Displaying publications 61 - 80 of 142 in total

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  1. Fulltext Sequence and phylogeny of the complete mitochondrial genome of the Himalayan jungle crow (Corvidae: Corvus macrorhynchos intermedius) from Pakistan
    Iqbal F, Ayub Q, Song BK, Wilson R, Fahim M, Rahman S
    Mitochondrial DNA B Resour, 2019 Dec 18;5(1):348-350.
    PMID: 33366551 DOI: 10.1080/23802359.2019.1704637
    Corvus macrorhynchos formerly referred to as the jungle crow or the large-billed crow is a polytypic species with unresolved taxonomy, comprising various subspecies widespread across South, Southeast, and East Asia. In this study, we report the complete mitogenome of one of these subspecies, Corvus macrorhynchos intermedius (Himalaya crow), from Pakistan. The mitochondrial genome is circular, 16,927 bp and contains typical animal mitochondrial genes (13 protein-coding genes, 2 ribosomal RNA, and 22 transfer RNA) and one non-coding region (D-loop) with a nucleotide content of A (30.6%), T (24.8%), G (14.8%), and C (29.8%). Phylogenetic analysis using the whole mitochondrial genome showed that C. m. intermedius and only reported subspecies Corvus macrorhynchos culminatus (Indian Jungle crow) are genetically distinct and it supports the recognition of the latter as a separate biospecies.
    Matched MeSH terms: Nucleotides
  2. Fulltext The presence of single-nucleotide polymorphisms in Hps4 gene in a subset of schizophrenic patients in Pahang: a preliminary study
    Norafiza Zainuddin, Maizatul Akma Mamat, Norlelawati A. Talib
    International Journal of Allied Health Sciences, 2017;1(2):14-27.
    MyJurnal
    Schizophrenia is a devastating mental disorder that affects people’s normal life with heterogeneous features of its clinical presentation, as well as its molecular attribute. In order to identify the potential molecular aberration, particularly single nucleotide polymorphism (SNP) which could be important in the aetiology of schizophrenia, polymerase chain reaction (PCR)-DNA sequencing approach was utilized for targeting the exon (and intron) 9 of the Hermansky-Pudlak syndrome type 4 (HPS4) gene. DNAs were extracted from peripheral blood of nine schizophrenic patients and one normal individual prior to PCR-DNA sequencing. Following DNA sequencing, a SNP (A>G) which is rs713998 at nucleotide position 22618 of exon 9 of the HPS4 gene was observed in eight schizophrenia samples. Moreover, DNA sequencing results also revealed an intronic aberration/SNP which is rs3747129 (C>T) at nucleotide position 22789 of intron 9 of the HPS4 gene in four schizophrenia samples. A SNP which is rs739289 (G>T) at nucleotide position 22677 of the intron was also found in eight schizophrenia samples. The importance of both the exonic and intronic aberrations is yet to be confirmed with further research involving larger population and other relevant clinical parameters. That notwithstanding, these preliminary results suggested that single nucleotide aberrations, particularly SNPs might have a role in the development of schizophrenia
    Matched MeSH terms: Nucleotides
  3. Fulltext Detection of all four dengue virus serotypes and identification of four mismatched nucleotides between DENV4 specific primer rTS4 and DENV 4 sequences in Sandakan and Kudat (2016-2017)
    Tin Sabai Aung, Amalina Emran, Chua Tock Hing, Tin Tin Thein, Win Win Than, Aye Aye Wynn, et al.
    Malaysian Journal of Medicine and Health Sciences, 2019;15(106):49-49.
    MyJurnal
    Introduction: Dengue is caused by dengue virus (DENV) which is a member of the genus Flavivirus of the family Flaviviridae. The prevalence of dengue has been increasing all over the world especially in Southeast Asia and Western Pacific regions. In 2016 - 2017 dengue outbreaks were reported in Sandakan and Kudat of Sabah, Malay-sia. The aim of this study was to determine the serotypes of dengue viruses circulating in these two sites during the outbreaks. Methods: A total of 200 dengue patients’ sera tested positive with NS1 and IgM & IgG rapid test (PanBio) were collected from Hospital Duchess of Kent Sandakan and Hospital Kudat between June 2016 and December 2017. PCR was done at the Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah. One-Step Reverse transcriptase PCR (RT-PCR) and nested PCR was performed using C-prM amplimers designed by Lanciotti et al and later redesigned by Chien et al, followed by sequencing some of the PCR products. Results: Out of 200 sera tested 128 were PCR positive. All the four dengue serotypes were detected with PCR products with specific sizes in gel electrophoresis. However, in four samples, no serotype-specific band was amplified by the nested PCR, while they were dengue-positive in RT-PCR showing 511 base pair amplicon. Sequencing results revealed all four samples were found to belong to DENV4. The sequences of these samples were aligned with that of DENV 4 reverse primer rTS4. The DENV4 specific primer rTS4 was found to have four mismatched nucleotides to the DENV4 sequences. Conclusion: There was a co-circulation of DENV1 to 4 in Sandakan and Kudat in the study period. DENV1 was the predominant serotype. DENV4 specific C-prM primer rTS4 should be redesigned for the local DENV4 strain in Sabah in future research.
    Matched MeSH terms: Nucleotides
  4. Fulltext Dataset of complete genome assembly and analysis of mycobacterium tuberculosis strain SIT745/EAI1-MYS
    Abdullah M, Suraiya S, Mohamad S, Harun A
    Data Brief, 2020 Aug;31:105949.
    PMID: 32671154 DOI: 10.1016/j.dib.2020.105949
    In this dataset, we report the genome assembly and data analysis of Mycobacterium tuberculosis strain SIT745/EAI1-MYS. Previously, this strain was isolated from a Malaysian patient with extra-pulmonary tuberculosis, and identification of this strain is done by spoligotype patterns with fifteen known Shared International Type (SITs). Further analysis showed that this strain has a remarkable phylogeographical specificity for Malaysia. Based on the National Center for Biotechnology Information (NCBI) nucleotide database information, the complete genome consists of 150 contigs with various sequence lengths and was not assembled. In this assembly, the aforementioned contigs along with reference sequence from Mycobacterium tuberculosis strain H37Rv and Mycobacterium bovis strain AF2122/97 was used for gap closures, were assembled into a single circular chromosome length of approximately 4.42 Mega bases (Mb) with an average GC content of 65.6%. The single circular chromosome was shown to contain 4,009 protein-coding sequences, 3 ribosomal RNAs, 45 transfer RNAs, and 12 superclasses distributed with 277 subsystems which constitute nearly 1900 genes, respectively. The genome information will provide fundamental knowledge of this organism as well as insight for understanding genomic and proteomic profiling, phylogenetic relationship.
    Matched MeSH terms: Nucleotides
  5. Fulltext Identification of Mycobacterium tuberculosis-specific DNA marker using MAMA-PCR
    Chin Kai Ling, Jaeyres Jani, Zainal Arifin Mustapha
    Malaysian Journal of Medicine and Health Sciences, 2019;15(106):36-36.
    MyJurnal
    Introduction: Tuberculosis (TB), commonly caused by Mycobacterium tuberculosis (Mtb), is one of the ten leading causes of death worldwide. The gold standard, microbiological culture for detection and differentiation of mycobac-teria are time-consuming and laborious. The use of fast, easy and sensitive nucleic acid amplification tests (NAATs) for diagnosis of TB remains challenging because there is a high degree of homology within Mtb complex (MTBC) members and absence of target genes in the genome of some strains. This study aimed to identify new candidate genetic marker and to design specific primers to detect Mtb using in silico methods. Methods: Using Basic Local Alignment Search Tool (BLAST) program, Mtb H37Rv chromosome reference genome sequence was mapped with other MTBC members and a single nucleotide polymorphism (SNP) at Rv1970 was found to be specific only for Mtb strains. Mismatch amplification mutation assay (MAMA) combine with polymerase chain reaction (PCR) was used as an alternative method to detect the point mutation. MAMA primers targeting the SNP were designed using Primer-BLAST and the PCR assay was optimized via Taguchi method. Results: The assay amplified a 112 bp gene fragment and was able to detect all Mtb strains, but not the other MTBC members and non-tuberculous Mycobacte-ria. The detection limit of the assay was 60 pg/μl. Conclusion: Bioinformatics has provided predictive identification of many new target markers. The designed primers were found to be highly specific at single-gene target resolution for detection of Mtb.
    Matched MeSH terms: Nucleotides
  6. Fulltext Effects of pH on Phosphorus Recovery from Different Composition of Food Waste Using Anaerobic Batch Digestion
    Selaman, R., Newati Wid
    Borneo Journal of Medical Sciences, 2018;12(101):63-64.
    MyJurnal
    Anaerobic digestion is a process by which microorganisms break down biodegradable material in the absence of oxygen. The process involves hydrolysis, acidogenesis and methanogenesis stages. Anaerobic digestion of food waste has been widely investigated for biogas recovery but limited study was performed on phosphorus recovery, which is reported depleting. Food waste is produced every day and dumped on landfill for final disposal which may lead to environmental issues such as odour problems and greenhouse gases release, due to decomposing of food waste, hence impacts global climate change. In anaerobic digestion pH is a very crucial parameter in an attempt to recover phosphorus as it highly influences the production of organic acids during acidogenesis.
    Matched MeSH terms: Deoxyuracil Nucleotides
  7. POPULATION GENETICS OF LONGTAIL TUNA (Thunnus tonggol) (BLEEKER, 1851) FROM EAST MALAYSIA BASED ON MITOCHONDRIAL DNA D-LOOP MARKER
    NURUL AZLIANA MOHD YASIN, NOORHANI SYAHIDA KASIM, TUN NURUL AIMI MAT JAAFAR, RUMEAIDA MAT PIAH, WAHIDAH MOHD ARSHAAD, SITI AZIZAH MOHD NOR, et al.
    UMT Journal of Undergraduate Research, 2020;2(2):49-56.
    MyJurnal
    Present study investigates the genetic diversity and genetic distribution of the longtail tuna Thunnus tonggol collected from east Malaysia (Borneo states of Sabah and Sarawak) based on mitochondrial DNA D-loop sequence analysis. 58 fish samples were obtained, specifically from Kota Kinabalu, KK (n = 22), Miri, MR (n=20) and Bintulu, BT (n = 17). DNA template was isolated using the salt extraction method. Final length of 404 base pair (bp) D-loop sequences revealed 52 haplotypes that comprise of 77 variable sites (38 of parsimony informative and 39 singleton). A total of 20 haplotypes were found in KK, 19 haplotypes in MR and 16 haplotypes in BT. Molecular diversity indices revealed high haplotype diversity and low nucleotide diversity in all populations; KK (h = 0.9913 ± 0.0165, π = 0.00239 ± 0.0127), MR (h = 0.9942 ± 0.0193, π = 0.0226 ± 0.0121) and BT (h = 0.9926 ± 0.0230, π = 0.0196 ± 0.0171). Population comparison pairwise FST show that KK and BT were significantly genetically differentiated. The result from this study will be beneficial for fisheries management and also to provide information on the population genetics of T. tonggol in East Malaysian waters.
    Matched MeSH terms: Nucleotides
  8. Fulltext CYTOCHROME OXIDASE I (COI) DIVERGENCE ASSESSMENT OF FAMILY NEMIPTERIDAE FROM MALAYSIAN WATERS
    LIEW YOU EN, SALWANI ABDULLAH, TAN MIN PAU, MAZLAN ABD GHAFFAR, ALIAS MAN, TUN NURUL AIMI MAT JAAFAR
    UMT Journal of Undergraduate Research, 2019;1(1):41-48.
    MyJurnal
    DNA Barcoding, primarily focusing on cytochrome coxidase subunit I (COI) gene has been appraised as an effective tool for species identification. Nonetheless, species identification based on molecular approach is essential for discrimination of look-alike species. In this study, we focused on the marine fishes Family Nemipteridae, one of the commercially important group distributed within the surrounding seas of Malaysia. Some of the samples were collected during the National Demersal Trawl Survey in the Exclusive Economic Zone of East Coast Peninsular Malaysia by the Department of Fishery Malaysia. A 652bp region of COI was sequenced for 74 individuals from nine putative species. Additional 34 COIsequences from GenBank were also included in this study making the total number of samples analysed to 108 individuals. The averageKimura 2-parameter (K2P) nucleotide divergence was 0.34% among individuals within species and 6.97% within genera. All putative species formed monophyletic clades in both Neighbour-joining (NJ) and Maximum-likelihood (ML) trees. However, there was a potential misidentification in specimen identified as Nemipterus tambuloides,as the specimen did not group with their own taxa. It was genetically grouped in Nemipterus thosaporni clade. This study supports the effectiveness of COIgene in species discrimination of Family Nemipteridae.
    Matched MeSH terms: Nucleotides
  9. Fulltext Sequencing and Annotated of Goat's Milk using Bioinformatics Tool: ClustalX
    Muhammad Najmi Mohammad Fauzi, Aisyah Aqilah Abu Bakar, Liyana Amalina Adnan, Tg Ainul Farha Tg Abdul Rahman, A’wani Aziz Nurdalila
    Malaysian Journal of Science, Health & Technology, 2021;7(1):28-33.
    MyJurnal
    Bioinformatics tool is a software program made to extract meaningful information from the mass of molecular biology or biological databases and carry out sequence or structural analysis. The method of determining the order of nucleotides within a deoxyribonucleic acid (DNA) molecule is known as DNA sequencing. This analysis is meant to be run to the commercialized or factorymade goat's milk (pasteurised) from various states in Malaysia to identify the milk's authenticity, either it is pure or mixed with other foreign substances from other animals. The main objective is to compare DNA sequences of commercialized and raw goat's milk (handmilking and non-pasteurised). To achieve this, we used ClustalX to align and compare the obtained DNA from both milk samples. The sequences will be aligned using ClustalX software. ClustalX is a provider of an automated system for performing multiple alignments of sequences and profiles and evaluating the outcomes. The usage of ClustalX is helpful as it is cost-effective, user-friendly, and showing a high accuracy of the analysis.

    Matched MeSH terms: Nucleotides
  10. Construction of A Preliminary Three-Dimensional Structure Simian betaretrovirus Serotype-2 (SRV-2) Reverse Transcriptase Isolated from Indonesian Cynomolgus Monkey
    Saepuloh U, Iskandriati D, Pamungkas J, Solihin DD, Mariya SS, Sajuthi D
    Trop Life Sci Res, 2020 Oct;31(3):47-61.
    PMID: 33214855 DOI: 10.21315/tlsr2020.31.3.4
    Simian betaretrovirus serotype-2 (SRV-2) is an important pathogenic agent in Asian macaques. It is a potential confounding variable in biomedical research. SRV-2 also provides a valuable viral model compared to other retroviruses which can be used for understanding many aspects of retroviral-host interactions and immunosuppression, infection mechanism, retroviral structure, antiretroviral and vaccine development. In this study, we isolated the gene encoding reverse transcriptase enzyme (RT) of SRV-2 that infected Indonesian cynomolgus monkey (Mf ET1006) and predicted the three dimensional structure model using the iterative threading assembly refinement (I-TASSER) computational programme. This SRV-2 RT Mf ET1006 consisted of 547 amino acids at nucleotide position 3284-4925 of whole genome SRV-2. The polymerase active site located in the finger/palm subdomain characterised by three conserved catalytic aspartates (Asp90, Asp165, Asp166), and has a highly conserved YMDD motif as Tyr163, Met164, Asp165 and Asp166. We estimated that this SRV-2 RT Mf ET1006 structure has the accuracy of template modelling score (TM-score 0.90 ± 0.06) and root mean square deviation (RMSD) 4.7 ± 3.1Å, indicating that this model can be trusted and the accuracy can be seen from the appearance of protein folding in tertiary structure. The superpositionings between SRV-2 RT Mf ET1006 and Human Immunodeficiency Virus-1 (HIV-1) RT were performed to predict the structural in details and to optimise the best fits for illustrations. This SRV-2 RT Mf ET1006 structure model has the highest homology to HIV-1 RT (2B6A.pdb) with estimated accuracy at TM-score 0.911, RMSD 1.85 Å, and coverage of 0.953. This preliminary study of SRV-2 RT Mf ET1006 structure modelling is intriguing and provide some information to explore the molecular characteristic and biochemical mechanism of this enzyme.
    Matched MeSH terms: Nucleotides
  11. Fulltext Population Genetic Structure of Ornate Threadfin Bream (Nemipterus hexodon) in Thailand
    Supmee V, Songrak A, Suppapan J, Sangthong P
    Trop Life Sci Res, 2021 Mar;32(1):63-82.
    PMID: 33936551 DOI: 10.21315/tlsr2021.32.1.4
    Ornate threadfin bream (Nemipterus hexodon) is an economically important fishery species in Southeast Asia. In Thailand, N. hexodon decreased dramatically due to overexploitation for commercial purposes. To construct an effective sustainable management plan, genetic information is necessary. Thus, in our study, the population genetic structure and demographic history of N. hexodon were investigated using 419 bp of the mitochondrial DNA sequence in cytochrome oxidase subunit I gene (mtDNA COI). A total of 142 samples was collected from nine localities in the Gulf of Thailand (Chonburi, Samut Songkhram, Surat Thani, Nakhon Si Thammarat, Songkhla), and the Andaman Sea (Satun, Trang, Krabi, Phang Nga). Fourteen polymorphic sites defined 18 haplotypes, revealing a high haplotype diversity and low nucleotide diversity among nine localities. The analysis of molecular variance (AMOVA) analysis, pairwise F
    ST
    , and minimum spanning network result revealed that the genetic structure of N. hexodon was separated into two populations: the Gulf of Thailand and the Andaman Sea population. The genetic structure of N. hexodon can be explained by a disruption of gene flow from the geographic barrier and the Pleistocene isolation of the marine basin hypothesis. Neutrality tests, Bayesian skyline analysis, mismatch distribution, and the estimated values of population growth suggested that N. hexodon had experienced a population expansion. The genetic information would certainly help us gain insight into the population genetic structure of N. hexodon living on the coast of Thailand.
    Matched MeSH terms: Nucleotides
  12. Complete Genome Sequences of Three Historically Important, Spatiotemporally Distinct, and Genetically Divergent Strains of Zika Virus: MR-766, P6-740, and PRVABC-59
    Yun SI, Song BH, Frank JC, Julander JG, Polejaeva IA, Davies CJ, et al.
    Genome Announc, 2016;4(4).
    PMID: 27540058 DOI: 10.1128/genomeA.00800-16
    Here, we report the 10,807-nucleotide-long consensus RNA genome sequences of three spatiotemporally distinct and genetically divergent Zika virus strains, with the functionality of their genomic sequences substantiated by reverse genetics: MR-766 (African lineage, Uganda, 1947), P6-740 (Asian lineage, Malaysia, 1966), and PRVABC-59 (Asian lineage-derived American strain, Puerto Rico, 2015).
    Matched MeSH terms: Nucleotides
  13. Fulltext Detection of aerolysin and hemolysin genes in Aeromonas spp. isolated from environmental and shellfish sources by polymerase chain reaction
    Yousr, A.H., Nipis, S., Rusul, G.R.A., Son, R.
    International Food Research Journal, 2007;14(2):115-122.
    MyJurnal
    Polymerase chain reaction (PCR) technique was used to assay for the detection of specific genes in the genomes of the Aeromonas spp. isolated from environmental and shellfish sources, particularly aero and hlyA genes, responsible for aerolysin and hemolysin toxins production in this genus. The results showed that: (i) the 1500 bp amplicon of the hlyA gene was detected in 20/38 of the Aeromonas hydrophila, 13/38 of the A. caviae and 6/9 of the A. veronii biovar sobria isolates; (ii) the 690 bp amplicon of the aero gene was detected in 20/38 of A. hydrophila, 17/38 of A. caviae and 6/9 of A. veronii biovar sobria isolates; (iii) the nucleotide blast results of aerolysin gene sequences of the representative strains of A. hydrophila, A. caviae and A. veronii biovar sobria revealed a high homology of 94%, 95% and 95% with published sequences, respectively and ; (iv) the protein blast showed 97%, 94% and 96% homology when compared to the published sequences, respectively. The finding of A. hydrophila virulence genes in other members of the genus Aeromonas, may give a new perspective to the significance of these results. The method described here may be a useful detection tool to assist in further investigation of aero and hlyA genes in the genus Aeromonas, especially for food microbiologist.
    Matched MeSH terms: Nucleotides
  14. Fulltext Determination of flavonoids in Citrus grandis (Pomelo) peels and their inhibition activity on lipid peroxidation in fish tissue
    Zarina, Z., Tan S.Y.
    International Food Research Journal, 2013;20(1):313-317.
    MyJurnal
    The peels of pomelo contribute 30% of the fruit weight and yet it has been dump without recognizing the possible nutritional value of the peels. Study has been carried out to identify flavonoid content of the peels and analysed the activity of the flavonoid towards inhibition of lipid peroxidation. Optimization of flavonoid extraction was conducted using aqueous solvent (methanol and ethanol), extraction time (1-3 h) and extraction temperature (50°C-80°) via water bath extraction. The total content of flavonoids was quantitatively determined by using coloration methods with chromogenic system of NaNO2–Al (NO3)3–NaOH and and it was found that the extraction at 65ºC for 2 h in aqueous ethanol was the optimized condition for maximum flavonoids i.e. 190.42mg/L. A spectrophometric analysis was performed to evaluate flavonoid activity towards lipid peroxidation in the fish tissue. There was reduction in Peroxide value (PV) indicated the inhibition of lipid peroxidation in fish treated with pomelo peel as evidence of concurrency of positive flavonoid activity.
    Matched MeSH terms: Deoxyuracil Nucleotides
  15. Genetic variation in the glucose-6-phosphate dehydrogenase gene in Kelantan Malays with neonatal jaundice
    Mohd Yusoff, N., Choo, K.E., Ghazali, S., Ibrahim, I., Mohd Hussin, Z.A., Mohd Yunus, et al.
    Malaysian Journal of Paediatrics and Child Health, 2000;12(1):11-15.
    MyJurnal
    Glucose-6-phosphate dehydrogenase (G6PD) deficiency is an X-linked red blood cell enzymopathy common in malaria endemic areas. Individuals affected by this disease show a wide variety of clinical signs including neonatal jaundice. In this preliminary report we describe the heterogeneity of G6PD deficient gene in neonatal jaundice in the Malay population in Kelantan. Thirteen G6PD deficient Malay neonates with hyperbilirubinemia were subjected to mutation analysis of the G6PD gene for known candidate mutations. Molecular defects were identified in the 13 patients studied. Though all of these were mis-sense mutations, identified nucleotide changes were heterogeneous. Six patients were found to have a C to T nucleotide change at nucleotide 563 of the G6PD gene (C563T), corresponding to G6PD Mediterranean; three cases had a single nucleotide change at T383C (G6PD Vanua Lava), two cases had G487A (G6PD Mahidol) and two cases had G1376T (G6PD Canton). These findings suggest that there are heterogeneous mutations of the G6PD gene associated with neonatal jaundice in the Malay population in Kelantan.
    Matched MeSH terms: Nucleotides
  16. Fulltext Interleukin 1β (+3954; -511) Genotype Polymorphism and its Association with Severe Chronic Generalized Periodontitis in the Malaysian Population
    Arora S, Ramachandra SS, Abdullah F, Gundavarapu KC
    Contemp Clin Dent, 2017 Jan-Mar;8(1):102-105.
    PMID: 28566859 DOI: 10.4103/ccd.ccd_1177_16
    INTRODUCTION: Single-nucleotide polymorphisms (SNPs) in interleukin 1β (IL-1β) gene have been known to be associated with increased susceptibility to chronic periodontitis among various ethnic populations. SNPs are more commonly observed at loci + 3954 and - 511. The aim of this study was to evaluate the role of IL-1β gene polymorphism at loci +3954 and - 511, and its association with severe chronic generalized periodontitis among the ethnic Malay, Chinese, and Indians within the Malaysian population.

    MATERIALS AND METHODS: Saliva samples from 120 subjects (60 cases and 60 controls) in the age group of 25-50 years were collected for isolation of genetic material using Norgen technique. Clinical attachment loss of ≥5 mm was considered as severe chronic generalized periodontitis. SNP's at loci +3954 and - 511 were identified and analyzed using Kompetitive Allele Specific Polymerase Chain Reaction Genotyping System (KASP™). Differences in the allele/genotype frequencies were assessed by Chi-square test (P < 0.05).

    RESULTS: On the comparison between cases and controls of IL-1β genotype polymorphism (+3954 and - 511), the difference in the genotype frequencies was statistically insignificant in all the three ethnicities. The genotype frequency in both groups in all three ethnicities of the Malaysian population was similar.

    CONCLUSION: IL-1β genotype polymorphism at +3954 and - 511 was found to be not associated with severe chronic generalized periodontitis among the three ethnicities in Malaysia. Studies with larger sample size should be done to confirm the findings of this study.
    Matched MeSH terms: Nucleotides
  17. Fulltext Detection of Genetically Modified Organisms (GMOs) using molecular techniques in food and feed samples from Malaysia and Vietnam
    Tung Nguyen, C.T., Son, R., Raha, A.R., Lai, O.M., Clemente Michael Wong, V.L.
    International Food Research Journal, 2008;15(2):155-166.
    MyJurnal
    Food labeling in accordance with Novel Food Regulation has been enforced in the European Community since 1997 with a series of updated legislations namely, EC/258/97, EC/1139/98, EC/49/2000, EC/50/2000 and EC/1829/2003. Guidelines and labeling regulations for the use of GMOs materials in food and feed products has also been introduced in Malaysia and Vietnam. Therefore, the demand for the establishment and development of a robust and rapid operation procedure for GMO detection has increased recently in both countries. The procedure of GMO detection emphasizes not only on detection tests but also on confirmation assays. This study employed PCR technology for detection and direct DNA sequencing for confirmation procedures respectively. The results demonstrated for the first time the presence of GM plants with glyphosate-resistant trait led by the control of P35S promoter and NOS terminator in either Malaysian or Vietnamese feed with high frequency (20 positive samples out of 24 analyzed samples). The P35S promoter, EPSPS gene and NOS terminator sequences obtained showed some mutations on single-stranded and double-stranded targeted sequences caused by single nucleotide insertion or single nucleotide changes. These results reinforce the need for development of detection procedures to comply with food/feed labeling system.
    Matched MeSH terms: Nucleotides
  18. Fulltext Integrated microRNA, gene expression and transcription factors signature in papillary thyroid cancer with lymph node metastasis
    Ab Mutalib NS, Othman SN, Mohamad Yusof A, Abdullah Suhaimi SN, Muhammad R, Jamal R
    PeerJ, 2016;4:e2119.
    PMID: 27350898 DOI: 10.7717/peerj.2119
    Background. Papillary thyroid carcinoma (PTC) is the commonest thyroid malignancy originating from the follicle cells in the thyroid. Despite a good overall prognosis, certain high-risk cases as in those with lymph node metastasis (LNM) have progressive disease and poorer prognosis. MicroRNAs are a class of non-protein-coding, 19-24 nucleotides single-stranded RNAs which regulate gene expression and these molecules have been shown to play a role in LNM. The integrated analysis of miRNAs and gene expression profiles together with transcription factors (TFs) has been shown to improve the identification of functional miRNA-target gene-TF relationships, providing a more complete view of molecular events underlying metastasis process. Objectives. We reanalyzed The Cancer Genome Atlas (TCGA) datasets on PTC to identify differentially expressed miRNAs/genes in PTC patients with LNM-positive (LNM-P) versus lymph node negative (LNN) PTC patients and to investigate the miRNA-gene-TF regulatory circuit that regulate LNM in PTC. Results. PTC patients with LNM (PTC LNM-P) have a significantly shorter disease-free survival rate compared to PTC patients without LNM (PTC LNN) (Log-rank Mantel Cox test, p = 0.0049). We identified 181 significantly differentially expressed miRNAs in PTC LNM-P versus PTC LNN; 110 were upregulated and 71 were downregulated. The five topmost deregulated miRNAs were hsa-miR-146b, hsa-miR-375, hsa-miR-31, hsa-miR-7-2 and hsa-miR-204. In addition, 395 miRNAs were differentially expressed between PTC LNM-P and normal thyroid while 400 miRNAs were differentially expressed between PTC LNN and normal thyroid. We found four significant enrichment pathways potentially involved in metastasis to the lymph nodes, namely oxidative phosphorylation (OxPhos), cell adhesion molecules (CAMs), leukocyte transendothelial migration and cytokine-cytokine receptor interaction. OxPhos was the most significantly perturbed pathway (p = 4.70E-06) involving downregulation of 90 OxPhos-related genes. Significant interaction of hsa-miR-301b with HLF, HIF and REL/NFkB transcription factors were identified exclusively in PTC LNM-P versus PTC LNN. Conclusion. We found evidence of five miRNAs differentially expressed in PTC LNM-P. Alteration in OxPhos pathway could be the central event in metastasis to the lymph node in PTC. We postulate that hsa-miR-301b might be involved in regulating LNM in PTC via interactions with HLF, HIF and REL/NFkB. To the best of our knowledge, the roles of these TFs have been studied in PTC but the precise role of this miRNA with these TFs in LNM in PTC has not been investigated.
    Matched MeSH terms: Nucleotides
  19. Implication of CDKAL1 single-nucleotide polymorphism rs 9465871 in obese and non-obese Egyptian children
    Ismail NA, Ragab S, Abd El Dayem SM, Baky ANAE, Hamed M, Ahmed Kamel S, et al.
    Med J Malaysia, 2018 10;73(5):286-290.
    PMID: 30350806
    INTRODUCTION: CDKAL1 single-nucleotide polymorphism rs 9465871variant is a risk locus for Type 2 Diabetes (T2DM).The study evaluated the associations of CDKAL1- rs9465871 with glycosylated hemoglobin A1C Level (HbA1c), fasting insulin level, insulin resistance and metabolic syndrome among obese and non- obese Egyptian children.

    MATERIALS AND METHODS: The study included 43 obese children and 40 normal weight children. Anthropometric body measurements, bio-specimen and biochemistry assays were done. Genotyping of rs9465871 (CDKAL1) was conducted.

    RESULTS: The percentages of the CC, CT, and TT genotypes of rs9465871in the lean children were 15%, 42.5%, and 42.5%, respectively. Regarding obese children, the frequencies were 18.6%, 58.1% and 23.3% respectively with no significant statistical difference. Comparison between the CDKAL1 rs 9465871 polymorphism showed that the highest value of fasting insulin was recorded in CC genotype (22.80± 15.18 [uIU/mL] P

    Matched MeSH terms: Nucleotides
  20. Improved nucleic acid extraction protocols for Ganoderma boninense, G. miniatocinctum and G. tornatum
    Nagappan J, Chin CF, Angel LPL, Cooper RM, May ST, Low EL
    Biotechnol Lett, 2018 Dec;40(11-12):1541-1550.
    PMID: 30203158 DOI: 10.1007/s10529-018-2603-7
    The first and most crucial step of all molecular techniques is to isolate high quality and intact nucleic acids. However, DNA and RNA isolation from fungal samples are usually difficult due to the cell walls that are relatively unsusceptible to lysis and often resistant to traditional extraction procedures. Although there are many extraction protocols for Ganoderma species, different extraction protocols have been applied to different species to obtain high yields of good quality nucleic acids, especially for genome and transcriptome sequencing. Ganoderma species, mainly G. boninense causes the basal stem rot disease, a devastating disease that plagues the oil palm industry. Here, we describe modified DNA extraction protocols for G. boninense, G. miniatocinctum and G. tornatum, and an RNA extraction protocol for G. boninense. The modified salting out DNA extraction protocol is suitable for G. boninense and G. miniatocinctum while the modified high salt and low pH protocol is suitable for G. tornatum. The modified DNA and RNA extraction protocols were able to produce high quality genomic DNA and total RNA of ~ 140 to 160 µg/g and ~ 80 µg/g of mycelia respectively, for Single Molecule Real Time (PacBio Sequel® System) and Illumina sequencing. These protocols will benefit those studying the oil palm pathogens at nucleotide level.
    Matched MeSH terms: Nucleotides
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