Biology subjects

Thorpe, S.

Publications and source records attributed to Thorpe, S..

13 recordsLinked to original sources

bioRxiv2026

Continuous mass photometry by single molecule trapping

The dynamic choreography of biomolecular interactions underpins the processes of life, but its direct observation remains challenging. Here, we introduce confined diffusion mass photometry, enabling hour-long, mass-resolved observation of individual biomolecules, their complexes and interactions with up to sub-kDa mass precision and ms temporal resolution. Our approach represents a quantitative time-resolved single-molecule measurement modality for studying complex biomolecular mechanisms in action.

biophysics↗

bioRxiv2026

Conditioning dentinal collagen by glycation improves long-term bond strength

ObjectivesThis study examined methylglyoxal (MGO) as a collagen crosslinker to reinforce demineralized dentin, enhance its enzymatic resistance, and improve long-term durability of the resin-dentin bond. MethodsDemineralized dentinal collagen films were treated with 0.5, 1, or 3 M MGO and subsequently exposed to collagenase to assess their resistance to enzymatic degradation. MGO-induced crosslink formation was monitored using Attenuated Total Reflectance-Fourier Transform Infrared spectroscopy (ATR-FTIR) spectroscopy by tracking the carbohydrate-associated band at 1180 cm-{superscript 1}. The apparent elastic modulus of the treated specimens was measured using a three-point bending test. For bond strength evaluation, resin-dentin beams were prepared and tested using microtensile bond strength (TBS) to assess the influence of MGO pretreatment on interfacial adhesion. ResultsThe ATR-FTIR spectra demonstrated increased intensity in the carbohydrate double bands (1000-1180 cm-{superscript 1}) in glycated samples compared to the control. Glycation with 3 M MGO exhibited the highest resistance to enzymatic degradation, persisting for up to 60 hours with a 78-fold increase in resistance factor compared to the control group (p < 0.05). Furthermore, glycation with 3 M MGO resulted in a 4-fold increase in elastic modulus compared with the control group. Notably, the functionalized dentin retained its improved mechanical properties even after collagenase exposure, whereas the control group experienced a significant 68.2% reduction in elastic modulus (p = 0.002). While MGO pretreatment did not influence resin infiltration or initial TBS ({approx}30-35 MPa), it maintained its original bond strength after one month of collagenase challenge. In contrast, the control group exhibited a significant reduction, decreasing to 17 {+/-} 5.5 MPa compared with its initial value (p < 0.01). ConclusionMGO demonstrated efficacy in enhancing the mechanical properties and enzymatic stability of collagen as well as improving the resistance of the bonded interface to enzymatic degradation. SignificanceMGO pretreatment maintains the long-term stability of the resin-dentin interface by protecting dentinal collagen from enzymatic degradation, without compromising initial bonding performance. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=113 SRC="FIGDIR/small/701305v1_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@54ae32org.highwire.dtl.DTLVardef@1787fdforg.highwire.dtl.DTLVardef@130b40org.highwire.dtl.DTLVardef@47c5f9_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2025

Electrochemical guided mode resonance biosensor for simultaneous refractive index and electrochemical measurements

A comprehensive miniaturised biosensing platform needs to detect multiple analytes, which often rely on different transduction mechanisms for their detection and quantification. This necessitates the development of multimodal sensors capable of simultaneous measurements without interference between measurement modalities. Guided mode resonance (GMR) biosensors are highly sensitive to refractive index changes and well suited to out-of-plane optical coupling, but have not previously been implemented in a multimodal configuration. Here, we present the electrochemical guided mode resonance (EC-GMR) sensor, a Si3N4 GMR photonic grating integrated with an indium tin oxide (ITO) electrode that enables concurrent optical and electrochemical sensing. Finite difference time domain (FDTD) simulations show that the resonance wavelength of the GMR shifts as a function of ITO thickness and applied bias. These findings are validated experimentally using EC-GMR devices fabricated with a range of ITO thicknesses. We demonstrate that the EC-GMR achieves a refractive index sensitivity of 84.4 nm/RIU while simultaneously measuring the double-layer capacitance. To highlight its multimodal capability, we characterise the optical and electrochemical responses of methylene blue, a widely used redox reporter in biosensing. By integrating photonic and electrochemical modalities in a compact format, the EC-GMR platform provides critical analytical information beyond that which could be obtained from a traditional single-modality sensor. This approach extends the analytical utility of GMR sensors and represents a robust, adaptable solution for diverse biosensing applications, from clinical diagnostics to environmental monitoring.

biophysics↗

bioRxiv2025

Deep learning-based event classification of mass photometry data for optimal mass measurement at the single-molecule level

Mass photometry (MP) is a powerful technique for studying biomolecular structure, interactions, and dynamics in solution. It detects and quantifies small reflectivity changes at a glass-water interface during protein (un)binding, with signals typically averaged over 100 milliseconds. However, particle motion at the point of single-molecule measurement can compromise key metrics such as mass resolution, sensitivity, and concentration. We present a three-dimensional convolutional residual network trained via supervised learning to classify landing events based on their spatiotemporal dynamics. By analysing 3D event thumbnails, our method isolates optimal single-molecule measurements, eliminating cumulative histogram artifacts and improving resolving power by up to a factor of 2. Validated across diverse experimental datasets--including resolved and partially resolved samples, and varying masses, concentrations, and integration times--our approach delivers robust performance under (sub)optimal conditions. Our approach provides measurement-level data-driven feedback, facilitating high quality MP measurements in challenging scenarios.

biophysics↗

bioRxiv2024

Best practice mass photometry: A guide to optimal single molecule mass measurement

Mass photometry (MP) has emerged as a powerful approach to study biomolecular structure, dynamics and interactions. The capabilities of the method ultimately hinge on the ability to accurately measure the tiny optical contrast generated by individual molecules landing at a glass-water interface, which enables mass-resolved quantification of biomolecular mixtures. Ideally, this capability is only limited by shot noise inherent to photon detection, but in practice depends on additional parameters and details of the assay. Here, we focus on the key parameters affecting MP performance, and present simple steps that can be taken to achieve optimal MP performance in terms of mass resolution, quantitative detection limit and analyte concentration range without compromising the ease and simplicity of the technique.

biophysics↗

bioRxiv2024

The Impact of a Natural Ingredients based Intervention Targeting the Nine Hallmarks of Aging on DNA methylation

Aging interventions have progressed in recent years due to the growing curiosity about how lifestyle impacts longevity. This study assessed the effects of SRW Laboratories Cel System nutraceutical range on epigenetic methylation patterns, inflammation, physical performance, body composition, and epigenetic biomarkers of aging. A 1-year study was conducted with 51 individuals, collecting data at baseline, 3 months, 6 months, and 12 months. Participants were encouraged to walk 10 minutes and practice 5 minutes of mindfulness daily. Significant improvements in muscle strength, body function, and body composition metrics were observed. Epigenetic clock analysis showed a decrease in biological age with significant reductions in stem cell division rates. Immune cell subset analysis indicated significant changes, with increases in eosinophils and CD8T cells and decreases in B memory, CD4T memory, and T-regulatory cells. Predicted epigenetic biomarker proxies (EBPs) showed significant changes in retinol/TTHY, a regulator of cell growth, proliferation, and differentiation, and deoxycholic acid glucuronide levels, a metabolite of deoxycholic acid generated in the liver. Gene ontology analysis revealed significant CpG methylation changes in genes involved in critical biological processes related to aging, such as oxidative stress-induced premature senescence, pyrimidine deoxyribonucleotide metabolic process, TRAIL binding, hyaluronan biosynthetic process, neurotransmitter loading into synaptic vesicles, pore complex assembly, collagen biosynthetic process, protein phosphatase 2A binding activity, and activation of transcription factor binding. Our findings suggest that the Cel System supplement range may effectively reduce biological age and improve health metrics, warranting further investigation into its mechanistic pathways and long-term efficacy.

genomics↗

bioRxiv2023

Intercomparison of growth models for Antarctic krill (Euphausia superba): towards a generalised understanding

Antarctic krill is a key species of the Southern Ocean, impacted by climate change and human exploitation. Understanding how these changes affect the distribution and abundance of krill is crucial for generating projections of change for Southern Ocean ecosystems. Krill growth is an important indicator of habitat suitability and a series of models have been developed and used to examine krill growth potential at different spatial and temporal scales. The available models have been developed using a range of empirical and mechanistic approaches, which provide alternative perspectives and cross-validation of analyses of the key processes influencing krill growth. Here we undertake an intercomparison of a suite of the available models to understand their sensitivities to major driving variables. This illustrates that the results are strongly determined by the model structure and technical characteristics, and the data on which they were developed and validated. Our results emphasize the importance of assessing the constraints and requirements of individual krill growth models to ensure their appropriate application. The study also demonstrates the value of the development of alternative modelling approaches to identify key processes affecting the dynamics of krill. Of critical importance for modelling the growth of krill is appropriately assessing and accounting for differences in estimates of food availability resulting from alternative methods of observation. We suggest that an intercomparison approach is particularly valuable in the development and application of models for the assessment of krill growth potential at circumpolar scales and for future projections. As another result of the intercomparison, the implementations of the models used in this study are now publicly available for future use and analyses.

ecology↗

bioRxiv2022

CD98 is critical for a conserved inflammatory response to diverse injury stimuli relevant to IPF exacerbations and COVID pneumonitis

Progressive fibrosing interstitial lung diseases (PFILDs) cause substantial morbidity and mortality. Antifibrotic agents slow progression, but most of the clinical need remains unmet. The archetypal PFILD is idiopathic pulmonary fibrosis (IPF). Chronic progression is driven by transforming growth factor (TGF-){beta}1 signalling. It is punctuated by inflammatory flares known as acute exacerbations (AE-IPF), which are associated with accelerated decline and high mortality. We hypothesized that acute injury responses underlying exacerbations and the mechanisms of chronic fibrosis overlap at the molecular level, via a cell surface assembly nucleated by galectin-3 that we term the gal-3-fibrosome. We focused upon a putative pro-inflammatory galectin-3 ligand, the CD98:integrin complex. Our data indicate CD98 and {beta}1-integrin co-localise with galectin-3 within epithelial cells in IPF lung tissue, and within 40 nm in human lung tissue treated with TGF-{beta}1 compared to controls. CD98 is required for interleukin (IL-)6 and IL-8 responses to biochemical and biophysical conditions mimicking stimuli of AE-IPF in vivo, ex vivo and in cells, and for an interstitial neutrophilic response in a mouse model. We demonstrate this pathway progresses via intracellular influx of Ca2+ mediated by TRPV4, and NF-{kappa}B activation, operating in positive feedback. Lastly we show the CD98- and galectin-3-dependence of IL-6 and IL-8 responses to the SARS-CoV-2 spike protein receptor binding domain and the conservation of this response pattern between lung epithelial cells and monocyte-derived macrophages. Taken together our findings identify CD98 as a key mediator of both pro-fibrotic and acute inflammatory responses in the lung with relevance to AE- and chronic progression of IPF, and the priming of fibrotic lungs for acute inflammatory responses. They similarly implicate CD98 and galectin-3 as mediators of COVID pneumonitis and worse outcomes in ILD patients with COVID.

cell biology↗

bioRxiv2022

Retinoid acid receptor β mechanically regulates the activity of pancreatic cancer cells

Pancreatic ductal adenocarcinoma (PDAC) is the most common and lethal form of pancreatic cancer, characterised by stromal remodelling, elevated matrix stiffness and high metastatic rate. Retinoids, compounds derived from vitamin A, have a history of clinical use in cancer for their anti-proliferative and differentiation effects, and more recently have been explored as anti-stromal therapies in PDAC for their ability to induce mechanical quiescence in cancer associated fibroblasts. Here we demonstrate that retinoic acid receptor {beta} (RAR-{beta}) transcriptionally represses myosin light chain 2 (MLC-2) expression, a key regulatory component of the contractile actomyosin machinery. In turn, MLC-2 downregulation results in decreased cytoskeletal stiffness and traction force generation, impaired response to mechanical stimuli via mechanosensing and reduced ability to invade through the basement membrane.

bioengineering↗

bioRxiv2022

Transformation of Human Mesenchymal Stem Cells into High-Grade Sarcomas by YAP1 and K-RAS Reflects the Undifferentiated Pleomorphic Sarcoma-Myxofibrosarcoma Disease Spectrum

High-grade complex karyotype sarcomas are a heterogeneous group of more than seventy tumors that vary in histology, clinical course, and patient demographics. Despite these clear differences, these high-grade sarcomas are treated similarly with a uniformly high metastatic rate. Pre-clinical models that allow for rigorous comparisons of distinct human sarcoma subtypes would advance insights into the relationships between sarcomas and inform therapeutic decisions. We describe the robust transformation of human mesenchymal stem cells into multiple subtypes of high-grade sarcoma. Using a pooled genetic screening approach, we identified key drivers and potential modifiers of transformation. YAP1 and KRAS were validated as drivers of two distinct sarcoma subtypes, undifferentiated pleomorphic sarcoma (UPS) and myxofibrosarcoma (MFS), respectively. In addition, the pathology of tumors driven by CDK4 and PIK3CA reflected leiomyosarcoma (LMS) and osteosarcoma (OS) indicating that further iterations of this model could result in additional sarcoma subtypes. Histologically and phenotypically these tumors reflect human sarcomas including the pathognomonic complex karyotype. In addition, CDK4 and PIK3CA driven tumors demonstrated endogenous YAP1 amplification which is seen across a subset of human tumors. While all tumors overlapped transcriptionally with the TCGA sarcoma data, further analysis confirmed that YAP1 and KRAS tumors recapitulate the UPS and MFS subtypes. Co-analysis of TCGA and model tumors support that these sarcoma subtypes lie along a spectrum of disease and adds guidance for further transcriptome-based refinement of sarcoma subtyping. Within complex karyotype sarcomas, there are multiple genetic changes but identifying those that are clinically relevant has been challenging. Comparing differentially expressed genes in YAP1 and KRAS tumors to human UPS and MFS identified the enrichment of oxidative phosphorylation pathways in both YAP1 tumors and UPS. Treatment of a panel of sarcoma cell lines with the combination of an oxidative phosphorylation inhibitor and Hippo pathway inhibitor led to a significant impairment in growth identifying new therapeutic targets. A subset of human UPS tumors showed an even greater enrichment in these pathways indicating this model can be used to identify clinically relevant subtypes. This model can be used to begin to understand pathways and mechanisms driving human sarcoma development, the relationship between sarcoma subtypes and to identify and test new therapeutic vulnerabilities for this aggressive and heterogeneous disease. Statement of SignificanceWe have created the first model to study the development, growth, and metastasis of multiple human sarcoma subtypes. This system can be used as a platform to investigate sarcoma biology and identify new therapeutic targets across a heterogeneous disease.

cancer biology↗

bioRxiv2020

Evidence for face selectivity in early vision

The commonly accepted "simple-to-complex" model of visual processing in the brain posits that visual tasks on complex objects such as faces are based on representations in high-level visual areas. Yet, recent experimental data showing the visual systems ability to localize faces in natural images within 100ms (Crouzet et al., 2010) challenge the prevalent hierarchical description of the visual system, and instead suggest the hypothesis of face-selectivity in early visual areas. In the present study, we tested this hypothesis with human participants in two eye tracking experiments, an fMRI experiment and an EEG experiment. We found converging evidence for neural representations selective for upright faces in V1/V2, with latencies starting around 40 ms post-stimulus onset. Our findings suggest a revision of the standard "simple-to-complex" model of hierarchical visual processing. Significance statementVisual processing in the brain is classically described as a series of stages with increasingly complex object representations: early visual areas encode simple visual features (such as oriented bars), and high-level visual areas encode representations for complex objects (such as faces). In the present study, we provide behavioral, fMRI, and EEG evidence for representations of complex objects - namely faces - in early visual areas. Our results challenge the standard "simple-to-complex" model of visual processing, suggesting that it needs to be revised to include neural representations for faces at the lowest levels of the visual hierarchy. Such early object representations would permit the rapid and precise localization of complex objects, as has previously been reported for the object class of faces.

neuroscience↗

bioRxiv2019

Simulating the evolutionary trajectories of metabolic pathways for insect symbionts in the Sodalis genus

1Insect-bacterial symbioses are ubiquitous, but there is still much to uncover about how these relationships establish, persist and evolve. The tsetse endosymbiont Sodalis glossinidius displays intriguing metabolic adaptations to its microenvironment, but the process by which this relationship evolved remains to be elucidated. The recent chance discovery of the free-living secies of the Sodalis genus, S. praecaptivus, provides a serendipitous starting point from which to investigate the evolution of this symbiosis. Here, we present a flux balance model for S. praecaptivus. Metabolic modelling is used in combination with a multi-objective evolutionary algorithm to explore the trajectories that S. glossinidius may have undertaken after becoming internalised. The time-dependent loss of key genes is shown to influence the evolved populations, providing possible targets for future in vitro genetic manipulation. This method provides an unusually detailed perspective on possible evolutionary trajectories for S. glossinidius in this fundamental process of evolutionary and ecological change.

evolutionary biology↗

bioRxiv2018

Algorithm for Reliable Detection of Beat Onsets in Cerebral Blood Flow Velocity Signals

Transcranial Doppler (TCD) ultrasound has been demonstrated to be a valuable tool for assessing cerebral hemodynamics via measurement of cerebral blood flow velocity (CBFV), with a number of established clinical indications. However, CBFV waveform analysis depends on reliable pulse onset detection, an inherently difficult task for CBFV signals acquired via TCD. We study the application of a new algorithm for CBFV pulse segmentation, which locates pulse onsets in a sequential manner using a moving difference filter and adaptive thresholding. The test data set used in this study consists of 92,012 annotated CBFV pulses, whose quality is representative of real world data. On this test set, the algorithm achieves a true positive rate of 99.998% (2 false negatives), positive predictive value of 99.998% (2 false positives), and mean temporal offset error of 6.10 {+/-} 4.75 ms. We do note that in this context, the way in which true positives, false positives, and false negatives are defined caries some nuance, so care should be taken when drawing comparisons to other algorithms. Additionally, we find that 97.8% and 99.5% of onsets are detected within 10 ms and 30 ms, respectively, of the true onsets. The algorithms performance in spite of the large degree of variation in signal quality and waveform morphology present in the test data suggests that it may serve as a valuable tool for the accurate and reliable identification of CBFV pulse onsets in neurocritical care settings.

bioinformatics↗