Biology subjects

Chung, S. H.

Publications and source records attributed to Chung, S. H..

13 recordsLinked to original sources

bioRxiv2025

User-Assisted Approach for Accurate Nonrigid Registration of Images and Traces

Fully automated registration algorithms are prone to getting trapped in solutions corresponding to local minima of their objective functions, leading to errors that are easy to detect but challenging to correct. Traditional solutions often involve iterative parameter tuning, data preprocessing and preregistering, and multiple algorithm reruns--an approach that is both time-consuming and does not guarantee satisfactory results. Therefore, for tasks where registration accuracy is more important than speed, it is appropriate to explore alternative, user-assisted registration strategies. In such tasks, finding and correcting errors in automated registration is often more time-consuming than directly integrating user input during the registration process. Therefore, this study evaluates a user-assisted approach for accurate nonrigid registration of images and traces. By leveraging the corresponding sets of fiducial points provided by the user to guide the registration, the algorithm computes an optimal nonrigid transformation that combines linear and nonlinear components. Our findings demonstrate that the registration accuracy of this approach improves consistently with the increased complexity of the linear transformation and as more fiducial points are provided. As a result, accuracy sufficient for many biomedical applications can be achieved within minutes, requiring only a small number of user-provided fiducial points.

bioengineering↗

bioRxiv2024

Tensions on the actin cytoskeleton and apical cell junctions in the C. elegans spermatheca are influenced by spermathecal anatomy, ovulation state and activation of myosin

Cells generate mechanical forces mainly through myosin motor activity on the actin cytoskeleton. In C. elegans, actomyosin stress fibers drive contractility of the smooth muscle-like cells of the spermatheca, a distensible, tube-shaped tissue in the hermaphrodite reproductive system and the site of oocyte fertilization. Stretching of the spermathecal cells by oocyte entry triggers activation of the small GTPase Rho. In this study, we asked how forces are distributed in vivo using the spermatheca, and explored how this tissue responds to alterations in myosin activity. Using laser ablation, we show that the basal actomyosin fibers are under tension in the occupied spermatheca. Reducing actomyosin contractility by depletion of the phospholipase C-{varepsilon}/PLC-1 or non-muscle myosin II/NMY-1, leads to distended spermathecae occupied by one or more embryos, but does not alter tension on the basal actomyosin fibers. This suggests that much of the tension on the basal actin fibers in the occupied spermatheca is due to the presence of the embryo. However, activating myosin through depletion of the Rho GAP SPV-1 increases tension on the actomyosin fibers, consistent with earlier studies showing Rho drives spermathecal contractility. On the inner surface of the spermathecal tube, tension on the apical junctions is decreased by depletion of PLC-1 and NMY-1. Surprisingly, when basal contractility is increased through SPV-1 depletion, the tension on apical junctions also decreases, with the most significant effect on the junctions aligned in perpendicular to the axis of the spermatheca. This suggests tension on the outer basal surface may compress the apical side, and suggests the three-dimensional shape of the spermatheca plays a role in force distribution and contractility during ovulation.

cell biology↗

bioRxiv2024

Normalized level set model for segmentation of low-contrast objects in 2- and 3- dimensional images

Analyses of biomedical images often rely on accurate segmentation of structures of interest. Traditional segmentation methods based on thresholding, watershed, fast marching, and level set perform well in high-contrast images containing structures of similar intensities. However, such methods can under-segment or miss entirely low-intensity objects on noisy backgrounds. Machine learning segmentation methods promise superior performance but require large training datasets of labeled images which are difficult to create, particularly in 3D. Here, we propose an algorithm based on the Local Binary Fitting (LBF) level set method, specifically designed to improve the segmentation of low-contrast structures.

bioengineering↗

bioRxiv2023

Real-time targeted illumination in widefield microscopy achieves confocal quality neuronal images

Widefield fluorescence imaging has significant challenges in visualizing neuronal fibers near cell bodies. Specifically, out-of-focus and scattered light from the bright cellbody often obscures nearby dim fibers and degrades their signal-to-background ratio. Scanning techniques can solve this problem but are limited by reduced imaging speed and increased cost. We greatly reduce stray light by modulating the illumination intensity to different structures. We use a digital micromirror device in the illumination channel of a common widefield microscope and use real-time image processing to pattern the illumination. With the setup, we illuminate bright cell bodies with minimal light intensity, and illuminate in focus fiber-like structures with high light intensity to reveal weak signals. Thus, we minimize the background and enhance the visibility of fibers in the final image. This targeted illumination significantly improves fiber contrast while maintaining a fast-imaging speed and low cost. Using a targeted illumination setup in a widefield microscope, we demonstrate confocal quality imaging of complex neurons in live C. elegans and zebrafish larva, as well as in in vitro mice brain slice.

neuroscience↗

bioRxiv2023

Assembly and operation of a cooling stage to immobilize C. elegans on their culture plates

High-resolution in vivo microscopy approaches can reveal subtle information and fine details inside the model animal Caenorhabditis elegans (C. elegans) but requires strong animal immobilization. Unfortunately, most current immobilization techniques require substantial manual effort, rendering high-resolution imaging low-throughput. We greatly simplify the C. elegans immobilization procedure by using a cooling approach that can easily immobilize entire populations of C. elegans directly on their cultivation plates. The cooling stage can establish and maintain a wide range of temperatures on the cultivation plate and ensures even temperature distribution across the agarose surface. In this article, we document the whole process of building the cooling stage from scratch. We envision that a typical researcher can build an operational cooling stage in their lab following our protocol without difficulty. We show how to utilize the cooling stage under three protocols, which have advantages for different experiments. We also show an example cooling profile of the stage as it approaches its final temperature and include some helpful tips in using cooling immobilization.

bioengineering↗

bioRxiv2022

Expression of thioredoxin-1 in the ASJ neuron corresponds with and enhances intrinsic regenerative capacity under lesion conditioning in C. elegans

A conditioning lesion of the peripheral sensory axon triggers robust central axon regeneration in mammals. We trigger conditioned regeneration in the C. elegans ASJ neuron by laser surgery or genetic disruption of sensory pathways. Conditioning upregulates trx-1 expression, as indicated by trx-1 promoter-driven green fluorescent protein and fluorescence in situ hybridization, suggesting trx-1 levels and associated fluorescence indicate regenerative capacity. Redox activity of trx-1 functionally enhances conditioned regeneration, but both redox-dependent and -independent activity inhibit non-conditioned regeneration. Six strains isolated in a forward genetic screen for reduced fluorescence, which suggests diminished regenerative potential, also show reduced axon outgrowth. We demonstrate an association between trx-1 expression and the conditioned state that we leverage to rapidly assess regenerative capacity.

neuroscience↗

bioRxiv2022

Use of sugarcane mosaic virus for virus-induced gene silencing in maize

Previously, sugarcane mosaic virus (SCMV) was developed as a vector for transient expression of heterologous genes in Zea mays (maize). Here we show that SCMV can also be applied for virus-induced gene silencing (VIGS) of endogenous maize genes. Comparison of sense and antisense VIGS constructs targeting maize PDS (phytoene desaturase) showed that antisense constructs resulted in a greater reduction in gene expression. In a time course of gene expression after infection with VIGS constructs targeting PDS, Les22 (Lesion mimic 22), and Ij1 (Iodent japonica1), efficient expression silencing was observed two, three, and four weeks after infection with SCMV. However, at week five, expression of Les22 and Ij1 was no longer significantly reduced compared to control plants. The defense signaling molecule jasmonate-isoleucine (JA-Ile) can be inactivated by 12C-hydroxylation and hydrolysis, and knockout of these genes leads to increased herbivore resistance. JA-Ile hydroxylases and hydrolases have been investigated in Arabidopsis, rice, and Nicotiana attenuata. To determine whether the maize homologs of these genes function in plant defense, we silenced expression of ZmCYP94B1 (predicted JA-Ile hydroxylase) and ZmJIH1 (predicted JA-Ile hydrolase) by VIGS with SCMV. Although ZmCYP94B1 and ZmJIH1gene expression silencing increased resistance to Spodoptera frugiperda (fall armyworm), Schistocerca americana (American birdwing grasshopper), and Rhopalosiphum maidis (corn leaf aphid), there was no additive effect from silencing the expression of both genes. Further work will be required to determine the more precise functions of these enzymes in regulating maize defenses.

plant biology↗

bioRxiv2022

Transverse and axial resolution of femtosecond laser ablation

Femtosecond lasers are capable of precise ablation that produce surgical dissections in vivo. The transverse and axial resolution of the laser damage inside the bulk are important parameters of ablation. The transverse resolution is routinely quantified, but the axial resolution is more difficult to measure and is less commonly performed. In some in vivo samples, fine dissections can also be difficult to visualize, but in vitro samples may allow clear imaging. Using a 1040-nm, 400-fs pulsed laser, we performed ablation inside agarose and glass, producing clear and persistent damage spots. Near the ablation threshold of both media, we found that the axial resolution is similar to the transverse resolution. We also ablated neuron cell bodies and fibers in C. elegans and demonstrate submicrometer resolution in both the transverse and axial directions, consistent with our results in agarose and glass. Using simple yet rigorous methods, we define the resolution of laser ablation in transparent media along all directions.

bioengineering↗

bioRxiv2021

Immobilization of C. elegans on cultivation plates by thermoelectric cooling for high-throughput subcellular-resolution microscopy

Despite its profound impact on biology, most high-resolution in vivo microscopy approaches remain low throughput because current immobilization techniques require significant manual effort. We greatly accelerate imaging of the nematode Caenorhabditis elegans by implementing a simple cooling approach to easily immobilize entire populations directly on their cultivation plates. We optimize and characterize cooling immobilization. Counterintuitively, relatively warmer temperatures immobilize animals significantly more effectively than colder temperatures utilized in prior studies. This enhanced immobilization enables clear submicron-resolution fluorescence imaging, which is challenging to achieve with most current immobilization techniques. We demonstrate 64x magnification 3D imaging and timelapse recording of neurons in adults and embryos without motion blur. Compared to standard azide immobilization, cooling immobilization reduces the animal preparation and recovery time by >98%, significantly increasing experimental speed. By obviating individual animal manipulation, our approach could also empower automated imaging of large C. elegans populations within standard experimental setups and workflows.

bioengineering↗

bioRxiv2021

Rapid screening of pest resistance genes in maize using a sugarcane mosaic virus vector

Spodoptera frugiperda (fall armyworm) is a notorious pest that threatens maize production world-wide. Current control measures involve the use of chemical insecticides and transgenic maize expressing Bacillus thuringiensis (Bt) toxins. Although several additional transgenes have confirmed insecticidal activity in other plants, limited research has been conducted in maize, at least partially due to the technical difficulty of maize transformation. Here, we describe implementation of a sugarcane mosaic virus (SCMV) vector for rapidly testing the efficacy of transgenes for the control of S. frugiperda in maize. Four categories of proteins were tested using the SCMV vector: (i) maize defense signaling proteins: peptide elicitors (Pep1 and Pep3) and jasmonate acid conjugating enzymes (JAR1a and JAR1b); (ii) maize defensive proteins: the previously identified ribosome-inactivating protein (RIP2) and maize proteinase inhibitor (MPI), and two proteins with predicted but unconfirmed anti-insect activities, an antimicrobial peptide (AMP) and a lectin (JAC1); (iii) lectins from other plant species: Allium cepa agglutinin (ACA) and Galanthus nivalis agglutinin (GNA); and (iv) spider and scorpion toxins: peptides from Urodacus yaschenkoi (UyCT3 and UyCT5) and Hadronyche versuta (Hvt). In most cases, S. frugiperda larval growth on maize was reduced by transient SCMV-mediated overexpression of genes encoding these proteins. Additionally, experiments with some of the SCMV-expressed genes showed effectiveness against two aphid species, Rhopalosiphum maidis (corn leaf aphid) and Myzus persicae (green peach aphid). Together, these results demonstrate that SCMV vectors can be exploited as a rapid screening method for testing the efficacy and insecticidal activity of candidate genes in maize.

plant biology↗

bioRxiv2020

Confocal imaging capacity on a widefield microscope using a spatial light modulator

Confocal microscopes can reject out-of-focus and scattered light; however, widefield microscopes are far more common in biological laboratories due to their accessibility and lower cost. We report confocal imaging capacity on a widefield microscope by adding a spatial light modulator (SLM) and utilizing custom illumination and acquisition methods. We discuss our illumination strategy and compare several procedures for postprocessing the acquired image data. We assessed the performance of this system for rejecting out-of-focus light by comparing images taken using our widefield microscope, our SLM-enhanced setup, and a commercial confocal microscope. The optical sectioning capability, assessed on thin fluorescent film, was 0.85 {+/-} 0.04 m for our SLM-enhanced setup and 0.68 {+/-} 0.04 m for a confocal microscope, while a widefield microscope exhibited no sectioning capability. We demonstrate our setup by imaging the same set of neurons in C. elegans on widefield, SLM, and confocal microscopes. SLM enhancement greatly reduces background from the cell body, allowing visualization of dim fibers nearby. Our SLM-enhanced setup identified 93% of the dim neuronal fibers seen in confocal images while a widefield microscope only identified 48% of the same fibers. Our microscope add-on represents a very simple (2-component) and inexpensive (<$600) approach to enable widefield microscopes to optically section thick samples.

bioengineering↗

bioRxiv2020

Host immune responses after suprachoroidal delivery of AAV8 in nonhuman primate eyes

The suprachoroid is a potential space located between the sclera and choroid of the eye which provides a novel route for ocular drug or viral vector delivery. Suprachoroidal injection of AAV8 using transscleral microneedles enables widespread transgene expression in eyes of nonhuman primates, but may cause intraocular inflammation. We characterized the host humoral and cellular immune responses after suprachoroidal delivery of AAV8 expressing green fluorescent protein (GFP) in rhesus macaques, and found that it can induce a mild chorioretinitis that resolves after systemic corticosteroid administration, with recovery of photoreceptor morphology but persistent immune cell infiltration after 3 months. Suprachoroidal AAV8 triggered B-cell and T-cell responses against GFP, but only mild antibody responses to the viral capsid as compared to intravitreal injections of the same vector and dose. Systemic biodistribution studies showed lower AAV8 levels in liver and spleen after suprachoroidal injection compared with intravitreal delivery. Our findings suggest that suprachoroidal AAV8 primarily triggers host immune responses to GFP, likely due to sustained transgene expression in scleral fibroblasts outside the blood-retinal barrier, but elicits less humoral immune reactivity to the viral capsid than intravitreal delivery due to lower egress into systemic circulation. Thus, suprachoroidal AAV delivery of human transgenes may have significant translational potential for retinal gene therapy.

genetics↗

bioRxiv2019

Ytterbium-doped fibre femtosecond laser offers robust design with deep and precise microsurgery

Laser microsurgery is a powerful tool for neurobiology used to ablate cells and sever neurites in-vivo. We compare a relatively new laser source to two well-established designs. Rare-earth-doped mode-locked fibre laser that produce high power pulsed radiation recently gained popularity for industrial uses. Such systems are manufactured at high standards of robustness and low maintenance requirements typical of solid-state lasers. We demonstrate that an Ytterbium-doped fibre femtosecond laser is comparable in precision to other femtosecond lasers, but with added reliability. It is more precise and can lesion deeper in tissue than a solid-state nanosecond laser. These advantages are not specific to the model system ablated for our demonstration, namely neurites in the nematode C. elegans, but are applicable to other systems and transparent tissue where a precise submicron resolution dissection is required.

neuroscience↗