Biology subjects

Ch'ng, Q.

Publications and source records attributed to Ch'ng, Q..

6 recordsLinked to original sources

bioRxiv2026

An integrated pipeline to count individual transcripts with single-cell resolution

Quantifying transcript abundance at single-cell resolution is important for understanding gene regulation in intact multicellular organisms. In Caenorhabditis elegans, RNA fluorescence in situ hybridization has been widely used to visualize transcripts, but conventional smFISH approaches can be limited by low signal-to-noise, poor performance with short transcripts, and workflows that do not readily support absolute transcript counting in identified cells. Here, we present an integrated experimental and computational pipeline for quantitative transcript analysis in whole-mount C. elegans embryos, larvae, and adults. The pipeline combines Hybridization Chain Reaction (HCR), confocal microscopy, RS-FISH spot detection, manual cell annotation in FIJI, and custom MATLAB-based spot assignment to quantify individual transcripts within defined cells. We show that this approach enables sensitive, specific, and multiplexed detection of transcripts, including short insulin-like peptide mRNAs, with single-cell resolution. Known spatial expression patterns were resolved in embryos, larvae, and adults, and probe specificity was validated using deletion mutants that remove HCR probe-binding sites. Applying this pipeline to ins-4, ins-6, and daf-28 in ASI and ASJ sensory neurons revealed cell-specific and context-dependent regulatory relationships across multiple mutant backgrounds. This workflow provides an accessible method for absolute transcript counting in anatomically intact C. elegans and should support mechanistic studies of gene regulation, cellular heterogeneity, and transcriptional network function.

molecular biology↗

bioRxiv2026

Advanced in High-Resolution Cryo Volume Electron Microscopy (cvEM) Imaging for Unicellular and Multicellular Organisms

Cryo-Focused Ion Beam Scanning Electron Microscopy (cryoFIB-SEM) using samples fixed by high-pressure freezing uniquely enables high resolution cryo-volume Electron Microscope (cvEM) images of cell ultrastructure to be obtained from whole cells and complex tissues in their near native state. As the freezing process also preserves fluorescence, the link between three-dimensional (3D) ultrastructure and biological process is also enabled by targeted cryo-Correlative Light and Electron Microscopy (CLEM). However, the overall viability of cvEM is challenged by sample preparation, charge balance during imaging, sample sensitivity to beam damage, contamination, and very long acquisition times. Here we detail new experimental workflows to significantly reduce each of these effects and demonstrate the improvement in resolution possible with results from the nematode Caenorhabditis elegans and the ciliated protozoon Paramecium bursaria containing many endosymbiotic algae. These results demonstrate the versatility and potential wide-ranging utility of cvEM for 3D ultrastructural imaging of whole multicellular and unicellular organisms.

biophysics↗

bioRxiv2025

The neuropeptide neuromedin U receptor nmur-1 buffers insulin receptor signaling in bacteria-dependent C. elegans survival

Distinct microbial environments exert diverse effects on the physiology and survival of the nematode Caenorhabditis elegans. Here, we show that C. elegans grown on two Escherichia coli strains exhibit different survival dynamics. Wild-type C. elegans on the B type OP50 exhibit more early deaths compared to C. elegans on K-12 type CS180. These early deaths on OP50 are characterized by swollen pharynges (P-deaths) due to bacterial accumulation within the tissue. In contrast, animals on CS180 are more resistant to P-deaths. These bacteria-dependent differences in P-deaths depend on bacterial lipopolysaccharide structures and the activities of the C. elegans neuropeptide neuromedin U receptor NMUR-1, which reduces P-deaths on OP50, but not on CS180. Surprisingly, however, NMUR-1 promotes the opposite response when the insulin receptor DAF-2 has reduced function -- where NMUR-1 now stimulates P-deaths on OP50, but again with no effect on CS180. We also find that NMUR-1 acts in sensory neurons to promote its bi-directional effects on longevity, which depend on the FOXO transcription factor DAF-16. In addition, NMUR-1 downregulates the expression of the insulin-like peptide daf-28, but only when DAF-2 function is not reduced. This suggests a regulatory mechanism through which NMUR-1 maintains insulin receptor DAF-2 signaling at a suitable level. Thus, our studies reveal that NMUR-1 serves to buffer the dynamic range of DAF-2 receptor signaling, thereby optimizing pharyngeal health and survival in response to specific bacteria.

physiology↗

bioRxiv2025

Extracting biological structure and heterogeneity from the nano to the macro scale

Fluorescence microscopy is an essential tool in biology. It has revealed great variability at multiple scales, in macromolecular complexes, cells, and organisms. Understanding this variability will reveal the mechanisms by which genetically or biochemically identical systems adopt different biological states. Achieving this requires the ability to extract both the underlying biological structure and how it varies across the population. Currently the field lacks general techniques to deal with arbitrary structures and different types of variability. Here we present SQUASSH, a new convolutional neural network-based approach to freely fit structural models to fluorescence microscopy data that simultaneously quantifies variability to reveal correlations, dynamics, and systematic distortions. SQUASSH is highly versatile: it accommodates diverse imaging modalities at length scales from nm to mm. This approach opens up applications such as imaging nanoscale macromolecular structures, revealing patterns in shape changes from organelle to tissue scale, and characterizing systems biology of dynamical processes.

cell biology↗

bioRxiv2022

Specific sensory neurons and insulin-like peptides modulate food type-dependent oogenesis and fertilization in Caenorhabditis elegans

AbstractAn animals responses to environmental cues are critical for its reproductive program. Thus, a mechanism that allows the animal to sense and adjust to its environment should make for a more efficient reproductive physiology. Here we demonstrate that in Caenorhabditis elegans specific sensory neurons influence onset of oogenesis through insulin signaling in response to food-derived cues. The chemosensory neurons ASJ modulate oogenesis onset through the insulin-like peptide (ILP) INS-6. In contrast, other sensory neurons, the olfactory neurons AWA, regulate food type-dependent differences in C. elegans fertilization rates, but not onset of oogenesis. AWA modulates fertilization rates at least partly in parallel to insulin receptor signaling, since the insulin receptor DAF-2 regulates fertilization independently of food type, which requires ILPs other than INS-6. Together our findings suggest that optimal reproduction requires the integration of diverse food-derived inputs through multiple neuronal signals acting on the C. elegans germline.

developmental biology↗

bioRxiv2019

A Multicellular Network Mechanism for Temperature-Robust Food Sensing

Responsiveness to external cues is a hallmark of biological systems. In complex environments, organisms must remain responsive to specific inputs even as other internal or external factors fluctuate. Here we show how Caenorhabditis elegans can discriminate between food levels to modulate lifespan despite temperature perturbations. While robustness of fixed outputs has been described, our findings uncover a more complex robustness process that maintains food-responsiveness. This end-to-end robustness from environment to physiology is mediated by food-sensing neurons that communicate via TGF-{beta} and serotonin signals to form a multicellular gene network. Mechanistically, specific regulations in this network change with temperature to maintain similar food-responsiveness in the lifespan output. Together, our findings provide a basis for gene-environment interactions and unveil computations that integrate environmental cues to govern physiology.

systems biology↗