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Bacterial sRNAs: regulation in stress

Hoe CH, Raabe CA, Rozhdestvensky TS, Tang TH

Int J Med Microbiol, 2013 Jul;303(5):217-29.
PMID: 23660175 DOI: 10.1016/j.ijmm.2013.04.002

Bacteria are often exposed to a hostile environment and have developed a plethora of cellular processes in order to survive. A burgeoning list of small non-coding RNAs (sRNAs) has been identified and reported to orchestrate crucial stress responses in bacteria. Among them, cis-encoded sRNA, trans-encoded sRNA, and 5'-untranslated regions (UTRs) of the protein coding sequence are influential in the bacterial response to environmental cues, such as fluctuation of temperature and pH as well as other stress conditions. This review summarizes the role of bacterial sRNAs in modulating selected stress conditions and highlights the alliance between stress response and clustered regularly interspaced short palindromic repeats (CRISPR) in bacterial defense.
Antimicrobial susceptibility and pulsed-field gel electrophoresis of Shigella sonnei strains in Malaysia (1997-2000)

Hoe CH, Yasin RM, Koh YT, Thong KL

J Appl Microbiol, 2005;99(1):133-40.
PMID: 15960673

Antimicrobial resistance of Shigella sonnei from Malaysia was determined and subtyping was carried by pulsed-field gel electrophoresis (PFGE) to assess the extent of genetic diversity of these strains.
Prevalence of multidrug-resistant Shigella isolated in Malaysia

Thong KL, Hoe CH, Koh YT, Yasin RM

J Health Popul Nutr, 2002 Dec;20(4):356-8.
PMID: 12659418
Fulltext Utilization of Small RNA Genes to Distinguish Vibrio cholerae Biotypes via Multiplex Polymerase Chain Reaction

Ahmed SA, Raabe CA, Cheah HL, Hoe CH, Rozhdestvensky TS, Tang TH

Am J Trop Med Hyg, 2019 06;100(6):1328-1334.
PMID: 30963989 DOI: 10.4269/ajtmh.18-0525

The diarrheal disease "cholera" is caused by Vibrio cholerae, and is primarily confined to endemic regions, mostly in Africa and Asia. It is punctuated by outbreaks and creates severe challenges to public health. The disease-causing strains are most-often members of serogroups O1 and O139. PCR-based methods allow rapid diagnosis of these pathogens, including the identification of their biotypes. However, this necessitates the selection of specific target sequences to differentiate even the closely related biotypes of V. cholerae. Oligonucleotides for selective amplification of small RNA (sRNA) genes that are specific to these V. cholerae subtypes were designed. The resulting multiplex PCR assay was validated using V. cholerae cultures (i.e., 19 V. cholerae and 22 non-V. cholerae isolates) and spiked stool samples. The validation using V. cholerae cultures and spiked stool suspensions revealed detection limits of 10-100 pg DNA per reaction and 1.5 cells/mL suspension, respectively. The multiplex PCR assay that targets sRNA genes for amplification enables the sensitive and specific detection, as well as the differentiation of V. cholerae-O1 classical, O1 El Tor, and O139 biotypes. Most importantly, the assay enables fast and cheaper diagnosis compared with classic culture-based methods.
Interleukin-28 Polymorphism: Ethnic variations and the response to chronic hepatitis C treatment in Malaysia

Hoe CH, Suan MAM, Hoe CH, Tang TH, Kiew KK, Hassan MRA, et al.

Med J Malaysia, 2018 08;73(4):260.
PMID: 30121693

No abstract provided.
Macrophage polarization in THP-1 cell line and primary monocytes: A systematic review

Mohd Yasin ZN, Mohd Idrus FN, Hoe CH, Yvonne-Tee GB

Differentiation, 2022;128:67-82.
PMID: 36370526 DOI: 10.1016/j.diff.2022.10.001

Macrophages derived from human monocytic leukemia THP-1 cell line are often used as the alternative of human primary macrophage. However, the polarization method of THP-1 to macrophages varies between different laboratories, which may unknowingly affect the relevance of research output across research groups. In this regard, a systematic search was developed in Pubmed, BioOne, Scopus, and Science Direct to identify articles focusing on THP-1 polarization into M1 and M2 macrophages. All selected articles were read and discussed by two independent reviewers. The selection process was based on selected keywords on the title, abstract and full-text level. A total of 85 articles were selected and categorized based on the field of studies, method of THP-1 differentiation, and markers or genes expressed upon differentiation. THP-1 derived macrophages were mainly used together with primary monocyte-derived macrophages in cellular inflammation studies, while it was commonly employed alone in cancer research. THP-1 derived macrophages are also of paramount importance in biomaterials studies to prevent unfavorable immune responses in-vivo. We explored various methods of THP-1 differentiation and suggested several common genes encountered to characterize M1 and M2 macrophages differentiated from THP-1. The systematic review highlights the relevance of using THP-1 derived macrophage as a useful alternative to primary macrophage. Although it is not possible to derive a standard method of THP-1 polarization into M1 and M2 macrophages from this review, it may lead researchers to obtain reproducible polarization protocol based on commonly used stimulants and markers of differentiation.
Fulltext Rapid diagnosis of leptospirosis by multiplex PCR

Ahmed SA, Sandai DA, Musa S, Hoe CH, Riadzi M, Lau KL, et al.

Malays J Med Sci, 2012 Jul;19(3):9-16.
PMID: 23610544 MyJurnal

Traditionally, the most common diagnostic approach used for diagnosing leptospirosis was the demonstration of immune-seroconversion in acute and convalescent patient serum samples. Recently, a variety of molecular techniques, including conventional and real-time polymerase chain reaction (PCR), have been developed for the specific detection of pathogenic bacteria from the genus Leptospira. PCR is a sensitive, specific, and rapid technique that has been successfully used to detect several microorganisms; including those of clinical significance.
Fulltext Non-protein coding RNA genes as the novel diagnostic markers for the discrimination of Salmonella species using PCR

Nithya R, Ahmed SA, Hoe CH, Gopinath SC, Citartan M, Chinni SV, et al.

PLoS One, 2015;10(3):e0118668.
PMID: 25774907 DOI: 10.1371/journal.pone.0118668

Salmonellosis, a communicable disease caused by members of the Salmonella species, transmitted to humans through contaminated food or water. It is of paramount importance, to generate accurate detection methods for discriminating the various Salmonella species that cause severe infection in humans, including S. Typhi and S. Paratyphi A. Here, we formulated a strategy of detection and differentiation of salmonellosis by a multiplex polymerase chain reaction assay using S. Typhi non-protein coding RNA (sRNA) genes. With the designed sequences that specifically detect sRNA genes from S. Typhi and S. Paratyphi A, a detection limit of up to 10 pg was achieved. Moreover, in a stool-seeding experiment with S. Typhi and S. Paratyphi A, we have attained a respective detection limit of 15 and 1.5 CFU/mL. The designed strategy using sRNA genes shown here is comparatively sensitive and specific, suitable for clinical diagnosis and disease surveillance, and sRNAs represent an excellent molecular target for infectious disease.
Fulltext Differential polarization and the expression of efferocytosis receptor MerTK on M1 and M2 macrophages isolated from coronary artery disease patients

Mohd Idrus FN, Ahmad NS, Hoe CH, Azlan M, Norfuad FA, Yusof Z, et al.

BMC Immunol, 2021 03 24;22(1):21.
PMID: 33761885 DOI: 10.1186/s12865-021-00410-2

BACKGROUND: Differential polarization of macrophage into M1 and M2 mediates atherosclerotic plaque clearance through efferocytosis. Higher expression of Mer proto-oncogene tyrosine kinase (MerTK) on M2 macrophage helps in maintaining macrophage efferocytic efficiency. In healthy individuals, macrophage polarization into M1 and M2 occurs in tissues in concomitance with the acquisition of functional phenotypes depending on specific microenvironment stimuli. However, whether the macrophage differential polarization and MerTK expression vary in coronary artery disease (CAD) patients remain unknown.
OBJECTIVE: This study aimed to elucidate the polarization of M1 and M2 macrophage from CAD patients as well as to investigate the expression of MerTK in these macrophage phenotypes.
METHODS: A total of 14 (n) CAD patients were recruited and subsequently grouped into "no apparent CAD", "non-obstructive CAD" and "obstructive CAD" according to the degree of stenosis. Thirty ml of venous blood was withdrawn to obtain monocyte from the patients. The M1 macrophage was generated by treating the monocyte with GMCSF, LPS and IFN-γ while MCSF, IL-4 and IL-13 were employed to differentiate monocyte into M2 macrophage. After 7 days of polarization, analysis of cell surface differentiation markers (CD86+/CD80+ for M1 and CD206+/CD200R+ for M2) and measurement of MerTK expression were performed using flow cytometry.
RESULTS: Both M1 and M2 macrophage expressed similar level of CD86, CD80 and CD206 in all groups of CAD patients. MerTK expression in no apparent CAD patients was significantly higher in M2 macrophage compared to M1 macrophage [12.58 ± 4.40 vs. 6.58 ± 1.37, p = 0.040].
CONCLUSION: Differential polarization of macrophage into M1 and M2 was highly dynamic and can be varied due to the microenvironment stimuli in atherosclerotic plaque. Besides, higher expression of MerTK in patients with the least coronary obstructive suggest its vital involvement in efferocytosis.
Fulltext Validation of Faecal Pyruvate Kinase Isoenzyme Type M2 (Faecal M2PK Quick) Test in Detection of Colorectal Adenoma and Adenocarcinoma Among High-Risk Malaysian Population

Mohd Suan MA, Ng YZ, Henry GF, Md Said R, Kollanthavelu S, Mustapha MI, et al.

Asian Pac J Cancer Prev, 2023 Sep 01;24(9):3183-3186.
PMID: 37774070 DOI: 10.31557/APJCP.2023.24.9.3183

BACKGROUND: Colorectal neoplasia is a multistep process that can lead to the development of colorectal cancer. Colonoscopy is the gold standard for diagnosis and screening of colorectal cancer, but its uptake is often hindered by unpleasant experiences and logistic obstacles. Therefore, non-invasive biomarker tests such as the M2-pyruvate kinase (M2PK) test have been explored as a potential screening tool.
OBJECTIVE: This study aims to evaluate the efficacy of the M2PK Quick Stool Test (ScheBo®) in detecting colorectal adenoma and adenocarcinoma in high-risk Malaysian populations using colonoscopy as the comparison.
METHODS: A prospective, cross-sectional, multicenter study was conducted from December 2017 to December 2019 in four hospitals in Malaysia. Participants were eligible if they met any of the following criteria: personal or family history of colorectal polyps or cancer, inherited syndromes, altered bowel habits, rectal bleeding, unintended weight loss, loss of appetite, abdominal pain or cramps, or unexplained iron deficiency, or an Asia-Pacific Colorectal Screening score of 4-7. Participants provided a stool sample that was tested for M2PK using the M2PK Quick Test. Participants then underwent a colonoscopy, and any lesions found were biopsied and sent for histopathological examination.
RESULTS: A total of 562 participants were included in the study, of whom 89 had a positive M2PK test. Presence of adenoma and/or dysplastic lesions were confirmed in 14.4% and adenocarcinoma in 3.0% of the participants. The M2PK Quick Stool Test showed a sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of 58.8%, 85.5%, 11.2% and 98.5%, respectively in detecting colorectal adenocarcinoma. For detection of colorectal adenoma, this test yielded a sensitivity, specificity, PPV and NPV of 27.3%, 86.3%, 27.0% and 86.5%, respectively.
CONCLUSIONS: The M2PK Quick Stool Test showed a moderate accuracy in detecting colorectal adenocarcinoma and adenomas in the studied population.