Biology subjects

Mills, B.

Publications and source records attributed to Mills, B..

7 recordsLinked to original sources

bioRxiv2026

A Human Precision Cut Kidney Slice Platform for Studying Glomerular Biology and Therapeutic Responses

Introduction: Short term human precision cut kidney slice cultures (PCKS) represent a tractable experimental that contains mature kidney cell types within their native anatomic context and that can be manipulated in vitro. In this study, we employ genomic tools to analyze the PCKS response to culture conditions and their suitability for study of glomerular disease biology. Methods: The impact of culture medium and oxygenation on PCKS viability and gene expression was explored using spatial transcriptomics and traditional histologic approaches. The biological response of PCKS to IFN{gamma} stimulation and signaling suppression by the JAK1/2 inhibitor baricitinib were also explored. Results: A genome wide atlas of glomerular and tubulointerstitial gene expression patterns was generated from PCKS cultured in different media and oxygenation conditions and at various timepoints in culture. IFN{gamma} induced APOL1 gene and protein expression in glomeruli, which could be suppressed by baricitinib. Expression changes were reproducible in PCKS derived from multiple donors. Conclusions: PCKS are reproducibly responsive to IFN{gamma} stimulation, which will allow dissection of APOL1 mediated glomerular disease mechanisms in a human tissue model system. Spatial transcriptomic profiling of tissue responses helps to tailor culture medium/oxygenation to optimize the PCKS system to address specific biological questions.

cell biology↗

bioRxiv2026

Endomicroscopic fluorescence lifetime imaging enables molecular detection and targeted sampling in the distal human lung

PurposeAccurate molecular characterisation of infection and inflammation within the distal human lung remains challenging, particularly in critically ill patients, due to limited access to the alveolar space and delayed diagnostic workflows. Molecular imaging approaches capable of real-time detection and targeted sampling could substantially improve diagnostic precision and the future translational development of molecular imaging probes and therapeutics. MethodsIn a preclinical setting, we evaluated a clinic-ready endomicroscopic fluorescence lifetime imaging microscopy (eFLIM) platform combined with molecularly targeted SmartProbes for in situ detection of bacteria and activated neutrophils in the distal human lung. A multifunctional 1.9-mm diameter imaging and sampling catheter (Eyes on Target; EoT) enabled real-time fluorescence intensity and lifetime imaging alongside directed alveolar microlavage via a 1.2-mm working channel. Fluorescence intensity and lifetime signatures of Gram-negative bacteria, Gram-positive bacteria, and activated neutrophils were characterised using three wash-free SmartProbes: NBD-PMX, Merocy-Van, and a neutrophil activation probe (NAP). Imaging and sampling performance were assessed in ventilated ex vivo human lungs. ResultsEoT reliably navigated to alveolar regions across all lung lobes in both phantom and ventilated human lung models. eFLIM distinguished alveolar microanatomy and enabled probe-specific molecular detection within the distal lung. Increased NBD-PMX signal was detected in Escherichia coli-instilled lobes, while Merocy-Van lifetime signatures selectively identified Staphylococcus aureus-instilled regions. Activated neutrophils were detected throughout lung tissue following NAP administration. Directed alveolar microlavage enabled recovery of cellular material and bacterial DNA from imaged regions for downstream analysis. ConclusioneFLIM using EoT combined with molecular SmartProbes enables real-time molecular imaging and targeted sampling within the distal human lung. This platform provides a translatable approach for evaluating infection and inflammation at the alveolar level and supports the clinical development of molecular imaging probes for pulmonary disease.

microbiology↗

bioRxiv2026

Development and evaluation of a pan-fungal lateral flow device for the rapid identification of pathogen class in microbial keratitis

PurposeTo develop a pan-fungal lateral flow device (LFD); evaluating device performance with samples obtained from ex vivo porcine cornea infection models. MethodsFungal {beta}-glucan (PF1), human CLEC7A/Dectin-1/CLECSF12 protein (Fc Tag; PF2), and fungal melanin (PF3) antibodies were evaluated for binding to clinically relevant fungal and bacterial species (Aspergillus flavus, Fusarium keratoplasticum, Candida albicans, Pseudomonas aeruginosa, Staphylococcus aureus) by immunofluorescence staining. PF1 and PF2 were evaluated in proof-of-concept, in-house LFD strips using cultured pathogens and ex vivo porcine corneal infection samples. The lead antibody (PF1) was validated in a commercially-developed prototype LFD. ResultsPF1 and PF2 discriminated target fungi from bacteria by immunofluorescence microscopy and in-house LFD strips. The lead candidate PF1 demonstrated good sensitivity (0.75) and specificity (0.94) with cultured fungal hyphae. Samples obtained from infected ex vivo cornea by clinically relevant methods confirmed excellent sensitivity (scrapes: 1.00, swabs: 0.94) and specificity (scrapes: 1.00, swabs: 0.83). The commercially-developed PF1-LFD prototype achieved perfect sensitivity (1.00) and specificity (1.00) when detecting and discriminating fungi from non-fungal ex vivo corneal swab samples. ConclusionsFeasibility of pan-fungal LFD application in microbial keratitis diagnosis was demonstrated - using {beta}-glucan as a pan-fungal target and a clinically relevant microbial keratitis ex vivo model. LFDs were able to differentiate fungal from bacterial samples, detect antigen present in corneal swabs, and provide a read-out within 20 minutes. Sensitivity and specificity values are comparable to currently used diagnostic tests. Translational RelevanceEarly discrimination of fungal keratitis cases is important to adapt treatment, and improve patient outcome.

microbiology↗

bioRxiv2025

INDITEK-2.0: A Bayesian inverse eco-evolutionary modelling framework for reconstructing Phanerozoic biodiversity

O_LIMechanistic eco-evolutionary models are powerful tools for understanding how life diversified over geological timescales, yet estimating their parameters remains a key challenge. The high computational requirements of these models make probabilistic inversion methods unfeasible. C_LIO_LIWe address this challenge with INDITEK-2.0, a new, cost-efficient eco-evolutionary model that integrates a Bayesian inverse modelling framework for probabilistic estimation of parameters. C_LIO_LITo validate this framework, we conducted a proof-of-concept study. We first generated synthetic biodiversity data for marine invertebrates using INDITEK-2.0 with known parameter values. To mimic field data, some realistic random Gaussian errors were added to the data. We then used our Bayesian inverse modelling framework to recover these original (true) parameter values from the dataset of current biodiversity distributions after 500 million years of diversification. Our solution is a probability distribution on the parameter space, and we show that the method successfully recovered the target parameter values with a relatively low degree of uncertainity. C_LIO_LIINDITEK-2.0s ability to probabilistically infer underlying eco-evolutionary processes provides a new modelling tool for reconstructing the evolutionary history of biodiversity across Earths ecosystems and taxonomic groups. C_LI

ecology↗

bioRxiv2025

Far-Ultraviolet Light Causes Direct DNA Damage in Human Lung Cells and Tissues

Far-ultraviolet C (Far-UVC) radiation, with a wavelength range from 200 to 235 nm, is germicidal and holds potential for clinical applications. However, its use against deep-seated and internal infections, such as those affecting the lungs, remains less well established. The safety profile of Far-UVC irradiation requires further investigation across different human tissues. In this study, we utilised a krypton-chloride (KrCl) excimer lamp and a pulsed laser system to examine the effects of Far-UVC irradiation on human lung cells in vitro and primary human tracheal tissue. Primary human tracheal tissue and cells exposed to continuous wave (222 nm) and pulsed 206 nm and 222 nm light at doses of 5, 25, and 50 mJ/cm2 exhibited Deoxyribonucleic acid (DNA) damage, including phosphorylation of {gamma}H2AX (Ser139). The continuous wave and pulsed 222 nm irradiation caused the formation of pyrimidine-pyrimidone (6-4) photoproducts. Irradiated human lung cells demonstrated reduced viability in vitro, and increased lactate dehydrogenase release into the culture medium 48 hours post-irradiation. Our findings reveal that even low doses of Far-UVC (206 nm, 222 nm) light can penetrate monolayers of human lung epithelial cells, causing direct DNA damage in the form of (6-4) photoproducts and DNA double-strand breaks, ultimately leading to cell death.

cell biology↗

bioRxiv2023

Canary in the Forest? Tree mortality and canopy dieback of western redcedar linked to drier and warmer summer conditions

Tree mortality and partial canopy dieback are increasing in many forest ecosystems from unfavorable climate conditions. Examining how tree growth and mortality are affected by climate variability can help identify proximate causes of tree mortality and canopy dieback. We investigated anomalously high mortality rates and partial canopy dieback of western redcedar (Thuja plicata, WRC), a culturally, ecologically, and economically important species in the Pacific Northwest (USA), using tree-ring methods. We sampled trees in three tree status groups--no canopy dieback, partial canopy dieback, and trees that died (0-30 years ago)--from 11 sites in coastal (maritime climate) and interior (continental climate) populations of WRC trees. In our study, WRC tree mortality was portended by on average 4-5 years of declining radial growth. Warmer and drier climate conditions in May and June that extend the annual July-September dry season reduced radial growth in 9 of 11 sites (1975-2020). Defining drought events as warm, dry May-June climate, we found that WRC trees recovered radial growth to pre-drought rates within three years when post-drought climate conditions were average or cooler and wetter than average. However, radial growth recovery from drought was slower or absent when conditions were warmer and drier during the post-drought recovery period, which appeared to lead to the widespread mortality event across coastal populations. Annually resolved tree mortality in coastal populations predominately occurred in 2017-2018 (80% of sampled trees) and coincided with exceedingly hot temperatures and the longest regionally dry period for May to September (1970-2020). In interior populations, tree mortality was associated with warmer, drier conditions from August to September. Our findings forewarn that a warming climate and more frequent and severe seasonal droughts will likely increase the vulnerability of WRC to canopy dieback and mortality and possibly other drought-sensitive trees in one of the worlds largest carbon sinks.

ecology↗

bioRxiv2020

Dual Energy X-ray Absorptiometry (DEXA) as a Longitudinal Outcome Measure of Cancer-Related Muscle Wasting in Mice

IntroductionPancreatic ductal adenocarcinoma (PDAC) is notorious for its associated skeletal muscle wasting (SMW) and mortality. Currently, the relationships between PDAC, SMW, and survival are poorly understood. Thus, there is a great need for a faithful small animal model with a quantitative longitudinal outcome measure that recapitulates clinical PDAC, to define SMW onset and assess progression. Therefore, we aimed to validate dual energy X-ray absorptiometry (DEXA) as a longitudinal outcome of lean body mass, and demonstrate its utility to quantify SMW in the KCKO murine model of PDAC. MethodsIn vivo body composition of: 1) untreated mice at 5, 8, 12, 18, and 22 weeks of age (n=4), and 2) a cohort of mice with (n=20) and without PDAC (n=10), was determined via DEXA, and lean mass of the lower hind limbs was predicted via a region of interest analysis by two independent observers. Total body weight was determined. Tibialis anterior (TA) muscles were weighed and processed for histomorphometry immediately post-mortem. Statistical differences between groups were assessed using t-tests and ANOVA. Linear regression models and correlation analysis were used to measure the association between TA and DEXA mass, and reproducibility of DEXA was quantified via the intraclass correlation coefficient (ICC). ResultsLean mass in growing untreated mice determined by DEXA correlated with TA mass (r2 = 0.94; p <0.0001) and body weight (r2 = 0.89; p <0.0001). DEXA measurements were highly reproducible between observers (ICC = 0.95; 95% CI: 0.89-0.98). DEXA and TA mass also correlated in the PDAC cohort (r2 = 0.76; p <0.0001). Significant SMW in tumor-bearing mice was detected within 38 days of implantation by DEXA, TA mass, and histomorphometry. ConclusionsDEXA is a longitudinal outcome measure of lower limb lean mass in mice. The KCKO syngeneic model is a bona fide model of PDAC-associated SMW that can be quantified with longitudinal DEXA.

cancer biology↗