Publications
550 results found
Bharadwaj A, Kalita R, Kumar A, et al., 2024, A cost-effective, modular, research-grade optical microscope, Current Science, Vol: 126, Pages: 244-2554, ISSN: 0011-3891
Optical microscopy is a ubiquitous tool in the physical and life sciences and in histopathology, where visible light microscopy is used to analyse clinical tissue sections at the micron scale to help diagnose diseases. In recent years, microscope technologies have dramatically evolved, but these have generally come with increased cost and complexity. To widen access to advanced microscopy capabilities, we have developed a cost-effective modular platform for optical microscopy (www.openscopes.com). Many of these instruments can be based around a new low-cost and flexible microscope stand, ‘openFrame’, for which the core components are open source. openFrame can support implementations of a wide range of microscope modalities for diverse applications, including research, pathology and training. Unlike many commercial microscopes that are often designed for specific applications and cannot be easily upgraded or adapted for different imaging modalities, openFramebased instruments can be relatively easily maintained, upgraded or adapted to another modality without requiring manufacturer support. To this end, openFramebased instruments are envisaged to operate with opensource software, enabling researchers to assemble and modify their microscopes with minimal challenges presented by proprietary (closed) hardware or software. Here, we describe the implementation of a low-cost, research-grade modular optical microscope applicable to research and pathology.
Lightley J, Kumar S, Lim MQ, et al., 2023, <i>openFrame</i>: A modular, sustainable, open microscopy platform with single-shot, dual-axis optical autofocus module providing high precision and long range of operation, JOURNAL OF MICROSCOPY, ISSN: 0022-2720
Gleneadie HJJ, Fernandez-Ruiz B, Sardini A, et al., 2023, Endogenous bioluminescent reporters reveal a sustained increase in utrophin gene expression upon EZH2 and ERK1/2 inhibition, COMMUNICATIONS BIOLOGY, Vol: 6
Darling C, Davis SPX, Kumar S, et al., 2023, Single-shot optical projection tomography for high-speed volumetric imaging of dynamic biological samples, JOURNAL OF BIOPHOTONICS, Vol: 16, ISSN: 1864-063X
Lightley J, Kumar S, Garcia E, et al., 2022, Robust, single-shot, optical autofocus system utilizing cylindrical lenses to provide high precision and long range of operation
<jats:title>ABSTRACT</jats:title><jats:p>We present a robust, “real-time” optical autofocus system for microscopy that provides high accuracy (<230 nm) and long range (∼130 µm) with a 1.4 numerical aperture oil immersion objective lens. This autofocus can operate in a closed loop, single-shot functionality over a range of ±37.5 µm and can also operate as a 2-step process up to ±68 µm. A real-time autofocus capability is useful for experiments with long image data acquisition times, including single molecule localization microscopy, that may be impacted by defocusing resulting from drift of components, e.g., due to changes in temperature or mechanical drift. It is also vital for automated slide scanning or multiwell plate imaging where the sample may not be in the same horizontal plane for every field of view during the image data acquisition. To realise high precision and long range, we implement orthogonal optical readouts using cylindrical lenses. We demonstrate the performance of this new optical autofocus system with automated multiwell plate imaging and single molecule localisation microscopy and illustrate the benefit of using a superluminescent diode as the autofocus light source.</jats:p>
Van de Pette M, Dimond A, Galvao AM, et al., 2022, Epigenetic changes induced by in utero dietary challenge result in phenotypic variability in successive generations of mice, Nature Communications, Vol: 13, ISSN: 2041-1723
Transmission of epigenetic information between generations occurs in nematodes, flies and plants, mediated by specialised small RNA pathways, modified histones and DNA methylation. Similar processes in mammals can also affect phenotype through intergenerational or trans-generational mechanisms. Here we generate a luciferase knock-in reporter mouse for the imprinted Dlk1 locus to visualise and track epigenetic fidelity across generations. Exposure to high-fat diet in pregnancy provokes sustained re-expression of the normally silent maternal Dlk1 in offspring (loss of imprinting) and increased DNA methylation at the somatic differentially methylated region (sDMR). In the next generation heterogeneous Dlk1 mis-expression is seen exclusively among animals born to F1-exposed females. Oocytes from these females show altered gene and microRNA expression without changes in DNA methylation, and correct imprinting is restored in subsequent generations. Our results illustrate how diet impacts the foetal epigenome, disturbing canonical and non-canonical imprinting mechanisms to modulate the properties of successive generations of offspring.
Kalita R, Flanagan W, Lightley J, et al., 2021, Single-shot phase contrast microscopy using polarisation-resolved differential phase contrast, JOURNAL OF BIOPHOTONICS, Vol: 14, ISSN: 1864-063X
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- Citations: 4
Guglielmi L, Heliot C, Kumar S, et al., 2021, Smad4 controls signaling robustness and morphogenesis by differentially contributing to the Nodal and BMP pathways, NATURE COMMUNICATIONS, Vol: 12
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- Citations: 7
Wysoczanski R, Baker J, Fenwick P, et al., 2021, Image analysis of tissue macrophages to confirm differential phagocytosis between groups by microscopy and automated bacterial quantification, Publisher: EUROPEAN RESPIRATORY SOC JOURNALS LTD, ISSN: 0903-1936
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- Citations: 1
Garcia E, Lightley J, Kumar S, et al., 2021, Application of direct stochastic optical reconstruction microscopy (dSTORM) to the histological analysis of human glomerular disease, JOURNAL OF PATHOLOGY CLINICAL RESEARCH, Vol: 7, Pages: 438-445
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- Citations: 2
Lightley J, Gorlitz F, Kumar S, et al., 2021, Robust deep learning optical autofocus system applied to automated multiwell plate single molecule localization microscopy, JOURNAL OF MICROSCOPY, ISSN: 0022-2720
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- Citations: 4
Garcia E, Lightley J, Kumar S, et al., 2021, Application of direct stochastic optical reconstruction microscopy (dSTORM) to the histological analysis of human glomerular disease, Publisher: SPRINGER, Pages: S142-S142, ISSN: 0945-6317
Cannon T, Lagarto J, Dyer B, et al., 2021, Characterisation of NADH fluorescence properties under one-photon excitation with respect to temperature, pH and binding to lactate dehydrogenase, Optical Society of America Continuum, Vol: 4, Pages: 1610-1625
Reduced nicotinamide adenine dinucleotide (NADH) is the principal electron donor in glycolysis and oxidative metabolism and is thus recognized as a key biomarker for probing metabolic state. While the fluorescence characteristics of NADH have been investigated extensively, there are discrepancies in the published data due to diverse experimental conditions, instrumentation and microenvironmental parameters that can affect NADH fluorescence. Using a cuvette-based time-resolved spectrofluorimeter employing one-photon excitation at 375 nm, we characterized the fluorescence intensity, lifetime, spectral response, anisotropy and time-resolved anisotropy of NADH in aqueous solution under varying microenvironmental conditions, namely temperature, pH, and binding to lactate dehydrogenase (LDH). Our results demonstrate how temperature, pH, and binding partners each impact the fluorescence signature of NADH and highlight the complexity of the fluorescence data when different parameters produce competing effects. We hope that the data presented in this study will provide a reference for potential sources of variation in experiments measuring NADH fluorescence.
Jones DC, Alexandrov Y, Curry N, et al., 2021, Multidimensional spectroscopy and imaging of defects in synthetic diamond: excitation-emission-lifetime luminescence measurements with multiexponential fitting and phasor analysis, Journal of Physics D: Applied Physics, Vol: 54, Pages: 1-13, ISSN: 0022-3727
We report the application of phasor analysis and nonlinear iterative fitting to complex spatial and spectroscopic luminescence decay data obtained from multidimensional microscopy of a CVD diamond grown on a HPHT substrate. This spectral and lifetime-resolved analysis enabled spatial mapping of variations in concentrations of nitrogen vacancy (NV) defects in both charge states and the quenching of NV− defects, as well as the identification of SiV− luminescence. These imaging and spectroscopic modalities may be important for reliable fabrication of quantum devices based on such defects in diamond, which will require well-defined and characterised quantum electronic properties.
Kalita R, Lightley J, Kumar S, et al., 2021, Single-shot quantitative phase contrast using polarisation-resolved differential phase microscopy, ISSN: 1605-7422
We present a robust, low-cost single-shot implementation of differential phase microscopy utilising a polarisation-sensitive camera to simultaneously acquire 4 images from which the phase gradients and quantitative phase image can be calculated.
Lightley J, Görlitz F, Kumar S, et al., 2021, ROBUST OPTICAL AUTOFOCUS SYSTEM UTILIZING NEURAL NETWORKS APPLIED TO AUTOMATED MULTIWELL PLATE STORM MICROSCOPY, ISSN: 1605-7422
We present a robust, low-cost neural network-based optical autofocus system that can operate over a range of ±100µm with submicron precision, enabling automated high-content super-resolved imaging with a 1.3 NA objective lens.
Darling C, Davis SPX, Kumar S, et al., 2021, Single-Shot Volumetric Imaging Using Optical Projection Tomography, ISSN: 1605-7422
We present a single-shot volumetric imaging method, utilising optical projection tomography. We record projections simultaneously, implementing compressive sensing and machine learning to record up to 70 (camera limited) 1x1x1.9mm volumes/second.
Jones B, McGlone ER, Fang Z, et al., 2021, Genetic and biased agonist-mediated reductions in β-arrestin recruitment prolong cAMP signalling at glucagon family receptors, Journal of Biological Chemistry, Vol: 296, Pages: 1-15, ISSN: 0021-9258
Receptors for the peptide hormones glucagon-like peptide-1 (GLP-1R), glucose-dependent insulinotropic polypeptide (GIPR) and glucagon (GCGR) are important regulators of insulin secretion and energy metabolism. GLP-1R agonists have been successfully deployed for the treatment of type 2 diabetes, but it has been suggested that their efficacy is limited by target receptor desensitisation and downregulation due to recruitment of β-arrestins. Indeed, recently described GLP-1R agonists with reduced β-arrestin-2 recruitment have delivered promising results in preclinical and clinical studies. We therefore aimed to determine if the same phenomenon could apply to the closely related GIPR and GCGR. In HEK293 cells depleted of both β-arrestin isoforms the duration of G protein-dependent cAMP/PKA signalling was increased in response to the endogenous ligand for each receptor. Moreover, in wild-type cells, “biased” GLP-1, GCG and GIP analogues with selective reductions in β-arrestin-2 recruitment led to reduced receptor endocytosis and increased insulin secretion over a prolonged stimulation period, although the latter effect was only seen at high agonist concentrations. Biased GCG analogues increased the duration of cAMP signalling, but this did not lead to increased glucose output from hepatocytes. Our study provides a rationale for development of GLP-1R, GIPR and GCGR agonists with reduced β-arrestin recruitment, but further work is needed to maximally exploit this strategy for therapeutic purposes.
Lightley J, Gorlitz F, Kumar S, et al., 2021, ROBUST OPTICAL AUTOFOCUS SYSTEM UTILIZING NEURAL NETWORKS APPLIED TO AUTOMATED MULTIWELL PLATE STORM MICROSCOPY, European Conferences on Biomedical Optics - Advances in Microscopic Imaging III, Publisher: SPIE-INT SOC OPTICAL ENGINEERING, ISSN: 0277-786X
Darling C, Davis SPX, Kumar S, et al., 2021, Single-Shot Volumetric Imaging Using Optical Projection Tomography, European Conferences on Biomedical Optics - Advances in Microscopic Imaging III, Publisher: SPIE-INT SOC OPTICAL ENGINEERING, ISSN: 0277-786X
Kalita R, Lightley J, Kumar S, et al., 2021, Single-shot quantitative phase contrast using polarisation-resolved differential phase microscopy, European Conferences on Biomedical Optics - Advances in Microscopic Imaging III, Publisher: SPIE-INT SOC OPTICAL ENGINEERING, ISSN: 0277-786X
Wysoczanski R, Baker JR, Fenwick P, et al., 2020, Analysis of defective phagocytosis in COPD using super-resolution microscopy and automated bacterial quantification, Publisher: EUROPEAN RESPIRATORY SOC JOURNALS LTD, ISSN: 0903-1936
Georgiadou E, Haythorne E, Dickerson MT, et al., 2020, The pore-forming subunit MCU of the mitochondrial Ca2+ uniporter is required for normal glucose-stimulated insulin secretion in vitro and in vivo in mice, Diabetologia, Vol: 63, Pages: 1368-1381, ISSN: 0012-186X
Aims/hypothesisMitochondrial oxidative metabolism is central to glucose-stimulated insulin secretion (GSIS). Whether Ca2+ uptake into pancreatic beta cell mitochondria potentiates or antagonises this process is still a matter of debate. Although the mitochondrial Ca2+ importer (MCU) complex is thought to represent the main route for Ca2+ transport across the inner mitochondrial membrane, its role in beta cells has not previously been examined in vivo.MethodsHere, we inactivated the pore-forming subunit of the MCU, encoded by Mcu, selectively in mouse beta cells using Ins1Cre-mediated recombination. Whole or dissociated pancreatic islets were isolated and used for live beta cell fluorescence imaging of cytosolic or mitochondrial Ca2+ concentration and ATP production in response to increasing glucose concentrations. Electrophysiological recordings were also performed on whole islets. Serum and blood samples were collected to examine oral and i.p. glucose tolerance.ResultsGlucose-stimulated mitochondrial Ca2+ accumulation (p< 0.05), ATP production (p< 0.05) and insulin secretion (p< 0.01) were strongly inhibited in beta cell-specific Mcu-null (βMcu-KO) animals, in vitro, as compared with wild-type (WT) mice. Interestingly, cytosolic Ca2+ concentrations increased (p< 0.001), whereas mitochondrial membrane depolarisation improved in βMcu-KO animals. βMcu-KO mice displayed impaired in vivo insulin secretion at 5 min (p< 0.001) but not 15 min post-i.p. injection of glucose, whilst the opposite phenomenon was observed following an oral gavage at 5 min. Unexpectedly, glucose tolerance was improved (p< 0.05) in young βMcu-KO (<12 weeks), but not in older animals vs WT mice.Conclusions/interpretationMCU is crucial for mitochondrial Ca2+ uptake in pancreatic beta cells and is required for normal GSIS. The apparent compensatory mechanisms that maintain glucose tolerance in βMcu-KO mice remain
Fang Z, Chen S, Pickford P, et al., 2020, The influence of peptide context on signaling and trafficking of glucagon-like peptide-1 receptor biased agonists, ACS Pharmacology & Translational Science, Vol: 3, Pages: 345-360, ISSN: 2575-9108
Signal bias and membrane trafficking have recently emerged as important considerations in the therapeutic targeting of the glucagon-like peptide-1 receptor (GLP-1R) in type 2 diabetes and obesity. In the present study, we have evaluated a peptide series with varying sequence homology between native GLP-1 and exendin-4, the archetypal ligands on which approved GLP-1R agonists are based. We find notable differences in agonist-mediated cyclic AMP signaling, recruitment of β-arrestins, endocytosis, and recycling, dependent both on the introduction of a His → Phe switch at position 1 and the specific midpeptide helical regions and C-termini of the two agonists. These observations were linked to insulin secretion in a beta cell model and provide insights into how ligand factors influence GLP-1R function at the cellular level.
Lagarto JL, Nickdel MB, Kelly DJ, et al., 2020, Autofluorescence lifetime reports cartilage damage in osteoarthritis, Scientific Reports, Vol: 10, ISSN: 2045-2322
Osteoarthritis (OA) is the most common arthritis and its hallmark is degradation of articular cartilage by proteolytic enzymes leading to loss of joint function. It is challenging to monitor the status of cartilage in vivo and this study explores the use of autofluorescence lifetime (AFL) measurements to provide a label-free optical readout of cartilage degradation that could enable earlier detection and evaluation of potential therapies. We previously reported that treatment of ex vivo porcine cartilage with proteolytic enzymes resulted in decreased AFL. Here we report changes in AFL of ex vivo mouse knee joints, porcine metacarpophalangeal joints, normal human metatarsophalangeal articular tissue and human OA tibial plateau tissues measured with or without treatment using a compact single-point time resolved spectrofluorometer. Our data show that proteolytically damaged areas in porcine metacarpophalangeal joints present a reduced AFL and that inducing aggrecanases in mouse and human joints also significantly reduces AFL. Further, human cartilage from OA patients presents a significantly lower AFL compared to normal human cartilage. Our data suggest that AFL can detect areas of cartilage erosion and may potentially be utilised as a minimally-invasive diagnostic readout for early stage OA in combination with arthroscopy devices.
Jones DC, Alexandrov Y, Curry N, et al., 2020, A multidimensional imaging and spectroscopic microscope
We present a multidimensional luminescence microscope for characterisation of emission from defects in diamond. We have applied the photoluminescence, hyperspectral and time-resolved luminescence imaging capabilities of this novel instrument to natural and synthetic diamonds.
Gorlitz F, Wysoczanski R, Kumar S, et al., 2020, Towards easier, faster super-resolved microscopy, Conference on Single Molecule Spectroscopy and Superresolution Imaging XIII, Publisher: SPIE-INT SOC OPTICAL ENGINEERING, ISSN: 0277-786X
Garcia E, Guo W, Kumar S, et al., 2020, FLIM, FRET and high content analysis, Symposium on Multiphoton Microscopy in the Biomedical Sciences XX held at SPIE BiOS Conference, Publisher: SPIE-INT SOC OPTICAL ENGINEERING, ISSN: 0277-786X
Davis SPX, Kumar S, Alexandrov Y, et al., 2019, Convolutional neural networks for reconstruction of undersampled optical projection tomography data applied to in vivo imaging of zebrafish., Journal of Biophotonics, Vol: 12, ISSN: 1864-063X
Optical projection tomography (OPT) is a 3D mesoscopic imaging modality that can utilize absorption or fluorescence contrast. 3D images can be rapidly reconstructed from tomographic data sets sampled with sufficient numbers of projection angles using the Radon transform, as is typically implemented with optically cleared samples of the mm-to-cm scale. For in vivo imaging, considerations of phototoxicity and the need to maintain animals under anesthesia typically preclude the acquisition of OPT data at a sufficient number of angles to avoid artifacts in the reconstructed images. For sparse samples, this can be addressed with iterative algorithms to reconstruct 3D images from undersampled OPT data, but the data processing times present a significant challenge for studies imaging multiple animals. We show here that convolutional neural networks (CNN) can be used in place of iterative algorithms to remove artifacts - reducing processing time for an undersampled in vivo zebrafish dataset from 77 to 15 minutes. We also show that using CNN produces reconstructions of equivalent quality to CS with 40% fewer projections. We further show that diverse training data classes, for example ex vivo mouse tissue data, can be used for CNN-based reconstructions of OPT data of other species including live zebrafish.
Corcoran D, Juskaite V, Xu Y, et al., 2019, DDR1 autophosphorylation is a result of aggregation into dense clusters, Scientific Reports, Vol: 9, ISSN: 2045-2322
The collagen receptor DDR1 is a receptor tyrosine kinase that promotes progression ofa wide range of human disorders. Little is known about how ligand binding triggers DDR1 kinase activity. We previously reported that collagen induces DDR1 activation through lateral dimer association and phosphorylation between dimers, a process that requires specific transmembrane association. Here we demonstrate ligand-induced DDR1 clustering by widefield and super-resolution imaging and provide evidence for a mechanism whereby DDR1 kinase activity is determined by its molecular density. Ligand binding resulted in initial DDR1 reorganisation into morphologically distinct clusters with unphosphorylated DDR1. Further compaction over time led to clusters with highly aggregated and phosphorylated DDR1. Ligand-induced DDR1 clustering was abolished by transmembrane mutations but did not require kinase activity. Our results significantly advance our understanding of the molecular events underpinning ligand-induced DDR1 kinase activity and provide an explanation for the unusually slow DDR1 activation kinetics.
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