Displaying publications 1 - 20 of 137 in total

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  1. Fulltext Crystal structure of 2-meth-oxy-2-[(4-methyl-phen-yl)sulfan-yl]-1-phenyl-ethan-1-one
    Zukerman-Schpector J, Olivato PR, Traesel HJ, Valença J, Rodrigues DN, Tiekink ER
    Acta Crystallogr E Crystallogr Commun, 2015 Jan 1;71(Pt 1):o3-4.
    PMID: 25705490 DOI: 10.1107/S205698901402550X
    In the title β-thio-carbonyl compound, C16H16O2S, the carbonyl and meth-oxy O atoms are approximately coplanar [O-C-C-O torsion angle = -18.2 (5)°] and syn to each other, and the tolyl ring is orientated to lie over them. The dihedral angle between the planes of the two rings is 44.03 (16)°. In the crystal, supra-molecular chains are formed along the c axis mediated by C-H⋯O inter-actions involving methine and methyl H atoms as donors, with the carbonyl O atom accepting both bonds; these pack with no specific inter-molecular inter-actions between them.
    Matched MeSH terms: Organic Chemicals
  2. Fulltext Comparative metabolomics of Phialemonium curvatum as an omnipotent fungus cultivated on crude palm oil versus glucose
    Zamani AI, Barig S, Ibrahim S, Mohd Yusof H, Ibrahim J, Low JYS, et al.
    Microb Cell Fact, 2020 Sep 09;19(1):179.
    PMID: 32907579 DOI: 10.1186/s12934-020-01434-w
    BACKGROUND: Sugars and triglycerides are common carbon sources for microorganisms. Nonetheless, a systematic comparative interpretation of metabolic changes upon vegetable oil or glucose as sole carbon source is still lacking. Selected fungi that can grow in acidic mineral salt media (MSM) with vegetable oil had been identified recently. Hence, this study aimed to investigate the overall metabolite changes of an omnipotent fungus and to reveal changes at central carbon metabolism corresponding to both carbon sources.

    RESULTS: Targeted and non-targeted metabolomics for both polar and semi-polar metabolites of Phialemonium curvatum AWO2 (DSM 23903) cultivated in MSM with palm oil (MSM-P) or glucose (MSM-G) as carbon sources were obtained. Targeted metabolomics on central carbon metabolism of tricarboxylic acid (TCA) cycle and glyoxylate cycle were analysed using LC-MS/MS-TripleQ and GC-MS, while untargeted metabolite profiling was performed using LC-MS/MS-QTOF followed by multivariate analysis. Targeted metabolomics analysis showed that glyoxylate pathway and TCA cycle were recruited at central carbon metabolism for triglyceride and glucose catabolism, respectively. Significant differences in organic acids concentration of about 4- to 8-fold were observed for citric acid, succinic acid, malic acid, and oxaloacetic acid. Correlation of organic acids concentration and key enzymes involved in the central carbon metabolism was further determined by enzymatic assays. On the other hand, the untargeted profiling revealed seven metabolites undergoing significant changes between MSM-P and MSM-G cultures.

    CONCLUSIONS: Overall, this study has provided insights on the understanding on the effect of triglycerides and sugar as carbon source in fungi global metabolic pathway, which might become important for future optimization of carbon flux engineering in fungi to improve organic acids production when vegetable oil is applied as the sole carbon source.

    Matched MeSH terms: Organic Chemicals/metabolism*
  3. Incorporation of surface plasmon resonance with novel valinomycin doped chitosan-graphene oxide thin film for sensing potassium ion
    Zainudin AA, Fen YW, Yusof NA, Al-Rekabi SH, Mahdi MA, Omar NAS
    Spectrochim Acta A Mol Biomol Spectrosc, 2018 Feb 15;191:111-115.
    PMID: 29024848 DOI: 10.1016/j.saa.2017.10.013
    In this study, the combination of novel valinomycin doped chitosan-graphene oxide (C-GO-V) thin film and surface plasmon resonance (SPR) system for potassium ion (K+) detection has been developed. The novel C-GO-V thin film was deposited on the gold surface using spin coating technique. The system was used to monitor SPR signal for K+ in solution with and without C-GO-V thin film. The K+ can be detected by measuring the SPR signal when C-GO-V thin film is exposed to K+ in solution. The sensor produces a linear response for K+ ion up to 100ppm with sensitivity and detection limit of 0.00948°ppm-1 and 0.001ppm, respectively. These results indicate that the C-GO-V film is high potential as a sensor element for K+ that has been proved by the SPR measurement.
    Matched MeSH terms: Organic Chemicals
  4. Co-composting of palm oil mill sludge-sawdust
    Yaser AZ, Abd Rahman R, Kalil MS
    Pak J Biol Sci, 2007 Dec 15;10(24):4473-8.
    PMID: 19093514
    Composting of Palm Oil Mill Sludge (POMS) with sawdust was conducted in natural aerated reactor. Composting using natural aerated reactor is cheap and simple. The goal of this study is to observe the potential of composting process and utilizing compost as media for growing Cymbopogun citratus, one of Malaysia herbal plant. The highest maximum temperature achieved is about 40 degrees C and to increase temperature bed, more biodegradable substrate needs to be added. The pH value decrease along the process with final pH compost is acidic (pH 5.7). The highest maximum organic losses are about 50% with final C/N ratio of the compost is about 19. Final compost also showed some fertilizing value but need to be adjusted to obtain an ideal substrate. Addition of about 70% sandy soil causes highest yield and excellent root development for C. citratus in potted media. Beside that, compost from POMS-sawdust also found to have fertilizer value and easy to handle. Composting of POMS with sawdust shows potential as an alternative treatment to dispose and recycle waste components.
    Matched MeSH terms: Organic Chemicals/analysis
  5. Influence of lipolysis and droplet size on tocotrienol absorption from self-emulsifying formulations
    Yap SP, Yuen KH
    Int J Pharm, 2004 Aug 20;281(1-2):67-78.
    PMID: 15288344
    A single dose comparative bioavailability study was conducted to evaluate the bioavailability of tocotrienols from two self-emulsifying formulations, one of which produced an emulsion that readily lipolysed under in vitro condition (SES-A), while the other produced a finer dispersion with negligible lipolysis (SES-B) in comparison with that of a non-self-emulsifying formulation in soya oil. The study was conducted according to a three-way crossover design using six healthy human volunteers. Statistically significant differences were observed between the logarithmic transformed peak plasma concentration (Cmax) and total area under the plasma concentration-time curve (AUC(0-infinity)) values of both SES-A and -B compared to NSES-C indicating that SES-A and -B achieved a higher extent of absorption compared to NSES-C. Moreover, the 90% confidence interval of the AUC(0-infinity) values of both SES-A and -B over those of NSES-C were between 2-3 suggesting an increase in bioavailability of about two-three times compared to NSES-C. Both SES-A and -B also achieved a faster onset of absorption. However, both SES-A and -B had comparable bioavailability, despite the fact that SES-B was able to form emulsions with smaller droplet size. Thus, it appeared that both droplet sizes as well as the rate and extent of lipolysis of the emulsion products formed were important for enhancing the bioavailability of the tocotrienols from the self-emulsifying systems.
    Matched MeSH terms: Organic Chemicals
  6. Relating molecular descriptors to frontier orbital energy levels, singlet and triplet excited states of fused tricyclics using machine learning
    Woon KL, Chong ZX, Ariffin A, Chan CS
    J Mol Graph Model, 2021 06;105:107891.
    PMID: 33765526 DOI: 10.1016/j.jmgm.2021.107891
    Fused tricyclic organic compounds are an important class of organic electronic materials. In designing molecules for organic electronics, knowing what chemical structure that be used to tune the molecular property is one of the keys that can help to improve the material performance. In this research, we applied machine learning and data analytic approaches in addressing this problem. The energy states (Lowest Unoccupied Molecular Orbital (HOMO), Highest Occupied Molecular Orbitals (LUMO), singlet (Es) and triplet (ET) energy) of more than 10 thousand fused tricyclics are calculated. Corresponding descriptors are also generated. We find that the Coulomb matrix is a poorer descriptor than high-level descriptors in a multilayer perceptron neural network. Correlations as high as 0.95 is obtained using a multilayer perceptron neural network with Mean Absolute Error as low as 0.08 eV. The descriptors that are important in tuning the energy levels are revealed using the Random Forest algorithm. Correlations of such descriptors are also plotted. We found that the higher the number of tertiary amines, the deeper are the HOMO and LUMO levels. The presence of NN in the aromatic rings can be used to tune the ES. However, there is no single dominant descriptor that can be correlated with the ET. A collection of descriptors is found to give a far better correlation with ET. This research demonstrated that machine learning and data analytics in guiding how certain chemical substructures correlate with the molecule energy states.
    Matched MeSH terms: Organic Chemicals*
  7. Organic-solvent stability of elastase strain K overexpressed in an Escherichia-Pseudomonas expression system
    Wong CF, Salleh AB, Basri M, Abd Rahman RN
    Biotechnol Appl Biochem, 2010 Sep;57(1):1-7.
    PMID: 20726840 DOI: 10.1042/BA20100224
    The structural gene of elastase strain K (elastase from Pseudomonas aeruginosa strain K), namely HindIII1500PstI, was successfully sequenced to contain 1497 bp. The amino acid sequence, deduced from the nucleotide sequence, revealed that the mature elastase consists of 301 amino acids, with a molecular mass of 33.1 kDa, and contains a conserved motif HEXXH, zinc ligands and residues involved in the catalysis of elastase strain K. The structural gene was successfully cloned to a shuttle vector, pUCP19, and transformed into Escherichia coli strains TOP10, KRX, JM109 and Tuner™ pLacI as well as P. aeruginosa strains PA01 (A.T.C.C. 47085) and S5, with detection of significant protein expression. Overexpression was detected from transformants KRX/pUCP19/HindIII1500PstI of E. coli and PA01/pUCP19/HindIII1500PstI of P. aeruginosa, with increases in elastolytic activity to 13.83- and 5.04-fold respectively relative to their controls. In addition, recombinant elastase strain K showed considerable stability towards numerous organic solvents such as methanol, ethanol, acetone, toluene, undecan-1-ol and n-dodecane, which typically pose a detrimental effect on enzymes; our finding provides further information to support the potential application of the enzyme in synthetic industries, particularly peptide synthesis.
    Matched MeSH terms: Organic Chemicals/chemistry
  8. Detection and Quantification of Chikungunya Virus by Real-Time RT-PCR Assay
    Wang SM, Ali UH, Sekaran SD, Thayan R
    Methods Mol Biol, 2016;1426:105-17.
    PMID: 27233265 DOI: 10.1007/978-1-4939-3618-2_10
    Real-time PCR assay has many advantages over conventional PCR methods, including rapidity, quantitative measurement, low risk of contamination, high sensitivity, high specificity, and ease of standardization (Mackay et al., Nucleic Acids Res 30:1292-1305, 2002). The real-time PCR system relies upon the measurement of a fluorescent reporter during PCR, in which the amount of emitted fluorescence is directly proportional to the amount of the PCR product in a reaction (Gibsons et al., Genome Res 6:995-1001, 1996). Here, we describe the use of SYBR Green I-based and TaqMan(®) real-time reverse transcription polymerase chain reaction (RT-PCR) for the detection and quantification of Chikungunya virus (CHIKV).
    Matched MeSH terms: Organic Chemicals
  9. Fulltext Application of ultrasonication at different microbial growth stages during apple juice fermentation by Lactobacillus plantarum: Investigation on the metabolic response
    Wang H, Tao Y, Li Y, Wu S, Li D, Liu X, et al.
    Ultrason Sonochem, 2021 May;73:105486.
    PMID: 33639530 DOI: 10.1016/j.ultsonch.2021.105486
    In this work, low-intensity ultrasonication (58.3 and 93.6 W/L) was performed at lag, logarithmic and stationary growth phases of Lactobacillus plantarum in apple juice fermentation, separately. Microbial responses to sonication, including microbial growth, profiles of organic acids profile, amino acids, phenolics, and antioxidant capacity, were examined. The results revealed that obvious responses were made by Lactobacillus plantarum to ultrasonication at lag and logarithmic phases, whereas sonication at stationary phase had a negligible impact. Sonication at lag and logarithmic phases promoted microbial growth and intensified biotransformation of malic acid to lactic acid. For example, after sonication at lag phase for 0.5 h, microbial count and lactic acid content in the ultrasound-treated samples at 58.3 W/L reached 7.91 ± 0.01 Log CFU/mL and 133.70 ± 7.39 mg/L, which were significantly higher than that in the non-sonicated samples. However, the ultrasonic effect on microbial growth and metabolism of organic acids attenuated with fermentation. Moreover, ultrasonication at lag and logarithmic phases had complex influences on the metabolism of apple phenolics such as chlorogenic acid, caffeic acid, procyanidin B2, catechin and gallic acid. Ultrasound could positively affect the hydrolysis of chlorogenic acid to caffeic acid, the transformation of procyanidin B2 and decarboxylation of gallic acid. The metabolism of organic acids and free amino acids in the sonicated samples was statistically correlated with phenolic metabolism, implying that ultrasound may benefit phenolic derivation by improving the microbial metabolism of organic acids and amino acids.
    Matched MeSH terms: Organic Chemicals/metabolism
  10. Manipulation of the conformation and enzymatic properties of T1 lipase by site-directed mutagenesis of the protein core
    Wahab RA, Basri M, Rahman RN, Salleh AB, Rahman MB, Chor LT
    Appl Biochem Biotechnol, 2012 Jun;167(3):612-20.
    PMID: 22581079 DOI: 10.1007/s12010-012-9728-2
    In silico and experimental investigations were conducted to explore the effects of substituting hydrophobic residues, Val, Met, Leu, Ile, Trp, and Phe into Gln 114 of T1 lipase. The in silico investigations accurately predicted the enzymatic characteristics of the mutants in the experimental studies and provided rationalization for some of the experimental observations. Substitution with Leu successfully improved the conformational stability and enzymatic characteristics of T1 lipase. However, replacement of Gln114 with Trp negatively affected T1 lipase and resulted in the largest disruption of protein stability, diminished lipase activity and inferior enzymatic characteristics. These results suggested that the substitution of a larger residue in a densely packed area of the protein core can have considerable effects on the structure and function of an enzyme. This is especially true when the residue is next to the catalytic serine as demonstrated with the Phe and Trp mutation.
    Matched MeSH terms: Organic Chemicals/chemistry
  11. Metal-organic frameworks for pesticidal persistent organic pollutants detection and adsorption - A mini review
    Wagner M, Andrew Lin KY, Oh WD, Lisak G
    J Hazard Mater, 2021 07 05;413:125325.
    PMID: 33601143 DOI: 10.1016/j.jhazmat.2021.125325
    The global population growth demands intensification of anthropogenic processes, thus leading to inter alia pollution of both land and aquatic environments with toxic organic compounds. Particularly harmful synthetic compounds are classified as persistent organic pollutants (POPs). Their relatively high chemical resistance resulted in a worldwide ban or strict control on the use of POPs. The majority of POPs were commonly used as pesticides, and unfortunately, some of them are still utilized as an aid in agricultural practices. Therefore, environmental monitoring in terms of reliable detection and quantification of pesticidal POPs is an ever-increasing need. Chemical sensors and adsorption materials crafted for specific pesticide operate on host-guest interactions should provide selectivity and sensitivity, thus leading to the detection of target molecule down to the nanomolar range. This could be achieved with materials exhibiting a very large active surface area, well-defined structure, and high stability. The novel materials studied in that context are metal-organic frameworks (MOFs). The structure of various MOFs can be functionalized to provide desired host-guest interactions. In this mini-review, we critically discuss the application of MOFs for the detection and adsorption of selected pesticides that are classified as POPs according to the Stockholm Convention.
    Matched MeSH terms: Organic Chemicals
  12. Fulltext Development and evaluation of a one-step SYBR-Green I-based real-time RT-PCR assay for the detection and quantification of Chikungunya virus in human, monkey and mosquito samples
    Ummul Haninah A, Vasan SS, Ravindran T, Chandru A, Lee HL, Shamala Devi S
    Trop Biomed, 2010 Dec;27(3):611-23.
    PMID: 21399603 MyJurnal
    This paper reports the development of a one-step SYBR-Green I-based realtime RT-PCR assay for the detection and quantification of Chikungunya virus (CHIKV) in human, monkey and mosquito samples by targeting the E1 structural gene. A preliminary evaluation of this assay has been successfully completed using 71 samples, consisting of a panel of negative control sera, sera from healthy individuals, sera from patients with acute disease from which CHIKV had been isolated, as well as monkey sera and adult mosquito samples obtained during the chikungunya fever outbreak in Malaysia in 2008. The assay was found to be 100-fold more sensitive than the conventional RT-PCR with a detection limit of 4.12x10(0) RNA copies/μl. The specificity of the assay was tested against other related viruses such as Dengue (serotypes 1-4), Japanese encephalitis, Herpes Simplex, Parainfluenza, Sindbis, Ross River, Yellow fever and West Nile viruses. The sensitivity, specificity and efficiency of this assay were 100%, 100% and 96.8% respectively. This study on early diagnostics is of importance to all endemic countries, especially Malaysia, which has been facing increasingly frequent and bigger outbreaks due to this virus since 1999.
    Matched MeSH terms: Organic Chemicals/metabolism
  13. Landfill leachate treatment by an experimental subsurface flow constructed wetland in tropical climate countries
    Ujang Z, Soedjono E, Salim MR, Shutes RB
    Water Sci Technol, 2005;52(12):243-50.
    PMID: 16477992
    Municipal leachate was treated in an experimental unit of constructed wetlands of subsurface flow type. The parameters studied were organics (BOD and COD), solids and heavy metals (Zn, Ni, Cu, Cr and Pb). Using two types of emergent plants of Scirpus globulosus and Eriocaulon sexangulare, more than 80% removal was achieved for all the parameters. E. sexangulare removed organics and heavy metals better than Scirpus globulosus. A higher concentration of heavy metals in the influent did not change the removal efficiency.
    Matched MeSH terms: Organic Chemicals/isolation & purification; Organic Chemicals/metabolism
  14. The effect of aeration and non-aeration time on simultaneous organic, nitrogen and phosphorus removal using an intermittent aeration membrane bioreactor
    Ujang Z, Salim MR, Khor SL
    Water Sci Technol, 2002;46(9):193-200.
    PMID: 12448469
    A laboratory-scale membrane bioreactor (MBR) was fed with synthetic wastewater to investigate the possibility of simultaneous removal of organic, nitrogen and phosphorus by intermittent aeration. The MBR consists of two compartments using a microfiltration membrane with 0.2 microm pore size and a surface area of 0.35 m2. Hydraulic retention time was set at 24 hours and solid retention time 25 days. MLSS concentration in the reactor was in the range of 2,500-3,800 mg/L. The MLSS internal recycling ratio was maintained at 100% influent flow rate. Intermittent aeration was applied in this study to provide an aerobic-anaerobic cycle. Three stages of operations were conducted to investigate the effect of aeration and non-aeration on simultaneous organic and nutrient removal. In Stage 1, time cycles of aeration and non-aeration were set at 90/150 min and 150/90 min in the first and second compartment, the removal efficiency was 97%, 94% and 70% for COD, nitrogen and phosphorus respectively. In Stage 2, time cycles of aeration and non-aeration were set at 60/120 min and 120/60 min in the first and second compartment, the removal efficiency was 97%, 96% and 71% for COD, nitrogen and phosphorus respectively. In Stage 3, time cycles of aeration and non-aeration were set at 120/120 min and 120/120 min in compartment 1 and 2, the removal efficiency was 98%, 96% and 78% for COD, nitrogen and phosphorus respectively. Results show that longer non-aeration time in the second compartment provided better performances of biological phosphorus removal.
    Matched MeSH terms: Organic Chemicals/isolation & purification
  15. Fulltext Cartilage regeneration by chondrogenic induced adult stem cells in osteoarthritic sheep model
    Ude CC, Sulaiman SB, Min-Hwei N, Hui-Cheng C, Ahmad J, Yahaya NM, et al.
    PLoS One, 2014;9(6):e98770.
    PMID: 24911365 DOI: 10.1371/journal.pone.0098770
    In this study, Adipose stem cells (ADSC) and bone marrow stem cells (BMSC), multipotent adult cells with the potentials for cartilage regenerations were induced to chondrogenic lineage and used for cartilage regenerations in surgically induced osteoarthritis in sheep model.
    Matched MeSH terms: Organic Chemicals/metabolism
  16. Bone marrow and adipose stem cells can be tracked with PKH26 until post staining passage 6 in in vitro and in vivo
    Ude CC, Shamsul BS, Ng MH, Chen HC, Norhamdan MY, Aminuddin BS, et al.
    Tissue Cell, 2012 Jun;44(3):156-63.
    PMID: 22402173 DOI: 10.1016/j.tice.2012.02.001
    Tracking of transplanted cells has become an important procedure in cell therapy. We studied the in vitro dye retention, survival and in vivo tracking of stem cells with PKH26 dye. Sheep BMSCs and ADSCs were labeled with 2, 4 and 8 μmol of PKH26 and monitored for six passages. Labeled BMSCs and ADSCs acquired mean cumulative population doubling of 12.7±0.4 and 14.6±0.5; unlabeled samples had 13.8±0.5 and 15.4±0.6 respectively. Upon staining with 2, 4 and 8 μmol PKH26, BMSCs had retentions of 40.0±5.8, 60.0±2.9 and 95.0±2.9%, while ADSCs had 92.0±1.2, 95.0±1.2 and 98.0±1.2%. ADSCs retentions were significantly higher at 2 and 4 μmol. On dye retention comparison at 8 μmol and 4 μmol for BMSCs and ADSCs; ADSCs were significantly higher at passages 2 and 3. The viability of BMSCs reduced from 94.0±1.2% to 90.0±0.6% and ADSCs from 94.0±1.2% to 52.0±1.2% (p<0.05) after 24h. BMSCs had significant up regulation of the cartilage genes for both the labeled and the unlabeled samples compared to ADSCs (p<0.05). PKH26 fluorescence was detected on the resected portions of the regenerated neo-cartilage. The recommended concentration of PKH26 for ADSCs is 2 μmol and BMSCs is 8 μmol, and they can be tracked up to 49 days.
    Matched MeSH terms: Organic Chemicals/chemistry*
  17. Toward Long-Term Stable and Efficient Large-Area Organic Solar Cells
    Tsai PT, Lin KC, Wu CY, Liao CH, Lin MC, Wong YQ, et al.
    ChemSusChem, 2017 07 10;10(13):2778-2787.
    PMID: 28516516 DOI: 10.1002/cssc.201700601
    Here, we report that long-term stable and efficient organic solar cells (OSCs) can be obtained through the following strategies: i) combination of rapid-drying blade-coating deposition with an appropriate thermal annealing treatment to obtain an optimized morphology of the active layer; ii) insertion of interfacial layers to optimize the interfacial properties. The resulting devices based on poly[4,8-bis(5-(2-ethylhexyl)thiophen-2-yl)benzo[1,2-b;4,5-b']dithiophene-2,6-diyl-alt-(4-(2-ethylhexyl)-3-fluorothieno[3,4-b]thiophene-2-carboxylate-2,6-diyl)] (PBDTTT-EFT):[6,6]-phenyl C71 butyric acid methyl ester (PC71 BM) blend as the active layer exhibits a power conversion efficiency (PCE) up to 9.57 %, which represents the highest efficiency ever reported for blade-coated OSCs. Importantly, the conventional structure devices based on poly(3-hexylthiophene) (P3HT):phenyl-C61 -butyric acid methyl ester (PCBM) blend can retain approximately 65 % of their initial PCE for almost 2 years under operating conditions, which is the best result ever reported for long-term stable OSCs under operational conditions. More encouragingly, long-term stable large-area OSCs (active area=216 cm2 ) based on P3HT:PCBM blend are also demonstrated. Our findings represent an important step toward the development of large-area OSCs with high performance and long-term stability.
    Matched MeSH terms: Organic Chemicals/chemistry*
  18. Detection of Newcastle disease virus using a SYBR Green I real time polymerase chain reaction
    Tan SW, Omar AR, Aini I, Yusoff K, Tan WS
    Acta Virol., 2004;48(1):23-8.
    PMID: 15230471
    A two-step SYBR Green I real time polymerase chain reaction (PCR, real time PCR) for the detection of Newcastle disease virus (NDV) was developed. A melting curve analysis was performed to distinguish specific from non-specific products and primer dimers. Regardless of different virus pathotypes the melting temperature (Tm) ranged from 86 degrees C to 87 degrees C. The sensitivity of the real time PCR was compared with the reverse transcription (RT)-nested PCR enzyme-linked immunosorbent assay (ELISA, RT-nested PCR ELISA). Whereas the detection limit of the real time PCR was 10 pg DNA, the RT-nested PCR ELISA and conventional PCR could only detect up to 1 ng and 10 ng DNA, respectively. Thus the real time PCR offers a sensitive, rapid and convenient method for screening large number of NDV specimens.
    Matched MeSH terms: Organic Chemicals*
  19. Detection and differentiation of velogenic and lentogenic Newcastle disease viruses using SYBR Green I real-time PCR with nucleocapsid gene-specific primers
    Tan SW, Ideris A, Omar AR, Yusoff K, Hair-Bejo M
    J Virol Methods, 2009 Sep;160(1-2):149-56.
    PMID: 19447142 DOI: 10.1016/j.jviromet.2009.05.006
    SYBR Green I real-time PCR was developed for detection and differentiation of Newcastle disease virus (NDV). Primers based on the nucleocapsid (NP) gene were designed to detect specific sequence of velogenic strains and lentogenic/vaccine strains, respectively. The assay was developed and tested with NDV strains which were characterized previously. The velogenic strains were detected only by using velogenic-specific primers with a threshold cycle (C(t)) 18.19+/-3.63 and a melting temperature (T(m)) 86.0+/-0.28 degrees C. All the lentogenic/vaccine strains, in contrast, were detected only when lentogenic-specific primers were used, with the C(t) value 14.70+/-2.32 and T(m) 87.4+/-0.21 degrees C. The assay had a dynamic detection range which spans over a 5log(10) concentration range, 10(9)-10(5) copies of DNA plasmid/reaction. The velogenic and lentogenic amplifications showed high PCR efficiency of 100% and 104%, respectively. The velogenic and lentogenic amplifications were highly reproducible with assay variability 0.45+/-0.31% and 1.30+/-0.65%, respectively. The SYBR Green I real-time PCR assay detected successfully the virus from tissue samples and oral swabs collected from the velogenic and lentogenic NDV experimental infection, respectively. In addition, the assay detected and differentiated accurately NDV pathotypes from suspected field samples where the results were in good agreement with both virus isolation and analysis of the fusion (F) cleavage site sequence. The assay offers an attractive alternative method for the diagnosis of NDV.
    Matched MeSH terms: Organic Chemicals/metabolism
  20. Rapid detection of porcine DNA in processed food samples using a streamlined DNA extraction method combined with the SYBR Green real-time PCR assay
    Tan LL, Ahmed SA, Ng SK, Citartan M, Raabe CA, Rozhdestvensky TS, et al.
    Food Chem, 2020 Mar 30;309:125654.
    PMID: 31678669 DOI: 10.1016/j.foodchem.2019.125654
    A specialized DNA extraction method and a SYBR Green quantitative polymerase chain reaction (SyG-qPCR) assay were combined to generate a ready-to-use kit for rapid detection of porcine admixtures in processed meat products. Our qPCR assay utilized repetitive LINE-1 elements specific to the genome of Sus scrofa domesticus (pig) as a target and incorporated internal controls. We improved the genomic DNA extraction method, and reduced extraction times to the minimum. The method was validated for specificity, sensitivity (0.001% w/w) and robustness, and values were compared with those of a commercially available kit. We also tested our method using 121 processed food products and consistently detected amplification only in samples containing pork. Due to its efficiency and cost-effectiveness, our method represents a valuable new method for detecting food adulteration with pork that is superior to existing quality control approaches.
    Matched MeSH terms: Organic Chemicals/chemistry*
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