared to conventional confocal imaging systems. Furthermore, optimised immunohistochemistry and optical clearing of hCSs afforded improved imaging at depth. This permitted visualization of the morphology of the inner lumen of neural rosettes. ConclusionWe present an optimized methodology that takes advantage of an ALSM system that can rapidly image intact 3D brain organoids at high resolution while retaining a large field of view. This imaging modality can be applied to both non-cleared and cleared in vitro human brain spheroids derived from hiPSCs for precise examination of their internal 3D structures. Furthermore, this process represents a rapid, highly efficient method to examine and quantify in 3D the formation of key structures required for the coordination of neurodevelopmental processes in both health and disease states. We posit that this approach would facilitate investigation of human neurodevelopmental processes.

neuroscience↗

bioRxiv2018

Observing the Cell in Its Native State: Imaging Subcellular Dynamics in Multicellular Organisms

True physiological imaging of subcellular dynamics requires studying cells within their parent organisms, where all the environmental cues that drive gene expression, and hence the phenotypes we actually observe, are present. A complete understanding also requires volumetric imaging of the cell and its surroundings at high spatiotemporal resolution without inducing undue stress on either. We combined lattice light sheet microscopy with two-channel adaptive optics to achieve, across large multicellular volumes, noninvasive aberration-free imaging of subcellular processes, including endocytosis, organelle remodeling during mitosis, and the migration of axons, immune cells, and metastatic cancer cells in vivo. The technology reveals the phenotypic diversity within cells across different organisms and developmental stages, and may offer insights into how cells harness their intrinsic variability to adapt to different physiological environments.\n\nOne Sentence SummaryCombining lattice light sheet microscopy with adaptive optics enables high speed, high resolution in vivo 3D imaging of dynamic processes inside cells under physiological conditions within their parent organisms.

cell biology↗