Displaying publications 1 - 20 of 1546 in total

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  1. 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
  2. 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
  3. 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*
  4. 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*
  5. 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
  6. 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
  7. 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*
  8. MyJurnal
    The aim of this study was to examine vegetarian burger patties manufactured by two producers in Malaysia for the presence of Listeria monocytogenes. Brand A was produced by an established food manufacturer
    while Brand B was produced by a small-scaled food producer. A total of 108 samples of vegetarian burger
    patties produced by both manufacturers were sampled from retail market and were analyzed by combined
    MPN-PCR and MPN plating method. Of all the samples tested, ten (9.3%) were found to be contaminated with L. monocytogenes. The L. monocytogenes contamination level in vegetarian burger patties manufactured by producer A (20.9% of the samples were contaminated with 3-1100 MPN/g of L. monocytogenes) was significantly higher (P
    Matched MeSH terms: Polymerase Chain Reaction
  9. Yew, Teh Jia, Khairulmizam Samsudin, Nur Izura Udzir, Shaiful Jahari Hashim
    MyJurnal
    Recent rootkit-attack mitigation work neglected to address the integrity of the mitigation tool itself. Both detection and prevention arms of current rootkit-attack mitigation solutions can be given credit for the advancement of multiple methodologies for rootkit defense but if the defense system itself is compromised, how is the defense system to be trusted? Another deficiency not addressed is how platform integrity can be preserved without availability of current RIDS or RIPS solutions, which operate only upon the loading of the kernel i.e. without availability of a trusted boot environment. To address these deficiencies, we present our architecture for solving rootkit persistence – Rootkit Guard (RG). RG is a marriage between TrustedGRUB (providing trusted boot), IMA (Integrity Measurement Architecture) (serves as RIDS) and SELinux (serves as RIPS). TPM hardware is utilised to provide total integrity of our platform via storage of the aggregate of the clean snapshot of our platform OS kernel into TPM hardware registers (i.e. the PCR) – of which no software attacks have been demonstrated to date. RG solves rootkit persistence by leveraging on one vital but simple strategy: the mounting of rootkit defense via prevention of the execution of configuration binaries or build initialisation scripts. We adopted the technique of rootkit persistence prevention via thwarting the initialisation of a rootkit’s installation procedure; if the rootkit is successfully installed, proper deployment via thwarting of the rootkit’s
    configuration is prevented. We had subjected the RG to 8 real world Linux 2.6 rootkits and the RG was successful in solving rootkit persistence in all 8 evaluated rootkits. In terms of performance, the RG introduced a maximum of 11% overhead and an average of 4% overhead, hence permitting deployment in production environments.
    Matched MeSH terms: Polymerase Chain Reaction
  10. MOHAMAD, O., HO, W. S.
    MyJurnal
    Sanger sequencing has been the major method in directly sequencing DNA, and has dominated the DNA sequencing market for nearly past 30 years (Varshney et al., 2009). Along with PCR, we cannot underestimate how important this technology has been to research in various elds of molecular biology. It has revolutionized genetics by allowing us to gain unprecedented insights into the
    workings of different organisms.
    Matched MeSH terms: Polymerase Chain Reaction
  11. 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
  12. 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
  13. New, C.Y., Abdul Rahman, R., Son, R., Mohammed, A.S.
    Food Research, 2018;2(4):378-390.
    MyJurnal
    The safety level of microwaved foods remains at vague as this subject was less addressed
    scientifically. A study was initiated to address the matter by investigating on the
    survivability of Salmonella and Shiga-toxigenic Escherichia coli (STEC) O157 in
    microwave heated ready-to-eat (RTE) foods using the Most Probable Number coupled
    Polymerase Chain Reaction (MPN-PCR) technique. A total of 329 samples of various
    ready-to-eat (RTE) convenience meals were collected around Wilayah Persekutuan Kuala
    Lumpur and Selangor regions. Salmonella was positively identified in 66 samples (20.1%,
    Matched MeSH terms: Polymerase Chain Reaction
  14. 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
  15. Lau YL, Lai MY, Anthony CN, Chang PY, Palaeya V, Fong MY, et al.
    Am. J. Trop. Med. Hyg., 2015 Jan;92(1):28-33.
    PMID: 25385862 DOI: 10.4269/ajtmh.14-0309
    In this study, three molecular assays (real-time multiplex polymerase chain reaction [PCR], merozoite surface antigen gene [MSP]-multiplex PCR, and the PlasmoNex Multiplex PCR Kit) have been developed for diagnosis of Plasmodium species. In total, 52 microscopy-positive and 20 malaria-negative samples were used in this study. We found that real-time multiplex PCR was the most sensitive for detecting P. falciparum and P. knowlesi. The MSP-multiplex PCR assay and the PlasmoNex Multiplex PCR Kit were equally sensitive for diagnosing P. knowlesi infection, whereas the PlasmoNex Multiplex PCR Kit and real-time multiplex PCR showed similar sensitivity for detecting P. vivax. The three molecular assays displayed 100% specificity for detecting malaria samples. We observed no significant differences between MSP-multiplex PCR and the PlasmoNex multiplex PCR kit (McNemar's test: P = 0.1489). However, significant differences were observed comparing real-time multiplex PCR with the PlasmoNex Multiplex PCR Kit (McNemar's test: P = 0.0044) or real-time multiplex PCR with MSP-multiplex PCR (McNemar's test: P = 0.0012).
    Matched MeSH terms: Multiplex Polymerase Chain Reaction; Real-Time Polymerase Chain Reaction
  16. Wong YP, Chua KH, Thong KL
    J. Microbiol. Methods, 2014 Dec;107:133-7.
    PMID: 25307691
    Nosocomial infections are a major public health concern worldwide. Early and accurate identification of nosocomial pathogens which are often multidrug resistant is crucial for prompt treatment. Hence, an alternative real-time polymerase chain reaction coupled with high resolution melting-curve analysis (HRMA) was developed for identification of five nosocomial bacteria. This assay targets species-specific regions of each nosocomial bacteria and produced five distinct melt curves with each representing a particular bacterial species. The melting curves were characterized by peaks of 78.8 ± 0.2 °C for Acinetobacter baumannii, 82.7 ± 0.2 °C for Escherichia coli, 86.3 ± 0.3 °C for Klebsiella pneumoniae, 88.8 ± 0.2 °C for Pseudomonas aeruginosa and 74.6 ± 02 °C for methicillin-resistant Staphylococcus aureus. The assay was able to specifically detect the five bacterial species with an overall detection limit of 2 × 10(-2) ng/μL. In conclusion, the HRM assay developed is a simple and rapid method for identification of the selected nosocomial pathogens.
    Matched MeSH terms: Polymerase Chain Reaction/methods*
  17. Sue MJ, Yeap SK, Omar AR, Tan SW
    Biomed Res Int, 2014;2014:653014.
    PMID: 24971343 DOI: 10.1155/2014/653014
    Polymerase chain reaction-enzyme linked immunosorbent assay (PCR-ELISA) is an immunodetection method that can quantify PCR product directly after immobilization of biotinylated DNA on a microplate. This method, which detects nucleic acid instead of protein, is a much more sensitive method compared to conventional PCR method, with shorter analytical time and lower detection limit. Its high specificity and sensitivity, together with its semiquantitative ability, give it a huge potential to serve as a powerful detection tool in various industries such as medical, veterinary, and agricultural industries. With the recent advances in PCR-ELISA, it is envisaged that the assay is more widely recognized for its fast and sensitive detection limit which could improve overall diagnostic time and quality.
    Matched MeSH terms: Polymerase Chain Reaction/methods*
  18. Chan PL, Rose RJ, Abdul Murad AM, Zainal Z, Low ET, Ooi LC, et al.
    PLoS ONE, 2014;9(6):e99774.
    PMID: 24927412 DOI: 10.1371/journal.pone.0099774
    The somatic embryogenesis tissue culture process has been utilized to propagate high yielding oil palm. Due to the low callogenesis and embryogenesis rates, molecular studies were initiated to identify genes regulating the process, and their expression levels are usually quantified using reverse transcription quantitative real-time PCR (RT-qPCR). With the recent release of oil palm genome sequences, it is crucial to establish a proper strategy for gene analysis using RT-qPCR. Selection of the most suitable reference genes should be performed for accurate quantification of gene expression levels.
    Matched MeSH terms: Real-Time Polymerase Chain Reaction/methods*
  19. Manjeri G, Muhamad R, Faridah QZ, Tan SG
    J. Genet., 2012 Nov 22;91(3):e92-6.
    PMID: 23257301
    Matched MeSH terms: Polymerase Chain Reaction/methods*
  20. Ling LP, Adibah AB, Tan SG, Christianus A, Faridah QZ
    J. Genet., 2011 Dec;90(3):e101-4.
    PMID: 22232191
    Matched MeSH terms: Polymerase Chain Reaction/methods
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