Biology subjects

Lim, Y. J.

Publications and source records attributed to Lim, Y. J..

9 recordsLinked to original sources

bioRxiv2025

Combining Multi-site FRAP and HILO-TIRF microscopy using a Spatial Light Modulator

Fluorescence Recovery After Photobleaching (FRAP) has remained a powerful tool to probe intracellular dynamics. FRAP relies on two aspects: (1) localised excitation resulting in photobleaching, and (2) fluorescence recovery of the bleached volume which provides insight into kinetics. Existing FRAP systems are limited by a trade-off between time and spatial multiplexing due to galvanometric scanning methods, precluding the study of multiple independent positions simultaneously as well as advanced widefield imaging modes. Hence, they may not capture the dynamic and non-isotropic environments in biological studies. In this paper, we utilise phase profiles corresponding to an array of fresnel lenses and diffractive masks to switch between simultaneous FRAP of independent spatial positions whilst maintaining epifluorescence, highly inclined laminated optical sheet (HILO), and total internal reflection fluorescence (TIRF) microscopy modalities. Our approach bridges high contrast fluorescence imaging (HILO and TIRF) and a multi-position FRAP technique using a single spatial light modulator. As such, this technique enables high contrast bleaching and screening across volumes, which we envision will be of value to areas such as single particle tracking and single molecule imaging where dynamic photobleaching is necessary to measure fast events across the field of view in a single versatile instrument.

biophysics↗

bioRxiv2025

Using rotational integration of oblique interferometric scattering (RO-iSCAT) to track axial spatiotemporal responses of membrane protrusions

Despite the crucial importance of dynamic membrane protrusions for understanding phagocytosis, cellular communication and mechanobiology, current imaging modalities struggle to quantitatively track their real-time, 3D spatiotemporal dynamics with sufficient molecular specificity and minimal perturbation. Many membrane protrusions studies still utilize confocal microscopy where its axial resolution and high phototoxicity remains a key limiting factor for live axial imaging. We discovered that multiple rotational oblique interference scattering (RO-iSCAT) leverages off-axis illumination to induce a larger lateral shift in out-of-focus iSCAT signals compared to in-focus signals. This phenomenon provides a foundation to generate speckle-free widefield interferometric signals with a 10-fold signal to noise ratio improvement, eliminating the need for any background subtraction. RO-iSCAT enables real-time, label-free, and minimally invasive imaging of diverse membrane protrusions within complex co-cultures. RO-iSCAT enables nanoscale-sensitive tracking of membrane protrusion dynamics along the axial direction. This allows for the construction of dynamic axial variance maps, facilitating quantitative measurements of membrane protrusion formation at tens to hundreds of nanometer displacements, without requiring 3D volumetric imaging. RO-iSCAT empowers real time quantitatively dissection of the axial spatiotemporal complexities of membrane protrusions and unlock future insights into fundamental processes like cell migration, durotaxis, and intercellular communication. Key pointsO_LIDiscovered that multiple integrated rotational oblique interference scattering (RO-iSCAT) generates speckle-free widefield interferometric signals with a 10-fold signal to noise ratio improvement, eliminating the need for any background subtraction. C_LIO_LIRemoved need for 3D volumetric imaging to quantified axial motion of membrane protrusion forming tethers, trails and bridge with within [~] tens of nanometer accuracy. C_LIO_LIEnabled classification of membrane protrusions that, despite possessing identical chemical compositions, are differentiated by their interactions, thus offering a qualitative comparison of membrane protrusions at the nanoscale in living cells. C_LI Summary Figure O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=130 SRC="FIGDIR/small/644841v1_ufig1.gif" ALT="Figure 1"> View larger version (38K): org.highwire.dtl.DTLVardef@b183a4org.highwire.dtl.DTLVardef@39a944org.highwire.dtl.DTLVardef@197f019org.highwire.dtl.DTLVardef@1438b3_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2025

Imaging throughput of compact handheld microscopes for quantitative single cell studies

High-throughput live-cell imaging within incubator environments often necessitates a compromise between optical resolution and instrument/computational complexity. In this work, we demonstrate that controlled defocusing, a default function in all optical microscopes, can be utilized as a primary contrast mechanism for large-scale cell analysis (7000 cells per field of view). Our results suggest that even at a low numerical aperture (NA [~] 0.01) and using just epi-illumination, defocused images can generate a uniform negative contrast across the cell body. This negative contrast improves automated cell segmentation efficiency over a wide field of view compared to in-focus imaging. We further evaluated the accessibility of this defocus imaging approach for both 2D and 3D cultures by implementing an automated cell segmentation protocol on a commercial off-the-shelf digital Universal Serial Bus (USB) microscope. The compact form factor of the digital USB microscope facilitates minimal pixel sampling, enabling high-throughput single-cell detection and continuous tracking across a large adherent cell population over several days. Our assessments of the utility of defocus imaging for 2D and 3D tissue cultures were further supported by monitoring the negative contrast changes during the migration and dissociation of 3D tissue spheroids. Our results show that negative contrast profiles from defocus images enable the quantification of cell proliferation, division, migration, and cell-to-cluster dissociation within standard culture environments. This defocusing methodology offers a scalable approach to extensive high-content screening through simplified instrumentation controls. Key pointsO_LIDefocused images of adherent cells using low NA optics homogenizes intracellular intensity hotspots, creating uniform negative contrast for whole cell segmentation; similar to shadow imaging in fluorescence. C_LIO_LIInverting look-up-table (LUT) combined with defocus imaging on large population of adherent cells in standard culture flask taken by standard digital USB microscopes allow for rapid, routine tracking of thousands of cells per field of view. C_LIO_LINegative contrast image profiles from defocusing enable the quantification cell proliferation, division, migration for 2D monolayer and 3D tissue spheroid cultures. C_LI

biophysics↗

bioRxiv2023

Soluble CTLA-4 raises the threshold for T-cell activation and modulates anti-tumour immunity

CTLA-4 is a crucial immune checkpoint receptor involved in the maintenance of immune homeostasis, tolerance, and tumour control. Antibodies targeting CTLA-4 have been promising treatment for numerous cancers, but the mechanistic basis of their anti-tumoral immune boosting effects are poorly understood. Although the ctla4 gene also encodes an alternatively-spliced soluble variant (sCTLA-4), preclinical/clinical evaluation of anti-CTLA-4-based immunotherapies have not considered the contribution of this isoform. Here, we explore the functional properties of sCTLA-4 and evaluate the efficacy of isoform-specific anti-sCTLA-4 antibody targeting in murine cancer model. We show that expression of sCTLA-4 in tumour cells suppresses CD8+ T-cells in vitro, and accelerates growth and experimental metastasis of murine tumours in vivo. These effects were accompanied by modification of the immune infiltrate, notably restraining CD8+ T-cells in a non-effector state. sCTLA-4 blockade with isoform-specific antibody reversed this restraint, enhancing intratumoural CD8+ T-cell activation and cytolytic potential, correlating with therapeutic efficacy and tumour control. This previously unappreciated role of sCTLA-4 suggests that better understanding of the biology and function of multi-gene products of immune checkpoint receptors needs to be fully elucidated for improved cancer immunotherapy.

cancer biology↗

bioRxiv2022

Combined scattering, interferometry and fluorescence oblique illumination for live cell nanoscale imaging

To determine the molecular and/or mechanical basis of cell migration using live cell imaging tools, it is necessary to correlate multiple 3D spatiotemporal events simultaneously. Fluorescence nanoscopy and label free nanoscale imaging can complement each other by providing both molecular specificity and structural dynamics of sub-cellular structure. In doing so, a combined imaging system would permit quantitative 3D spatial temporal detail of individual cellular components. In this paper, we empirically determined a series of optimal azimuthal scanning angles and rotating beam to achieve simultaneous and label-free nanoscale and fluorescence imaging. Label-free nanoscale imaging here refers to interferometric, brightfield (BF) and darkfield (DF) rotating coherence scattering (ROCS) microscopy, while fluorescence refers to high inclined Laminated Oblique (HiLO) and total internal reflection fluorescence (TIRF) imaging. The combined capabilities of interferometric, scattering and fluorescence imaging enables (1) the identification of molecular targets (substrate or organelle), (2) quantification of 3D cell morphodynamics, and (3) tracking of intracellular organelles in 3D. This combined imaging tool was then used to characterize migrating platelets and adherent endothelial cells, both critical to the process of infection and wound healing. The combined imaging results of over [~]1000 platelets, suggested that serum albumin (bovine) was necessary for platelets to migrate and scavenge fibrin/fibrinogen. Furthermore, we determine new asynchronous membrane fluctuations between the leading and rear edge of a migrating platelet. We further demonstrated that interferometric imaging permitted the quantification of mitochondria dynamics on lung microvascular cells (HMVEC). Our data suggests that axial displacement of mitochondria is minimized when it is closer to the nucleus or the leading edge of a cell membrane that exhibits retrograde motion. Taken together, this combined imaging platform has proven to quantify multiple spatial temporal events of a migrating cell, that will undoubtedly open ways to new quantitative correlative nanoscale live cell imaging.

biophysics↗

bioRxiv2022

Patterning Fluid Shear Stress Landscapes with Multiphoton Inner Laser Lithography (MILL) for Live Cell Adhesion and Translocation

Heterogenous fluid shear stress is known to provide mechanical cues for cell adhesion and translocation. To assemble 3D microstructures using current fabrication methods in a single channel and recapitulate in vivo heterogenous fluid flow would require hours of fabrication and specialized equipment. Inspired by the traditional art form of inside painting, we developed a technique for 3D fabrication of micro-patterned flow channels and mixed in vivo fluid flow in a matter of minutes. We termed this technique Multiphoton Inner Laser Lithography (MILL). We further showed that when combined with adaptive optics, MILL is compatible with both flat and curved channel shapes. MILL recapitulated in vivo tissue topology and 3D fluid flow within tissue stroma (low fluid shear, 0 - 3.5 dynes/cm2) and blood vessel (high fluid shear, 0 - 80 dynes/cm2). We demonstrate fibroblast cell and platelets adhere and translocate differently between laminar flow patterns that are homogenous versus heterogeneous in real time. Parallel strips of MILL channels were assembled for simultaneous platelet function test to quantify the efficacy of an antithrombotic GPVI Fab (~2000 microthrombi per test). The MILL technique can be readily reproduced in vivo fluid flow in minutes and benefit preclinical screening of drug pharmacokinetics. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=98 SRC="FIGDIR/small/496569v2_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@1efbe9eorg.highwire.dtl.DTLVardef@cbab5aorg.highwire.dtl.DTLVardef@15ed255org.highwire.dtl.DTLVardef@42d14e_HPS_FORMAT_FIGEXP M_FIG C_FIG Significant pointsO_LIMILL channels are made from commercially available off the shelf components using a standard multiphoton imaging system C_LIO_LIVarying degrees of in vivo heterogenous laminar flow is shown to directly influence cells translocating on thinly coated collagen surfaces C_LIO_LIParallel strips of MILL channels were assembled for simultaneous platelet function tests (~2000 microthrombi per test). C_LI

bioengineering↗

bioRxiv2020

COSI for label-free multiparameter quantitative imaging of intra-thrombus stability in vitro.

Although existing microfluidics in vitro assays recapitulate blood vessel microenvironment using surface-immobilized agonists under biofluidic flows, these assays do not quantify intra-thrombus mass and activities of adhesive platelets at agonist margin and uses fluorescence labeling, therefore limiting clinical translation potential. Here, we describe a real time label-free in vitro quantitative imaging flow assay called Coherent Optical Scattering and phase Interferometry (COSI) that evaluates both intra-thrombus and adhesive-only platelet dynamics using only changes in refractive index. By combining coherent optical scattering and optical interferometry, we evaluated and quantified both intra-thrombus mass with picogram accuracy and adhesive platelet-only events/dynamics with high spatial-temporal resolution (400 nm/s) under fluid shear stress using only changes in refractive index. Using oblique illumination, COSI provide a [~] 4 {micro}m thin axial slice that quantifies the magnitude of physical of surface adhesive platelets (spreading, adhesion and consolidation) in a developing thrombus without labelling under fluid shear stress. We achieve real time visualization of recruitment of single platelet into thrombus and further correlate it to the developing mass of a thrombus. The adhesive platelet activity exhibit stabilized surface activity of around 2 {micro}m/s and intra-thrombus mass exchange were balanced at around 1 picogram after treatment of a broad range metalloproteinase inhibitor (250 {micro}M GM6001). SignificanceThe combination of phase imaging with transmitted light and backscattering imaging via oblique illumination in COSI unpicked intra-thrombus mass and adhesive platelet-only activity events at picogram and sub-micrometer precision with millisecond time resolution under fluid shear stress. COSI maps the longitudinal time dynamics of adhesive platelets along changing thrombus mass under metalloproteinase inhibition, and demonstrates potential for real-time correlative microfluidic label-free imaging for flow-dependent biological adhesive events.

bioengineering↗

bioRxiv2020

Clustering of CD3ζ is sufficient to initiate T cell receptor signaling

T cell activation is initiated when ligand binding to the T cell receptor (TCR) triggers intracellular phosphorylation of the TCR-CD3 complex. However, it remains unknown how biophysical properties of TCR engagement result in biochemical phosphorylation events. Here, we constructed an optogenetic tool that induces spatial clustering of CD3{zeta} chains in a light controlled manner. We showed that spatial clustering of the CD3{zeta} intracellular tail alone was sufficient to initialize T cell triggering including phosphorylation of CD3{zeta}, Zap70, PLC{gamma}, ERK and initiated Ca2+ flux. In reconstituted COS-7 cells, only Lck expression was required to initiate CD3{zeta} phosphorylation upon CD3{zeta} clustering, which leads to the recruitment of tandem SH2 domain of Zap70 from cell cytosol to the newly formed CD3{zeta} clusters at the plasma membrane. Taken together, our data suggest that clustering of the TCR can initialize proximal TCR signaling and thus constitute a biophysical mechanism of TCR triggering.

immunology↗

bioRxiv2019

The Impact of Uremia and Intestinal Dysbiosis on Hepatic Drug Metabolism in a Rat Model of Progressive Chronic Kidney Disease

Nonrenal clearance pathways such as drug metabolism are decreased in chronic kidney disease (CKD). Although the mechanism remains elusive, uremic toxin retention and an altered gut microbiota are suspected to influence cytochrome P450s (CYPs) contributing to the unpredictable pharmacokinetics in patients with CKD. We characterized dysbiosis and uremia in CKD to elucidate associations between CYP expression and CKD progression. Rats fed control or CKD-inducing adenine diet were subsequently studied at five time points over 42 days. CYP expression and activity were compared to alterations in the 1) plasma and liver metabolome and 2) gut bacterial microbiota. CYP3A2 and CYP2C11 were downregulated in CKD by [≥]76% (p<0.001) concurrently with or slightly prior to CKD onset as defined by serum creatinine. Metabolite profiles were altered prior to changes in the gut microbiota, and gut-derived uremic toxins including indoxyl sulfate, phenyl sulfate and 4-ethylphenyl sulfate correlated with CYP3A2 or CYP2C11 expression. Bacterial genera Turicibacter and Parabacteroides were identified as being characteristic of CKD. In conclusion, CYP3A2 and CYP2C11 are downregulated before dysbiosis and correlate with select uremic toxins.

pharmacology and toxicology↗