Biology subjects

Milne, S.

Publications and source records attributed to Milne, S..

6 recordsLinked to original sources

bioRxiv2026

Junctional Nanodomains Organised by Extended Synaptotagmin-1 Underlie Inflammatory Signalling in Sensory Neurons

Endoplasmic reticulum-plasma membrane (ER-PM) junctions coordinate Ca2+ signalling and nociceptor excitability during inflammation, but the molecular scaffold governing assembly of signalling complexes remains unclear. Here, we identify Extended Synaptotagmin-1 (Esyt1) as a key, dynamic regulator of inflammatory pain signalling. In nociceptive DRG neurons, Esyt1 is co-expressed with ANO1 and IP3R1. Time-resolved proximity ligation assays and super-resolution microscopy showed that bradykinin rapidly increased ANO1-Esyt1 nanoscale proximity, while IP3R1-Esyt1 interactions were dynamically reorganised during ANO1-IP3R1 complex formation. Esyt1 knockdown reduced bradykinin-evoked ANO1 activity, impaired store-operated Ca2+ entry (SOCE), decreased STIM1-Orai1 complex formation, and disrupted ER Ca2+ store refilling. Simultaneous imaging of Ca2+ dynamics and ANO1 activity demonstrated functional coupling between SOCE and ANO1 that required Esyt1. Furthermore, in-vivo Esyt1-knockdown significantly reduced bradykinin-induced nocifensive behaviour. Together, these findings identify Esyt1 as a Ca2+-responsive scaffold that organises ER-PM signalling nanodomains and promotes inflammatory pain signalling.

neuroscience↗

bioRxiv2025

Stand age drives changes in the biodiversity and microclimate of oil palm plantations

Tree plantation age strongly dictates its environment. As they mature, the canopy closes and habitat complexity tends to increase, which in turn affects biodiversity. However, for oil palm, one of the most important and widespread tree plantations, we lack a detailed understanding of how this process affects microclimate and biodiversity. We therefore compiled environmental and biodiversity data of oil palm plantations that were repeatedly sampled over a 6 year period in Malaysian Borneo. Using these data, we made a chronosequence of the microclimate and biodiversity of oil palm plantations between the ages 5 and 18. We found that oil palm plantations increasingly buffer temperature and humidity over time, becoming cooler and less dry. Animal responses differed between taxa: spider and beetle abundance increased, ant abundance decreased, and mammal and dung-beetle abundances stayed constant. The diversity of beetles in general increased and family-level community composition changed, while dung-beetle and mammal diversity stayed constant. Some taxa are therefore likely limited by the harsh microclimate of young plantations, while increased habitat complexity and fruit and leaf production in older plantations could also drive increased abundances of other taxa. Our results reveal that oil palm plantations undergo considerable changes, even over a decade after establishment. Correspondingly, plantation age should be considered in studies into oil palm plantations impact on climate and biodiversity, and landscape level diversity could be increased by allowing multiple oil palm stand-ages to co-exist.

ecology↗

bioRxiv2023

Single-cell RNA-sequencing of bronchoscopy specimens: development of a rapid, minimal-handling protocol

Single-cell RNA-sequencing (scRNA-seq) is an important tool for understanding disease pathophysiology, including airways diseases. Currently, the majority of scRNA-seq studies in airways diseases have used invasive methods (airway biopsy, surgical resection) which carry inherent risks and thus present a major limitation to scRNA-seq investigation of airway pathology. Bronchial brushing, where the airway mucosa is sampled using a cytological brush, is a viable, less invasive method of obtaining airway cells for scRNA-seq. Here we are describing the development of a rapid and minimal-handling protocol for preparing single cell suspensions from bronchial brush specimens for scRNA-seq. Our optimized protocol maximises cell recovery and cell quality, and may facilitate large-scale profiling of the airway transcriptome at single cell resolution. Lay abstractSingle-cell RNA-sequencing (scRNA-seq) measures the gene expression of individual cells, and may be useful for understanding disease processes. scRNA-seq may be used to investigate lung diseases, but using invasive methods such as biopsy or surgery limits our ability to conduct large research studies. Bronchial brushing, where a soft brush is used to collect cells from inside the lungs, is a safer method but we need a better way to isolate individual cells from the brush specimens. We developed a method that is faster and involves less handling of the specimens compared to other published methods. Our method may therefore be useful for conducting large scRNA-seq studies in lung diseases.

genomics↗

bioRxiv2022

Logging alters tropical forest structure, while conversion reduces biodiversity and functioning

The impacts of degradation and deforestation on tropical forests are poorly understood, particularly at landscape scales. We present an extensive ecosystem analysis of the impacts of logging and conversion of tropical forest to oil palm from a large-scale study in Borneo, synthesizing responses from 82 variables categorized into four ecological levels spanning a broad suite of ecosystem properties: 1) structure and environment, 2) species traits, 3) biodiversity, and 4) ecosystem functions. Responses were highly heterogeneous and often complex and non-linear. Variables that were directly impacted by the physical process of timber extraction, such as soil structure, were sensitive to even moderate amounts of logging, whereas measures of biodiversity and ecosystem functioning were generally resilient to logging but more affected by conversion to oil palm plantation. One-Sentence SummaryLogging tropical forest mostly impacts structure while biodiversity and functions are more vulnerable to habitat conversion.

ecology↗

bioRxiv2020

Gene Expression Network Analysis Provides Potential Targets Against SARS-CoV-2

ABSTRACTBACKGROUND Cell entry of SARS-CoV-2, the novel coronavirus causing COVID-19, is facilitated by host cell angiotensin-converting enzyme 2 (ACE2) and transmembrane serine protease 2 (TMPRSS2). We aimed to identify and characterize genes that are co-expressed with ACE2 and TMPRSS2, and to further explore their biological functions and potential as druggable targets.METHODS Using the gene expression profiles of 1,038 lung tissue samples, we performed a weighted gene correlation network analysis (WGCNA) to identify modules of co-expressed genes. We explored the biology of co-expressed genes using bioinformatics databases, and identified known drug-gene interactions.RESULTS ACE2 was in a module of 681 co-expressed genes; 12 genes with moderate-high correlation with ACE2 (r>0.3, FDR<0.05) had known interactions with existing drug compounds. TMPRSS2 was in a module of 1,086 co-expressed genes; 15 of these genes were enriched in the gene ontology biologic process ‘Entry into host cell’, and 53 TMPRSS2-correlated genes had known interactions with drug compounds.CONCLUSION Dozens of genes are co-expressed with ACE2 and TMPRSS2, many of which have plausible links to COVID-19 pathophysiology. Many of the co-expressed genes are potentially targetable with existing drugs, which may help to fast-track the development of COVID-19 therapeutics.Competing Interest StatementS.M. reports personal fees from Novartis and Boehringer-Ingelheim, outside the submitted work. W.T. reports fees to Institution from Roche-Ventana, AbbVie, Merck-Sharp-Dohme and Bristol-Myers-Squibb, outside the submitted work. M.B. reports research grants paid to University from Astra Zeneca, Novartis, outside the submitted work. D.D.S. reports research funding from AstraZeneca and received honoraria for speaking engagements from Boehringer Ingelheim and AstraZeneca over the past 36 months, outside of the submitted work.View Full Text

genomics↗

bioRxiv2019

The protective effect of club cell secretory protein (CC-16) on COPD risk and progression: a Mendelian randomisation study

BackgroundThere are currently no robust biomarkers of chronic obstructive pulmonary disease (COPD) risk or progression. Club cell secretory protein-16 (CC-16) is associated with the clinical expression of COPD. We aimed to determine if there is a causal effect of serum CC-16 level on COPD risk and/or progression using Mendelian randomisation (MR) analysis. MethodsWe performed a genome-wide association meta-analysis for serum CC-16 in two COPD cohorts (Lung Health Study [LHS], n=3,850 and ECLIPSE, n=1,702). We then used the CC-16-associated single-nucleotide polymorphisms (SNPs) in MR analysis to estimate the causal effect of serum CC-16 on COPD risk (International COPD Genetics Consortium/UK-Biobank dataset; n=35,735 cases, n=222,076 controls) and progression (change in forced expiratory volume in 1 s [FEV1] in LHS and ECLIPSE). We also determined the associations between SNPs associated with CC-16 and gene expression using n=1,111 lung tissue samples from the Lung eQTL Study. ResultsWe identified 7 SNPs independently associated (p<5x10-8) with serum CC-16 levels; 6 of these were novel. MR analysis suggested a protective causal effect of increased serum CC-16 on COPD risk (p=0.008) and progression (LHS only, p=0.02). Five of the SNPs were also associated with gene expression in lung tissue, including that of the CC-16-encoding gene SCGB1A1 (false discovery rate<0.1). ConclusionWe have identified several novel genetic variants associated with serum CC-16 level in COPD cohorts. These genetic associations suggest a potential causal effect of serum CC-16 on COPD risk and progression. Further investigation of CC-16 as a biomarker or therapeutic target in COPD is warranted. KEY MESSAGESWhat is the key question? Can genetics help uncover a causal effect of serum CC-16 level on COPD risk and/or progression? What is the bottom line? There is a protective effect of genetically-increased serum CC-16 on both COPD risk and progression (as measured by change in FEV1 over time), which may be due to increased expression of the CC-16-encoding gene SCGB1A1 in the lung. Why read on? This is the first study to demonstrate a possible causal effect of serum CC-16 in people with COPD, and highlights the potential for CC-16 as a biomarker or therapeutic target.

genomics↗