Displaying publications 1 - 20 of 1907 in total

  1. Bonny SQ, Hossain MAM, Uddin SMK, Pulingam T, Sagadevan S, Johan MR
    Crit Rev Food Sci Nutr, 2022;62(5):1317-1335.
    PMID: 33146031 DOI: 10.1080/10408398.2020.1841728
    Vibrio parahaemolyticus, Vibrio cholerae and Vibrio vulnificus are the most significant aquatic pathogens of the genera Vibrio, account for most Vibrio-associated outbreaks worldwide. Rapid identification of these pathogens is of great importance for disease surveillance, outbreak investigations and food safety maintenance. Traditional culture dependent methods are time-consuming and labor-intensive whereas culture-independent polymerase chain reaction (PCR) based assays are reliable, consistent, rapid and reproducible. This review covers the recent development and applications of PCR based techniques, which have accelerated advances in the analysis of nucleic acids to identify three major pathogenic vibrios. Emphasis has been given to analytical approaches as well as advantages and limits of the available methods. Overall, this review article possesses the substantial merit to be used as a reference guide for the researchers to develop improved PCR based techniques for the differential detection and quantification of Vibrio species.
    Matched MeSH terms: Polymerase Chain Reaction
  2. Hashimoto T, Ozaki A, Bhandari D, Sawano T, Murayama A, Shrestha S, et al.
    Travel Med Infect Dis, 2021;43:102145.
    PMID: 34298174 DOI: 10.1016/j.tmaid.2021.102145
    Matched MeSH terms: Real-Time Polymerase Chain Reaction
  3. Awang H, Hamzah FH, Ahmad MH, Mahmood MF, Wahab A, Embong K, et al.
    Infect Dis (Lond), 2021 05;53(5):390-392.
    PMID: 33512265 DOI: 10.1080/23744235.2021.1876913
    Matched MeSH terms: Reverse Transcriptase Polymerase Chain Reaction; Real-Time Polymerase Chain Reaction
  4. Nurulhikma Md. Isa, Ismanizan Ismail, Zamri Zainal
    Kapsaisinoid merupakan alkaloid yang memberikan ciri kepedasan pada cili serta khusus pada genus Capsicum. Sebatian kapsaisinoid terdiri daripada dua komponen utama iaitu kapsaisin dan dihidrokapsaisin. Dalam kajian ini, pengklonan cDNA Kapsaisin sintase (Cs) telah berjaya dilakukan menerusi kaedah transkripsi berbalik PCR (RT-PCR) dan klon cDNA tersebut dinamakan CUKMCS yang bersaiz 981 pb. Pencarian homologi menggunakan program blastx dan blastp yang terdapat pada pangkalan data NCBI mendapati CUKMCS mempunyai persamaan yang sangat tinggi terhadap Cs pada Capsicum frutescens, Capsicum annuum dan Capsicum chacoense. Saiz ramalan protein CUKMCS diangggarkan sekitar 36 kDa. Penentuan pengekspresan transkrip Cs pada 5 tisu yang berbeza mendapati transkrip dikesan pada tisu plasenta, mesokarp dan biji manakala tiada transkrip Cs dikesan pada daun dan akar
    Matched MeSH terms: Polymerase Chain Reaction; Reverse Transcriptase Polymerase Chain Reaction
  5. Fu JYL, Chong YM, Sam IC, Chan YF
    J Virol Methods, 2022 Mar;301:114462.
    PMID: 35026305 DOI: 10.1016/j.jviromet.2022.114462
    Emerging SARS-CoV-2 variants of concern (VOC) have been associated with enhanced transmissibility and immune escape. Next-generation sequencing (NGS) of the whole genome is the gold standard for variant identification for surveillance but is time-consuming and costly. Rapid and cost-effective assays that detect SARS-CoV-2 variants are needed. We evaluated Allplex SARS-CoV-2 Master Assay and Variants I Assay to detect HV69/70 deletion, Y144 deletion, E484K, N501Y, and P681H spike mutations in 248 positive samples collected in Kuala Lumpur, Malaysia, between January and May 2021. Spike variants were detected in 78/248 (31.5 %), comprising 60 VOC B.1.351 (beta) and 18 B.1.1.7 (alpha). With NGS as reference for 115 samples, the sensitivity for detecting the spike mutations was 98.7 % with the Master Assay and 100 % with the Variants I Assay. The emergence of beta variants correlated with increasing COVID-19 infections in Malaysia. The prevalence of alpha VOC and lineage B.1.466.2 was low. These assays detect mutations present in alpha, beta and gamma VOCs. Of the VOCs which have subsequently emerged, the assays should detect omicron (B.1.1.529) but not B.1.617.2 (delta). In conclusion, spike variant PCR assays can be used to rapidly monitor selected SARS-CoV-2 VOCs in resource-limited settings, but require updates as new variants emerge.
    Matched MeSH terms: Reverse Transcriptase Polymerase Chain Reaction; Multiplex Polymerase Chain Reaction
  6. Kee PS, Karunanathie H, Maggo SDS, Kennedy MA, Chua EW
    Methods Mol Biol, 2023;2967:181-192.
    PMID: 37608112 DOI: 10.1007/978-1-0716-3358-8_15
    Polymerase chain reaction (PCR) is a laboratory technique used to amplify a targeted region of DNA, demarcated by a set of oligonucleotide primers. Long-range PCR is a form of PCR optimized to facilitate the amplification of large fragments. Using the adapted long-range PCR protocol described in this chapter, we were able to generate PCR products of 6.6, 7.2, 13, and 20 kb from human genomic DNA samples. For some of the long PCRs, successful amplification was not possible without the use of PCR enhancers. Thus, we also evaluated the impact of some enhancers on long-range PCR and included the findings as part of this updated chapter.
    Matched MeSH terms: Polymerase Chain Reaction*
  7. Thanh TT, Anh NT, Tham NT, Van HM, Sabanathan S, Qui PT, et al.
    Virol J, 2015 Jun 09;12:85.
    PMID: 26050791 DOI: 10.1186/s12985-015-0316-2
    BACKGROUND: Hand foot and mouth disease (HFMD) is a disease of public health importance across the Asia-Pacific region. The disease is caused by enteroviruses (EVs), in particular enterovirus A71 (EV-A71). In EV-A71-associated HFMD, the infection is sometimes associated with severe manifestations including neurological involvement and fatal outcome. The availability of a robust diagnostic assay to distinguish EV-A71 from other EVs is important for patient management and outbreak response.

    METHODS: We developed and validated an internally controlled one-step single-tube real-time RT-PCR in terms of sensitivity, linearity, precision, and specificity for simultaneous detection of EVs and EV-A71. Subsequently, the assay was then applied on throat and rectal swabs sampled from 434 HFMD patients.

    RESULTS: The assay was evaluated using both plasmid DNA and viral RNA and has shown to be reproducible with a maximum assay variation of 4.41 % and sensitive with a limit of detection less than 10 copies of target template per reaction, while cross-reactivity with other EV serotypes was not observed. When compared against a published VP1 nested RT-PCR using 112 diagnostic throat and rectal swabs from 112 children with a clinical diagnosis of HFMD during 2014, the multiplex assay had a higher sensitivity and 100 % concordance with sequencing results which showed EVs in 77/112 (68.8 %) and EV-A71 in 7/112 (6.3 %). When applied to clinical diagnostics for 322 children, the assay detected EVs in throat swabs of 257/322 (79.8 %) of which EV-A71 was detected in 36/322 (11.2 %) children. The detection rate increased to 93.5 % (301/322) and 13.4 % (43/322) for EVs and EV-A71, respectively, when rectal swabs from 65 throat-negative children were further analyzed.

    CONCLUSION: We have successfully developed and validated a sensitive internally controlled multiplex assay for rapid detection of EVs and EV-A71, which is useful for clinical management and outbreak control of HFMD.

    Matched MeSH terms: Reverse Transcriptase Polymerase Chain Reaction/methods*; Reverse Transcriptase Polymerase Chain Reaction/standards; Multiplex Polymerase Chain Reaction/methods*; Multiplex Polymerase Chain Reaction/standards; Real-Time Polymerase Chain Reaction/methods*; Real-Time Polymerase Chain Reaction/standards
  8. Chua EW, Miller AL, Kennedy MA
    Anal Biochem, 2015 May 15;477:115-7.
    PMID: 25766577 DOI: 10.1016/j.ab.2015.02.023
    We compared four brands of microtubes with respect to their suitability for long-range polymerase chain reactions (PCRs). One of the four brands was found to have an inhibitory effect, decreasing PCR yields. The effect was universal across different PCR or enzyme systems. Increased ultraviolet absorbance suggests leaching of unknown chemical species into PCR mixtures. However, this could not be confirmed by high-performance liquid chromatography-mass spectrometry analysis. Nevertheless, our article demonstrates a clear impact of the choice of microtubes on long-range PCR success. Due consideration should be given to the PCR microtubes when determining optimal reaction conditions for long-range PCR.
    Matched MeSH terms: Polymerase Chain Reaction/instrumentation*
  9. Wong RSY
    Malays J Pathol, 2021 Apr;43(1):3-8.
    PMID: 33903299
    The severe acute respiratory syndrome coronavirus 2 is a novel coronavirus that causes the coronavirus disease 2019 (COVID-19). COVID-19 has been declared a pandemic by the World Health Organisation since March 2020. To date, the number of confirmed COVID-19 cases has exceeded 47 million and more than 1.2 million people have lost their lives to the disease. The disease is spreading at an exponential rate with no signs of slowing down. COVID-19 testing and early diagnosis play a crucial role in not just patient management, but also the prevention of the further spread of the disease. Various diagnostic approaches have been applied to detect SARS-CoV-2 infection. This article will critically review these diagnostic approaches and compare each with the gold-standard, which is viral RNA detection using reverse transcriptase-polymerase chain reaction (RT-PCR).
    Matched MeSH terms: Reverse Transcriptase Polymerase Chain Reaction/methods
  10. Teh KJ, Tang HY, Lim LS, Pung HS, Gan SY, Lai NS
    Eur Rev Med Pharmacol Sci, 2023 May;27(10):4378-4385.
    PMID: 37259718 DOI: 10.26355/eurrev_202305_32443
    Lyme borreliosis is caused by the Gram-negative spirochetes Borrelia spp., particularly Borrelia burgdorferi sensu lato complex. The disease is transmitted through the bite of the infected black-legged Ixodes tick. Lyme borreliosis extensively occurs in the Northern Hemisphere, mainly in the United States. Lyme borreliosis cases are also detected in Asian countries including Korea, Nepal, China, Taiwan, and Japan. However, there is an inadequate understanding of Lyme borreliosis in the Southeast Asian region. Hence, this review aims to provide a brief update on the prevalence of Lyme borreliosis infection in Southeast Asia based on the latest literature on this issue. Lyme borreliosis has been discovered in human serum in Indonesia, Malaysia, and Singapore. The human serum samples were mainly examined with ELISA test using Borrelia spp. IgG and IgM antigens. Borrelia spp. also has been detected in ticks found on host animals such as Sundamys muelleri and Python in Malaysia, Thailand, and Laos. Polymerase chain reaction (PCR) is used to detect the presence of Borrelia DNAs in the samples. The published studies have demonstrated that Borrelia spp. exists in Southeast Asia and although the incidence is relatively low, it is believed that Lyme disease cases are under-reported.
    Matched MeSH terms: Polymerase Chain Reaction/methods
  11. Kim JH, Chong CK, Sinniah M, Sinnadurai J, Song HO, Park H
    J Clin Virol, 2015 Apr;65:11-9.
    PMID: 25766980 DOI: 10.1016/j.jcv.2015.01.018
    BACKGROUND: Dengue is a mosquito-borne disease that causes a public health problem in tropical and subtropical countries. Current immunological diagnostics based on IgM and/or nonstructural protein 1 (NS1) antigen are limited for acute dengue infection due to low sensitivity and accuracy.
    OBJECTIVES: This study aimed to develop a one-step multiplex real-time RT-PCR assay showing higher sensitivity and accuracy than previous approaches.
    STUDY DESIGN: Serotype-specific primers and probes were designed through the multiple alignment of NS1 gene. The linearity and limit of detection (LOD) of the assay were determined. The assay was clinically validated with an evaluation panel that was immunologically tested by WHO and Malaysian specimens.
    RESULTS: The LOD of the assay was 3.0 log10 RNA copies for DENV-1, 2.0 for DENV-3, and 1.0 for DENV-2 and DENV-4. The assay showed 95.2% sensitivity (20/21) in an evaluation panel, whereas NS1 antigen- and anti-dengue IgM-based immunological assays exhibited 0% and 23.8-47.6% sensitivities, respectively. The assay showed 100% sensitivity both in NS1 antigen- and anti-dengue IgM-positive Malaysian specimens (26/26). The assay provided the information of viral loads and serotype with discrimination of heterotypic mixed infection.
    CONCLUSIONS: The assay could be clinically applied to early dengue diagnosis, especially during the first 5 days of illness and approximately 14 days after infection showing an anti-dengue IgM-positive response.
    Matched MeSH terms: Reverse Transcriptase Polymerase Chain Reaction/methods*; Multiplex Polymerase Chain Reaction/methods*
  12. Liew KS, Ho WS, Pang SL, Julaihi A
    Physiol Mol Biol Plants, 2015 Jan;21(1):163-5.
    PMID: 25649417 DOI: 10.1007/s12298-014-0262-2
    Duabanga moluccana (or locally known as sawih) is an indigenous fast growing tropical tree species that confers various advantages for the timber industry and for planted forests development. In this paper, we isolated and characterized 8 polymorphic microsatellite markers from the D. moluccana genome using ISSR-suppression PCR techniques. The number of alleles and PIC values ranged from 3 to 8 alleles per locus and from 0.488 to 0.792, respectively. Three microsatellite loci were deviated from Hardy-Weinberg equilibrium (P 
    Matched MeSH terms: Polymerase Chain Reaction
  13. Wong FL, Hamidah NH, Hawa AA, Nurul AN, Leong CF, Saw F, et al.
    Malays J Pathol, 2011 Dec;33(2):107-12.
    PMID: 22299211
    Molecular pathogenesis of chronic myeloid leukemia (CML) is well established and molecular monitoring for patients with CML has become an important practice in the management of patients on imatinib therapy. In the present study, we report the use of RQ-PCR method for detection of BCR-ABL fusion gene for our CML cases. We performed a two-step RQ-PCR on bone marrow aspirates or peripheral blood of 37 CML patients. Quantitative expression of BCR-ABL fusion gene was carried out relative to the expression of a housekeeping gene as endogenous control to compensate for uneven cell numbers, RNA quality, or variations in reverse transcription efficiencies. Twenty-four of these patients were pre-treated with hydroxyurea or alpha interferon prior to the imatinib therapy. Their BCR-ABL fusion gene levels were monitored for 18 months. All samples processed were evaluable. The PCR amplification efficiency of the ABL gene is 90.5% (0.2158) and the BCR-ABL gene, 93.4% (0.1573).
    Matched MeSH terms: Reverse Transcriptase Polymerase Chain Reaction/methods*; Real-Time Polymerase Chain Reaction/methods*
  14. Edwin Shiaw CS, Shiran MS, Cheah YK, Tan GC, Sabariah AR
    Med J Malaysia, 2010 Jun;65(2):133-7.
    PMID: 23756798 MyJurnal
    This study was done to evaluate various DNA and RNA extractions from archival FFPE tissues. A total of 30 FFPE blocks from the years of 2004 to 2006 were assessed with each modified and adapted method. Extraction protocols evaluated include the modified enzymatic extraction method (Method A), Chelex-100 extraction method (Method B), heat-induced retrieval in alkaline solution extraction method (Methods C and D) and one commercial FFPE DNA Extraction kit (Qiagen, Crawley, UK). For RNA extraction, 2 extraction protocols were evaluated including the enzymatic extraction method (Method 1), and Chelex-100 RNA extraction method (Method 2). Results show that the modified enzymatic extraction method (Method A) is an efficient DNA extraction protocol, while for RNA extraction, the enzymatic method (Method 1) and the Chelex-100 RNA extraction method (Method 2) are equally efficient RNA extraction protocols.
    Matched MeSH terms: Polymerase Chain Reaction
  15. Poh CL, Tan EL
    Methods Mol Biol, 2011;665:65-77.
    PMID: 21116796 DOI: 10.1007/978-1-60761-817-1_5
    Enteroviruses are positive stranded RNA viruses belonging to the genus Enterovirus of the Picornaviridae family. Human enteroviruses are transmitted through the fecal-oral route and have been shown to cause mild to life-threatening diseases. Various diagnostic methods have been developed to detect enteroviruses from clinical specimens but many were impeded by requirements for special reagents, lengthy procedures, low sensitivity or cross-reactivity. This chapter describes rapid and highly sensitive methods of enteroviral detection directly from clinical specimens based on a conventional one-step Reverse Transcription polymerase chain reaction (RT-PCR) and a one-step real-time RT-PCR.
    Matched MeSH terms: Polymerase Chain Reaction/methods*; Reverse Transcriptase Polymerase Chain Reaction/methods
  16. Rahman MM, Wong KK, Alfizah H, Hussin S, Isahak I
    Pak J Med Sci, 2015 Jul-Aug;31(4):791-4.
    PMID: 26430404 DOI: 10.12669/pjms.314.7003
    To determine the efficacy of cell culture, immunoflourescence Assay (IFA) and real time polymerase chain reaction (rRT-PCR) in relation to diagnosis of influenza and Respiratory Syncytial Virus (RSV).
    Matched MeSH terms: Real-Time Polymerase Chain Reaction
  17. Chua KH, Lee PC, Chai HC
    Malar J, 2016;15:134.
    PMID: 26931146 DOI: 10.1186/s12936-016-1183-z
    Detection of Plasmodium spp. is sometimes inconvenient especially in rural areas that are distant from a laboratory. In this study a portable diagnostic test of Plasmodium spp. was developed using insulated isothermal polymerase chain reaction (iiPCR) as an alternative approach to improve this situation.
    Matched MeSH terms: Polymerase Chain Reaction
  18. 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.
    Matched MeSH terms: Real-Time Polymerase Chain Reaction
  19. Shakinah Ravindran, Wai Kan Woo, Safwan Saufi, Wan Nur Amni, Intan Ishak, Ghows Azzam, et al.
    Trop Life Sci Res, 2019;30(2):1-12.
    Penentuan jantina burung adalah penting untuk tujuan kajian ekologi dan biologi evolusi, serta program pembiakan dan konservasi terutamanya bagi burung yang mempunyai ciri monomorfik. Bagi burung pungguk jelapang Tyto alba, pengesahan jantina adalah penting untuk konservasi serta program pengenalan bagi kawalan tikus perosak. Penentuan jantina secara molekular untuk subspesies Asia Tenggara, Tyto alba javanica, telah dijalankan menggunakan Reaksi Rantai Polimerase (PCR) diikuti 3% gel agaros elektroforesis. Primer P2/P8 and 2550F/2718R untuk amplifikasi gen CHD (Chromo Helicase DNA-binding gene) diuji dan kedua-dua set primer memberi keputusan yang berjaya. Set primer 2550F/2718R memberi hasil yang lebih baik kerana jurang di antara jalur berganda lebih terang. DNA yang diekstrak dari darah, darah yang dicairkan, serta DNA yang diekstrak dari bulu burung digunakan untuk menentukan jantina burung. DNA yang diekstrak dari bulu memberi keputusan yang kurang memuaskan akibat pencemaran serta kuantiti DNA yang rendah. Penentuan jantina menggunakan darah yang dicairkan merupakan kaedah yang menjimatkan kos serta masa. Penjujukan gen CHD dari Tyto alba javanica menunjukkan 98% hingga 99% kesamaan identiti bila dibandingkan gen CHD Tyto alba alba.
    Matched MeSH terms: Polymerase Chain Reaction
  20. Ferniah RS, Kasiamdari RS, Priyatmojo A, Daryono BS
    Trop Life Sci Res, 2018 Jul;29(2):29-37.
    PMID: 30112139 DOI: 10.21315/tlsr2018.29.2.3
    Cross-breeding is a method of producing progeny with better resistance to pathogens. Resistance to pathogens usually involves pathogenesis-related (PR) proteins. Class II chitinase is an example of a defensive PR protein in plants. The class II chitinase in chilli is coded by the CaChi2 gene. In this study, we crossed susceptible with resistant chilli cultivars, analysed the F1 resistance response against pathogenic F. oxysporum, and analysed the level of CaChi2 gene expression in the F1. Data were collected using disease severity index (DSI) determination and gene expression analysis by qRT-PCR (quantitative Reverse Transcriptase Polymerase Chain Reaction). Results showed that the DSI of F1 was not significantly different from the resistant ancestor. The relative CaChi2 expression level of F1 was higher than the susceptible ancestor but not significantly different from the resistant ancestor. We concluded that the F1 can be categorised as resistant to F. oxysporum, and the CaChi2 gene is involved in the molecular defense response.
    Matched MeSH terms: Reverse Transcriptase Polymerase Chain Reaction
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