Displaying publications 61 - 80 of 306 in total

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  1. Fulltext Molecular quantitation and characterization of Vibrio cholerae from different seafood obtained from wetmarket and supermarket
    Vengadesh, L., Son, R., Yoke-Kqueen, C.
    International Food Research Journal, 2012;19(1):45-50.
    MyJurnal
    Vibrio cholerae still represents a significant threat to human health worldwide despite the advances in hygiene, consumer knowledge, food treatment and food processing. In Malaysia, statistics in year 2009 have shown that among the food and water borne diseases, food poisoning has the highest incidence rate of 36.17 per 100,000 populations and with a mortality rate of 0.01 per 100,000 populations. In this study, 22 seafood samples comprising of fish, squid, crustacean and mollusks purchased from wet market and supermarket were analyzed. The Most Probable Number (MPN) and real time PCR was used to enumerate the Vibrio cholerae in seafood sample. The results showed that MPN-real time PCR of the samples from wet market had a maximum of >1100 MPN/g compare to 93 MPN/g enumerated from the MPN plate. The MPN-real time PCR in the samples from supermarket indicated 290 MPN/g as compared to 240 MPN/g enumerated from the MPN plate. The standard curves showed that there was a good linear correlation between the Ct values. The minimum level of detection of Vibrio cholerae standard DNA at targeted gene was 3 x 10-5 ng/μl.
    Matched MeSH terms: Real-Time Polymerase Chain Reaction
  2. Fulltext Development of a SYBR green based real-time polymerase chain reaction assay for specific detection and quantification of Vibrio parahaemolyticus from food and environmental samples
    Micky, V., Nur Quraitu’ Aini, T., Velnetti, L., Patricia Rowena, M.B., Christy, C., Lesley Maurice, B.
    International Food Research Journal, 2014;21(3):921-927.
    MyJurnal
    Vibrio parahaemolyticus is a foodborne pathogen and their human infection is regularly associated with the consumption of raw or undercooked seafood and contaminated water supplies. Many conventional biochemical identification and confirmation procedures are performed to detect the presence of this pathogen, both from seafood or environmental samples. However, these procedures not only require two or more days to complete, they do not have the capabilities to determine the number of V. parahaemolyticus cells in any given samples. Thus, in this study we describe the development of a rapid SYBR green based real-time PCR assay, targeting the thermo labile (tl) gene of V. parahaemolyticus for the detection and enumeration of this bacterium from seafood and environmental samples. We report that the real-time PCR assay and the primers designed are highly specific, and only generated the desired amplicons with V. parahaemolyticus DNA samples against other bacteria and fungi species. Our assay is also highly sensitive, and, is able to detect V. parahaemolyticus with high coefficient values in concentrations as low as 1.0 pg/μl DNA for pure genomic DNA solutions and 10 cells/ml in serially diluted cell suspension and spiked samples. This assay can be completed in less than 3 hours and may be used as a tool for rapid determination of V. parahaemolyticus densities in the food industries, environmental risk assessment and for clinical diagnostics purposes.
    Matched MeSH terms: Real-Time Polymerase Chain Reaction
  3. Fulltext Technical aspects in understanding effects of gamma irradiation on flower colour changes in Dendrobium Sonia
    Sakinah Ariffin, Azhar Mohamad, Ratnam, Wickneswari
    Jurnal Sains Nuklear Malaysia, 2012;24(1):91-101.
    MyJurnal
    Colour is one of the most important traits in orchids and has created great interest in breeding programmes. Gamma irradiation is an alternative way for generation of somaclonal variation for new flower colours. Phenotypic changes are usually observed during screening and selection of mutants. Understanding of targeted gene expression level and evaluation of the changes facilitate in the development of functional markers for selection of desired flower colour mutants. Four Dendrobium orchid sequences (NCBI accessions: AM490639, AY41319, FM209429 and DQ462460) were selected to design gene specific primers based on information for chalcone synthase (CHS) from NCBI database. Quantitative real-time PCR (qPCR) was used to understand flower colour expression quantitatively derived from the CHS gene activities in different flower tissues (petal and sepal) from control Dendrobium Sonia (red purple), mutant DS 35-1/M (purple pink) and mutant DS 35-WhiteA. It was found that expression of CHS gene was highest in sepals of white flowers and lowest in both sepals and petals of purple pink flowers. Genomic DNA was amplified and PCR products were sequenced, aligned and compared. Sequence variations of CHS partial gene in Dendrobium Sonia mutants with different flower colour showed that two protein positions have been changed as compared to the control. These non-synonymous mutations may have contributed to the colour alterations in the white and purple pink mutants. This paper describes important procedures to quantify gene expression such as RNA isolation (quantity and quality), cDNA synthesis and primer design steps for CHS genes.
    Matched MeSH terms: Real-Time Polymerase Chain Reaction
  4. Fulltext Effect of Ganoderma lucidum polysaccharides on the growth of Bifidobacterium spp. as assessed using Real-time PCR
    Yamin, S., Shuhaimi, M., Arbakariya, A., Khalilah, A. K., Anas, O., Yazid, A. M., et al.
    International Food Research Journal, 2012;19(3):1199-1205.
    MyJurnal
    The use of component from Ganoderma lucidum as prebiotic source is interesting as the G. lucidum itself was known for more than a decade in the traditional Chinese medicine. In this work, Ganoderma lucidum crude polysaccharides (GLCP) and Polysaccharide-fraction number 2 (PF-2) were used as carbon sources in the fermentation with Bifidobacterium sp. The results showed the potential of prebiotic effect of the G. lucidum extract in batch-culture fermentation based on increment in the growth of bacteria used (0.4 – 1.5 log10 CFU/mL) after 18h fermentation. Fermentation was further done using faecal materials as bacterial inocula and bacterial growth changes were examined using real-time PCR. The results showed the ability of GLCP and PF-2 to support the growth of Bifidobacterium genus with 0.3 and 0.7 log10 cells/ml increased, respectively. Interestingly, Lactobacillus which is known as beneficial bacterial genus also showed growth increment with 0.7 and 1 log10 cells/ml increased. The competition for carbon sources thus inhibits the growth of potentially harmful genus, Salmonella (0.3 and 0.5 log10 cells/ml) in comparison to the control.
    Matched MeSH terms: Real-Time Polymerase Chain Reaction
  5. Changes in rumen protozoal community by condensed tannin fractions of different molecular weights from a Leucaena leucocephala hybrid in vitro
    Saminathan M, Gan HM, Abdullah N, Wong CMVL, Ramiah SK, Tan HY, et al.
    J Appl Microbiol, 2017 Apr 23.
    PMID: 28434189 DOI: 10.1111/jam.13477
    AIMS: To evaluate the effects of condensed tannins (CTs) fractions of differing molecular weights (MWs) from a Leucaena leucocephala hybrid-Rendang on the rumen protozoal community in vitro.

    METHODS AND RESULTS: The effects of unfractionated CTs (F0) and CT fractions of different MWs (F1 > F2 > F3 > F4 > F5) on protozoal population and community were evaluated in vitro using rumen microbes and ground guinea grass as the substrate. Higher-MW CT fractions F1 and F2 significantly (P real-time PCR analysis showed that the total protozoa was significantly (P 

    Matched MeSH terms: Real-Time Polymerase Chain Reaction
  6. Fulltext Sybr Green Real-Time PCR is a useful method in screening for high risk human papilloma virus types 16 and 18 in neoplastic cervical cancer
    Nor Rizan, K., Abdul Manaf ,A., Sabariah, A.R., Siti Aishah, M.A., Noorjahan Banu, M.A., Zubaidah, Z.
    Medicine & Health, 2011;6(1):59-67.
    MyJurnal
    Human papillomavirus (HPV) plays an important role in the pathogenesis of cervical cancer. HPV has been found in 99.7% of cervical cancers worldwide. In Malaysia, it is the second most common cancer among women in all major ethnic groups. The main purpose of this study was to establish the method of SyBrGreen Real-Time PCR and apply it for identification of multiple infections of the two high risk HPV subtypes. In this study, 57 positive samples for HPV 16 and HPV 18 were used to establish a simple
    and sensitive method to detect and identify HPV infection in the cervical neoplasia at different stages of the disease by using real-time ABICycler SyBrGreen 1 technology. The results showed 67 HPV genomes in 57 samples. HPV 16 genome was detected in 55/67 (82%) cases while HPV 18 was detected in 8/67 (12%) cases with 4 cases showing multiple infections of HPV 16 and HPV 18. HPV 16 was the most prevalent followed by HPV 18. Using SyBr Green Real-Time PCR techniques, the results
    showed that DNA melting curve for HPV 16 had a peak around 80.2ºC and Ct value of 20 cycles whereas the DNA melting curve for HPV 18 around 79.2ºC and Ct value of 22 cycles. In conclusion, a SyBr Green Real-Time PCR method has the potential for clinical usage in detection and identification of HPV infection in cervical neoplasia at different stages of the disease.
    Matched MeSH terms: Real-Time Polymerase Chain Reaction
  7. Fulltext Validation of oligonucleotide microarray gene expression profiles by real-time PCR using SYBR-Green 1 fluorescence
    Nik Norliza Nik Hassan, Rozita Rosli, Abdul Munir Abdul Murad, Nor Kaslina Kornain, Sabariah, A.R., Rohan Malek Johan, et al.
    Buletin Persatuan Genetik Malaysia, 2008;14(1):1-16.
    MyJurnal
    DNA microarray technology has permitted large scale parallel analysis of gene expression of several diseases, including cancers. Real-time PCR has become a well-established procedure for
    quantifying levels of gene expression. We evaluated Real-Time PCR to validate differentially expressed genes identified by DNA arrays. Gene expression of three different grade of transitional cell carcinoma (TCC) of human bladder cancer was determined using microarray slide containing cancer-related genes. Data obtained were sorted according based on the ratios between Cy3 and Cy5 dyes used and revealed 119, 235 and 183 differentially expressed genes in TCC WHO Grades I, II and III, respectively. Real-time PCR used SYBR Green-1 dye detection to validate relative change in gene expression. Real- Time PCR confirmed the change in gene expression of 17 of 28 (75%) genes identified by microarray. Real-Time PCR also suggest that genes identified by microarray with two or higher fold change cannot be eliminated as false nor be accepted as true without validation. Real-Time PCR based on SYBR Green- 1 is well-suited to validate DNA array results because it is quantitative, rapid and requires less RNA compared to the conventional assays.
    Matched MeSH terms: Real-Time Polymerase Chain Reaction
  8. Fulltext Detection of human herpesvirus 6 (HHV-6) in saliva of healthy adults in Malaysia
    Choo, H.L., Shoji, Y., Leong, C.O.
    Malaysian Journal of Medicine and Health Sciences, 2012;8(2):55-64.
    MyJurnal
    Human herpesvirus-6 (HHV-6) levels have been considered as markers for various diseases. The aim of this study was to evaluate the prevalence of HHV-6 infection in healthy adults in Malaysia. Methods: The level of HHV-6 in saliva was investigated in 36 healthy adults, age 19 to 23 years, at Kuala Lumpur, Malaysia using variant-specific TaqmanTM quantitative real-time PCR (qPCR). Results: The amount of HHV-6 DNA in the saliva of healthy adults ranged from negative to 10,000 HHV-6 genomes/ml of saliva (median, 360 genomes/ml of saliva). Of the 36 samples tested, 30 (83%) contained HHV-6 DNA. HHV-6B was the only variant detected in the saliva of all the positive cases. Conclusions: The detection of HHV-6 DNA in saliva by real-time PCR assay provides a sensitive and specific quantitation of HHV-6. Our pilot study suggests the wide prevalence of HHV-6 in saliva from
    healthy adults.
    Matched MeSH terms: Real-Time Polymerase Chain Reaction
  9. Gut health and serum growth hormone levels of broiler chickens fed dietary chitin and chitosan from cricket and shrimp
    Ibitoye EB, Lokman IH, Hezmee MNM, Goh YM, Zuki ABZ, Jimoh AA, et al.
    Poult Sci, 2019 Feb 01;98(2):745-752.
    PMID: 30265345 DOI: 10.3382/ps/pey419
    Growth hormones (GH) alone does not explain the growth rate in the chicken as growth in an animal is multi-factorial. Normal morphology of the intestinal villus and crypt, with adequate regulation of intestinal nutrient transporters, is essential to a healthy gut. Nutrition plays a significant role in gut health management, but information on the effect of dietary chitin and chitosan on gut morphology, gene expression of nutrient transporter, and serum levels of GH in broiler chickens is scanty. Thus, this study aimed at evaluating the comparative effect of dietary chitin and chitosan from cricket and shrimp on the small intestinal morphology, relative gene expression of intestinal nutrient transporters and serum level of GH in the broiler. A total of 150 day-old male Cobb500 broiler chicks were randomly allotted to one of the five treatment groups (n = 30). Treatment 1 was fed basal diet only, treatments 2 to 5 were fed a basal diet with 0.5 g cricket chitin, cricket chitosan, shrimp chitin, and shrimp chitosan, respectively, per kg diet. At days 21 and 42, duodenal and jejunal samples were assessed for structural morphology and jejunum for the relative gene expression of PepT1, EAAT3, SGLT1, and SGLT5 using quantitative real-time PCR. Results bared that dietary cricket chitosan and shrimp chitosan significantly (P < 0.05) improved jejunal villus height and reduced crypt depth without improving the body weight (BW). The gut morphology of birds under cricket chitin was poor and significantly (P < 0.05) different from other treated groups. Both the dietary chitin and chitosan at day 21 and only dietary chitosan at day 42 significantly (P < 0.05) down-regulated the relative mRNA expression of PepT1, EAAT3, SGLT1, and SGLT5 of broiler chickens. Treated groups differ non-significantly at both phases, while cricket chitin numerically increased the relative expression of PepT1, EAAT3, and SGLT1. Therefore, the potential of cricket chitin to improve BW and to up-regulate nutrient transporters is worthy of further exploration.
    Matched MeSH terms: Real-Time Polymerase Chain Reaction
  10. Fulltext HLA-B*15:02 screening in epileptic patients using a high resolution melting-real time PCR (HRM-QPCR) method
    Zam Zureena Mohd Rani, Nor Azian Abdul Murad, Saberi Saimun, Sri Noraima Othman, Rahman Jamal, Sue-Mian Then, et al.
    Neurology Asia, 2018;23(2):137-144.
    MyJurnal
    Background: The HLA-B*15:02 polymorphism in epileptic patients is known to be associated with carbamazepine-induced Stevens-Johnson syndrome (SJS). The prevalence of HLA-B*15:02 polymorphism seemed to be ethnic-specific with a higher frequency of HLA-B*15:02 in Asian compared to the Europeans. This study was performed to determine the frequency of the HLA-B*15:02 polymorphism in epileptic patients at the Chancellor Tuanku Muhriz Hospital-UKM Medical Centre (HCTM-UKMMC) using high resolution melting-real time PCR (HRM-QPCR) method.
    Methods: We performed a fast and effective in-house high resolution melting-real time polymerase chain reaction method and compared it with the conventional multiplex-PCR method. The specificity and sensitivity of each test were also determined using DNA from saliva.
    Results: Using the conventional multiplexPCR approach for screening, 25 out of 64 (39.1%) epileptic patients were positive for HLA-B*15:02. However, using the HRM-QPCR technique, 24/64 (37.5%) of the patients were positive. The one patient who tested positive by the multiplex-PCR but negative using the HRM-QPCR turned out to be negative by DNA sequencing. The HRM-QPCR and DNA sequencing showed 100% sensitivity and specificity. The multiplex-PCR showed 100% sensitivity and 98.4% specificity compared to both HRM-QPCR and DNA sequencing. The HRM-QPCR is also more cost-effective (time-consuming when compared to the multiplex-PCR ($25.15 USD/test).
    Conclusion: Our result suggested that multiplex PCR, HRM-QPCR and Sanger sequencing can be used for detection of HLA-B*15:02. However, a qualitative method such as multiplex PCR should be confirmed with other quantitative methods such as HRM-QPCR and Sanger sequencing.
    Keywords: Epilepsy, carbamazepine-induced Steven Johnson syndrome, multiplex-polymerase chain reaction, high resolution melting-real time polymerase chain reaction (HRM-QPCR), DNA sequencing
    Matched MeSH terms: Real-Time Polymerase Chain Reaction
  11. Electrospun poly(3-hydroxybutyrate-co-3-hydroxyhexanoate)/silk fibroin film is a promising scaffold for bone tissue engineering
    Ang SL, Shaharuddin B, Chuah JA, Sudesh K
    Int J Biol Macromol, 2020 Feb 15;145:173-188.
    PMID: 31866541 DOI: 10.1016/j.ijbiomac.2019.12.149
    Polyhydroxyalkanoates (PHAs) are biodegradable polyesters produced by microorganisms, under unbalanced growth conditions, as a carbon storage compound. PHAs are composed of various monomers such as 3-hydroxybutyrate (3HB) and 3-hydroxyhexanoate (3HHx). Silk fibroin (SF) derived from Bombyx mori cocoons, is a widely studied protein polymer commonly used for biomaterial applications. In this study, non-woven electrospun films comprising a copolymer of 3HB and 3HHx [P(3HB-co-3HHx)], SF and their blends were prepared by electrospinning technique. The growth and osteogenic differentiation of human umbilical cord-derived mesenchymal stem cells (hUC-MSCs) were studied using different types of fabricated electrospun films. The differentiation study revealed that electrospun P(3HB-co-3HHx)/SF film supports the differentiation of hUC-MSCs into the osteogenic lineage, confirmed by histological analysis using Alizarin Red staining, energy dispersive X-ray (EDX) and quantitative real-time PCR analysis (qPCR). Electrospun P(3HB-co-3HHx)/SF film up-regulated the expression of osteogenic marker genes, alkaline phosphatase (ALP) and osteocalcin (OCN), by 1.6-fold and 2.8-fold respectively, after 21 days of osteogenic induction. In conclusion, proliferation and osteogenic differentiation of hUC-MSCs were enhanced through the blending of P(3HB-co-3HHx) and SF. The results from this study suggest that electrospun P(3HB-co-3HHx)/SF film is a promising biomaterial for bone tissue engineering.
    Matched MeSH terms: Real-Time Polymerase Chain Reaction
  12. Fulltext Rapid identification of melioidosis agent by an insulated isothermal PCR on a field-deployable device
    Chua KH, Tan EW, Chai HC, Puthucheary SD, Lee PC, Puah SM
    PeerJ, 2020;8:e9238.
    PMID: 32518734 DOI: 10.7717/peerj.9238
    Background: Burkholderia pseudomallei causes melioidosis, a serious illness that can be fatal if untreated or misdiagnosed. Culture from clinical specimens remains the gold standard but has low diagnostic sensitivity.

    Method: In this study, we developed a rapid, sensitive and specific insulated isothermal Polymerase Chain Reaction (iiPCR) targeting bimA gene (Burkholderia Intracellular Motility A; BPSS1492) for the identification of B. pseudomallei. A pair of novel primers: BimA(F) and BimA(R) together with a probe were designed and 121 clinical B. pseudomallei strains obtained from numerous clinical sources and 10 ATCC non-targeted strains were tested with iiPCR and qPCR in parallel.

    Results: All 121 B. pseudomallei isolates were positive for qPCR while 118 isolates were positive for iiPCR, demonstrating satisfactory agreement (97.71%; 95% CI [93.45-99.53%]; k = 0.87). Sensitivity of the bimA iiPCR/POCKIT assay was 97.52% with the lower detection limit of 14 ng/µL of B. pseudomallei DNA. The developed iiPCR assay did not cross-react with 10 types of non-targeted strains, indicating good specificity.

    Conclusion: This bimA iiPCR/POCKIT assay will undoubtedly complement other methodologies used in the clinical laboratory for the rapid identification of this pathogen.

    Matched MeSH terms: Real-Time Polymerase Chain Reaction
  13. Fulltext Real-time reverse transcription loop-mediated isothermal amplification for rapid detection of SARS-CoV-2
    Lau YL, Ismail I, Mustapa NI, Lai MY, Tuan Soh TS, Hassan A, et al.
    PeerJ, 2020;8:e9278.
    PMID: 32547882 DOI: 10.7717/peerj.9278
    Background: Highly sensitive real-time reverse transcription polymerase chain reaction (RT-qPCR) methods have been developed for the detection of SARS-CoV-2. However, they are costly. Loop-mediated isothermal amplification (LAMP) assay has emerged as a novel alternative isothermal amplification method for the detection of nucleic acid.

    Methods: A rapid, sensitive and specific real-time reverse transcription LAMP (RT-LAMP) assay was developed for SARS-CoV-2 detection.

    Results: This assay detected one copy/reaction of SARS-CoV-2 RNA in 30 min. Both the clinical sensitivity and specificity of this assay were 100%. The RT-LAMP showed comparable performance with RT-qPCR. Combining simplicity and cost-effectiveness, this assay is therefore recommended for use in resource resource-limited settings.

    Matched MeSH terms: Real-Time Polymerase Chain Reaction
  14. Fulltext Performance Evaluation of Commercial Dengue Diagnostic Tests for Early Detection of Dengue in Clinical Samples
    Mat Jusoh TNA, Shueb RH
    J Trop Med, 2017;2017:4687182.
    PMID: 29379526 DOI: 10.1155/2017/4687182
    The shattering rise in dengue virus infections globally has created a need for an accurate and validated rapid diagnostic test for this virus. Rapid diagnostic test (RDT) and reverse transcription-polymerase chain reaction (RT-PCR) diagnostic detection are useful tools for diagnosis of early dengue infection. We prospectively evaluated the diagnostic performance of nonstructural 1 (NS1) RDT and real-time RT-PCR diagnostic kits in 86 patient serum samples. Thirty-six samples were positive for dengue NS1 antigen while the remaining 50 were negative when tested with enzyme-linked immunosorbent assay (ELISA). Commercially available RDTs for NS1 detection, RTK ProDetect™, and SD Bioline showed high sensitivity of 94% and 89%, respectively, compared with ELISA. GenoAmp® Trioplex Real-Time RT-PCR and RealStar® Dengue RT-PCR tests presented a comparable kappa agreement with 0.722. The result obtained from GenoAmp® Real-Time RT-PCR Dengue test showed that 14 samples harbored dengue virus type 1 (DENV-1), 8 samples harbored DENV-2, 2 samples harbored DENV-3, and 1 sample harbored DENV-4. 1 sample had a double infection with DENV-1 and DENV-2. The NS1 RDTs and real-time RT-PCR tests were found to be a useful diagnostic for early and rapid diagnosis of acute dengue and an excellent surveillance tool in our battle against dengue.
    Matched MeSH terms: Real-Time Polymerase Chain Reaction
  15. Fulltext Assessment of Aedes albopictus reference genes for quantitative PCR at different stages of development
    Dzaki N, Azzam G
    PLoS One, 2018;13(3):e0194664.
    PMID: 29554153 DOI: 10.1371/journal.pone.0194664
    Members of the Aedes genus of mosquitoes are widely recognized as vectors of viral diseases. Ae.albopictus is its most invasive species, and are known to carry viruses such as Dengue, Chikugunya and Zika. Its emerging importance puts Ae.albopictus on the forefront of genetic interaction and evolution studies. However, a panel of suitable reference genes specific for this insect is as of now undescribed. Nine reference genes, namely ACT, eEF1-γ, eIF2α, PP2A, RPL32, RPS17, PGK1, ILK and STK were evaluated. Expression patterns of the candidate reference genes were observed in a total of seventeen sample types, separated by stage of development and age. Gene stability was inferred from obtained quantification data through three widely cited evaluation algorithms i.e. BestKeeper, geNorm, and NormFinder. No single gene showed a satisfactory degree of stability throughout all developmental stages. Therefore, we propose combinations of PGK and ILK for early embryos; RPL32 and RPS17 for late embryos, all four larval instars, and pupae samples; eEF1-γ with STK for adult males; eEF1-γ with RPS17 for non-blood fed females; and eEF1-γ with eIF2α for both blood-fed females and cell culture. The results from this study should be able to provide a more informed selection of normalizing genes during qPCR in Ae.albopictus.
    Matched MeSH terms: Real-Time Polymerase Chain Reaction/methods; Real-Time Polymerase Chain Reaction/standards*; Real-Time Polymerase Chain Reaction/veterinary
  16. Development of a TaqMan minor groove binding probe-based quantitative reverse transcription polymerase chain reaction for the detection and quantification of Zika virus
    Chin KL, Teoh BT, Sam SS, Loong SK, Tan KK, Azizan NS, et al.
    Trop Biomed, 2022 Dec 01;39(4):518-523.
    PMID: 36602210 DOI: 10.47665/tb.39.4.005
    Zika virus (ZIKV) infection has emerged as a global health concern following epidemic outbreaks of severe neurological disorders reported in Pacific and Americas since 2016. Therefore, a rapid, sensitive and specific diagnostic test for ZIKV infection is critical for the appropriate patient management and the control of disease spread. A TaqMan minor groove binding (MGB) probe-based quantitative reverse transcription-polymerase chain reaction (qRT-PCR) assay was developed based on the conserved sequence regions of 463 ZIKV NS2B genes. The designed ZIKV qRT-PCR assay was evaluated for its detection limit, strain coverage and cross-reactivity. We further assessed the clinical applicability of qRT-PCR assay for ZIKV RNA detection using a total 18 simulated clinical specimens. The detection limit of the qRT-PCR assay was 11.276 ZIKV RNA copies at the 95% probability level (probit analysis, p<= 0.05). Both Asian and African ZIKV strains were detected by the qRT-PCR assay without cross-reacting with DENV-1, DENV-2, DENV-3, DENV-4, CHIKV, JEV, LGTV, GETV and SINV. The qRT-PCR assay demonstrated a perfect agreement (k = 1.000, P < 0.001) with the reference assay; the sensitivity and specificity of the qRT-PCR assay were 100% (95% CI= 79.6-100) and 100% (95% CI= 43.9-100) respectively. The qRT-PCR assay developed in this study is a useful diagnostic tool for the broad coverage detection and quantification of both the Asian and African ZIKV strains.
    Matched MeSH terms: Real-Time Polymerase Chain Reaction
  17. Fulltext Real-time PCR assay in differentiating Entamoeba histolytica, Entamoeba dispar, and Entamoeba moshkovskii infections in Orang Asli settlements in Malaysia
    Lau YL, Anthony C, Fakhrurrazi SA, Ibrahim J, Ithoi I, Mahmud R
    Parasit Vectors, 2013;6(1):250.
    PMID: 23985047 DOI: 10.1186/1756-3305-6-250
    Amebiasis caused by Entamoeba histolytica is the third leading cause of death worldwide. This pathogenic amoeba is morphologically indistinguishable from E. dispar and E. moshkovskii, the non-pathogenic species. Polymerase chain reaction is the current method of choice approved by World Health Organization. Real-time PCR is another attractive molecular method for diagnosis of infectious diseases as post-PCR analyses are eliminated and turnaround times are shorter. The present work aimed to compare the results of Entamoeba species identification using the real-time assay against the established nested PCR method.
    Matched MeSH terms: Real-Time Polymerase Chain Reaction/methods*
  18. Real-time polymerase chain reaction for diagnosis and quantitation of negative strand of chikungunya virus
    Chiam CW, Chan YF, Loong SK, Yong SS, Hooi PS, Sam IC
    Diagn Microbiol Infect Dis, 2013 Oct;77(2):133-7.
    PMID: 23886793 DOI: 10.1016/j.diagmicrobio.2013.06.018
    Quantitative real-time polymerase chain reaction (qRT-PCR) is useful for diagnosis and studying virus replication. We developed positive- and negative-strand qRT-PCR assays to detect nsP3 of chikungunya virus (CHIKV), a positive-strand RNA alphavirus that causes epidemic fever, rash, and arthritis. The positive- and negative-strand qRT-PCR assays had limits of quantification of 1 and 3 log10 RNA copies/reaction, respectively. Compared to a published E1 diagnostic assay using 30 laboratory-confirmed clinical samples, the positive-strand nsP3 qRT-PCR assay had higher R(2) and efficiency and detected more positive samples. Peak viral load of 12.9 log(10) RNA copies/mL was reached on day 2 of illness, and RNA was detectable up to day 9, even in the presence of anti-CHIKV IgM. There was no correlation between viral load and persistent arthralgia. The positive-strand nsP3 assay is suitable for diagnosis, while the negative-strand nsP3 assay, which uses tagged primers to increase specificity, is useful for study of active viral replication kinetics.
    Matched MeSH terms: Real-Time Polymerase Chain Reaction/methods*
  19. Quantification of Her-2/Neu gene in breast cancer patients using real time-polymerase chain reaction (Q-PCR) and correlation with immunohistochemistry findings
    Abdul Murad NA, Razak ZA, Hussain RM, Syed Hussain SN, Ko Ching Huat C, Che Md Ali SA, et al.
    Asian Pac J Cancer Prev, 2013;14(3):1655-9.
    PMID: 23679251
    BACKGROUND: HER-2/neu is a proto-oncogene that encodes a transmembrane tyrosine kinase growth factor which is crucial for stimulating growth and cellular motility. Overexpression of HER-2/neu is observed in 10-35% of human breast cancers and is associated with pathogenesis, prognosis as well as response to therapy. Given the imperative role of HER-2/neu overexpression in breast cancer, it is important to determine the magnitude of amplification which may facilitate a better prognosis as well as personalized therapy in affected patients. In this study, we determined HER-2/neu protein expression by immunohistochemistry (IHC) concurrently with HER-2/neu DNA amplification by quantitative real time-polymerase chain reaction (Q-PCR).

    MATERIALS AND METHODS: A total of 53 paired tissue samples from breast cancer patients were frozen-sectioned to characterize the tumour and normal tissues. Only tissues with 80% tumour cells were used in this study. For confirmation, Q-PCR was used to determine the HER-2/neu DNA amplification.

    RESULTS: We found 20/53 (37.7%) of the tumour tissues to be positive for HER-2/neu protein overexpression using IHC. Out of these twenty, only 9/53 (17%) cases were in agreement with the Q-PCR results. The concordance rate between IHC and Q-PCR was 79.3%. Approximately 20.7% of positive IHC cases showed no HER-2/neu gene amplification using Q-PCR.

    CONCLUSION: In conclusion, IHC can be used as an initial screening method for detection of the HER-2/neu protein overexpression. Techniques such as Q-PCR should be employed to verify the IHC results for uncertain cases as well as determination of HER-2/neu gene amplification.

    Matched MeSH terms: Real-Time Polymerase Chain Reaction*
  20. Detection and discrimination of Mycobacterium tuberculosis complex
    Issa R, Mohd Hassan NA, Abdul H, Hashim SH, Seradja VH, Abdul Sani A
    Diagn Microbiol Infect Dis, 2012 Jan;72(1):62-7.
    PMID: 22078904 DOI: 10.1016/j.diagmicrobio.2011.09.021
    A real-time quantitative polymerase chain reaction (qPCR) was developed for detection and discrimination of Mycobacterium tuberculosis (H37Rv and H37Ra) and M. bovis bacillus Calmette-Guérin (BCG) of the Mycobacterium tuberculosis complex (MTBC) from mycobacterial other than tuberculosis (MOTT). It was based on the melting curve (Tm) analysis of the gyrB gene using SYBR(®) Green I detection dye and the LightCycler 1.5 system. The optimal conditions for the assay were 0.25 μmol/L of primers with 3.1 mmol/L of MgCl(2) and 45 cycles of amplification. For M. tuberculosis (H37Rv and H37Ra) and M. bovis BCG of the MTBC, we detected the crossing points (Cp) at cycles of 16.96 ± 0.07, 18.02 ± 0.14, and 18.62 ± 0.09, respectively, while the Tm values were 90.19 ± 0.06 °C, 90.27 ± 0.09 °C, and 89.81 ± 0.04 °C, respectively. The assay was sensitive and rapid with a detection limit of 10 pg of the DNA template within 35 min. In this study, the Tm analysis of the qPCR assay was applied for the detection and discrimination of MTBC from MOTT.
    Matched MeSH terms: Real-Time Polymerase Chain Reaction/methods*
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