Displaying publications 1 - 20 of 237 in total

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  1. 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
  2. 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
  3. 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*
  4. George R, Donald PM, Nagraj SK, Idiculla JJ, Hj Ismail R
    Malays J Med Sci, 2013 Jan;20(1):76-80.
    PMID: 23785258 MyJurnal
    Sex determination is the most important step in personal identification in forensic investigations. DNA-based sex determination analysis is comparatively more reliable than the other conventional methods of sex determination analysis. Advanced technology like real-time polymerase chain reaction (PCR) offers accurate and reproducible results and is at the level of legal acceptance. But still there are situations like chimerism where an individual possess both male and female specific factors together in their body. Sex determination analysis in such cases can give erroneous results. This paper discusses the phenomenon of chimerism and its impact on sex determination analysis in forensic investigations.
    Matched MeSH terms: Real-Time Polymerase Chain Reaction
  5. Chin, Yuet Meng, Arison Mohamad, Zubaidah Zakaria
    MyJurnal
    For many years counting cells and identifying them under the microscope has been the conventional method to determine the number of abnormal and normal cells in cancers. During the last decade, studies have shown that the detection and quantification of residual tumor cells is important in predicting the clinical outcome of several types of hematological malignancies. Detection of
    minimal residual disease (MRD) is now becoming routinely implemented in treatment protocols and is increasingly used for guiding therapy and for evaluation of new treatment modalities (Raanani & Hashomer, 2004). A wide variety of techniques have been developed to detect residual malignant cells beyond the sensitivity of conventional approaches by cell morphology. One of these technology is by real time quantitative (RQ) polymerase chain reaction (PCR) using the Taqman and LightCycler systems.
    Matched MeSH terms: Real-Time Polymerase Chain Reaction
  6. Hossain MAM, Ali ME, Sultana S, Asing, Bonny SQ, Kader MA, et al.
    J. Agric. Food Chem., 2017 May 17;65(19):3975-3985.
    PMID: 28481513 DOI: 10.1021/acs.jafc.7b00730
    Cattle, buffalo, and porcine materials are widely adulterated, and their quantification might safeguard health, religious, economic, and social sanctity. Recently, conventional polymerase chain reaction (PCR) and PCR-restriction fragment length polymorphism (RFLP) assays have been documented but they are just suitable for identification, cannot quantify adulterations. We described here a quantitative tetraplex real-time PCR assay with TaqMan Probes to quantify contributions from cattle, buffalo, and porcine materials simultaneously. Amplicon-sizes were very short (106-, 90-, and 146-bp for cattle, buffalo, and porcine) because longer targets could be broken down, bringing serious ambiguity in molecular diagnostics. False negative detection was eliminated through an endogenous control (141-bp site of eukaryotic 18S rRNA). Analysis of 27 frankfurters and 27 meatballs reflected 84-115% target recovery at 0.1-10% adulterations. Finally, a test of 36 commercial products revealed 71% beef frankfurters, 100% meatballs, and 85% burgers contained buffalo adulteration, but no porcine was found in beef products.
    Matched MeSH terms: Real-Time Polymerase Chain Reaction/instrumentation; Real-Time Polymerase Chain Reaction/methods*
  7. Mohamad NA, Mustafa S, Khairil Mokhtar NF, El Sheikha AF
    J. Sci. Food Agric., 2018 Sep;98(12):4570-4577.
    PMID: 29505123 DOI: 10.1002/jsfa.8985
    BACKGROUND: The pharmaceutical industry has boosted gelatin consumption worldwide. This is supported by the availability of cost-effective gelatin production from porcine by-products. However, cross-contamination of gelatin materials, where porcine gelatin was unintentionally included in the other animal sources of gelatin, has caused significant concerns about halal authenticity. The real-time polymerase chain reaction (PCR) has enabled a highly specific and sensitive animal species detection method in various food products. Hence, such a technique was employed in the present study to detect and quantify porcine DNA in gelatin using a molecular beacon probe, with differences in performance between mitochondrial (cytochrome b gene) and chromosomal DNA-(MPRE42 repetitive element) based porcine-specific PCR assays being compared.

    RESULTS: A higher sensitivity was observed in chromosomal DNA (MPRE-PCR assay), where this assay allows the detection of gelatin DNA at amounts as as low as 1 pg, whereas mitochondrial DNA (CBH-PCR assay) can only detect at levels down to 10 pg of gelatin DNA. When an analysis with commercial gelatin and gelatin capsule samples was conducted, the same result was observed, with a significantly more sensitive detection being provided by the repetitive element of chromosomal DNA.

    CONCLUSION: The present study has established highly sensitive DNA-based porcine detection systems derived from chromosomal DNA that are feasible for highly processed products such as gelatin and gelatin capsules containing a minute amount of DNA. This sensitive detection method can also be implemented to assist the halal authentication process of various food products available on the market. © 2018 Society of Chemical Industry.

    Matched MeSH terms: Real-Time Polymerase Chain Reaction/instrumentation; Real-Time Polymerase Chain Reaction/methods*
  8. Teoh BT, Sam SS, Tan KK, Johari J, Abd-Jamil J, Hooi PS, et al.
    Sci Rep, 2016 06 09;6:27663.
    PMID: 27278716 DOI: 10.1038/srep27663
    Timely and accurate dengue diagnosis is important for differential diagnosis and immediate implementation of appropriate disease control measures. In this study, we compared the usefulness and applicability of NS1 RDT (NS1 Ag Strip) and qRT-PCR tests in complementing the IgM ELISA for dengue diagnosis on single serum specimen (n = 375). The NS1 Ag Strip and qRT-PCR showed a fair concordance (κ = 0.207, p = 0.001). While the NS1 Ag Strip showed higher positivity than qRT-PCR for acute (97.8% vs. 84.8%) and post-acute samples (94.8% vs. 71.8%) of primary infection, qRT-PCR showed higher positivity for acute (58.1% vs. 48.4%) and post-acute (50.0% vs.41.4%) samples in secondary infection. IgM ELISA showed higher positivity in samples from secondary dengue (74.2-94.8%) than in those from primary dengue (21.7-64.1%). More primary dengue samples showed positive with combined NS1 Ag Strip/IgM ELISA (99.0% vs. 92.8%) whereas more secondary samples showed positive with combined qRT-PCR/IgM ELISA (99.4% vs. 96.2%). Combined NS1 Ag Strip/IgM ELISA is a suitable combination tests for timely and accurate dengue diagnosis on single serum specimen. If complemented with qRT-PCR, combined NS1 Ag Strip/IgM ELISA would improve detection of secondary dengue samples.
    Matched MeSH terms: Real-Time Polymerase Chain Reaction/methods*; Real-Time Polymerase Chain Reaction/standards
  9. Selvarajah GT, Bonestroo FAS, Timmermans Sprang EPM, Kirpensteijn J, Mol JA
    BMC Vet. Res., 2017 Nov 25;13(1):354.
    PMID: 29178874 DOI: 10.1186/s12917-017-1281-3
    BACKGROUND: Quantitative PCR (qPCR) is a common method for quantifying mRNA expression. Given the heterogeneity present in tumor tissues, it is crucial to normalize target mRNA expression data using appropriate reference genes that are stably expressed under a variety of pathological and experimental conditions. No studies have validated specific reference genes in canine osteosarcoma (OS). Previous gene expression studies involving canine OS have used one or two reference genes to normalize gene expression. This study aimed to validate a panel of reference genes commonly used for normalization of canine OS gene expression data using the geNorm algorithm. qPCR analysis of nine canine reference genes was performed on 40 snap-frozen primary OS tumors and seven cell lines.

    RESULTS: Tumors with a variety of clinical and pathological characteristics were selected. Gene expression stability and the optimal number of reference genes for gene expression normalization were calculated. RPS5 and HNRNPH were highly stable among OS cell lines, while RPS5 and RPS19 were the best combination for primary tumors. Pairwise variation analysis recommended four and two reference genes for optimal normalization of the expression data of canine OS tumors and cell lines, respectively.

    CONCLUSIONS: Appropriate combinations of reference genes are recommended to normalize mRNA levels in canine OS tumors and cell lines to facilitate standardized and reliable quantification of target gene expression, which is essential for investigating key genes involved in canine OS metastasis and for comparative biomarker discovery.

    Matched MeSH terms: Real-Time Polymerase Chain Reaction/methods; Real-Time Polymerase Chain Reaction/veterinary
  10. Subramaniam, K.S., Wong, M.S., Woo, Y.L., Mat Adenan, N.A., Mohamed, Z., Chung, I., et al.
    JUMMEC, 2013;16(1):1-5.
    MyJurnal
    Genetic mutations in endometrial cancer (EC) have been extensively studied in the Western population but not much in Asian cohorts. This study has demonstrated that PTEN and PIK3CA mutations are commonly found in EC among Malaysian women. Following RNA extraction from 20 cancerous and 18 non-cancerous tissues, the presence of mutations in 9 exons of PTEN and 3 exons of PIK3CA genes were detected using real-time PCR, accompanied by High Resolution Melt (HRM) analysis. Sequencing confirmed specificity of each PCR product. The mutations for both genes were detected in the samples with varying frequencies. Notably, all samples expressed mutation of PTEN at exon 7 but none in exon 4. Further analysis demonstrated that strong concurrent mutations occurred between exons 7 of PTEN with exon 20 region 1 of PIK3CA gene (90%). Our data showed mutations are present in EC and not the non-cancerous tissues. Larger samples are being collected to validate this observation.
    Matched MeSH terms: Real-Time Polymerase Chain Reaction
  11. MyJurnal
    Malaysia, Biosafety Bill 2006 was approved by Parliament in July 2007, and labeling legislation will be implemented soon. In this study, duplex polymerase chain reaction (PCR) was carried out to detect
    endogenous soybean lectin gene and exogenous cp4-epsps (5’-enolpyruvylshikimate-3-phospate synthase) gene simultaneously. Additionally, real-time PCR utilizing SYBR Green fluorescence dye were established for the quantitative analysis of Roundup Ready soybean (RRS), which is based on the two established calibration curve from cloned fragment of cp4-epsps gene and lectin gene respectively. Approximately, 39.5% (45/114) of the samples examined in this study contain RRS, animal feeds (31), processed food (13) and raw soybean (1). Additionally, 75.6% (34/45) of the positive samples were found contained RRS above 0.9%. The sensitive GMO quantitative approach described in this study enable the analysis of various samples and this will facilitate the labeling process.
    Matched MeSH terms: Real-Time Polymerase Chain Reaction
  12. Jasbeer, K., Ghazali, F.M., Cheah, Y.K., Son, R.
    MyJurnal
    The introduction of new agricultural commodities and products derived from modernbiotechnology may have an impact on human and animal health, the environment and economiesof countries. As more Genetically Modified Organisms (GMO) enter markets worldwide, themonitoring of GMOs is being preferred for obvious reasons such as determination of seed purity,verification of non-GMO status of agricultural crops and fulfilling GMO labeling provisions, tomention a few. Numerous GMO analytical methods which include screening, identification andquantification have been developed to reliably determine the presence and/or amount of GMOin agricultural commodities, in raw agricultural materials and in processed and refined ingredients.The detection of GMOs relies on the detection of transgenic DNA or protein material. For routineanalysis, a good sample preparation technique should reproducibly generate DNA/protein ofsufficient quality, purity and yield while minimizing the effects of inhibition andcontamination.
    The key sample preparation steps include homogenization, pretreatment, extraction andpurification. Due to the fact that analytical laboratories receive samples that are often processedand refined, the quality and quantity of transgenic target analyte (e.g. protein and DNA) frequentlychallenge the sensitivity of any detection method. With the development of GMO analysistechniques, the Polymerase Chain Reaction (PCR) technique has been the mainstay for GMOdetection, and the real-time PCR is the most effective and important method for GMOquantification. The choice of target sequence; for example a promoter, a terminator, a gene, or ajunction between two of these elements, is the single most important factor controlling the specificity of the PCR method. Recent developments include event-specific methods, particularlyuseful for identification and quantification of GM content. Although PCR technology has obvious
    limitations, the potentially high degree of sensitivity and specificity explains why PCR in its various
    formats, is currently the leading analytical technology employed in GMO analysis. Comparatively, immunoassays are becoming attractive tools for rapid field monitoring for the integrity of agricultural commodities in identity preservation systems, whereby non-specialised personnel can employ them in cost-effective manner. This review discusses various popular extraction methodologies and summarises the current status of the most widely used and easily applicable GMO analysis technologies in laboratories, namely the PCR and immunoassay technologies.
    Matched MeSH terms: Real-Time Polymerase Chain Reaction
  13. Anand S, Rajan M, Venkateshbabu N, Kandaswamy D, Shravya Y, Rajeswari K
    Open Dent J, 2016;10:160-5.
    PMID: 27386000 DOI: 10.2174/1874210601610010160
    AIM: To compare the antibacterial efficacy of Azadirachta indica (Neem), Commiphora myrrha (Myrrh), Glycyrrhiza glabra (Liquorice) with 2% Chlorhexidine (CHX) against E. faecalis by using Real Time PCR.

    MATERIALS AND METHODS: A total of fifty teeth specimens (n=50) were inoculated with E. faecalis for 21 days. Specimens were divided into five groups (Group 1: Myrrh, Group 2: Neem, Group 3: Liquorice, Group 4: 2% CHX and Group 5: Saline (negative control)). The intracanal medicaments were packed inside the tooth. After 5 days, the remaining microbial load was determined by using real time PCR.

    RESULTS: Threshold cycle (Ct) values of Myrrh extract, Neem extract, Liquorice Extract, 2% CHX and saline were found to be 30.94, 23.85, 21.38, 30.93 and 17.8 respectively.

    CONCLUSION: Myrrh extract showed inhibition of E.faecalis equal to that of 2% CHX followed by Neem, Liquorice and Saline.

    Matched MeSH terms: Real-Time Polymerase Chain Reaction
  14. Gunasegar S, Himratul-Aznita WH
    FEMS Yeast Res., 2019 Mar 01;19(2).
    PMID: 30476044 DOI: 10.1093/femsyr/foy123
    Candida albicans ATCC 14053 and Candida parapsilosis ATCC 22019 hyphal-wall protein 1 (HWP1) are involved in hyphae formation and pathogenesis. The transcriptional agglutinin-like sequence 3 (ALS3) genes in both species are responsible for the development of biofilm and colonization on tooth surfaces. Therefore, we investigated the expression of HWP1 and ALS3 quantitatively in C. albicans and C. parapsilosis and examined the biofilm structure upon exposure to various nicotine concentrations. In vitro, biofilms of Candida species were developed directly on slides using the Lab-Tek Chamber Slide System and visualized by confocal laser scanning microscopy. Quantitative real-time polymerase chain reaction was used to measure HWP1 and ALS3 expression in C. albicans ATCC 14053 and C. parapsilosis ATCC 22019. The results indicated that nicotine multiplied the number of yeast cells and increased the extracellular polysaccharides of Candida species. We also found that 1-2 mg/mL nicotine could enhance the formation of biofilm. The findings also revealed that the expression of HWP1 and ALS3 in Candida species were increased as the nicotine concentration increased. Therefore, nicotine influences the biofilm development of oral-associated C. albicans ATCC 14053 and C. parapsilosis ATCC 22019.
    Matched MeSH terms: Real-Time Polymerase Chain Reaction
  15. Hanafy NA, Badr MS, Nasr GM
    Open Access Maced J Med Sci, 2018 Sep 25;6(9):1577-1580.
    PMID: 30337968 DOI: 10.3889/oamjms.2018.400
    BACKGROUND: Toxoplasma gondii is a common parasitic infection of humans. Infection is usually mild. Serious complications can occur in pregnant and immunocompromised patients.

    AIM: The present study aims to investigate the performance of 2 different PCR protocols; real-time quantitative molecular assays (qPCR) and conventional molecular assays (cPCR), using 2 different sets of primers and by using cloned purified Toxoplasma genomic substances to be evaluated as reference samples.

    METHODS: The target DNA was provided in 8 different quantities.

    RESULTS: Amplification failure was reported only with the cPCR in samples of low concentrations using both primer sets. Quantitative PCR detected the 8 different dilutions of the purified Toxoplasma gondii using the 2 sets of primers while cPCR was sensitive to detect only 6 different dilutions.

    CONCLUSION: Generally real-time quantitative molecular assays, is easy to use method compared to conventional PCR assay and produces more reliable results within only one hour time but still the possible application of qPCRs in routine diagnosis necessitates analysis of a large number of clinical samples in further studies to make the proper choice.

    Matched MeSH terms: Real-Time Polymerase Chain Reaction
  16. Che Engku Noramalina Che-Engku-Chik, Siti Sarah Othman, Helmi Wasoh, Nor Azah Yusof, Jaafar Abdullah, Mohd Hazani Mat Zaid
    MyJurnal
    Despite the continued effort globally made to control the growing case of Tuberculosis (TB), it
    continues to be regarded as the second deadliest disease after the HIV. There are various
    methods developed to diagnose TB, most of which having the criteria of sensitive, selective,
    cheap and portable to be used in robust applications. Even with the advancement in medication,
    the important keys including early stage diagnosis is yet to be considered. In diagnosing TB, the
    only technique remained as the gold standard method is the culturing method, which is the Acid
    Fast Bacilli (AFB) staining. On the other hand, molecular technique utilising Polymerase Chain
    Reaction (PCR) assay is preferred as a non-culturing method. Additionally, as molecular
    techniques become advanced, real-time PCR or quantitative PCR (qPCR) using multiple probes
    in one shot has raised interest among researchers, because it can skip the process of gel
    electrophoresis. Recently, researchers have been working on electrochemical DNA sensors
    which are sensitive, selective, rapid, cheap and can meet with point of care (POC) testing
    requirements to diagnose TB.
    Matched MeSH terms: Real-Time Polymerase Chain Reaction
  17. Azlina Ahmad-Annuar, Ai Sze Ching
    Sains Malaysiana, 2015;44:1481-1488.
    As researchers seek to determine the cellular mechanisms underlying biological processes, they have turned to analyze the functional role of microRNAs to understand this process in details. Here, we investigated the expression pattern of two microRNAs, miR-124 and -134 in maturing neurons and found that the choice of endogenous controls influenced the observed expression levels of these microRNAs. We have cultured rat hippocampal neurons and performed quantitative PCR on the microRNAs using Taqman gene expression assays. The expression of miRNAs was normalised with selected endogenous controls. Using BestKeeper and NormFinder software, we found that 18S rRNA and 5S rRNA to be unsuitable as endogenous controls in this system, while normalising to U6 snRNA produced more consistent results. Our study would like to highlight the importance of empirically testing proposed endogenous controls in any model system before data interpretation is carried out.
    Matched MeSH terms: Real-Time Polymerase Chain Reaction
  18. Rashidah Iberahim, Norefrina Shafinaz Md. Nor, Wan Ahmad Yaacob, Nazlina Ibrahim
    Sains Malaysiana, 2018;47:1431-1438.
    The present study was aimed at determining the compounds available in Eleusine indica methanol extract and the effects on
    herpes simplex virus type 1 (HHV1) replication cycle and progeny infectivity. Twelve compounds mostly from the flavonoid
    and phenolic groups were identified by Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS) analysis. The
    effect on replication phases of HHV1 was determined by time-of-addition, time-removal and virus yield reduction assays
    with expression of selected genes analysed by quantitative Real Time-Polymerase Chain Reaction (qRT-PCR). The extract
    inhibited plaque formation the most during the first 2 h and at 24 h of infection. Plaque formation inhibition was also
    noted at all other time points but at lesser percentage. Treatment with E. indica reduced progeny infectivity when treated
    for 10 h and was dose-dependent. E. indica methanol extract inhibited immediate early, early and late phases of HHV1
    replication cycle by modifying the expression of UL
    54, UL
    27 and UL
    30 genes during the infection. Immunostaining of
    infected cells confirmed that E. indica inhibited mainly Glycoproteins B but not Glycoprotein C and D. Thus, the methanol
    extract of E. indica has the ability to alter HHV1 replication cycle at almost all stages and reduce progeny infectivity.
    Matched MeSH terms: Real-Time Polymerase Chain Reaction
  19. Zhang L, Cenci A, Rouard M, Zhang D, Wang Y, Tang W, et al.
    Sci Rep, 2019 Jun 03;9(1):8199.
    PMID: 31160634 DOI: 10.1038/s41598-019-44637-x
    Fusarium wilt disease, caused by Fusarium oxysporum f. sp. cubense, especially by tropical race 4 (Foc TR4), is threatening the global banana industry. Musa acuminata Pahang, a wild diploid banana that displays strong resistance to Foc TR4, holds great potential to understand the underlying resistance mechanisms. Microscopic examination reports that, in a wounding inoculation system, the Foc TR4 infection processes in roots of Pahang (resistant) and a triploid cultivar Brazilian (susceptible) were similar by 7 days post inoculation (dpi), but significant differences were observed in corms of both genotypes at 14 dpi. We compare transcriptomic responses in the corms of Pahang and Brazilian, and show that Pahang exhibited constitutive defense responses before Foc TR4 infection and inducible defense responses prior to Brazilian at the initial Foc TR4 infection stage. Most key enzymatic genes in the phenylalanine metabolism pathway were up-regulated in Brazilian, suggesting that lignin and phytotoxin may be triggered during later stages of Foc TR4 infection. This study unravels a few potential resistance candidate genes whose expression patterns were assessed by RT-qPCR assay and improves our understanding the defense mechanisms of Pahang response to Foc TR4.
    Matched MeSH terms: Real-Time Polymerase Chain Reaction
  20. Moriya S, Tan VP, Yee AK, Parhar IS
    Neurosci. Lett., 2019 08 24;708:134330.
    PMID: 31201839 DOI: 10.1016/j.neulet.2019.134330
    In Parkinson's disease (PD), several genes have been identified as the PD-related genes, however, the regulatory mechanisms of these gene expressions have not been fully identified. In this study, we investigated the effect of inflammation, one of the major risk factors in PD on expressions of the PD-related genes. Lipopolysaccharide (LPS) was intraperitoneally administered to mature male zebrafish and gene expressions in the brains were examined by real-time PCR. In the inflammation-related genes, expressions of tnfb, il1b and il6 were increased at 2 days post administration in the 10 μg group, and tnfb expression was also increased at 4 days post administration in the 1 μg and 10 μg group. In the PD-related genes, pink1 expression was significantly decreased at 4 days, atp13a2 expression was significantly increased at 7 days, and uchl1 expression was significantly decreased at 7 days. This suggests that pink1, atp13a2 and uchl1 expressions are regulated by inflammation, and this regulatory mechanism might be involved in the progress of PD.
    Matched MeSH terms: Real-Time Polymerase Chain Reaction
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