Biology subjects

Tan, K. H.

Publications and source records attributed to Tan, K. H..

5 recordsLinked to original sources

bioRxiv2026

Isolation and Characterization of a Novel Calcium-Precipitating Alkali-Tolerant Lysinibacillus sphaericus in Local Urban Environment

Concrete is an extensively used construction material in infrastructures due to cost-effectiveness and durability. However, its low tensile strength makes it prone to cracking, posing persistent maintenance challenges. Traditional repair methods are often expensive and difficult to implement, especially for critical structures. Recent studies propose a potential solution involving alkaliphilic or alkali-tolerant calcium-carbonate producing bacteria in aiding concrete crack repair through microbial-induced calcium carbonate precipitation (MICP) via urea hydrolysis. Considering the adaptive nature of bacteria, we hypothesize that naturally occurring concrete-inhabiting microbes possess properties crucial for mending cracks. Therefore, this study aims to isolate and evaluate these inherent microbes and their MICP ability. Six concrete samples were collected and cultured on Alkaline Nutrient Agar for microbial isolation. Urease activity was assessed phenotypically and genotypically. MICP activity was observed and validated under Scanning Electron Microscope/Energy Dispersive Spectroscopy (SEM/EDS). Out of the 49 isolates cultured, Lysinibacillus sphaericus PUMA0250 emerges as the most promising isolate for practical implementation, showing high pH survivability in an in-house formulated concrete agar medium (pH 12.6). L. sphaericus PUMA0250 exhibited MICP activity via urea hydrolysis and harbored all crucial genes involved in urease-mediated MICP. SEM/EDS analysis confirmed the structure and composition of the produced calcium carbonate precipitate. This study demonstrates the potential of L. sphaericus PUMA0250 to be incorporated into concrete to assess its healing efficiency. Its ability to thrive in the alkaline concrete environment and produce calcium by-products may aid concrete crack repair, opening microbiological avenues for sustainable and efficient concrete repair methodologies. IMPORTANCEAlthough concrete is widely used in construction, the construction material is prone to cracking, leading to costly repairs and structural degradation. This study isolated Lysinibacillus sphaericus PUMA0250 from tropical urban concrete, that can survive the highly alkaline environment typical of concrete structures in equatorial climate. Importantly, it produces calcium carbonate, a mineral that can help in concrete repair. These findings contribute to our understanding of how microbes that naturally produce calcium carbonate by-products can be used to repair concrete. For such applications, microbes must be able to withstand extreme conditions, including high pH and low nutrient availability. Our discovery of a resilient, native isolate highlights the potential of tropical concrete microbiomes as sources for self-healing construction technologies. This work lays the foundation for more sustainable, low-maintenance building materials and opens new possibilities in microbiology-driven solutions for urban infrastructure challenges.

microbiology↗

bioRxiv2024

Non-destructive viability assessment of cancer cell spheroids using dynamic optical coherence tomography with trypan blue validation

3D cell cultures are widely used in biomedical research for the recapitulation of in vivo microenvironments. Viability assessment and monitoring of these intricate conformations remain an open problem as standard cell viability protocols based on colorimetry or microscopy are not directly applicable to intact 3D samples. Optical coherence tomography (OCT) has been explored extensively for subsurface structural and quasi-functional analysis of 3D cell cultures and tissue. Recent studies of dynamic OCT as a source of cellular contrast have found qualitative associations with necrosis in cell spheroids, suggesting potential as a viability marker. We present empirical and validated evidence for dynamic OCT as a quantitative indicator of cell viability in 3D cultures. We analysed over 240 MCF-7 cancer cell spheroids with dynamic OCT and corresponding viability measurements using the trypan blue exclusion assay. Significant effects of common reagents Dimethyl sulfoxide (DMSO) and Phosphate-Buffered Saline (PBS) on OCT readouts were noted. We proposed a regression-based OCT brightness normalisation technique that removed reagent-induced OCT intensity biases and helped improve correspondence to the viability assay. These results offer a quantitative biological foundation for further advances of dynamic OCT as a novel non-invasive modality for 3D culture monitoring.

bioengineering↗

bioRxiv2023

Fluorescent Peptide-based Probe for the Detection of Alpha-synuclein Aggregates in the Gut

BackgroundParkinsons disease (PD) is diagnosed clinically by motor symptoms, with no molecular diagnostic test currently available. By the time motor symptoms manifest, significant irreversible neurodegeneration has already occurred, limiting the effectiveness of neuroprotective therapies and drug interventions. Recent identification of pathological alpha-synuclein (-syn) aggregates in the gastrointestinal (GI) tract of prodromal PD patients offer a potential avenue for early disease diagnosis. This study aims to explore specific fluorescence labelling of -syn aggregates in the GI tract using a peptide-based probe for early diagnosis of PD. MethodsWe used primary hippocampal neuronal cells and wild-type mouse tissues with the addition of pre-formed -syn fibrils to identify the most suitable peptide fluorescent probe (P1) for staining -syn aggregates in cells and tissues. We validated the probe labelling in GI tract tissues from three mouse models, including PFF-injected mice and two transgenic PD mouse strains. We quantified labelling accuracy by confocal imaging and protein analysis. ResultsWe found that P1 labelled -syn aggregates with high accuracy (87% in comparison to Serine129-phosphorylated -syn antibody) and high specificity for labelling their aggregated forms over monomeric forms. In GI tract tissues, P1 labelled -syn aggregates across tissue layers (mucosa, sub-mucosa, muscularis externa) and achieved comparable performance to antibody staining. Higher degree of probe labelling was found in older mice due to increased accumulation of -syn aggregates with ageing. Notably, -syn aggregates were readily detectable in the colonic mucosae using P1, indicating the potential use of this probe for early PD diagnosis during colonic examinations like colonoscopy. ConclusionWe have developed a peptide-based fluorescent probe and demonstrated its rapid and specific labelling of -syn aggregates. We highlight the probes ability to label these aggregates rapidly over -syn monomers and survey the abundance of -syn aggregates throughout the entire length of the GI tract. These support the further development of P1 as a specific fluorescent imaging biomarker for colonic -syn aggregates for the early detection of PD.

neuroscience↗

bioRxiv2022

Deep ultraviolet-excited fluorescence histology with fibre optic illumination for microtopography and quantitative tissue mapping

Cellular imaging of thick samples requires physical sectioning or laser scanning microscopy, generally incompatible with high-throughput requirements. We developed fibre optic microscopy with ultraviolet (UV) surface excitation (FUSE), a portable, quantitative fluorescence imaging platform for thick tissue that substantially advances prior UV excitation approaches with illumination engineering and computational methods. Optic fibres delivered <300nm light with directional control, enabling unprecedented 50X widefield imaging on thick tissue with sub-nuclear clarity, and 3D topography of surface microstructure. Generative modelling of high-magnification images using our normalising flow architecture FUSE-Flow (open-source) enhanced low-magnification imaging by variational inference. Comprehensive validation comprised multi-scale fluorescence histology compared with standard H&E, and quantitative analyses of senescence, antibiotic toxicity, and nuclear DNA content in tissue models via efficient sampling of entire murine organs by thick slices up to 0.4x8x12mm and 1.3 million cells per surface. This technology addresses long-standing laboratory gaps for high-throughput studies for rapid cellular insights. TeaserLarge-field functional cellular insights into thick tissue with generative AI enables accelerated decision-making

bioengineering↗

bioRxiv2021

Developmental and Intergenerational Landscape of Human Circulatory Lipidome and its Association with Obesity Risk

Lipids play a vital role in human health and development, but changes to their circulatory levels during gestation and in early life are poorly understood. Here we present the first developmental and intergenerational landscape of the human circulatory lipidome, derived by profiling of 480 lipid species representing 25 lipid classes, in mothers and their offspring (n=2491). Levels of 66% of the profiled lipids increased in maternal circulation during gestation, while cord blood had higher concentrations of acylcarnitines and lysophospholipids. The offspring lipidome at age six years revealed striking similarities with postnatal maternal lipidome (adult) in its lipid composition and concentrations. Comparison of lipids associated with child and maternal adiposity identified a 92% overlap, implying intergenerational similarities in the lipid signatures of obesity risk. We also catalogued lipid signatures linked with maternal adiposity during gestation and offspring birthweight, and validated (>70% overlap) the findings in an independent birth-cohort (n=1935).

systems biology↗