Displaying publications 81 - 100 of 1868 in total

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  1. Increased Expression of Phosphatidylinositol 3-Kinase p110α and Gene Amplification of PIK3CA in Nasopharyngeal Carcinoma
    Yip WK, He PY, Abdullah MA, Yusoff S, Seow HF
    Pathol Oncol Res, 2016 Apr;22(2):413-9.
    PMID: 26581613 DOI: 10.1007/s12253-015-0007-8
    Molecular alterations in PIK3CA oncogene that encodes the p110α catalytic subunit of phosphatidylinositol 3-kinase (PI3K p110α) are commonly found in human cancers. In this study, we examined the expression of PI3K p110α and PIK3CA gene amplification in 74 nasopharyngeal carcinoma (NPC) cases. Immunohistochemical staining demonstrated overexpression of PI3K p110α protein in 44.6% (33/74) of NPCs and 4.8% (2/42) of the adjacent normal nasopharyngeal mucosa. Copy number of PIK3CA gene was successfully analyzed in 51 of the total NPC cases and 19 non-malignant nasopharynx tissues by quantitative real-time PCR. Using mean + 2(standard deviation) of copy numbers in the non-malignant nasopharynx tissues as a cutoff value, PIK3CA copy number gain was found in 10 of 51 (19.6%) NPC cases. High PI3K p110α expression level was correlated with increased PIK3CA copy number (Spearman's rho =0.324, P = 0.02). PI3K p110α expression and PIK3CA copy number did not associate with Akt phosphorylation, and patient and tumor variables. This study suggests that PI3K p110α overexpression, which is attributed, at least in part, to PIK3CA gene amplification, may contribute to NPC pathogenesis. However, these molecular aberrations may not be responsible for activation of Akt signaling in NPC.
    Matched MeSH terms: Real-Time Polymerase Chain Reaction
  2. Activation of phosphatidylinositol 3-kinase/Akt signaling by EGF downregulates membranous E-cadherin and β-catenin and enhances invasion in nasopharyngeal carcinoma cells
    Yip WK, Seow HF
    Cancer Lett, 2012 May 28;318(2):162-72.
    PMID: 22182447 DOI: 10.1016/j.canlet.2011.12.018
    Dysregulation of E-cadherin and β-catenin function in cell-cell adhesion is common in nasopharyngeal carcinoma (NPC) and correlates with metastatic disease. In this study, we examined the role of EGF-activated phosphatidylinositol 3-kinase (PI3K)-Akt signaling in E-cadherin and β-catenin regulation. We found that reduced membranous E-cadherin and β-catenin expression was positively correlated with Akt phosphorylation in NPC tissues. EGF treatment disrupted cell-cell adhesion and resulted in mesenchymal morphological features in NPC cell lines (TW01, TW04, and TW06). Western blot analysis showed that the E-cadherin protein level was partially reduced in TW04 cells only and the β-catenin levels were not considerably affected upon EGF treatment. In contrast, quantitative real-time RT-PCR showed that the E-cadherin, but not β-catenin, mRNA levels were markedly reduced by EGF in all cell lines. Immunofluorescent staining revealed that E-cadherin and β-catenin appeared to be markedly reduced on the cell surface and more localized in the cytoplasm. Inhibition of PI3K by LY294002 did not abolish the EGF-induced downregulation of E-cadherin protein or mRNA in TW04 cells but moderately increased the β-catenin protein level in TW01 cells and mRNA level in TW06 cells. However, LY294002 substantially restored or increased cell surface E-cadherin and β-catenin in all EGF-treated cell lines, in concordance with the inhibition of cell morphological changes. Moreover, LY294002 significantly blocked EGF-driven cell invasion, correlating with the elevation of membranous E-cadherin and β-catenin levels. In conclusion, EGF-induced epithelial-to-mesenchymal transition may not be only dependent on downregulation of E-cadherin protein/mRNA but also on mislocalization of E-cadherin and β-catenin. The mechanisms involved may be related, at least in part, to the PI3K-Akt pathway.
    Matched MeSH terms: Real-Time Polymerase Chain Reaction
  3. Fulltext A case-controlled validation study of a blood-based seven-gene biomarker panel for colorectal cancer in Malaysia
    Yip KT, Das PK, Suria D, Lim CR, Ng GH, Liew CC
    J Exp Clin Cancer Res, 2010;29:128.
    PMID: 20846378 DOI: 10.1186/1756-9966-29-128
    BACKGROUND: Colorectal cancer (CRC) screening is key to CRC prevention and mortality reduction, but patient compliance with CRC screening is low. We previously reported a blood-based test for CRC that utilizes a seven-gene panel of biomarkers. The test is currently utilized clinically in North America for CRC risk stratification in the average-risk North American population in order to improve screening compliance and to enhance clinical decision making.
    METHODS: In this study, conducted in Malaysia, we evaluated the seven-gene biomarker panel validated in a North American population using blood samples collected from local patients. The panel employs quantitative RT-PCR (qRT-PCR) to analyze gene expression of the seven biomarkers (ANXA3, CLEC4D, TNFAIP6, LMNB1, PRRG4, VNN1 and IL2RB) that are differentially expressed in CRC patients as compared with controls. Blood samples from 210 patients (99 CRC and 111 controls) were collected, and total blood RNA was isolated and subjected to quantitative RT-PCR and data analysis.
    RESULTS: The logistic regression analysis of seven-gene panel has an area under the curve (AUC) of 0.76 (95% confidence interval: 0.70 to 0.82), 77% specificity, 61% sensitivity and 70% accuracy, comparable to the data obtained from the North American investigation of the same biomarker panel.
    CONCLUSIONS: Our results independently confirm the results of the study conducted in North America and demonstrate the ability of the seven biomarker panel to discriminate CRC from controls in blood samples drawn from a Malaysian population.
    Matched MeSH terms: Reverse Transcriptase Polymerase Chain Reaction
  4. Fulltext Genetic variability within and among Haemonchus contortus isolates from goats and sheep in China
    Yin F, Gasser RB, Li F, Bao M, Huang W, Zou F, et al.
    Parasit Vectors, 2013 Sep 25;6(1):279.
    PMID: 24499637 DOI: 10.1186/1756-3305-6-279
    BACKGROUND: Haemonchus contortus (order Strongylida) is a common parasitic nematode infecting small ruminants and causing significant economic losses worldwide. Knowledge of genetic variation within and among H. contortus populations can provide a foundation for understanding transmission patterns, the spread of drug resistance alleles and might assist in the control of haemonchosis.

    METHODS: 152 H. contortus individual adult worms were collected from seven different geographical regions in China. The second internal transcribed spacer (ITS-2) of the nuclear ribosomal DNA and mitochondrial nicotinamide dehydrogenase subunit 4 gene (nad4) were amplified by polymerase chain reaction (PCR) and sequenced directly. The sequence variations and population genetic diversities were determined.

    RESULTS: Nucleotide sequence analyses revealed 18 genotypes (ITS-2) and 142 haplotypes (nad4) among the 152 worms, with nucleotide diversities of 2.6% and 0.027, respectively, consistent with previous reports from other countries, including Australia, Brazil, Germany, Italy, Malaysia, Sweden, the USA and Yemen. Population genetic analyses revealed that 92.4% of nucleotide variation was partitioned within populations; there was no genetic differentiation but a high gene flow among Chinese populations; some degree of genetic differentiation was inferred between some specimens from China and those from other countries.

    CONCLUSIONS: This is the first study of genetic variation within H. contortus in China. The results revealed high within-population variations, low genetic differentiation and high gene flow among different populations of H. contortus in China. The present results could have implications for studying the epidemiology and ecology of H. contortus in China.

    Matched MeSH terms: Polymerase Chain Reaction
  5. Fulltext Vitamin D Deficiency and Janus kinase 2 V617F Mutation Status in Essential Thrombocythemia and Polycythemia Vera
    Yikilmaz AŞ, Akinci S, Bakanay ŞM, Dilek İ
    Malays J Med Sci, 2020 Feb;27(1):70-77.
    PMID: 32158346 DOI: 10.21315/mjms2020.27.1.7
    Introduction: Vitamin D, which is known for its effects on calcium and bone metabolism, has recently been associated with haematological malignancies. We aimed to investigate the relationship between disease findings and vitamin D deficiency in essential thrombocythemia (ET) and polycythemia vera (PV).

    Material and Methods: This retrospective cohort study conducted in Turkey included 73 patients diagnosed with PV or ET according to WHO criteria between 2012 and 2018. Vitamin D deficiency was defined as 25-OH vitamin D < 20 ng/mL. Polymerase chain reaction (PCR) was used to detect the Janus kinase 2 (JAK2) V617F mutation.

    Results: Vitamin D deficiency was found in 66.7% of PV and 74.2% of ET patients. The median follow-up time of ET and PV patients was 48 months and 47 months, respectively. Patients with the JAK2 mutation had a higher prevalence of a history of thrombosis and age older than 65 years. There was a significant relationship between JAK2 positivity and vitamin D deficiency.

    Conclusion: There was a remarkably higher prevalence of vitamin D deficiency in JAK2 mutation-positive ET and PV patients. These patients should be carefully evaluated for vitamin D deficiency. More studies are required to further investigate the association between JAK2 and vitamin D.

    Matched MeSH terms: Polymerase Chain Reaction
  6. Fulltext Edible bird's nest attenuates procoagulation effects of high-fat diet in rats
    Yida Z, Imam MU, Ismail M, Ismail N, Hou Z
    Drug Des Devel Ther, 2015;9:3951-9.
    PMID: 26251574 DOI: 10.2147/DDDT.S87772
    Edible bird's nest (EBN) is popular in Asia, and has long been used traditionally as a supplement. There are, however, limited evidence-based studies on its efficacy. EBN has been reported to improve dyslipidemia, which is closely linked to hypercoagulation states. In the present study, the effects of EBN on high-fat diet- (HFD-) induced coagulation in rats were evaluated. Rats were fed for 12 weeks with HFD alone or in combination with simvastatin or EBN. Food intake was estimated, and weight measurements were made during the experimental period. After sacrifice, serum oxidized low-density lipoprotein (oxLDL), adiponectin, leptin, von willibrand factor, prostacyclin, thromboxane and lipid profile, and whole blood coagulation indices (bleeding time, prothrombin time, activated partial thromboplastin time, red blood count count, and platelet count) were estimated. Furthermore, hepatic expression of coagulation-related genes was evaluated using multiplex polymerase chain reaction. The results indicated that EBN could attenuate HFD-induced hypercholesterolemia and coagulation similar to simvastatin, partly through transcriptional regulation of coagulation-related genes. The results suggested that EBN has the potential for lowering the risk of cardiovascular disease-related hypercoagulation due to hypercholesterolemia.
    Matched MeSH terms: Multiplex Polymerase Chain Reaction
  7. Fulltext Rootkit guard (RG) - an architecture for rootkit resistant file-system implementation based on TPM
    Yew, Teh Jia, Khairulmizam Samsudin, Nur Izura Udzir, Shaiful Jahari Hashim
    Pertanika Journal of Science & Technology, 2013;21(2):507-520.
    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
  8. Epstein-Barr virus-encoded latent membrane protein-1 upregulates 14-3-3σ and Reprimo to confer G(2)/M phase cell cycle arrest
    Yeo KS, Mohidin TB, Ng CC
    C. R. Biol., 2012 Dec;335(12):713-21.
    PMID: 23312294 DOI: 10.1016/j.crvi.2012.11.002
    Epstein-Barr virus (EBV) is a ubiquitous tumor-causing virus which infects more than 90% of the world population asymptomatically. Recent studies suggest that LMP-1, -2A and -2B cooperate in the tumorigenesis of EBV-associated epithelial cancers such as nasopharygeal carcinoma, oral and gastric cancer. In this study, LMPs were expressed in the HEK293T cell line to reveal their oncogenic mechanism via investigation on their involvement in the regulation of the cell cycle and genes that are involved. LMPs were expressed in HEK293T in single and co-expression manner. The transcription of cell cycle arrest genes were examined via real-time PCR. Cell cycle progression was examined via flow cytometry. 14-3-3σ and Reprimo were upregulated in all LMP-1 expressing cells. Moreover, cell cycle arrest at G(2)/M progression was detected in all LMP-1 expressing cells. Therefore, we conclude that LMP-1 may induce cell cycle arrest at G(2)/M progression via upregulation of 14-3-3σ and Reprimo.
    Matched MeSH terms: Real-Time Polymerase Chain Reaction
  9. Golden SusPtrit: a genetically well transformable barley line for studies on the resistance to rust fungi
    Yeo FK, Hensel G, Vozábová T, Martin-Sanz A, Marcel TC, Kumlehn J, et al.
    Theor Appl Genet, 2014 Feb;127(2):325-37.
    PMID: 24247233 DOI: 10.1007/s00122-013-2221-7
    KEY MESSAGE: We developed 'Golden SusPtrit', i.e., a barley line combining SusPtrit's high susceptibility to non-adapted rust fungi with the high amenability of Golden Promise for transformation. Nonhost and partial resistance to Puccinia rust fungi in barley are polygenically inherited. These types of resistance are principally prehaustorial, show high diversity between accessions of the plant species and are genetically associated. To study nonhost and partial resistance, as well as their association, candidate gene(s) for resistance must be cloned and tested in susceptible material where SusPtrit would be the line of choice. Unfortunately, SusPtrit is not amenable to Agrobacterium-mediated transformation. Therefore, a doubled haploid (DH) mapping population (n = 122) was created by crossing SusPtrit with Golden Promise to develop a 'Golden SusPtrit', i.e., a barley line combining SusPtrit's high susceptibility to non-adapted rust fungi with the high amenability of Golden Promise for transformation. We identified nine genomic regions occupied by resistance quantitative trait loci (QTLs) against four non-adapted rust fungi and P. hordei isolate 1.2.1 (Ph.1.2.1). Four DHs were selected for an Agrobacterium-mediated transformation efficiency test. They were among the 12 DH lines most susceptible to the tested non-adapted rust fungi. The most efficiently transformed DH line was SG062N (11-17 transformants per 100 immature embryos). The level of non-adapted rust infection on SG062N is either similar to or higher than the level of infection on SusPtrit. Against Ph.1.2.1, the latency period conferred by SG062N is as short as that conferred by SusPtrit. SG062N, designated 'Golden SusPtrit', will be a valuable experimental line that could replace SusPtrit in nonhost and partial resistance studies, especially for stable transformation using candidate genes that may be involved in rust-resistance mechanisms.
    Matched MeSH terms: Polymerase Chain Reaction
  10. Gene isolation using degenerate primers targeting protein motif: A laboratory exercise
    Yeo BPH, Foong LC, Tam SM, Lee V, Hwang SS
    Biochem Mol Biol Educ, 2018 01;46(1):47-53.
    PMID: 29131478 DOI: 10.1002/bmb.21089
    Structures and functions of protein motifs are widely included in many biology-based course syllabi. However, little emphasis is placed to link this knowledge to applications in biotechnology to enhance the learning experience. Here, the conserved motifs of nucleotide binding site-leucine rich repeats (NBS-LRR) proteins, successfully used for the isolation and characterization of many plant resistance gene analogues (RGAs), is featured in the development of a series of laboratory experiments using important molecular biology techniques. A set of previously isolated RGA sequences is used as the model for performing sequence alignment and visualising 3D protein structure using current bioinformatics programs (Clustal Omega and Argusdock software). A pair of established degenerate primer sequences is provided for the prediction of targeted amino acids sequences in the RGAs. Reverse transcription-polymerase chain reaction (RT-PCR) is used to amplify RGAs from total RNA samples extracted from the tropical wild relative of black pepper, Piper colubrinum (Piperaceae). This laboratory exercise enables students to correlate specific DNA sequences with respective amino acid codes and the interaction between conserved motifs of resistance genes with putatively targeted proteins. © 2017 by The International Union of Biochemistry and Molecular Biology, 46(1):47-53, 2018.
    Matched MeSH terms: Reverse Transcriptase Polymerase Chain Reaction
  11. Fulltext Dengue patients exhibit higher levels of PrM and E antibodies than their asymptomatic counterparts
    Yeo AS, Rathakrishnan A, Wang SM, Ponnampalavanar S, Manikam R, Sathar J, et al.
    Biomed Res Int, 2015;2015:420867.
    PMID: 25815314 DOI: 10.1155/2015/420867
    Dengue virus infection is a common tropical disease which often occurs without being detected. These asymptomatic cases provide information in relation to the manifestation of immunological aspects. In this study, we developed an ELISA method to compare neutralizing effects of dengue prM and E antibodies between dengue patients and their asymptomatic household members. Recombinant D2 premembrane (prM) was constructed, cloned, and tested for antigenicity. The recombinant protein was purified and tested with controls by using an indirect ELISA method. Positive dengue serum samples with their asymptomatic pair were then carried out onto the developed ELISA. In addition, commercially available recombinant envelope (E) protein was used to develop an ELISA which was tested with the same set of serum samples in the prM ELISA. Asymptomatic individuals showed preexisting heterotypic neutralizing antibodies. The recombinant prM was antigenically reactive in the developed ELISA. Dengue patients had higher prM and E antibodies compared to their household members. Our study highlights the neutralizing antibodies levels with respect to dengue prM and E between dengue patients and asymptomatic individuals.
    Matched MeSH terms: Polymerase Chain Reaction
  12. Anion exchanger 1 mutations associated with distal renal tubular acidosis in the Thai population
    Yenchitsomanus PT, Sawasdee N, Paemanee A, Keskanokwong T, Vasuvattakul S, Bejrachandra S, et al.
    J Hum Genet, 2003;48(9):451-456.
    PMID: 12938018 DOI: 10.1007/s10038-003-0059-6
    We have previously demonstrated that compound heterozygous (SAO/G701D) and homozygous (G701D/G701D) mutations of the anion exchanger 1 (AE1) gene, encoding erythroid and kidney AE1 proteins, cause autosomal recessive distal renal tubular acidosis (AR dRTA) in Thai patients. It is thus of interest to examine the prevalence of these mutations in the Thai population. The SAO and G701D mutations were examined in 844 individuals from north, northeast, central, and south Thailand. Other reported mutations including R602H, DeltaV850, and A858D were also examined in some groups of subjects. The SAO mutation was common in the southern Thai population; its heterozygote frequency was 7/206 and estimated allele frequency 1.70%. However, this mutation was not observed in populations of three other regions of Thailand. In contrast, the G701D mutation was not found in the southern population but was observed in the northern, northeastern, and central populations, with heterozygote frequencies of 1/216, 3/205, and 1/217, and estimated allele frequencies of 0.23%, 0.73%, and 0.23%, respectively. The higher allele frequency of the G701D mutation in the northeastern Thai population corresponds to our previous finding that all Thai patients with AR dRTA attributable to homozygous G701D mutation originate from this population. This suggests that the G701D allele that is observed in this region might arise in northeastern Thailand. The presence of patients with compound heterozygous SAO/G701D in southern Thailand and Malaysia and their apparently absence in northeastern Thailand indicate that the G701D allele may have migrated to the southern peninsular region where SAO is common, resulting in pathogenic allelic interaction.
    Matched MeSH terms: Polymerase Chain Reaction
  13. Pilot study of the sensitivity and specificity of the DNA integrity assay for stool-based detection of colorectal cancer in Malaysian patients
    Yehya AH, Yusoff NM, Khalid IA, Mahsin H, Razali RA, Azlina F, et al.
    Asian Pac J Cancer Prev, 2012;13(5):1869-72.
    PMID: 22901138
    BACKGROUND: To assess the diagnostic potential of tumor-associated high molecular weight DNA in stool samples of 32 colorectal cancer (CRC) patients compared to 32 healthy Malaysian volunteers by means of polymerase chain reaction (PCR).

    METHODS: Stool DNA was isolated and tumor-associated high molecular weight DNA (1.476 kb fragment including exons 6-9 of the p53 gene) was amplified using PCR and visualized on ethidium bromide-stained agarose gels.

    RESULTS: Out of 32 CRC patients, 18 were positive for the presence of high molecular weight DNA as compared to none of the healthy individuals, resulting in an overall sensitivity of 56.3% with 100% specificity. Out of 32 patients, 23 had tumor on the left side and 9 on the right side, 16 and 2 being respectively positive. This showed that high molecular weight DNA was significantly (p=0.022) more detectable in patients with left side tumor (69.6% vs 22.2%). Out of 32 patients, 22 had tumors larger than 1.0 cm, 18 of these (81.8%) being positive for long DNA as compared to not a single patient with tumor size smaller than 1.0 cm (p<0.001).

    CONCLUSION: We detected CRC-related high molecular weight p53 DNA in stool samples of CRC patients with an overall sensitivity of 56.3% with 100% specificity, with a strong tumor size dependence.

    Matched MeSH terms: Polymerase Chain Reaction
  14. Fulltext A simple and inexpensive physical lysis method for DNA and RNA extraction from freshwater microalgae
    Yee W, Abdul-Kadir R, Lee LM, Koh B, Lee YS, Chan HY
    3 Biotech, 2018 Aug;8(8):354.
    PMID: 30105179 DOI: 10.1007/s13205-018-1381-1
    In this work, a simple and inexpensive physical lysis method using a cordless drill fitted with a plastic pellet pestle and 150 mg of sterile sea sand was established for the extraction of DNA from six strains of freshwater microalgae. This lysis method was also tested for RNA extraction from two microalgal strains. Lysis duration between 15 and 120 s using the cetyltrimethyl ammonium bromide (CTAB) buffer significantly increased the yield of DNA from four microalgalstrains (Monoraphidium griffithii NS16, Scenedesmus sp. NS6, Scenedesmus sp. DPBC1 and Acutodesmus sp. DPBB10) compared to control. It was also found that grinding was not required to obtain DNA from two strains of microalgae (Choricystis sp. NPA14 and Chlamydomonas sp. BM3). The average DNA yield obtained using this lysis method was between 62.5 and 78.9 ng/mg for M. griffithii NS16, 42.2-247.0 ng/mg for Scenedesmus sp. NS6, 70.2-110.9 ng/mg for Scenedesmus sp. DPBC1 and 142.8-164.8 ng/mg for Acutodesmus sp. DPBB10. DNA obtained using this method was sufficiently pure for PCR amplification. Extraction of total RNA from M. griffithii NS16 and Mychonastes sp. NPD7 using this lysis method yielded high-quality RNA suitable for RT-PCR. This lysis method is simple, cheap and would enable rapid nucleic acid extraction from freshwater microalgae without requiring costly materials and equipment such as liquid nitrogen or beadbeaters, and would facilitate molecular studies on microalgae in general.
    Matched MeSH terms: Polymerase Chain Reaction; Reverse Transcriptase Polymerase Chain Reaction
  15. Male-specific RNA coliphages detected by plaque assay and RT-PCR in tropical river waters and animal fecal matter
    Yee SY, Fong NY, Fong GT, Tak OJ, Hui GT, Su Ming Y
    Int J Environ Health Res, 2006 Feb;16(1):59-68.
    PMID: 16507481
    Male-specific RNA coliphages (FRNA) have been recommended as indicators of fecal contamination and of the virological quality of water. In this study, 16 river water and 183 animal fecal samples were examined for the presence of FRNA coliphages by a plaque assay using Salmonella typhimurium WG49 and WG25 to differentiate between male-specific and somatic phages, a RNase spot test to differentiate between DNA and RNA phages and a reverse transcriptase-polymerase chain reaction (RT-PCR) for the specific identification of FRNA phages. The overall recovery rate for F-specific coliphages was 8.0%. (4.4% from animal fecal matter and 50% from river water samples). Plaque counts were generally low (< 6 x 10(2) pfu per g feces or ml water), with FRNA (6.5%) and Male-specific DNA coliphages (FDNA) (7.0%) phages occurring at almost equal frequencies. The RT-PCR was positive in all FRNA plaques and was able to identify FRNA phages in mixed populations of FRNA, FDNA and somatic phages.
    Matched MeSH terms: Reverse Transcriptase Polymerase Chain Reaction/methods
  16. Identification of hybrids of painted and milky storks using FTA card-collected blood, molecular markers, and morphologies
    Yee EY, Zainuddin ZZ, Ismail A, Yap CK, Tan SG
    Biochem Genet, 2013 Oct;51(9-10):789-99.
    PMID: 23846110 DOI: 10.1007/s10528-013-9607-8
    Suspicious hybrids of painted storks and milky storks were found in a Malaysian zoo. Blood of these birds was sampled on FTA cards for DNA fingerprinting. Of 44 optimized primers, 6 produced diagnostic markers that could identify hybrids. The markers were based on simple, direct PCR-generated multilocus banding patterns that provided two sets of genetic data, one for each of the two stork species and another for the hybrids. It also revealed that large DNA fragments (3,000 bp) could be amplified from blood collected on FTA cards. When the results of each individual bird's DNA fingerprint were compared with plumage characters, the hybrids were found to express a range of intermediate phenotypic traits of the pure breeds with no dominant plumage characteristic from either parental species.
    Matched MeSH terms: Polymerase Chain Reaction
  17. Fulltext In Vivo Antioxidant and Hypolipidemic Effects of Fermented Mung Bean on Hypercholesterolemic Mice
    Yeap SK, Beh BK, Ho WY, Mohd Yusof H, Mohamad NE, Ali NM, et al.
    Evid Based Complement Alternat Med, 2015;2015:508029.
    PMID: 26074993 DOI: 10.1155/2015/508029
    Legumes have previously been reported with hypolipidemic effect caused by the presence of flavonoid. This study was carried out to evaluate the antioxidant and hypolipidemic effects of fermented mung bean on hypercholesterolemic mice. Blood from all mice was collected and subjected to serum lipid and liver profiles biochemical analysis and quantitative RT-PCR for atherosclerosis related gene expressions. Besides, livers were collected for antioxidant assays and histopathology evaluation. Fermented mung bean was found to reduce the level of serum lipid and liver enzyme profiles of hypercholesterolemic mice. Furthermore, liver antioxidant and nitric oxide levels were also significantly restored by fermented mung bean in a dosage dependent manner. The gene expression study indicated that Apoe and Bcl2a1a were upregulated while Npy and Vwf expressions were downregulated after the treatment. The effects of fermented mung bean were greater than nonfermented mung bean. These results indicated that fermented mung bean possessed antioxidants that lead to its hypolipidemic effect on hypercholesterolemic mice.
    Matched MeSH terms: Reverse Transcriptase Polymerase Chain Reaction
  18. Fulltext Non-tuberculous mycobacterial ocular infection masquerading as choroidal tumour - a diagnostic conundrum
    Yeap KC, Sivagurunathan PD, Raman P, Khalid KHM
    GMS Ophthalmol Cases, 2019;9:Doc25.
    PMID: 31355123 DOI: 10.3205/oc000114
    Purpose: To report a rare case of non-tuberculous mycobacterial (NTM) choroiditis masquerading as choroidal tumour, where the initial diagnosis was masked by keratitis. Casedescription: A 57-year-old heroin chaser with a pre-existing left eye blindness due to past blunt trauma presented with diffuse bacterial keratitis on the same side. Systemic examination revealed multiple non-tender cervical lymphadenopathies. B-scan ultrasonography showed a hyperechoic choroidal mass with surrounding exudative retinal detachment, resembling a choroidal tumour. However, computed tomography (CT) and magnetic resonance imaging (MRI) scan findings were suggestive of inflammatory choroidal changes. Inflammatory markers were significantly raised and infective screening was positive for HIV and Hepatitis C. Tuberculosis workup was normal. In view of intractable pain, evisceration was done and his vitreous humour was sent for polymerase chain reaction (PCR). It was reported to be positive for Mycobacterium Fortuitum. Conclusion: NTM ocular infections are rare, challenging to diagnose, and potentially sight threatening. Early recognition and prompt treatment is life and vision saving.
    Matched MeSH terms: Polymerase Chain Reaction
  19. Enzyme-linked amperometric electrochemical genosensor assay for the detection of PCR amplicons on a streptavidin-treated screen-printed carbon electrode
    Yean CY, Kamarudin B, Ozkan DA, Yin LS, Lalitha P, Ismail A, et al.
    Anal Chem, 2008 Apr 15;80(8):2774-9.
    PMID: 18311943 DOI: 10.1021/ac702333x
    A general purpose enzyme-based amperometric electrochemical genosensor assay was developed wherein polymerase chain reaction (PCR) amplicons labeled with both biotin and fluorescein were detected with peroxidase-conjugated antifluorescein antibody on a screen-printed carbon electrode (SPCE). As a proof of principle, the response selectivity of the genosensor was evaluated using PCR amplicons derived from lolB gene of Vibrio cholerae. Factors affecting immobilization, hybridization, and nonspecific binding were optimized to maximize sensitivity and reduce assay time. On the basis of the background amperometry signals obtained from nonspecific organisms and positive signals obtained from known V. cholerae, a threshold point of 4.20 microA signal was determined as positive. Under the optimum conditions, the limit of detection (LOD) of the assay was 10 CFU/mL of V. cholerae. The overall precision of this assay was good, with the coefficient of variation (CV) being 3.7% using SPCE and intermittent pulse amperometry (IPA) as an electrochemical technique. The assay is sensitive, safe, and cost-effective when compared to conventional agarose gel electrophoresis, real-time PCR, and other enzyme-linked assays for the detection of PCR amplicons. Furthermore, the use of a hand-held portable reader makes it suitable for use in the field.
    Matched MeSH terms: Polymerase Chain Reaction/methods*
  20. A nanoplex PCR assay for the rapid detection of vancomycin and bifunctional aminoglycoside resistance genes in Enterococcus species
    Yean CY, Yin LS, Lalitha P, Ravichandran M
    BMC Microbiol, 2007 Dec 11;7:112.
    PMID: 18070365
    BACKGROUND: Enterococci have emerged as a significant cause of nosocomial infections in many parts of the world over the last decade. The most common enterococci strains present in clinical isolates are E. faecalis and E. faecium which have acquired resistant to either gentamicin or vancomycin. The conventional culture test takes 2-5 days to yield complete information of the organism and its antibiotic sensitivity pattern. Hence our present study was focused on developing a nanoplex PCR assay for the rapid detection of vancomycin and bifunctional aminoglycoside resistant enterococci (V-BiA-RE). This assay simultaneously detects 8 genes namely 16S rRNA of Enterococcus genus, ddl of E. faecalis and E. faecium, aacA-aphD that encodes high level gentamicin resistance (HLGR), multilevel vancomycin resistant genotypes such as vanA, vanB, vanC and vanD and one internal control gene.

    RESULTS: Unique and specific primer pairs were designed to amplify the 8 genes. The specificity of the primers was confirmed by DNA sequencing of the nanoplex PCR products and BLAST analysis. The sensitivity and specificity of V-BiA-RE nanoplex PCR assay was evaluated against the conventional culture method. The analytical sensitivity of the assay was found to be 1 ng at the DNA level while the analytical specificity was evaluated with 43 reference enterococci and non-enterococcal strains and was found to be 100%. The diagnostic accuracy was determined using 159 clinical specimens, which showed that 97% of the clinical isolates belonged to E. faecalis, of which 26% showed the HLGR genotype, but none were vancomycin resistant. The presence of an internal control in the V-BiA-RE nanoplex PCR assay helped us to rule out false negative cases.

    CONCLUSION: The nanoplex PCR assay is robust and can give results within 4 hours about the 8 genes that are essential for the identification of the most common Enterococcus spp. and their antibiotic sensitivity pattern. The PCR assay developed in this study can be used as an effective surveillance tool to study the prevalence of enterococci and their antibiotic resistance pattern in hospitals and farm animals.

    Matched MeSH terms: Polymerase Chain Reaction/economics; Polymerase Chain Reaction/methods*
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