Biology subjects

Cheung, K. C.

Publications and source records attributed to Cheung, K. C..

10 recordsLinked to original sources

bioRxiv2026

Strategies to improve neurite outgrowth from primary neurons ingelatin methacrylate hydrogels polymerized with visible lightexposure inside a microscale 3D model

Gelatin methacrylate (GelMA) hydrogels offer many advantageous properties such as excellent biocompatibility, tunable stiffness, and rapid fabrication, making them attractive materials for neural systems-on-a-chip devices used to study axonal outgrowth in three-dimensional (3D) environments. In this study, we evaluate properties of GelMA hydrogels crosslinked with visible blue light and application of these hydrogels for encapsulation of primary dorsal root ganglion (DRG) explants inside a custom microscale device. We selected low GelMA polymer concentrations of 3 % and 6 % w/v for hydrogel preparation to create soft materials and demonstrate the effect of degree of functionalization (DoF) on stiffness of GelMA in a blue light-induced crosslinking system. Additionally, a decrease in crosslinking efficiency and stiffness of GelMA was observed upon reconstitution of the polymer in DMEM cell culture media compared to PBS. To evaluate the axonal outgrowth, DRG explants were encapsulated in various GelMA formulations and cultured for 7 days. Following incubation, the explants were fixed and immunochemically labelled with anti-beta-III-tubulin antibody. We further describe an application of custom-developed semi-automated image analysis tool together with linear mixed effects modeling to evaluate axonal outgrowth across different GelMA formulations. Among the formulations tested in our study, 3 % GelMA 95 % DoF hydrogels supported the longest neurite outgrowth suggesting that matrix properties influenced neurite extension.

bioengineering↗

bioRxiv2026

Multiplexed hormone immunoassays for women's health on a regenerable silicon photonic chip

Hormone dynamics are central to a multitude of conditions in women's health; however, limitations in the cost, convenience, and multiplexing capacity of current hormone assays preclude routine longitudinal hormone testing. This limitation severely restricts our understanding in this historically neglected field, presenting a need for improved bioanalytical tools to support hormone-informed care. Silicon photonic resonator sensors have excellent multiplexing capacity and scalable fabrication, and offer strong potential to meet this important need. Here we demonstrate, for the first time, multiplexed silicon photonic detection of two urinary hormone biomarkers, follicle-stimulating hormone (FSH) and pregnanediol-3-glucuronide (PdG), using sub-wavelength grating ring resonators and a polydopamine-based, regenerable surface chemistry. We combine a sandwich immunoassay for FSH and an antigen-down competitive immunoassay for PdG on the same chip, both amplified using a commercially available quantum-dot-streptavidin conjugate and with on-chip regeneration over multiple measurement cycles. In artificial urine, this proof-of-principle multiplexed assay achieves limits of detection of 0.594 ng/mL for FSH and 19.1 ng/mL for PdG. This architecture is inherently scalable to tens of hormone targets on a millimetre-scale chip (a >10x multiplexing improvement over typical lateral-flow immunoassays) enabling future low-cost, quantitative at-home hormone panels that could transform research, diagnostics, and treatment in women's health.

bioengineering↗

bioRxiv2026

Effects of MRI on an Injectable Hydrogel with Magnetically Alignable Microstructures for Oriented Cell Growth

Injectable biomaterials with aligned microstructures play a critical role in tissue engineering and drug-delivery applications where control over the position and orientation of cells and nano/micron-scale architectures enhance intervention efficacy. Patients are often subject to MRI scans; for patient safety and treatment efficacy, we investigated the effects of MRI on a biomaterial treatment consisting of aligned magnetic microstructures being developed for guiding cell growth. Under MRI exposure, potential movement of aligned structures could be detrimental to nearby cells, and potential MRI-induced heating could adversely affect traumatized tissue. In this work, the alignment state and heat conduction of such a treatment were studied using a 9.4 T preclinical MRI. The treatment comprises short magnetic rod-shaped polycaprolactone fibers (rods) with embedded magnetic nanoparticles in a surrounding hydrogel (gelatin methacrylate), with rod alignment observed before and after a 45-minute MRI scan. No change in rod alignment state was observed, and no heat generation was measured. A theoretical framework was developed which supports the experimental observation that the biomaterial is stable under MRI. This work can be extended to other biomaterial systems with aligned architectures used in tissue engineering applications such as spinal cord, muscle and tendon.

bioengineering↗

bioRxiv2025

SPIN: Inkjet-Driven Nanowell Workflow for Scalable and Sensitive Single-Cell Proteomics

Single-cell proteomics is emerging as a powerful approach to resolve cellular heterogeneity, yet sample processing remains challenging due to limited input material and the absence of protein amplification. We present a protocol centered on an image-guided, machine-learning-driven inkjet single-cell printer integrated with a dew-point-controlled nanowell chip to reduce loss, increase throughput, and improve reproducibility. The system dispenses single cells at >1 Hz into sealed nanoliter wells with minimal surface contact, virtually eliminating evaporation; a high-thermal-conductivity aluminum substrate and precise environmental control further ensure exceptional reproducibility. Relative to a commercial dispenser, the workflow yields significantly higher protein and peptide recovery without bias toward high-abundance species, delivering uniformly deep coverage. Biological pathway analysis emphasizes the robustness of this workflow, as there is a near 100% protein completeness detected among the enzymes in the Kreb cycle in both A549 and astrocytes, suggesting the consistency across all samples evaluated. This platform addresses core processing bottlenecks and enables reliable, scalable single-cell proteomics.

systems biology↗

bioRxiv2025

What Could Go Wrong? Promoting Success by Planning for Failure in Label-Free Biosensor Assay Development

Label-free biosensors offer powerful platforms for detecting molecular interactions, but developing robust assays on these systems presents several challenges due to the complexity of the testing systems and intersection of disciplines. In this work, we describe a lightweight, 3-step experimental workflow supporting troubleshooting and root cause analysis that we developed during the design and optimization of silicon photonic biosensor assays in an academic research setting. Because such environments often lack the resources and formal quality-management infrastructure available in industry, our approach emphasizes practicality and ease of adoption. Drawing from our own assay failures and successes, we identify common failure modes, propose structured troubleshooting workflows, and provide case studies illustrating the application of established frameworks, including the Five Whys, the Plan-Do-Check-Act cycle, Open-Narrow-Close and the Ishikawa (fishbone) diagram. By applying this framework to our research, we increased our assay yield by a factor of 2, from ~45% to ~90%. This paper aims to support other teams engaged in label-free assay development by equipping them with practical tools and experimental best practices. HighlightsO_LIWe doubled assay yield from ~45% to ~90% by planning for failure, not just success. C_LIO_LITailored troubleshooting frameworks help pinpoint and solve various assay failures. C_LIO_LIApplying innovative problem-solving to workflows accelerates biosensor development. C_LIO_LISystematic troubleshooting improves assay development across a range of lab settings. C_LIO_LIA 3-step workflow highlighting what could go wrong supports continuous improvement. C_LI

bioengineering↗

bioRxiv2025

Resonating with replicability: factors shaping assay yield and variability in microfluidics-integrated silicon photonic biosensors

The integration of biosensors and microfluidics has facilitated the development of compact analytical devices capable of performing automated and information-rich detection of myriad targets, both in the lab and at the point of need. However, optimization of microfluidics-integrated biosensor systems and replicability challenges present roadblocks in validation and commercialization. Understanding factors contributing to yield and replicability in biosensor performance is key to the development of biosensor optimization frameworks and technology translation beyond the research setting. Hence, for the first time, we present a detailed analysis of factors affecting performance, assay yield, and intra- and inter-assay replicability in microfluidics-integrated silicon photonic (SiP) evanescent-field microring resonator biosensors. Strategies for mitigating bubbles--a major operational hurdle and contributor to instability and variability in microfluidics-integrated biosensors--are analyzed to improve assay yield. Effective bubble mitigation is demonstrated by combining microfluidic device degassing, plasma treatment, and microchannel pre-wetting with surfactant solution. Both intrinsic and analyte-detection performance metrics and their replicability are quantified for the first time for sub-wavelength grating-based SiP biosensors, highlighting a path to further optimization. Lastly, the effects of sensor functionalization on analyte detection performance and replicability are evaluated. We compare polydopamine-vs. Protein A-mediated bioreceptor immobilization chemistries and spotting-vs. flow-mediated bioreceptor patterning approaches. We find that simple polydopamine-mediated, spotting-based functionalization improves spike protein (1 {micro}g/mL) detection signal by 8.2x and 5.8x compared to polydopamine/flow and Protein A/flow approaches, respectively, and yields an inter-assay coefficient of variability below the standard 20% threshold for immunoassay validation. Overall, this work proposes a practical framework through which evanescent-field SiP biosensors, and microfluidics-integrated biosensors more generally, can be characterized, compared, and optimized to facilitate efficient biosensor development.

bioengineering↗

bioRxiv2023

Deepurify: a multi-modal deep language model to remove contamination from metagenome-assembled genomes

Metagenome-assembled genomes (MAGs) offer valuable insights into the exploration of microbial dark matter using metagenomic sequencing data. However, there is a growing concern that contamination in MAGs may significantly impact the downstream analysis results. Existing MAG decontamination methods heavily rely on marker genes but do not fully leverage genomic sequences. To address the limitations, we have introduced a novel decontamination approach named Deepurify, which utilizes a multi-modal deep language model employing contrastive learning to learn taxonomic similarities of genomic sequences. Deepurify utilizes inferred taxonomic lineages to guide the allocation of contigs into a MAG-separated tree and employs a tree traversal strategy for maximizing the total number of medium- and high-quality MAGs. Extensive experiments were conducted on two simulated datasets, CAMI I, and human gut metagenomic sequencing data. These results demonstrate that Deepurify significantly outperforms other decontamination methods.

genomics↗

bioRxiv2023

Cryo-EM structure of TMEM63C suggests it functions as a monomer

The TMEM63 family proteins (A, B, and C), calcium-permeable channels in animals that are preferentially activated by hypo-osmolality, have been implicated in various physiological functions. Deficiency of these channels would cause many diseases including hearing loss. However, their structures and physiological roles are not yet well understood. In this study, we determined the cryo-EM structure of the mouse TMEM63C at 3.56 [A], and revealed structural differences compared to its plant orthologues OSCAs. Further structural guided mutagenesis and electrophysiological studies demonstrated the important roles of the coupling of TM0 and TM6 in channel activity. Additionally, we confirmed that the physiological state of TMEM63C is monomer, while TMEM63B is a mix of monomer and dimer in cells, suggesting that oligomerization is a novel regulatory mechanism for TMEM63 proteins.

biophysics↗

bioRxiv2020

Pollutants in Hong Kong Soils: Organochlorine Pesticides and Polychlorinated Biphenyls

Organochlorine pesticides (OCPs) and polychlorinated biphenyls (PCBs) were investigated in 138 soil samples collected in Hong Kong. Results showed that within the selected OCPs, only DDT and its metabolites (DDD and DDE) were frequently detected. Of 138 soil samples, 18% were non-detected for any DDT residues, while 25% were contaminated sporadically with DDT only (non-detected to 1090 {micro}g kg-1) and 57% contained various combinations of DDT, DDD and DDE (2.03 to 1118 {micro}g kg-1). In contrast, total PCBs ({sum}66 congeners) contamination was distributed more evenly (0.22 to 154 {micro}g kg-1) than DDTs, but serious contamination was found in industrial areas and soils collected near highways. Concentrations of 7 indicator PCBs ranged between non-detected to 34.5 {micro}g kg-1. The ratios of DDT/metabolites were typically greater than 1, thus suggesting recent application of DDT. Medium-range deposition from industrial areas within as well as away from the city is also suspected to be the origins of DDTs and PCBs found in Hong Kong soils. The concentrations of DDTs and PCBs in all soil samples did not exceed the recommended values in soil quality guidelines except 3 samples for DDT from locations far away from densely populated districts such as Tuen Mun and Tin Shui Wai. Therefore, DDTs and PCBs were not of significant concern in terms of their impacts on public health and environment.

pharmacology and toxicology↗

bioRxiv2020

Pollutants in Hong Kong Soil: As, Cd, Cr, Cu, Hg, Pb and Zn

Six heavy metals (Hg, Cu, Cd, Cr, Pb, Zn) and 1 metalloid (As) in surface soils of Hong Kong were investigated in 10 land use categories (urban park, greening area, country park, rural area, restored landfill, agricultural farmland, orchard farm, crematorium, industrial and near highway area). Edaphic Hg concentration in Hong Kong was firstly reported here. Clustering of land uses was observed based on total pollutants concentrations (sum of 7 metals). The most polluted cluster consisted of industrial and highway areas (median: 617 to 833 mg kg-1) and the runner-up cluster included urban park, greening area and restored landfill (median: 400 to 500 mg kg-1). However, this general finding was not observed for Hg, where higher concentration was found in agricultural farmland (median 109 g kg-1). The use of low quality fertilizers, together with the contribution from exhausts and wearable parts from automobiles were believed to be the major sources of Cr, Cu and Zn in Hong Kong, while the application of Hg-containing agrochemicals maybe the main mechanism of Hg contamination in agricultural soil. Based on the daily intake assumption of 0.2 g d-1 of soil particles by USEPA, direct ingestion of Hg-containing soils is not a major exposure pathway for population in Hong Kong. When comparing the edaphic heavy metal concentrations with Dutch soil quality guidelines demonstrated that Hg, Cd and Pb were not in level of health concerns, while Cu, Cr and Zn in less than 6% of total samples were found to exceed the Dutch intervention values sporadically. In contrast, suburban soils from northern and northeastern Hong Kong were mostly contaminated with As (10% of total samples) at concentration that could be potentially causing adverse health impacts to the nearby population. Pollutant in Hong Kong soils seriesO_LIChung, M. K., Hu, R., Cheung, K. C. & Wong, M. H. Pollutants in Hong Kong soils: Polycyclic aromatic hydrocarbons. Chemosphere 67, 464-473 (2007). http://doi.org/10.1016/j.chemosphere.2006.09.062 C_LIO_LIChung, M. K., Cheung, K. C. & Wong, M. H. Pollutants in Hong Kong Soil: As, Cd, Cr, Cu, Hg, Pb and Zn https://doi.org/10.1101/2020.02.16.951558 C_LIO_LIChung, M. K., Hu, R., Cheung, K. C. & Wong, M. H. Pollutants in Hong Kong Soils: Organochlorine Pesticides and Polychlorinated Biphenyls https://doi.org/10.1101/2020.02.16.951541 C_LI

pharmacology and toxicology↗