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  1. Genomic Instability and Cellular Senescence: Lessons From the Budding Yeast
    Lee JW, Ong EBB
    Front Cell Dev Biol, 2020;8:619126.
    PMID: 33511130 DOI: 10.3389/fcell.2020.619126
    Aging is a complex biological process that occurs in all living organisms. Aging is initiated by the gradual accumulation of biomolecular damage in cells leading to the loss of cellular function and ultimately death. Cellular senescence is one such pathway that leads to aging. The accumulation of nucleic acid damage and genetic alterations that activate permanent cell-cycle arrest triggers the process of senescence. Cellular senescence can result from telomere erosion and ribosomal DNA instability. In this review, we summarize the molecular mechanisms of telomere length homeostasis and ribosomal DNA stability, and describe how these mechanisms are linked to cellular senescence and longevity through lessons learned from budding yeast.
  2. Unravelling bacterial virulence factors in yeast: From identification to the elucidation of their mechanisms of action
    Wong Z, Ong EBB
    Arch Microbiol, 2024 Jun 15;206(7):303.
    PMID: 38878203 DOI: 10.1007/s00203-024-04023-2
    Pathogenic bacteria employ virulence factors (VF) to establish infection and cause disease in their host. Yeasts, Saccharomyces cerevisiae and Saccharomyces pombe, are useful model organisms to study the functions of bacterial VFs and their interaction with targeted cellular processes because yeast processes and organelle structures are highly conserved and similar to higher eukaryotes. In this review, we describe the principles and applications of the yeast model for the identification and functional characterisation of bacterial VFs to investigate bacterial pathogenesis. The growth inhibition phenotype caused by the heterologous expression of bacterial VFs in yeast is commonly used to identify candidate VFs. Then, subcellular localisation patterns of bacterial VFs can provide further clues about their target molecules and functions during infection. Yeast knockout and overexpression libraries are also used to investigate VF interactions with conserved eukaryotic cell structures (e.g., cytoskeleton and plasma membrane), and cellular processes (e.g., vesicle trafficking, signalling pathways, and programmed cell death). In addition, the yeast growth inhibition phenotype is also useful for screening new drug leads that target and inhibit bacterial VFs. This review provides an updated overview of new tools, principles and applications to study bacterial VFs in yeast.
  3. Correction to : Unravelling bacterial virulence factors in yeast: from identification to the elucidation of their mechanisms of action
    Wong Z, Ong EBB
    Arch Microbiol, 2024 Jun 29;206(7):331.
    PMID: 38951198 DOI: 10.1007/s00203-024-04073-6
  4. Enhancing yeast growth with carboxylates under multiple nutrient limitations
    Yusof TY, Lian MQ, Ong EBB, Teh AH
    3 Biotech, 2021 Sep;11(9):409.
    PMID: 34471591 DOI: 10.1007/s13205-021-02955-w
    Yeast cell death is triggered when essential nutrients such as potassium and lipid are limited but ammonium is in excess. When ammonium and glucose were maintained at 100% of the normal concentration while all the other essential nutrients in yeast nitrogen base (YNB) were reduced to 2%, yeast growth was halted by ammonium toxicity. Yeast started to grow again when either ammonium was also reduced to 2% or gluconate was added, but simultaneously adding gluconate as well as reducing all the nutrients except glucose 50-fold revived yeast growth to a greater extent, i.e. a quarter of the normal growth. Gluconate, as well as formate and alginate, stimulated yeast growth by buffering the drop in pH. Yeast cells were seemingly more susceptible to low pH under the nutrient-limited conditions, entering the stationary phase at pH higher than that of the normal condition. Carboxylate salts may prove a cost-efficient replacement for large proportions of the essential nutrients as yeast cells, in the presence of 2 mg ml-1 gluconate, could still achieve nearly 90% of the normal growth when cultured in only 10% of the normal YNB concentration.
  5. Fulltext Deletion of Salmonella enterica serovar Typhi tolC reduces bacterial adhesion and invasion toward host cells
    Hussain A, Ong EBB, Balaram P, Ismail A, Kien PK
    Front Microbiol, 2023;14:1301478.
    PMID: 38029101 DOI: 10.3389/fmicb.2023.1301478
    BACKGROUND: S. Typhi is a Gram-negative bacterium that causes typhoid fever in humans. Its virulence depends on the TolC outer membrane pump, which expels toxic compounds and antibiotics. However, the role of TolC in the host cell adhesion and invasion by S. Typhi is unclear.

    OBJECTIVE: We aimed to investigate how deleting the tolC affects the adhesion and invasion of HT-29 epithelial and THP-1 macrophage cells by S. Typhi in vitro.

    METHODS: We compared the adhesion and invasion rates of the wild-type and the tolC mutant strains of S. Typhi using in vitro adhesion and invasion assays. We also measured the expression levels of SPI-1 genes (invF, sipA, sipC, and sipD) using quantitative PCR.

    RESULTS: We found that the tolC mutant showed a significant reduction in adhesion and invasion compared to the wild-type strain in both cell types. We also observed that the expression of SPI-1 genes was downregulated in the tolC mutant.

    DISCUSSION: Our results suggest that TolC modulates the expression of SPI-1 genes and facilitates the adhesion and invasion of host cells by S. Typhi. Our study provides new insights into the molecular mechanisms of S. Typhi pathogenesis and antibiotic resistance. However, our study is limited by the use of in vitro models and does not reflect the complex interactions between S. Typhi and host cells in vivo.

  6. TolC facilitates the intracellular survival and immunomodulation of Salmonella Typhi in human host cells
    Hussain A, Ong EBB, Balaram P, Ismail A, Kien PK
    Virulence, 2024 Dec;15(1):2395831.
    PMID: 39185619 DOI: 10.1080/21505594.2024.2395831
    Salmonella enterica serovar Typhi (S. Typhi) causes typhoid fever, a systemic infection that affects millions of people worldwide. S. Typhi can invade and survive within host cells, such as intestinal epithelial cells and macrophages, by modulating their immune responses. However, the immunomodulatory capability of S. Typhi in relation to TolC-facilitated efflux pump function remains unclear. The role of TolC, an outer membrane protein that facilitates efflux pump function, in the invasion and immunomodulation of S. Typhi, was studied in human intestinal epithelial cells and macrophages. The tolC deletion mutant of S. Typhi was compared with the wild-type and its complemented strain in terms of their ability to invade epithelial cells, survive and induce cytotoxicity in macrophages, and elicit proinflammatory cytokine production in macrophages. The tolC mutant, which has a defective outer membrane, was impaired in invading epithelial cells compared to the wild-type strain, but the intracellular presence of the tolC mutant exhibited greater cytotoxicity and induced higher levels of proinflammatory cytokines (IL-1β and IL-8) in macrophages compared to the wild-type strain. These effects were reversed by complementing the tolC mutant with a functional tolC gene. Our results suggest that TolC plays a role in S. Typhi to efficiently invade epithelial cells and suppress host immune responses during infection. TolC may be a potential target for the development of novel therapeutics against typhoid fever.
  7. Evaluation of Salmonella Typhi antigen YncE alongside HlyE for the detection of typhoid fever and its carriers
    Franklin F, Chong CW, Chua LH, Anthony AA, Liew MWO, Aziah I, et al.
    Med Microbiol Immunol, 2020 Oct;209(5):593-601.
    PMID: 32246197 DOI: 10.1007/s00430-020-00667-1
    Typhoid fever is a disease caused by Salmonella Typhi that was implicated in millions of illnesses worldwide annually. Individuals that do not recover fully from typhoid fever can become asymptomatic carriers of the disease. Host antibodies against the S. Typhi antigens, HlyE (for acute typhoid) and YncE (for carriers) were previously reported to be useful biomarkers for the disease. Here, we expressed and purified recombinant HlyE and YncE antigens and tested the IgG, IgA and IgM responses in 422 sera samples retrieved from acute typhoid patients, other febrile, food handlers, and healthy individuals. The results showed that HlyE-IgG, -IgA and -IgM ELISAs have a collective sensitivity of 83% while YncE-IgG and -IgA ELISAs identified 16 possible carriers based on their antibody profiles. The identification of sensitive biomarkers for typhoid carrier detection is crucial for disease eradication.
  8. Genetic relatedness in extended-spectrum beta-lactamase-producing Escherichia coli from clinical isolates using enterobacterial repetitive intergenic consensus polymerase chain reaction
    Tanko N, Tolulope OA, Olajumoke BR, Ong EBB, Yahaya M, Olalekan OB
    Int J Health Sci (Qassim), 2021 9 23;15(5):18-27.
    PMID: 34548859
    Objectives: The aim of this study is to determine the genetic relatedness of extended-spectrum beta-lactamases (ESBL)-producing Escherichia coli using the enterobacterial repetitive intergenic consensus-polymerase chain reaction (ERIC-PCR) technique.

    Methods: Suspected Gram-negative bacteria with their identities from the clinical samples were confirmed using Microgen GN-A-ID Kit. The double-disc synergy test was used to confirm for ESBL-producing E. coli. The susceptibility of the organisms was tested against eleven antimicrobial agents. A singleplex PCR assay was carried out targeting TEM, SHV, CTX-M, and OXA. ERIC-PCR performed, and band patterns obtained were visually evaluated. A dendrogram of the ERIC-PCR fingerprint pattern was done with the aid of DendroUPGMA using the cluster method.

    Results: Of the 576 clinical samples collected, 23 isolates were confirmed E. coli, and all (100%) are ESBL producers. The highest antibiotic resistance rate was recorded in cefixime (95.6%), and the least was amikacin (17.4%). The predominant ESBL gene is blaTEM genes (95.6%). Gel analysis of ERIC-PCR revealed 1-6 bands. The profiles of the ERIC-PCR differentiated the 23 E. coli isolates into four ERIC cluster types.

    Conclusion: More than 80% of the isolates are sensitive to amikacin, with greater than 95% harboring blaTEM genes. Overall, ERIC obtained from the clinical specimens indicated some evidence in the genetic relatedness of the ESBL genes among E. coli isolates.

  9. Comparison of microplate- and bottle-based methods to age yeast for chronological life span assays
    Kwong MMY, Lee JW, Samian MR, Watanabe N, Osada H, Ong EBB
    J Microbiol Methods, 2019 12;167:105743.
    PMID: 31629019 DOI: 10.1016/j.mimet.2019.105743
    This study compared the chronological life span and survival of Saccharomyces cerevisiae aged in a microplate or bottle, under different aeration and calorie restriction conditions. Our data shows that limited aeration in the microplate-aged culture contributed to slower outgrowth but extended yeast CLS compared to the bottle-aged culture.
  10. Fulltext Identification of Tropical Plant Extracts That Extend Yeast Chronological Life Span
    Kwong MMY, Lee JW, Samian MR, Wahab HA, Watanabe N, Ong EBB
    Cells, 2021 10 11;10(10).
    PMID: 34685698 DOI: 10.3390/cells10102718
    Certain plant extracts (PEs) contain bioactive compounds that have antioxidant and lifespan-extending activities on organisms. These PEs play different roles in cellular processes, such as enhancing stress resistance and modulating longevity-defined signaling pathways that contribute to longevity. Here, we report the discovery of PEs that extended chronological life span (CLS) in budding yeast from a screen of 222 PEs. We identified two PEs, the leaf extracts of Manihot esculenta and Wodyetia bifurcata that extended CLS in a dose-dependent manner. The CLS-extending PEs also conferred oxidative stress tolerance, suggesting that these PEs might extend yeast CLS through the upregulation of stress response pathways.
  11. Intensification of Inclusion Body Processing via Temperature-Based Refolding
    Wong RS, Alias NNM, Ong EBB, Liew MWO
    Methods Mol Biol, 2023;2617:189-200.
    PMID: 36656525 DOI: 10.1007/978-1-0716-2930-7_13
    Inclusion bodies (IB) are dense insoluble aggregates of mostly misfolded polypeptides that usually result from recombinant protein overexpression. IB formation has been observed in protein expression systems such as E. coli, yeast, and higher eukaryotes. To recover soluble recombinant proteins in their native state, IB are commonly first solubilized with a high concentration of denaturant. This is followed by concurrent denaturant removal or reduction and a transition into a refolding-favorable chemical environment to facilitate the refolding of solubilized protein to its native state. Due to the high concentration of denaturant used, conventional refolding approaches can result in dilute products and are buffer inefficient. To circumvent the limitations of conventional refolding approaches, a temperature-based refolding approach which combines a low concentration of denaturant (0.5 M guanidine hydrochloride, GdnHCl) with a high temperature (95 °C) during solubilization was proposed. In this chapter, we describe a temperature-based refolding approach for the recovery of core streptavidin (cSAV) from IB. Through the temperature-based approach, intensification was achieved through the elimination of a concentration step which would be required by a dilution approach and through a reduction in buffer volumes required for dilution or denaturant removal. High-temperature treatment during solubilization may have also resulted in the denaturation and aggregation of undesired host-cell proteins, which could then be removed through a centrifugation step resulting in refolded cSAV of high purity without the need for column purification. Refolded cSAV was characterized by biotin-binding assay and SDS-PAGE, while purity was determined by RP-HPLC.
  12. Fulltext Screening of selected ageing-related proteins that extend chronological life span in yeast Saccharomyces cerevisiae
    Lee JW, Ong TG, Samian MR, Teh AH, Watanabe N, Osada H, et al.
    Sci Rep, 2021 Dec 17;11(1):24148.
    PMID: 34921163 DOI: 10.1038/s41598-021-03490-7
    Ageing-related proteins play various roles such as regulating cellular ageing, countering oxidative stress, and modulating signal transduction pathways amongst many others. Hundreds of ageing-related proteins have been identified, however the functions of most of these ageing-related proteins are not known. Here, we report the identification of proteins that extended yeast chronological life span (CLS) from a screen of ageing-related proteins. Three of the CLS-extending proteins, Ptc4, Zwf1, and Sme1, contributed to an overall higher survival percentage and shorter doubling time of yeast growth compared to the control. The CLS-extending proteins contributed to thermal and oxidative stress responses differently, suggesting different mechanisms of actions. The overexpression of Ptc4 or Zwf1 also promoted rapid cell proliferation during yeast growth, suggesting their involvement in cell division or growth pathways.
  13. Exploring the role of impedance spectroscopy in assessing 405 nm laser-induced inactivation of saccharomyces cerevisiae
    Ang BJ, Suardi N, Ong EBB, Khasim SNH, Gemanam SJ, Mustafa IS, et al.
    Photochem Photobiol Sci, 2024 Apr 09.
    PMID: 38592591 DOI: 10.1007/s43630-024-00564-z
    Impedance spectroscopy was employed to assess the electrical properties of yeast following 405 nm laser irradiation, exploring the effects of visible, non-ionizing laser-induced inactivation as a more selective and safer alternative for photoinactivation applications compared to the use of DNA targeting, ionizing UV light. Capacitance and impedance spectra were obtained for yeast suspensions irradiated for 10, 20, 30, and 40 min using 100 and 200 mW laser powers. Noticeable differences in capacitance spectra were observed at lower frequencies (40 Hz to 1 kHz), with a significant increase at 40 min for both laser powers. β-dispersion was evident in the impedance spectra in the frequency range of 10 kHz to 10 MHz. The characteristic frequency of dielectric relaxation steadily shifted to higher frequencies with increasing irradiation time, with a drastic change observed at 40 min for both laser powers. These changes signify a distinct alteration in the physical state of yeast. A yeast spot assay demonstrated a decrease in cell viability with increasing laser irradiation dose. The results indicate a correlation between changes in electrical properties, cell viability, and the efficacy of 405 nm laser-induced inactivation. Impedance spectroscopy is shown to be an efficient, non-destructive, label-free method for monitoring changes in cell viability in photobiological effect studies. The development of impedance spectroscopy-based real-time studies in photoinactivation holds promise for advancing our understanding of light-cell interactions in medical applications.
  14. Fulltext Performance of Immunodiagnostic Tests for Typhoid Fever: A Systematic Review and Meta-Analysis
    Najib MA, Mustaffa KMF, Ong EBB, Selvam K, Khalid MF, Awang MS, et al.
    Pathogens, 2021 Sep 13;10(9).
    PMID: 34578216 DOI: 10.3390/pathogens10091184
    Typhoid fever, also known as typhoid, is a life-threatening bacterial infection that remains a global health concern. The infection is associated with a significant morbidity and mortality rate, resulting in an urgent need for specific and rapid detection tests to aid prevention and management of the disease. The present review aims to assess the specificity and sensitivity of the available literature on the immunodiagnostics of typhoid fever. A literature search was conducted using three databases (PubMed, ProQuest and Scopus) and manual searches through the references of identified full texts to retrieve relevant literature published between 1 January 2011 and 31 December 2020. Of the 577 studies identified in our search, 12 were included in further analysis. Lipopolysaccharides (LPS) and hemolysin E (HlyE) were the most frequently studied antigens. The specimens examined in these studies included serum and saliva. Using blood culture as the gold standard, anti-LPS IgA gave the highest sensitivity of 96% (95% CI: 93-99) and specificity of 96% (95% CI: 93-99) for distinguishing between typhoid cases and healthy controls, whereas the combination of anti-LPS and anti-flagellin total IgGAM gave the highest sensitivity of 93% (95% CI: 86-99) and specificity of 95% (95% CI: 89-100) for distinguishing typhoid cases and other febrile infections. A comparably high sensitivity of 92% (95% CI: 86-98) and specificity of 89% (95% CI: 78-100) were shown in testing based on detection of the combination of anti-LPS (IgA and IgM) and anti-HlyE IgG as well as a slightly lower sensitivity of 91% (95% CI: 74-100) in the case of anti-50kDa IgA. Anti-50kDa IgM had the lowest sensitivity of 36% (95% CI: 6-65) against both healthy and febrile controls. The development of a rapid diagnostic test targeting antibodies against lipopolysaccharides combined with flagellin appeared to be a suitable approach for the rapid detection test of typhoid fever. Saliva is added benefit for rapid typhoid diagnosis since it is less invasive. As a result, further studies could be done to develop additional approaches for adopting such samples.
  15. Fulltext Isolation and characterization of DNA aptamers against the HlyE antigen of Salmonella Typhi
    Ahmad Najib M, Winter A, Mustaffa KMF, Ong EBB, Selvam K, Khalid MF, et al.
    Sci Rep, 2024 Nov 18;14(1):28416.
    PMID: 39557915 DOI: 10.1038/s41598-024-78685-9
    Aptamers have emerged as prominent ligands in clinical diagnostics because they provide various advantages over antibodies, such as quicker generation time, reduced manufacturing costs, minimal batch-to-batch variability, greater modifiability, and improved thermal stability. In the present study, we isolated and characterized DNA aptamers that can specifically bind to the hemolysin E (HlyE) antigen of Salmonella Typhi for future development of typhoid diagnostic tests. The DNA aptamers against Salmonella Typhi HlyE were isolated using systematic evolution of ligands by exponential enrichment (SELEX), and their binding affinity and specificity were assessed utilizing enzyme-linked oligonucleotide assay (ELONA). A total of 11 distinct aptamers were identified, and the binding affinities and species selectivities of the three most probable aptamers were determined. Kd values were obtained in the nanomolar range, with the highest affinity of 83.6 nM determined for AptHlyE97. In addition, AptHlyE11, AptHlyE45 and AptHlyE97 clearly distinguished S. Typhi HlyE from other tested bacteria, such as Salmonella Paratyphi A, Salmonella Paratyphi B, Shigella flexneri, Klebsiella pneumonia and Escherichia coli, therefore displaying desirable specificity. These novel aptamers could be used as diagnostic ligands for the future development of inexpensive and effective point-of-care tests for typhoid surveillance, especially in developing countries of the tropics and subtropics.
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