Displaying publications 421 - 440 of 3445 in total

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  1. Mariam Ahmad Zawawi, Mohamed Kamel Abd Ghani, Gopal G, Hidayatulfathi Othman, Hartini Yusof, Norhisham Haron
    Sains Malaysiana, 2012;41:1095-1098.
    entamoeba histolytica dan/atau entamoeba dispar merupakan protozoa usus yang mempunyai prevalens infeksi yang tinggi dalam kalangan masyarakat pedalaman terutamanya masyarakat Orang Asli. Ia tersebar secara meluas di kawasan tropika dan subtropika serta di negara membangun berbanding negara maju. Sebanyak 111 sampel feses kanak-kanak Orang Asli daripada suku kaum Jahai telah diterima dan disaring untuk entamoeba histolytica dan/atau entamoeba dispar menggunakan kaedah apusan langsung yang memberi hasil positif terhadap 43 sampel atau 38.7%. Oleh sebab amaun sampel yang diterima adalah sedikit, hanya 66 sampel feses sahaja yang dapat diperiksa menggunakan tiga jenis teknik diagnostik berbeza iaitu apusan langsung, kepekatan formalin-eter dan pewarnaan trikrom. Hasil kajian mendapati, prevalens yang tinggi bagi infeksi entamoeba histolytica dan/atau entamoeba dispar iaitu 50% menggunakan
    ketiga-tiga teknik diagnosis. Prevalens infeksi yang tinggi juga turut ditunjukkan pada kanak-kanak perempuan iaitu 62.5% berbanding kanak-kanak lelaki 30.8% (p<0.05). Selain itu, daripada segi umur, kanak-kanak yang berumur 7-9 tahun adalah lebih terdedah kepada infeksi entamoeba histolytica dan/atau entamoeba dispar dengan prevalens 60.7% (p>0.05). Teknik pewarnaan trikrom menunjukkan pengesanan 100% ke atas infeksi entamoeba histolytica dan/atau entamoeba dispar, diikuti teknik kepekatan formalin-eter 78.8% dan apusan langsung 72.7%. Prevalens infeksi entamoeba histolytica dan/atau entamoeba dispar yang tinggi dalam kalangan kanak-kanak Orang Asli di Pos Sungai Rual ini berhubungkait dengan pelbagai faktor iaitu status sosioekonomi yang rendah, kekurangan pengetahuan tentang penjagaan kesihatan serta kebersihan diri yang rendah. Peningkatan prevalens infeksi dalam kajian ini juga menunjukkan pentingnya penggunaan teknik diagnostik yang lebih berkesan dalam pemeriksaan rutin bagi mendapatkan hasil diagnosis yang lebih tepat.
    Matched MeSH terms: DNA, Protozoan
  2. SHAHRUL HISHAM ZAINAL ARIFFIN, ROSLINA SHAMSUDIN, NURUL ATIKAH AHMAD, ZULKIFLIE ZAMROD
    Sains Malaysiana, 2012;41:423-430.
    Sistem minigenom telah digunakan untuk mengkaji replikasi dan transkripsi virus RNA tidak bersegmen. Objektif kajian ini adalah untuk membina sistem minigenom bagi virus NDV strain tempatan, AF2240 serta bagi mengkaji mekanisme transkripsi dan replikasi virus ini. Bagi tujuan ini lima plasmid digunakan iaitu pMGNDV, pCITENP, pCITEP, pTriEX-T7, dan pGEML. Kesemua plasmid diekstrak secara berskala besar dan dimendakkan menggunakan polietilina glikol. Hasil ekstrak ini digunakan untuk transfeksi ke dalam sel. Translasi in vitro dilakukan dengan menggunakan pCITENP, pCITEP, dan pTriEX-T7 untuk memastikan kesemua konstruk ini berfungsi. Hasil pemblotan western menunjukkan protein bersaiz ~100 kDa (T7), ~53 kDa (NP), ~53 dan 55 kDa (P) berjaya diekspreskan. Protein CAT diperoleh apabila plasmid yang mengekodkan minigenom NDV ditransfeksi bersama plasmid yang mengekodkan protein nukleokapsid (NP), fosfoprotein (P) dan subunit besar polimerase (L) ke dalam sel BHK-21. Dianggarkan 55 pg protein CAT berjaya diperoleh menggunakan kit CAT ELISA. Hasil pemblotan western turut menunjukkan protein CAT bersaiz 25 kDa dihasilkan. Kesimpulannnya, system minigenom ini berupaya untuk berfungsi dan mampu mengekspreskan gen asing di dalam sel mamalia BHK-21.
    Matched MeSH terms: DNA Viruses
  3. Thavoncharoensub N, Maruyama K, Heh CH, Hoong Leong K, Shi H, Shigematsu Y, et al.
    PMID: 30929604 DOI: 10.1080/15257770.2019.1586919
    8-OxodGTP is generated by the reaction between dGTP and reactive oxygen species and a considered mutagenic nucleotide. It can be incorporated into the duplex DNA during replication processes by the DNA polymerase, and thus the repair enzyme removes oxodGTP from the nucleotide pools in living cells. On the other hand, the γ-modified triphosphates show interesting properties for use as biological tools. Therefore, the γ-N-pyrenylalkyl-oxodGTP derivatives were synthesized and their effect on the enzymatic reactions were evaluated. The γ-N-pyrenylmethyl-oxodGTP was found to be accepted by the DNA polymerase just like oxodGTP, but showed a competitive inhibition property for the human oxodGTPase.
    Matched MeSH terms: DNA-Directed DNA Polymerase/chemistry
  4. Czamara D, Eraslan G, Page CM, Lahti J, Lahti-Pulkkinen M, Hämäläinen E, et al.
    Nat Commun, 2019 06 11;10(1):2548.
    PMID: 31186427 DOI: 10.1038/s41467-019-10461-0
    Epigenetic processes, including DNA methylation (DNAm), are among the mechanisms allowing integration of genetic and environmental factors to shape cellular function. While many studies have investigated either environmental or genetic contributions to DNAm, few have assessed their integrated effects. Here we examine the relative contributions of prenatal environmental factors and genotype on DNA methylation in neonatal blood at variably methylated regions (VMRs) in 4 independent cohorts (overall n = 2365). We use Akaike's information criterion to test which factors best explain variability of methylation in the cohort-specific VMRs: several prenatal environmental factors (E), genotypes in cis (G), or their additive (G + E) or interaction (GxE) effects. Genetic and environmental factors in combination best explain DNAm at the majority of VMRs. The CpGs best explained by either G, G + E or GxE are functionally distinct. The enrichment of genetic variants from GxE models in GWAS for complex disorders supports their importance for disease risk.
    Matched MeSH terms: DNA/blood*; DNA Methylation/genetics*
  5. Yong HS, Chua KO, Song SL, Liew YJ, Eamsobhana P, Chan KG
    Mol Biol Rep, 2021 Aug;48(8):6047-6056.
    PMID: 34357549 DOI: 10.1007/s11033-021-06608-2
    BACKGROUND: Tephritid fruit flies of the genus Dacus are members of the tribe Dacini, subfamily Dacinae. There are some 274 species worldwide, distributed in Africa and the Asia-Pacific. To date, only five complete mitochondrial genomes (mitogenomes) of Dacus fruit flies have been published and are available in the GenBank.

    METHODS AND RESULTS: In view of the lack of study on their mitogenome, we sequenced (by next generation sequencing) and annotated the complete mitogenome of D. vijaysegarani from Malaysia to determine its features and phylogenetic relationship. The whole mitogenome of D. vijaysegarani has identical gene order with the published mitogenomes of the genus Dacus, with 13 protein-coding genes, two rRNA genes, 22 tRNAs, a non-coding A + T rich control region, and intergenic spacer and overlap sequences. Phylogenetic analysis based on 15 mitochondrial genes (13 PCGs and two rRNA genes), reveals Dacus, Zeugodacus and Bactrocera forming a distinct clade. The genus Dacus forms a monophyletic group in the subclade containing also the Zeugodacus group; this Dacus-Zeugodacus subclade is distinct from the Bactrocera subclade. D. (Mellesis) vijaysegarani forms a lineage with D. (Mellesis) trimacula in the subcluster containing also the lineage of D. (Mellesis) conopsoides and D. (Callantra) longicornis. D. (Dacus) bivittatus and D. (Didacus) ciliatus form a distinct subcluster. Based on cox1 sequences, the Malaysia and Vietnam taxa of D. vijaysegarani may not be conspecific.

    CONCLUSIONS: Overall, the mitochondrial genome of D. vijaysegarani provided essential molecular data that could be useful for further studies for species diagnosis, evolution and phylogeny research of other tephritid fruit flies in the future.

    Matched MeSH terms: DNA, Mitochondrial/genetics; Sequence Analysis, DNA/methods
  6. Glökler J, Lim TS, Ida J, Frohme M
    Crit Rev Biochem Mol Biol, 2021 12;56(6):543-586.
    PMID: 34263688 DOI: 10.1080/10409238.2021.1937927
    The introduction of nucleic acid amplification techniques has revolutionized the field of medical diagnostics in the last decade. The advent of PCR catalyzed the increasing application of DNA, not just for molecular cloning but also for molecular based diagnostics. Since the introduction of PCR, a deeper understanding of molecular mechanisms and enzymes involved in DNA/RNA replication has spurred the development of novel methods devoid of temperature cycling. Isothermal amplification methods have since been introduced utilizing different mechanisms, enzymes, and conditions. The ease with which isothermal amplification methods have allowed nucleic acid amplification to be carried out has had a profound impact on the way molecular diagnostics are being designed after the turn of the millennium. With all the advantages isothermal amplification brings, the issues or complications surrounding each method are heterogeneous making it difficult to identify the best approach for an end-user. This review pays special attention to the various isothermal amplification methods by classifying them based on the mechanistic characteristics which include reaction formats, amplification information, promoter, strand break, and refolding mechanisms. We would also compare the efficiencies and usefulness of each method while highlighting the potential applications and detection methods involved. This review will serve as an overall outlook on the journey and development of isothermal amplification methods as a whole.
    Matched MeSH terms: DNA
  7. Yang JH, Toda MJ, Suwito A, Hashim R, Gao JJ
    Zookeys, 2017.
    PMID: 28769630 DOI: 10.3897/zookeys.665.11609
    The genus Dichaetophora Duda comprises 61 described species classified into four species groups: agbo, tenuicauda, acutissima and sinensis. This genus is distributed exclusively in the Old World, and is rich in species in the tropical and subtropical areas of the Oriental, Australasian, and Afrotropical regions. In this paper, a new species group, the trilobita group, is established for six new species discovered from the Oriental region. The delimitation of these species is firstly performed in light of morphology and further with the aid of DNA sequences of the mitochondrial COI and COII (cytochrome c oxydase, subunits I and II, respectively) genes, considering also their respective geographical origins. Then, the new species (trilobita Yang & Gao, sp. n., heterochroma Yang & Gao, sp. n., flatosternata Yang & Gao, sp. n., borneoensis Yang & Gao, sp. n., javaensis Yang & Gao, sp. n., and sumatraensis Yang & Gao, sp. n.) are described, and a key, based on not only morphological but also molecular information, is provided.
    Matched MeSH terms: DNA
  8. Zainun MY, Simarani K
    Sci Total Environ, 2018 Mar;616-617:269-278.
    PMID: 29117585 DOI: 10.1016/j.scitotenv.2017.10.266
    The municipal landfill is an example of human-made environment that harbours some complex diversity of microorganism communities. To evaluate this complexity, the structures of bacterial communities in active (operational) and closed (non-operational) landfills in Malaysia were analysed with culture independent metagenomics approaches. Several points of soil samples were collected from 0 to 20cm depth and were subjected to physicochemical test, such as temperature, pH, and moisture content. In addition, the heavy metal contamination was determined by using ICPMS. The bacterial enumeration was examined on nutrient agar (NA) plates aerobically at 30°C. The soil DNA was extracted, purified and amplified prior to sequence the 16S rRNA gene for statistical and bioinformatics analyses. As a result, the average of bacteria for the closed landfill was higher compared to that for the active landfill at 9.16×107 and 1.50×107, respectively. The higher bacterial OTUs sequenced was also recorded in closed landfills compared to active landfill i.e. 6625 and 4552 OTUs respectively. The data from both landfills showed that the predominant phyla belonged to Proteobacteria (55.7%). On average, Bacteroidetes was the second highest phylum followed by Firmicutes for the active landfill. While the phyla for communities in closed landfill were dominated by phyla from Acidobacteria and Actinobacteria. There was also Euryarchaeota (Archaea) which became a minor phylum that was detected in active landfill, but almost completely absent in closed landfill. As such, the composition of bacterial communities suggests some variances between the bacterial communities found in active and closed landfills. Thus, this study offers new clues pertaining to bacterial diversity pattern between the varied types of landfills studied.
    Matched MeSH terms: DNA, Bacterial/isolation & purification; DNA, Archaeal/isolation & purification
  9. Shen KN, Loh KH, Chen CH, Hsiao CD
    Mitochondrial DNA A DNA Mapp Seq Anal, 2016 11;27(6):4122-4123.
    PMID: 25585497
    In this study, the complete mitogenome sequence of the Blue-face angelfish, Pomacanthus xanthometapon (Perciformes: Pomacanthidae) has been sequenced by the next-generation sequencing method. The assembled mitogenome consisting of 16,533 bp includes 13 protein coding genes, 22 transfer RNAs, and two ribosomal RNAs genes. The overall base composition of Blue-face angelfish is 28.7% for A, 28.9% for C, 15.9% for G, 26.6% for T and show 84% identities to flame angelfish Centropyge loriculus. The complete mitogenome of the Blue-face angelfish provides essential and important DNA molecular data for further phylogeography and evolutionary analysis for marine angelfish phylogeny.
    Matched MeSH terms: DNA, Mitochondrial/genetics; Sequence Analysis, DNA/methods
  10. Nascimento SM, Mendes MCQ, Menezes M, Rodríguez F, Alves-de-Souza C, Branco S, et al.
    Harmful Algae, 2017 12;70:73-89.
    PMID: 29169570 DOI: 10.1016/j.hal.2017.11.001
    A new species of toxic benthic dinoflagellate is described based on laboratory cultures isolated from two locations from Brazil, Rio de Janeiro and Bahia. The morphology was studied with SEM and LM. Cells are elliptical in right thecal view and flat. They are 37-44μm long and 29-36μm wide. The right thecal plate has a V shaped indentation where six platelets can be identified. The thecal surface of both thecal plates is smooth and has round or kidney shaped and uniformly distributed pores except in the central area of the cell, and a line of marginal pores. Some cells present an elongated depression on the central area of the apical part of the right thecal plate. Prorocentrum caipirignum is similar to Prorocentrum lima in its morphology, but can be differentiated by the general cell shape, being elliptical while P. lima is ovoid. In the phylogenetic trees based on ITS and LSU rDNA sequences, the P. caipirignum clade appears close to the clades of P. lima and Prorocentrum hoffmannianum. The Brazilian strains of P. caipirignum formed a clade with strains from Cuba, Hainan Island and Malaysia and it is therefore likely that this new species has a broad tropical distribution. Prorocentrum caipirignum is a toxic species that produces okadaic acid and the fast acting toxin prorocentrolide.
    Matched MeSH terms: DNA, Ribosomal/genetics; DNA, Protozoan/genetics
  11. Tang LP, Lee SS, Zeng NK, Cai Q, Zhang P, Yang ZL
    Mycologia, 2017 12 04;109(4):557-567.
    PMID: 29200380 DOI: 10.1080/00275514.2017.1394789
    Some Amanita specimens collected from Malaysia are critically investigated by morphological examination and molecular analysis of two gene fragments, the nuc rDNA partial 28S (28S) gene and the internal transcriber spacer (ITS1-5.8S-ITS2 = ITS) regions. Six phylogenetic species of Amanita section Caesareae are recognized among the studied collections. One of them is described as new, A. malayensis. Four of the phylogenetic species correspond with existing morphology-based taxa: A. aporema, A. javanica, A. princeps, and A. similis. The remaining species is not described because of the paucity of material. Detailed descriptions and the distribution of these southeastern Asian species are provided, along with a key to the species of section Caesareae from Malaysia.
    Matched MeSH terms: DNA, Fungal/genetics; DNA, Ribosomal Spacer/genetics
  12. Moey LH, Abdul Azize NA, Yakob Y, Leong HY, Keng WT, Chen BC, et al.
    Pediatr Neonatol, 2018 08;59(4):397-403.
    PMID: 29203193 DOI: 10.1016/j.pedneo.2017.11.006
    BACKGROUND: Fructose-1,6-bisphosphatase (FBPase) deficiency is a rare autosomal recessive inborn error of gluconeogenesis. We reported the clinical findings and molecular genetic data in seven Malaysian patients with FBPase deficiency.

    METHODS: All patients diagnosed with FBPase deficiency from 2010 to 2015 were included in this study. Their clinical and laboratory data were collected retrospectively.

    RESULTS: All the patients presented with recurrent episodes of hypoglycemia, metabolic acidosis, hyperlactacidemia and hepatomegaly. All of them had the first metabolic decompensation prior to 2 years old. The common triggering factors were vomiting and infection. Biallelic mutations in FBP1 gene (MIM*611570) were identified in all seven patients confirming the diagnosis of FBPase deficiency. In four patients, genetic study was prompted by detection of glycerol or glycerol-3-phosphate in urine organic acids analysis. One patient also had pseudo-hypertriglyceridemia. Seven different mutations were identified in FBP1, among them four mutations were new: three point deletions (c.392delT, c.603delG and c.704delC) and one splice site mutation (c.568-2A > C). All four new mutations were predicted to be damaging by in silico analysis. One patient presented in the neonatal period and succumbed due to sepsis and multi-organ failure. Among six survivors (current age ranged from 4 to 27 years), four have normal growth and cognitive development. One patient had short stature and another had neurological deficit following status epilepticus due to profound hypoglycemia.

    CONCLUSION: FBPase deficiency needs to be considered in any children with recurrent hypoglycemia and metabolic acidosis. Our study expands the spectrum of FBP1 gene mutations.

    Matched MeSH terms: DNA Helicases/genetics*; DNA-Binding Proteins/genetics*
  13. Mohamad FS, Mat Zaid MH, Abdullah J, Zawawi RM, Lim HN, Sulaiman Y, et al.
    Sensors (Basel), 2017 Dec 02;17(12).
    PMID: 29207463 DOI: 10.3390/s17122789
    This article describes chemically modified polyaniline and graphene (PANI/GP) composite nanofibers prepared by self-assembly process using oxidative polymerization of aniline monomer and graphene in the presence of a solution containing poly(methyl vinyl ether-alt-maleic acid) (PMVEA). Characterization of the composite nanofibers was carried out by Fourier transform infrared (FTIR) and Raman spectroscopy, transmission electron microscopy (TEM) and scanning electron microscopy (SEM). SEM images revealed the size of the PANI nanofibers ranged from 90 to 360 nm in diameter and was greatly influenced by the proportion of PMVEA and graphene. The composite nanofibers with an immobilized DNA probe were used for the detection of Mycobacterium tuberculosis by using an electrochemical technique. A photochemical indicator, methylene blue (MB) was used to monitor the hybridization of target DNA by using differential pulse voltammetry (DPV) method. The detection range of DNA biosensor was obtained from of 10-6-10-9 M with the detection limit of 7.853 × 10-7 M under optimum conditions. The results show that the composite nanofibers have a great potential in a range of applications for DNA sensors.
    Matched MeSH terms: DNA
  14. Zhang H, Gao J, Ma Z, Liu Y, Wang G, Liu Q, et al.
    Front Cell Infect Microbiol, 2022;12:1082809.
    PMID: 36530420 DOI: 10.3389/fcimb.2022.1082809
    BACKGROUND: Wolbachia is gram-negative and common intracellular bacteria, which is maternally inherited endosymbionts and could expand their propagation in host populations by means of various manipulations. Recent reports reveal the natural infection of Wolbachia in Aedes Aegypti in Malaysia, India, Philippines, Thailand and the United States. At present, none of Wolbachia natural infection in Ae. aegypti has been reported in China.

    METHODS: A total of 480 Ae. aegypti adult mosquitoes were collected from October and November 2018 based on the results of previous investigations and the distribution of Ae. aegypti in Yunnan. Each individual sample was processed and screened for the presence of Wolbachia by PCR with wsp primers. Phylogenetic trees for the wsp gene was constructed using the neighbour-joining method with 1,000 bootstrap replicates, and the p-distance distribution model of molecular evolution was applied.

    RESULTS: 24 individual adult mosquito samples and 10 sample sites were positive for Wolbachia infection. The Wolbachia infection rate (IR) of each population ranged from 0 - 41.7%. The infection rate of group A alone was 0%-10%, the infection rate of group B alone was 0%-7.7%, and the infection rate of co-infection with A and B was 0-33.3%.

    CONCLUSIONS: Wolbachia infection in wild Ae. aegypti in China is the first report based on PCR amplification of the Wolbachia wsp gene. The Wolbachia infection is 5%, and the wAlbA and wAlbB strains were found to be prevalent in the natural population of Ae. aegypti in Yunnan Province.

    Matched MeSH terms: DNA Primers
  15. Haarindraprasad R, Gopinath SCB, Veeradassan P
    Biotechnol Appl Biochem, 2022 Dec;69(6):2698-2712.
    PMID: 34997977 DOI: 10.1002/bab.2316
    A "Janus particle" refers to the production of two materials in a single system and shows a difference in physical characteristics, and two surfaces participate in the formation with different chemistries. This research generated the Janus using a hybrid of zinc oxide (ZnO) and gold (Au) on the sensor surface toward making high-performance DNA sensors. The Janus ZnO/Au-textured film was synthesized via the one-step sol-gel method, which involves a suitable ratio of a mixture of ZnO sol seed solution. The synthesized Janus ZnO/Au-textured film undergoes a low-temperature aqueous hydrothermal route to synthesize quasi-one-dimensional nanowires. The average grain size in the Janus ZnO/Au nanotextured wire was 41.60 nm. The fabricated nanotextured wire was further optimized by tuning the thickness and characterized by XRD and high-resolution microscopy. Electrical characterization was conducted on the Janus ZnO/Au nanotextured wire coupled with an interdigitated electrode sensor to detect the specific leptospirosis DNA strand. The generated device is capable of detecting lower DNA concentration at 1 × 10-13 M with a sensitivity of 8.54 MΩ M-1 cm-2 . The high performance is attained on linear concentrations of 10-6 -10-13 M with the determination coefficient, "I = 135437.63C-3609.07" R2 = 0.9551. A potential strategy is proposed as a base for developing different high-performance sensors.
    Matched MeSH terms: DNA
  16. Kurina I, Popenko A, Klimenko N, Koshechkin S, Chuprikova L, Filipenko M, et al.
    Mol Cell Probes, 2020 Aug;52:101570.
    PMID: 32304824 DOI: 10.1016/j.mcp.2020.101570
    Nowadays the advent of innovative high-throughput sequencing allows obtaining high-quality microbiome profiling. However, PCR-based tests are still considered the "golden standard" for many clinical applications. Here, we designed a qPCR-based platform with fluorescent-labeled oligonucleotide probes for assessing human gut microbiome composition. The system allows conducting qualitative and semiquantitative analysis for 12 prokaryotic taxa that are prevalent in the human gut and associated with diseases, diet, age and other factors. The platform was validated by comparing microbiome profile data obtained with two different methods - the platform and high-throughput 16S rRNA sequencing - across 42 stool samples. The test can form the basis for precise and cost-efficient microbiome assay for large-scale surveys including clinical trials with interventions related to diet and disease risks.
    Matched MeSH terms: DNA Probes/metabolism; DNA Primers/metabolism
  17. Lim L, Ab Majid AH
    Sci Rep, 2021 Apr 19;11(1):8465.
    PMID: 33875727 DOI: 10.1038/s41598-021-87946-w
    With the development of new metagenomic techniques, the microbial community structure of common bed bugs, Cimex lectularius, is well-studied, while information regarding the constituents of the bacterial communities associated with tropical bed bugs, Cimex hemipterus, is lacking. In this study, the bacteria communities in the blood-fed and starved tropical bed bugs were analysed and characterized by amplifying the v3-v4 hypervariable region of the 16S rRNA gene region, followed by MiSeq Illumina sequencing. Across all samples, Proteobacteria made up more than 99% of the microbial community. An alpha-proteobacterium Wolbachia and gamma-proteobacterium, including Dickeya chrysanthemi and Pseudomonas, were the dominant OTUs at the genus level. Although the dominant OTUs of bacterial communities of blood-fed and starved bed bugs were the same, bacterial genera present in lower numbers were varied. The bacteria load in starved bed bugs was also higher than blood-fed bed bugs.
    Matched MeSH terms: DNA/analysis; DNA/genetics*; DNA Barcoding, Taxonomic
  18. Zainuddin Z, Teh LK, Suhaimi AW, Salleh MZ, Ismail R
    Clin Chim Acta, 2003 Oct;336(1-2):97-102.
    PMID: 14500040 DOI: 10.1016/s0009-8981(03)00319-x
    BACKGROUND: Cytochrome P4502C9 (CYP2C9), a principle drug-metabolizing enzyme is polymorphic in humans and is responsible for important pharmacokinetic and pharmacodynamic variations of CYP2C9 substrates. We developed an allele-specific multiplex polymerase chain reaction (PCR) method for the detection of common CYP2C9 alleles.
    METHOD: Genomic DNA was extracted from blood obtained from 40 unrelated healthy Malaysian Indian volunteers. The DNA was subjected to a first PCR that was used to amplify both exons 3 and 7 simultaneously in one reaction tube and a second PCR that was used to detect the polymorphic sites of CYP2C9 alleles using allele-specific primers. Sequencing was performed to validate the test results.
    RESULTS: We were successful in amplifying the fragments of interest from the DNA samples. The method was also reproducible and specific. The amplified sequences showed 100% homology to CYP2C9 sequence.
    CONCLUSION: This is the first nested allele-specific multiplex PCR method reported to allow for the simultaneously detection of five CYP2C9 alleles.
    Matched MeSH terms: DNA/blood; DNA Primers/genetics
  19. Zainal Abidin DH, Mohd Nor SA, Lavoué S, A Rahim M, Jamaludin NA, Mohammed Akib NA
    Sci Rep, 2021 Sep 07;11(1):17800.
    PMID: 34493747 DOI: 10.1038/s41598-021-97324-1
    The Merbok Estuary comprises one of the largest remaining mangrove forests in Peninsular Malaysia. Its value is significant as it provides important services to local and global communities. It also offers a unique opportunity to study the structure and functioning of mangrove ecosystems. However, its biodiversity is still partially inventoried, limiting its research value. A recent checklist based on morphological examination, reported 138 fish species residing, frequenting or subject to entering the Merbok Estuary. In this work, we reassessed the fish diversity of the Merbok Estuary by DNA barcoding 350 specimens assignable to 134 species initially identified based on morphology. Our results consistently revealed the presence of 139 Molecular Operational Taxonomic Units (MOTUs). 123 of them are congruent with morphology-based species delimitation (one species = one MOTU). In two cases, two morphological species share the same MOTU (two species = one MOTU), while we unveiled cryptic diversity (i.e. COI-based genetic variability > 2%) within seven other species (one species = two MOTUs), calling for further taxonomic investigations. This study provides a comprehensive core-list of fish taxa in Merbok Estuary, demonstrating the advantages of combining morphological and molecular evidence to describe diverse but still poorly studied tropical fish communities. It also delivers a large DNA reference collection for brackish fishes occurring in this region which will facilitate further biodiversity-oriented research studies and management activities.
    Matched MeSH terms: DNA/genetics; DNA Barcoding, Taxonomic*
  20. Syukriani Y, Wulandari AS, Wanranto B, Hidayat Y
    Sci Justice, 2023 Mar;63(2):229-237.
    PMID: 36870702 DOI: 10.1016/j.scijus.2023.01.003
    The existence of the Chinese population in the predominantly Malay population in Indonesia can be traced back thousands of years, and it has been suspected that it played an essential role in the history of the Malay population origin in Maritime South East Asia. With the fact that the Malay-Indonesian population is currently predominant compared to the Chinese population in Indonesia (Chinese-Indonesian), the selection of the origin of the STRs allele frequency panel population becomes an issue in DNA profiling, including in paternity testing. This study analyses the genetic relationship between the Chinese-Indonesian and Malay-Indonesian populations and how this affects the Paternity Index (PI) ​​calculation in paternity test cases. The study of the relationship between populations was carried out using neighbour-joining (NJ) tree analysis and multidimensional scaling (MDS) on the allele frequency panel of 19 autosomal STRs loci of Malay-Indonesian (n = 210) and Chinese-Indonesian (n = 78) populations. Four population groups were used as references: Malay-Malaysian, Filipino, Chinese, and Caucasian. An MDS analysis was also performed based on the pairwise FST calculation. The combined Paternity Index (CPI) calculation was carried out on 132 paternity cases from the Malay-Indonesian population with inclusive results using a panel of allele frequencies from the six populations. The pairwise FST MDS indicates a closer relationship between the Chinese-Indonesian and Malay-Indonesian compared to the Chinese population, which is in line with the CPIs comparison test. The outcome suggests that the alternative use of allele frequency database between Malay-Indonesian and Chinese-Indonesian for CPI calculations is not very influential. These results can also be considered in studying the extent of genetic assimilation between the two populations. In addition, these results support the robustness claim of multivariate analysis to represent phenomena that phylogenetic analyses may not be able to demonstrate, especially for massive panel data.
    Matched MeSH terms: DNA
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