Biology subjects

Yap, E. P. H.

Publications and source records attributed to Yap, E. P. H..

3 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↗

bioRxiv2025

Clarifying the priming requirement and activator specificity for the NLRP3 inflammasome in human keratinocytes in vitro

While NLRP3 has been extensively studied in myeloid cells, its existence and regulation in epithelial cells, including keratinocytes, are unclear. In fact, whether human keratinocytes express a functional NLRP3 inflammasome at all remains a matter of debate in the inflammasome field. Here, we provide additional evidence that NLRP3 is repressed in human keratinocytes cultured under non-inflammatory conditions but can be sharply induced by interferon-{gamma} (IFN{gamma})--but not lipopolysaccharide (LPS). In this IFN{gamma}-primed state, not all established NLRP3 activators are specific to NLRP3. We report that nigericin-driven keratinocyte pyroptosis occurs via both NLRP1 and NLRP3, whereas Staphylococcus aureus -hemolysin (Hla) exclusively and nonredundantly activates NLRP3, even though both require K+ efflux. Furthermore, in the presence of T cells, certain virulent S. aureus strains can cause NLRP3-dependent pyroptotic death in keratinocytes in vitro through the cooperative actions of superantigens (SAgs) and Hla. In summary, our findings establish the strict inducibility and functional relevance of the NLRP3 inflammasome in non-myeloid, epithelial cells in vitro. These results resolve conflicting reports and position keratinocytes as a context-specific, non-hematopoietic cellular model for studying NLRP3 activation in host-microbe interactions at barrier tissues. KEY FINDINGSO_LIAdditional evidence that NLRP3 is absent in resting, nonstimulated human keratinocytes in vitro C_LIO_LIIFN{gamma}, but not LPS, is a potent priming signal for NLRP3 in human keratinocytes in vitro C_LIO_LIIn IFN{gamma}-primed keratinocytes, S. aureus -hemolysin (Hla) selectively activates NLRP3, whereas nigericin activates both NLRP1 and NLRP3 in vitro C_LIO_LISAg and Hla kill keratinocytes via NLRP3-driven pyroptosis in the presence of T cells in vitro C_LI GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=156 SRC="FIGDIR/small/669639v1_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@4996f4org.highwire.dtl.DTLVardef@155a2a9org.highwire.dtl.DTLVardef@12a21a0org.highwire.dtl.DTLVardef@105bc15_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2020

Rapid direct nucleic acid amplification test without RNA extraction for SARS-CoV-2 using a portable PCR thermocycler

There is an ongoing worldwide coronavirus disease 2019 (Covid-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). At present, confirmatory diagnosis is by reverse transcription polymerase chain reaction (RT-PCR), typically taking several hours and requiring a molecular laboratory to perform. There is an urgent need for rapid, simplified and cost-effective detection methods. We have developed and analytically validated a protocol for direct rapid extraction-free PCR (DIRECT-PCR) detection of SARS-CoV-2 without the need for nucleic acid purification. As few as 6 RNA copies per reaction of viral nucleocapsid (N) gene from respiratory samples such as sputum and nasal exudate can be detected directly using our one-step inhibitor-resistant assay. The performance of this assay was validated on a commercially available portable PCR thermocycler. Viral lysis, reverse transcription, amplification and detection are achieved in a single-tube homogeneous reaction within 36 minutes. This minimized hands-on time, reduces turnaround-time for sample-to-result and obviates the need for RNA purification reagents. It could enable wider use of Covid-19 testing for diagnosis, screening and research in countries and regions where laboratory capabilities are limiting.

microbiology↗